Influence of manure age and sunlight on the community structure of cattle fecal bacteria as revealed by Illumina sequencing

NASA Astrophysics Data System (ADS)

Wong, K.; Shaw, T. I.; Oladeinde, A.; Molina, M.

2013-12-01

Fecal pollution of environmental waters is a major concern for the general public because exposure to fecal-associated pathogens can have severe impacts on human health. Stream and river impairment due to fecal pollution is largely the result of agricultural activities in the United States. In the last few years, numerous metagenomic studies utilized next generation sequencing to develop microbial community profiles by massively sequencing the 16sRNA hypervariable region. This technology supports the application of water quality assessment such as pathogen detection and fecal source tracking. The bacteria communities of samples in these studies were determined when they were freshly collected; therefore, little is known about how feces age or how environmental stress influences the microbial ecology of fecal materials. In this study we monitored bacteria community changes in cattle feces for 57 days after excretion (day 0, 2, 4 8, 15, 22, 29, 43, 57) by sequencing the 16s variable region 4, using Illumnia MiSeq. Twelve cattle feces were studied; half of the samples were directly exposed to sunlight (unshaded) and half were shaded. Results indicate that the relative abundance (RA) profile in both shaded and unshaded samples rapidly changed from day 0 to 15, but stabilized from day 22 to 57. Firmcutes were the most abundant phylum (~40%) at day 0, but were reduced to <10% by day 57. The RA of Proteobacteria was only 1% at day 0, but increased to ~50% by day 57in both shaded and unshaded samples. By the end of the study, shaded and unshaded samples had a similar RA of Firmcutes and Proteobacteria but the RA of Bacteroidetes and Actinobacteria was, respectively, about 7% lower and 10% higher for unshaded samples. UV intensity, moisture, and temperature were significantly different between shaded and unshaded plots, indicating that these environmental stresses could influence the structure of fecal bacteria community in the natural environment. According to the rarefaction curve analysis, richness of bacteria diversity in feces decreased as time progressed. Some pathogens such as Campylobacter were detected only at the beginning, meaning they substantially decayed during the course of our study. Overall, this study indicated: (1) sunlight can influence the community structure and (2) after excretion the fecal bacteria diversity can be significantly changed over time. Future studies should therefore use not only the microbial signature of fresh but also moderately aged fecal samples to develop more accurate community profiles for fecal source tracking.

The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks.

PubMed

Amanidaz, Nazak; Zafarzadeh, Ali; Mahvi, Amir Hossein

2015-12-01

This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms.

The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks

PubMed Central

AMANIDAZ, Nazak; ZAFARZADEH, Ali; MAHVI, Amir Hossein

2015-01-01

Background: This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. Methods: This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. Results: In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Conclusion: Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms. PMID:26811820

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

USGS Publications Warehouse

Layton, Blythe A.; Cao, Yiping; Ebentier, Darcy L.; Hanley, Kaitlyn; Ballesté, Elisenda; Brandão, João; Byappanahalli, Muruleedhara N.; Converse, Reagan; Farnleitner, Andreas H.; Gentry-Shields, Jennifer; Gourmelon, Michèle; Lee, Chang Soo; Lee, Jiyoung; Lozach, Solen; Madi, Tania; Meijer, Wim G.; Noble, Rachel; Peed, Lindsay; Reischer, Georg H.; Rodrigues, Raquel; Rose, Joan B.; Schriewer, Alexander; Sinigalliano, Chris; Srinivasan, Sangeetha; Stewart, Jill; ,; Laurie, C.; Wang, Dan; Whitman, Richard; Wuertz, Stefan; Jay, Jenny; Holden, Patricia A.; Boehm, Alexandria B.; Shanks, Orin; Griffith, John F.

2013-01-01

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman®, HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman® was found to be the most effective marker of human fecal contamination in this California-based study.

Identification and determination of the viability of Giardia lamblia cysts and Cryptosporidium parvum and Cryptosporidium hominis oocysts in human fecal and water supply samples by fluorescent in situ hybridization (FISH) and monoclonal antibodies.

PubMed

Lemos, Vanessa; Graczyk, Thaddeus K; Alves, Margarida; Lobo, Maria Luísa; Sousa, Maria C; Antunes, Francisco; Matos, Olga

2005-12-01

In the present study, fluorescent in situ hybridization (FISH) and monoclonal antibodies (MAbs) were evaluated for species-specific detection and viability determination of Giardia lamblia, Cryptosporidium parvum, and Cryptosporidium hominis in human fecal and water supply samples. A total of 50 fecal human samples positive for G. lamblia cysts, 38 positive for C. parvum, and 23 positive for C. hominis were studied. Also, 18 water supply samples positive for Giardia spp. and Cryptosporidium spp. by the United States Environmental Protection Agency (USEPA) Method 1623 were studied by FISH and fluorescein isothiocyanate (FITC)-conjugated MAbs. Eighteen percent of the fecal samples parasitologically positive for G. lamblia presented viable and nonviable cysts, and 5% of those positive for Cryptosporidium spp. presented viable and nonviable oocysts. Of the 18 water supply samples analyzed, 6 (33%) presented Giardia spp. viable and nonviable cysts and 2 (11%) presented viable and nonviable Cryptosporidium spp. oocysts. G. lamblia identification was confirmed by polymerase chain reaction (PCR) and sequencing of the beta-giardin gene in the fecal and water samples found positive by FISH and FITC-conjugated MAbs. C. parvum and Cryptosporidium muris were identified, by PCR and sequencing of the small subunit of ribosomal RNA gene, in seven and one water samples, respectively. Our results confirm that this technique enables simultaneous visualization, species-specific identification, and viability determination of the organisms present in human fecal and water supply samples.

Detection of feline coronavirus in cheetah (Acinonyx jubatus) feces by reverse transcription-nested polymerase chain reaction in cheetahs with variable frequency of viral shedding.

PubMed

Gaffney, Patricia M; Kennedy, Melissa; Terio, Karen; Gardner, Ian; Lothamer, Chad; Coleman, Kathleen; Munson, Linda

2012-12-01

Cheetahs (Acinonyx jubatus) are a highly threatened species because of habitat loss, human conflict, and high prevalence of disease in captivity. An epidemic of feline infectious peritonitis and concern for spread of infectious disease resulted in decreased movement of cheetahs between U.S. zoological facilities for managed captive breeding. Identifying the true feline coronavirus (FCoV) infection status of cheetahs is challenging because of inconsistent correlation between seropositivity and fecal viral shedding. Because the pattern of fecal shedding of FCoV is unknown in cheetahs, this study aimed to assess the frequency of detectable fecal viral shedding in a 30-day period and to determine the most efficient fecal sampling strategy to identify cheetahs shedding FCoV. Fecal samples were collected from 16 cheetahs housed at seven zoological facilities for 30 to 46 consecutive days; the samples were evaluated for the presence of FCoV by reverse transcription-nested polymerase chain reaction (RT-nPCR). Forty-four percent (7/16) of cheetahs had detectable FCoV in feces, and the proportion of positive samples for individual animals ranged from 13 to 93%. Cheetahs shed virus persistently, intermittently, or rarely over 30-46 days. Fecal RT-nPCR results were used to calculate the probability of correctly identifying a cheetah known to shed virus given multiple hypothetical fecal collection schedules. The most efficient hypothetical fecal sample collection schedule was evaluation of five individual consecutive fecal samples, resulting in a 90% probability of identifying a known shedder. Demographic and management risk factors were not significantly associated (P < or = 0.05) with fecal viral shedding. Because some cheetahs shed virus intermittently to rarely, fecal sampling schedules meant to identify all known shedders would be impractical with current tests and eradication of virus from the population unreasonable. Managing the captive population as endemically infected with FCoV may be a more feasible approach.

Mycobacterium avium subsp. paratuberculosis from free-ranging deer and rabbits surrounding Minnesota dairy herds

PubMed Central

2005-01-01

Abstract The objectives of this study were to estimate the prevalence of Mycobacterium avium subsp. paratuberculosis (MAP) among deer and rabbits surrounding infected and noninfected Minnesota dairy farms using fecal culture, and to describe the frequency that farm management practices were used that could potentially lead to transmission of infection between these species. Fecal samples from cows and the cow environment were collected from 108 Minnesota dairy herds, and fecal pellets from free-ranging white-tailed deer and eastern cottontail rabbits were collected from locations surrounding 114 farms; all samples were tested using bacterial culture. In addition, a questionnaire was administered to 114 herd owners. Sixty-two percent of the dairy herds had at least 1 positive fecal pool or environmental sample. A total of 218 rabbit samples were collected from 90% of the herds, and 309 deer samples were collected from 47% of the herds. On 2 (4%) of the farms sampled, 1 deer fecal sample was MAP positive. Both farms had samples from the cow fecal pool and cow environment that were positive by culture. On 2 (2%) other farms, 1 rabbit fecal sample was positive by culture to MAP, with one of these farms having positive cow fecal pools and cow environmental samples. Pasture was used on 79% of the study farms as a grazing area for cattle, mainly for dry cows (75%) and bred or prebred heifers (87%). Of the 114 farms, 88 (77%) provided access to drylot for their cattle, mainly for milking cows (77/88; 88%) and bred heifers (87%). Of all study farms, 90 (79%) used some solid manure broadcasting on their crop fields. Of all 114 farms, the estimated probability of daily physical contact between cattle manure and deer or rabbits was 20% and 25%, respectively. Possible contact between cattle manure and deer or rabbits was estimated to occur primarily from March through December. The frequency of pasture or drylot use and manure spreading on crop fields may be important risk factors for transmission of MAP among dairy cattle, deer, and rabbits. Although the MAP prevalence among rabbits and deer is low, their role as MAP reservoirs should be considered. PMID:15745220

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.

2010-03-01

Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomicmore » units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.« less

Characterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators

PubMed Central

Wu, Cindy H.; Sercu, Bram; Van De Werfhorst, Laurie C.; Wong, Jakk; DeSantis, Todd Z.; Brodie, Eoin L.; Hazen, Terry C.; Holden, Patricia A.; Andersen, Gary L.

2010-01-01

Background Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Methodology/Principal Findings Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and α-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC∶A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. Conclusions/Significance This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health. PMID:20585654

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

PubMed Central

Tedjo, Danyta I.; Jonkers, Daisy M. A. E.; Savelkoul, Paul H.; Masclee, Ad A.; van Best, Niels; Pierik, Marieke J.; Penders, John

2015-01-01

Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80°C, -20°C for 1 week, at +4°C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80°C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80°C versus the other methods and -80°C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80°C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4°C or room temperature) or freezing at -20°C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders. PMID:26024217

Applicability of universal Bacteroidales genetic marker for microbial monitoring of drinking water sources in comparison to conventional indicators.

PubMed

Shahryari, A; Nikaeen, M; Khiadani Hajian, M; Nabavi, F; Hatamzadeh, M; Hassanzadeh, A

2014-11-01

Water quality monitoring is essential for the provision of safe drinking water. In this study, we compared a selection of fecal indicators with universal Bacteroidales genetic marker to identify fecal pollution of a variety of drinking water sources. A total of 60 samples were collected from water sources. The microbiological parameters included total coliforms, fecal coliforms, Escherichia coli and fecal streptococci as the fecal indicator bacteria (FIB), Clostridium perfringens and H2S bacteria as alternative indicators, universal Bacteroidales genetic marker as a promising alternative fecal indicator, and Salmonella spp., Shigella spp., and E. coli O157 as pathogenic bacteria. From 60 samples analyzed, Bacteroidales was the most frequently detected indicator followed by total coliforms. However, the Bacteroidales assay failed to detect the marker in nine samples positive for FIB and other alternative indicators. The results of our study showed that the absence of Bacteroidales is not necessarily an evidence of fecal and pathogenic bacteria absence and may be unable to ensure the safety of the water. Further research, however, is required for a better understanding of the use of a Bacteroidales genetic marker as an indicator in water quality monitoring programs.

[Isolation methods and diversity of culturable fecal actinobacteria associated with Panthera tigris tigris in Yunnan Safari Park].

PubMed

Cao, Yanru; Jiang, Yi; Li, Youlong; Chen, Xiu; Jin, Rongxian; He, Wenxiang

2012-07-04

We studied the isolation methods and diversity of culturable fecal actinobacteria associated with Panthera tigris tigris by using culture-dependent approaches. Fresh fecal samples of healthy Panthera tigris tigris were collected from Yunnan Safari Park. Pretreatment of the samples, isolation media and inhibitors were tested for actinobacteria isolation. 16S rRNA genes of actinobacteria were sequenced and subjected to phylogenetic analysis. The abundance of culturable actinobacteria was 1.10 x 10(8) cfu/g colony forming units (CFU) per gram of feces (wet weight). We obtained 110 purified cultural actinobacterium strains. The analysis based on 16S rRNA gene sequences showed that these strains were distributed in 10 different families and 12 genera of actinobacteria at least, and most of them were non-filamentous, such as Arthrobacter, Dietzia, Kocuria, Corynebacterium and Microbacterium. Streptomyces was the mainly classical filamentous actinobacteria, and up to 64% of total. Drying and heating up the fecal samples can greatly increase the rate of the actinobacteria. Many kinds of inhibitors and chemical defined media are suitable for isolation of fecal actinobacteria. The culturable actinobacteria are abundant in Panthera tigris tigris feces. Our study found an effective method to isolate animals' fecal actinobacteria and it's useful for studying and exploiting animals' fecal actinobacteria.

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

PubMed Central

Staley, C.; Sadowsky, M. J.; Gyawali, P.; Sidhu, J. P. S.; Palmer, A.; Beale, D. J.; Toze, S.

2015-01-01

In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. PMID:26231650

Influence of Coliform Source on Evaluation of Membrane Filters

PubMed Central

Brodsky, M. H.; Schiemann, D. A.

1975-01-01

Four brands of membrane filters were examined for total and fecal coliform recovery performance by two experimental approaches. Using diluted EC broth cultures of water samples, Johns-Manville filters were superior to Sartorius filters for fecal coliform but equivalent for total coliform recovery. Using river water samples, Johns-Manville filters were superior to Sartorius filters for total coliform but equivalent for fecal coliform recovery. No differences were observed between Johns-Manville and Millipore or Millipore and Sartorius filters for total or fecal coliform recoveries using either approach, nor was any difference observed between Millipore and Gelman filters for fecal coliform recovery from river water samples. These results indicate that the source of the coliform bacteria has an important influence on the conclusions of membrane filter evaluation studies. PMID:1106318

Effect of selected gastrointestinal parasites and viral agents on fecal S100A12 concentrations in puppies as a potential comparative model.

PubMed

Heilmann, Romy M; Grellet, Aurélien; Grützner, Niels; Cranford, Shannon M; Suchodolski, Jan S; Chastant-Maillard, Sylvie; Steiner, Jörg M

2018-04-17

Previous data suggest that fecal S100A12 has clinical utility as a biomarker of chronic gastrointestinal inflammation (idiopathic inflammatory bowel disease) in both people and dogs, but the effect of gastrointestinal pathogens on fecal S100A12 concentrations is largely unknown. The role of S100A12 in parasite and viral infections is also difficult to study in traditional animal models due to the lack of S100A12 expression in rodents. Thus, the aim of this study was to evaluate fecal S100A12 concentrations in a cohort of puppies with intestinal parasites (Cystoisospora spp., Toxocara canis, Giardia sp.) and viral agents that are frequently encountered and known to cause gastrointestinal signs in dogs (coronavirus, parvovirus) as a comparative model. Spot fecal samples were collected from 307 puppies [median age (range): 7 (4-13) weeks; 29 different breeds] in French breeding kennels, and fecal scores (semiquantitative system; scores 1-13) were assigned. Fecal samples were tested for Cystoisospora spp. (C. canis and C. ohioensis), Toxocara canis, Giardia sp., as well as canine coronavirus (CCV) and parvovirus (CPV). S100A12 concentrations were measured in all fecal samples using an in-house radioimmunoassay. Statistical analyses were performed using non-parametric 2-group or multiple-group comparisons, non-parametric correlation analysis, association testing between nominal variables, and construction of a multivariate mixed model. Fecal S100A12 concentrations ranged from < 24-14,363 ng/g. Univariate analysis only showed increased fecal S100A12 concentrations in dogs shedding Cystoisospora spp. (P = 0.0384) and in dogs infected with parvovirus (P = 0.0277), whereas dogs infected with coronavirus had decreased fecal S100A12 concentrations (P = 0.0345). However, shedding of any single enteropathogen did not affect fecal S100A12 concentrations in multivariate analysis (all P > 0.05) in this study. Only fecal score and breed size had an effect on fecal S100A12 concentrations in multivariate analysis (P < 0.0001). An infection with any single enteropathogen tested in this study is unlikely to alter fecal S100A12 concentrations, and these preliminary data are important for further studies evaluating fecal S100A12 concentrations in dogs or when using fecal S100A12 concentrations as a biomarker in patients with chronic idiopathic gastrointestinal inflammation.

Evaluation of a quantitative H2S MPN test for fecal microbes analysis of water using biochemical and molecular identification.

PubMed

McMahan, Lanakila; Grunden, Amy M; Devine, Anthony A; Sobsey, Mark D

2012-04-15

The sensitivity and specificity of the H(2)S test to detect fecal bacteria in water has been variable and uncertain in previous studies, partly due to its presence-absence results. Furthermore, in groundwater samples false-positive results have been reported, with H(2)S-positive samples containing no fecal coliforms or Escherichia coli. False-negative results also have been reported in other studies, with H(2)S-negative samples found to contain E. coli. Using biochemical and molecular methods and a novel quantitative test format, this research identified the types and numbers of microbial community members present in natural water samples, including fecal indicators and pathogens as well as other bacteria. Representative water sources tested in this study included cistern rainwater, a protected lake, and wells in agricultural and forest settings. Samples from quantitative H(2)S tests of water were further cultured for fecal bacteria by spread plating onto the selective media for detection and isolation of Aeromonas spp., E. coli, Clostridium spp., H(2)S-producers, and species of Salmonella and Shigella. Isolates were then tested for H(2)S production, and identified to the genus and species level using biochemical methods. Terminal Restriction Fragment Length Polymorphisms (TRFLP) was the molecular method employed to quantitatively characterize microbial community diversity. Overall, it was shown that water samples testing positive for H(2)S bacteria also had bacteria of likely fecal origin and waters containing fecal pathogens also were positive for H(2)S bacteria. Of the microorganisms isolated from natural water, greater than 70 percent were identified using TRFLP analysis to reveal a relatively stable group of organisms whose community composition differed with water source and over time. These results further document the validity of the H(2)S test for detecting and quantifying fecal contamination of water. Copyright © 2011 Elsevier Ltd. All rights reserved.

Vegetable Contamination by the Fecal Bacteria of Poultry Manure: Case Study of Gardening Sites in Southern Benin

PubMed Central

Atidégla, Séraphin C.; Huat, Joël; Agbossou, Euloge K.; Saint-Macary, Hervé; Glèlè Kakai, Romain

2016-01-01

A study was conducted in southern Benin to assess the contamination of vegetables by fecal coliforms, Escherichia coli, and fecal streptococci as one consequence of the intensification of vegetable cropping through fertilization with poultry manure. For this purpose, on-farm trials were conducted in 2009 and 2010 at Yodo-Condji and Ayi-Guinnou with three replications and four fertilization treatments including poultry manure and three vegetable crops (leafy eggplant, tomato, and carrot). Sampling, laboratory analyses, and counts of fecal bacteria in the samples were performed in different cropping seasons. Whatever the fertilization treatment, the logs of mean fecal bacteria count per g of fresh vegetables were variable but higher than AFNOR criteria. The counts ranged from 8 to 10 fecal coliforms, from 5 to 8 fecal streptococci, and from 2 to 6 Escherichia coli, whereas AFNOR criteria are, respectively, 0, 1, and 0. The long traditional use of poultry manure and its use during the study helped obtain this high population of fecal pathogens. Results confirmed that the contamination of vegetables by fecal bacteria is mainly due to the use of poultry manure. The use of properly composted poultry manure with innovative cropping techniques should help reduce the number and incidence of pathogens. PMID:27069914

Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River.

PubMed

Sun, Haohao; He, Xiwei; Ye, Lin; Zhang, Xu-Xiang; Wu, Bing; Ren, Hongqiang

2017-03-01

The fecal bacteria in natural waters may pose serious risks on human health. Although many source tracking methods have been developed and used to determine the possible sources of the fecal pollution, little is known about the overall diversity and abundance of fecal bacterial community in natural waters. In this study, a method based on fecal bacterial sequence library was introduced to evaluate the fecal bacterial profile in the Yangtze River (Nanjing section). Our results suggested that the Yangtze River water harbors diverse fecal bacteria. Fifty-eight fecal operational taxonomic units (97% identity level) were detected in the Yangtze River water samples and the relative abundance of fecal bacteria in these samples ranged from 0.1 to 8%. It was also found that the relative abundances of the fecal bacteria in locations near to the downstream of wastewater treatment plants were obviously higher than those in other locations. However, the high abundance of fecal bacteria could decrease to the normal level in 2~4 km in the river due to degradation or dilution, and the overall fecal bacteria level changed little when the Yangtze River flew through the Nanjing City. Moreover, the fecal bacteria in the Yangtze River water were found to be highly associated (Spearman rho = 0.804, P < 0.001) with the potential pathogenic bacteria. Collectively, the findings in this study reveal the diversity, abundance, and possible sources of fecal bacteria in the Yangtze River and advance our understandings of the fecal bacteria community in the natural waters.

Distribution and variability of fecal-indicator bacteria in Scioto and Olentangy rivers in the Columbus, Ohio, area

USGS Publications Warehouse

Myers, Donna N.

1992-01-01

This report presents the results of a study by the U.S. Geological Survey, in cooperation with the City of Columbus, Ohio, to determine the distribution and variability of fecal-indicator bacteria in Scioto and Olentangy Rivers. Fecal-indicator bacteria are among the contaminants of concern to recreational users of these rivers in the Columbus area. Samples were collected to be analyzed for fecal-coliform and Escherichia coli (E. coli) bacteria and selected water-quality constituents and physical properties at 10 sites-- 4 on the Olentangy River and 6 on the Scioto River during the recreational seasons in 1987, 1988, and 1989. Measurements of streamflow also were made at these sites at various frequencies during base flow and runoff. The concentrations of fecal-coliform and E. coli bacteria in the Scioto and Olentangy Rivers spanned a range of five orders of magnitude, from less than 20 to greater than 2,000,000 col/100 mL (colonies per 100 milliliters). In addition, the concentrations of fecal coliform and E. coli bacteria are well correlated (r=0.97) in the study area. At times, relatively high concentrations, for fecal-indicator bacteria (concentrations greater than 51,000 col/100 mL for fecal-coliform and E. coli ) were found in Olentangy River at Woody Hayes Drive and at Goodale Street, and in Scioto River at Greenlawn Avenue and at Columbus. Intermediate concentrations of fecal-indicator bacteria (from 5,100 to 50,000 col/100 mL for fecal coliform and (from 510 to 50,000 col/100 mL for E. coli ) were found in Scioto River at Town Street and below O'Shaughnessy Dam near Dublin, Ohio, and in Olentangy River at Henderson Road. The lowest (median) concentrations of fecal-indicator bacteria (from 20 to 5,000 col/100 mL for fecal coliform and from 20 to 500 col/100 mL for E. coli ) were found at Olentangy River near Worthington, Ohio, Scioto River at Dublin Road Water Treatment Plant and below Griggs Reservoir. Fecal-coliform concentrations exceeded the geometric mean and single-sample Ohio Water Quality Standards for recreation less frequently than E. coli concentrations. The E. coli numerical water-quality standards are more difficult to meet than the fecal coliform standards because they are as much as an order of magnitude lower in some instances. The geometric mean bathing-water and primary-contact standards for fecal-coliform and E. coli bacteria were exceeded in more samples for Olentangy River at Goodale Street than for any other site. The single-sample bathing-water standard for fecal-coliform bacteria was exceeded in 83 percent of all samples and for E. coli in 91 percent of samples for Olentangy River at Goodale Street. Compared to Olentangy River at Goodale Street, geometric means and single-samples exceeded the bathing-water standards somewhat less frequently for Scioto River at Town Street and far less frequently for Scioto River at Dublin Road Water Treatment Plant. In contrast to results for fecal-indicator bacteria, the differences between sites for pH and for concentrations for total alkalinity, total chloride, total nonfilterable residue, total nitrate plus nitrite as nitrogen, total phosphorus, and total organic carbon were small. The large contribution of streamflow and discharge of fecal-indicator bacteria from Olentangy River to Scioto River has a major effect on the Scioto River downstream from the confluence of Olentangy River during periods of rainfall and runoff. Fecal-indicator discharges were calculated for times before, during, and at 24-hour intervals for 48 to 72 hours after two runoff-producing storms. Fecal-coliform and E. coli concentrations were lower in samples collected before runoff and during receding streamflows at 24- to 48-hours after the storms than in samples collected during runoff. The fecal-indicator discharges entering Scioto River from Olentangy River ranged from 22.6 to nearly 100 percent of the total for two storms studied. Controlling nonpoint, unregulated,

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

PubMed Central

Eriksson, Per; Mourkas, Evangelos; González-Acuna, Daniel; Olsen, Björn; Ellström, Patrik

2017-01-01

ABSTRACT Introduction: Advances in the development of nucleic acid-based methods have dramatically facilitated studies of host–microbial interactions. Fecal DNA analysis can provide information about the host’s microbiota and gastrointestinal pathogen burden. Numerous studies have been conducted in mammals, yet birds are less well studied. Avian fecal DNA extraction has proved challenging, partly due to the mixture of fecal and urinary excretions and the deficiency of optimized protocols. This study presents an evaluation of the performance in avian fecal DNA extraction of six commercial kits from different bird species, focusing on penguins. Material and methods: Six DNA extraction kits were first tested according to the manufacturers’ instructions using mallard feces. The kit giving the highest DNA yield was selected for further optimization and evaluation using Antarctic bird feces. Results: Penguin feces constitute a challenging sample type: most of the DNA extraction kits failed to yield acceptable amounts of DNA. The QIAamp cador Pathogen kit (Qiagen) performed the best in the initial investigation. Further optimization of the protocol resulted in good yields of high-quality DNA from seven bird species of different avian orders. Conclusion: This study presents an optimized approach to DNA extraction from challenging avian fecal samples. PMID:29152162

A PILOT STUDY TO COMPARE MICROBIAL AND CHEMICAL INDICATORS OF HUMAN FECAL CONTAMINATION IN WATER

EPA Science Inventory

Limitations exist in applying traditional microbial methods for the detection of human fecal contamination of water. A pilot study was undertaken to compare the microbial and chemical indicators of human fecal contamination of water. Sixty-four water samples were collected in O...

Utility of Helicobacter spp. associated GFD markers for detecting avian fecal pollution in natural waters of two continents.

PubMed

Ahmed, W; Harwood, V J; Nguyen, K; Young, S; Hamilton, K; Toze, S

2016-01-01

Avian fecal droppings may negatively impact environmental water quality due to the presence of high concentrations of fecal indicator bacteria (FIB) and zoonotic pathogens. This study was aimed at evaluating the performance characteristics and utility of a Helicobacter spp. associated GFD marker by screening 265 fecal and wastewater samples from a range of avian and non-avian host groups from two continents (Brisbane, Australia and Florida, USA). The host-prevalence and -specificity of this marker among fecal and wastewater samples tested from Brisbane were 0.58 and 0.94 (maximum value of 1.00). These values for the Florida fecal samples were 0.30 (host-prevalence) and 1.00 (host-specificity). The concentrations of the GFD markers in avian and non-avian fecal nucleic acid samples were measured at a test concentration of 10 ng of nucleic acid at Brisbane and Florida laboratories using the quantitative PCR (qPCR) assay. The mean concentrations of the GFD marker in avian fecal nucleic acid samples (5.2 × 10(3) gene copies) were two orders of magnitude higher than non-avian fecal nucleic acid samples (8.6 × 10(1) gene copies). The utility of this marker was evaluated by testing water samples from the Brisbane River, Brisbane and a freshwater creek in Florida. Among the 18 water samples tested from the Brisbane River, 83% (n = 18) were positive for the GFD marker, and the concentrations ranged from 6.0 × 10(1)-3.2 × 10(2) gene copies per 100 mL water. In all, 92% (n = 25) water samples from the freshwater creek in Florida were also positive for the GFD marker with concentrations ranging from 2.8 × 10(1)-1.3 × 10(4) gene copies per 100 mL water. Based on the results, it can be concluded that the GFD marker is highly specific to avian host groups, and could be used as a reliable marker to detect the presence and amount of avian fecal pollution in environmental waters. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution.

PubMed

Peed, Lindsay A; Nietch, Christopher T; Kelty, Catherine A; Meckes, Mark; Mooney, Thomas; Sivaganesan, Mano; Shanks, Orin C

2011-07-01

Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between human and other animal sources of fecal pollution making it difficult to identify diffuse pollution sources. Human-associated quantitative real-time PCR (qPCR) methods in combination with low-order headwatershed sampling, precipitation information, and high-resolution geographic information system land use data can be useful for identifying diffuse source of human fecal pollution in receiving waters. To test this assertion, this study monitored nine headwatersheds over a two-year period potentially impacted by faulty septic systems and leaky sanitary sewer lines. Human fecal pollution was measured using three different human-associated qPCR methods and a positive significant correlation was seen between abundance of human-associated genetic markers and septic systems following wet weather events. In contrast, a negative correlation was observed with sanitary sewer line densities suggesting septic systems are the predominant diffuse source of human fecal pollution in the study area. These results demonstrate the advantages of combining water sampling, climate information, land-use computer-based modeling, and molecular biology disciplines to better characterize diffuse sources of human fecal pollution in environmental waters.

Administration of Bifidobacterium breve PS12929 and Lactobacillus salivarius PS12934, two strains isolated from human milk, to very low and extremely low birth weight preterm infants: a pilot study.

PubMed

Moles, Laura; Escribano, Esperanza; de Andrés, Javier; Montes, María Teresa; Rodríguez, Juan M; Jiménez, Esther; Sáenz de Pipaón, Miguel; Espinosa-Martos, Irene

2015-01-01

The preterm infant gut has been described as immature and colonized by an aberrant microbiota. Therefore, the use of probiotics is an attractive practice in hospitals to try to reduce morbidity and mortality in this population. The objective of this pilot study was to elucidate if administration of two probiotic strains isolated from human milk to preterm infants led to their presence in feces. In addition, the evolution of a wide spectrum of immunological compounds, including the inflammatory biomarker calprotectin, in both blood and fecal samples was also assessed. For this purpose, five preterm infants received two daily doses (~10(9) CFU) of a 1:1 mixture of Bifidobacterium breve PS12929 and Lactobacillus salivarius PS12934. Bacterial growth was detected by culture-dependent techniques in all the fecal samples. The phylum Firmicutes dominated in nearly all fecal samples while L. salivarius PS12934 was detected in all the infants at numerous sample collection points and B. breve PS12929 appeared in five fecal samples. Finally, a noticeable decrease in the fecal calprotectin levels was observed along time.

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches

PubMed Central

Hamilton, K. A.; Gyawali, P.; Toze, S.; Haas, C. N.

2016-01-01

ABSTRACT Avian and possum fecal droppings may negatively impact roof-harvested rainwater (RHRW) water quality due to the presence of zoonotic pathogens. This study was aimed at evaluating the performance characteristics of a possum feces-associated (PSM) marker by screening 210 fecal and wastewater samples from possums (n = 20) and a range of nonpossum hosts (n = 190) in Southeast Queensland, Australia. The host sensitivity and specificity of the PSM marker were 0.90 and 0.95 (maximum value, 1.00), respectively. The mean concentrations of the GFD marker in possum fecal DNA samples (8.8 × 107 gene copies per g of feces) were two orders of magnitude higher than those in the nonpossum fecal DNA samples (5.0 × 105 gene copies per g of feces). The host sensitivity, specificity, and concentrations of the avian feces-associated GFD marker were reported in our recent study (W. Ahmed, V. J. Harwood, K. Nguyen, S. Young, K. Hamilton, and S. Toze, Water Res 88:613–622, 2016, http://dx.doi.org/10.1016/j.watres.2015.10.050). The utility of the GFD and PSM markers was evaluated by testing a large number of tank water samples (n = 134) from the Brisbane and Currumbin areas. GFD and PSM markers were detected in 39 of 134 (29%) and 11 of 134 (8%) tank water samples, respectively. The GFD marker concentrations in PCR-positive samples ranged from 3.7 × 102 to 8.5 × 105 gene copies per liter, whereas the concentrations of the PSM marker ranged from 2.0 × 103 to 6.8 × 103 gene copies per liter of water. The results of this study suggest the presence of fecal contamination in tank water samples from avian and possum hosts. This study has established an association between the degradation of microbial tank water quality and avian and possum feces. Based on the results, we recommend disinfection of tank water, especially for tanks designated for potable use. IMPORTANCE The use of roof-harvested rainwater (RHRW) for domestic purposes is a globally accepted practice. The presence of pathogens in rainwater tanks has been reported by several studies, supporting the necessity for the management of potential health risks. The sources of fecal pollution in rainwater tanks are unknown. However, the application of microbial source tracking (MST) markers has the potential to identify the sources of fecal contamination in a rainwater tank. In this study, we provide evidence of avian and possum fecal contamination in tank water samples using molecular markers. This study established a potential link between the degradation of the microbial quality of tank water and avian and possum feces. PMID:27208100

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota.

PubMed

Horng, Katti R; Ganz, Holly H; Eisen, Jonathan A; Marks, Stanley L

2018-01-01

Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and -80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer ( F -value = 6.87, DF  = 3, P  < 0.001), storage temperature ( F -value=1.77, DF  = 3, P  = 0.037), and duration of sample storage ( F -value = 3.68, DF  = 3, P  < 0.001). Changes in bacterial composition were observed in samples stored in -80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations ( DF  = 8.57, P  < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content.

PubMed

Lewis, Zachery T; Davis, Jasmine C C; Smilowitz, Jennifer T; German, J Bruce; Lebrilla, Carlito B; Mills, David A

2016-01-01

Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.

Ground-water quality and effects of poultry confined animal feeding operations on shallow ground water, upper Shoal Creek basin, Southwest Missouri, 2000

USGS Publications Warehouse

Mugel, Douglas N.

2002-01-01

Forty-seven wells and 8 springs were sampled in May, October, and November 2000 in the upper Shoal Creek Basin, southwest Missouri, to determine if nutrient concentrations and fecal bacteria densities are increasing in the shallow aquifer as a result of poultry confined animal feeding operations (CAFOs). Most of the land use in the basin is agricultural, with cattle and hay production dominating; the number of poultry CAFOs has increased in recent years. Poultry waste (litter) is used as a source of nutrients on pasture land as much as several miles away from poultry barns.Most wells in the sample network were classified as ?P? wells, which were open only or mostly to the Springfield Plateau aquifer and where poultry litter was applied to a substantial acreage within 0.5 mile of the well both in spring 2000 and in several previous years; and ?Ag? wells, which were open only or mostly to the Springfield Plateau aquifer and which had limited or no association with poultry CAFOs. Water-quality data from wells and springs were grouped for statistical purposes as P1, Ag1, and Sp1 (May 2000 samples) and P2, Ag2, and Sp2 (October or November 2000 samples). The results of this study do not indicate that poultry CAFOs are affecting the shallow ground water in the upper Shoal Creek Basin with respect to nutrient concentrations and fecal bacteria densities. Statistical tests do not indicate that P wells sampled in spring 2000 have statistically larger concentrations of nitrite plus nitrate or fecal indicator bacteria densities than Ag wells sampled during the same time, at a 95-percent confidence level. Instead, the Ag wells had statistically larger concentrations of nitrite plus nitrate and fecal coliform bacteria densities than the P wells.The results of this study do not indicate seasonal variations from spring 2000 to fall 2000 in the concentrations of nutrients or fecal indicator bacteria densities from well samples. Statistical tests do not indicate statistically significant differences at a 95-percent confidence level for nitrite plus nitrate concentrations or fecal indicator bacteria densities between either P wells sampled in spring and fall 2000, or Ag wells sampled in spring and fall 2000. However, analysis of samples from springs shows that fecal streptococcus bacteria densities were statistically smaller in fall 2000 than in spring 2000 at a 95-percent confidence level.Nitrite plus nitrate concentrations in spring 2000 samples ranged from less than the detection level [0.02 mg/L (milligram per liter) as nitrogen] to 18 mg/L as nitrogen. Seven samples from three wells had nitrite plus nitrate concentrations at or larger than the maximum contaminant level (MCL) of 10 mg/L as nitrogen. The median nitrite plus nitrate concentrations were 0.28 mg/L as nitrogen for P1 samples, 4.6 mg/L as nitrogen for Ag1 samples, and 3.9 mg/L as nitrogen for Sp1 samples.Fecal coliform bacteria were detected in 1 of 25 P1 samples and 5 of 15 Ag1 samples. Escherichia coli (E. coli) bacteria were detected in 3 of 24 P1 samples and 1 of 13 Ag1 samples. Fecal streptococcus bacteria were detected in 8 of 25 P1 samples and 6 of 15 Ag1 samples. Bacteria densities in samples from wells ranged from less than 1 to 81 col/100 mL (colonies per 100 milliliters) of fecal coliform, less than 1 to 140 col/100 mL of E. coli, and less than 1 to 130 col/100 mL of fecal streptococcus. Fecal indicator bacteria densities in samples from springs were substantially larger than in samples from wells. In Sp1 samples, bacteria densities ranged from 12 to 3,300 col/100 mL of fecal coliform, 40 to 2,700 col/100 mL of E. coli, and 42 to 3,100 col/100 mL of fecal streptococcus.

Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources in Homosassa Springs, Florida

USGS Publications Warehouse

Griffin, Dale W.; Stokes, Rodger; Rose, J.B.; Paul, J.H.

2000-01-01

A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study.

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water.

PubMed

Ahmed, W; Staley, C; Sadowsky, M J; Gyawali, P; Sidhu, J P S; Palmer, A; Beale, D J; Toze, S

2015-10-01

In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Seed germination from lowland tapir (Tapirus terrestris) fecal samples collected during the dry season in the Northern Brazilian Amazon.

PubMed

Barcelos, Adriana Renata; Bobrowiec, Paulo Estefano D; Sanaiotti, Tânia Margarete; Gribel, Rogério

2013-03-01

This study evaluated the potential of lowland tapirs as seed dispersers in the northern Brazilian Amazon. The study analyzed the viability of seeds after passage through the gut. Fecal samples were collected from 6 different vegetation physiognomies in Viruá National Park during the dry season. The samples were then kept in a greenhouse for 16 months to allow the seeds to germinate. The seedling species were identified and classified according to the type of fruit, plant habit, seed size and type of ingestion. Of the 111 fecal samples, 94 (84.7%) had viable seeds of 75 species. Melastomataceae was the most frequent family with viable seeds in the fecal samples (69.1% of samples, N= 18 species). The data suggest that the importance of the lowland tapirs as dispersers is not restricted to the species consumed actively by frugivory but also extends to species accidentally consumed during browsing. The occurrence of both large and small viable seeds in the fecal samples as well as a number of large drupes, which probably cannot be transported via endozoochory by any other animal species, provide evidence of the ecological importance of lowland tapirs to the dynamics of the forest-campinarana vegetation mosaic in the region. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

Comparison of individual, pooled, and composite fecal sampling methods for detection of Salmonella on U.S. dairy operations

USDA-ARS?s Scientific Manuscript database

The objectives of this study were to estimate the prevalence of Salmonella for individual, pooled, and composite fecal samples and to compare culture results from each sample type for determining herd Salmonella infection status and identifying Salmonella serotype(s). The USDA’s National Animal Hea...

Comparison of Gull Feces-Specific Assays Targeting the 16S rRNA Genes of Catellicoccus marimammalium and Streptococcus spp.

PubMed Central

Ryu, Hodon; Griffith, John F.; Khan, Izhar U. H.; Hill, Stephen; Edge, Thomas A.; Toledo-Hernandez, Carlos; Gonzalez-Nieves, Joel

2012-01-01

Two novel gull-specific quantitative PCR (qPCR) assays were developed using 16S rRNA gene sequences from gull fecal clone libraries: a SYBR green assay targeting Streptococcus spp. (gull3) and a hydrolysis TaqMan assay targeting Catellicoccus marimammalium (gull4). The objectives of this study were to compare the host specificity of a previous C. marimammalium qPCR assay (gull2) with that of the new markers and to examine the presence of the three gull markers in environmental water samples from different geographic locations. Most of the gull fecal samples tested (n = 255) generated positive signals with the gull2 and gull4 assays (i.e., >86%), whereas only 28% were positive with gull3. Low prevalence and abundance of tested gull markers (0.6 to 15%) were observed in fecal samples from six nonavian species (n = 180 fecal samples), whereas the assays cross-reacted to some extent (13 to 31%) with other (nongull) avian fecal samples. The gull3 assay was positive against fecal samples from 11 of 15 avian species, including gull. Of the presumed gull-impacted water samples (n = 349), 86%, 59%, and 91% were positive with the gull2, the gull3, and the gull4 assays, respectively. Approximately 5% of 239 non-gull-impacted water samples were positive with the gull2 and the gull4 assays, whereas 21% were positive witg the gull3 assay. While the relatively high occurrence of gull2 and gull4 markers in waters impacted by gull feces suggests that these assays could be used in environmental monitoring studies, the data also suggest that multiple avian-specific assays will be needed to accurately assess the contribution of different avian sources in recreational waters. PMID:22226950

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks.

PubMed

Hale, Vanessa L; Tan, Chia L; Knight, Rob; Amato, Katherine R

2015-06-01

Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at -80 °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2 weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8 weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at -20 °C, freezing at -80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8weeks) prior to microbial extraction and analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Fecal indicators and zoonotic pathogens in household drinking water taps fed from rainwater tanks in Southeast Queensland, Australia.

PubMed

Ahmed, W; Hodgers, L; Sidhu, J P S; Toze, S

2012-01-01

In this study, the microbiological quality of household tap water samples fed from rainwater tanks was assessed by monitoring the numbers of Escherichia coli bacteria and enterococci from 24 households in Southeast Queensland (SEQ), Australia. Quantitative PCR (qPCR) was also used for the quantitative detection of zoonotic pathogens in water samples from rainwater tanks and connected household taps. The numbers of zoonotic pathogens were also estimated in fecal samples from possums and various species of birds by using qPCR, as possums and birds are considered to be the potential sources of fecal contamination in roof-harvested rainwater (RHRW). Among the 24 households, 63% of rainwater tank and 58% of connected household tap water (CHTW) samples contained E. coli and exceeded Australian drinking water guidelines of <1 CFU E. coli per 100 ml water. Similarly, 92% of rainwater tanks and 83% of CHTW samples also contained enterococci. In all, 21%, 4%, and 13% of rainwater tank samples contained Campylobacter spp., Salmonella spp., and Giardia lamblia, respectively. Similarly, 21% of rainwater tank and 13% of CHTW samples contained Campylobacter spp. and G. lamblia, respectively. The number of E. coli (P = 0.78), Enterococcus (P = 0.64), Campylobacter (P = 0.44), and G. lamblia (P = 0.50) cells in rainwater tanks did not differ significantly from the numbers observed in the CHTW samples. Among the 40 possum fecal samples tested, Campylobacter spp., Cryptosporidium parvum, and G. lamblia were detected in 60%, 13%, and 30% of samples, respectively. Among the 38 bird fecal samples tested, Campylobacter spp., Salmonella spp., C. parvum, and G. lamblia were detected in 24%, 11%, 5%, and 13% of the samples, respectively. Household tap water samples fed from rainwater tanks tested in the study appeared to be highly variable. Regular cleaning of roofs and gutters, along with pruning of overhanging tree branches, might also prove effective in reducing animal fecal contamination of rainwater tanks.

Fecal Indicators and Zoonotic Pathogens in Household Drinking Water Taps Fed from Rainwater Tanks in Southeast Queensland, Australia

PubMed Central

Hodgers, L.; Sidhu, J. P. S.; Toze, S.

2012-01-01

In this study, the microbiological quality of household tap water samples fed from rainwater tanks was assessed by monitoring the numbers of Escherichia coli bacteria and enterococci from 24 households in Southeast Queensland (SEQ), Australia. Quantitative PCR (qPCR) was also used for the quantitative detection of zoonotic pathogens in water samples from rainwater tanks and connected household taps. The numbers of zoonotic pathogens were also estimated in fecal samples from possums and various species of birds by using qPCR, as possums and birds are considered to be the potential sources of fecal contamination in roof-harvested rainwater (RHRW). Among the 24 households, 63% of rainwater tank and 58% of connected household tap water (CHTW) samples contained E. coli and exceeded Australian drinking water guidelines of <1 CFU E. coli per 100 ml water. Similarly, 92% of rainwater tanks and 83% of CHTW samples also contained enterococci. In all, 21%, 4%, and 13% of rainwater tank samples contained Campylobacter spp., Salmonella spp., and Giardia lamblia, respectively. Similarly, 21% of rainwater tank and 13% of CHTW samples contained Campylobacter spp. and G. lamblia, respectively. The number of E. coli (P = 0.78), Enterococcus (P = 0.64), Campylobacter (P = 0.44), and G. lamblia (P = 0.50) cells in rainwater tanks did not differ significantly from the numbers observed in the CHTW samples. Among the 40 possum fecal samples tested, Campylobacter spp., Cryptosporidium parvum, and G. lamblia were detected in 60%, 13%, and 30% of samples, respectively. Among the 38 bird fecal samples tested, Campylobacter spp., Salmonella spp., C. parvum, and G. lamblia were detected in 24%, 11%, 5%, and 13% of the samples, respectively. Household tap water samples fed from rainwater tanks tested in the study appeared to be highly variable. Regular cleaning of roofs and gutters, along with pruning of overhanging tree branches, might also prove effective in reducing animal fecal contamination of rainwater tanks. PMID:22020514

Salmonella Prevalence and Antimicrobial Susceptibility from the National Animal Health Monitoring System Sheep 2011 Study.

PubMed

Dargatz, David A; Marshall, Katherine L; Fedorka-Cray, Paula J; Erdman, Matthew M; Kopral, Christine A

2015-12-01

Salmonella is a major cause of foodborne illness and can cause clinical disease in animals. Understanding the on-farm ecology of Salmonella will be helpful in decreasing the risk of foodborne transmission. An objective of this study was to determine the prevalence of Salmonella among fecal samples collected on sheep operations in the United States. Another objective was to compare the use of composite fecal samples with fecal samples collected from individual sheep as a tool for screening sheep flocks for Salmonella. Sheep fecal samples (individual and composite) were collected on operations in 22 states. Salmonella isolates were characterized with regard to species, serotype, and antimicrobial susceptibility profile. Most operations (72.1%) had at least one positive sample and overall 26.9% of samples were positive. The percentage of positive samples varied by animal age class. Composite and individual samples gave similar results. The majority of the isolates (94%) were Salmonella enterica subspecies diarizonae serotype 61:-:1,5,7. Nearly all of the isolates (91.2%) tested for antimicrobial susceptibility were susceptible to all antimicrobials in the panel. The findings suggest that salmonellae typically associated with foodborne disease transmission are infrequently found on sheep operations in the United States.

Fecal shedding of non-O157 serogroups of Shiga toxin-producing Escherichia coli in feedlot cattle vaccinated with an Escherichia coli O157:H7 SRP vaccine or fed a Lactobacillus-based direct-fed microbial.

PubMed

Cernicchiaro, N; Renter, D G; Cull, C A; Paddock, Z D; Shi, X; Nagaraja, T G

2014-05-01

The objectives of this study were to determine whether fecal shedding of non-O157 Shiga toxin-producing Escherichia coli (STEC) in feedlot cattle was affected by the use of an E. coli O157:H7 vaccine or a direct-fed microbial (DFM) and whether the shedding of a particular non-O157 STEC serogroup within feces was associated with shedding of O157 or other non-O157 STEC serogroups. A total of 17,148 cattle in 40 pens were randomized to receive one, both, or neither (control) of the two interventions: a vaccine based on the siderophore receptor and porin proteins (E. coli SRP vaccine, two doses) and a DFM product (low-dose Bovamine). Fresh fecal samples (30 samples per pen) were collected weekly from pen floors for four consecutive weeks beginning approximately 56 days after study allocation. DNA extracted from enriched samples was tested for STEC O157 and non-O157 serogroups O26, O45, O103, O111, O121, and O145 and for four major virulence genes (stx1, stx2, eae, and ehxA) using an 11-gene multiplex PCR assay. Generalized linear mixed models were used to analyze the effects of treatments and make within-sample comparisons of the presence of O-serogroup-specific genes. Results of cumulative prevalence measures indicated that O157 (14.6%), O26 (10.5%), and O103 (10.3%) were the most prevalent STEC O serogroups. However, the vaccine, DFM, or both had no significant effect (P > 0.05) on fecal prevalence of the six non-O157 STEC serogroups in feedlot cattle. Within-sample comparisons of the presence of STEC serogroup-specific genes indicated that fecal shedding of E. coli O157 in cattle was associated with an increased probability (P < 0.05) of fecal shedding of STEC O26, O45, O103, and O121. Our study revealed that neither the E. coli O157:H7 vaccine, which reduced STEC O157 fecal shedding, nor the DFM significantly affected fecal shedding of non-O157 STEC serogroups, despite the fact that the most prevalent non-O157 STEC serogroups tended to occur concurrently with O157 STEC strains within fecal samples.

Determination of Baylisascaris schroederi Infection in Wild Giant Pandas by an Accurate and Sensitive PCR/CE-SSCP Method

PubMed Central

Zhang, Wenping; Yie, Shangmian; Yue, Bisong; Zhou, Jielong; An, Renxiong; Yang, Jiangdong; Chen, Wangli; Wang, Chengdong; Zhang, Liang; Shen, Fujun; Yang, Guangyou; Hou, Rong; Zhang, Zhihe

2012-01-01

It has been recognized that other than habitat loss, degradation and fragmentation, the infection of the roundworm Baylisascaris schroederi (B. schroederi) is one of the major causes of death in wild giant pandas. However, the prevalence and intensity of the parasite infection has been inconsistently reported through a method that uses sedimentation-floatation followed by a microscope examination. This method fails to accurately determine infection because there are many bamboo residues and/or few B. schroederi eggs in the examined fecal samples. In the present study, we adopted a method that uses PCR and capillary electrophoresis combined with a single-strand conformation polymorphism analysis (PCR/CE-SSCP) to detect B. schroederi infection in wild giant pandas at a nature reserve, and compared it to the traditional microscope approach. The PCR specifically amplified a single band of 279-bp from both fecal samples and positive controls, which was confirmed by sequence analysis to correspond to the mitochondrial COII gene of B. schroederi. Moreover, it was demonstrated that the amount of genomic DNA was linearly correlated with the peak area of the CE-SSCP analysis. Thus, our adopted method can reliably detect the infectious prevalence and intensity of B. schroederi in wild giant pandas. The prevalence of B. schroederi was found to be 54% in the 91 fecal samples examined, and 48% in the fecal samples of 31 identified individual giant pandas. Infectious intensities of the 91 fecal samples were detected to range from 2.8 to 959.2 units/gram, and from 4.8 to 959.2 units/gram in the fecal samples of the 31 identified giant pandas. For comparison, by using the traditional microscope method, the prevalence of B. schroederi was found to be only 33% in the 91 fecal samples, 32% in the fecal samples of the 31 identified giant pandas, and no reliable infectious intensity was observed. PMID:22911871

Determination of Baylisascaris schroederi infection in wild giant pandas by an accurate and sensitive PCR/CE-SSCP method.

PubMed

Zhang, Wenping; Yie, Shangmian; Yue, Bisong; Zhou, Jielong; An, Renxiong; Yang, Jiangdong; Chen, Wangli; Wang, Chengdong; Zhang, Liang; Shen, Fujun; Yang, Guangyou; Hou, Rong; Zhang, Zhihe

2012-01-01

It has been recognized that other than habitat loss, degradation and fragmentation, the infection of the roundworm Baylisascaris schroederi (B. schroederi) is one of the major causes of death in wild giant pandas. However, the prevalence and intensity of the parasite infection has been inconsistently reported through a method that uses sedimentation-floatation followed by a microscope examination. This method fails to accurately determine infection because there are many bamboo residues and/or few B. schroederi eggs in the examined fecal samples. In the present study, we adopted a method that uses PCR and capillary electrophoresis combined with a single-strand conformation polymorphism analysis (PCR/CE-SSCP) to detect B. schroederi infection in wild giant pandas at a nature reserve, and compared it to the traditional microscope approach. The PCR specifically amplified a single band of 279-bp from both fecal samples and positive controls, which was confirmed by sequence analysis to correspond to the mitochondrial COII gene of B. schroederi. Moreover, it was demonstrated that the amount of genomic DNA was linearly correlated with the peak area of the CE-SSCP analysis. Thus, our adopted method can reliably detect the infectious prevalence and intensity of B. schroederi in wild giant pandas. The prevalence of B. schroederi was found to be 54% in the 91 fecal samples examined, and 48% in the fecal samples of 31 identified individual giant pandas. Infectious intensities of the 91 fecal samples were detected to range from 2.8 to 959.2 units/gram, and from 4.8 to 959.2 units/gram in the fecal samples of the 31 identified giant pandas. For comparison, by using the traditional microscope method, the prevalence of B. schroederi was found to be only 33% in the 91 fecal samples, 32% in the fecal samples of the 31 identified giant pandas, and no reliable infectious intensity was observed.

A human fecal contamination index for ranking impaired ...

EPA Pesticide Factsheets

Human fecal pollution of surface water remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for recreational water quality risk management. The transition from a research subject to a management tool requires the integration of standardized water sampling, laboratory, and data analysis procedures. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and Bayesian data algorithm to establish a human fecal contamination index that can be used to rank impaired recreational water sites polluted with human waste. Stability and bias of index predictions were investigated under various parameters including siteswith different pollution levels, sampling period time range (1-15 weeks), and number of qPCR replicates per sample (2-14 replicates). Sensitivity analyses were conducted with simulated data sets (100 iterations) seeded with HF183/BacR287 qPCR laboratory measurements from water samples collected from three Southern California sites (588 qPCR measurements). Findings suggest that site ranking is feasible and that all parameters tested influence stability and bias in human fecal contamination indexscoring. Trends identified by sensitivity analyses will provide managers with the information needed to design and conduct field studies to rank impaired recreational water sites based

Factors affecting genotyping success in giant panda fecal samples.

PubMed

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong; Zhang, He-Min

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH -20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at -20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates ( P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.

Factors affecting genotyping success in giant panda fecal samples

PubMed Central

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies. PMID:28560107

Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene

USGS Publications Warehouse

Lamendella, R.; Domingo, J.W.S.; Oerther, D.B.; Vogel, J.R.; Stoeckel, D.M.

2007-01-01

We evaluated the efficacy, sensitivity, host-specificity, and spatial/temporal dynamics of human- and ruminant-specific 16S rRNA gene Bacteroidetes markers used to assess the sources of fecal pollution in a fecally impacted watershed. Phylogenetic analyses of 1271 fecal and environmental 16S rRNA gene clones were also performed to study the diversity of Bacteroidetes in this watershed. The host-specific assays indicated that ruminant feces were present in 28-54% of the water samples and in all sampling seasons, with increasing frequency in downstream sites. The human-targeted assays indicated that only 3-5% of the water samples were positive for human fecal signals, although a higher percentage of human-associated signals (19-24%) were detected in sediment samples. Phylogenetic analysis indicated that 57% of all water clones clustered with yet-to-be-cultured Bacteroidetes species associated with sequences obtained from ruminant feces, further supporting the prevalence of ruminant contamination in this watershed. However, since several clusters contained sequences from multiple sources, future studies need to consider the potential cosmopolitan nature of these bacterial populations when assessing fecal pollution sources using Bacteroidetes markers. Moreover, additional data is needed in order to understand the distribution of Bacteroidetes host-specific markers and their relationship to water quality regulatory standards. ?? 2006 Federation of European Microbiological Societies.

Fecal-indicator bacteria in streams alonga gradient of residential development

USGS Publications Warehouse

Frenzel, Steven A.; Couvillion, Charles S.

2002-01-01

Fecal-indicator bacteria were sampled at 14 stream sites in Anchorage, Alaska, USA, as part of a study to determine the effects of urbanization on water quality. Population density in the subbasins sampled ranged from zero to 1,750 persons per square kilometer. Higher concentrations of fecal-coliform, E. coli, and enterococci bacteria were measured at the most urbanized sites. Although fecal-indicator bacteria concentrations were higher in summer than in winter, seasonal differences in bacteria concentrations generally were not significant. Areas served by sewer systems had significantly higher fecal-indicator bacteria concentrations than did areas served by septic systems. The areas served by sewer systems also had storm drains that discharged directly to the streams, whereas storm sewers were not present in the areas served by septic systems. Fecal-indicator bacteria concentrations were highly variable over a two-day period of stable streamflow, which may have implications for testing of compliance to water-quality standards.

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile.

PubMed

Kumar, Ranjit; Maynard, Craig L; Eipers, Peter; Goldsmith, Kelly T; Ptacek, Travis; Grubbs, J Aaron; Dixon, Paula; Howard, Donna; Crossman, David K; Crowley, Michael R; Benjamin, William H; Lefkowitz, Elliot J; Weaver, Casey T; Rodriguez, J Martin; Morrow, Casey D

2016-01-13

Fecal microbiota transplants (FMT) are an effective treatment for patients with gut microbe dysbiosis suffering from recurrent C. difficile infections. To further understand how FMT reconstitutes the patient's gut commensal microbiota, we have analyzed the colonization potential of the donor, recipient and recipient post transplant fecal samples using transplantation in gnotobiotic mice. A total of nine samples from three human donors, recipient's pre and post FMT were transplanted into gnotobiotic mice. Microbiome analysis of three donor fecal samples revealed the presence of a high relative abundance of commensal microbes from the family Bacteriodaceae and Lachnospiraceae that were almost absent in the three recipient pre FMT fecal samples (<0.01%). The microbe composition in gnotobiotic mice transplanted with the donor fecal samples was similar to the human samples. The recipient samples contained Enterobacteriaceae, Lactobacillaceae, Enterococcaceae in relative abundance of 43, 11, 8%, respectively. However, gnotobiotic mice transplanted with the recipient fecal samples had an average relative abundance of unclassified Clostridiales of 55%, approximately 7000 times the abundance in the recipient fecal samples prior to transplant. Microbiome analysis of fecal samples from the three patients early (2-4 weeks) after FMT revealed a microbe composition with the relative abundance of both Bacteriodaceae and Lachnospiraceae that was approximately 7% of that of the donor. In contrast, gnotobioitc mice transplanted with the fecal samples obtained from the three at early times post FMT revealed increases in the relative abundance of Bacteriodaceae and Lachnospiraceae microbe compositions to levels similar to the donor fecal samples. Furthermore, the unclassified Clostridiales in the recipient samples post FMT was reduced to an average of 10%. We have used transplantation into gnotobiotic mice to evaluate the colonization potential of microbiota in FMT patients early after transplant. The commensal microbes present at early times post FMT out competed non-commensal microbes (e.g. such as unclassified Clostridiales) for niche space. The selective advantage of these commensal microbes to occupy niches in the gastrointestinal tract helps to explain the success of FMT to reconstitute the gut microbe community of patients with recurrent C. difficile infections.

Eukaryotic viruses in wastewater samples from the United States

USGS Publications Warehouse

Symonds, E.M.; Griffin, Dale W.; Breitbart, M.

2009-01-01

Human fecal matter contains a large number of viruses, and current bacterial indicators used for monitoring water quality do not correlate with the presence of pathogenic viruses. Adenoviruses and enteroviruses have often been used to identify fecal pollution in the environment; however, other viruses shed in fecal matter may more accurately detect fecal pollution. The purpose of this study was to develop a baseline understanding of the types of viruses found in raw sewage. PCR was used to detect adenoviruses, enteroviruses, hepatitis B viruses, herpesviruses, morbilliviruses, noroviruses, papillomaviruses, picobirnaviruses, reoviruses, and rotaviruses in raw sewage collected throughout the United States. Adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples and 25% and 33% of final effluent samples, respectively. Enteroviruses and noroviruses were detected in 75% and 58% of raw sewage samples, respectively, and both viral groups were found in 8% of final effluent samples. This study showed that adenoviruses, enteroviruses, noroviruses, and picobirnaviruses are widespread in raw sewage. Since adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples, they are potential markers of fecal contamination. Additionally, this research uncovered previously unknown sequence diversity in human picobirnaviruses. This baseline understanding of viruses in raw sewage will enable educated decisions to be made regarding the use of different viruses in water quality assessments. Copyright ?? 2009, American Society for Microbiology. All Rights Reserved.

Environmental sampling to predict fecal prevalence of Salmonella in an intensively monitored dairy herd.

PubMed

Van Kessel, J S; Karns, J S; Wolfgang, D R; Hovingh, E; Jayarao, B M; Van Tassell, C P; Schukken, Y H

2008-10-01

Although dairy cattle are known reservoirs for salmonellae, cattle that are shedding this organism are often asymptomatic and difficult to identify. A dairy herd that was experiencing a sustained, subclinical outbreak of Salmonella enterica subsp. enterica Cerro was monitored for 2 years. Fecal samples from the lactating cows were collected every 6 to 8 weeks and tested for the presence of Salmonella. Fecal prevalence of Salmonella fluctuated throughout the observation period and ranged from 8 to 88%. Manure composites and water trough samples were collected along with the fecal samples, and bulk milk and milk filters were cultured for the presence of Salmonella on a weekly basis. Over 90% of the manure composites--representing high-animal-traffic areas-were positive at each sampling. Salmonella was detected in 11% of milk samples and in 66% of the milk filters. Results of weekly bulk milk quality testing (i.e., bulk tank somatic cell score, standard plate count, preliminary incubation count) were typically well within acceptable ranges. Milk quality variables had low correlations with herd Salmonella fecal prevalence. When observed over time, sampling period average prevalence of Salmonella in milk filters closely paralleled fecal prevalence of Salmonella in the herd. Based on results of this study, milk filters appear to be an effective method for monitoring shedding prevalence at the herd level. In-line filter testing is also a more sensitive measure of Salmonella, and perhaps other pathogens, in raw milk than testing the milk alone.

Diet composition and terrestrial prey selection of the Laysan teal on Laysan Island

USGS Publications Warehouse

Reynolds, M.H.; Slotterback, J.W.; Walters, J.R.

2006-01-01

The Laysan teal (Anas laysanensis) is an endangered dabbling duck endemic to the Hawaiian Archipelago but currently restricted to a single breeding population on Laysan Island. We studied its diet using fecal analysis and behavioral observations. Laysan teal fecal samples (N=118) contained prey items in 15 primary prey categories with a mean of 2.9 (range 0-7) taxa per sample. Sixty-two of these fecal samples were quantified with 2,270 prey items identified (mean items per sample 37; range 0-205). Based on fecal analysis and behavioral observations, we learned that the Laysan teal is not strictly a macroinsectivore as previously reported, but consumed seeds, succulent leaves, and algae, in addition to adult and larval diptera, ants, lepidoptera, coleoptera, and Artemia. We compared abundance of invertebrates from two terrestrial foraging substrates, soil and standing vegetation, to the abundance of invertebrate prey items counted in fecal samples collected from these habitats for the same period. In the soil substrate, Laysan teal selected two of the most abundant invertebrates, lepidoptera larvae and coleoptera. In the standing vegetation, Laysan teal selected the most abundant taxa: coleoptera. Amphipods were consumed in proportion to their abundance, and small gastropods (Tornatellides sp.), isopods, and arachnids were avoided or were identified in fecal matter in disproportion to their abundance in the foraging habitat. We compared fecal composition of samples collected in aquatic and terrestrial habitats and detected significant differences in samples' species compositions. The conservation implications of the adult Laysan teal's diet are positive, since results indicate that the Laysan teal are opportunistic insectivores, and exhibit dietary flexibility that includes seeds and other food. Dietary flexibility improves the possibility of successfully reestablishing populations on other predator-free islands.

Quantification of Shiga Toxin-Converting Bacteriophages in Wastewater and in Fecal Samples by Real-Time Quantitative PCR ▿

PubMed Central

Imamovic, Lejla; Ballesté, Elisenda; Jofre, Juan; Muniesa, Maite

2010-01-01

Shiga toxin-converting bacteriophages (Stx phages) are involved in the pathogenicity of some enteric bacteria, such as Escherichia coli O157:H7. Stx phages are released from their bacterial hosts after lytic induction and remain free in the environment. Samples were analyzed for the presence of free Stx phages by an experimental approach based on the use of real-time quantitative PCR (qPCR), which enables stx to be detected in the DNA from the viral fraction of each sample. A total of 150 samples, including urban raw sewage samples, wastewater samples with fecal contamination from cattle, pigs, and poultry, and fecal samples from humans and diverse animals, were used in this study. Stx phages were detected in 70.0% of urban sewage samples (10 to 103 gene copies [GC] per ml) and in 94.0% of animal wastewater samples of several origins (10 to 1010 GC per ml). Eighty-nine percent of cattle fecal samples were positive for Stx phages (10 to 105 GC per g of sample), as were 31.8% of other fecal samples of various origins (10 to 104 GC per g of sample). The stx2 genes and stx2 variants were detected in the viral fraction of some of the samples after sequencing of stx2 fragments amplified by conventional PCR. The occurrence and abundance of Stx phages in the extraintestinal environment confirm the role of Stx phages as a reservoir of stx in the environment. PMID:20622134

Evaluation of fecal elastase and serum cholecystokinin in dogs with a false positive fecal elastase test.

PubMed

Steiner, J M; Rehfeld, J F; Pantchev, N

2010-01-01

An assay for the measurement of pancreatic elastase in dog feces has been introduced. The goal of this study was to evaluate the rate of false-positive fecal-elastase test results in dogs with suspected exocrine pancreatic insufficiency (EPI) and to assess serum cholecystokinin (CCK) concentrations in dogs with a false positive fecal elastase test result. Twenty-six fecal and serum samples from dogs suspected of EPI, for which samples had been submitted to a commercial laboratory (Vet Med Labor) for analysis. Prospective study. Serum trypsin-like immunoreactivity (TLI) was measured in 26 dogs with a decreased fecal elastase concentration of <10 microg/g feces. Serum CCK concentrations were measured in 21 of these dogs. Of 26 dogs with a decreased fecal elastase concentration, 6 (23%) had serum TLI concentrations within or above the reference range. Serum CCK concentrations were significantly higher in dogs with a true positive fecal elastase test result (median: 1.1 pmol/L; range: 0.1-3.3 pmol/L) than in those with a false positive fecal elastase test result (median: 0.1 pmol/L; range: 0.1-0.9 pmol/L; P value = .0163). The rate of false positive fecal elastase test results was high in this group of dogs, suggesting that diagnosis of EPI must be confirmed by other means. The decreased CCK concentration in dogs with a false positive fecal elastase test result could suggest that false positive results are because of decreased stimulation of exocrine pancreatic function caused by other conditions.

Using host-associated genetic markers to investigate sources of fecal contamination in two Vermont streams

USGS Publications Warehouse

Medalie, Laura; Matthews, Leslie J.; Stelzer, Erin A.

2011-01-01

The use of host-associated Bacteroidales-based 16S ribosomal ribonucleic acid genetic markers was investigated as a tool for providing information to managers on sources of bacterial impairment in Vermont streams. The study was conducted during 2009 in two watersheds on the U.S. Environmental Protection Agency's 303(d) List of Impaired Waters, the Huntington and the Mettawee Rivers. Streamwater samples collected during high-flow and base-flow conditions were analyzed for concentrations of Escherichia coli (E. coli) and Bacteroidales genetic markers (General AllBac, Human qHF183 and BacHum, Ruminant BoBac, and Canid BacCan) to identify humans, ruminants, and canids as likely or unlikely major sources of fecal contamination. Fecal reference samples from each of the potential source groups, as well as from common species of wildlife, were collected during the same season and from the same watersheds as water samples. The results were combined with data from other states to assess marker cross reaction and to relate marker results to E. coli, the regulated water-quality parameter, with a higher degree of statistical significance. Results from samples from the Huntington River collected under different flow conditions on three dates indicated that humans were unlikely to be a major source of fecal contamination, except for a single positive result at one station that indicated the potential for human sources. Ruminants (deer, moose, cow, or sheep) were potential sources of fecal contamination at all six stations on the Huntington River during one high-flow event and at all but two stations during the other high-flow event. Canids were potential sources of fecal contamination at some stations during two high-flow events, with genetic-marker concentrations in samples from two of the six stations showing consistent positive results for canids for both storm dates. A base-flow sample showed no evidence of major fecal contamination in the Huntington River from humans, ruminants, or canids. Results from samples from the Mettawee River watershed collected during high-flow conditions (12 storm samples on 2 dates at 6 stations) indicated that there was no evidence of fecal contamination from humans in seven samples and possible evidence in five samples. Results for humans were positive for only one station during both storm events. For two of the five samples with evidence for human fecal contamination, results for two different human genetic markers agreed, but results from three samples were inconsistent. In samples from five of the six Mettawee stations, ruminants were a potential source of fecal contamination on at least one of the three sampled dates, including three positive results for the base-flow sample. Yet samples from all of the stations that showed positive results for ruminants did so for only one or two of the three sampled dates. Samples from only one of the six stations gave consistent results, which were negative for ruminants for all three dates. In the Mettawee River base-flow sample, humans were an unlikely source of major fecal contamination. Factors that may influence results and conclusions include the timing of sample collection relative to the storm event; variability of E. coli and Bacteroidales concentrations in fecal reference samples and in water; sampling and analytical errors; the potential cross reactivity of host-associated genetic markers; and different persistence and survival rates of E. coli bacteria and Bacteroidales genetic markers on land, in water, and by season. These factors interfere with the ability to directly relate Bacteroidales concentrations to E. coli concentrations in river samples. It must be recognized that while use of Bacteroidales genetic markers as a source tracking tool coupled with the interpretive approach described in this report cannot be used quantitatively to pinpoint sources, it can be used to exclude potential sources as major contributors to fecal contamination.

Identification of fecal contamination sources in water using host-associated markers.

PubMed

Krentz, Corinne A; Prystajecky, Natalie; Isaac-Renton, Judith

2013-03-01

In British Columbia, Canada, drinking water is tested for total coliforms and Escherichia coli, but there is currently no routine follow-up testing to investigate fecal contamination sources in samples that test positive for indicator bacteria. Reliable microbial source tracking (MST) tools to rapidly test water samples for multiple fecal contamination markers simultaneously are currently lacking. The objectives of this study were (i) to develop a qualitative MST tool to identify fecal contamination from different host groups, and (ii) to evaluate the MST tool using water samples with evidence of fecal contamination. Singleplex and multiplex polymerase chain reaction (PCR) were used to test (i) water from polluted sites and (ii) raw and drinking water samples for presence of bacterial genetic markers associated with feces from humans, cattle, seagulls, pigs, chickens, and geese. The multiplex MST assay correctly identified suspected contamination sources in contaminated waterways, demonstrating that this test may have utility for heavily contaminated sites. Most raw and drinking water samples analyzed using singleplex PCR contained at least one host-associated marker. Singleplex PCR was capable of detecting host-associated markers in small sample volumes and is therefore a promising tool to further analyze water samples submitted for routine testing and provide information useful for water quality management.

Naturally colonized beef cattle populations fed combinations of yeast culture and an ionophore in finishing diets containing dried distiller's grains with solubles had similar fecal shedding of Escherichia coli O157:H7.

PubMed

Swyers, K L; Carlson, B A; Nightingale, K K; Belk, K E; Archibeque, S L

2011-06-01

Beef steers (n = 252) were used to evaluate the effects of dietary supplement on fecal shedding of Escherichia coli O157:H7. Seven pens of 9 steers (63 steers per treatment) were fed diets supplemented with or without yeast culture (YC) or monensin (MON) and their combination (YC × MON). YC and MON were offered at 2.8 g/kg and 33 mg/kg of dry matter intake, respectively. Environmental sponge samples (from each pen floor, feed bunk, and water trough) were collected on day 0. Rectal fecal grab samples were collected on days 0, 28, 56, 84, 110, and 125. Samples were collected and pooled by pen and analyzed for presumptive E. coli O157:H7 colonies, which were confirmed by a multiplex PCR assay and characterized by pulsed-field gel electrophoresis (PFGE) typing. On day 0, E. coli O157:H7 was detected in 7.0% of feed bunk samples and 14.3% of pen floor samples but in none of the water trough samples. The 71.4% prevalence of E. coli O157:H7 in fecal samples on day 0 decreased significantly (P < 0.05) over time. E. coli O157:H7 fecal shedding was not associated with dietary treatment (P > 0.05); however, in cattle fed YC and YC × MON fecal shedding was 0% by day 28. Eight Xba I PFGE subtypes were identified, and a predominant subtype and three closely related subtypes (differing by three or fewer bands) accounted for 78.7% of environmental and fecal isolates characterized. Results from this study indicate that feeding YC to cattle may numerically decrease but not eliminate fecal shedding of E. coli O157:H7 at the onset of treatment and that certain E. coli O157 subtypes found in the feedlot environment may persist in feedlot cattle.

Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators

USGS Publications Warehouse

Haack, S.K.; Duris, J.W.; Fogarty, L.R.; Kolpin, D.W.; Focazio, M.J.; Furlong, E.T.; Meyer, M.T.

2009-01-01

The objective of this study was to compare fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli [EC], and enterococci [ENT]) concentrations with a wide array of typical organic wastewater chemicals and selected bacterial genes as indicators of fecal pollution in water samples collected at or near 18 surface water drinking water intakes. Genes tested included esp (indicating human-pathogenic ENT) and nine genes associated with various animal sources of shiga-toxin-producing EC (STEC). Fecal pollution was indicated by genes and/or chemicals for 14 of the 18 tested samples, with little relation to FIB standards. Of 13 samples with <50 EC 100 mL-1, human pharmaceuticals or chemical indicators of wastewater treatment plant effluent occurred in six, veterinary antibiotics were detected in three, and stx1 or stx2 genes (indicating varying animal sources of STEC) were detected in eight. Only the EC eaeA gene was positively correlated with FIB concentrations. Human-source fecal pollution was indicated by the esp gene and the human pharmaceutical carbamazepine in one of the nine samples that met all FIB recreational water quality standards. Escherichia coli rfbO157 and stx2c genes, which are typically associated with cattle sources and are of potential human health significance, were detected in one sample in the absence of tested chemicals. Chemical and gene-based indicators of fecal contamination may be present even when FIB standards are met, and some may, unlike FIB, indicate potential sources. Application of multiple water quality indicators with variable environmental persistence and fate may yield greater confidence in fecal pollution assessment and may inform remediation decisions. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Modulation of gut microbiota and increase in fecal water content in mice induced by administration of Lactobacillus kefiranofaciens DN1.

PubMed

Jeong, Dana; Kim, Dong-Hyeon; Kang, Il-Byeong; Kim, Hyunsook; Song, Kwang-Young; Kim, Hong-Seok; Seo, Kun-Ho

2017-02-22

Lactobacillus kefiranofaciens is the key probiotic bacterium in kefir. In this study, we investigated the effects of oral consumption of L. kefiranofaciens on the fecal quality and intestinal microbiota of mice. Four-week-old Balb/c mice were divided into two groups (n = 8 each) and administered 0.2 mL of saline (control group) or saline containing 2 × 10 8 cfu L. kefiranofaciens DN1 (LKF_DN1 group) for two weeks. At the end of the experiment, their fecal samples were collected and the fecal quality and microbiota were assessed. The LKF_DN1 group exhibited higher total fecal weight and fecal weight per stool sample than the control group (p < 0.05). Interestingly, the fecal water content was significantly higher in the fecal samples of the LKF_DN1 group than in those of the control group (p < 0.05). The numbers of total bacteria, Firmicutes, Bacteroidetes, Lactobacillus, and Prevotella were significantly higher in the LKF_DN1 group than in the control group (p < 0.05). In contrast, the number of opportunistic pathogens, including Proteobacteria and Enterobacteriaceae, and the percentage of genus Clostridium among the total bacteria were significantly reduced in the LKF_DN1 group (p < 0.05). Our data suggest that regular L. kefiranofaciens DN1 administration could alleviate constipation and improve gut microbiota.

Trail Creek I: Assessing the Water Quality of Streams using Fecal Indicator Bacteria and Microbial Source Tracking

NASA Astrophysics Data System (ADS)

Saintil, T.; Radcliffe, D. E.; Rasmussen, T. C.; Kannan, A.

2017-12-01

Fecal coliforms are indicators for disease-causing pathogens. The United States Environmental Protection Agency (US. EPA) recommends the use of E. coli and Enterococci because they are highly correlated with pathogenic organisms in recreational waters. This standard method helps to determine the overall water quality and the potential health risks. Studies have shown that it is difficult to estimate the exact sources of fecal contamination because both human and certain animal species contain E. coli and Enterococci in their waste. Certain strains of E. coli and Enterococci are also able to survive outside of their hosts, which should not be the case for an appropriate fecal indicator. As a result, microbial source tracking (MST) studies use gene specific markers to identify the possible contributors to water pollution whether human or animal. Trail Creek is a second-order stream located in Athens-Clarke County, GA. The 33-km2 watershed is approximately 64% forests, 18% pastures and 16% residential communities. Trail Creek is on the TMDL list and an extended study on the relationships between the different factors causing elevated fecal bacteria is needed. Synoptic sampling events were conducted during baseflow conditions at six locations. Storm sampling events (> 8 mm) were captured using automated samplers at two locations. These samplers were equipped with pressure transducers which record stage at 30-minute intervals. The samples were analyzed for fecal coliform, E. Coli and Enterococci. Water quality parameters including temperature, specific conductance, dissolved oxygen, pH, and turbidity were also recorded. Relationships between the parameters and fecal indicator bacteria show inconsistent patterns and high variability. Using quantitative PCR and MST techniques, the human specific marker (HF183) and ruminant marker (Rum2Bac) were used to identify the fecal sources in both baseflow and storm samples. The presence and abundance of the different markers at each site will be presented. The findings will be useful for adopting best management practices and implementing green infrastructure for the reduction of fecal pollution.

Fecal Leukocytes in Children Infected with Diarrheagenic Escherichia coli▿

PubMed Central

Mercado, Erik H.; Ochoa, Theresa J.; Ecker, Lucie; Cabello, Martin; Durand, David; Barletta, Francesca; Molina, Margarita; Gil, Ana I.; Huicho, Luis; Lanata, Claudio F.; Cleary, Thomas G.

2011-01-01

The purpose of this study was to determine the presence and quantity of fecal leukocytes in children infected with diarrheagenic Escherichia coli and to compare these levels between diarrhea and control cases. We analyzed 1,474 stool samples from 935 diarrhea episodes and 539 from healthy controls of a cohort study of children younger than 2 years of age in Lima, Peru. Stools were analyzed for common enteric pathogens, and diarrheagenic E. coli isolates were studied by a multiplex real-time PCR. Stool smears were stained with methylene blue and read by a blinded observer to determine the number of polymorphonuclear leukocytes per high-power field (L/hpf). Fecal leukocytes at >10 L/hpf were present in 11.8% (110/935) of all diarrheal episodes versus 1.1% (6/539) in controls (P < 0.001). Among stool samples with diarrheagenic E. coli as the only pathogen isolated (excluding coinfection), fecal leukocytes at >10 L/hpf were present in 8.5% (18/212) of diarrhea versus 1.3% (2/157) of control samples (P < 0.01). Ninety-five percent of 99 diarrheagenic E. coli diarrhea samples were positive for fecal lactoferrin. Adjusting for the presence of blood in stools, age, sex, undernutrition, and breastfeeding, enterotoxigenic E. coli (ETEC) isolation as a single pathogen, excluding coinfections, was highly associated with the presence of fecal leukocytes (>10 L/hpf) with an odds ratio (OR) of 4.1 (95% confidence interval [CI], 1.08 to 15.51; P < 0.05). Although diarrheagenic E. coli was isolated with similar frequencies in diarrhea and control samples, clearly it was associated with a more inflammatory response during symptomatic infection; however, in general, these pathogens elicited a mild inflammatory response. PMID:21325554

Sewage Reflects the Microbiomes of Human Populations

PubMed Central

Newton, Ryan J.; McLellan, Sandra L.; Dila, Deborah K.; Vineis, Joseph H.; Morrison, Hilary G.; Eren, A. Murat

2015-01-01

ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. PMID:25714718

Fecal-indicator bacteria in the Allegheny, Monongahela, and Ohio Rivers, near Pittsburgh, Pennsylvania, July-September 2001

USGS Publications Warehouse

Fulton, John W.; Buckwalter, Theodore F.

2004-01-01

This report presents the results of a study by the Allegheny County Health Department (ACHD) and the U.S. Geological Survey (USGS) to determine the concentrations of fecal-indicator bacteria in the Allegheny, Monongahela, and Ohio Rivers (Three Rivers) in Allegheny County, Pittsburgh, Pa. Water-quality samples and river-discharge measurements were collected from July to September 2001 during dry- (72-hour dry antecedent period), mixed-, and wet-weather (48-hour dry antecedent period and at least 0.3 inch of rain in a 6-hour period) conditions at five sampling sites on the Three Rivers in Allegheny County. Water samples were collected weekly to establish baseline conditions and during successive days after three wet-weather events. Water samples were analyzed for fecal-indicator organisms including fecal-coliform (FC) bacteria, Escherichia coli (E. coli), and enterococci bacteria. Water samples were collected by the USGS and analyzed by the ACHD Laboratory. At each site, left-bank and right-bank surface-water samples were collected in addition to a composite sample (discharge-weighted sample representative of the channel cross section as a whole) at each site. Fecal-indicator bacteria reported in bank and composite samples were used to evaluate the distribution and mixing of bacteria-source streams in receiving waters such as the Three Rivers. Single-event concentrations of enterococci, E. coli, and FC during dry-weather events were greater than State and Federal water-quality standards (WQS) in 11, 28, and 28 percent of the samples, respectively; during mixed-weather events, concentrations of fecal-indicator bacteria were greater than WQS in 28, 37, and 43 percent of the samples, respectively; and during wet-weather events, concentrations of fecal-indicator bacteria were greater than WQS in 56, 71, and 81 percent of samples, respectively. Single-event, wet-weather concentrations exceeded those during dry-weather events for all sites except the Allegheny River at Oakmont. For this site, dilution during wet-weather events or the lack of source streams upgradient of the site may have caused this anomaly. Additionally, single-event concentrations of E. coli and FC frequently exceeded the WQS reported during wet-weather events. It is difficult to establish a short-term trend in fecal-indicator bacteria concentrations as a function of time after a wet-weather event due to factors including the spatial variability of sources contributing fecal material, dry-weather discharges, resuspension of bottom sediments, and flow augmentation from reservoirs. Relative to E. coli and enterococci, FC concentrations appeared to decrease with time, which may be attributed to the greater die-off rate for FC bacteria. Fecal-indicator bacteria concentrations at a site are dependent on the spatial distribution of point sources upstream of the station, the time-of-travel, rate of decay, and the degree of mixing and resuspension. Therefore, it is difficult to evaluate whether the left, right, and composite concentrations reported at a particular site are significantly different. To evaluate the significance of the fecal-indicator bacteria concentrations and turbidity reported in grab and composite samples during dry-, mixed-, and wet-weather events, data sets were evaluated using Wilcoxon rank sum tests. Tests were conducted using the fecal-indicator bacteria colonies and turbidity reported for each station for a given weather event. For example, fecal coliform counts reported in the left-bank sample were compared against the right-bank and composite samples, respectively, for the Ohio River at Sewickley site during dry-, mixed-, and wet-weather events. The statistical analyses suggest that, depending on the sampling site, the fecal-bacteria concentrations measured at selected locations vary spatially within a channel (left bank compared to right, right bank compared to composite). The most significant differences occurred between feca

Use of Occult Blood Detection Cards for Real-Time PCR-Based Diagnosis of Schistosoma Mansoni Infection

PubMed Central

Schunk, Mirjam; Kebede Mekonnen, Seleshi; Wondafrash, Beyene; Mengele, Carolin; Fleischmann, Erna; Herbinger, Karl-Heinz; Verweij, Jaco J.; Geldmacher, Christof; Bretzel, Gisela; Löscher, Thomas; Zeynudin, Ahmed

2015-01-01

Background In Schistosoma mansoni infection, diagnosis and control after treatment mainly rely on parasitological stool investigations which are laborious and have limited sensitivity. PCR methods have shown equal or superior sensitivity but preservation and storage methods limit their use in the field. Therefore, the use of occult blood detection cards (fecal cards) for easy sampling and storage of fecal samples for further PCR testing was evaluated in a pilot study. Methodology Stool specimens were collected in a highly endemic area for S. mansoni in Ethiopia and submitted in an investigator-blinded fashion to microscopic examination by Kato-Katz thick smear as well as to real-time PCR using either fresh frozen stool samples or stool smears on fecal cards which have been stored at ambient temperature for up to ten months. Principal Findings Out of 55 stool samples, 35 were positive by microscopy, 33 and 32 were positive by PCR of frozen samples and of fecal card samples, respectively. When microscopy was used as diagnostic “gold standard”, the sensitivity of PCR on fresh stool was 94.3% (95%-CI: 86.6; 100) and on fecal cards 91.4% (95%-CI: 82.2; 100). Conclusions The use of fecal cards proved to be a simple and useful method for stool collection and prolonged storage prior to PCR based diagnosis of S. mansoni infection. This technique may be a valuable approach for large scale surveillance and post treatment assessments PMID:26360049

Use of Occult Blood Detection Cards for Real-Time PCR-Based Diagnosis of Schistosoma Mansoni Infection.

PubMed

Schunk, Mirjam; Kebede Mekonnen, Seleshi; Wondafrash, Beyene; Mengele, Carolin; Fleischmann, Erna; Herbinger, Karl-Heinz; Verweij, Jaco J; Geldmacher, Christof; Bretzel, Gisela; Löscher, Thomas; Zeynudin, Ahmed

2015-01-01

In Schistosoma mansoni infection, diagnosis and control after treatment mainly rely on parasitological stool investigations which are laborious and have limited sensitivity. PCR methods have shown equal or superior sensitivity but preservation and storage methods limit their use in the field. Therefore, the use of occult blood detection cards (fecal cards) for easy sampling and storage of fecal samples for further PCR testing was evaluated in a pilot study. Stool specimens were collected in a highly endemic area for S. mansoni in Ethiopia and submitted in an investigator-blinded fashion to microscopic examination by Kato-Katz thick smear as well as to real-time PCR using either fresh frozen stool samples or stool smears on fecal cards which have been stored at ambient temperature for up to ten months. Out of 55 stool samples, 35 were positive by microscopy, 33 and 32 were positive by PCR of frozen samples and of fecal card samples, respectively. When microscopy was used as diagnostic "gold standard", the sensitivity of PCR on fresh stool was 94.3% (95%-CI: 86.6; 100) and on fecal cards 91.4% (95%-CI: 82.2; 100). The use of fecal cards proved to be a simple and useful method for stool collection and prolonged storage prior to PCR based diagnosis of S. mansoni infection. This technique may be a valuable approach for large scale surveillance and post treatment assessments.

Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage.

PubMed

Carroll, Ian M; Ringel-Kulka, Tamar; Siddle, Jennica P; Klaenhammer, Todd R; Ringel, Yehuda

2012-01-01

The handling and treatment of biological samples is critical when characterizing the composition of the intestinal microbiota between different ecological niches or diseases. Specifically, exposure of fecal samples to room temperature or long term storage in deep freezing conditions may alter the composition of the microbiota. Thus, we stored fecal samples at room temperature and monitored the stability of the microbiota over twenty four hours. We also investigated the stability of the microbiota in fecal samples during a six month storage period at -80°C. As the stability of the fecal microbiota may be affected by intestinal disease, we analyzed two healthy controls and two patients with irritable bowel syndrome (IBS). We used high-throughput pyrosequencing of the 16S rRNA gene to characterize the microbiota in fecal samples stored at room temperature or -80°C at six and seven time points, respectively. The composition of microbial communities in IBS patients and healthy controls were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. The composition of the microbiota in fecal samples stored for different lengths of time at room temperature or -80°C clustered strongly based on the host each sample originated from. Our data demonstrates that fecal samples exposed to room or deep freezing temperatures for up to twenty four hours and six months, respectively, exhibit a microbial composition and diversity that shares more identity with its host of origin than any other sample.

Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case-control study.

PubMed

Hasegawa, Kohei; Stewart, Christopher J; Mansbach, Jonathan M; Linnemann, Rachel W; Ajami, Nadim J; Petrosino, Joseph F; Camargo, Carlos A

2017-07-26

Emerging evidence demonstrated that the structure of fecal microbiome is associated with the likelihood of bronchiolitis in infants. However, no study has examined functional profiles of fecal microbiome in infants with bronchiolitis. In this context, we conducted a case-control study. As a part of multicenter prospective study, we collected stool samples from 40 infants hospitalized with bronchiolitis (cases). We concurrently enrolled 115 age-matched healthy controls. First, by applying 16S rRNA gene sequencing to these 155 fecal samples, we identified the taxonomic profiles of fecal microbiome. Next, based on the taxonomy data, we inferred the functional capabilities of fecal microbiome and tested for differences in the functional capabilities between cases and controls. Overall, the median age was 3 months and 45% were female. Among 274 metabolic pathways surveyed, there were significant differences between bronchiolitis cases and healthy controls for 37 pathways, including lipid metabolic pathways (false discovery rate [FDR] <0.05). Particularly, the fecal microbiome of bronchiolitis cases had consistently higher abundances of gene function related to the sphingolipid metabolic pathways compared to that of controls (FDR <0.05). These pathways were more abundant in infants with Bacteroides-dominant microbiome profile compared to the others (FDR <0.001). On the basis of the predicted metagenome in this case-control study, we found significant differences in the functional potential of fecal microbiome between infants with bronchiolitis and healthy controls. Although causal inferences remain premature, our data suggest a potential link between the bacteria-derived metabolites, modulations of host immune response, and development of bronchiolitis.

A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method.

PubMed

Cao, Yiping; Sivaganesan, Mano; Kelty, Catherine A; Wang, Dan; Boehm, Alexandria B; Griffith, John F; Weisberg, Stephen B; Shanks, Orin C

2018-01-01

Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and management. However, there are currently no standardized approaches for field implementation and interpretation of qPCR data. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and a novel Bayesian weighted average approach to establish a human fecal contamination score (HFS) that can be used to prioritize sampling sites for remediation based on measured human waste levels. The HFS was then used to investigate 975 study design scenarios utilizing different combinations of sites with varying sampling intensities (daily to once per week) and number of qPCR replicates per sample (2-14 replicates). Findings demonstrate that site prioritization with HFS is feasible and that both sampling intensity and number of qPCR replicates influence reliability of HFS estimates. The novel data analysis strategy presented here provides a prescribed approach for the implementation and interpretation of human-associated HF183/BacR287 qPCR data with the goal of site prioritization based on human fecal pollution levels. In addition, information is provided for future users to customize study designs for optimal HFS performance. Published by Elsevier Ltd.

Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000

USGS Publications Warehouse

Hyer, Kenneth; Moyer, Douglas

2003-01-01

Surface-water impairment by fecal coliform bacteria is a water-quality issue of national scope and importance. In Virginia, more than 175 stream segments are on the Commonwealth's 1998 303(d) list of impaired waters because of elevated concentrations of fecal coliform bacteria. These fecal coliform-impaired stream segments require the development of total maximum daily load (TMDL) and associated implementation plans, but accurate information on the sources contributing these bacteria usually is lacking. The development of defendable fecal coliform TMDLs and management plans can benefit from reliable information on the bacteria sources that are responsible for the impairment. Bacterial source tracking (BST) recently has emerged as a powerful tool for identifying the sources of fecal coliform bacteria that impair surface waters. In a demonstration of BST technology, three watersheds on Virginia's 1998 303(d) list with diverse land-use practices (and potentially diverse bacteria sources) were studied. Accotink Creek is dominated by urban land uses, Christians Creek by agricultural land uses, and Blacks Run is affected by both urban and agricultural land uses. During the 20-month field study (March 1999?October 2000), water samples were collected from each stream during a range of flow conditions and seasons. For each sample, specific conductance, dissolved oxygen concentration, pH, turbidity, flow, and water temperature were measured. Fecal coliform concentrations of each water sample were determined using the membrane filtration technique. Next, Escherichia coli (E. coli) were isolated from the fecal coliform bacteria and their sources were identified using ribotyping (a method of 'genetic fingerprinting'). Study results provide enhanced understanding of the concentrations and sources of fecal coliform bacteria in these three watersheds. Continuum sampling (sampling along the length of the streams) indicated that elevated concentrations of fecal coliform bacteria (maximum observed concentration of 290,000 colonies/100 milliliters (col/100mL) could occur along the entire length of each stream, and that the samples collected at the downstream monitoring station of each stream were generally representative of the entire upstream reach. Seasonal patterns were observed in the base-flow fecal coliform concentrations of all streams; concentrations were typically highest in the summer and lowest in the winter. Fecal coliform concentrations were lowest during periods of base flow (typically 200?2,000 col/100mL) and increased by 3?4 orders of magnitude during storm events (as high as 700,000 col/100mL). Multiple linear regression models were developed to predict fecal coliform concentrations as a function of streamflow and other water-quality parameters. The source tracking technique provided identification of bacteria contributions from diverse sources that included (but were not limited to) humans, cattle, poultry, horses, dogs, cats, geese, ducks, raccoons, and deer. Seasonal patterns were observed in the contributions of cattle and poultry sources. There were relations between the identified sources of fecal coliform bacteria and the land-use practices within each watershed. There were only minor differences in the distribution of bacteria sources between low-flow periods and high-flow periods. A coupled approach that utilized both a large available source library and a smaller, location-specific source library provided the most success in identifying the unknown E. coli isolates. BST data should provide valuable support and guidance for producing more defendable and scientifically rigorous watershed models. Incorporation of these bacteria-source data into watershed management strategies also should result in the selection of more efficient source-reduction scenarios for improving water quality.

Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

USGS Publications Warehouse

Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

2012-01-01

During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

Fecal-indicator bacteria concentrations in the Illinois River between Hennepin and Peoria, Illinois: 2007-08

USGS Publications Warehouse

Dupre, David H.; Hortness, Jon E.; Terrio, Paul J.; Sharpe, Jennifer B.

2012-01-01

The Illinois Environmental Protection Agency has designated portions of the Illinois River in Peoria, Woodford, and Tazewell Counties, Illinois, as impaired owing to the presence of fecal coliform bacteria. The U.S. Geological Survey, in cooperation with the Tri-County Regional Planning Commission, examined the water quality in the Illinois River and major tributaries within a 47-mile reach between Peoria and Hennepin, Ill., during water year 2008 (October 2007–September 2008). Investigations included synoptic (snapshot) sampling at multiple locations in a 1-day period: once in October 2007 during lower streamflow conditions, and again in June 2008 during higher streamflow conditions. Five locations in the study area were monitored for the entire year at monthly or more frequent intervals. Two indicator bacteria were analyzed in each water sample: fecal coliform and Escherichia coli (E. coli). Streamflow information from previously established monitoring locations in the study area was used in the analysis. Correlation analyses were used to characterize the relation between the two fecal-indicator bacteria and the relation of either indicator to streamflow. Concentrations of the two measured fecal-indicator bacteria correlated well for all samples analyzed (r = 0.94, p E. coli: rho = -0.43, p = 0.0157). The correlation between fecal indicators and streamflow in tributaries or in the Illinois River at Hennepin was found to be statistically significant, yet moderate in strength with coefficient values ranging from r = 0.4 to 0.6. Indirect observations from the June 2008 higher flow synoptic event may indicate continued effects from combined storm and sanitary sewers in the vicinity of the Illinois River near Peoria, Ill., contributing to observed single-sample exceedance of the State criterion for fecal coliform.

Comparison of fecal pooling strategies for detection of Mycobacterium avium ssp. paratuberculosis in cattle.

PubMed

McKenna, S L B; Ritter, C; Dohoo, I; Keefe, G P; Barkema, H W

2018-05-23

In herds with typical moderate to low within-herd prevalence, testing for Mycobacterium avium ssp. paratuberculosis (MAP), the infectious agent of Johne's disease, will be more cost-effective if individual fecal samples are cultured in composite pools. However, sensitivity to classify a pool containing 1 or more positive individual samples as positive may depend on pool size and number of individual positive samples within a pool. Fecal samples collected from 994 dairy cows sampled at slaughter were cultured to detect MAP. Culturing was done both individually and as composite pooled samples using the TREK ESP Culture System II broth medium (Thermo Fisher Scientific, Trek Diagnostic Systems Inc., Cleveland, OH). Composite samples consisted of pools containing feces from 3, 5, 8, 10, or 15 cows. The number of individual fecal culture-positive cows within each pool ranged from 0 to 4. Culture of individual fecal samples detected MAP in 36 (3.6%) of the 994 cows. Individual samples that were detected within the first 50 d by TREK ESP Culture System II were more likely to lead to a positive pool result. In total, 840 pooled fecal samples were examined for presence of MAP, and of those, 272 pools actually contained feces from fecal culture-positive cows. The crude sensitivity (proportion of pools that contained at least 1 fecal-positive cow that tested positive) for pools of 3, 5, 8, 10, and 15 was 47, 67, 44, 59, and 39%, respectively. Across pools, an increase of the number of fecal culture-positive samples from 1 to 2 enhanced overall crude sensitivity from 44 to 71%. However, sensitivity did not further increase for pools with 3 or 4 fecal culture-positive samples (63 and 60%, respectively). Additionally, a simulation analysis assessing probability of pooled fecal samples being positive in herds of 50 and 100 cows was conducted. The simulation assumed that 1, 2, or 5 cows per herd were MAP fecal culture-positive and that pools of 5 and 10 were used. This low-prevalence herd simulation indicated that weighted mean herd probabilities of detecting a positive herd ranged between 52 and 99.3%, with the lowest probability for pools of 10 with 1 positive cow in the herd and the highest probability for pools of 5 with 5 positive cows in the herd. However, overall, pools of 5 and 10 had similar diagnostic capabilities, enabling cost savings by utilizing pools of 10. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Validation of a fecal scoring scale in puppies during the weaning period.

PubMed

Grellet, Aurélien; Feugier, Alexandre; Chastant-Maillard, Sylvie; Carrez, Bruno; Boucraut-Baralon, Corine; Casseleux, Gregory; Grandjean, Dominique

2012-10-01

In puppies weaning is a high risk period. Fecal changes are frequent and can be signs of infection by digestive pathogens (bacteria, viruses, parasites) and indicators of nutritional and environmental stress. The aim of this study was to define a pathological fecal score for weaning puppies, and to study the impact on that score of two intestinal viruses (canine parvovirus type 2 and canine coronavirus). For this, the quality of stools was evaluated on 154 puppies between 4 and 8 weeks of age (100 from small breeds and 54 from large breeds). The scoring was performed immediately after a spontaneous defecation based on a 13-point scale (from 1; liquid to 13; dry and hard feces). Fecal samples were frozen for further viral analysis. Each puppy was weighed once a week during the study period. The fecal score regarded as pathological was the highest score associated with a significant reduction in average daily gain (ADG). Fecal samples were checked by semi-quantitative PCR or RT-PCR for canine parvovirus type 2 and canine coronavirus identification, respectively. The quality of feces was affected by both age and breed size. In small breeds, the ADG was significantly reduced under a fecal score of 6 and 7 for puppies at 4-5 and 6-8 weeks of age, respectively. In large breeds, the ADG was significantly reduced under a fecal score of 5 whatever the age of the puppy. Whereas a high viral load of canine parvovirus type 2 significantly impacted feces quality, no effect was recorded for canine coronavirus. This study provides an objective threshold for evaluation of fecal quality in weaning puppies. It also emphasizes the importance to be given to age and breed size in that evaluation. Copyright © 2012 Elsevier B.V. All rights reserved.

Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters.

PubMed

Converse, Reagan R; Blackwood, A Denene; Kirs, Marek; Griffith, John F; Noble, Rachel T

2009-11-01

Concentrations of fecal indicator bacteria (FIB; e.g. Escherichia coli, and Enterococcus sp.) can only be used in limited ways for determining the source of fecal contamination in recreational waters because they cannot distinguish human from non-human fecal contamination. Several Bacteroides spp. have been suggested as potential alternative indicators. We have developed a rapid, culture-independent method for quantifying fecal Bacteroides spp. using quantitative PCR (QPCR) targeting the 16S rRNA gene. The assay specifically targets and quantifies the most common human Bacteroides spp. The details of the method are presented, including analyses of a wide range of fecal samples from different organisms. Specificity and performance of the QPCR assay were also tested via a laboratory experiment where human sewage and gull guano were inoculated into a range of environmental water samples. Concentrations of fecal Bacteroides spp., total Enterococcus sp., Enterococcus faecium, Enterococcus faecalis, and Enterococcus casseliflavus were measured using QPCR, and total Enterococcus sp. and E. coli were quantified by membrane filtration (MF). Samples spiked with gull guano were highly concentrated with total Enterococcus sp., E. coli, E. faecalis, and E. casseliflavus, demonstrating that these indicators are prominent in animal feces. On the other hand, fecal Bacteroides spp. concentrations were high in samples containing sewage and were relatively low in samples spiked with gull guano. Sensitivity and specificity results suggest that the rapid fecal Bacteroides spp. QPCR assay may be a useful tool to effectively predict the presence and concentration of human-specific fecal pollution.

Sample treatment optimization for fish stool metabolomics.

PubMed

Hano, Takeshi; Ito, Mana; Ito, Katsutoshi; Uchida, Motoharu

2018-06-07

Gut microbiota play an essential role in an organism's health. The fecal metabolite profiling content reflects these microbiota-mediated physiological changes in various organisms, including fish. Therefore, metabolomics analysis of fish feces should provide insight into the dynamics linking physiology and gut microbiota. However, metabolites are often unstable in aquatic environments, making fecal metabolites difficult to examine in fish. In this study, a novel method using gas chromatography-mass spectrometry (GC-MS) was developed and optimized for the preparation of metabolomics samples from the feces of the marine fish, red sea bream (Pagrus major). The preparation methodology was optimized, focusing on rinsing frequency and rinsing solvent. Feces (collected within 4 h of excretion) were rinsed three times with sterilized 2.5% NaCl solution or 3.0% artificial seawater (ASW). Among the 86 metabolites identified in the NaCl-rinsed samples, 57 showed superior recovery to that in ASW-rinsed samples, indicating that NaCl is a better rinsing solvent, particularly for amino acids, organic acids, and fatty acids. To evaluate rinsing frequency, fecal samples were rinsed with NaCl solution 0, 1, 3, or 5 times. The results indicate that three or more rinses enabled robust and stable detection of metabolites encapsulated within the solid fecal residue. Furthermore, these data suggest that rinsing is unnecessary when studying sugars, amino acids, and sterols, again highlighting the need for appropriate rinsing solvent and frequency. This study provides further insight into the use of fecal samples to evaluate and promote fish health during farming and supports the application of this and similar analyses to study the effects of environmental fluctuations and/or contamination. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of high-performance chemical isotope labeling LC-MS for profiling the human fecal metabolome.

PubMed

Xu, Wei; Chen, Deying; Wang, Nan; Zhang, Ting; Zhou, Ruokun; Huan, Tao; Lu, Yingfeng; Su, Xiaoling; Xie, Qing; Li, Liang; Li, Lanjuan

2015-01-20

Human fecal samples contain endogenous human metabolites, gut microbiota metabolites, and other compounds. Profiling the fecal metabolome can produce metabolic information that may be used not only for disease biomarker discovery, but also for providing an insight about the relationship of the gut microbiome and human health. In this work, we report a chemical isotope labeling liquid chromatography-mass spectrometry (LC-MS) method for comprehensive and quantitative analysis of the amine- and phenol-containing metabolites in fecal samples. Differential (13)C2/(12)C2-dansyl labeling of the amines and phenols was used to improve LC separation efficiency and MS detection sensitivity. Water, methanol, and acetonitrile were examined as an extraction solvent, and a sequential water-acetonitrile extraction method was found to be optimal. A step-gradient LC-UV setup and a fast LC-MS method were evaluated for measuring the total concentration of dansyl labeled metabolites that could be used for normalizing the sample amounts of individual samples for quantitative metabolomics. Knowing the total concentration was also useful for optimizing the sample injection amount into LC-MS to maximize the number of metabolites detectable while avoiding sample overloading. For the first time, dansylation isotope labeling LC-MS was performed in a simple time-of-flight mass spectrometer, instead of high-end equipment, demonstrating the feasibility of using a low-cost instrument for chemical isotope labeling metabolomics. The developed method was applied for profiling the amine/phenol submetabolome of fecal samples collected from three families. An average of 1785 peak pairs or putative metabolites were found from a 30 min LC-MS run. From 243 LC-MS runs of all the fecal samples, a total of 6200 peak pairs were detected. Among them, 67 could be positively identified based on the mass and retention time match to a dansyl standard library, while 581 and 3197 peak pairs could be putatively identified based on mass match using MyCompoundID against a Human Metabolome Database and an Evidence-based Metabolome Library, respectively. This represents the most comprehensive profile of the amine/phenol submetabolome ever detected in human fecal samples. The quantitative metabolome profiles of individual samples were shown to be useful to separate different groups of samples, illustrating the possibility of using this method for fecal metabolomics studies.

Potential for gulls to transport bacteria from human waste sites to beaches.

PubMed

Alm, Elizabeth W; Daniels-Witt, Quri R; Learman, Deric R; Ryu, Hodon; Jordan, Dustin W; Gehring, Thomas M; Santo Domingo, Jorge

2018-02-15

Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape. Copyright © 2017 Elsevier B.V. All rights reserved.

FECAL CORTISOL LEVELS IN SCIMITAR-HORNED ORYX, ORYX DAMMAH, REVEALS DIFFERENCES BETWEEN CAPTIVE ENVIRONMENTS.

PubMed

Pauling, Cassandra D; Lankford, Scott E; Jackson, Victoria L

2017-12-01

Due to the intensive management of the scimitar-horned oryx, Oryx dammah, involving both captivity and reintroductions, understanding the stress associated with environmental situations this endangered species might experience would be particularly helpful. Fecal cortisol levels were measured across seasons, between captive management programs, and among varying reproductive states in animals held at Fossil Rim Wildlife Center (FRWC) and Kansas City Zoo (KCZ). A total of 72 samples were collected from FRWC and 69 samples were collected from KCZ. The herd size and sex ratio changed for both locations in the middle of sampling due to translocations and birth. The herd sizes ranged from 25 to 28 individuals at FRWC and 22 to 24 individuals at KCZ. An ELISA was optimized and utilized to investigate fecal cortisol variances across seasons, captive management programs, and among varying reproductive states. Fecal cortisol levels ranged from 68.9 to 668.7 pg/g throughout this study, but key differences were found in response to reproductive status, environmental conditions, and social status. The highest level of fecal cortisol measured (668.7 pg/g) was in a pregnant female 9 days prior to parturition. During winter months, an increase in fecal cortisol levels occurred in both herds (FRWC 160.3 pg/g to 335.1 pg/g and KCZ 118.8 pg/g to 505.0 pg/g). In addition, when intact males were held together in an enclosure, the dominant males had lower fecal cortisol levels compared with submissive males during three of the four sampling periods. Understanding how these data relate to the physiologic stress response will require further study, but these results can be utilized to help establish expected fecal cortisol ranges in multiple environments and can aid current captive scimitar-horned oryx management programs, as well as future reintroduction efforts.

Water quality and sources of fecal coliform bacteria in the Meduxnekeag River, Houlton, Maine

USGS Publications Warehouse

Culbertson, Charles W.; Huntington, Thomas G.; Stoeckel, Donald M.; Caldwell, James M.; O'Donnell, Cara

2014-01-01

In response to bacterial contamination in the Meduxnekeag River and the desire to manage the watershed to reduce contaminant sources, the Houlton Band of Maliseet Indians (HBMI) and the U.S. Geological Survey began a cooperative effort to establish a baseline of water-quality data that can be used in future studies and to indicate potential sources of nutrient and bacterial contamination. This study was conducted during the summer of 2005 in the Meduxnekeag River Basin near Houlton, Maine. Continuously recorded specific conductance can be a good indicator for water quality. Specific conductance increased downstream from the town of Houlton, between runoff events, and decreased sharply following major runoff events. Collections of discrete samples during the summer of 2005 indicated seasonal positive concentration-discharge relations for total phosphorus and total nitrogen; these results indicate that storm runoff may mobilize and transport these nutrients from the terrestrial environment to the river. Data collected by the HBMI on fecal coliform bacteria indicated that bacterial contamination enters the Meduxnekeag River from multiple paths including tributaries and surface drains (ditches) in developed areas in Houlton, Maine. The Houlton wastewater treatment discharge was not an important source of bacterial contamination. Bacteroidales-based tests for general fecal contamination (Bac32 marker) were predominantly positive in samples that had excessive fecal contamination as indicated by Enterococci density greater than 104 colony-forming units per 100 millilters. Of the 22 samples tested for Bacteroidales-based markers of human-associated fecal contamination (HF134 and HF183), 8 were positive. Of the 22 samples tested for Bacteroidales-based markers of ruminant-associated fecal contamination (CF128 and CF193), 7 were positive. Human fecal contamination was detected consistently at two sites (surface drains in urban areas in the town of Houlton) and occasionally detected at one site (Moose Brook) but was not detected at other sites. Fecal contamination (as indicated by fecal coliform density) apparently is localized under normal flow conditions with the highest levels restricted to drains in urban areas and to a lesser extent B Stream, Pearce Brook, and Big Brook, all tributaries to the main stem of the Meduxnekeag River. Coliphage were enumerated as an alternate indicator of fecal contamination with the intent of typing the virus into host-associated classes (human or ruminant), as was done for Enterococci; however, insufficient coliphage were isolated to provide more than preliminary indications. In spite of low coliphage enumeration, the preliminary results strengthen the conclusion that the Enterococci data correctly indicated the samples that contained human and ruminant fecal contamination. The finding that contamination was in many of the tributaries following storms in mid-July indicates that storm runoff likely carries fecal contaminants to more locations than runoff under lower flow conditions.

Feedlot- and Pen-Level Prevalence of Enterohemorrhagic Escherichia coli in Feces of Commercial Feedlot Cattle in Two Major U.S. Cattle Feeding Areas.

PubMed

Cull, Charley A; Renter, David G; Dewsbury, Diana M; Noll, Lance W; Shridhar, Pragathi B; Ives, Samuel E; Nagaraja, Tiruvoor G; Cernicchiaro, Natalia

2017-06-01

The objective of this study was to determine feedlot- and pen-level fecal prevalence of seven enterohemorrhagic Escherichia coli (EHEC) belonging to serogroups (O26, O45, O103, O111, O121, O145, and O157, or EHEC-7) in feces of feedlot cattle in two feeding areas in the United States. Cattle pens from four commercial feedlots in each of the two major U.S. beef cattle areas were sampled. Up to 16 pen-floor fecal samples were collected from each of 4-6 pens per feedlot, monthly, for a total of three visits per feedlot, from June to August, 2014. Culture procedures including fecal enrichment in E. coli broth, immunomagnetic separation, and plating on selective media, followed by confirmation through polymerase chain reaction (PCR) testing, were conducted. Generalized linear mixed models were fitted to estimate feedlot-, pen-, and sample-level fecal prevalence of EHEC-7 and to evaluate associations between potential demographic and management risk factors with feedlot and within-pen prevalence of EHEC-7. All study feedlots and 31.0% of the study pens had at least one non-O157 EHEC-positive fecal sample, whereas 62.4% of pens tested positive for EHEC O157; sample-level prevalence estimates ranged from 0.0% for EHEC O121 to 18.7% for EHEC O157. Within-pen prevalence of EHEC O157 varied significantly by sampling month; similarly within-pen prevalence of non-O157 EHEC varied significantly by month and by the sex composition of the pen (heifer, steer, or mixed). Feedlot management factors, however, were not significantly associated with fecal prevalence of EHEC-7. Intraclass correlation coefficients for EHEC-7 models indicated that most of the variation occurred between pens, rather than within pens, or between feedlots. Hence, the potential combination of preharvest interventions and pen-level management strategies may have positive food safety impacts downstream along the beef chain.

Ionic liquid-based reagents improve the stability of midterm fecal sample storage.

PubMed

Hao, Lilan; Xia, Zhongkui; Yang, Huanming; Wang, Jian; Han, Mo

2017-08-01

Fecal samples are widely used in metagenomic research, which aims to elucidate the relationship between human health and the intestinal microbiota. However, the best conditions for stable and reliable storage and transport of these samples at room temperature are still unknown, and whether samples stored at room temperature for several days will maintain their microbiota composition is still unknown. Here, we established and tested a preservation method using reagents containing imidazolium- or pyridinium-based ionic liquids. We stored human fecal samples in these reagents for up to 7 days at different temperatures. Subsequently, all samples were sequenced and compared with fresh samples and/or samples treated under other conditions. The 16S rRNA sequencing results suggested that ionic liquid-based reagents could stabilize the composition of the microbiota in fecal samples during a 7-day storage period, particularly when stored at room temperature. Thus, this method may have implications in the storage of fecal samples for metagenomic research. Copyright © 2017 Elsevier B.V. All rights reserved.

Herd-level prevalence of Map infection in dairy herds of southern Chile determined by culture of environmental fecal samples and bulk-tank milk qPCR.

PubMed

Kruze, J; Monti, G; Schulze, F; Mella, A; Leiva, S

2013-09-01

Paratuberculosis, an infectious disease of domestic and wild ruminants caused by Mycobacterium avium subsp. paratuberculosis (Map), is an economically important disease in dairy herds worldwide. In Chile the disease has been reported in domestic and wildlife animals. However, accurate and updated estimations of the herd-prevalence in cattle at national or regional level are not available. The objectives of this study were to determine the herd-level prevalence of dairy herds with Map infected animals of Southern Chile, based on two diagnostic tests: culture of environmental fecal samples and bulk-tank milk qPCR. Two composite environmental fecal samples and one bulk-tank milk sample were collected during September 2010 and September 2011 from 150 dairy farms in Southern Chile. Isolation of Map from environmental fecal samples was done by culture of decontaminated samples on a commercial Herrold's Egg Yolk Medium (HEYM) with and without mycobactin J. Suspicious colonies were confirmed to be Map by conventional IS900 PCR. Map detection in bulk-tank milk samples was done by real time IS900 PCR assay. PCR-confirmed Map was isolated from 58 (19.3%) of 300 environmental fecal samples. Holding pens and manure storage lagoons were the two more frequent sites found positive for Map, representing 35% and 33% of total positive samples, respectively. However, parlor exits and cow alleyways were the two sites with the highest proportion of positive samples (40% and 32%, respectively). Herd prevalence based on environmental fecal culture was 27% (true prevalence 44%) compared to 49% (true prevalence 87%) based on bulk-tank milk real time IS900 PC. In both cases herd prevalence was higher in large herds (>200 cows). These results confirm that Map infection is wide spread in dairy herds in Southern Chile with a rough herd-level prevalence of 28-100% depending on the herd size, and that IS900 PCR on bulk-tank milk samples is more sensitive than environmental fecal culture to detect Map-infected dairy herds. Copyright © 2013 Elsevier B.V. All rights reserved.

Utility of Microbial Source-Tracking Markers for Assessing Fecal Contamination in the Portage River Watershed, Northwestern Ohio, 2008

USGS Publications Warehouse

Kephart, Christopher M.; Bushon, Rebecca N.

2010-01-01

An influx of concentrated animal feeding operations in northwest Ohio has prompted local agencies to examine the effects of these industrial farms on water quality in the upper Portage River watershed. The utility of microbial source-tracking (MST) tools as a means of characterizing sources of fecal contamination in the watershed was evaluated. From 2007 to 2008, scientists with the U.S. Geological Survey, Bowling Green State University, and the Wood County Health Department collected and analyzed 17 environmental samples and 13 fecal source samples for Bacteroides-based host-associated DNA markers. At many of the environmental sites tested, MST marker results corroborated the presumptive fecal contamination sources. Results from this demonstration study support the utility of using MST with host-specific molecular markers to characterize the sources of fecal contamination in the Portage River watershed.

Frequent detection of a human fecal indicator in the urban ocean: environmental drivers and covariation with enterococci.

PubMed

Jennings, Wiley C; Chern, Eunice C; O'Donohue, Diane; Kellogg, Michael G; Boehm, Alexandria B

2018-03-01

Fecal pollution of surface waters presents a global human health threat. New molecular indicators of fecal pollution have been developed to address shortcomings of traditional culturable fecal indicators. However, there is still little information on their fate and transport in the environment. The present study uses spatially and temporally extensive data on traditional (culturable enterococci, cENT) and molecular (qPCR-enterococci, qENT and human-associated marker, HF183/BacR287) indicator concentrations in marine water surrounding highly-urbanized San Francisco, California, USA to investigate environmental and anthropogenic processes that impact fecal pollution. We constructed multivariable regression models for fecal indicator bacteria at 14 sampling stations. The human marker was detected more frequently in our study than in many other published studies, with detection frequency at some stations as high as 97%. The odds of cENT, qENT, and HF183/BacR287 exceeding health-relevant thresholds were statistically elevated immediately following discharges of partially treated combined sewage, and cENT levels dissipated after approximately 1 day. However, combined sewer discharges were not important predictors of indicator levels typically measured in weekly monitoring samples. Instead, precipitation and solar insolation were important predictors of cENT in weekly samples, while precipitation and water temperature were important predictors of HF183/BacR287 and qENT. The importance of precipitation highlights the significance of untreated storm water as a source of fecal pollution to the urban ocean, even for a city served by a combined sewage system. Sunlight and water temperature likely control persistence of the indicators via photoinactivation and dark decay processes, respectively.

Characterizing the fecal microbiota of infants with botulism.

PubMed

Shirey, T Brian; Dykes, Janet K; Lúquez, Carolina; Maslanka, Susan E; Raphael, Brian H

2015-11-23

Infant botulism is the most prevalent form of botulism in the USA, representing 68.5 % of cases reported from 2001-2012. Infant botulism results when botulinum toxin-producing clostridia (BTPC) colonize the infant gut with concomitant in vivo production of the highly potent botulinum neurotoxin (BoNT). The gut microbiota of infants with botulism is largely uncharacterized; therefore, it remains unclear whether the microbiota profile of these patients are distinct in composition, abundance, or diversity. To address this uncertainty, we employed 16S rRNA gene profiling to characterize the fecal microbiota in 14 stool samples among laboratory-confirmed and non-confirmed infant botulism cases. Seven bacterial phyla were identified among all 14 infant stool samples examined. Compared to samples from non-confirmed cases, the fecal microbiota of infant botulism patients displayed significantly higher Proteobacteria abundance. Of the 20 bacterial families identified, Enterobacteriaceae was significantly more abundant in samples from infants with botulism. Firmicutes abundance and the abundance ratio of Firmicutes/Proteobacteria was significantly lower in samples from infants with botulism. Lactobacillus spp. abundance was notably reduced in 12 of the 14 samples. Clostridium botulinum and Clostridium baratii were identified in low relative abundances in confirmed and non-confirmed samples based on their 16S rRNA gene profiles, although their toxigenicity remained undetermined. No significant differences were observed in the number of operational taxonomic units (OTUs) observed or in fecal microbiota diversity between laboratory-confirmed and non-confirmed samples. Correlations between individual phylum abundances and infant age were variable, and no significant differences were shown in number of OTUs observed or in fecal microbiota diversity between samples delineated by overall mean age. Significant differences in Proteobacteria, Firmicutes, and Enterobacteriaceae abundances were identified in the fecal microbiota of infants with botulism when compared to samples from non-confirmed cases. Fecal microbiota diversity was not significantly altered in infants with botulism, and a limited presence of BTPC was shown. It could not be determined whether the fecal microbiota profiles shown here were comparable prior to patient illness, or whether they were the direct result of infant botulism. The results of this study do, however, provide a detailed and descriptive observation into the infant gut microbiota after intestinal colonization by BTPC.

Fluoroquinolones and qnr genes in sediment, water, soil, and human fecal flora in an environment polluted by manufacturing discharges.

PubMed

Rutgersson, Carolin; Fick, Jerker; Marathe, Nachiket; Kristiansson, Erik; Janzon, Anders; Angelin, Martin; Johansson, Anders; Shouche, Yogesh; Flach, Carl-Fredrik; Larsson, D G Joakim

2014-07-15

There is increasing concern that environmental antibiotic pollution promotes transfer of resistance genes to the human microbiota. Here, fluoroquinolone-polluted river sediment, well water, irrigated farmland, and human fecal flora of local villagers within a pharmaceutical industrial region in India were analyzed for quinolone resistance (qnr) genes by quantitative PCR. Similar samples from Indian villages farther away from industrial areas, as well as fecal samples from Swedish study participants and river sediment from Sweden, were included for comparison. Fluoroquinolones were detected by MS/MS in well water and soil from all villages located within three km from industrially polluted waterways. Quinolone resistance genes were detected in 42% of well water, 7% of soil samples and in 100% and 18% of Indian and Swedish river sediments, respectively. High antibiotic concentrations in Indian sediment coincided with high abundances of qnr, whereas lower fluoroquinolone levels in well water and soil did not. We could not find support for an enrichment of qnr in fecal samples from people living in the fluoroquinolone-contaminated villages. However, as qnr was detected in 91% of all Indian fecal samples (24% of the Swedish) it suggests that the spread of qnr between people is currently a dominating transmission route.

Effects of Holding Time, Storage, and the Preservation of ...

EPA Pesticide Factsheets

The purpose of this project was to answer questions related to storage of samples to be analyzed by the quantitative polymerase chain reaction (qPCR)-based assays for fecal indicator bacteria. The project was divided into two parts. The first part was to determine if filters that were used to collect fecal indicators could be stored frozen and analyzed at a later date and the second part was to determine if refrigerated water samples could be held for 24 to 48 hours prior to analysis by qPCR. Both of these studies answer questions that were important in the analysis of fresh and marine surface water samples for beach monitoring purposes. 1) Develop and evaluate qPCR assays and test methods for the detection and quantification of genetic markers from indicator bacteria that are associated with human fecal waste and from two new groups of general fecal indicator bacteria (E. coli and Clostridia) that historically have been widely used or are favored in specific regions 2) Determine the occurrence and densities of genetic markers detected by new qPCR assays developed under objective 1 and compare with occurrence and densities of genetic markers detected by previously developed qPCR assays for enterococci and total Bacterioidalesin waste waters and fecal material from different animal sources. 3) Determine stability of fecal indicator bacteria target DNA sequences in freezer archived filter retentates of ambient surface water samples 4) Determine the densitie

Mesquite seed density in fecal samples of Raramuri Criollo vs. Angus x Hereford cows grazing Chihuahuan Desert Rangeland

USDA-ARS?s Scientific Manuscript database

This study was part of a larger project investigating breed-related differences in feeding habits of Raramuri Criollo (RC) versus Angus x Hereford (AH) cows. Seed densities in fecal samples collected in July and August 2015 were analyzed to compare presumed mesquite bean consumption of RC and AH cow...

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data.

PubMed

Blekhman, Ran; Tang, Karen; Archie, Elizabeth A; Barreiro, Luis B; Johnson, Zachary P; Wilson, Mark E; Kohn, Jordan; Yuan, Michael L; Gesquiere, Laurence; Grieneisen, Laura E; Tung, Jenny

2016-08-16

Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples-unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.

Development and Evaluation of a Quantitative PCR Assay Targeting Sandhill Crane (Grus canadensis) Fecal Pollution

PubMed Central

Ryu, Hodon; Lu, Jingrang; Vogel, Jason; Elk, Michael; Chávez-Ramírez, Felipe; Ashbolt, Nicholas

2012-01-01

While the microbial water quality in the Platte River is seasonally impacted by excreta from migrating cranes, there are no methods available to study crane fecal contamination. Here we characterized microbial populations in crane feces using phylogenetic analysis of 16S rRNA gene fecal clone libraries. Using these sequences, a novel crane quantitative PCR (Crane1) assay was developed, and its applicability as a microbial source tracking (MST) assay was evaluated by determining its host specificity and detection ability in environmental waters. Bacteria from crane excreta were dominated by bacilli and proteobacteria, with a notable paucity of sequences homologous to Bacteroidetes and Clostridia. The Crane1 marker targeted a dominant clade of unclassified Lactobacillales sequences closely related to Catellicoccus marimammalium. The host distribution of the Crane1 marker was relatively high, being positive for 69% (66/96) of the crane excreta samples tested. The assay also showed high host specificity, with 95% of the nontarget fecal samples (i.e., n = 553; 20 different free-range hosts) being negative. Of the presumed crane-impacted water samples (n = 16), 88% were positive for the Crane1 assay, whereas none of the water samples not impacted by cranes were positive (n = 165). Bayesian statistical models of the Crane1 MST marker demonstrated high confidence in detecting true-positive signals and a low probability of false-negative signals from environmental water samples. Altogether, these data suggest that the newly developed marker could be used in environmental monitoring studies to study crane fecal pollution dynamics. PMID:22492437

An uncooked vegan diet shifts the profile of human fecal microflora: computerized analysis of direct stool sample gas-liquid chromatography profiles of bacterial cellular fatty acids.

PubMed Central

Peltonen, R; Ling, W H; Hänninen, O; Eerola, E

1992-01-01

The effect of an uncooked extreme vegan diet on fecal microflora was studied by direct stool sample gas-liquid chromatography (GLC) of bacterial cellular fatty acids and by quantitative bacterial culture by using classical microbiological techniques of isolation, identification, and enumeration of different bacterial species. Eighteen volunteers were divided randomly into two groups. The test group received an uncooked vegan diet for 1 month and a conventional diet of mixed Western type for the other month of the study. The control group consumed a conventional diet throughout the study period. Stool samples were collected. Bacterial cellular fatty acids were extracted directly from the stool samples and measured by GLC. Computerized analysis of the resulting fatty acid profiles was performed. Such a profile represents all bacterial cellular fatty acids in a sample and thus reflects its microflora and can be used to detect changes, differences, or similarities of bacterial flora between individual samples or sample groups. GLC profiles changed significantly in the test group after the induction and discontinuation of the vegan diet but not in the control group at any time, whereas quantitative bacterial culture did not detect any significant change in fecal bacteriology in either of the groups. The results suggest that an uncooked extreme vegan diet alters the fecal bacterial flora significantly when it is measured by direct stool sample GLC of bacterial fatty acids. PMID:1482187

Impact of exercise on fecal and cecal metabolome over aging: a longitudinal study in rats.

PubMed

Deda, Olga; Gika, Helen; Panagoulis, Theodoros; Taitzoglou, Ioannis; Raikos, Nikolaos; Theodoridis, Georgios

2017-01-01

Physical exercise can reduce adverse conditions during aging, while both exercise and aging act as metabolism modifiers. The present study investigates rat fecal and cecal metabolome alterations derived from exercise during rats' lifespan. Groups of rats trained life-long or for a specific period of time were under study. The training protocol consisted of swimming, 15-18 min per day, 3-5 days per week, with load of 4-0% of rat's weight. Fecal samples and cecal extracts were analyzed by targeted and untargeted metabolic profiling methods (GC-MS and LC-MS/MS). Effects of exercise and aging on the rats' fecal and cecal metabolome were observed. Fecal and cecal metabolomics are a promising field to investigate exercise biochemistry and age-related alterations.

Bacteriological quality of bottled drinking water versus municipal tap water in Dharan municipality, Nepal.

PubMed

Pant, Narayan Dutt; Poudyal, Nimesh; Bhattacharya, Shyamal Kumar

2016-06-07

Water-related diseases are of great concern in developing countries like Nepal. Every year, there are countless morbidity and mortality due to the consumption of unsafe drinking water. Recently, there have been increased uses of bottled drinking water in an assumption that the bottled water is safer than the tap water and its use will help to protect from water-related diseases. So, the main objective of this study was to analyze the bacteriological quality of bottled drinking water and that of municipal tap water. A total of 100 samples (76 tap water and 24 bottled water) were analyzed for bacteriological quality and pH. The methods used were spread plate method for total plate count (TPC) and membrane filter method for total coliform count (TCC), fecal coliform count (FCC), and fecal streptococcal count (FSC). pH meter was used for measuring pH. One hundred percent of the tap water samples and 87.5 % of the bottled water samples were found to be contaminated with heterotrophic bacteria. Of the tap water samples, 55.3 % were positive for total coliforms, compared with 25 % of the bottled water. No bottled water samples were positive for fecal coliforms and fecal streptococci, in contrast to 21.1 % and 14.5 % of the tap water samples being contaminated with fecal coliforms and fecal streptococci, respectively. One hundred percent of the tap water samples and 54.2 % of the bottled water samples had pH in the acceptable range. All of the municipal tap water samples and most of the bottled drinking water samples distributed in Dharan municipality were found to be contaminated with one or more than one type of indicator organisms. On the basis of our findings, we may conclude that comparatively, the bottled drinking water may have been safer (than tap water) to drink.

Changes in the fecal concentrations of cortisol and androgen metabolites in captive male jaguars (Panthera onca) in response to stress.

PubMed

Morato, R G; Bueno, M G; Malmheister, P; Verreschi, I T N; Barnabe, R C

2004-12-01

In the present study we determined the efficacy of the measurement of fecal cortisol and androgen metabolite concentrations to monitor adrenal and testicular activity in the jaguar (Panthera onca). Three captive male jaguars were chemically restrained and electroejaculated once or twice within a period of two months. Fecal samples were collected daily for 5 days before and 5 days after the procedure and stored at -20 degrees C until extraction. Variations in the concentrations of cortisol and androgen metabolites before and after the procedure were determined by solid phase cortisol and testosterone radioimmunoassay and feces dry weight was determined by drying at 37 degrees C for 24 h under vacuum. On four occasions, fecal cortisol metabolite levels were elevated above baseline (307.8 +/- 17.5 ng/g dry feces) in the first fecal sample collected after the procedure (100 to 350% above baseline). On one occasion, we did not detect any variation. Mean (+/- SEM) fecal androgen concentration did not change after chemical restraint and electroejaculation (before: 131.1 +/- 26.7, after: 213.7 +/- 43.6 ng/g dry feces). These data show that determination of fecal cortisol and androgen metabolites can be very useful for a noninvasive assessment of animal well-being and as a complement to behavioral, physiological, and pathological studies. It can also be useful for the study of the relationship between adrenal activity and reproductive performance in the jaguar.

Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

USGS Publications Warehouse

Johnston, Christopher; Byappanahalli, Muruleedhara N.; Gibson, Jacqueline MacDonald; Ufnar, Jennifer A.; Whitman, Richard L.; Stewart, Jill R.

2013-01-01

Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

PubMed Central

Koskey, Amber M.; Fisher, Jenny C.; Traudt, Mary F.; Newton, Ryan J.

2014-01-01

Gulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB. Enterococcaceae and Enterobacteriaceae were the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealed Catellicoccus marimammalium as the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcus indoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified as Enterococcus spp., 1.2% were identified as Streptococcus spp., and none were identified as C. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions of C. marimammalium 16S rRNA gene sequences (>50-fold) relative to typical mEI culturable Enterococcus spp. C. marimammalium therefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment. PMID:24242244

Effects of fecal sampling on preanalytical and analytical phases in quantitative fecal immunochemical tests for hemoglobin.

PubMed

Rapi, Stefano; Berardi, Margherita; Cellai, Filippo; Ciattini, Samuele; Chelazzi, Laura; Ognibene, Agostino; Rubeca, Tiziana

2017-07-24

Information on preanalytical variability is mandatory to bring laboratories up to ISO 15189 requirements. Fecal sampling is greatly affected by lack of harmonization in laboratory medicine. The aims of this study were to obtain information on the devices used for fecal sampling and to explore the effect of different amounts of feces on the results from the fecal immunochemical test for hemoglobin (FIT-Hb). Four commercial sample collection devices for quantitative FIT-Hb measurements were investigated. The volume of interest (VOI) of the probes was measured from diameter and geometry. Quantitative measurements of the mass of feces were carried out by gravimetry. The effects of an increased amount of feces on the analytical environment were investigated measuring the Hb values with a single analytical method. VOI was 8.22, 7.1 and 9.44 mm3 for probes that collected a target of 10 mg of feces, and 3.08 mm3 for one probe that targeted 2 mg of feces. The ratio between recovered and target amounts of devices ranged from 56% to 121%. Different changes in the measured Hb values were observed, in adding increasing amounts of feces in commercial buffers. The amounts of collected materials are related to the design of probes. Three out 4 manufacturers declare the same target amount using different sampling volumes and obtaining different amounts of collected materials. The introduction of a standard probes to reduce preanalytical variability could be an useful step for fecal test harmonization and to fulfill the ISO 15189 requirements.

Extraction of 3,4,4'-Trichlorocarbanilide from Rat Fecal Samples for Determination by High Pressure Liquid Chromatography-Tandem Mass Spectrometry.

PubMed

Kennedy, Rebekah C; Fling, Russell R; Terry, Paul D; Menn, Fu-Min; Chen, Jiangang; Borman, Christopher J

2015-07-15

Triclocarban (3,4,4'-Trichlorocarbanilide; TCC) in the environment has been well documented. Methods have been developed to monitor TCC levels from various matrices including water, sediment, biosolids, plants, blood and urine; however, no method has been developed to document the concentration of TCC in fecal content after oral exposure in animal studies. In the present study, we developed and validated a method that uses liquid extraction coupled with HPLC-MS/MS determination to measure TCC in feces. The limit of detection and limit of quantitation in control rats without TCC exposure was 69.0 ng/g and 92.9 ng/g of feces, respectively. The base levels of TCC in feces were lower than LOD. At 12 days of treatment, the fecal TCC concentration increased to 2220 µg/g among 0.2% w/w exposed animals. The concentration in fecal samples decreased over the washout period in 0.2% w/w treated animals to 0.399 µ/g feces after exposure was removed for 28 days. This method required a small amount of sample (0.1 g) with simple sample preparation. Given its sensitivity and efficiency, this method may be useful for monitoring TCC exposure in toxicological studies of animals.

Coccidia of whooping cranes

USGS Publications Warehouse

Forrester, Donald J.; Carpenter, J.W.; Blankinship, D.R.

1978-01-01

Coccidial oocysts were observed in 6 of 19 fecal samples from free-ranging whooping cranes (Grus americana) and 4 of 16 samples from captive whooping cranes. Eimeria gruis occurred in four free-ranging whooping cranes and E. reichenowi in two free-ranging and two captive whooping cranes. Fecal samples from two captive cranes contained oocysts of Isospora lacazei which was considered a spurious parasite. Oocysts of both species of Eimeria were prevalent in fecal samples collected from three free-ranging Canadian sandhill cranes (G. canadensis rowani) from whooping crane wintering grounds in Texas. These coccidia were prevalent also in fecal samples from 14 sandhill cranes (of 4 subspecies) maintained in captivity at the Patuxent Wildlife Research Center in Maryland.

Data for distribution of various species of fecal coliforms in urban, rural and private drinking water sources in ten years period - A case study: Kermanshah, Iran.

PubMed

Davoodi, Reza; Pirsaheb, Meghdad; Karimyan, Kamaladdin; Gupta, Vinod Kumar; Takhtshahi, Ali Reza; Sharafi, Hooshmand; Moradi, Masoud

2018-06-01

This study was aimed to investigate the distribution of various species of fecal coliform in urban, rural and private drinking water sources of Kermanshah, in the west of Iran. For this study, data of ten years period (2006-2016) assessments of microbial quality regarding various species of Fecal coliforms was taken from health centers associated with urban, rural and private resources of Kermanshah city. A total number of 8643 samples were taken, 1851 samples from rural, 365 from urban and 4834 from private resources. The results showed that Fecal coliforms , Escherichia coli ( E. coli ) had the widest distribution in all urban, rural and private water resources (22.3%, 45.9% and 34%, respectively). Moreover, E. coli (47.5%) and Klebsiella (0.4%) had, respectively, the highest and lowest distribution in all months considered. Based on the results, E.coli exists mostly in water resources; it is therefore of particular importance in the monitoring of water resources.

Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection.

PubMed

Weingarden, Alexa R; Chen, Chi; Bobr, Aleh; Yao, Dan; Lu, Yuwei; Nelson, Valerie M; Sadowsky, Michael J; Khoruts, Alexander

2014-02-15

Fecal microbiota transplantation (FMT) has emerged as a highly effective therapy for refractory, recurrent Clostridium difficile infection (CDI), which develops following antibiotic treatments. Intestinal microbiota play a critical role in the metabolism of bile acids in the colon, which in turn have major effects on the lifecycle of C. difficile bacteria. We hypothesized that fecal bile acid composition is altered in patients with recurrent CDI and that FMT results in its normalization. General metabolomics and targeted bile acid analyses were performed on fecal extracts from patients with recurrent CDI treated with FMT and their donors. In addition, 16S rRNA gene sequencing was used to determine the bacterial composition of pre- and post-FMT fecal samples. Taxonomic bacterial composition of fecal samples from FMT recipients showed rapid change and became similar to the donor after the procedure. Pre-FMT fecal samples contained high concentrations of primary bile acids and bile salts, while secondary bile acids were nearly undetectable. In contrast, post-FMT fecal samples contained mostly secondary bile acids, as did non-CDI donor samples. Therefore, our analysis showed that FMT resulted in normalization of fecal bacterial community structure and metabolic composition. Importantly, metabolism of bile salts and primary bile acids to secondary bile acids is disrupted in patients with recurrent CDI, and FMT corrects this abnormality. Since individual bile salts and bile acids have pro-germinant and inhibitory activities, the changes suggest that correction of bile acid metabolism is likely a major mechanism by which FMT results in a cure and prevents recurrence of CDI.

A case study characterizing animal fecal sources in surface water using a mitochondrial DNA marker.

PubMed

Bucci, John P; Shattuck, Michelle D; Aytur, Semra A; Carey, Richard; McDowell, William H

2017-08-01

Water quality impairment by fecal waste in coastal watersheds is a public health issue. The present study provided evidence for the use of a mitochondrial (mtDNA) marker to detect animal fecal sources in surface water. The accurate identification of fecal pollution is based on the notion that fecal microorganisms preferentially inhabit a host animal's gut environment. In contrast, mtDNA host-specific markers are inherent to eukaryotic host cells, which offers the advantage by detecting DNA from the host rather than its fecal bacteria. The present study focused on sampling water presumably from non-point sources (NPS), which can increase bacterial and nitrogen concentrations to receiving water bodies. Stream sampling sites located within the Piscataqua River Watershed (PRW), New Hampshire, USA, were sampled from a range of sites that experienced nitrogen inputs such as sewer and septic systems and suburban runoff. Three mitochondrial (mtDNA) gene marker assays (human, bovine, and canine) were tested from surface water. Nineteen sites were sampled during an 18-month period. Analyses of the combined single and multiplex assay results showed that the proportion of occurrence was highest for bovine (15.6%; n = 77) compared to canine (5.6%; n = 70) and human (5.7%; n = 107) mtDNA gene markers. For the human mtDNA marker, there was a statistically significant relationship between presence vs. absence and land use (Fisher's test p = 0.0031). This result was evident particularly for rural suburban septic, which showed the highest proportion of presence (19.2%) compared to the urban sewered (3.3%), suburban sewered (0%), and agricultural (0%) as well as forested septic (0%) sites. Although further testing across varied land use is needed, our study provides evidence for using the mtDNA marker in large watersheds.

A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus).

PubMed

Kistler, Whitney M; Parlos, Julie A; Peper, Steven T; Dunham, Nicholas R; Kendall, Ronald J

2016-01-01

Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53-0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population.

A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus)

PubMed Central

Kistler, Whitney M.; Parlos, Julie A.; Peper, Steven T.; Dunham, Nicholas R.; Kendall, Ronald J.

2016-01-01

Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53–0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population. PMID:27893772

Fecal and Mucosa-Associated Intestinal Microbiota in Patients with Diarrhea-Predominant Irritable Bowel Syndrome.

PubMed

Maharshak, Nitsan; Ringel, Yehuda; Katibian, David; Lundqvist, Ashley; Sartor, R Balfour; Carroll, Ian M; Ringel-Kulka, Tamar

2018-05-17

Irritable bowel syndrome (IBS) has been associated with changes in the intestinal microbiota. Only a few studies have explored differences in the mucosa-associated microbiota between IBS patients and healthy controls (HC). To characterize and compare the microbiota in mucosal and fecal samples from carefully selected patients with IBS-D and HC. The cohort was composed of 23 diarrhea-predominant IBS (IBS-D) patients and 24 HC. Fresh stool samples were collected from participants prior to the collection of colonic mucosal samples from an unprepped bowel. After DNA extraction, 16S rRNA genes were sequenced by 454 pyrosequencing and analyzed using the QIIME pipeline. The fecal microbiota (luminal niche) of IBS-D patients was found to have reduced enteric richness compared to HC (P < 0.05), whereas no differences were observed between the two groups within the mucosal microbiota. Within the luminal niche, the relative proportions of Faecalibacterium genus were found to be lower in IBS-D than in HC and the Dorea genus was higher in IBS-D. None of the taxa proportions were significantly different in IBS-D patients versus HC using an FDR of ≤ 0.1 when analyzing samples that appeared in > 25% samples of either niche. Fecal and mucosal microbiota of IBS-D patients and HC are very similar and are not sufficient to explain the reported altered physiology and symptomatology of IBS-D. Future studies should investigate intestinal microbiome-dependent functional activity in addition to the fecal and mucosal-associated microbial composition.

Levels of plasma and fecal glucocorticoid metabolites following an ACTH challenge in male and female coyotes (Canis latrans).

PubMed

Stevenson, Erika T; Gese, Eric M; Neuman-Lee, Lorin A; French, Susannah S

2018-03-01

Knowledge of endocrine stress responses can be advantageous for understanding how animals respond to their environment. One tool in wildlife endocrinology is to measure the adrenocortical activity as a parameter of disturbance of animals. Fecal glucocorticoid metabolites (GCMs) provide a noninvasive assessment of adrenocortical activity. Using an adrenocorticotropic hormone (ACTH) challenge administered to 28 captive coyotes (Canis latrans), we measured the levels of plasma cortisol, and fecal cortisol and corticosterone metabolites (i.e., GCMs). Our goal was to determine the dose-response in the plasma and fecal samples following the injection and determine if there were effects of sex, age, and time of day. Specifically, animals were anesthetized for ~ 90 min with treatment animals intravenously injected with exogenous ACTH and control animals receiving saline. We collected blood samples prior to injection and at 4 different time points post-injection. We also collected fecal samples 2 days pre- and 2 days post-injection to measure fecal GCMs and determine if an endocrine stress response could be detected in fecal samples. We found a definite response in cortisol levels in the plasma for coyotes to the ACTH challenge. There was a response in fecal corticosterone 1 day post-injection, but the control males showed a similar response indicating a handling effect. Fecal cortisol levels did not indicate a response to the ACTH challenge, and were significantly lower than corticosterone concentrations. We also found significant sex, but not age or diurnal, differences in fecal GCMs. Radioimmunoassays for fecal corticosterone levels appeared to be a reliable indicator of physiological stress in coyotes.

Survival, transport, and sources of fecal bacteria in streams and survival in land-applied poultry litter in the upper Shoal Creek basin, southwestern Missouri, 2001-2002

USGS Publications Warehouse

Schumacher, John G.

2003-01-01

Densities of fecal coliform bacteria along a 5.7-mi (mile) reach of Shoal Creek extending upstream from State Highway 97 (site 3) to State Highway W (site 2) and in two tributaries along this reach exceeded the Missouri Department of Natural Resources (MDNR) standard of 200 col/100 mL (colonies per 100 milliliters) for whole-body contact recreation. A combination of techniques was used in this report to provide information on the source, transport, and survival of fecal bacteria along this reach of Shoal Creek. Results of water-quality samples collected during dye-trace and seepage studies indicated that at summer low base-flow conditions, pastured cattle likely were a substantial source of fecal bacteria in Shoal Creek at the MDNR monitoring site (site 3) at State Highway 97. Using repeat element Polymerase Chain Reaction (rep-PCR), cattle were the presumptive source of about 50 percent of the Escherichia coli (E. coli) isolates in water samples from site 3. Cattle, horses, and humans were the most common presumptive source of E. coli isolates at sites further upstream. Poultry was identified by rep-PCR as a major source of E. coli in Pogue Creek, a tributary in the upper part of the study area. Results of the rep-PCR were in general agreement with the detection and distribution of trace concentrations of organic compounds commonly associated with human wastewater, such as caffeine, the antimicrobial agent triclosan, and the pharmaceutical compounds acetaminophen and thiabendazole (a common cattle anthelmintic). Significant inputs of fecal bacteria to Shoal Creek occurred along a 1.6-mi reach of Shoal Creek immediately upstream from site 3. During a 36-hour period in July 2001, average densities of fecal coliform and E. coli bacteria increased from less than or equal to 500 col/100 mL upstream from this stream reach (sample site 2c) to 2,100 and 1,400 col/100 mL, respectively, at the MDNR sampling site. Fecal bacteria densities exhibited diurnal variability at all five sampling sites along the 5.7-mi study reach of Shoal Creek, but the trends at successive downstream sites were out of phase and could not be explained by simple advection and dispersion. At base-flow conditions, the travel time of bacteria in Shoal Creek along the 5.7-mi reach between State Highway W (site 2) and the MDNR sampling site (site 3) was about 26 hours. Substantial dispersion and dilution occurs along the upper 4.1 mi of this reach because of inflows from a number of springs and tributaries and the presence of several long pools and channel meanders. Minimal dispersion and dilution occurs along the 1.6-mi reach immediately upstream from the MDNR sampling site. Measurements of fecal bacteria decay in Shoal Creek during July 2001 indicated that about 8 percent of fecal coliform and E. coli bacteria decay each hour with an average first-order decay constant of 0.084 h-1 (per hour). Results of field test plots indicated that substantial numbers of fecal bacteria present in poul try litter can survive in fields for as much as 8 weeks after the application of the litter to the land surface. Median densities of fecal coliform and E. coli in slurry-water samples collected from fields increased from less than 60 col/100 mL before the application of turkey and broiler litter, to as large as 420,000 and 290,000 col/100 mL after the application of litter. Bacteria densities in the test plots generally decreased in a exponential manner over time with decay rates ranging from 0.085 to 0.185 d-1 (per day) for fecal coliform to between 0.100 and 0.250 d-1 for E. coli. The apparent survival of significant numbers of fecal bacteria on fields where poultry litter has been applied indicates that runoff from these fields is a potential source of fecal bacteria to vicinity streams for many weeks following litter application.

Survival of fecal coliforms in dry-composting toilets.

PubMed

Redlinger, T; Graham, J; Corella-Barud, V; Avitia, R

2001-09-01

The dry-composting toilet, which uses neither water nor sewage infrastructure, is a practical solution in areas with inadequate sewage disposal and where water is limited. These systems are becoming increasingly popular and are promoted to sanitize human excreta and to recycle them into fertilizer for nonedible plants, yet there are few data on the safety of this technology. This study analyzed fecal coliform reduction in approximately 90 prefabricated, dry-composting toilets (Sistema Integral de Reciclamiento de Desechos Orgánicos [SIRDOs]) that were installed on the U.S.-Mexico border in Ciudad Juárez, Chihuahua, Mexico. The purpose of this study was to determine fecal coliform reduction over time and the most probable method of this reduction. Biosolid waste samples were collected and analyzed at approximately 3 and 6 months and were classified based on U.S. Environmental Protection Agency standards. Results showed that class A compost (high grade) was present in only 35.8% of SIRDOs after 6 months. The primary mechanism for fecal coliform reduction was found to be desiccation rather than biodegradation. There was a significant correlation (P = 0.008) between classification rating and percent moisture categories of the biosolid samples: drier samples had a greater proportion of class A samples. Solar exposure was critical for maximal class A biosolid end products (P = 0.001). This study only addressed fecal coliforms as an indicator organism, and further research is necessary to determine the safety of composting toilets with respect to other pathogenic microorganisms, some of which are more resistant to desiccation.

Survival of Fecal Coliforms in Dry-Composting Toilets

PubMed Central

Redlinger, Thomas; Graham, Jay; Corella-Barud, Verónica; Avitia, Raquel

2001-01-01

The dry-composting toilet, which uses neither water nor sewage infrastructure, is a practical solution in areas with inadequate sewage disposal and where water is limited. These systems are becoming increasingly popular and are promoted to sanitize human excreta and to recycle them into fertilizer for nonedible plants, yet there are few data on the safety of this technology. This study analyzed fecal coliform reduction in approximately 90 prefabricated, dry-composting toilets (Sistema Integral de Reciclamiento de Desechos Orgánicos [SIRDOs]) that were installed on the U.S.-Mexico border in Ciudad Juárez, Chihuahua, Mexico. The purpose of this study was to determine fecal coliform reduction over time and the most probable method of this reduction. Biosolid waste samples were collected and analyzed at approximately 3 and 6 months and were classified based on U.S. Environmental Protection Agency standards. Results showed that class A compost (high grade) was present in only 35.8% of SIRDOs after 6 months. The primary mechanism for fecal coliform reduction was found to be desiccation rather than biodegradation. There was a significant correlation (P = 0.008) between classification rating and percent moisture categories of the biosolid samples: drier samples had a greater proportion of class A samples. Solar exposure was critical for maximal class A biosolid end products (P = 0.001). This study only addressed fecal coliforms as an indicator organism, and further research is necessary to determine the safety of composting toilets with respect to other pathogenic microorganisms, some of which are more resistant to desiccation. PMID:11526002

Evaluation of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a screening method for the detection of influenza viruses in the fecal materials of water birds.

PubMed

Yoshida, Hiromi; Sakoda, Yoshihiro; Endo, Mayumi; Motoshima, Masayuki; Yoshino, Fumi; Yamamoto, Naoki; Okamatsu, Masatoshi; Soejima, Takahiro; Senba, Syouhei; Kanda, Hidetoshi; Kida, Hiroshi

2011-06-01

Migratory water birds are a natural reservoir for influenza A viruses. Viruses replicate in the intestines of ducks and are shed with the fecal materials. Virus isolation from collected fecal materials, therefore, is an integral part of the surveillance of avian influenza in water birds. In the present study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) was assessed for its usefulness in detecting the RNA of influenza A viruses in fecal materials. It was found that, RT-LAMP specifically and sensitively detects the matrix gene of influenza A viruses. Influenza A viruses were isolated from the fecal materials in which viral RNA were detected by RT-LAMP in 35 min. The present findings indicate that RT-LAMP is useful as a high throughput screening method for field samples prior to virus isolation, allowing the processing of hundreds of samples per day.

Use of Bacteroidales Microbial Source Tracking To Monitor Fecal Contamination in Fresh Produce Production

PubMed Central

Ravaliya, Kruti; Garcia, Santos; Heredia, Norma; Fabiszewski de Aceituno, Anna; Bartz, Faith E.; Leon, Juan S.; Jaykus, Lee-Ann

2014-01-01

In recent decades, fresh and minimally processed produce items have been associated with an increasing proportion of food-borne illnesses. Most pathogens associated with fresh produce are enteric (fecal) in origin, and contamination can occur anywhere along the farm-to-fork chain. Microbial source tracking (MST) is a tool developed in the environmental microbiology field to identify and quantify the dominant source(s) of fecal contamination. This study investigated the utility of an MST method based on Bacteroidales 16S rRNA gene sequences as a means of identifying potential fecal contamination, and its source, in the fresh produce production environment. The method was applied to rinses of fresh produce, source and irrigation waters, and harvester hand rinses collected over the course of 1 year from nine farms (growing tomatoes, jalapeño peppers, and cantaloupe) in Northern Mexico. Of 174 samples, 39% were positive for a universal Bacteroidales marker (AllBac), including 66% of samples from cantaloupe farms (3.6 log10 genome equivalence copies [GEC]/100 ml), 31% of samples from tomato farms (1.7 log10 GEC/100 ml), and 18% of samples from jalapeño farms (1.5 log10 GEC/100 ml). Of 68 AllBac-positive samples, 46% were positive for one of three human-specific markers, and none were positive for a bovine-specific marker. There was no statistically significant correlation between Bacteroidales and generic Escherichia coli across all samples. This study provides evidence that Bacteroidales markers may serve as alternative indicators for fecal contamination in fresh produce production, allowing for determination of both general contamination and that derived from the human host. PMID:24212583

Animal Feces Contribute to Domestic Fecal Contamination: Evidence from E. coli Measured in Water, Hands, Food, Flies, and Soil in Bangladesh.

PubMed

Ercumen, Ayse; Pickering, Amy J; Kwong, Laura H; Arnold, Benjamin F; Parvez, Sarker Masud; Alam, Mahfuja; Sen, Debashis; Islam, Sharmin; Kullmann, Craig; Chase, Claire; Ahmed, Rokeya; Unicomb, Leanne; Luby, Stephen P; Colford, John M

2017-08-01

Fecal-oral pathogens are transmitted through complex, environmentally mediated pathways. Sanitation interventions that isolate human feces from the environment may reduce transmission but have shown limited impact on environmental contamination. We conducted a study in rural Bangladesh to (1) quantify domestic fecal contamination in settings with high on-site sanitation coverage; (2) determine how domestic animals affect fecal contamination; and (3) assess how each environmental pathway affects others. We collected water, hand rinse, food, soil, and fly samples from 608 households. We analyzed samples with IDEXX Quantitray for the most probable number (MPN) of E. coli. We detected E. coli in source water (25%), stored water (77%), child hands (43%), food (58%), flies (50%), ponds (97%), and soil (95%). Soil had >120 000 mean MPN E. coli per gram. In compounds with vs without animals, E. coli was higher by 0.54 log 10 in soil, 0.40 log 10 in stored water and 0.61 log 10 in food (p < 0.05). E. coli in stored water and food increased with increasing E. coli in soil, ponds, source water and hands. We provide empirical evidence of fecal transmission in the domestic environment despite on-site sanitation. Animal feces contribute to fecal contamination, and fecal indicator bacteria do not strictly indicate human fecal contamination when animals are present.

Animal Feces Contribute to Domestic Fecal Contamination: Evidence from E. coli Measured in Water, Hands, Food, Flies, and Soil in Bangladesh

PubMed Central

2017-01-01

Fecal-oral pathogens are transmitted through complex, environmentally mediated pathways. Sanitation interventions that isolate human feces from the environment may reduce transmission but have shown limited impact on environmental contamination. We conducted a study in rural Bangladesh to (1) quantify domestic fecal contamination in settings with high on-site sanitation coverage; (2) determine how domestic animals affect fecal contamination; and (3) assess how each environmental pathway affects others. We collected water, hand rinse, food, soil, and fly samples from 608 households. We analyzed samples with IDEXX Quantitray for the most probable number (MPN) of E. coli. We detected E. coli in source water (25%), stored water (77%), child hands (43%), food (58%), flies (50%), ponds (97%), and soil (95%). Soil had >120 000 mean MPN E. coli per gram. In compounds with vs without animals, E. coli was higher by 0.54 log10 in soil, 0.40 log10 in stored water and 0.61 log10 in food (p < 0.05). E. coli in stored water and food increased with increasing E. coli in soil, ponds, source water and hands. We provide empirical evidence of fecal transmission in the domestic environment despite on-site sanitation. Animal feces contribute to fecal contamination, and fecal indicator bacteria do not strictly indicate human fecal contamination when animals are present. PMID:28686435

Presumptive Sources of Fecal Contamination in Four Tributaries to the New River Gorge National River, West Virginia, 2004

USGS Publications Warehouse

Mathes, Melvin V.; O'Brien, Tara L.; Strickler, Kriston M.; Hardy, Joshua J.; Schill, William B.; Lukasik, Jerzy; Scott, Troy M.; Bailey, David E.; Fenger, Terry L.

2007-01-01

Several methods were used to determine the sources of fecal contamination in water samples collected during September and October 2004 from four tributaries to the New River Gorge National River -- Arbuckle Creek, Dunloup Creek, Keeney Creek, and Wolf Creek. All four tributaries historically have had elevated levels of fecal coliform bacteria. The source-tracking methods used yielded various results, possibly because one or more methods failed. Sourcing methods used in this study included the detection of several human-specific and animal-specific biological or molecular markers, and library-dependent pulsed-field gel electrophoresis analysis that attempted to associate Escherichia coli bacteria obtained from water samples with animal sources by matching DNA-fragment banding patterns. Evaluation of the results of quality-control analysis indicated that pulsed-field gel electrophoresis analysis was unable to identify known-source bacteria isolates. Increasing the size of the known-source library did not improve the results for quality-control samples. A number of emerging methods, using markers in Enterococcus, human urine, Bacteroidetes, and host mitochondrial DNA, demonstrated some potential in associating fecal contamination with human or animal sources in a limited analysis of quality-control samples. All four of the human-specific markers were detected in water samples from Keeney Creek, a watershed with no centralized municipal wastewater-treatment facilities, thus indicating human sources of fecal contamination. The human-specific Bacteroidetes and host mitochondrial DNA markers were detected in water samples from Dunloup Creek, Wolf Creek, and to a lesser degree Arbuckle Creek. Results of analysis for wastewater compounds indicate that the September 27 sample from Arbuckle Creek contained numerous human tracer compounds likely from sewage. Dog, horse, chicken, and pig host mitochondrial DNA were detected in some of the water samples with the exception of the October 5 sample from Dunloup Creek. Cow, white-tailed deer, and Canada goose DNA were not detected in any of the samples collected from the four tributaries, despite the presence of these animals in the watersheds. Future studies with more rigorous quality-control analyses are needed to investigate the potential applicability and use of these emerging methods. Because many of the detections for the various methods could vary over time and with flow conditions, repeated sampling during both base flow and storm events would be necessary to more definitively determine the sources of fecal contamination for each watershed.

Evaluation of Bovine Feces-Associated Microbial Source Tracking Markers and Their Correlations with Fecal Indicators and Zoonotic Pathogens in a Brisbane, Australia, Reservoir

PubMed Central

Sritharan, T.; Palmer, A.; Sidhu, J. P. S.; Toze, S.

2013-01-01

This study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (BacCow-UCD and cowM3) and one viral [bovine adenovirus (B-AVs)] microbial source tracking (MST) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast Queensland, Australia. In addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal indicator bacteria (FIB), Campylobacter spp., Escherichia coli O157, and Salmonella spp. The overall host specificity values of the BacCow-UCD, cowM3, and B-AVs markers to differentiate between bovine and other nontarget host groups were 0.66, 0.88, and 1.00, respectively (maximum value of 1.00). The overall host sensitivity values of these markers, however, in composite bovine wastewater and individual bovine fecal DNA samples were 0.93, 0.90, and 0.60, respectively (maximum value of 1.00). Among the 36 water samples tested, 56%, 22%, and 6% samples were PCR positive for the BacCow-UCD, cowM3, and B-AVs markers, respectively. Among the 36 samples tested, 50% and 14% samples were PCR positive for the Campylobacter 16S rRNA and E. coli O157 rfbE genes, respectively. Based on the results, we recommend that multiple bovine feces-associated markers be used if possible for bovine fecal pollution tracking. Nonetheless, the presence of the multiple bovine feces-associated markers along with the presence of potential zoonotic pathogens indicates bovine fecal pollution in the reservoir water samples. Further research is required to understand the decay rates of these markers in relation to FIB and zoonotic pathogens. PMID:23417003

Fecal-indicator bacteria in surface waters of the Santee River Basin and coastal drainages, North and South Carolina, 1995-98

USGS Publications Warehouse

Wilhelm, Lance J.; Maluk, Terry L.

1998-01-01

IntroductionHigh levels of fecal-indicator bacteria in rivers and streams can indicate the possible presence of pathogenic (disease-causing) microorganisms. Cholera, typhoid fever, bacterial dysentery, infectious hepatitis, and cryptosporidiosis are some of the well known waterborne diseases that spread through water contaminated and fecal matter. Eye, ear, nose, and throat infections also can result from contact with contaminated water. In general, methods are not routinely used to detect pathogens in water. Instead, bacteria such as total coliforms, fecal coliforms, fecal streptococci, Escherichia coli (E coli), and enterococci are used as indicators of sanitary water quality, because they are present in high numbers in fecal material and have been shown to be associated with some waterborne disease-causing organisms. Indicator bacteria usually are harmless, more plentiful, and easier to detect than pathogens. The concentration of bacteria in a sample of water is usually expressed as the number of bacterial colonies per 100 milliliters of water sample.As part of the U.S. Geological Survey National Water-Quality Assessment Program, 145 samples were collected and analyzed for selected water-quality constituents, fecal coliforms, and fecal streptococci at 17 sites in North and South Carolina from October 1995 through September 1996. Of the original 17 sites, 4 in South Carolina were sampled for E. coli and total coliforms from April through September 1997. At two sites, this sampling continued from October 1997 through April 1998.

Use of fecal volatile organic compound analysis to discriminate between non-vaccinated and BCG—Vaccinated cattle prior to and after Mycobacterium bovis challenge

PubMed Central

Stahl, Randal; Waters, W. Ray; Palmer, Mitchell V.; Nol, Pauline; Rhyan, Jack C.; VerCauteren, Kurt C.; Koziel, Jacek A.

2017-01-01

Bovine tuberculosis is a zoonotic disease of global public health concern. Development of diagnostic tools to improve test accuracy and efficiency in domestic livestock and enable surveillance of wildlife reservoirs would improve disease management and eradication efforts. Use of volatile organic compound analysis in breath and fecal samples is being developed and optimized as a means to detect disease in humans and animals. In this study we demonstrate that VOCs present in fecal samples can be used to discriminate between non-vaccinated and BCG-vaccinated cattle prior to and after Mycobacterium bovis challenge. PMID:28686691

Sources and Pathways of Bacterial Contamination in Urban Streams and Ocean Beaches, Santa Barbara, California

NASA Astrophysics Data System (ADS)

Johnson, R. D.; Mendez, G. O.; La, J. X.; Izbicki, J. A.

2005-12-01

Streams and ocean beaches in Santa Barbara, California, occasionally have concentrations of fecal indicator bacteria that exceed public health standards for recreational water, forcing temporary beach closures. Possible sources of fecal bacteria contamination include transient human populations, animal populations, and leaking sewer lines. The purpose of this three-year study is to identify important sources of fecal bacteria affecting the urban streams and beaches and to identify important pathways of transport. Contamination may enter streams and beaches directly by surface runoff, but also may be transmitted short distances through shallow ground water. Our analysis of existing historical data shows that fecal indicator bacteria concentrations are higher in near-shore ocean water following extreme high tides. The possible role of near shore ground water in supplying contaminants to the sea will be investigated by sampling water from an array of shallow wells installed for this study between an older city sewer line and the ocean. The ground water flux to the ocean will be inferred from water levels in these wells, and further tested by radium isotope values in near shore ocean samples. Two additional well arrays will be installed to test for leakage from residential sewage hookups and measure associated exchanges between ground water, streams, and ocean. Preliminary data collected by this study show fecal indicator bacteria concentrations in urban reaches of Mission Creek and its tributaries, the principle drainage through the city, are higher during low flow periods than during periods of higher flow. Analysis of preliminary data also shows short-term temporal variations in bacterial concentrations during twenty-four hour periods. Human enterovirus has been detected in our sample from one urban-drain tributary to Mission Creek. In order to identify the origins of fecal indicator bacteria water samples from Mission Creek, its tributaries, urban drains, and associated shallow ground water will be analyzed for nutrients, dissolved organic carbon (including optical properties to characterize the composition of the organic carbon), fecal sterols, DNA (using Terminal-Restriction Fragment Length Poylmorphism), and phospholipid fatty acids.

Tracking the Primary Sources of Fecal Pollution in a Tropical Watershed in a One-Year Study

EPA Science Inventory

A study was conducted to determine the primary sources of fecal pollution in a subtropical watershed using host-specific assays developed in temperate regions. Water samples (n=534) from 10 different sites along the Rio Grande de Arecibo watershed were collected every two-three w...

Comparing protein and energy status of winter-fed white-tailed deer

USGS Publications Warehouse

Page, B.D.; Underwood, H.B.

2006-01-01

Although nutritional status in response to controlled feeding trials has been extensively studied in captive white-tailed deer (Odocoileus virginianus), there remains a considerable gap in understanding the influence of variable supplemental feeding protocols on free-ranging deer. Consequently, across the northern portion of the white-tailed deer range, numerous property managers are investing substantial resources into winter supplemental-feeding programs without adequate tools to assess the nutritional status of their populations. We studied the influence of a supplemental winter feeding gradient on the protein and energy status of free-ranging white-tailed deer in the Adirondack Mountains of New York. We collected blood and fecal samples from 31 captured fawns across 3 sites that varied considerably in the frequency, quantity, and method of supplemental feed distribution. To facilitate population-wide comparisons, we collected fresh fecal samples off the snow at each of the 3 sites with supplemental feeding and 1 reference site where no feeding occurred. Results indicated that the method of feed distribution, in addition to quantity and frequency, can affect the nutritional status of deer. The least intensively fed population showed considerable overlap in diet quality with the unfed population in a principal components ordination, despite the substantial time and financial resources invested in the feeding program. Data from fecal samples generally denoted a gradient in diet quality and digestibility that corresponded with the availability of supplements. Our results further demonstrated that fecal nitrogen and fecal fiber, indices of dietary protein and digestibility, can be estimated using regressions of fecal pellet mass, enabling a rapid qualitative assessment of diet quality.

Evaluation of PMS-PCR technology for detection of Mycobacterium avium subsp. paratuberculosis directly from bovine fecal specimens.

PubMed

Salgado, M; Steuer, P; Troncoso, E; Collins, M T

2013-12-27

Mycobacterium avium subsp. paratuberculosis (MAP) causes paratuberculosis, or Johne's disease, in animals. Diagnosis of MAP infection is challenging because of the pathogen's fastidious in vitro growth requirements and low-level intermittent shedding in feces during the preclinical phase of the infection. Detection of these "low-shedders" is important for effective control of paratuberculosis as these animals serve as sources of infection for susceptible calves. Magnetic separation technology, used in combination with culture or molecular methods for the isolation and detection of pathogenic bacteria, enhances the analytical sensitivity and specificity of detection methods. The aim of the present study was to evaluate peptide-mediated magnetic separation (PMS) capture technology coupled with IS900 PCR using the Roche real-time PCR system (PMS-PCR), in comparison with fecal culture using BACTEC-MGIT 960 system, for detection of MAP in bovine fecal samples. Among the 351 fecal samples 74.9% (263/351) were PMS-PCR positive while only 12.3% (43/351) were MGIT culture-positive (p=0.0001). All 43 MGIT culture-positive samples were also positive by PMS-PCR. Mean PMS-PCR crossing-point (Cp) values for the 13 fecal samples with the highest number of MAP, based on time to detection, (26.3) were significantly lower than for the 17 fecal samples with <100 MAP per 2g feces (30.06) (p<0.05). PMS-PCR technology provided results in a shorter time and yielded a higher number of positive results than MGIT culture. Earlier and faster detection of animals shedding MAP by PMS-PCR should significantly strengthen control efforts for MAP-infected cattle herds by helping to limit infection transmission at earlier stages of the infection. Copyright © 2013 Elsevier B.V. All rights reserved.

Assessment of the relative sensitivity of milk ELISA for detection of Mycobacterium avium ssp. paratuberculosis infectious dairy cows.

PubMed

Laurin, Emilie L; Sanchez, Javier; Chaffer, Marcelo; McKenna, Shawn L B; Keefe, Greg P

2017-01-01

Milk ELISA are commonly used for detection of Mycobacterium avium ssp. paratuberculosis (MAP) antibodies in dairy cows, due to low cost and quick processing for large numbers of samples. However, low sensitivity and variations from host and environmental factors can impede detection of MAP antibodies at early disease stages. The objectives of our study were to assess the sensitivity of milk ELISA in comparison with fecal tests and to evaluate how detectable antibody concentrations in milk vary with changes in fecal shedding of MAP, cow age, cow parity, days in milk, and time of year. To compare the sensitivity of a commercial milk ELISA with solid and broth fecal culture and with fecal real-time PCR, a longitudinal study was performed for the identification of MAP-infectious animals as determined by prior fecal testing for MAP shedding. In addition, associations between variation in milk MAP ELISA score and changes in fecal MAP shedding, host age, days in milk, and season were evaluated. Monthly milk and fecal samples were collected over 1 yr from 46 cows that were previously shedding MAP in their feces. Sensitivity of milk ELISA was 29.9% (95% CI: 24.8 to 35.1%), compared with 46.7% (40.7 to 52.7%) for fecal solid culture, 55.0% (49.3 to 60.7%) for fecal broth culture, and 78.4% (73.3 to 83.1%) for fecal direct real-time PCR. The effect of stage of lactation could not be separated from the effect of season, with increased milk ELISA scores at greater days in milk in winter. However, unpredictable monthly variations in results were observed among the 3 assays for individual cow testing, which highlights the importance of identifying patterns in pathogen and antibody detection over time in MAP-positive herds. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

SURVEY OF HOUSE RAT INTESTINAL PARASITES FROM SURABAYA DISTRICT, EAST JAVA, INDONESIA THAT CAN CAUSE OPPORTUNISTIC INFECTIONS IN HUMANS.

PubMed

Prasetyo, R H

2016-03-01

The purpose of this study was to investigate the prevalence of house rat zoonotic intestinal parasites from Surabaya District, East Java, Indonesia that have the potential to cause opportunistic infection in humans. House rat fecal samples were collected from an area of Surabaya District with a dense rat population during May 2015. Intestinal parasites were detected microscopically using direct smear of feces stained with Lugol's iodine and modified Ziehl-Neelsen stains. The fecal samples were also cultured for Strongyloides stercoralis. Ninety-eight house rat fecal samples were examined. The potential opportunistic infection parasite densities found in those samples were Strongyloides stercoralis in 53%, Hymenolepis nana in 42%, Cryptosporidium spp in 33%, and Blastocystis spp in 6%. This is the first report of this kind in Surabaya District. Measures need to be taken to control the house rat population in the study area to reduce the risk of the public health problem. Keywords: zoonotic intestinal parasites, opportunistic infection, house rat, densely populated area, Indonesia

A study of the level and dynamics of Eimeria populations in naturally infected, grazing beef cattle at various stages of production in the Mid-Atlantic USA.

PubMed

Lucas, Aaron S; Swecker, William S; Lindsay, David S; Scaglia, Guillermo; Neel, James P S; Elvinger, Francois C; Zajac, Anne M

2014-05-28

There is little information available on the species dynamics of eimerian parasites in grazing cattle in the central Appalachian region of the United States. Therefore, the objective of this study was to describe the level of infection and species dynamics of Eimeria spp. in grazing beef cattle of various age groups over the course of a year in the central Appalachian region. Rectal fecal samples were collected from male and female calves (n=72) monthly from May through October 2005, heifers only (n=36) monthly from November 2005 to April 2006, and cows (n=72) in May, July, and September, 2005. Eimeria spp. oocysts were seen in 399 of 414 (96%) fecal samples collected from the calves from May through October. Fecal oocysts counts (FOC) in the calves were lower (P<0.05) in May than all other months and no significant differences were detected from June through September. Eimeria spp. oocysts were detected in 198 of 213 (92%) of fecal samples collected from the 36 replacement heifers monthly from November to April and monthly mean FOC did not differ during this time period. The prevalence of oocyst shedding increased to 100% in calves in September and remained near 100% in the replacement heifers during the sampling period. Eimeria spp. oocysts were also detected in 150 of 200 (75%) samples collected in May, July, and September from the cows and mean FOC did not differ significantly over the sampling period. Eimeria spp. composition was dominated by Eimeria bovis in fecal samples collected from calves, replacement heifers and cows. Mixed Eimeria spp. infections were, however, common in all groups and 13 Eimeria spp. oocysts were identified throughout the sampling period. Copyright © 2014 Elsevier B.V. All rights reserved.

Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area

PubMed Central

Sinigalliano, C. D.; Gidley, M. L.; Shibata, T.; Whitman, D.; Dixon, T. H.; Laws, E.; Hou, A.; Bachoon, D.; Brand, L.; Amaral-Zettler, L.; Gast, R. J.; Steward, G. F.; Nigro, O. D.; Fujioka, R.; Betancourt, W. Q.; Vithanage, G.; Mathews, J.; Fleming, L. E.; Solo-Gabriele, H. M.

2007-01-01

Floodwaters in New Orleans from Hurricanes Katrina and Rita were observed to contain high levels of fecal indicator bacteria and microbial pathogens, generating concern about long-term impacts of these floodwaters on the sediment and water quality of the New Orleans area and Lake Pontchartrain. We show here that fecal indicator microbe concentrations in offshore waters from Lake Pontchartrain returned to prehurricane concentrations within 2 months of the flooding induced by these hurricanes. Vibrio and Legionella species within the lake were more abundant in samples collected shortly after the floodwaters had receded compared with samples taken within the subsequent 3 months; no evidence of a long-term hurricane-induced algal bloom was observed. Giardia and Cryptosporidium were detected in canal waters. Elevated levels of fecal indicator bacteria observed in sediment could not be solely attributed to impacts from floodwaters, as both flooded and nonflooded areas exhibited elevated levels of fecal indicator bacteria. Evidence from measurements of Bifidobacterium and bacterial diversity analysis suggest that the fecal indicator bacteria observed in the sediment were from human fecal sources. Epidemiologic studies are highly recommended to evaluate the human health effects of the sediments deposited by the floodwaters. PMID:17488814

ESTABLISHING NORMAL FECAL FLORA IN WILD AUSTRALIAN PASSERINE BIRDS BY USE OF THE FECAL GRAM STAIN.

PubMed

Latham, Benjamin; Leishman, Alan; Martin, John; Phalen, David

2017-09-01

The purpose of this study was to determine the normal fecal bacterial and fungal flora and parasite prevalence in wild passerine birds found at the Australian Botanic Garden (Mount Annan, New South Wales). Wild passerine birds (n = 186) from 28 species were captured with mist nets. Fecal Gram stains (n = 155) were made from 26 species and analyzed for bacterial density, Gram stain morphology, and the presence of yeast. Fecal wet preparations (n = 139) were made from 24 passerine species and were analyzed for parasites. Our results showed that 81.9% of passerines sampled had bacteria present in their feces. The bacteria found were entirely Gram positive and consisted predominantly of cocci. Individuals that were caught on multiple occasions were found to have stable bacterial populations, apart from the red-browed finch (Neochmia temporalis). Insectivores had higher bacterial densities and cocci proportions than nectarivores had. Yeasts were rare in most species, with the exception of the bell miner (Manorina melanophrys) and noisy miner (Manorina melanocephala). The yeast, Macrorhabdus ornithogaster, and parasites were not observed in any fecal samples. These results will help practitioners to assess the health of Australian passerine species submitted for care or housed in zoological collections.

Faecal matrix metalloprotease-9 is a more sensitive marker for diagnosing pouchitis than faecal calprotectin: results from a pilot study.

PubMed

Farkas, Klaudia; Bálint, Anita; Bor, Renáta; Földesi, Imre; Szűcs, Mónika; Nagy, Ferenc; Szepes, Zoltán; Annaházi, Anita; Róka, Richárd; Molnár, Tamás

2015-03-01

Potential non-invasive markers of pouchitis would have a great deal of significance within clinical practice. This study is aimed at assessing the diagnostic accuracy of fecal calprotectin and matrix metalloprotease-9 as potential markers in patients both with and without pouchitis. Stool and blood samples were collected from 33 ileal pouch-anal anastomosis patients before a follow-up pouchoscopy. Biopsy samples were taken for histological purposes. The presence of cuffitis and stenosis was evaluated with an endoscopy. Calprotectin and matrix metalloprotease-9 were quantified with an enzyme-linked immunosorbent assay. Pouchitis was detected in 30.3% of the patients. The levels of fecal calprotectin and matrix metalloprotease-9 increased significantly in patients with pouchitis. The sensitivity and specificity of matrix metalloprotease-9 was higher than that of fecal calprotectin. Only matrix metalloprotease-9 correlated significantly with the severity of pouchitis. Fecal matrix metalloprotease-9 has a high specificity in the diagnosis of pouchitis.

Pepper Mild Mottle Virus as an Indicator of Fecal Pollution ▿

PubMed Central

Rosario, Karyna; Symonds, Erin M.; Sinigalliano, Christopher; Stewart, Jill; Breitbart, Mya

2009-01-01

Accurate indicators of fecal pollution are needed in order to minimize public health risks associated with wastewater contamination in recreational waters. However, the bacterial indicators currently used for monitoring water quality do not correlate with the presence of pathogens. Here we demonstrate that the plant pathogen Pepper mild mottle virus (PMMoV) is widespread and abundant in wastewater from the United States, suggesting the utility of this virus as an indicator of human fecal pollution. Quantitative PCR was used to determine the abundance of PMMoV in raw sewage, treated wastewater, seawater exposed to wastewater, and fecal samples and/or intestinal homogenates from a wide variety of animals. PMMoV was present in all wastewater samples at concentrations greater than 1 million copies per milliliter of raw sewage. Despite the ubiquity of PMMoV in human feces, this virus was not detected in the majority of animal fecal samples tested, with the exception of chicken and seagull samples. PMMoV was detected in four out of six seawater samples collected near point sources of secondary treated wastewater off southeastern Florida, where it co-occurred with several other pathogens and indicators of fecal pollution. Since PMMoV was not found in nonpolluted seawater samples and could be detected in surface seawater for approximately 1 week after its initial introduction, the presence of PMMoV in the marine environment reflects a recent contamination event. Together, these data demonstrate that PMMoV is a promising new indicator of fecal pollution in coastal environments. PMID:19767474

Evaluation of the impact of refrigeration on next generation sequencing-based assessment of the canine and feline fecal microbiota.

PubMed

Weese, J Scott; Jalali, Mohammad

2014-09-30

Evaluation of factors that might impact microbiota assessment is important to avoid spurious results, particularly in field and multicenter studies where sample collection may occur distant from the laboratory. This study evaluated the impact of refrigeration on next generation sequence-based assessment of the canine and feline fecal microbiota. Fecal samples were collected from seven dogs and ten cats, and analysed at baseline and after 3, 7, 10 and 14 days of storage at 4°C. There were no differences in community membership or population structure between timepoints for either dogs or cats, nor were there any differences in richness, diversity and evenness. There were few differences in relative abundance of phyla or predominant genera, with the only differences being significant increases in Actinobacteria between Days 0-14 (P = 0.0184) and 1-14 (P = 0.0182) for canine samples, and a decrease in Erysipelotrichaceae incertae sedis between Day 0 and Day 7 (median 4.9 vs 2.2%, P = 0.046) in feline samples. Storage for at least 14 days at 4°C has limited impact on culture-independent assessment of the canine and feline fecal microbiota, although changes in some individual groups may occur.

Sewage reflects the microbiomes of human populations.

PubMed

Newton, Ryan J; McLellan, Sandra L; Dila, Deborah K; Vineis, Joseph H; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

2015-02-24

Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics. Copyright © 2015 Newton et al.

Occurrence of microbial indicators and Clostridium perfringens in wastewater, water column samples, sediments, drinking water, and Weddell seal feces collected at McMurdo Station, Antarctica

USGS Publications Warehouse

Lisle, J.T.; Smith, J.J.; Edwards, D.D.; McFeters, G.A.

2004-01-01

McMurdo Station, Antarctica, has discharged untreated sewage into McMurdo Sound for decades. Previous studies delineated the impacted area, which included the drinking water intake, by using total coliform and Clostridium perfringens concentrations. The estimation of risk to humans in contact with the impacted and potable waters may be greater than presumed, as these microbial indicators may not be the most appropriate for this environment. To address these concerns, concentrations of these and additional indicators (fecal coliforms, Escherichia coli, enterococci, coliphage, and enteroviruses) in the untreated wastewater, water column, and sediments of the impacted area and drinking water treatment facility and distribution system at McMurdo Station were determined. Fecal samples from Weddell seals in this area were also collected and analyzed for indicators. All drinking water samples were negative for indicators except for a single total coliform-positive sample. Total coliforms were present in water column samples at higher concentrations than other indicators. Fecal coliform and enterococcus concentrations were similar to each other and greater than those of other indicators in sediment samples closer to the discharge site. C. perfringens concentrations were higher in sediments at greater distances from the discharge site. Seal fecal samples contained concentrations of fecal coliforms, E. coli, enterococci, and C. perfringens similar to those found in untreated sewage. All samples were negative for enteroviruses. A wastewater treatment facility at McMurdo Station has started operation, and these data provide a baseline data set for monitoring the recovery of the impacted area. The contribution of seal feces to indicator concentrations in this area should be considered.

Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations

PubMed Central

Heaney, Christopher D.; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R.

2015-01-01

Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI] = 1.03, 5.94) and 2.30 times (95% CI = 0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI = 1.21, 6.80) and 3.36 (95% CI = 1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. PMID:25600418

Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations.

PubMed

Heaney, Christopher D; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R

2015-04-01

Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI]=1.03, 5.94) and 2.30 times (95% CI=0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI=1.21, 6.80) and 3.36 (95% CI=1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. Copyright © 2014 Elsevier B.V. All rights reserved.

First record of entodiniomorph ciliates in a carnivore, the maned wolf (Chrysocyon brachyurus), from Brazil.

PubMed

Vynne, Carly; Kinsella, John M

2009-06-01

The entodiniomorph ciliates (Ciliophora: Entodiniomorphida) are endosymbiotes widely found in the intestines of herbivorous mammals. These commensals commonly occur in the Artiodactyla and Perissodactyla and have also been described in the Proboscidea, Primates, Rodentia, and Diprotodontia. This study reports the first finding of a ciliate in a member of order Carnivora, the maned wolf (Chrysocyon brachyurus). Fecal samples from wild and captive maned wolves were screened using ethyl acetate sedimentation. Prevalence in fecal samples collected from free-ranging maned wolves in Brazil was 40% (6 of 15). Fecal samples from two of four captive individuals from the St. Louis Zoo also had the same species of ciliate. The largely frugivorous diet of the maned wolf likely explains the occurrence of these normally herbivore-associated endosymbiotes in a carnivore.

Fecal corticosterone reflects serum corticosterone in Florida sandhill cranes.

PubMed

Ludders, J W; Langenberg, J A; Czekala, N M; Erb, H N

2001-07-01

Florida sandhill cranes (Grus canadensis pratensis) were conditioned to confinement 6 hr/day for 7 days. On day 8, each bird's jugular vein was catheterized, blood samples were drawn, and each crane was confined for 6 hr. Using a randomized, restricted cross-over design, cranes were injected intravenously with either 0.9% NaCl solution or ACTH (cosyntropin; Cortrosyn; 0.25 mg). During the 6 hr of confinement, fecal samples (feces and urine) were collected from each of five cranes immediately after defecation. Individual fecal samples were collected approximately at hourly intervals and assayed for corticosterone. We showed previously that serum corticosterone did not vary significantly following saline injection, but peaked significantly 60 min after ACTH injection. Maximal fecal corticosterone concentrations (ng/g) were greater (P < 0.10; median 1087 ng/g) following ACTH stimulation compared to maximal fecal corticosterone concentrations at the end of acclimation (day 7; median 176) and following saline treatment (median 541). In cranes under controlled conditions, fecal corticosterone concentration reflects serum corticosterone levels, fecal corticosterone, Grus canadensis pratensis, sandhill cranes, serum corticosterone levels.

Comparison of milk culture, direct and nested polymerase chain reaction (PCR) with fecal culture based on samples from dairy herds infected with Mycobacterium avium subsp. paratuberculosis

PubMed Central

Gao, Anli; Odumeru, Joseph; Raymond, Melinda; Hendrick, Steven; Duffield, Todd; Mutharia, Lucy

2009-01-01

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in cattle and other farm ruminants, and is also a suspected pathogen of Crohn’s disease in humans. Development of diagnostic methods for MAP infection has been a challenge over the last few decades. The objective of this study was to investigate the relationship between different methods for detection of MAP in milk and fecal samples. A total of 134 milk samples and 110 feces samples were collected from 146 individual cows in 14 MAP-infected herds in southwestern Ontario. Culture, IS900 polymerase chain reaction (PCR) and nested PCR methods were used for detecting MAP in milk; results were compared with those of fecal culture. A significant relationship was found between milk culture, direct PCR, and nested PCR (P < 0.05). The fecal culture results were not related to any of the 3 assay methods used for the milk samples (P > 0.10). Although fecal culture showed a higher sensitivity than the milk culture method, the difference was not significant (P = 0.2473). The number of MAP colony-forming units (CFU) isolated by culture from fecal samples was, on average, higher than that isolated from milk samples (P = 0.0083). There was no significant correlation between the number of CFU cultured from milk and from feces (Pearson correlation coefficient = 0.1957, N = 63, P = 0.1243). The animals with high numbers of CFU in milk culture may not be detected by fecal culture at all, and vise versa. A significant proportion (29% to 41%) of the positive animals would be missed if only 1 culture method, instead of both milk and feces, were to be used for diagnosis. This suggests that the shedding of MAP in feces and milk is not synchronized. Most of the infected cows were low-level shedders. The proportion of low-level shedders may even be underestimated because MAP is killed during decontamination, thus reducing the chance of detection. Therefore, to identify suspected Johne’s-infected animals using the tests in this study, both milk and feces samples should be collected in duplicate to enhance the diagnostic rate. The high MAP kill rate identified in the culture methods during decontamination may be compensated for by using the nested PCR method, which had a higher sensitivity than the IS900 PCR method used. PMID:19337397

Detection of cytomegalovirus DNA in fecal samples as a method for CMV enterocolitis diagnosis after allogeneic stem cell transplantation.

PubMed

Zavrelova, Alzbeta; Radocha, Jakub; Pliskova, Lenka; Paterova, Pavla; Vejrazkova, Eva; Cyrany, Jiri; Gabalec, Filip; Podhola, Miroslav; Zak, Pavel

2018-05-16

Cytomegalovirus enterocolitis is a rare but potentially life threatening complication after allogeneic stem cell transplantation. Its early diagnosis and treatment are essential for a successful outcome. To determine the potential benefit of fecal CMV DNA detection in the diagnosis of CMV colitis among stem cell transplant recipients. Biopsies from the lower gastrointestinal tract, taken during 69 episodes of diarrhea, were compared with fecal samples previously examined for CMV DNA in 45 patients after allogeneic stem cell transplantation. Six confirmed cases of CMV colitis were observed, with 16 out of 69 (23%) fecal samples proving positive for CMV DNA. Only one positive sample correlated with histologically confirmed CMV colitis, and 15 samples were evaluated as false positive. These results provide a 16.7% sensitivity and 76.2% specificity in the diagnosis of CMV enterocolitis. The examination of fecal samples for the presence of CMV DNA has very low potential in the diagnosis of CMV enterocolitis after allogeneic stem cell transplantation; therefore, a biopsy of the gastrointestinal mucosa is still warranted for correct diagnosis.

Assessment and impact of microbial fecal pollution and human enteric pathogens in a coastal community.

PubMed

Lipp, E K; Farrah, S A; Rose, J B

2001-04-01

The goals of this study were to assess watersheds impacted by high densities of OSDS (onsite sewage disposal systems) for evidence of fecal contamination and evaluate the occurrence of human pathogens in coastal waters off west Florida. Eleven stations (representing six watersheds) were intensively sampled for microbial indicators of fecal pollution (fecal coliform bacteria, enterococci, Clostridium perfringens and coliphage) and the human enteric pathogens, Cryptosporidium, Giardia, and enteroviruses during the summer rainy season (May-September 1996). Levels of all indicators ranged between < 5 and > 4000 CFU/100 ml. Cryptosporidium and Giardia were detected infrequently (6.8% and 2.3% of samples tested positive, respectively). Conversely, infectious enteroviruses were detected at low levels in 5 of the 6 watersheds sampled. Using cluster analysis, sites were grouped into two categories, high and low risks, based on combined levels of indicators. These results suggest that stations of highest pollution risk were located within areas of high OSDS densities. Furthermore, data indicate a subsurface transport of contaminated water to surface waters. The high prevalence of enteroviruses throughout the study area suggests a chronic pollution problem and potential risk to recreational swimmers in and around Sarasota Bay.

[Investigation of Cryptosporidium sp. in workers of the Van municipality slaughterhouse and in slaughtered animals].

PubMed

Ciçek, Mutalip; Körkoca, Hanifi; Gül, Abdurrahman

2008-01-01

This study was carried out in order to investigate the prevalence of Cryptosporidium sp. in slaughtered animals and workers of the Van municipality slaughterhouse in Van. Animals slaughtered at different times and workers who had been working in different departments of the slaughter house were included in the study for three months. A total of 309 fecal specimens from animals including 167 sheep, 56 goats and 86 cattle and 87 fecal specimens from workers were examined for Cryptosporidium sp. oocysts. In slaughtered animals, the modified acid-fast staining method was used to determine the oocysts of Cryptosporidium sp. The fecal samples of slaughter workers were examined by using RIDA (R) Quick Cryptosporidium Strip Test (R-Biopharm, Germany) and the modified acid-fast staining method. Fecal samples found to be positive by stripe test were also confirmed with the ELISA method (R-Biopharm, Germany). Oocysts of Cryptosporidium sp. were found in fecal specimens of 22 sheep (13.17%), 6 goats (10.71%) and 7 cattle (8.13%). Intestinal parasites were observed in 34 fecal specimens of workers (39.08%). Cryptosporidium sp., Hymenolepis nana, Chilomastix mesnili, Endolimax nana, Iodamoeba bütschlii were found in the specimen of one worker (1.14%), Entamoeba coli in 4 workers (4.59%), Blastocystis hominis (9.19%) in 8 workers, and Giardia intestinalis (19.54%) in 17 workers.

Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa).

PubMed

Huang, Qianqian; Holman, Devin B; Alexander, Trevor; Hu, Tianming; Jin, Long; Xu, Zhongjun; McAllister, Tim A; Acharya, Surya; Zhao, Guoqi; Wang, Yuxi

2018-01-01

The present study assessed the effect of purple prairie clover (PPC) and PPC condensed tannins (CT) on the fecal microbiota of lambs using high-throughput 16S rRNA gene pyrosequencing. A total of 18 individual lambs were randomly divided into three groups and fed either green chop alfalfa (Alf), a 40:60 (DM basis; Mix) mixture of Alf and PPC, or Mix supplemented with polyethylene glycol (Mix-P) for 18 days. Fecal samples were collected on days 13 through 18 using digital rectal retrieval. The DNA of fecal samples was extracted and the microbial 16S rRNA gene amplicons were sequenced using 454 pyrosequencing. Regardless of diet, the bacterial community was dominated by Firmicutes and Bacteroidetes with many sequences unclassified at the genus level. Forage type and CT had no effect on the fecal microbial composition at the phylum level or on α-diversity. Compared to the Alf diet, the Mix diet reduced the relative abundance of Akkermansia (P = 0.03) and Asteroleplasma (P = 0.05). Fecal microbial populations in Alf and Mix-P clustered separately from each other when assessed using unweighted UniFrac (P < 0.05). These results indicate that PPC CT up to 36 g/kg DM in the diet had no major effect on fecal microbial flora at the phyla level and exerted only minor effects on the genera composition of fecal microbiota in lambs.

Genetic diversity and antimicrobial resistance among isolates of Escherichia coli O157: H7 from feces and hides of super-shedders and low-shedding pen-mates in two commercial beef feedlots

PubMed Central

2012-01-01

Background Cattle shedding at least 104 CFU Escherichia coli O157:H7/g feces are described as super-shedders and have been shown to increase transmission of E. coli O157:H7 to other cattle in feedlots. This study investigated relationships among fecal isolates from super-shedders (n = 162), perineal hide swab isolates (PS) from super-shedders (n = 137) and fecal isolates from low-shedder (< 104 CFU/g feces) pen-mates (n = 496) using pulsed-field gel electrophoresis (PFGE). A subsample of these fecal isolates (n = 474) was tested for antimicrobial resistance. Isolates of E. coli O157:H7 were obtained from cattle in pens (avg. 181 head) at 2 commercial feedlots in southern Alberta with each steer sampled at entry to the feedlot and prior to slaughter. Results Only 1 steer maintained super-shedder status at both samplings, although approximately 30% of super-shedders in sampling 1 had low-shedder status at sampling 2. A total of 85 restriction endonuclease digestion clusters (REPC; 90% or greater similarity) and 86 unique isolates (< 90% similarity) were detected, with the predominant REPC (30% of isolates) being isolated from cattle in all feedlot pens, although it was not associated with shedding status (super- or low-shedder; P = 0.94). Only 2/21 super-shedders had fecal isolates in the same REPC at both samplings. Fecal and PS isolates from individual super-shedders generally belonged to different REPCs, although fecal isolates of E. coli O157:H7 from super- and low-shedders showed greater similarity (P < 0.001) than those from PS. For 77% of super-shedders, PFGE profiles of super-shedder fecal and PS isolates were distinct from all low-shedder fecal isolates collected in the same pen. A low level of antimicrobial resistance (3.7%) was detected and prevalence of antimicrobial resistance did not differ among super- and low-shedder isolates (P = 0.69), although all super-shedder isolates with antimicrobial resistance (n = 3) were resistant to multiple antimicrobials. Conclusions Super-shedders did not have increased antimicrobial resistance compared to low-shedder pen mates. Our data demonstrated that PFGE profiles of individual super-shedders varied over time and that only 1/162 steers remained a super-shedder at 2 samplings. In these two commercial feedlots, PFGE subtypes of E. coli O157:H7 from fecal isolates of super- and low-shedders were frequently different as were subtypes of fecal and perineal hide isolates from super-shedders. PMID:23014060

Detection of antibodies against classical swine fever virus in fecal samples from wild boar.

PubMed

Seo, Sang won; Sunwoo, Sun young; Hyun, Bang hoon; Lyoo, Young S

2012-12-28

Classical swine fever (CSF) is a contagious viral disease that affects pigs. Wild boars can play an important epidemiological role in CSF outbreaks. In the past decades, studies conducted in many countries have reported that the CSF virus (CSFV) may persist in wild boar populations. The existence of CSFV in the free-ranging wild boar populations was indirectly confirmed by determining the prevalence of antibodies against CSFV in the serum of hunted wild boars. However, analyzing sero-prevalence in hunted wild boars to study the risk of CSF outbreaks is difficult due to insufficient number of samples, limitation of hunting area and biased age distribution of hunted wild boars. To improve this survey method, we collected feces of wild boars from their habitat and tested them using CSFV antibody enzyme-linked immunosorbent assay (ELISA) and CSF virus neutralization (VN) test. In this study, ELISA was found to be highly sensitive for detecting antibodies against CSFV in fecal samples. Most of doubtful or positive results obtained in CSFV ELISA were confirmed by VN tests. Despite the high coincidence rate of antibody-positive samples between CSFV ELISA and VN test, the possibility of false positive reaction should be considered. In the regional distribution, a fact that antibody-positive fecal and serum samples were found in geographically close area was shown. Hence, presence of antibodies in fecal samples may provide vital information regarding the risk of CSF outbreaks in wild boar groups in geographical proximity. Copyright © 2012 Elsevier B.V. All rights reserved.

Prevalence and distribution of Baylisascaris procyonis in urban raccoons (Procyon lotor) in Winnipeg, Manitoba.

PubMed

Sexsmith, Jennifer L; Whiting, Terry L; Green, Chris; Orvis, Sheldon; Berezanski, Dean J; Thompson, Amy B

2009-08-01

The prevalence of Baylisascaris procyonis was estimated in the urban raccoon population of Winnipeg through the fecal flotation of raccoon feces collected at active latrines and through gross postmortem and fecal flotation of samples collected from nuisance raccoons. Fecal flotation of latrine-collected feces was positive in 33 of 89 samples and, of 52 latrines identified, 26 were positive on 1 or more occasions. Trapped individual raccoons subjected to postmortem examination were positive in 57 of 114 animals captured. Comparing a single fecal flotation to the gold standard of finding adult worms in the small intestine had a sensitivity of 78.9% and specificity of 92.9%. This study suggests that carriage of Baylisascaris procyonis is widespread in raccoons in the Winnipeg urban ecosystem. Raccoon latrines in Winnipeg should be treated as infectious sites and efforts should be made to limit access of pets and people at risk to those sites.

Quantitative Real-Time PCR Fecal Source Identification in the ...

EPA Pesticide Factsheets

Rivers in the Tillamook Basin play a vital role in supporting a thriving dairy and cheese-making industry, as well as providing a safe water resource for local human and wildlife populations. Historical concentrations of fecal bacteria in these waters are at times too high to allow for safe use leading to economic loss, endangerment of local wildlife, and poor conditions for recreational use. In this study, we employ host-associated qPCR methods for human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), cattle (CowM2 and CowM3), canine (DG3 and DG37), and avian (GFD) fecal pollution combined with high-resolution geographic information system (GIS) land use data and general indicator bacteria measurements to elucidatewater quality spatial and temporal trends. Water samples (n=584) were collected over a 1-year period at 29 sites along the Trask, Kilchis, and Tillamook rivers and tributaries (Tillamook Basin, OR). A total of 16.6% of samples (n=97) yielded E. coli levels considered impaired based on Oregon Department of Environmental Quality bacteria criteria (406 MPN/100mL). Hostassociated genetic indicators were detected at frequencies of 39.2% (HF183/BacR287), 16.3% (HumM2), 74.6% (Rum2Bac), 13.0% (CowM2), 26.7% (CowM3), 19.8% (DG3), 3.2% (DG37), and 53.4% (GFD) across all water samples (n=584). Seasonal trends in avian, cattle, and human fecal pollution sources were evident over the study area. On a sample site basis, quantitative fecal source identification and

Estimation of Pig Fecal Contamination in a River Catchment by Real-Time PCR Using Two Pig-Specific Bacteroidales 16S rRNA Genetic Markers▿

PubMed Central

Mieszkin, Sophie; Furet, Jean-Pierre; Corthier, Gérard; Gourmelon, Michèle

2009-01-01

The microbiological quality of coastal or river water can be affected by fecal contamination from human or animal sources. To discriminate pig fecal pollution from other pollution, a library-independent microbial source tracking method targeting Bacteroidales host-specific 16S rRNA gene markers by real-time PCR was designed. Two pig-specific Bacteroidales markers (Pig-1-Bac and Pig-2-Bac) were designed using 16S rRNA gene Bacteroidales clone libraries from pig feces and slurry. For these two pig markers, 98 to 100% sensitivity and 100% specificity were obtained when tested by TaqMan real-time PCR. A decrease in the concentrations of Pig-1-Bac and Pig-2-Bac markers was observed throughout the slurry treatment chain. The two newly designed pig-specific Bacteroidales markers, plus the human-specific (HF183) and ruminant-specific (BacR) Bacteroidales markers, were then applied to river water samples (n = 24) representing 14 different sites from the French Daoulas River catchment (Brittany, France). Pig-1-Bac and Pig-2-Bac were quantified in 25% and 62.5%, respectively, of samples collected around pig farms, with concentrations ranging from 3.6 to 4.1 log10 copies per 100 ml of water. They were detected in water samples collected downstream from pig farms but never detected near cattle farms. HF183 was quantified in 90% of water samples collected downstream near Daoulas town, with concentrations ranging between 3.6 and 4.4 log10 copies per 100 ml of water, and BacR in all water samples collected around cattle farms, with concentrations ranging between 4.6 and 6.0 log10 copies per 100 ml of water. The results of this study highlight that pig fecal contamination was not as frequent as human or bovine fecal contamination and that fecal pollution generally came from multiple origins. The two pig-specific Bacteroidales markers can be applied to environmental water samples to detect pig fecal pollution. PMID:19329663

Occurrence of fecal coliform bacteria in selected streams in Wyoming, 1990-99

USGS Publications Warehouse

Clark, Melanie L.; Norris, Jodi R.

2000-01-01

The U.S. Geological Survey (USGS), in cooperation with the Wyoming Department of Environmental Quality (WDEQ), is collecting water samples for analysis of fecal coliform bacteria at 18 stream sites as part of a statewide network. Contamination by bacteria of fecal origin in streams where contact recreation is a designated water use is a concern because of potential public-health risk from the presence of enteric pathogens. Fecal coliform concentrations are temporally and spatially variable in Wyoming streams-concentrations ranged from less than 1 to 45,000 colonies per 100 milliliters of water during 1990-99. Fecal coliform concentrations were less than the water-quality criterion of 400 colonies per 100 milliliters in 83 percent of the samples, indicating fecal coliform contamination is not a widespread problem in these Wyoming streams. However, 14 of the 18 monitoring sites had at least one sample in which the fecal coliform concentration exceeded 400 colonies per 100 milliliters at some time during the 10-year period. Fecal coliform concentrations generally are higher during April through September than during October through March. The higher concentrations coincide with the time period when the public-health risk is higher because summer months are when contact recreation use is more likely occurring. Fecal coliform concentrations were positively correlated with discharge and stream temperature and generally were negatively correlated with pH, specific conductance, and dissolved oxygen.

Coccidian Parasites and Conservation Implications for the Endangered Whooping Crane (Grus americana)

PubMed Central

Bertram, Miranda R.; Hamer, Gabriel L.; Snowden, Karen F.; Hartup, Barry K.; Hamer, Sarah A.

2015-01-01

While the population of endangered whooping cranes (Grus americana) has grown from 15 individuals in 1941 to an estimated 304 birds today, the population growth is not sufficient to support a down-listing of the species to threatened status. The degree to which disease may be limiting the population growth of whooping cranes is unknown. One disease of potential concern is caused by two crane-associated Eimeria species: Eimeria gruis and E. reichenowi. Unlike most species of Eimeria, which are localized to the intestinal tract, these crane-associated species may multiply systemically and cause a potentially fatal disease. Using a non-invasive sampling approach, we assessed the prevalence and phenology of Eimeria oocysts in whooping crane fecal samples collected across two winter seasons (November 2012–April 2014) at the Aransas National Wildlife Refuge along the Texas Gulf coast. We also compared the ability of microscopy and PCR to detect Eimeria in fecal samples. Across both years, 26.5% (n = 328) of fecal samples were positive for Eimeria based on microscopy. Although the sensitivity of PCR for detecting Eimeria infections seemed to be less than that of microscopy in the first year of the study (8.9% vs. 29.3%, respectively), an improved DNA extraction protocol resulted in increased sensitivity of PCR relative to microscopy in the second year of the study (27.6% and 20.8%, respectively). The proportion of positive samples did not vary significantly between years or among sampling sites. The proportion of Eimeria positive fecal samples varied with date of collection, but there was no consistent pattern of parasite shedding between the two years. We demonstrate that non-invasive fecal collections combined with PCR and DNA sequencing techniques provides a useful tool for monitoring Eimeria infection in cranes. Understanding the epidemiology of coccidiosis is important for management efforts to increase population growth of the endangered whooping crane. PMID:26061631

Bacteriological quality of ground water used for household supply, Lower Susquehanna River basin, Pennsylvania and Maryland

USGS Publications Warehouse

Bickford, Tammy M.; Lindsey, Bruce D.; Beaver, M.R.

1996-01-01

This report describes the bacteriological results of a ground-water study conducted from 1993 to 1995 as part of the U.S. Geological Survey's National Water-Quality Assessment Program in the Lower Susquehanna River Basin study unit. Water samples collected from 146 household supply wells were analyzed for fecal-indicator organisms including total coliform, fecal coliform, Escherichia coli (E. coli), and fecal streptococcus concentrations. Supporting data used in the interpretations are selected water-quality constituents, well-construction information, and the environmental setting at the well site including land use, physiography, and bedrock type. Water from nearly 70 percent of the wells sampled had total coliform present and thus was not suitable for drinking without treatment. Fecal coliforms were found in water from approximately 25 percent of the sampled wells. E. coli testing was not conducted in 1993. Approximately 30 percent of the 88 sampled wells had waters with E. coli. Fecal streptococcus bacteria was present in water from about 65 percent of the wells sampled. Bacteriological contamination was more likely to occur in water from wells in agricultural areas than in water from wells in forested areas. Water from wells sampled in the Ridge and Valley Physiographic Province was more likely to have bacteria than water from wells in the Piedmont Physiographic Province. Differences in bacterial concentrations among bedrock types are only statistically significant for E. coli. Bacterial concentrations are weakly related to well-age but not to other well characteristics such as the total well depth or the casing length. Relations exist between bacterial concentrations and selected water-quality constituents. Most wells from which water was sampled did not have sanitary seals and very few were grouted. This may have contributed to the number of detections of bacteria. It is uncertain whether the bacteria detected are the result of widespread aquifer contamination or site-specific factors.

Prevalence of Giardia sp. Cryptosporidium parvum and Cryptosporidium andersoni (syn. C. muris) [correction of Cryptosporidium parvum and Cryptosporidium muris (C. andersoni)] in 109 dairy herds in five counties of southeastern New York.

PubMed

Wade, S E; Mohammed, H O; Schaaf, S L

2000-11-01

A cross-sectional study was undertaken to determine the prevalence of Giardia sp. (G. duodenalis group), Cryptosporidium parvum and Cryptosporidium andersoni (C. muris) [corrected] in dairy cattle in three different age groups, and to evaluate the association of age and season with prevalence. One hundred and nine dairy farms, from a total of 212 farms, in five counties of southeastern New York volunteered to participate. On these farms, 2943 fecal samples were collected from three defined age groups. The farms were randomly assigned for sampling within the four seasons of the year. Each farm was visited once during the study period from March 1993 to June 1994 to collect fecal samples. Demographic data on the study population was collected at the time of sampling by interviewing the farm owner or manager. At collection, fecal samples were scored as diarrheic or non-diarrheic, and each condition was later related to positive or negative infection with these parasites. Fecal samples were processed using a quantitative centrifugation concentration flotation technique and enumerated using bright field and phase contrast microscopy. In this study, the overall population prevalence for Giardia sp. was 8.9%; C. parvum, 0.9%; and C. muris, 1.1%. When considering animals most at the risk of infection (those younger than 6 months of age) Giardia sp. and C. parvum was found in 20.1 and 2.4% of the animals, respectively. Giardia sp. and C. muris were found in all age groups. There was no significant seasonal pattern of infection for any of these parasites.

Fecal Contamination on Produce from Wholesale and Retail Food Markets in Dhaka, Bangladesh.

PubMed

Harris, Angela R; Islam, Mohammad Aminul; Unicomb, Leanne; Boehm, Alexandria B; Luby, Stephen; Davis, Jennifer; Pickering, Amy J

2018-01-01

Fresh produce items can become contaminated with enteric pathogens along the supply chain at the preharvest (e.g., irrigation water, soil, fertilizer) or postharvest (e.g., vendor handling or consumer handling) stages. This study assesses the concentrations of fecal indicator bacteria Escherichia coli , enterococci (ENT), and Bacteriodales on surfaces of carrots, eggplants, red amaranth leaves, and tomatoes obtained from both a wholesale market (recently harvested) and neighborhood retail markets in Dhaka, Bangladesh. We detected E. coli in 100% of carrot and red amaranth rinses, 92% of eggplant rinses, and 46% of tomato rinses. Using a molecular microbial source tracking assay, we found that 32% of produce samples were positive for ruminant fecal contamination. Fecal indicator bacteria were more likely to be detected on produce collected in retail markets compared with that in the wholesale market; retail market produce were 1.25 times more likely to have E. coli detected ( P = 0.03) and 1.24 times more likely to have ENT detected ( P = 0.03) as compared with wholesale market produce. Bacteriodales was detected in higher concentrations in retail market produce samples compared with wholesale market produce samples (0.40 log 10 gene copies per 100 cm 2 higher, P = 0.03). Our results suggest that ruminant and general fecal contamination of produce in markets in Dhaka is common, and suggest that unsanitary conditions in markets are an important source of produce fecal contamination postharvest.

The role of land use and environmental factors on microbial pollution of mountainous limestone aquifers

NASA Astrophysics Data System (ADS)

Allocca, V.; Celico, F.; Petrella, E.; Marzullo, G.; Naclerio, G.

2008-07-01

Limestone aquifers in Southern Italy are often affected by bacterial contamination produced by pasture and agriculture. The main goals of this study were (1) to analyze the role of land use and environmental factors on microbial contamination and, (2) to identify, at field scale, the most suitable indicator of fecal pollution, by comparing fecal coliforms and fecal enterococci. Analyzing surface and spring water, it was noted that both fecal indicators showed a significant decrease during the period characterized by freezing and/or freeze-thaw intervals. The data analysis shows that fecal coliforms are characterized by a significant decrease in population (3 orders of magnitude, at least) during the freezing period, while fecal enterococci are temporarily inhibited. A taxonomic classification of fecal enterococci detected in spring water samples was performed by the API 20 Strep system and by sequencing of the ribosomal 16S DNA genes. The results showed that freezing conditions did not cause any significant change on the set of enterococcal species.

Ovarian cycle of southern brown howler monkey (Alouatta guariba clamitans) through fecal progestin measurement.

PubMed

Silvestre, Thiago; Zanetti, Eveline S; Duarte, José M B; Barriento, Fernando G; Hirano, Zelinda M B; Souza, Júlio C; Passos, Fernando C

2017-01-01

The ovarian cycle in howler monkeys (genus Alouatta) has beean investigated through several biological parameters (ranging between 16.3 and 29.5 days); however, no data exist concerning the ovarian activity of the southern brown howler monkey (Alouatta guariba clamitans). This study aimed to describe the ovarian cycle of A. g. clamitans by profiling fecal progestin concentrations. Over 20 weeks, fecal samples of eight captive adult females of A. g. clamitans were collected. The collections were made at dawn, 5 days a week, and the samples were frozen immediately following collection. Next, they were dried, pulverized and hormonal metabolites were extracted to determine progestin concentrations by enzyme immunoassay. Of the 758 samples tested, the mean concentration of fecal progestins was 2866.40 ± 470.03 ng/g of dry feces, while the mean concentration at baseline was 814.47 ± 164.36 ng/g of dry feces. Among the eight females, one showed no ovarian cyclicity and three presented periods of probable absence of cyclicity and low progestin concentrations. A mean duration of 16 ± 0.52 days was observed for the 35 cycles studied. The interluteal phase lasted 4 ± 0.37 days on average, with a mean concentration of fecal progestins of 467.98 ± 29.12 ng/g of dry feces, while the luteal phase lasted 11 ± 0.50 days, with a mean concentration of 4283.27 ± 193.31 ng/g of dry feces. Besides describing the characteristics of the ovarian cycle, possible causes for the low concentrations of fecal progestins and periods of absence of cyclicity are also discussed.

Different fecal microbiotas and volatile organic compounds in treated and untreated children with celiac disease.

PubMed

Di Cagno, Raffaella; Rizzello, Carlo G; Gagliardi, Francesca; Ricciuti, Patrizia; Ndagijimana, Maurice; Francavilla, Ruggiero; Guerzoni, M Elisabetta; Crecchio, Carmine; Gobbetti, Marco; De Angelis, Maria

2009-06-01

This study aimed at investigating the fecal microbiotas of children with celiac disease (CD) before (U-CD) and after (T-CD) they were fed a gluten-free diet and of healthy children (HC). Brothers or sisters of T-CD were enrolled as HC. Each group consisted of seven children. PCR-denaturing gradient gel electrophoresis (DGGE) analysis with V3 universal primers revealed a unique profile for each fecal sample. PCR-DGGE analysis with group- or genus-specific 16S rRNA gene primers showed that the Lactobacillus community of U-CD changed significantly, while the diversity of the Lactobacillus community of T-CD was quite comparable to that of HC. Compared to HC, the ratio of cultivable lactic acid bacteria and Bifidobacterium to Bacteroides and enterobacteria was lower in T-CD and even lower in U-CD. The percentages of strains identified as lactobacilli differed as follows: HC (ca. 38%) > T-CD (ca. 17%) > U-CD (ca. 10%). Lactobacillus brevis, Lactobacillus rossiae, and Lactobacillus pentosus were identified only in fecal samples from T-CD and HC. Lactobacillus fermentum, Lactobacillus delbrueckii subsp. bulgaricus, and Lactobacillus gasseri were identified only in several fecal samples from HC. Compared to HC, the composition of Bifidobacterium species of T-CD varied, and it varied even more for U-CD. Forty-seven volatile organic compounds (VOCs) belonging to different chemical classes were identified using gas-chromatography mass spectrometry-solid-phase microextraction analysis. The median concentrations varied markedly for HC, T-CD, and U-CD. Overall, the r(2) values for VOC data for brothers and sisters were equal to or lower than those for unrelated HC and T-CD. This study shows the effect of CD pathology on the fecal microbiotas of children.

A Pilot Study on Effects of Hydraulic Dredging and Disposal on Water Quality of the Upper Mississippi River (July 1976). GREAT I Water Quality Work Group

DTIC Science & Technology

1976-07-01

coliform, fecal coliform, and fecal streptococcus densities. Salmonellae and shigellae were not recovered from either upstream water samples or from...fecal streptococci, Clostridlum perfringens) and enteric pathogens (salmonellae, shigellae , enteroviruses, infectious hepatitus agent) have beeii shown...the Mississippi River that was polluted with Shigella sonnet (5,32). 49W 1.----Wq W P4 p TABLE 1. Incidence of selected enteric diseases during 1975 in

The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome

PubMed Central

Shankar, Vijay; Homer, Daniel; Rigsbee, Laura; Khamis, Harry J; Michail, Sonia; Raymer, Michael; Reo, Nicholas V; Paliy, Oleg

2015-01-01

The goal of this study was to determine if fecal metabolite and microbiota profiles can serve as biomarkers of human intestinal diseases, and to uncover possible gut microbe–metabolite associations. We employed proton nuclear magnetic resonance to measure fecal metabolites of healthy children and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS-D). Metabolite levels were associated with fecal microbial abundances. Using several ordination techniques, healthy and irritable bowel syndrome (IBS) samples could be distinguished based on the metabolite profiles of fecal samples, and such partitioning was congruent with the microbiota-based sample separation. Measurements of individual metabolites indicated that the intestinal environment in IBS-D was characterized by increased proteolysis, incomplete anaerobic fermentation and possible change in methane production. By correlating metabolite levels with abundances of microbial genera, a number of statistically significant metabolite–genus associations were detected in stools of healthy children. No such associations were evident for IBS children. This finding complemented the previously observed reduction in the number of microbe–microbe associations in the distal gut of the same cohort of IBS-D children. PMID:25635640

The networks of human gut microbe-metabolite associations are different between health and irritable bowel syndrome.

PubMed

Shankar, Vijay; Homer, Daniel; Rigsbee, Laura; Khamis, Harry J; Michail, Sonia; Raymer, Michael; Reo, Nicholas V; Paliy, Oleg

2015-08-01

The goal of this study was to determine if fecal metabolite and microbiota profiles can serve as biomarkers of human intestinal diseases, and to uncover possible gut microbe-metabolite associations. We employed proton nuclear magnetic resonance to measure fecal metabolites of healthy children and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS-D). Metabolite levels were associated with fecal microbial abundances. Using several ordination techniques, healthy and irritable bowel syndrome (IBS) samples could be distinguished based on the metabolite profiles of fecal samples, and such partitioning was congruent with the microbiota-based sample separation. Measurements of individual metabolites indicated that the intestinal environment in IBS-D was characterized by increased proteolysis, incomplete anaerobic fermentation and possible change in methane production. By correlating metabolite levels with abundances of microbial genera, a number of statistically significant metabolite-genus associations were detected in stools of healthy children. No such associations were evident for IBS children. This finding complemented the previously observed reduction in the number of microbe-microbe associations in the distal gut of the same cohort of IBS-D children.

Bacterial source tracking guides management of boat head waste in a coastal resort area.

PubMed

Mallin, Michael A; Haltom, Mary I; Song, Bongkeun; Tavares, Mary E; Dellies, Stephen P

2010-12-01

Fecal contamination of water bodies causes a public health problem and economic loss. To control such contamination management actions need to be guided by sound science. From 2007-2009 a study was undertaken to determine the sources of fecal bacteria contamination to the marine waters adjoining the Town of Wrightsville Beach, North Carolina, USA. The research effort included sampling for fecal coliform and Enterococcus bacteria, sampling for optical brighteners, dye studies, and use of molecular bacterial source tracking techniques including polymerase chain reaction (PCR) and terminal restriction fragment polymorphism (T-RFLP) fingerprinting of the Bacteroides-Prevotella group. Of the 96 samples collected from nine locations during the study, the water contact standard for Enterococcus was exceeded on 13 occasions. The T-RFLP fingerprint analyses demonstrated that the most widespread source of fecal contamination was human, occurring in 38% of the samples, with secondary ruminant and avian sources also detected. Optical brightener concentrations were low, reflecting a lack of sewage line leakage or spills. A lack of sewer leaks and lack of septic systems in the town pointed toward discharge from boat heads into the marine waters as the major cause of fecal contamination; this was supported by dye studies. Based on these data, the Town initiated action to have the U.S. Environmental Protection Agency declare the coastal waters (out to 3 nautical miles), the nearby Atlantic Intracoastal Waterway and its tributaries a no-discharge zone (NDZ) to alleviate the human fecal pollution. The Town garnered supporting resolutions from other local communities who jointly petitioned the North Carolina Department of Environmental and Natural Resources. This State regulatory agency supported the local government resolutions and sent an application for an NDZ to the EPA in April 2009. The EPA concurred, and in February 2010 the coastal waters of New Hanover County, NC, became the first marine area on the U.S. eastern seaboard between Delaware and the Florida Keys to be declared a no-discharge zone. Copyright © 2010 Elsevier Ltd. All rights reserved.

Effects of a fire alarm strobe light on fecal corticosterone metabolite concentrations in mice.

PubMed

Godfrey, Denice; Silverman, Jerald

2009-02-01

The type and location of fire alarms are important considerations in animal facility design. The Guide for the Care and Use of Laboratory Animals recommends minimizing animal exposure to such alarms. Nevertheless, it is often necessary to maintain fire alarms within animal housing or procedural areas. The authors exposed male mice to the flashing strobe light component of a standard fire alarm and evaluated mouse fecal corticosterone concentration, which is known to be an indicator of stress. Mice were exposed to the strobe light for 5 min during either the light or the dark phase of the light:dark cycle. The authors collected fecal samples every 6 h for 24 h before exposing mice to the alarm and every 6 h for 24 h after exposure. Fecal samples taken before exposure (baseline samples) showed a normal circadian pattern of corticosterone metabolite excretion. In fecal samples taken after mice were exposed to the fire alarm, metabolite concentrations did not significantly differ from baseline concentrations over time.

Nutrient digestibility and fecal characteristics are different among captive exotic felids fed a beef-based raw diet.

PubMed

Vester, Brittany M; Burke, Sarah L; Dikeman, Cheryl L; Simmons, Lee G; Swanson, Kelly S

2008-03-01

Nutrient digestibility has not been well characterized in exotic felids. The objective of this experiment was to evaluate differences in nutrient digestibility and fecal characteristics in five large exotic captive felid species, including bobcats, jaguars, cheetahs, Indochinese tigers, and Siberian tigers. All animals were individually housed and adapted to a beef-based raw diet (Nebraska Brand((R)) Special Beef Feline, North Platte, NE) for 16 d. Total fecal collections were conducted from days 17 to 20. Fecal samples were weighed and scored on collection. Diet and fecal samples were evaluated for dry matter, organic matter, protein, fat, and energy to determine total tract digestibility. Fresh fecal samples were collected to determine fecal pH, ammonia, phenol, indole, short-chain fatty acid, and branched-chain fatty acid concentrations. Fecal scores were greater (P<0.01) in Indochinese tigers when compared with all other species, and cheetahs had greater (P<0.01) fecal scores than jaguars and bobcats. Fat digestibility was greater (P<0.01) in Siberian tigers, Indochinese tigers, and bobcats (96%) compared with cheetahs and jaguars (94%). Digestible energy was greater (P<0.05) in bobcats and Indochinese tigers at 93.5 and 92.9%, respectively, compared with cheetahs and jaguars, 91.6%. Fecal pH was greater (P<0.01) in bobcats compared with all other species evaluated. Indole concentrations were greater (P<0.05) in cheetahs and jaguars compared with bobcats and Indochinese tigers. Fecal ammonia concentrations were increased (P<0.05) in cheetahs compared with all other species. The beef-based raw diet was highly digestible; however, differences in fat and digestible energy suggest that species should be considered when determining caloric needs of exotic felids. Zoo Biol 27:126-136, 2008. (c) 2008 Wiley-Liss, Inc.

Bayesian estimation of the sensitivity and specificity of individual fecal culture and Paralisa to detect Mycobacterium avium subspecies paratuberculosis infection in young farmed deer.

PubMed

Stringer, Lesley A; Jones, Geoff; Jewell, Chris P; Noble, Alasdair D; Heuer, Cord; Wilson, Peter R; Johnson, Wesley O

2013-11-01

A Bayesian latent class model was used to estimate the sensitivity and specificity of an immunoglobulin G1 serum enzyme-linked immunosorbent assay (Paralisa) and individual fecal culture to detect young deer infected with Mycobacterium avium subsp. paratuberculosis. Paired fecal and serum samples were collected, between July 2009 and April 2010, from 20 individual yearling (12-24-month-old) deer in each of 20 South Island and 18 North Island herds in New Zealand and subjected to culture and Paralisa, respectively. Two fecal samples and 16 serum samples from 356 North Island deer, and 55 fecal and 37 serum samples from 401 South Island deer, were positive. The estimate of individual fecal culture sensitivity was 77% (95% credible interval [CI] = 61-92%) with specificity of 99% (95% CI = 98-99.7%). The Paralisa sensitivity estimate was 19% (95% CI = 10-30%), with specificity of 94% (95% CI = 93-96%). All estimates were robust to variation of priors and assumptions tested in a sensitivity analysis. The data informs the use of the tests in determining infection status at the individual and herd level.

Usefulness of detection of clarithromycin-resistant Helicobacter pylori from fecal specimens for young adults treated with eradication therapy.

PubMed

Osaki, Takako; Mabe, Katsuhiro; Zaman, Cynthia; Yonezawa, Hideo; Okuda, Masumi; Amagai, Kenji; Fujieda, Shinji; Goto, Mitsuhide; Shibata, Wataru; Kato, Mototsugu; Kamiya, Shigeru

2017-10-01

To prevent Helicobacter pylori infection in the younger generation, it is necessary to investigate the prevalence of antibiotic-resistant H. pylori. The aim of this study was to evaluate the method of PCR-based sequencing to detect clarithromycin (CAM) resistance-associated mutations using fecal samples as a noninvasive method. DNA extracted from fecal specimens and isolates from gastric biopsy specimens were collected from patients with H. pylori infection. Antibiotic resistance to CAM was analyzed by molecular and culture methods. The detection rates of CAM resistance-associated mutations (A2142C or A2143G) were compared before and after eradication therapy. With CAM resistance of H. pylori evaluated by antibiotic susceptibility test as a gold standard, the sensitivity and the specificity of gene mutation detection from fecal DNA were 80% and 84.8%, respectively. In contrast, using DNA of isolated strains, the sensitivity and the specificity were 80% and 100%. Of the seven cases in which eradication was unsuccessful by triple therapy including CAM, CAM-resistant H. pylori, and resistance-associated mutations were detected in three cases, CAM-resistant H. pylori without the mutation was detected in two patients, and resistance-associated mutation was only detected in one patient. PCR-based sequencing to detect CAM resistance-associated mutations using isolates or fecal samples was useful for finding antibiotic-resistant H. pylori infection. Although the specificity of the detection from fecal samples compared with antibiotic susceptibility testing was lower than that from isolates, this fecal detection method is suitable especially for asymptomatic subjects including children. Further improvement is needed before clinical application. © 2017 John Wiley & Sons Ltd.

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence

USGS Publications Warehouse

Stoeckel, D.M.; Stelzer, E.A.; Stogner, R.W.; Mau, D.P.

2011-01-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections-augmented with local observations and land-use patterns-indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. ?? 2011 Elsevier Ltd.

Assessment of possible sources of microbiological contamination in the water column and streambed sediment of the Jacks Fork, Ozark National Scenic Riverways, Missouri - Phase III

USGS Publications Warehouse

Davis, Jerri V.; Barr, Miya N.

2006-01-01

In 1998, a 5 river-mile reach of the Jacks Fork was included on Missouri's list of impaired waters as required by Section 303(d) of the Federal Clean Water Act. The identified pollutant on the Jacks Fork was fecal coliform bacteria. The length of the impaired reach was changed to 7 miles on the Missouri 2002 303(d) list because of data indicating the fecal coliform bacteria problem existed over a broader area. The U.S. Geological Survey, in cooperation with the National Park Service, conducted a study to better understand the extent and sources of microbiological contamination within the Jacks Fork from Alley Spring to the mouth, which includes the 7-mile 303(d) reach. Ten sites were sampled from June 2003 through October 2003 and from June 2004 through October 2004. Water-column and streambed sediment samples were collected from main-stem and tributary sites mostly during base-flow conditions during a variety of recreational season river uses and analyzed for fecal coliform and Escherichia coli bacteria. Isolates of Escherichia coli obtained from water samples collected at five sites were submitted for rep-PCR analysis to identify presumptive sources of fecal indicator bacteria in the Jacks Fork. Results indicate that recreational users (including boaters and swimmers) are not the primary source of fecal coliform bacteria in the Jacks Fork; rather, the presence of fecal coliform bacteria is associated with other animals, of which horses are the primary source. Increases in fecal coliform bacteria densities in the Jacks Fork are associated with cross-country horseback trail-riding events.

Fecal microbiome of periparturient dairy cattle and associations with the onset of Salmonella shedding

PubMed Central

Opiyo, Stephen O.; Digianantonio, Rose; Williams, Michele L.; Wijeratne, Asela; Habing, Gregory

2018-01-01

Non-typhoidal Salmonella enterica is a zoonotic pathogen with critical importance in animal and public health. The persistence of Salmonella on farms affects animal productivity and health, and represents a risk for food safety. The intestinal microbiota plays a fundamental role in the colonization and invasion of this ubiquitous microorganism. To overcome the colonization resistance imparted by the gut microbiome, Salmonella uses invasion strategies and the host inflammatory response to survive, proliferate, and establish infections with diverse clinical manifestations. Cattle serve as reservoirs of Salmonella, and periparturient cows have high prevalence of Salmonella shedding; however, little is known about the association between the gut microbiome and the onset of Salmonella shedding during the periparturient period. Thus, the objective of this study was to assess the association between changes in bacterial communities and the onset of Salmonella shedding in cattle approaching parturition. In a prospective cohort study, fecal samples from 98 dairy cows originating from four different farms were collected at four time points relative to calving (-3 wks, -1 wk, +1 wk, +3 wks). All 392 samples were cultured for Salmonella. Sequencing of the V4 region of the 16S rRNA gene using the Illumina platform was completed to evaluate the fecal microbiome in a selected sample subset. Analyses of microbial composition, diversity, and structure were performed according to time points, farm, and Salmonella onset status. Individual cow fecal microbiomes, predominated by Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria phyla, significantly changed before and after parturition. Microbial communities from different farms were distinguishable based on multivariate analysis. Although there were significant differences in some bacterial taxa between Salmonella positive and negative samples, our results did not identify differences in the fecal microbial diversity or structure for cows with and without the onset of Salmonella shedding. These data suggest that determinants other than the significant changes in the fecal microbiome influence the periparturient onset of Salmonella shedding in dairy cattle. PMID:29750790

Cross-Comparison of Human Wastewater-Associated Molecular Markers in Relation to Fecal Indicator Bacteria and Enteric Viruses in Recreational Beach Waters.

PubMed

Hughes, B; Beale, D J; Dennis, P G; Cook, S; Ahmed, W

2017-04-15

Detection of human wastewater contamination in recreational waters is of critical importance to regulators due to the risks posed to public health. To identify such risks, human wastewater-associated microbial source tracking (MST) markers have been developed. At present, however, a greater understanding of the suitability of these markers for the detection of diluted human wastewater in environmental waters is necessary to predict risk. Here, we compared the process limit of detection (PLOD) and process limit of quantification (PLOQ) of six human wastewater-associated MST markers ( Bacteroides HF183 [HF183], Escherichia coli H8 [EC H8], Methanobrevibacter smithii nifH , human adenovirus [HAdV], human polyomavirus [HPyV], and pepper mild mottle virus [PMMoV]) in relation to a fecal indicator bacterium (FIB), Enterococcus sp. 23S rRNA (ENT 23S), and three enteric viruses (human adenovirus serotypes 40/41 [HAdV 40/41], human norovirus [HNoV], and human enterovirus [EV]) in beach water samples seeded with raw and secondary-treated wastewater. Among the six MST markers tested, HF183 was the most sensitive measure of human fecal pollution and was quantifiable up to dilutions of 10 -6 and 10 -4 for beach water samples seeded with raw and secondary-treated wastewater, respectively. Other markers and enteric viruses were detected at various dilutions (10 -1 to 10 -5 ). These MST markers, FIB, and enteric viruses were then quantified in beach water ( n = 12) and sand samples ( n = 12) from South East Queensland (SEQ), Australia, to estimate the levels of human fecal pollution. Of the 12 sites examined, beach water and sand samples from several sites had quantifiable concentrations of HF183 and PMMoV markers. Overall, our results indicate that while HF183 is the most sensitive measure of human fecal pollution, it should be used in conjunction with a conferring viral marker to avoid overestimating the risk of gastrointestinal illness. IMPORTANCE MST is an effective tool to help utilities and regulators improve recreational water quality around the globe. Human fecal pollution poses significant public health risks compared to animal fecal pollution. Several human wastewater-associated markers have been developed and used for MST field studies. However, a head-to-head comparison in terms of their performance to detect diluted human fecal pollution in recreational water is lacking. In this study, we cross-compared the performance of six human wastewater-associated markers in relation to FIB and enteric viruses in beach water samples seeded with raw and secondary-treated wastewater. The results of this study will provide guidance to regulators and utilities on the appropriate application of MST markers for tracking the sources of human fecal pollution in environmental waters and confer human health risks. Copyright © 2017 American Society for Microbiology.

Evaluation of Water Quality for Two St. Johns River Tributaries Receiving Septic Tank Effluent, Duval County, Florida

USGS Publications Warehouse

Wicklein, Shaun M.

2004-01-01

Tributary streamflow to the St. Johns River in Duval County is thought to be affected by septic tank leachate from residential areas adjacent to these tributaries. Water managers and the city of Jacksonville have committed to infrastructure improvements as part of a management plan to address the impairment of tributary water quality. In order to provide data to evaluate the effects of future remedial activities in selected tributaries, major ion and nutrient concentrations, fecal coliform concentrations, detection of wastewater compounds, and tracking of bacterial sources were used to document septic tank influences on the water quality of selected tributaries. The tributaries Fishing Creek and South Big Fishweir Creek were selected because they drain subdivisions identified as high priority locations for septic tank phase-out projects: the Pernecia and Murray Hill B subdivisions, respectively. Population, housing (number of residences), and septic tank densities for the Murray Hill B subdivision are greater than those for the Pernecia subdivision. Water-quality samples collected in the study basins indicate influences from ground water and septic tanks. Estimated concentrations of total nitrogen ranged from 0.33 to 2.86 milligrams per liter (mg/L), and ranged from less than laboratory reporting limit (0.02 mg/L) to 0.64 mg/L for total phosphorus. Major ion concentrations met the State of Florida Class III surface-water standards; total nitrogen and total phosphorus concentrations exceeded the U.S. Environmental Protection Agency Ecoregion XII nutrient criteria for rivers and streams 49 and 96 percent of the time, respectively. Organic wastewater compounds detected at study sites were categorized as detergents, antioxidants and flame retardants, manufactured polycarbonate resins, industrial solvents, and mosquito repellent. The most commonly detected compound was para-nonylphenol, a breakdown product of detergent. Results of wastewater sampling give evidence that stream water in the study basins is affected by septic tank effluent. Fecal coliform bacteria concentrations were measured on a monthly basis; of 115 samples, 63 percent exceeded the State of Florida fecal coliform bacteria standard for Class III surface waters of 800 colonies per 100 milliliters of water on any 1 day. Fecal coliform bacteria concentrations ranged from less than 20 colonies per 100 milliliters of sample to greater than or equal to 160,000 colonies per 100 milliliters of sample. Antibiotic resistance patterns of fecal coliform bacteria were used to identify the sources of fecal coliform bacteria. Significant sources of fecal coliform bacteria included wild animals, dogs, and humans. A majority of the fecal coliform bacteria were classified to be from human sources. Because the primary source of fecal coliform bacteria is from human sources, and most likely septic tank effluent, management of human sources may substantially improve microbiological water quality in both the Fishing Creek and South Branch Big Fishweir Creek basins.

Cross-Comparison of Human Wastewater-Associated Molecular Markers in Relation to Fecal Indicator Bacteria and Enteric Viruses in Recreational Beach Waters

PubMed Central

Hughes, B.; Beale, D. J.; Dennis, P. G.; Cook, S.

2017-01-01

ABSTRACT Detection of human wastewater contamination in recreational waters is of critical importance to regulators due to the risks posed to public health. To identify such risks, human wastewater-associated microbial source tracking (MST) markers have been developed. At present, however, a greater understanding of the suitability of these markers for the detection of diluted human wastewater in environmental waters is necessary to predict risk. Here, we compared the process limit of detection (PLOD) and process limit of quantification (PLOQ) of six human wastewater-associated MST markers (Bacteroides HF183 [HF183], Escherichia coli H8 [EC H8], Methanobrevibacter smithii nifH, human adenovirus [HAdV], human polyomavirus [HPyV], and pepper mild mottle virus [PMMoV]) in relation to a fecal indicator bacterium (FIB), Enterococcus sp. 23S rRNA (ENT 23S), and three enteric viruses (human adenovirus serotypes 40/41 [HAdV 40/41], human norovirus [HNoV], and human enterovirus [EV]) in beach water samples seeded with raw and secondary-treated wastewater. Among the six MST markers tested, HF183 was the most sensitive measure of human fecal pollution and was quantifiable up to dilutions of 10−6 and 10−4 for beach water samples seeded with raw and secondary-treated wastewater, respectively. Other markers and enteric viruses were detected at various dilutions (10−1 to 10−5). These MST markers, FIB, and enteric viruses were then quantified in beach water (n = 12) and sand samples (n = 12) from South East Queensland (SEQ), Australia, to estimate the levels of human fecal pollution. Of the 12 sites examined, beach water and sand samples from several sites had quantifiable concentrations of HF183 and PMMoV markers. Overall, our results indicate that while HF183 is the most sensitive measure of human fecal pollution, it should be used in conjunction with a conferring viral marker to avoid overestimating the risk of gastrointestinal illness. IMPORTANCE MST is an effective tool to help utilities and regulators improve recreational water quality around the globe. Human fecal pollution poses significant public health risks compared to animal fecal pollution. Several human wastewater-associated markers have been developed and used for MST field studies. However, a head-to-head comparison in terms of their performance to detect diluted human fecal pollution in recreational water is lacking. In this study, we cross-compared the performance of six human wastewater-associated markers in relation to FIB and enteric viruses in beach water samples seeded with raw and secondary-treated wastewater. The results of this study will provide guidance to regulators and utilities on the appropriate application of MST markers for tracking the sources of human fecal pollution in environmental waters and confer human health risks. PMID:28159789

Comparison of fecal culture and Danish Mix-ELISA for determination of Salmonella enterica subsp. enterica prevalence in growing swine.

PubMed

Funk, J A; Harris, I T; Davies, P R

2005-04-25

In the USA, control of food-borne salmonellosis associated with meat consumption has been predominantly focused at slaughter and processing. It is expected that standards at slaughter and processing will become more stringent, creating pressure to reduce prevalence of Salmonella-positive food animals through on-farm interventions. The aim of this study was to compare traditional fecal culture and the Danish Mix-ELISA (DME) for determination of Salmonella prevalence pre-harvest in swine. In Trial 1, five cohorts of individually identified pigs were longitudinally sampled during the growing period to compare the kinetics of prevalence as estimated by fecal culture and the DME. In Trial 2, the correlation between fecal prevalence and seroprevalence was estimated pre-marketing in 49 groups of pigs. In Trial 1, fecal prevalence and seroprevalence showed similar kinetics, with a tendency of a higher OD% cut-off to more closely approximate fecal prevalence. In Trial 2, correlations between fecal culture and the DME were 0.40, 0.36, 0.43, and 0.43 (p<0.001) for OD% cut-offs > or =10, 20, 30, and 40, respectively. Based on these results, a higher OD% cut-off would be recommended if more approximate estimation of fecal prevalence is desired and longitudinal sampling would be suggested for evaluating the impact of on-farm interventions for Salmonella reduction whether utilizing fecal culture or the DME. Further evaluation of the impact of Salmonella serovar present on farms on seroprevalence and the relationship of on-farm seroprevalence with food safety risk are needed prior to utilizing the DME for pre-harvest Salmonella diagnostics in the US swine herd.

Fecal-indicator bacteria in the Allegheny, Monongahela, and Ohio Rivers and selected tributaries, Allegheny County, Pennsylvania, 2001-2005

USGS Publications Warehouse

Buckwalter, Theodore F.; Zimmerman, Tammy M.; Fulton, John W.

2006-01-01

Concentrations of fecal-indicator bacteria were determined in 1,027 water-quality samples collected from July 2001 through August 2005 during dry- (72-hour dry antecedent period) and wet-weather (48-hour dry antecedent period and at least 0.3 inch of rain in a 24-hour period) conditions in the Allegheny, Monongahela, and Ohio Rivers (locally referred to as the Three Rivers) and selected tributaries in Allegheny County. Samples were collected at five sampling sites on the Three Rivers and at eight sites on four tributaries to the Three Rivers having combined sewer overflows. Water samples were analyzed for three fecal-indicator organisms fecal coliform, Escherichia coli (E. coli), and enterococci bacteria. Left-bank and right-bank surface-water samples were collected in addition to a cross-section composite sample at each site. Concentrations of fecal coliform, E. coli, and enterococci were detected in 98.6, 98.5, and 87.7 percent of all samples, respectively. The maximum fecal-indicator bacteria concentrations were collected from Sawmill Run, a tributary to the Ohio River; Sawmill Run at Duquesne Heights had concentrations of fecal coliform, E. coli, and enterococci of 410,000, 510,000, and 180,000 col/100 mL, respectively, following a large storm. The samples collected in the Three Rivers and selected tributaries frequently exceeded established recreational standards and criteria for bacteria. Concentrations of fecal coliform exceeded the Pennsylvania water-quality standard (200 col/100 mL) in approximately 63 percent of the samples. Sample concentrations of E. coli and enterococci exceeded the U.S. Environmental Protection Agency (USEPA) water-quality criteria (235 and 61 col/100 mL, respectively) in about 53 and 47 percent, respectively, of the samples. Fecal-indicator bacteria were most strongly correlated with streamflow, specific conductance, and turbidity. These correlations most frequently were observed in samples collected from tributary sites. Fecal-indicator bacteria concentrations and turbidity were correlated to the location of sample collection in the cross section. Most differences were between bank and composite samples; differences between right-bank and left-bank samples were rarely observed. The Allegheny River sites had more significant correlations than the Monongahela or Ohio River sites. Comparisons were made between fecal-indicator bacteria in composite samples collected during dry-weather, wet-weather day-one, wet-weather day-two (tributary sites only), and wet-weather day-three (Three Rivers sites only) events in the Three Rivers and selected tributary sites. The lowest median bacteria concentrations generally were observed in the dry-weather composite samples. All median bacteria concentrations in dry-weather composite samples in the five Three Rivers sites were below water-quality standards and criteria; bacteria concentrations in the upstream tributary sites rarely met all standards or criteria. Only Turtle Creek, Thompson Run, and Chartiers Creek had at least one median bacteria concentration below water-quality standards or criteria. Median bacteria concentrations in the composite samples generally were higher the day after a wet-weather event compared to dry-weather composite samples and other wet-weather composite samples collected. In the five Three Rivers sites, median bacteria concentrations 3 days after a wet-weather event in composite samples tended to fall below the water-quality standards and criteria; in the eight tributary sites, median bacteria concentrations in the dry-weather and wet-weather composite samples generally were above the water-quality standards or criteria. Composite samples collected at the upstream sites on the Three Rivers and selected tributaries generally had lower median bacteria concentrations than composite samples collected at the downstream sites during dry- and wet-weather events. Higher concentrations downstream may be because o

Quantitative PCR measurements of Escherichia coli including shiga toxin-producing E. coli (STEC) in animal feces and environmental waters.

PubMed

Ahmed, W; Gyawali, P; Toze, S

2015-03-03

Quantitative PCR (qPCR) assays were used to determine the concentrations of E. coli including shiga toxin-producing E. coli (STEC) associated virulence genes (eaeA, stx1, stx2, and hlyA) in ten animal species (fecal sources) and environmental water samples in Southeast Queensland, Australia. The mean Log10 concentrations and standard deviations of E. coli 23S rRNA across fecal sources ranged from 1.3 ± 0.1 (horse) to 6.3 ± 0.4 (cattle wastewater) gene copies at a test concentration of 10 ng of DNA. The differences in mean concentrations of E. coli 23S rRNA gene copies among fecal source samples were significantly different from each other (P < 0.0001). Among the virulence genes, stx2 (25%, 95% CI, 17-33%) was most prevalent among fecal sources, followed by eaeA (19%, 95% CI, 12-27%), stx1 (11%, 95% CI, 5%-17%) and hlyA (8%, 95% CI, 3-13%). The Log10 concentrations of STEC virulence genes in cattle wastewater samples ranged from 3.8 to 5.0 gene copies at a test concentration of 10 ng of DNA. Of the 18 environmental water samples tested, three (17%) were positive for eaeA and two (11%) samples were also positive for the stx2 virulence genes. The data presented in this study will aid in the estimation of quantitative microbial risk assessment (QMRA) from fecal pollution of domestic and wild animals in drinking/recreational water catchments.

Characterizing the temporal patterns of avian influenza virus introduction into Japan by migratory birds

PubMed Central

ONUMA, Manabu; KAKOGAWA, Masayoshi; YANAGISAWA, Masae; HAGA, Atsushi; OKANO, Tomomi; NEAGARI, Yasuko; OKANO, Tsukasa; GOKA, Koichi; ASAKAWA, Mitsuhiko

2017-01-01

The objectives of the present study were to observe the temporal pattern of avian influenza virus (AIV) introduction into Japan and to determine which migratory birds play an important role in introducing AIV. In total, 19,407 fecal samples from migratory birds were collected at 52 sites between October 2008 and May 2015. Total nucleic acids extracted from the fecal samples were subjected to reverse transcription loop–mediated isothermal amplification to detect viral RNA. Species identification of host migratory birds was conducted by DNA barcoding for positive fecal samples. The total number of positive samples was 352 (prevalence, 1.8%). The highest prevalence was observed in autumn migration, and a decrease in prevalence was observed. During autumn migration, central to southern Japan showed a prevalence higher than the overall prevalence. Thus, the main AIV entry routes may involve crossing the Sea of Japan and entry through the Korean Peninsula. Species identification was successful in 221 of the 352 positive samples. Two major species sequences were identified: the Mallard/Eastern Spot-billed duck group (115 samples; 52.0%) and the Northern pintail (61 samples; 27.6%). To gain a better understanding of the ecology of AIV in Japan and the introduction pattern of highly pathogenic avian influenza viruses, information regarding AIV prevalence by species, the prevalence of hatch-year migratory birds, migration patterns and viral subtypes in fecal samples using egg inoculation and molecular-based methods in combination is required. PMID:28484128

The microbiome in PTEN hamartoma tumor syndrome.

PubMed

Byrd, Victoria; Getz, Ted; Padmanabhan, Roshan; Arora, Hans; Eng, Charis

2018-03-01

Germline PTEN mutations defining PTEN hamartoma tumor syndrome (PHTS) confer heritable predisposition to breast, endometrial, thyroid and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA gene sequencing. PCoA revealed clustering of the fecal microbiome by cancer history ( P  = 0.03, R 2  = 0.04). Fecal samples from PHTS cancer patients had relatively more abundant operational taxonomic units (OTUs) from family Rikenellaceae and unclassified members of Clostridia compared to those from non-cancer patients, whereas families Peptostreptococcaceae, Enterobacteriaceae, and Bifidobacteriaceae represented relatively more abundant OTUs among fecal samples from PHTS non-cancer patients. Functional metagenomic prediction revealed enrichment of the folate biosynthesis, genetic information processing and cell growth and death pathways among fecal samples from PHTS cancer patients compared to non-cancer patients. We found no major shifts in overall diversity and no clustering by cancer history among oral wash or urine samples. Our observations suggest the utility of an expanded study to interrogate gut dysbiosis as a potential cancer risk modifier in PHTS patients. © 2018 The authors.

Parasite prevalence in fecal samples from shelter dogs and cats across the Canadian provinces.

PubMed

Villeneuve, Alain; Polley, Lydden; Jenkins, Emily; Schurer, Janna; Gilleard, John; Kutz, Susan; Conboy, Gary; Benoit, Donald; Seewald, Wolfgang; Gagné, France

2015-05-21

In Canada, surveys of enteric parasites in dogs and cats have been reported sporadically over the past 40 years, mostly focusing on a specific region. The present work was performed to determine the current prevalence of various parasites in fecal samples from shelter dogs and cats across the Canadian provinces. A total of 1086 dog and 636 cat fecal samples from 26 shelters were analysed using a sugar solution double centrifugal flotation technique. Prevalences (national, regional, provincial, age and parasite-specific), were calculated and compared using the Fisher-Exact test. A multiplex PCR was performed to distinguish Taenia spp, Echinococcus granulosus and E. multilocularis on samples positive for taeniid eggs. Overall, 33.9% of dogs and 31.8% of cats were positive for at least one parasite. Toxocara canis and T. cati were the most prevalent parasite present in fecal samples followed by Cystoisospora spp. Prevalence in dogs was similar across the Atlantic, East, West and Pacific regions, while prevalence in cats varied regionally. Eggs of E. granulosus/E. canadensis were detected in samples from dogs from BC, AB, and ON. Data from this study will help in the development of strategies, based on the level of risk per geographic location for the prevention and response to these parasites in pets and free-roaming and shelter animals in Canada.

The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli.

PubMed

Omulo, Sylvia; Lofgren, Eric T; Mugoh, Maina; Alando, Moshe; Obiya, Joshua; Kipyegon, Korir; Kikwai, Gilbert; Gumbi, Wilson; Kariuki, Samuel; Call, Douglas R

2017-05-01

Investigators often rely on studies of Escherichia coli to characterize the burden of antibiotic resistance in a clinical or community setting. To determine if prevalence estimates for antibiotic resistance are sensitive to sample handling and interpretive criteria, we collected presumptive E. coli isolates (24 or 95 per stool sample) from a community in an urban informal settlement in Kenya. Isolates were tested for susceptibility to nine antibiotics using agar breakpoint assays and results were analyzed using generalized linear mixed models. We observed a <3-fold difference between prevalence estimates based on freshly isolated bacteria when compared to isolates collected from unprocessed fecal samples or fecal slurries that had been stored at 4°C for up to 7days. No time-dependence was evident (P>0.1). Prevalence estimates did not differ for five distinct E. coli colony morphologies on MacConkey agar plates (P>0.2). Successive re-plating of samples for up to five consecutive days had little to no impact on prevalence estimates. Finally, culturing E. coli under different conditions (with 5% CO 2 or micro-aerobic) did not affect estimates of prevalence. For the conditions tested in these experiments, minor modifications in sample processing protocols are unlikely to bias estimates of the prevalence of antibiotic-resistance for fecal E. coli. Copyright © 2017 Elsevier B.V. All rights reserved.

Annual ovarian activity monitored by the noninvasive measurement of fecal concentrations of progesterone and 17β-estradiol metabolites in rusa deer (Rusa timorensis)

PubMed Central

SUDSUKH, Apichaya; TAYA, Kazuyoshi; WATANABE, Gen; WAJJWALKU, Worawidh; THONGPHAKDEE, Ampika; THONGTIP, Nikorn

2016-01-01

To clarify the reproductive cycle of female Rusa deer (Rusa timorensis), the fecal concentrations of progesterone and 17β-estradiol metabolites were measured. Fecal samples were collected on a weekly basis for one year (between October, 2012 and September, 2013) from five healthy adult hinds in Thailand. At the beginning of the study, three hinds were pregnant. Two hinds delivered one healthy offspring, and one hind delivered a stillborn calf. The mating period of Rusa hinds in Thailand is from November to April. In pregnant hinds, fecal progesterone metabolite concentration was high in late pregnancy and abruptly declined to the baseline around parturition, suggesting that the placenta secretes a large amount of progesterone. Fecal 17β-estradiol metabolite concentration remained elevated around the day of parturition. Both concentrations of fecal progesterone and 17β-estradiol metabolites in non-lactating hinds were significantly higher than those in lactating hinds, indicating that ovarian activity of lactating hinds is suppressed by the suckling stimulus of fawn during lactation. The present study demonstrated that monitoring of fecal steroid hormones is useful method for assessing ovarian function in this species. PMID:27570098

[Presence of fecal coliforms, Escherichia coli and DNAse- and coagulase-positive Staphylococcus aureus, in "colonial" cheese sold in the city of Blumenau, Estado de Santa Catarina, Brazil].

PubMed

Reibnitz, M G; Tavares, L B; García, J A

1998-01-01

Twenty cheese samples were collected at Blumenau (SC) and were submitted to analysis in order to verify the presence of fecal coliforms, Escherichia coli and Staphylococcus aureus. Among the 20 samples of cheese, analysis revealed that 70% and 20% respectively, were not within present legal specifications (Norma 001/87-DNVSA) for fecal coliforms and Escherichia coli. For Staphylococcus, 95% of the samples were not within present legal specifications.

Specificity of a Bacteroides thetaiotaomicron marker for human feces

USGS Publications Warehouse

Carson, C.A.; Christiansen, J.M.; Yampara-Iquise, H.; Benson, V.W.; Baffaut, C.; Davis, J.V.; Broz, R.R.; Kurtz, W.B.; Rogers, W.M.; Fales, W.H.

2005-01-01

A bacterial primer set, known to produce a 542-bp amplicon specific for Bacteroides thetaiotaomicron, generated this product in PCR with 1 ng of extracted DNA from 92% of 25 human fecal samples, 100% of 20 sewage samples, and 16% of 31 dog fecal samples. The marker was not detected in 1 ng of fecal DNA from 61 cows, 35 horses, 44 pigs, 24 chickens, 29 turkeys, and 17 geese. Copyright ?? 2005, American Society for Microbiology. All Rights Reserved.

Detection and quantification of Spirocerca lupi by HRM qPCR in fecal samples from dogs with spirocercosis.

PubMed

Rojas, Alicia; Segev, Gilad; Markovics, Alex; Aroch, Itamar; Baneth, Gad

2017-09-19

Spirocerca lupi, the dog oesophageal nematode, causes a potentially fatal disease in domestic dogs, and is currently clinically diagnosed by coproscopy and oesophagoscopy. To date, a single molecular method, a semi-nested PCR, targeting the cox1 gene, has been developed to aid in the diagnosis of spirocercosis. The present study describes three novel high-resolution melt (HRM) quantitative PCR (qPCR) assays targeting fragments of the ITS1, 18S and cytb loci of S. lupi. The performance of these molecular assays in feces was compared to fecal flotation and to the previously described cox1 gene semi-nested PCR in 18 fecal samples from dogs with clinical oesophageal spirocercosis diagnosed by oesophagoscopy. The HRM qPCR for ITS1 and 18S were both able to detect 0.2 S. lupi eggs per gram (epg), while the HRM qPCR for the cytb and the semi-nested PCR for the cox1 detected 6 epg and 526 epg, respectively. Spirocerca lupi was detected in 61.1%, 44.4%, 27.8%, 11.1% and 5.6% of the fecal samples of dogs diagnosed with spirocercosis by using the ITS1 and 18S HRM qPCR assays, fecal flotation, cytb HRM qPCR and cox1 semi-nested PCR, respectively. All dogs positive by fecal flotation were also positive by ITS1 and 18S HRM qPCRs. Quantification of S. lupi eggs was successfully achieved in the HRM qPCRs and compared to the fecal flotation with no significant difference in the calculated concentrations between the HRM qPCRs that detected the 18S and ITS1 loci and the fecal flotation. The HRM qPCR for the 18S cross-amplified DNA from Toxocara canis and Toxascaris leonina. In contrast, the HRM qPCR for ITS1 did not cross-amplify DNA from other canine gastrointestinal parasites. This study presents two new molecular assays with significantly increased sensitivity for confirming and quantifying fecal S. lupi eggs. Of these, the HRM qPCR for ITS1 showed the best performance in terms of the limit of detection and absence of cross-amplification with other parasites. These assays will be useful in detecting infection and for follow-up during therapy.

Identifying fecal pollution sources using 3M(™) Petrifilm (™) count plates and antibiotic resistance analysis in the Horse Creek Watershed in Aiken County, SC (USA).

PubMed

Harmon, S Michele; West, Ryan T; Yates, James R

2014-12-01

Sources of fecal coliform pollution in a small South Carolina (USA) watershed were identified using inexpensive methods and commonly available equipment. Samples from the upper reaches of the watershed were analyzed with 3M(™) Petrifilm(™) count plates. We were able to narrow down the study's focus to one particular tributary, Sand River, that was the major contributor of the coliform pollution (both fecal and total) to a downstream reservoir that is heavily used for recreation purposes. Concentrations of total coliforms ranged from 2,400 to 120,333 cfu/100 mL, with sharp increases in coliform counts observed in samples taken after rain events. Positive correlations between turbidity and fecal coliform counts suggested a relationship between fecal pollution and stormwater runoff. Antibiotic resistance analysis (ARA) compared antibiotic resistance profiles of fecal coliform isolates from the stream to those of a watershed-specific fecal source library (equine, waterfowl, canines, and untreated sewage). Known fecal source isolates and unknown isolates from the stream were exposed to six antibiotics at three concentrations each. Discriminant analysis grouped known isolates with an overall average rate of correct classification (ARCC) of 84.3 %. A total of 401 isolates from the first stream location were classified as equine (45.9 %), sewage (39.4 %), waterfowl (6.2 %), and feline (8.5 %). A similar pattern was observed at the second sampling location, with 42.6 % equine, 45.2 % sewage, 2.8 % waterfowl, 0.6 % canine, and 8.8 % feline. While there were slight weather-dependent differences, the vast majority of the coliform pollution in this stream appeared to be from two sources, equine and sewage. This information will contribute to better land use decisions and further justify implementation of low-impact development practices within this urban watershed.

Potential of fecal waste for the production of biomethane, bioethanol and biodiesel.

PubMed

Gomaa, Mohamed A; Abed, Raeid M M

2017-07-10

Fecal waste is an environmental burden that requires proper disposal, which ultimately becomes also an economic burden. Because fecal waste is nutrient-rich and contains a diverse methanogenic community, it has been utilized to produce biomethane via anaerobic digestion. Carbohydrates and lipids in fecal waste could reach up to 50% of the dry weight, which also suggests a potential as a feedstock for bioethanol and biodiesel production. We measured biomethane production from fecal waste of cows, chickens, goats and humans and compared the microbial community composition before and after anaerobic digestion. We also compared the fecal waste for cellulase production, saccharification and fermentation to produce bioethanol and for lipid content and fatty acid profiles to produce biodiesel. All fecal waste produced biomethane, with the highest yield of 433.4±77.1ml CH 4 /g VS from cow fecal waste. Production of bioethanol was achieved from all samples, with chicken fecal waste yielding as high as 1.6±0.25g/l. Sludge samples exhibited the highest extractable portion of lipids (20.9±0.08wt%) and conversion to fatty acid methyl esters (11.94wt%). Utilization of fecal waste for the production of biofuels is environmentally and economically beneficial. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigation of bacterial diversity in the feces of cattle fed different diets

USDA-ARS?s Scientific Manuscript database

The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dryrolled corn, 13% corn silage, a...

Feasibility of Providing Safe Mouth Care and Collecting Oral and Fecal Microbiome Samples from Nursing Home Residents with Dysphagia: Proof of Concept Study.

PubMed

Jablonski, Rita A; Winstead, Vicki; Azuero, Andres; Ptacek, Travis; Jones-Townsend, Corteza; Byrd, Elizabeth; Geisinger, Maria L; Morrow, Casey

2017-09-01

Individuals with dysphagia who reside in nursing homes often receive inadequate mouth care and experience poor oral health. From a policy perspective, the combination of absent evidence-based mouth care protocols coupled with insufficient dental coverage create a pool of individuals at great risk for preventable infectious illnesses that contribute to high health care costs. The purpose of the current study was to determine (a) the safety of a mouth care protocol tailored for individuals with dysphagia residing in nursing homes without access to suction equipment, and (b) the feasibility of collecting oral and fecal samples for microbiota analyses. The mouth care protocol resulted in improved oral hygiene without aspiration, and oral and fecal samples were safely collected from participants. Policies supporting ongoing testing of evidence-based mouth care protocols for individuals with dysphagia are important to improve quality, demonstrate efficacy, and save health care costs. [Journal of Gerontological Nursing, 43(9), 9-15.]. Copyright 2017, SLACK Incorporated.

A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania.

PubMed

Julian, Timothy R; Pickering, Amy J

2015-01-01

Diarrheal diseases are a leading cause of under-five mortality and morbidity in sub-Saharan Africa. Quantitative exposure modeling provides opportunities to investigate the relative importance of fecal-oral transmission routes (e.g. hands, water, food) responsible for diarrheal disease. Modeling, however, requires accurate descriptions of individuals' interactions with the environment (i.e., activity data). Such activity data are largely lacking for people in low-income settings. In the present study, we collected activity data and microbiological sampling data to develop a quantitative microbial exposure model for two female caretakers in peri-urban Tanzania. Activity data were combined with microbiological data of contacted surfaces and fomites (e.g. broom handle, soil, clothing) to develop example exposure profiles describing second-by-second estimates of fecal indicator bacteria (E. coli and enterococci) concentrations on the caretaker's hands. The study demonstrates the application and utility of video activity data to quantify exposure factors for people in low-income countries and apply these factors to understand fecal contamination exposure pathways. This study provides both a methodological approach for the design and implementation of larger studies, and preliminary data suggesting contacts with dirt and sand may be important mechanisms of hand contamination. Increasing the scale of activity data collection and modeling to investigate individual-level exposure profiles within target populations for specific exposure scenarios would provide opportunities to identify the relative importance of fecal-oral disease transmission routes.

Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling.

PubMed

Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca

2015-01-01

In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.

Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling

PubMed Central

Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca

2015-01-01

In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples. PMID:26035837

Quality evaluation of processed clay soil samples.

PubMed

Steiner-Asiedu, Matilda; Harrison, Obed Akwaa; Vuvor, Frederick; Tano-Debrah, Kwaku

2016-01-01

This study assessed the microbial quality of clay samples sold on two of the major Ghanaian markets. The study was a cross-sectional assessing the evaluation of processed clay and effects it has on the nutrition of the consumers in the political capital town of Ghana. The items for the examination was processed clay soil samples. Staphylococcus spp and fecal coliforms including Klebsiella, Escherichia, and Shigella and Enterobacterspp were isolated from the clay samples. Samples from the Kaneshie market in Accra recorded the highest total viable counts 6.5 Log cfu/g and Staphylococcal count 5.8 Log cfu/g. For fecal coliforms, Madina market samples had the highest count 6.5 Log cfu/g and also recorded the highest levels of yeast and mould. For Koforidua, total viable count was highest in the samples from the Zongo market 6.3 Log cfu/g. Central market samples had the highest count of fecal coliforms 4.6 Log cfu/g and yeasts and moulds 6.5 Log cfu/g. "Small" market recorded the highest staphylococcal count 6.2 Log cfu/g. The water activity of the clay samples were low, and ranged between 0.65±0.01 and 0.66±0.00 for samples collected from Koforidua and Accra respectively. The clay samples were found to contain Klebsiella spp. Escherichia, Enterobacter, Shigella spp. staphylococcus spp., yeast and mould. These have health implications when consumed.

Prevalence of parvovirus in Minnesota turkeys.

PubMed

Sharafeldin, T A; Singh, A; Abdel-Glil, M Y; Mor, S K; Porter, R E; Goyal, S M

2017-02-01

Poult enteritis syndrome (PES) is characterized by enteritis and decreased body weight gain in growing turkey poults between one d and 7 wk of age. Another syndrome called light turkey syndrome (LTS) causes a decrease in body weight of adult tom turkeys in Minnesota leading to huge economic losses. Reovirus, rotavirus, and astrovirus have been found in LTS and PES flocks in Minnesota. We tested 80 fecal pools collected from four LTS flocks and 35 fecal pools from non-LTS flocks for the presence of parvovirus. In addition, 116 fecal and meconium samples from turkeys submitted to the Minnesota Veterinary Diagnostic Laboratory (MVDL) also were tested. The samples were tested by PCR using primers for the non-structural 1 (NS1) gene of parvovirus. Of the 80 samples from LTS flocks, 41 were positive for parvovirus while 20 of 35 samples from non-LTS flocks were positive. The prevalence of parvovirus in fecal samples submitted to MVDL was relatively low; only five of the 116 pools were positive. The partial NS1 gene sequences from LTS and non-LTS samples showed 98 to 100% nt identity except for one divergent turkey parvovirus (TuPV) strain that revealed 90% identity and clustered with chicken-like parvoviruses. The presence of this divergent strain suggests circulation of a recombinant strain of TuPV in Minnesota turkeys. Our results indicate that TuPVs are circulating in both LTS and non-LTS flocks of turkeys in Minnesota, and further experimental studies are indicated to study the role of TuPV in LTS. © 2016 Poultry Science Association Inc.

Comparison and continuous estimates of fecal coliform and Escherichia coli bacteria in selected Kansas streams, May 1999 through April 2002

USGS Publications Warehouse

Rasmussen, Patrick P.; Ziegler, Andrew C.

2003-01-01

The sanitary quality of water and its use as a public-water supply and for recreational activities, such as swimming, wading, boating, and fishing, can be evaluated on the basis of fecal coliform and Escherichia coli (E. coli) bacteria densities. This report describes the overall sanitary quality of surface water in selected Kansas streams, the relation between fecal coliform and E. coli, the relation between turbidity and bacteria densities, and how continuous bacteria estimates can be used to evaluate the water-quality conditions in selected Kansas streams. Samples for fecal coliform and E. coli were collected at 28 surface-water sites in Kansas. Of the 318 samples collected, 18 percent exceeded the current Kansas Department of Health and Environment (KDHE) secondary contact recreational, single-sample criterion for fecal coliform (2,000 colonies per 100 milliliters of water). Of the 219 samples collected during the recreation months (April 1 through October 31), 21 percent exceeded the current (2003) KDHE single-sample fecal coliform criterion for secondary contact rec-reation (2,000 colonies per 100 milliliters of water) and 36 percent exceeded the U.S. Environmental Protection Agency (USEPA) recommended single-sample primary contact recreational criterion for E. coli (576 colonies per 100 milliliters of water). Comparisons of fecal coliform and E. coli criteria indicated that more than one-half of the streams sampled could exceed USEPA recommended E. coli criteria more frequently than the current KDHE fecal coliform criteria. In addition, the ratios of E. coli to fecal coliform (EC/FC) were smallest for sites with slightly saline water (specific conductance greater than 1,000 microsiemens per centimeter at 25 degrees Celsius), indicating that E. coli may not be a good indicator of sanitary quality for those streams. Enterococci bacteria may provide a more accurate assessment of the potential for swimming-related illnesses in these streams. Ratios of EC/FC and linear regression models were developed for estimating E. coli densities on the basis of measured fecal coliform densities for six individual and six groups of surface-water sites. Regression models developed for the six individual surface-water sites and six groups of sites explain at least 89 percent of the variability in E. coli densities. The EC/FC ratios and regression models are site specific and make it possible to convert historic fecal coliform bacteria data to estimated E. coli densities for the selected sites. The EC/FC ratios can be used to estimate E. coli for any range of historical fecal coliform densities, and in some cases with less error than the regression models. The basin- and statewide regression models explained at least 93 percent of the variance and best represent the sites where a majority of the data used to develop the models were collected (Kansas and Little Arkansas Basins). Comparison of the current (2003) KDHE geometric-mean primary contact criterion for fecal coliform bacteria of 200 col/100 mL to the 2002 USEPA recommended geometric-mean criterion of 126 col/100 mL for E. coli results in an EC/FC ratio of 0.63. The geometric-mean EC/FC ratio for all sites except Rattlesnake Creek (site 21) is 0.77, indicating that considerably more than 63 percent of the fecal coliform is E. coli. This potentially could lead to more exceedances of the recommended E. coli criterion, where the water now meets the current (2003) 200-col/100 mL fecal coliform criterion. In this report, turbidity was found to be a reliable estimator of bacteria densities. Regression models are provided for estimating fecal coliform and E. coli bacteria densities using continuous turbidity measurements. Prediction intervals also are provided to show the uncertainty associated with using the regression models. Eighty percent of all measured sample densities and individual turbidity-based estimates from the regression models were in agreement as exceedi

Bacteria holding times for fecal coliform by mFC agar method and total coliform and Escherichia coli by Colilert®-18 Quanti-Tray® method

USGS Publications Warehouse

Aulenbach, Brent T.

2010-01-01

Bacteria holding-time experiments of up to 62 h were performed on five surface-water samples from four urban stream sites in the vicinity of Atlanta, GA, USA that had relatively high densities of coliform bacteria (Escherichia coli densities were all well above the US Environmental Protection Agency criterion of 126 colonies (100 ml) − 1 for recreational waters). Holding-time experiments were done for fecal coliform using the membrane filtration modified fecal coliform (mFC) agar method and for total coliform and E. coli using the Colilert®-18 Quanti-Tray® method. The precisions of these analytical methods were quantified. Precisions determined for fecal coliform indicated that the upper bound of the ideal range of counts could reasonably be extended upward and would improve precision. For the Colilert®-18 method, analytical precisions were similar to the theoretical precisions for this method. Fecal and total coliform densities did not change significantly with holding times up to about 27 h. Limited information indicated that fecal coliform densities might be stable for holding times of up to 62 h, whereas total coliform densities might not be stable for holding times greater than about 27 h. E. coli densities were stable for holding times of up to 18 h—a shorter period than indicated from a previous studies. These results should be applicable to non-regulatory monitoring sampling designs for similar urban surface-water sample types.

Tracking pathogen transmission at the human-wildlife interface: banded mongoose and Escherichia coli.

PubMed

Pesapane, R; Ponder, M; Alexander, K A

2013-06-01

A primary challenge to managing emerging infectious disease is identifying pathways that allow pathogen transmission at the human-wildlife interface. Using Escherichia coli as a model organism, we evaluated fecal bacterial transmission between banded mongoose (Mungos mungo) and humans in northern Botswana. Fecal samples were collected from banded mongoose living in protected areas (n = 87, 3 troops) and surrounding villages (n = 92, 3 troops). Human fecal waste was collected from the same environment (n = 46). Isolates were evaluated for susceptibility to 10 antibiotics. Resistant E. coli isolates from mongoose were compared to human isolates using rep-PCR fingerprinting and MLST-PCR. Antimicrobial resistant isolates were identified in 57 % of the mongoose fecal samples tested (range 31-78% among troops). At least one individual mongoose fecal sample demonstrated resistance to each tested antibiotic, and multidrug resistance was highest in the protected areas (40.9%). E. coli isolated from mongoose and human sources in this study demonstrated an extremely high degree of genetic similarity on rep-PCR (AMOVA, F ST = 0.0027, p = 0.18) with a similar pattern identified on MLST-PCR. Human waste may be an important source of microbial exposure to wildlife. Evidence of high levels of antimicrobial resistance even within protected areas identifies an emerging health threat and highlights the need for improved waste management in these systems.

SPECIFICITY AND SENSITIVITY OF FECAL BACTEROIDETES HUMAN-SPECIFIC PRIMERS WITH FECAL AND WASTEWATER SAMPLES FROM THE U.S. MIDWEST AND NORTHEAST REGIONS

EPA Science Inventory

Numerous watersheds throughout the United States are impaired due to fecal contamination. Fecal Bacteroidetes is a group of anaerobic bacteria present in high concentrations in animal feces that has shown promise as a microbial source tracking indicator of human and othe...

Prevalence of internal parasites in beef cows in the United States: Results of the National Animal Health Monitoring System's (NAHMS) beef study, 2007-2008.

PubMed

Stromberg, Bert E; Gasbarre, Louis C; Ballweber, Lora R; Dargatz, David A; Rodriguez, Judith M; Kopral, Christine A; Zarlenga, Dante S

2015-10-01

During the United States Department of Agriculture (USDA) National Animal Health Monitoring System's (NAHMS) 2007-2008 beef study, 567 producers from 24 US States were offered the opportunity to collect fecal samples from weaned beef calves and have them evaluated for the presence of parasite eggs (Phase 1). Participating producers were provided with instructions and materials for sample collection. Up to 20 fresh fecal samples were collected from each of the 99 participating operations. Fresh fecal samples were submitted to one of 3 randomly assigned laboratories for evaluation. Upon arrival at the laboratories, all samples were processed for the enumeration of strongyle, Nematodirus, and Trichuris eggs using the modified Wisconsin technique. The presence or absence of coccidian oocysts and tapeworm eggs was also noted. In submissions where the strongyle eggs per gram exceeded 30, aliquots from 2 to 6 animals were pooled for DNA extraction. Extracted DNA was subjected to genus level polymerase chain reaction (PCR) identification for the presence of Ostertagia, Cooperia, Haemonchus, Oesophagostomum, and Trichostrongylus. In this study, 85.6% of the samples had strongyle type, Nematodirus, and Trichuris eggs. Among the samples evaluated, 91% had Cooperia, 79% Ostertagia, 53% Haemonchus, 38% Oesophagostomum, 18% Nematodirus, 7% Trichuris, and 3% Trichostrongylus. The prevalence of coccidia and tapeworm eggs was 59.9% and 13.7%, respectively.

Prevalence of internal parasites in beef cows in the United States: Results of the National Animal Health Monitoring System’s (NAHMS) beef study, 2007–2008

PubMed Central

Stromberg, Bert E.; Gasbarre, Louis C.; Ballweber, Lora R.; Dargatz, David A.; Rodriguez, Judith M.; Kopral, Christine A.; Zarlenga, Dante S.

2015-01-01

During the United States Department of Agriculture (USDA) National Animal Health Monitoring System’s (NAHMS) 2007–2008 beef study, 567 producers from 24 US States were offered the opportunity to collect fecal samples from weaned beef calves and have them evaluated for the presence of parasite eggs (Phase 1). Participating producers were provided with instructions and materials for sample collection. Up to 20 fresh fecal samples were collected from each of the 99 participating operations. Fresh fecal samples were submitted to one of 3 randomly assigned laboratories for evaluation. Upon arrival at the laboratories, all samples were processed for the enumeration of strongyle, Nematodirus, and Trichuris eggs using the modified Wisconsin technique. The presence or absence of coccidian oocysts and tapeworm eggs was also noted. In submissions where the strongyle eggs per gram exceeded 30, aliquots from 2 to 6 animals were pooled for DNA extraction. Extracted DNA was subjected to genus level polymerase chain reaction (PCR) identification for the presence of Ostertagia, Cooperia, Haemonchus, Oesophagostomum, and Trichostrongylus. In this study, 85.6% of the samples had strongyle type, Nematodirus, and Trichuris eggs. Among the samples evaluated, 91% had Cooperia, 79% Ostertagia, 53% Haemonchus, 38% Oesophagostomum, 18% Nematodirus, 7% Trichuris, and 3% Trichostrongylus. The prevalence of coccidia and tapeworm eggs was 59.9% and 13.7%, respectively. PMID:26424909

The influence of serial fecal sampling on the diagnosis of giardiasis in humans, dogs, and cats.

PubMed

Uchôa, Flávia Fernandes de Mendonça; Sudré, Adriana Pittella; Macieira, Daniel de Barros; Almosny, Nádia Regina Pereira

2017-08-24

Giardia infection is a common clinical problem in humans and pets. The diagnosis of giardiasis is challenging as hosts intermittently excrete protozoan cysts in their feces. In the present study, we comparatively evaluated two methods of serial fecal sampling in humans, dogs, and cats from Rio de Janeiro, Brazil. The Faust et al. technique was used to examine fecal specimens collected in triplicate from 133 patients (52 humans, 60 dogs, and 21 cats). Specimens from 74 patients were received from the group assigned to carry out sampling on consecutive days - 34 humans, 35 dogs, and 5 cats, and specimens from 59 patients were received from the group assigned to carry out sampling on non-consecutive, separate days - 18 human beings, 25 dogs, and 16 cats. G. duodenalis cysts were found in stools of 30 individuals. Multiple stool sampling resulted in an increase in the number of samples that were positive for Giardia in both groups. The authors therefore conclude that multiple stool sampling increases the sensitivity of the Faust et al . technique to detect G. duodenalis cysts in samples from humans, cats and dogs.

The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing.

PubMed

Kennedy, Nicholas A; Walker, Alan W; Berry, Susan H; Duncan, Sylvia H; Farquarson, Freda M; Louis, Petra; Thomson, John M; Satsangi, Jack; Flint, Harry J; Parkhill, Julian; Lees, Charlie W; Hold, Georgina L

2014-01-01

Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has received relatively little attention. The aim of this study was to analyze bacterial communities in volunteer and inflammatory bowel disease (IBD) patient fecal samples extracted using widely used DNA extraction kits in established gastrointestinal research laboratories. Fecal samples from two healthy volunteers (H3 and H4) and two relapsing IBD patients (I1 and I2) were investigated. DNA extraction was undertaken using MoBio Powersoil and MP Biomedicals FastDNA SPIN Kit for Soil DNA extraction kits. PCR amplification for pyrosequencing of bacterial 16S rRNA genes was performed in both laboratories on all samples. Hierarchical clustering of sequencing data was done using the Yue and Clayton similarity coefficient. DNA extracted using the FastDNA kit and the MoBio kit gave median DNA concentrations of 475 (interquartile range 228-561) and 22 (IQR 9-36) ng/µL respectively (p<0.0001). Hierarchical clustering of sequence data by Yue and Clayton coefficient revealed four clusters. Samples from individuals H3 and I2 clustered by patient; however, samples from patient I1 extracted with the MoBio kit clustered with samples from patient H4 rather than the other I1 samples. Linear modelling on relative abundance of common bacterial families revealed significant differences between kits; samples extracted with MoBio Powersoil showed significantly increased Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae, and lower Enterobacteriaceae, Lachnospiraceae, Clostridiaceae, and Erysipelotrichaceae (p<0.05). This study demonstrates significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits. This highlights the importance of ensuring that samples in a study are prepared with the same method, and the need for caution when cross-comparing studies that use different methods.

Seasonal Variations in Survival of Indicator Bacteria in Soil and Their Contribution to Storm-water Pollution

PubMed Central

Van Donsel, Dale J.; Geldreich, Edwin E.; Clarke, Norman A.

1967-01-01

Survival of a fecal coliform (Escherichia coli) and a fecal streptococcus (Streptococcus faecalis var. liquifaciens) was studied through several years at shaded and exposed outdoor soil plots. Death rates for both organisms were calculated for the different seasons at both sites. The 90% reduction times for the fecal coliform ranged from 3.3 days in summer to 13.4 days in autumn. For the fecal streptococcus, 90% reduction times were from 2.7 days in summer to 20.1 days in winter. During summer, the fecal coliform survived slightly longer than the fecal streptococcus; during autumn, survival was the same; and in spring and winter the fecal streptococcus survived much longer than the fecal coliform. Both organisms were isolated from storm-water runoff collected below a sampling site when counts were sufficiently high in soil. Isolation was more frequent during prolonged rains, lasting up to 10 days, than during short rain storms. There was evidence of aftergrowth of nonfecal coliforms in the soil as a result of temperature and rainfall variations. Such aftergrowth may contribute to variations in bacterial count of storm-water runoff which have no relation to the sanitary history of the drainage area. PMID:16349746

Ground-water-quality data for selected wells in the Beaver Creek watershed, West Tennessee

USGS Publications Warehouse

Williams, S.D.

1996-01-01

In 1993 the U.S. Geological Survey, in cooperation with the Tennessee Department of Environment and Conservation (TDEC), began an investigation of the quality of ground water in the Beaver Creek watershed in West Tennessee. A total of 408 water samples were collected from 91 wells during 5 sampling periods in 1994. Water samples were analyzed for selected water-quality properties, fecal coliform and streptococci bacteria, nutrients, and major inorganic constituents. Selected well- construction data and information on potential sources of contamination were also collected for the 91 wells sampled. Nitrate concentrations (measured as NO3) ranged from a detection limit of 0.1 to 91 milligrams per liter (mg/L). Nitrate concentrations exceeding 13 mg/L were detected in 71 of the samples collected. Nitrate concentrations in water samples collected from three wells exceeded the TDEC primary drinking water standard of 44 mg/L for nitrate (measured as NO3). Nitrite (measured as NO2), ammonium (measured as NH4), and orthophosphate (measured as PO4) concentrations in samples were generally less than 0.1 mg/L (detection limit). Fecal coliform bacteria were detected in 33 of the 408 water samples collected. Samples from 21 of the 91 wells contained fecal coliform bacteria during one or more of the five sampling periods. Fecal streptococci bacteria were detected in 123 of the 408 samples. Samples from 59 wells contained fecal streptococci bacteria during one or more of the five sampling periods.

Duplex quantitative real-time PCR assay for the detection and discrimination of the eggs of Toxocara canis and Toxocara cati (Nematoda, Ascaridoidea) in soil and fecal samples.

PubMed

Durant, Jean-Francois; Irenge, Leonid M; Fogt-Wyrwas, Renata; Dumont, Catherine; Doucet, Jean-Pierre; Mignon, Bernard; Losson, Bertrand; Gala, Jean-Luc

2012-12-07

Toxocarosis is a zoonotic disease caused by Toxocara canis (T. canis) and/or Toxocara cati (T. cati), two worldwide distributed roundworms which are parasites of canids and felids, respectively. Infections of humans occur through ingestion of embryonated eggs of T. canis or T. cati, when playing with soils contaminated with dogs or cats feces. Accordingly, the assessment of potential contamination of these areas with these roundworms eggs is paramount. A duplex quantitative real-time PCR (2qPCR) targeting the ribosomal RNA gene internal transcribed spacer (ITS2) has been developed and used for rapid and specific identification of T. canis and T. cati eggs in fecal and soil samples. The assay was set up on DNA samples extracted from 53 adult worms including T. canis, T. cati, T. leonina, Ascaris suum (A. suum) and Parascaris equorum (P. equorum). The assay was used to assess the presence of T. cati eggs in several samples, including 12 clean soil samples spiked with eggs of either T. cati or A. suum, 10 actual soil samples randomly collected from playgrounds in Brussels, and fecal samples from cats, dogs, and other animals. 2qPCR results on dogs and cats fecal samples were compared with results from microscopic examination. 2qPCR assay allowed specific detection of T. canis and T. cati, whether adult worms, eggs spiked in soil or fecal samples. The 2qPCR limit of detection (LOD) in spiked soil samples was 2 eggs per g of soil for a turnaround time of 3 hours. A perfect concordance was observed between 2qPCR assay and microscopic examination on dogs and cats feces. The newly developed 2qPCR assay can be useful for high throughput prospective or retrospective detection of T.canis and/or T. cati eggs in fecal samples as well as in soil samples from playgrounds, parks and sandpits.

National Risk Management Research Laboratory (NRMRL) Microbial Research

EPA Science Inventory

Experimental design: Three host-specific PCR assays were tested against fecal and water samples. Host-specificity assays were performed against targeted and nontargeted fecal sources. Detection limits were performed against diluted fecal and water DNA extracts. Groundwater an...

Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses.

PubMed

Conceição-Neto, Nádia; Zeller, Mark; Heylen, Elisabeth; Lefrère, Hanne; Mesquita, João Rodrigo; Matthijnssens, Jelle

2015-05-20

More knowledge about viral populations in wild animals is needed in order to better understand and assess the risk of zoonotic diseases. In this study we performed viral metagenomic analysis of fecal samples from three healthy carnivores: a badger (Meles meles), a mongoose (Herpestes ichneumon) and an otter (Lutra lutra) from Portugal. We detected the presence of novel highly divergent viruses in the fecal material of the carnivores analyzed, such as five gemycircularviruses. Four of these gemycircularviruses were found in the mongoose and one in the badger. In addition we also identified an RNA-dependent RNA polymerase gene from a putative novel member of the Nodaviridae family in the fecal material of the otter. Together these results underline that many novel viruses are yet to be discovered and that fecal associated viruses are not always related to disease. Our study expands the knowledge of viral species present in the gut, although the interpretation of the true host species of such novel viruses needs to be reviewed with great caution.

The diagnostic value of a new fecal marker, matrix metalloprotease-9, in different types of inflammatory bowel diseases.

PubMed

Farkas, Klaudia; Saródi, Zoltán; Bálint, Anita; Földesi, Imre; Tiszlavicz, László; Szűcs, Mónika; Nyári, Tibor; Tajti, János; Nagy, Ferenc; Szepes, Zoltán; Bor, Renáta; Annaházi, Anita; Róka, Richárd; Molnár, Tamás

2015-03-01

Only limited data are available regarding the diagnostic accuracy of fecal matrix metalloprotease-9 [MMP-9] for inflammatory bowel disease [IBD]. The aims of our study were to assess the diagnostic accuracy of fecal MMP-9 in patients with active Crohn's disease [CD], ulcerative colitis [UC], and pouchitis, and to compare the diagnostic accuracy of fecal MMP-9 and fecal calprotectin [CP] in IBD. Stool and blood samples were collected in 50 CD, 54 UC, and 34 ileal pouch-anal anastomosis patients before control endoscopies were performed. Biopsies were taken for histologic purposes. The activities of CD, UC, and pouchitis were defined with the use of clinical, endoscopic, and histologic activity scores. Fecal CP and MMP-9 levels were quantified by enzyme-linked immunosorbent assay. Active CD, UC, and pouchitis were detected in 38%, 54%, and 29% of the patients, respectively. A significant correlation was revealed between fecal CP and the clinical activities of CD and UC, and between fecal CP and the endoscopic activity of UC and pouchitis. Fecal MMP-9 did not correlate with any of the activity indices of CD; however, strong associations were shown between fecal MMP-9 and clinical, endoscopic, and histologic activities of both UC and pouchitis. This is the first study assessing the diagnostic accuracy of MMP-9 in different types of IBD. Our results showed that fecal MMP-9 has high sensitivity in the detection of endoscopically active UC and pouchitis. These non-invasive methods help assess intestinal inflammation. Copyright © 2015 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

PubMed Central

Fisher, Jenny C.; Eren, A. Murat; Green, Hyatt C.; Shanks, Orin C.; Morrison, Hilary G.; Vineis, Joseph H.; Sogin, Mitchell L.

2015-01-01

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

Assessing hog lagoon waste contamination in the Cape Fear Watershed using Bacteroidetes 16S rRNA gene pyrosequencing.

PubMed

Arfken, Ann M; Song, Bongkeun; Mallin, Michael A

2015-09-01

Hog lagoons can be major sources of waste and nutrient contamination to watersheds adjacent to pig farms. Fecal source tracking methods targeting Bacteroidetes 16S rRNA genes in pig fecal matter may underestimate or fail to detect hog lagoon contamination in riverine environments. In order to detect hog lagoon wastewater contamination in the Cape Fear Watershed, where a large number of hog farms are present, we conducted pyrosequencing analyses of Bacteroidetes 16S rRNA genes in hog lagoon waste and identified new hog lagoon-specific marker sequences. Additional pyrosequencing analyses of Bacteroidetes 16S rRNA genes were conducted with surface water samples collected at 4 sites during 5 months in the Cape Fear Watershed. Using an operational taxonomic unit (OTU) identity cutoff value of 97 %, these newly identified hog lagoon markers were found in 3 of the river samples, while only 1 sample contained the pig fecal marker. In the sample containing the pig fecal marker, there was a relatively high percentage (14.1 %) of the hog lagoon markers and a low pig fecal marker relative abundance of 0.4 % in the Bacteroidetes 16S rRNA gene sequences. This suggests that hog lagoon contamination must be somewhat significant in order for pig fecal markers to be detected, and low levels of hog lagoon contamination cannot be detected targeting only pig-specific fecal markers. Thus, new hog lagoon markers have a better detection capacity for lagoon waste contamination, and in conjunction with a pig fecal marker, provide a more comprehensive and accurate detection of hog lagoon waste contamination in susceptible watersheds.

Next-generation sequencing identification of pathogenic bacterial genes and their relationship with fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal.

PubMed

Ghaju Shrestha, Rajani; Tanaka, Yasuhiro; Malla, Bikash; Bhandari, Dinesh; Tandukar, Sarmila; Inoue, Daisuke; Sei, Kazunari; Sherchand, Jeevan B; Haramoto, Eiji

2017-12-01

Bacteriological analysis of drinking water leads to detection of only conventional fecal indicator bacteria. This study aimed to explore and characterize bacterial diversity, to understand the extent of pathogenic bacterial contamination, and to examine the relationship between pathogenic bacteria and fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal. Sixteen water samples were collected from shallow dug wells (n=12), a deep tube well (n=1), a spring (n=1), and rivers (n=2) in September 2014 for 16S rRNA gene next-generation sequencing. A total of 525 genera were identified, of which 81 genera were classified as possible pathogenic bacteria. Acinetobacter, Arcobacter, and Clostridium were detected with a relatively higher abundance (>0.1% of total bacterial genes) in 16, 13, and 5 of the 16 samples, respectively, and the highest abundance ratio of Acinetobacter (85.14%) was obtained in the deep tube well sample. Furthermore, the bla OXA23-like genes of Acinetobacter were detected using SYBR Green-based quantitative PCR in 13 (35%) of 37 water samples, including the 16 samples that were analyzed for next-generation sequencing, with concentrations ranging 5.3-7.5logcopies/100mL. There was no sufficient correlation found between fecal indicator bacteria, such as Escherichia coli and total coliforms, and potential pathogenic bacteria, as well as the bla OXA23-like gene of Acinetobacter. These results suggest the limitation of using conventional fecal indicator bacteria in evaluating the pathogenic bacteria contamination of different water sources in the Kathmandu Valley. Copyright © 2017 Elsevier B.V. All rights reserved.

Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study.

PubMed

Harwood, Valerie J; Boehm, Alexandria B; Sassoubre, Lauren M; Vijayavel, Kannappan; Stewart, Jill R; Fong, Theng-Theng; Caprais, Marie-Paule; Converse, Reagan R; Diston, David; Ebdon, James; Fuhrman, Jed A; Gourmelon, Michele; Gentry-Shields, Jennifer; Griffith, John F; Kashian, Donna R; Noble, Rachel T; Taylor, Huw; Wicki, Melanie

2013-11-15

An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination. Human viruses used as source identifiers included adenoviruses (HAdV), enteroviruses (EV), norovirus Groups I and II (NoVI and NoVII), and polyomaviruses (HPyVs). Bacteriophages were also employed, including somatic coliphages and F-specific RNA bacteriophages (FRNAPH) as general indicators of fecal contamination. Bacteriophage methods targeting human fecal sources included genotyping of FRNAPH isolates and plaque formation on bacterial hosts Enterococcus faecium MB-55, Bacteroides HB-73 and Bacteroides GB-124. The use of small sample volumes (≤50 ml) resulted in relatively insensitive theoretical limits of detection (10-50 gene copies or plaques × 50 ml(-1)) which, coupled with low virus concentrations in samples, resulted in high false-negative rates, low sensitivity, and low negative predictive values. On the other hand, the specificity of the human virus methods was generally close to 100% and positive predictive values were ∼40-70% with the exception of NoVs, which were not detected. The bacteriophage methods were generally much less specific toward human sewage than virus methods, although FRNAPH II genotyping was relatively successful, with 18% sensitivity and 85% specificity. While the specificity of the human virus methods engenders great confidence in a positive result, better concentration methods and larger sample volumes must be utilized for greater accuracy of negative results, i.e. the prediction that a human contamination source is absent. Copyright © 2013 Elsevier Ltd. All rights reserved.

Patterns of Antimicrobial Resistance Observed in Escherichia coli Isolates Obtained from Domestic- and Wild-Animal Fecal Samples, Human Septage, and Surface Water

PubMed Central

Sayah, Raida S.; Kaneene, John B.; Johnson, Yvette; Miller, RoseAnn

2005-01-01

A repeated cross-sectional study was conducted to determine the patterns of antimicrobial resistance in 1,286 Escherichia coli strains isolated from human septage, wildlife, domestic animals, farm environments, and surface water in the Red Cedar watershed in Michigan. Isolation and identification of E. coli were done by using enrichment media, selective media, and biochemical tests. Antimicrobial susceptibility testing by the disk diffusion method was conducted for neomycin, gentamicin, streptomycin, chloramphenicol, ofloxacin, trimethoprim-sulfamethoxazole, tetracycline, ampicillin, nalidixic acid, nitrofurantoin, cephalothin, and sulfisoxazole. Resistance to at least one antimicrobial agent was demonstrated in isolates from livestock, companion animals, human septage, wildlife, and surface water. In general, E. coli isolates from domestic species showed resistance to the largest number of antimicrobial agents compared to isolates from human septage, wildlife, and surface water. The agents to which resistance was demonstrated most frequently were tetracycline, cephalothin, sulfisoxazole, and streptomycin. There were similarities in the patterns of resistance in fecal samples and farm environment samples by animal, and the levels of cephalothin-resistant isolates were higher in farm environment samples than in fecal samples. Multidrug resistance was seen in a variety of sources, and the highest levels of multidrug-resistant E. coli were observed for swine fecal samples. The fact that water sample isolates were resistant only to cephalothin may suggest that the resistance patterns for farm environment samples may be more representative of the risk of contamination of surface waters with antimicrobial agent-resistant bacteria. PMID:15746342

Development and testing of real-time PCR assays for determining fecal loading and source identification (cattle, human, etc.) in surface water and groundwater

NASA Astrophysics Data System (ADS)

McKay, L. D.; Layton, A.; Gentry, R.

2004-12-01

A multi-disciplinary group of researchers at the University of Tennessee is developing and testing a series of microbial assay methods based on real-time PCR to detect fecal bacterial concentrations and host sources in water samples. Real-time PCR is an enumeration technique based on the unique and conserved nucleic acid sequences present in all organisms. The first research task was development of an assay (AllBac) to detect total amount of Bacteroides, which represents up to 30 percent of fecal mass. Subsequent assays were developed to detect Bacteroides from cattle (BoBac) and humans (HuBac) using 16sRNA genes based on DNA sequences in the national GenBank, as well as sequences from local fecal samples. The assays potentially have significant advantages over conventional bacterial source tracking methods because: 1. unlike traditional enumeration methods, they do not require bacterial cultivation; 2. there are no known non-fecal sources of Bacteroides; 3. the assays are quantitative with results for total concentration and for each species expressed in mg/l; and 4. they show little regional variation within host species, meaning that they do not require development of extensive local gene libraries. The AllBac and BoBac assays have been used in a study of fecal contamination in a small rural watershed (Stock Creek) near Knoxville, TN, and have proven useful in identification of areas where cattle represent a significant fecal input and in development of BMPs. It is expected that these types of assays (and future assays for birds, hogs, etc.) could have broad applications in monitoring fecal impacts from Animal Feeding Operations, as well as from wildlife and human sources.

Removal of bacterial fecal indicators, coliphages and enteric adenoviruses from waters with high fecal pollution by slow sand filtration.

PubMed

Bauer, Rosalie; Dizer, Halim; Graeber, Ingeborg; Rosenwinkel, Karl-Heinz; López-Pila, Juan M

2011-01-01

The aim of the present study was to estimate the performance of slow sand filtration (SSF) facilities, including the time needed for reaching stabilization (maturation), operated with surface water bearing high fecal contamination, representing realistic conditions of rivers in many emerging countries. Surface water spiked with wastewater was infiltrated at different pore water velocities (PWV) and samples were collected at different migration distances. The samples were analyzed for phages and to a lesser extent for fecal bacteria and enteric adenoviruses. At the PWV of 50 cm/d, at which somatic phages showed highest removal, their mean log(10) removal after 90 cm migration was 3.2. No substantial differences of removal rates were observed at PWVs between 100 and 900 cm/d (2.3 log(10) mean removal). The log(10) mean removal of somatic phages was less than the observed for fecal bacteria and tended more towards that of enteric adenoviruses This makes somatic phages a potentially better process indicator than Escherichia coli for the removal of viruses in SSF. We conclude that SSF, and by inference in larger scale river bank filtration (RBF), is an excellent option as a component in multi-barrier systems for drinking water treatment also in areas where the sources of raw water are considerably fecally polluted, as often found in many emerging countries. Copyright © 2010 Elsevier Ltd. All rights reserved.

Application of fecal near-infrared spectroscopy and nutritional balance software to monitor diet quality and body condition in beef cows grazing Arizona rangeland.

PubMed

Tolleson, D R; Schafer, D W

2014-01-01

Monitoring the nutritional status of range cows is difficult. Near-infrared spectroscopy (NIRS) of feces has been used to predict diet quality in cattle. When fecal NIRS is coupled with decision support software such as the Nutritional Balance Analyzer (NUTBAL PRO), nutritional status and animal performance can be monitored. Approximately 120 Hereford and 90 CGC composite (50% Red Angus, 25% Tarentaise, and 25% Charolais) cows grazing in a single herd were used in a study to determine the ability of fecal NIRS and NutbalPro to project BCS (1 = thin and 9 = fat) under commercial scale rangeland conditions in central Arizona. Cattle were rotated across the 31,000 ha allotment at 10 to 20 d intervals. Cattle BCS and fecal samples (approximately 500 g) composited from 5 to 10 cows were collected in the pasture approximately monthly at the midpoint of each grazing period. Samples were frozen and later analyzed by NIRS for prediction of diet crude protein (CP) and digestible organic matter (DOM). Along with fecal NIRS predicted diet quality, animal breed type, reproductive status, and environmental conditions were input to the software for each fecal sampling and BCS date. Three different evaluations were performed. First, fecal NIRS and NutbalPro derived BCS was projected forward from each sampling as if it were a "one-time only" measurement. Second, BCS was derived from the average predicted weight change between 2 sampling dates for a given period. Third, inputs to the model were adjusted to better represent local animals and conditions. Fecal NIRS predicted diet quality varied from a minimum of approximately 5% CP and 57% DOM in winter to a maximum of approximately 11% CP and 60% DOM in summer. Diet quality correlated with observed seasonal changes and precipitation events. In evaluation 1, differences in observed versus projected BCS were not different (P > 0.1) between breed types but these values ranged from 0.1 to 1.1 BCS in Herefords and 0.0 to 0.9 in CGC. In evaluation 2, differences in observed versus projected BCS were not different (P > 0.1) between breed types but these values ranged from 0.00 to 0.46 in Hereford and 0.00 to 0.67 in CGC. In evaluation 3, the range of differences between observed and projected BCS was 0.04 to 0.28. The greatest difference in projected versus observed BCS occurred during periods of lowest diet quality. Body condition was predicted accurately enough to be useful in monitoring the nutrition of range beef cows under the conditions of this study.

Fecal-indicator bacteria in the Newfound Creek watershed, western North Carolina, during a high and low streamflow condition, 2003

USGS Publications Warehouse

Giddings, Elise M.; Oblinger, Carolyn J.

2004-01-01

Water quality in the Newfound Creek watershed has been shown to be affected by bacteria, sediment, and nutrients. In this study, Escherichia coli (E. coli) bacteria were sampled at five sites in Newfound Creek and five tributary sites during low flow on May 28, 2003, and high flow on November 19, 2003. In addition, a subset of five sites was sampled for fecal coliform bacteria, E. coli bacteria in streambed sediments (low flow only), and coliphage virus for serotyping. Coliphage virus serotyping has been used to identify human and animal sources of bacterial contamination. A streamflow gage was installed and operated to support ongoing water-quality studies in the watershed. Fecal coliform densities ranged from 92 to 27,000 colony-forming units per 100 milliliters of water for E. coli and 140 to an estimated 29,000 colony-forming units per 100 milliliters of water for fecal coliform during the two sampling visits. Ninety percent of the E. coli and fecal coliform samples exceeded corresponding U.S. Environmental Protection Agency or North Carolina water-quality criteria for recreational and ambient waters. During low flow, the middle part of the Newfound Creek watershed and the Dix Creek tributary had the highest densities of E. coli bacteria. During the high-flow sampling, all tributaries contained high densities of E. coli bacteria, although Dix Creek and Round Hill Branch were the largest contributors of these bacteria to Newfound Creek. Coliphage virus serotyping results were inconclusive because most samples did not contain the male-specific RNA coliphage needed for serotyping. Positive results indicated, however, that during low flow, non-human sources of bacteria were present in Sluder Branch, and during high flow, human sources of bacteria were present in Round Hill Branch. Sampling of bacteria in streambed sediments during low flow indicated that sediments do not appear to be a substantial source of bacteria relative to the water column, with the exception of an area near the confluence of Sluder Branch and Newfound Creek.

Quantification of the Flavonoid-Degrading Bacterium Eubacterium ramulus in Human Fecal Samples with a Species-Specific Oligonucleotide Hybridization Probe

PubMed Central

Simmering, Rainer; Kleessen, Brigitta; Blaut, Michael

1999-01-01

To investigate the occurrence of the flavonoid-degrading bacterium Eubacterium ramulus in the human intestinal tract, an oligonucleotide probe designated S-S-E.ram-0997-a-A-18 was designed and validated, with over 90 bacterial strains representing the dominant described human fecal flora. Application of S-S-E.ram-0997-a-A-18 to fecal samples from 20 subjects indicated the presence of E. ramulus in each individual tested in numbers from 4.4 × 107 to 2.0 × 109 cells/g of fecal dry mass. Six fecal E. ramulus isolates were recognized by S-S-E.ram-0997-a-A-18 but exhibited different band patterns when analyzed by randomly amplified polymorphic DNA. PMID:10427069

Quantitative CrAssphage PCR Assays for Human Fecal ...

EPA Pesticide Factsheets

Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal indicator bacteria are used; however, they cannot distinguish human fecal waste from pollution from other animals. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome. Based upon initial screening, two novel crAssphage qPCR assays (CPQ_056 and CPQ_064) were designed and evaluated in reference fecal samples and water matrices. The assays exhibited high specificities (98.6%) when tested against a large animal fecal reference library and were highly abundant in raw sewage and sewage impacted water samples. In addition, CPQ_056 and CPQ_064 assay performance was compared to HF183/BacR287 and HumM2 methods in paired experiments. Findings confirm viral crAssphage qPCR assays perform at a similar level to well established bacterial human-associated fecal source identification technologies. These new viral based assays could become important water quality management and research tools. To inform the public.

Depletion of Stercobilin in Fecal Matter from a Mouse Model of Autism Spectrum Disorders

PubMed Central

Sekera, Emily R.; Rudolph, Heather L.; Carro, Stephen D.; Morales, Michael J.; Bett, Glenna C. L.; Rasmusson, Randall L.; Wood, Troy D.

2017-01-01

Introduction Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders lacking a clinical biomarker for diagnosis. Emerging evidence shows that intestinal microflora from ASD subjects can be distinguished from controls, suggesting metabolite differences due to the action of intestinal microbes may provide a means for identifying potential biomarkers for ASD. Objectives The aim of this study was to determine if quantitative differences in levels of stercobilin and stercobilinogen, metabolites produced by biological action of intestinal microflora, exist in the fecal matter between an ASD mouse model population and controls. Methods Pairs of fecal samples were collected from two mouse groups, an ASD model group with Timothy syndrome 2 (TS2-NEO) and a gender-matched control group. After centrifugation, supernatant was spiked with an 18O-labeled stercobilin isotopomer and subjected to solid phase extraction for processing. Extracted samples were spotted on a stainless steel plate and subjected to matrix-assisted laser desorption and ionization mass spectrometry using dihydroxybenzoic acid as the matrix (n = 5). Peak areas for bilins and 18O-stercobilin isotopomers were determined in each fecal sample. Results A 40–45% depletion in stercobilin in TS2-NEO fecal samples compared with controls was observed with p < 0.05; a less dramatic depletion was observed for stercobilinogen. Conclusions The results show that stercobilin depletion in feces is observed for an ASD mouse model vs. controls. This may help to explain recent observations of a less diverse microbiome in humans with ASD and may prove helpful in developing a clinical ASD biomarker. PMID:29147105

Comparison of microbial populations in the small intestine, large intestine and feces of healthy horses using terminal restriction fragment length polymorphism

PubMed Central

2013-01-01

Background The composition of the microbiota of the equine intestinal tract is complex. Determining whether the microbial composition of fecal samples is representative of proximal compartments of the digestive tract could greatly simplify future studies. The objectives of this study were to compare the microbial populations of the duodenum, ileum, cecum, colon and rectum (feces) within and between healthy horses, and to determine whether rectal (fecal) samples are representative of proximal segments of the gastrointestinal tract. Intestinal samples were collected from ten euthanized horses. 16S rRNA gene PCR-based TRFLP was used to investigate microbiota richness in various segments of the gastrointestinal tract, and dice similarity indices were calculated to compare the samples. Results Within horses large variations of microbial populations along the gastrointestinal tract were seen. The microbiota in rectal samples was only partially representative of other intestinal compartments. The highest similarity was obtained when feces were compared to the cecum. Large compartmental variations were also seen when microbial populations were compared between six horses with similar dietary and housing management. Conclusion Rectal samples were not entirely representative of intestinal compartments in the small or large intestine. This should be taken into account when designing studies using fecal sampling to assess other intestinal compartments. Similarity between horses with similar dietary and husbandry management was also limited, suggesting that parts of the intestinal microbiota were unique to each animal in this study. PMID:23497580

Ape Conservation Physiology: Fecal Glucocorticoid Responses in Wild Pongo pygmaeus morio following Human Visitation

PubMed Central

Muehlenbein, Michael P.; Ancrenaz, Marc; Sakong, Rosman; Ambu, Laurentius; Prall, Sean; Fuller, Grace; Raghanti, Mary Ann

2012-01-01

Nature-based tourism can generate important revenue to support conservation of biodiversity. However, constant exposure to tourists and subsequent chronic activation of stress responses can produce pathological effects, including impaired cognition, growth, reproduction, and immunity in the same animals we are interested in protecting. Utilizing fecal samples (N = 53) from 2 wild habituated orangutans (Pongo pygmaeus morio) (in addition to 26 fecal samples from 4 wild unhabituated orangutans) in the Lower Kinabatangan Wildlife Sanctuary of Sabah, Malaysian Borneo, we predicted that i) fecal glucocorticoid metabolite concentrations would be elevated on the day after tourist visitation (indicative of normal stress response to exposure to tourists on the previous day) compared to samples taken before or during tourist visitation in wild, habituated orangutans, and ii) that samples collected from habituated animals would have lower fecal glucocorticoid metabolites than unhabituated animals not used for tourism. Among the habituated animals used for tourism, fecal glucocorticoid metabolite levels were significantly elevated in samples collected the day after tourist visitation (indicative of elevated cortisol production on the previous day during tourist visitation). Fecal glucocorticoid metabolite levels were also lower in the habituated animals compared to their age-matched unhabituated counterparts. We conclude that the habituated animals used for this singular ecotourism project are not chronically stressed, unlike other species/populations with documented permanent alterations in stress responses. Animal temperament, species, the presence of coping/escape mechanisms, social confounders, and variation in amount of tourism may explain differences among previous experiments. Acute alterations in glucocorticoid measures in wildlife exposed to tourism must be interpreted conservatively. While permanently altered stress responses can be detrimental, preliminary results in these wild habituated orangutans suggest that low levels of predictable disturbance can likely result in low physiological impact on these animals. PMID:22438916

Ape conservation physiology: fecal glucocorticoid responses in wild Pongo pygmaeus morio following human visitation.

PubMed

Muehlenbein, Michael P; Ancrenaz, Marc; Sakong, Rosman; Ambu, Laurentius; Prall, Sean; Fuller, Grace; Raghanti, Mary Ann

2012-01-01

Nature-based tourism can generate important revenue to support conservation of biodiversity. However, constant exposure to tourists and subsequent chronic activation of stress responses can produce pathological effects, including impaired cognition, growth, reproduction, and immunity in the same animals we are interested in protecting. Utilizing fecal samples (N = 53) from 2 wild habituated orangutans (Pongo pygmaeus morio) (in addition to 26 fecal samples from 4 wild unhabituated orangutans) in the Lower Kinabatangan Wildlife Sanctuary of Sabah, Malaysian Borneo, we predicted that i) fecal glucocorticoid metabolite concentrations would be elevated on the day after tourist visitation (indicative of normal stress response to exposure to tourists on the previous day) compared to samples taken before or during tourist visitation in wild, habituated orangutans, and ii) that samples collected from habituated animals would have lower fecal glucocorticoid metabolites than unhabituated animals not used for tourism. Among the habituated animals used for tourism, fecal glucocorticoid metabolite levels were significantly elevated in samples collected the day after tourist visitation (indicative of elevated cortisol production on the previous day during tourist visitation). Fecal glucocorticoid metabolite levels were also lower in the habituated animals compared to their age-matched unhabituated counterparts. We conclude that the habituated animals used for this singular ecotourism project are not chronically stressed, unlike other species/populations with documented permanent alterations in stress responses. Animal temperament, species, the presence of coping/escape mechanisms, social confounders, and variation in amount of tourism may explain differences among previous experiments. Acute alterations in glucocorticoid measures in wildlife exposed to tourism must be interpreted conservatively. While permanently altered stress responses can be detrimental, preliminary results in these wild habituated orangutans suggest that low levels of predictable disturbance can likely result in low physiological impact on these animals.

The prevalence of verotoxins, Escherichia coli O157:H7, and Salmonella in the feces and rumen of cattle at processing.

PubMed

Van Donkersgoed, J; Graham, T; Gannon, V

1999-05-01

Fecal samples collected from cattle at processing during a 1-year period were tested for verotoxins (VT1, VT2), Escherichia coli O157:H7, and Salmonella. Verotoxins were detected in 42.6% (95% CI, 39.8% to 45.4%), E. coli O157:H7 in 7.5% (95% CI, 6.1% to 9.1%), and Salmonella in 0.08% (95% CI, 0.004% to 0.5%) of the fecal samples. In yearling cattle, the median within-lot prevalence (percentage of positive samples within a lot) was 40% (range, 0% to 100%) for verotoxins and 0% for E. coli O157:H7 (range, 0% to 100%) and Salmonella (range, 0% to 17%). One or more fecal samples were positive for verotoxins in 80.4% (95% CI, 72.8% to 86.4%) of the lots of yearling cattle, whereas E. coli O157:H7 were detected in 33.6% (95% CI, 26.0% to 42.0%) of the lots. In cull cows, the median within-lot prevalence was 50% (range, 0% to 100%) for verotoxins and 0% (range, 0% to 100%) for E. coli O157:H7 and Salmonella (range, 0% to 0%). Verotoxins were detected in one or more fecal samples from 78.0% (95% CI, 70.4% to 84.2%) of the lots of cull cows, whereas E. coli O157:H7 were detected in only 6.0% (95% CI, 3.0% to 11.4%) of the lots of cull cows. The prevalence of verotoxins in fecal samples was lower in yearling cattle than in cull cows, whereas the prevalence of E. coli O157:H7 in fecal samples was higher in yearling cattle than in cull cows. The prevalence of E. coli O157:H7 in fecal samples was highest in the summer months. Rumen fill, body condition score, sex, type of cattle (dairy, beef), and distance travelled to the plant were not associated with the fecal prevalence of verotoxins or E. coli O157:H7. The prevalence of verotoxins in fecal samples of cull cows was associated with the source of the cattle. It was highest in cows from the auction market (52%) and farm/ranch (47%) and lowest in cows from the feedlot (31%). In rumen samples, the prevalence of verotoxins was 6.4% (95% CI, 4.2% to 9.4%), and it was 0.8% (95% CI, 0.2% to 2.3%) for E. coli O157:H7, and 0.3% (95% CI, 0.007% to 1.5%) for Salmonella.

Lactobacillus paracasei A survives gastrointestinal passage and affects the fecal microbiota of healthy infants.

PubMed

Marzotto, Marta; Maffeis, Claudio; Paternoster, Thomas; Ferrario, Rossano; Rizzotti, Lucia; Pellegrino, Maristella; Dellaglio, Franco; Torriani, Sandra

2006-11-01

This study focuses on the potentiality of a putative probiotic strain, Lactobacillus paracasei A, to survive gastrointestinal (GI) passage and modulate the resident microbiota of healthy infants. In a placebo-controlled study, 26 children aged 12-24 months received 100 g/day of either fermented milk containing strain A or pasteurized yogurt for four weeks. Fecal samples were analyzed before starting the administration, after 1, 3 and 4 weeks of consumption and after washout. The fate of strain A was followed by means of a newly developed PCR targeting a strain-specific genomic marker. The composition and dynamics of fecal microbial communities during the study were analyzed by culturing on selective media and by the PCR-denaturing gradient gel electrophoresis (DGGE) technique using universal and group-specific (Lactobacillus and Bifidobacterium) primers. The variation in enzymatic activities in infant feces during probiotic consumption was also analyzed. Strain A survived in fecal samples in most (92%) of the infants examined after 1 week of consumption, and temporarily dominated the intestinal Lactobacillus community. The administration of L. paracasei A led to a significant increment in the Lactobacillus population, while a moderate effect upon the main bacterial groups in the GI ecosystem was observed. Strain A also affected the diversity of the Lactobacillus and Bifidobacterium populations. The fecal bacterial structure of 1 - 2-year-old infants seems to combine neonate and adult-like features. The microbiota of these subjects promptly responded to probiotic consumption, later restoring the endogenous equilibrium.

Quality evaluation of processed clay soil samples

PubMed Central

Steiner-Asiedu, Matilda; Harrison, Obed Akwaa; Vuvor, Frederick; Tano-Debrah, Kwaku

2016-01-01

Introduction This study assessed the microbial quality of clay samples sold on two of the major Ghanaian markets. Methods The study was a cross-sectional assessing the evaluation of processed clay and effects it has on the nutrition of the consumers in the political capital town of Ghana. The items for the examination was processed clay soil samples. Results Staphylococcus spp and fecal coliforms including Klebsiella, Escherichia, and Shigella and Enterobacterspp were isolated from the clay samples. Samples from the Kaneshie market in Accra recorded the highest total viable counts 6.5 Log cfu/g and Staphylococcal count 5.8 Log cfu/g. For fecal coliforms, Madina market samples had the highest count 6.5 Log cfu/g and also recorded the highest levels of yeast and mould. For Koforidua, total viable count was highest in the samples from the Zongo market 6.3 Log cfu/g. Central market samples had the highest count of fecal coliforms 4.6 Log cfu/g and yeasts and moulds 6.5 Log cfu/g. “Small” market recorded the highest staphylococcal count 6.2 Log cfu/g. The water activity of the clay samples were low, and ranged between 0.65±0.01 and 0.66±0.00 for samples collected from Koforidua and Accra respectively. Conclusion The clay samples were found to contain Klebsiella spp. Escherichia, Enterobacter, Shigella spp. staphylococcus spp., yeast and mould. These have health implications when consumed. PMID:27642456

Laboratory Testing of Donors and Stool Samples for Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection

PubMed Central

Neish, Emma M.; Miller, Nancy S.; Dhere, Tanvi; Burd, Eileen M.; Carpentieri, Cynthia; Sitchenko, Kaitlin L.

2017-01-01

ABSTRACT Fecal microbiota transplantation is an efficacious and inexpensive therapy for recurrent Clostridium difficile infection, yet its safety is thought to depend on appropriate fecal donor screening. FDA guidance for regulation of this procedure is in flux, but screening and manufacture of fecal material from asymptomatic donors present many challenges to clinical laboratories. This minireview summarizes FDA regulatory changes, principles of donor selection, and recommended laboratory screening practices for fecal microbiota transplantation. PMID:28077694

Factors Influencing Fecal Contamination in Pond of Bangladesh

NASA Astrophysics Data System (ADS)

Knappett, P. S.; Escamilla, V.; Layton, A.; McKay, L. D.; Emch, M.; Mailloux, B. J.; Williams, D. E.; Huq, M. R.; Alam, M.; Farhana, L.; Ferguson, A. S.; Sayler, G. S.; Ahmed, K.; Serre, M. L.; Akita, Y.; Yunus, M.; van Geen, A.

2010-12-01

Occurrence of diarrheal disease in villages in rural Bangladesh remains relatively common, even though many households have switched to tubewell water for drinking and cooking. One factor contributing to this may be exposure to fecal contamination in ponds, which are often used for bathing and fishing. The objective of this study is to determine the dominant sources of fecal pollution in typical ponds and to explore the relationship between local population, latrine density, latrine quality and concentrations of fecal bacteria and pathogens in pond water. Forty-three ponds were sampled and analyzed for E. coli using culture-based methods and for E. coli, Bacteroides and adenovirus using quantitative PCR. Population and sanitation infrastructure were surveyed and compared to levels of pond fecal contamination. Molecular fecal source tracking using Bacteroides, determined that humans were the dominant source of fecal contamination in 79% of the ponds. Ponds directly receiving latrine effluent had the highest concentrations of fecal indicator bacteria. Concentrations of fecal indicator bacteria correlated with population surveyed within a distance of 30-70 m (p<0.01) and total latrines surveyed within 50-70 m (p<0.05). Unsanitary latrines with visible effluent within the pond drainage basin were also significantly correlated to fecal indicator concentrations (p<0.05). The vast majority of the surveyed ponds contained unsafe levels of fecal contamination primarily due to unsanitary latrines, and to lesser extent to sanitary latrines and cattle. Since the majority of fecal pollution is from humans, use of pond water could help explain the persistence of diarrheal disease in rural Bangladesh.

Fecal total iron concentration is inversely associated with fecal Lactobacillus in preschool children.

PubMed

Kalipatnapu, Sasank; Kuppuswamy, Sivaraman; Venugopal, Giriprasad; Kaliaperumal, Venkatesh; Ramadass, Balamurugan

2017-08-01

Iron deficiency is associated with stunting and poor performance in children. Oral iron supplementation is widely promoted to correct iron deficiency. However, excess iron may be toxic to beneficial luminal gut bacteria and could support growth of pathobionts. The aim of this study is to analyze the fecal total iron concentration and fecal Lactobacillus levels in a cohort of stunted and normal children. The study was undertaken in two different locations. One of them is a rural area, and the other is a semi-urban-slum area; both areas are located in the Vellore district of Tamilnadu state. Twenty children (10 stunted and 10 normal growth) aged 2 to 5 years from each area were recruited. Both groups were nearly identical demographically. Fecal samples were collected. Fecal total iron was estimated, and fecal DNA was extracted and subjected to 16S rDNA-targeted real-time PCR to determine the relative predominance of Lactobacillus and Escherichia coli. The fecal total iron concentration in rural children (3656 μg/g wet wt. of feces) was significantly higher when compared with semi-urban-slum children (114.9 μg/g wet wt. of feces, P < 0.005). Inversely, fecal Lactobacillus in rural children (median 3.18 × 10 -3 relative difference compared with total bacteria) was significantly lower when compared with semi-urban-slum children (median 59.33 × 10 -3 , p < 0.005). There was no significant change observed between normal and stunted children. E. coli levels remained unaffected. The present study documents an inverse relationship between fecal iron concentration and fecal Lactobacillus concentration in children belonging to two different localities independent of their nutritional status. © 2017 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Influence of wet distiller's grains on prevalence of Escherichia coli O157:H7 and Salmonella in feedlot cattle and antimicrobial susceptibility of generic Escherichia coli isolates.

PubMed

Edrington, Tom S; MacDonald, Jim C; Farrow, Russell L; Callaway, Todd R; Anderson, Robin C; Nisbet, David J

2010-05-01

The current research examined the inclusion of 20% wet distiller's grains (WDG) fed with steam-flaked corn (SFC) or dry-rolled corn (DRC) in diets fed to feedlot cattle on fecal prevalence of Escherichia coli O157:H7 and Salmonella. Crossbred beef heifers (n = 272; average initial body weight (BW) = 354 kg) were blocked by BW and pen size and randomly assigned to treatment. Fecal samples from freshly voided fecal pats were collected from each pen on the day cattle shipped for slaughter (237 fecal samples: 72, 125, and 40 from cattle 132, 160, and 181 days on feed, respectively). Fecal samples were cultured quantitatively and qualitatively for the above pathogens. Populations of E. coli O157:H7 and Salmonella were generally low with very few samples containing quantifiable populations. Similarly, after enrichment, few samples were E. coli O157:H7 positive in any collection with no treatment differences (p > 0.10). More samples were Salmonella positive during the first collection with an increased (p < 0.05) prevalence observed in the SFC and DRC treatments compared with DRC + WDG treatment. No other treatment differences were observed for Salmonella. Putative fecal coliform isolates (18 per treatment; first collection) were examined for antimicrobial susceptibility, and the majority were susceptible to all of the antibiotics examined. Most of the resistance was observed in the SFC (n = 3) and DRC (n = 4) treatments, and only one isolate in each of the two WDG treatments demonstrated resistance (one antibiotic each, streptomycin and tetracycline). All multidrug resistance (2-4 antibiotics) was observed in isolates cultured from the DRC and SFC treatments (n = 2 isolates in each treatment). Results of the current research found no significant effect of feeding WDG to feedlot cattle on fecal prevalence, at time of shipment for slaughter, of E. coli O157:H7, and only modest differences (decreases) in Salmonella prevalence with no apparent affect on antimicrobial susceptibility of fecal coliform isolates.

Chapter A7. Section 7.2. Fecal Indicator Viruses

USGS Publications Warehouse

Bushon, Rebecca N.

2003-01-01

More than 100 types of human pathogenic viruses may be present in fecal-contaminated waters. Coliphages are used as indicators of virus-related fecal contamination and of the microbiological quality of waters. This report provides information on the equipment, sampling protocols, and laboratory methods that are in standard use by U.S. Geological Survey (USGS) personnel for the collection of data on fecal indicator viruses.

Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area

PubMed Central

Leight, Andrew K.; Crump, Byron C.; Hood, Raleigh R.

2018-01-01

Routine monitoring of shellfish growing waters for bacteria indicative of human sewage pollution reveals little about the bacterial communities that co-occur with these indicators. This study investigated the bacterial community, potential pathogens, and fecal indicator bacteria in 40 water samples from a shellfish growing area in the Chesapeake Bay, USA. Bacterial community composition was quantified with deep sequencing of 16S rRNA gene amplicons, and absolute gene abundances were estimated with an internal standard (Thermus thermophilus genomes). Fecal coliforms were quantified by culture, and Vibrio vulnificus and V. parahaemolyticus with quantitative PCR. Fecal coliforms and V. vulnificus were detected in most samples, and a diverse assemblage of potential human pathogens were detected in all samples. These taxa followed two general patterns of abundance. Fecal coliforms and 16S rRNA genes for Enterobacteriaceae, Aeromonas, Arcobacter, Staphylococcus, and Bacteroides increased in abundance after a 1.3-inch rain event in May, and, for some taxa, after smaller rain events later in the season, suggesting that these are allochthonous organisms washed in from land. Clostridiaceae and Mycobacterium 16S rRNA gene abundances increased with day of the year and were not positively related to rainfall, suggesting that these are autochthonous organisms. Other groups followed both patterns, such as Legionella. Fecal coliform abundance did not correlate with most other taxa, but were extremely high following the large rainstorm in May when they co-occurred with a broad range of potential pathogen groups. V. vulnificus were absent during the large rainstorm, and did not correlate with 16S rRNA abundances of Vibrio spp. or most other taxa. These results highlight the complex nature of bacterial communities and the limited utility of using specific bacterial groups as indicators of pathogen presence. PMID:29593669

Linking on-farm dairy management practices to storm-flow fecal coliform loading for California coastal watersheds.

PubMed

Lewis, D J; Atwill, E R; Lennox, M S; Hou, L; Karle, B; Tate, K W

2005-08-01

How and where to improve water quality within an agricultural watershed requires data at a spatial scale that corresponds with individual management decision units on an agricultural operation. This is particularly true in the context of water quality regulations, such as Total Maximum Daily Loads (TMDLs), that identify agriculture as one source of non-point source pollution through larger tributary watershed scale and above and below water quality investigations. We have conducted a systems approach study of 10 coastal dairies and ranches to document fecal coliform concentration and loading to surface waters at the management decision unit scale. Water quality samples were collected on a storm event basis from loading units that included: manure management systems; gutters; storm drains; pastures; and corrals and lots. In addition, in-stream samples were collected above and below the dairy facilities and from a control watershed, managed for light grazing and without a dairy facility or human residence and corresponding septic system. Samples were analyzed for fecal coliform concentration by membrane filtration. Instantaneous discharge was measured for each collected sample. Storm runoff was also calculated using the curve number method (SCS, 1985). Results for a representative dairy as well as the entire 10 dairy data set are presented. Fecal coliform concentrations demonstrate high variability both within and between loading units. Fecal coliform concentrations for pastures range from 206 to 2,288,888 cfu/100 ml and for lots from 1,933 to 166,105,000 cfu/100 ml. Mean concentrations for pastures and lots are 121,298 (SE = 62,222) and 3,155,584 (SE = 1,902,713) cfu/100 ml, respectively. Fecal coliform load from units of concentrated animals and manure are significantly more than units such as pastures while storm flow amounts were significantly less. Compared with results from earlier tributary scale studies in the watershed, this systems approach has generated water quality data that is beneficial for management decisions because of its scale and representation of current management activities. These results are facilitating on-farm changes through the cooperative efforts of dairy managers, regulatory agency staff, and sources of technical and financial assistance.

Soiled-bedding Sentinel Detection of Murine Norovirus 4

PubMed Central

Manuel, Christopher A; Hsu, Charlie C; Riley, Lela K; Livingston, Robert S

2008-01-01

According to serologic surveys, murine norovirus (MNV) is the most prevalent viral pathogen infecting mice used in biomedical research. However, the use of sentinel mice to detect MNV-infected mouse populations has not been evaluated thoroughly. To this end, an experimental method of soiled bedding transfer was created to mimic a quarterly sentinel monitoring program. Soiled bedding (15 or 30 cm3) from ICR mice experimentally infected with MNV4 was transferred weekly to cages of pair-housed 4-wk-old ICR mice. After 12 wk, both mice in 80% (4 of 5) of cages receiving either 15 or 30 cm3 of soiled bedding were seropositive for MNV and were shedding virus in feces. To evaluate the stability of MNV RNA in mouse feces, fecal pellets from MNV-infected sentinel mice were stored at room temperature for as long as 14 d. After storage, all fecal samples tested positive for MNV by RT-PCR. To determine whether fecal samples could be pooled for MNV detection, 1 MNV-positive fecal pellet was combined with either 9 or 19 MNV-negative fecal pellets. All pooled fecal samples were positive for MNV by RT-PCR at both dilutions. These data indicate that although MNV-infected mouse populations can be detected by exposing sentinel mice to MNV-contaminated bedding, detection failures can occur. In addition, there was high agreement in the MNV infection status of cohoused sentinel mice. These data also demonstrate that MNV is readily detectable in pooled fecal samples and in mouse feces stored at room temperature for 2 wk. PMID:18459710

Use of Clostridium perfringens as a fecal indicator to detect intertidal disposal at backcountry marine campsites in Prince William Sound, Alaska

Treesearch

Gino Graziano; Paul Twardock; Rusty Myers; Roman Dial; David Scheel

2007-01-01

Human waste disposal is a health concern in many backcountry areas. This study measured Clostridium perfringens in beach sediments of Prince William Sound, Alaska, to detect fecal contamination resulting from intertidal disposal. Analysis involved holding times that exceeded eight hours. In repeatedly sampled stored sediments, C. perfringens...

Canine fecal contamination in a metropolitan area (Milan, north-western Italy): prevalence of intestinal parasites and evaluation of health risks.

PubMed

Zanzani, Sergio Aurelio; Di Cerbo, Anna Rita; Gazzonis, Alessia Libera; Genchi, Marco; Rinaldi, Laura; Musella, Vincenzo; Cringoli, Giuseppe; Manfredi, Maria Teresa

2014-01-01

Intestinal parasites of dogs represent a serious threat to human health due to their zoonotic potential. Thus, metropolitan areas presenting high concentrations of pets and urban fecal contamination on public areas are at sanitary risk. Major aim of this survey was to determine prevalence of zoonotic parasites in dog fecal samples collected from public soil of Milan (north-western Italy). Differences in parasites prevalence distribution were explored by a geographical information system- (GIS-) based approach, and risk factors (human density, sizes of green parks, and dog areas) were considered. The metropolitan area was divided into 157 rectangular subareas and sampling was performed following a 1-kilometer straight transect. A total of 463 fecal samples were analyzed using centrifugation-flotation technique and ELISA to detect Giardia and Cryptosporidium coproantigens. A widespread fecal contamination of soil was highlighted, being fecal samples found in 86.8% of the subareas considered. The overall prevalence of intestinal parasites was 16.63%. Zoonotic parasites were found, such as Trichuris vulpis (3.67%), Toxocara canis (1.72%), Strongyloides stercoralis (0.86%), Ancylostomatidae (0.43%), and Dipylidium caninum (0.43%). Giardia duodenalis was the most prevalent zoonotic protozoa (11.06%), followed by Cryptosporidium (1.10%). Faeces from subareas characterized by broad green areas showed to be particularly prone to infection.

Canine Fecal Contamination in a Metropolitan Area (Milan, North-Western Italy): Prevalence of Intestinal Parasites and Evaluation of Health Risks

PubMed Central

Zanzani, Sergio Aurelio; Di Cerbo, Anna Rita; Gazzonis, Alessia Libera; Genchi, Marco; Rinaldi, Laura; Musella, Vincenzo; Cringoli, Giuseppe

2014-01-01

Intestinal parasites of dogs represent a serious threat to human health due to their zoonotic potential. Thus, metropolitan areas presenting high concentrations of pets and urban fecal contamination on public areas are at sanitary risk. Major aim of this survey was to determine prevalence of zoonotic parasites in dog fecal samples collected from public soil of Milan (north-western Italy). Differences in parasites prevalence distribution were explored by a geographical information system- (GIS-) based approach, and risk factors (human density, sizes of green parks, and dog areas) were considered. The metropolitan area was divided into 157 rectangular subareas and sampling was performed following a 1-kilometer straight transect. A total of 463 fecal samples were analyzed using centrifugation-flotation technique and ELISA to detect Giardia and Cryptosporidium coproantigens. A widespread fecal contamination of soil was highlighted, being fecal samples found in 86.8% of the subareas considered. The overall prevalence of intestinal parasites was 16.63%. Zoonotic parasites were found, such as Trichuris vulpis (3.67%), Toxocara canis (1.72%), Strongyloides stercoralis (0.86%), Ancylostomatidae (0.43%), and Dipylidium caninum (0.43%). Giardia duodenalis was the most prevalent zoonotic protozoa (11.06%), followed by Cryptosporidium (1.10%). Faeces from subareas characterized by broad green areas showed to be particularly prone to infection. PMID:25478583

Evaluation of an inhouse rapid ELISA test for detection of giardia in domestic sheep (Ovis aries).

PubMed

Wilson, Jolaine M; Hankenson, F Claire

2010-11-01

Sheep (Ovis aries) are increasingly used at our institution as models of human disease. Within the research environment, routine husbandry and handling of sheep has potential for transmission of zoonotic agents, including Giardia. The prevalence of Giardia in sheep may approach 68%. Classic diagnostic testing involves microscopic examination for fecal cysts or trophozoites; however, limitations of microscopy include time, labor, and potential false-negative results due to intermittent shedding. We wished to determine whether a commercial rapid ELISA used for Giardia detection in dogs and cats could be used in sheep. Fecal samples collected from sheep (n = 93) were tested with a combination of 6 methods: reference laboratory fecal flotation, reference laboratory ELISA, inhouse fecal flotation, and commercially available tests (enzyme immunoassay, direct fluorescence antibody assay, and rapid ELISA). Prevalence of Giardia infection in facility sheep was 11.8% (11 of 93 animals). Of the 11 samples considered positive, 3 were confirmed by multiple testing methods, and 5 were positive by microscopy alone. Inhouse fecal flotation for 8 samples was positive on only 1 of 2 consecutive testing days. The rapid ELISA test exhibited 0% sensitivity for sheep giardiasis. Overall, the examined methods had low sensitivities and low positive predictive values. Despite limitations, microscopic analysis of repeat fecal samples remained the most accurate diagnostic method for ovine giardiasis among the methods tested.

The prevalence of Escherichia coli O157:H7 fecal shedding in feedlot pens is affected by the water-to-cattle ratio: A randomized controlled trial.

PubMed

Beauvais, Wendy; Gart, Elena V; Bean, Melissa; Blanco, Anthony; Wilsey, Jennifer; McWhinney, Kallie; Bryan, Laura; Krath, Mary; Yang, Ching-Yuan; Manriquez Alvarez, Diego; Paudyal, Sushil; Bryan, Kelsey; Stewart, Samantha; Cook, Peter W; Lahodny, Glenn; Baumgarten, Karina; Gautam, Raju; Nightingale, Kendra; Lawhon, Sara D; Pinedo, Pablo; Ivanek, Renata

2018-01-01

Escherichia coli O157:H7 fecal shedding in feedlot cattle is common and is a public health concern due to the risk of foodborne transmission that can result in severe, or even fatal, disease in people. Despite a large body of research, few practical and cost-effective farm-level interventions have been identified. In this study, a randomized controlled trial was conducted to assess the effect of reducing the level of water in automatically refilling water-troughs on fecal shedding of E. coli O157:H7 in feedlot cattle. Pens in a feedlot in the Texas Panhandle were randomly allocated as control (total number: 17) or intervention (total number: 18) pens. Fecal samples (2,759 in total) were collected both at baseline and three weeks after the intervention, and tested for the presence of E. coli O157:H7 using immunomagnetic bead separation and selective culture. There was a strong statistical association between sampling date and the likelihood of a fecal sample testing positive for E. coli O157:H7. Pen was also a strong predictor of fecal prevalence. Despite accounting for this high level of clustering, a statistically significant association between reduced water levels in the trough and increased prevalence of E. coli O157:H7 in the feces was observed (Odds Ratio = 1.6; 95% Confidence Interval: 1.2-2.0; Likelihood Ratio Test: p = 0.02). This is the first time that such an association has been reported, and suggests that increasing water-trough levels may be effective in reducing shedding of E. coli O157:H7 in cattle feces, although further work would be needed to test this hypothesis. Controlling E. coli O157:H7 fecal shedding at the pre-harvest level may lead to a reduced burden of human foodborne illness attributed to this pathogen in beef.

The prevalence of Escherichia coli O157:H7 fecal shedding in feedlot pens is affected by the water-to-cattle ratio: A randomized controlled trial

PubMed Central

Gart, Elena V.; Bean, Melissa; Blanco, Anthony; Wilsey, Jennifer; McWhinney, Kallie; Bryan, Laura; Krath, Mary; Yang, Ching-Yuan; Manriquez Alvarez, Diego; Paudyal, Sushil; Bryan, Kelsey; Stewart, Samantha; Cook, Peter W.; Lahodny, Glenn; Baumgarten, Karina; Gautam, Raju; Nightingale, Kendra; Lawhon, Sara D.; Pinedo, Pablo; Ivanek, Renata

2018-01-01

Escherichia coli O157:H7 fecal shedding in feedlot cattle is common and is a public health concern due to the risk of foodborne transmission that can result in severe, or even fatal, disease in people. Despite a large body of research, few practical and cost-effective farm-level interventions have been identified. In this study, a randomized controlled trial was conducted to assess the effect of reducing the level of water in automatically refilling water-troughs on fecal shedding of E. coli O157:H7 in feedlot cattle. Pens in a feedlot in the Texas Panhandle were randomly allocated as control (total number: 17) or intervention (total number: 18) pens. Fecal samples (2,759 in total) were collected both at baseline and three weeks after the intervention, and tested for the presence of E. coli O157:H7 using immunomagnetic bead separation and selective culture. There was a strong statistical association between sampling date and the likelihood of a fecal sample testing positive for E. coli O157:H7. Pen was also a strong predictor of fecal prevalence. Despite accounting for this high level of clustering, a statistically significant association between reduced water levels in the trough and increased prevalence of E. coli O157:H7 in the feces was observed (Odds Ratio = 1.6; 95% Confidence Interval: 1.2–2.0; Likelihood Ratio Test: p = 0.02). This is the first time that such an association has been reported, and suggests that increasing water-trough levels may be effective in reducing shedding of E. coli O157:H7 in cattle feces, although further work would be needed to test this hypothesis. Controlling E. coli O157:H7 fecal shedding at the pre-harvest level may lead to a reduced burden of human foodborne illness attributed to this pathogen in beef. PMID:29414986

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence.

PubMed

Stoeckel, Donald M; Stelzer, Erin A; Stogner, Robert W; Mau, David P

2011-05-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections--augmented with local observations and land-use patterns--indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. Copyright © 2011 Elsevier Ltd. All rights reserved.

Distributions of Fecal Markers in Wastewater from Different Climatic Zones for Human Fecal Pollution Tracking in Australian Surface Waters

PubMed Central

Sidhu, J. P. S.; Smith, K.; Beale, D. J.; Gyawali, P.; Toze, S.

2015-01-01

Recreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp., HFMs Bacteroides HF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia. E. coli mean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 106 gene copies per ml), followed by those of HF183 (8.0 × 105 gene copies per ml) and Enterococcus spp. (3.6 × 105 gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated that Bacteroides HF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters. PMID:26682850

Feline fecal virome reveals novel and prevalent enteric viruses

PubMed Central

Ng, Terry Fei Fan; Mesquita, João Rodrigo; Nascimento, Maria São José; Kondov, Nikola O.; Wong, Walt; Reuter, Gábor; Knowles, Nick J.; Vega, Everardo; Esona, Mathew D.; Deng, Xutao; Vinjé, Jan; Delwart, Eric

2014-01-01

Humans keep more than 80 million cats worldwide, ensuring frequent contacts with their viruses. Despite such interactions the enteric virome of cats remains poorly understood. We analyzed a fecal sample from a single healthy cat from Portugal using viral metagenomics and detected five eukaryotic viral genomes. These viruses included a novel picornavirus (proposed genus “Sakobuvirus”) and bocavirus (feline bocavirus 2), a variant of feline astrovirus 2 and sequence fragments of a highly divergent feline rotavirus and picobirnavirus. Feline sakobuvirus A represents the prototype species of a proposed new genus in the Picornaviridae family, distantly related to human salivirus and kobuvirus. Feline astroviruses (mamastrovirus 2) are the closest relatives of the classic human astroviruses (mamastrovirus 1), suggestive of past cross-species transmission. Presence of these viruses by PCR among Portuguese cats was detected in 13% (rotavirus), 7% (astrovirus), 6% (bocavirus), 4% (sakobuvirus), and 4% (picobirnavirus) of 55 feline fecal samples. Co-infections were frequent with 40% (4/10) of cats shedding more than one of these viruses. Our study provides an initial unbiased description of the feline fecal virome indicating a high level of asymptomatic infections. Availability of the genome sequences of these viruses will facilitate future tropism and disease association studies. PMID:24793097

Antibiotic resistance profiles of coagulase-positive and coagulase-negative staphylococci from pit latrine fecal sludge in a peri-urban South African community.

PubMed

Beukes, Lorika S; Schmidt, Stefan

2018-04-16

The aim of this study was to assess pit latrine samples from a peri-urban community in KwaZulu-Natal (South Africa) for the presence of multidrug-resistant (MDR) Staphylococcus spp. Standard procedures were used to isolate Staphylococcus spp. from pit latrine fecal sludge samples, with confirmation at genus level by polymerase chain reaction (PCR). Sixty-eight randomly selected pit latrine Staphylococcus spp. isolates were further characterized by using established disk diffusion procedures. An average Staphylococcus spp. count of 2.1 × 10 5  CFU per g fecal material was established using two randomly selected pit latrine samples. Of the 68-selected Staphylococcus spp. pit latrine isolates, 49% were identified as coagulase positive, 51% as coagulase negative and 65% (12 coagulase positive, 32 coagulase negative isolates) were categorized as MDR. The majority (66/68) of Staphylococcus spp. isolates displayed resistance to fusidic acid while only 5/68 isolates displayed resistance to chloramphenicol. The pit latrine samples analyzed in this study are a source of MDR Staphylococcus spp., highlighting the need for proper hygiene and sanitation regimes in rural communities using these facilities.

Microbiological quality of Puget Sound Basin streams and identification of contaminant sources

USGS Publications Warehouse

Embrey, S.S.

2001-01-01

Fecal coliforms, Escherichia coli, enterococci, and somatic coliphages were detected in samples from 31 sites on streams draining urban and agricultural regions of the Puget Sound Basin Lowlands. Densities of bacteria in 48 and 71 percent of the samples exceeded U.S. Environmental Protection Agency's freshwater recreation criteria for Escherichia coli and enterococci, respectively, and 81 percent exceeded Washington State fecal coliform standards. Male-specific coliphages were detected in samples from 15 sites. Male-specific F+RNA coliphages isolated from samples taken at South Fork Thornton and Longfellow Creeks were serotyped as Group II, implicating humans as potential contaminant sources. These two sites are located in residential, urban areas. F+RNA coliphages in samples from 10 other sites, mostly in agricultural or rural areas, were serotyped as Group I, implicating non-human animals as likely sources. Chemicals common to wastewater, including fecal sterols, were detected in samples from several urban streams, and also implicate humans, at least in part, as possible sources of fecal bacteria and viruses to the streams.

Integral strategy for evaluation of fecal indicator performance in bird-influenced saline inland waters.

PubMed

Kirschner, Alexander K T; Zechmeister, Thomas C; Kavka, Gerhard G; Beiwl, Christian; Herzig, Alois; Mach, Robert L; Farnleitner, Andreas H

2004-12-01

Wild birds are an important nonpoint source of fecal contamination of surface waters, but their contribution to fecal pollution is mostly difficult to estimate. Thus, to evaluate the relation between feces production and input of fecal indicator bacteria (FIB) into aquatic environments by wild waterfowl, we introduced a new holistic approach for evaluating the performance of FIB in six shallow saline habitats. For this, we monitored bird abundance, fecal pellet production, and the abundance of FIB concomitantly with a set of environmental variables over a 9-month period. For estimating fecal pellet production, a new protocol of fecal pellet counting was introduced, which was called fecal taxation (FTX). We could show that, over the whole range of investigated habitats, bird abundance, FTX values, and FIB abundance were highly significantly correlated and could demonstrate the good applicability of the FTX as a meaningful surrogate parameter for recent bird abundances and fecal contamination by birds in shallow aquatic ecosystems. Presumptive enterococci (ENT) were an excellent surrogate parameter of recent fecal contamination in these saline environments for samples collected at biweekly to monthly sampling intervals while presumptive Escherichia coli and fecal coliforms (FC) were often undetectable. Significant negative correlations with salinity indicated that E. coli and FC survival was hampered by osmotic stress. Statistical analyses further revealed that fecal pollution-associated parameters represented one system component independent from other environmental variables and that, besides feces production, rainfall, total suspended solids (direct), and trophy (indirect) had significant positive effects on ENT concentrations. Our holistic approach of linking bird abundance, feces production, and FIB detection with environmental variables may serve as a powerful model for application to other aquatic ecosystems.

Integral Strategy for Evaluation of Fecal Indicator Performance in Bird-Influenced Saline Inland Waters

PubMed Central

Kirschner, Alexander K. T.; Zechmeister, Thomas C.; Kavka, Gerhard G.; Beiwl, Christian; Herzig, Alois; Mach, Robert L.; Farnleitner, Andreas H.

2004-01-01

Wild birds are an important nonpoint source of fecal contamination of surface waters, but their contribution to fecal pollution is mostly difficult to estimate. Thus, to evaluate the relation between feces production and input of fecal indicator bacteria (FIB) into aquatic environments by wild waterfowl, we introduced a new holistic approach for evaluating the performance of FIB in six shallow saline habitats. For this, we monitored bird abundance, fecal pellet production, and the abundance of FIB concomitantly with a set of environmental variables over a 9-month period. For estimating fecal pellet production, a new protocol of fecal pellet counting was introduced, which was called fecal taxation (FTX). We could show that, over the whole range of investigated habitats, bird abundance, FTX values, and FIB abundance were highly significantly correlated and could demonstrate the good applicability of the FTX as a meaningful surrogate parameter for recent bird abundances and fecal contamination by birds in shallow aquatic ecosystems. Presumptive enterococci (ENT) were an excellent surrogate parameter of recent fecal contamination in these saline environments for samples collected at biweekly to monthly sampling intervals while presumptive Escherichia coli and fecal coliforms (FC) were often undetectable. Significant negative correlations with salinity indicated that E. coli and FC survival was hampered by osmotic stress. Statistical analyses further revealed that fecal pollution-associated parameters represented one system component independent from other environmental variables and that, besides feces production, rainfall, total suspended solids (direct), and trophy (indirect) had significant positive effects on ENT concentrations. Our holistic approach of linking bird abundance, feces production, and FIB detection with environmental variables may serve as a powerful model for application to other aquatic ecosystems. PMID:15574941

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents.

PubMed

Mayer, René E; Reischer, Georg H; Ixenmaier, Simone K; Derx, Julia; Blaschke, Alfred Paul; Ebdon, James E; Linke, Rita; Egle, Lukas; Ahmed, Warish; Blanch, Anicet R; Byamukama, Denis; Savill, Marion; Mushi, Douglas; Cristóbal, Héctor A; Edge, Thomas A; Schade, Margit A; Aslan, Asli; Brooks, Yolanda M; Sommer, Regina; Masago, Yoshifumi; Sato, Maria I; Taylor, Huw D; Rose, Joan B; Wuertz, Stefan; Shanks, Orin C; Piringer, Harald; Mach, Robert L; Savio, Domenico; Zessner, Matthias; Farnleitner, Andreas H

2018-05-01

Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750-4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log 10 7.2-8.0 marker equivalents (ME) 100 mL -1 ) and biologically treated wastewater samples (median log 10 4.6-6.0 ME 100 mL -1 ) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.

OCCURRENCE OF INTRINSIC VANCOMYCIN RESISTANT ENTEROCOCCI IN ANIMAL FECES

EPA Science Inventory

A survey was conducted to determine the occurrence of vancomycin resistant enterococci (VRE) in animal and human fecal samples. Fecal samples from 14 animal species and humans were analyzed by quantitative culture for enterococci and VRE. Over 800 VRE isolates were characterize...

Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples

EPA Science Inventory

There are numerous PCR-based methods available to characterize human fecal pollution in ambient waters. Each assay employs distinct oligonucleotides and many target different genes and microorganisms leading to potential variations in method performance. Laboratory comparisons ...

Investigation of bacterial diversity in the feces of cattle fed different diets.

PubMed

Kim, M; Kim, J; Kuehn, L A; Bono, J L; Berry, E D; Kalchayanand, N; Freetly, H C; Benson, A K; Wells, J E

2014-02-01

The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.

Correlation of quantitative PCR for a poultry-specific brevibacterium marker gene with bacterial and chemical indicators of water pollution in a watershed impacted by land application of poultry litter.

PubMed

Weidhaas, Jennifer L; Macbeth, Tamzen W; Olsen, Roger L; Harwood, Valerie J

2011-03-01

The impact of fecal contamination from human and agricultural animal waste on water quality is a major public health concern. Identification of the dominant source(s) of fecal pollution in a watershed is necessary for assessing the safety of recreational water and protecting water resources. A field study was conducted using quantitative PCR (qPCR) for the 16S rRNA gene of Brevibacterium sp. LA35 to track feces-contaminated poultry litter in environmental samples. Based on sensitivity and specificity characteristics of the qPCR method, the Bayesian conditional probability that detection of the LA35 marker gene in a water sample represented a true-positive result was 93%. The marker's covariance with fecal indicator bacteria (FIB) and metals associated with poultry litter was also assessed in litter, runoff, surface water, and groundwater samples. LA35 was detected in water and soil samples collected throughout the watershed, and its concentration covaried with concentrations of Escherichia coli, enterococci, As, Cu, P, and Zn. Significantly greater concentrations of FIB, As, Cu, P, and Zn were observed in edge-of-field runoff samples in which LA35 was detected, compared to samples in which it was not detected. Furthermore, As, Cu, P, and Zn concentrations covaried in environmental samples in which LA35 was detected and typically did not in samples in which the marker gene was not detected. The covariance of the poultry-specific LA35 marker gene with these known contaminants from poultry feces provides further evidence that it is a useful tool for assessing the impact of poultry-derived fecal pollution in environmental waters.

State of the art molecular markers for fecal pollution source tracking in water.

PubMed

Roslev, Peter; Bukh, Annette S

2011-03-01

Most environmental waters are susceptible to fecal contamination from animal and/or human pollution sources. To attenuate or eliminate such contamination, it is often critical that the pollution sources are rapidly and correctly identified. Fecal pollution source tracking (FST) is a promising research area that aims to identify the origin(s) of fecal pollution in water. This mini-review focuses on the potentials and limitations of library independent molecular markers that are exclusively or strongly associated with fecal pollution from humans and different animals. Fecal-source-associated molecular markers include nucleic acid sequences from prokaryotes and viruses associated with specific biological hosts, but also sequences such as mitochondrial DNA retrieved directly from humans and animals. However, some fecal-source-associated markers may not be absolutely specific for a given source type, and apparent specificity and frequency established in early studies are sometimes compromised by new studies suggesting variation in specificity and abundance on a regional, global and/or temporal scale. It is therefore recommended that FST studies are based on carefully selected arrays of markers, and that identification of human and animal contributions are based on a multi-marker toolkit with several markers for each source category. Furthermore, future FST studies should benefit from increased knowledge regarding sampling strategies and temporal and spatial variability of marker ratios. It will also be important to obtain a better understanding of marker persistence and the quantitative relationship between marker abundance and the relative contribution from individual fecal pollution source types. A combination of enhanced pathogen screening methods, and validated quantitative source tracking techniques could then contribute significantly to future management of environmental water quality including improved microbial risk assessment.

Storm loads of culturable and molecular fecal indicators in an inland urban stream.

PubMed

Liao, Hehuan; Krometis, Leigh-Anne H; Cully Hession, W; Benitez, Romina; Sawyer, Richard; Schaberg, Erin; von Wagoner, Emily; Badgley, Brian D

2015-10-15

Elevated concentrations of fecal indicator bacteria in receiving waters during wet-weather flows are a considerable public health concern that is likely to be exacerbated by future climate change and urbanization. Knowledge of factors driving the fate and transport of fecal indicator bacteria in stormwater is limited, and even less is known about molecular fecal indicators, which may eventually supplant traditional culturable indicators. In this study, concentrations and loading rates of both culturable and molecular fecal indicators were quantified throughout six storm events in an instrumented inland urban stream. While both concentrations and loading rates of each fecal indicator increased rapidly during the rising limb of the storm hydrographs, it is the loading rates rather than instantaneous concentrations that provide a better estimate of transport through the stream during the entire storm. Concentrations of general fecal indicators (both culturable and molecular) correlated most highly with each other during storm events but not with the human-associated HF183 Bacteroides marker. Event loads of general fecal indicators most strongly correlated with total runoff volume, maximum discharge, and maximum turbidity, while event loads of HF183 most strongly correlated with the time to peak flow in a hydrograph. These observations suggest that collection of multiple samples during a storm event is critical for accurate predictions of fecal indicator loading rates and total loads during wet-weather flows, which are required for effective watershed management. In addition, existing predictive models based on general fecal indicators may not be sufficient to predict source-specific genetic markers of fecal contamination. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of Quantitative PCR Assays Targeting the 16S rRNA Genes of Enterococcus spp. and Their Application to the Identification of Enterococcus Species in Environmental Samples

PubMed Central

Ryu, Hodon; Henson, Michael; Elk, Michael; Toledo-Hernandez, Carlos; Griffith, John; Blackwood, Denene; Noble, Rachel; Gourmelon, Michèle; Glassmeyer, Susan

2013-01-01

The detection of environmental enterococci has been determined primarily by using culture-based techniques that might exclude some enterococcal species as well as those that are nonculturable. To address this, the relative abundances of enterococci were examined by challenging fecal and water samples against a currently available genus-specific assay (Entero1). To determine the diversity of enterococcal species, 16S rRNA gene-based group-specific quantitative PCR (qPCR) assays were developed and evaluated against eight of the most common environmental enterococcal species. Partial 16S rRNA gene sequences of 439 presumptive environmental enterococcal strains were analyzed to study further the diversity of enterococci and to confirm the specificities of group-specific assays. The group-specific qPCR assays showed relatively high amplification rates with targeted species (>98%), although some assays cross-amplified with nontargeted species (1.3 to 6.5%). The results with the group-specific assays also showed that different enterococcal species co-occurred in most fecal samples. The most abundant enterococci in water and fecal samples were Enterococcus faecalis and Enterococcus faecium, although we identified more water isolates as Enterococcus casseliflavus than as any of the other species. The prevalence of the Entero1 marker was in agreement with the combined number of positive signals determined by the group-specific assays in most fecal samples, except in gull feces. On the other hand, the number of group-specific assay signals was lower in all water samples tested, suggesting that other enterococcal species are present in these samples. While the results highlight the value of genus- and group-specific assays for detecting the major enterococcal groups in environmental water samples, additional studies are needed to determine further the diversity, distributions, and relative abundances of all enterococcal species found in water. PMID:23087032

Detection of Bovine and Porcine Adenoviruses for Tracing the Source of Fecal Contamination

PubMed Central

Maluquer de Motes, Carlos; Clemente-Casares, Pilar; Hundesa, Ayalkibet; Martín, Margarita; Girones, Rosina

2004-01-01

In this study, a molecular procedure for the detection of adenoviruses of animal origin was developed to evaluate the level of excretion of these viruses by swine and cattle and to design a test to facilitate the tracing of specific sources of environmental viral contamination. Two sets of oligonucleotides were designed, one to detect porcine adenoviruses and the other to detect bovine and ovine adenoviruses. The specificity of the assays was assessed in 31 fecal samples and 12 sewage samples that were collected monthly during a 1-year period. The data also provided information on the environmental prevalence of animal adenoviruses. Porcine adenoviruses were detected in 17 of 24 (70%) pools of swine samples studied, with most isolates being closely related to serotype 3. Bovine adenoviruses were present in 6 of 8 (75%) pools studied, with strains belonging to the genera Mastadenovirus and Atadenovirus and being similar to bovine adenoviruses of types 2, 4, and 7. These sets of primers produced negative results in nested PCR assays when human adenovirus controls and urban-sewage samples were tested. Likewise, the sets of primers previously designed for detection of human adenovirus also produced negative results with animal adenoviruses. These results indicate the importance of further studies to evaluate the usefulness of these tests to trace the source of fecal contamination in water and food and for environmental studies. PMID:15006765

Detection of bovine and porcine adenoviruses for tracing the source of fecal contamination.

PubMed

Maluquer de Motes, Carlos; Clemente-Casares, Pilar; Hundesa, Ayalkibet; Martín, Margarita; Girones, Rosina

2004-03-01

In this study, a molecular procedure for the detection of adenoviruses of animal origin was developed to evaluate the level of excretion of these viruses by swine and cattle and to design a test to facilitate the tracing of specific sources of environmental viral contamination. Two sets of oligonucleotides were designed, one to detect porcine adenoviruses and the other to detect bovine and ovine adenoviruses. The specificity of the assays was assessed in 31 fecal samples and 12 sewage samples that were collected monthly during a 1-year period. The data also provided information on the environmental prevalence of animal adenoviruses. Porcine adenoviruses were detected in 17 of 24 (70%) pools of swine samples studied, with most isolates being closely related to serotype 3. Bovine adenoviruses were present in 6 of 8 (75%) pools studied, with strains belonging to the genera Mastadenovirus and Atadenovirus and being similar to bovine adenoviruses of types 2, 4, and 7. These sets of primers produced negative results in nested PCR assays when human adenovirus controls and urban-sewage samples were tested. Likewise, the sets of primers previously designed for detection of human adenovirus also produced negative results with animal adenoviruses. These results indicate the importance of further studies to evaluate the usefulness of these tests to trace the source of fecal contamination in water and food and for environmental studies.

Molecular Determination of Fasciola Spp. Isolates from Domestic Ruminants Fecal Samples in the Northwest of Iran

PubMed Central

IMANI BARAN, Abbas; CHERAGHI SARAY, Habib; KATIRAEE, Farzad

2017-01-01

Background: Fasciola species are the main causes for fascioliasis with great financial losses and are among the most important food/water-borne parasites worldwide. The basic proceedings such as epidemiology and effective control of fascioliasis rely mainly on precise identification of Fasciola species. The present study was conducted to determine the Fasciola species in ruminant fecal samples from East Azerbaijan Province in Iran. Methods: Overall, 2012 fecal samples were collected and processed initially for microscopic examination of Fasciola eggs in 2014–15. Then, recovered eggs were subjected to molecular identification. A fragment of 618 bp of the 28S rRNA gene pertaining to Fasciola genus was amplified under PCR. The amplified fragment was restricted by fast digest Ava II enzyme in order to a Restriction Fragment Length Polymorphism. Results: Based on microscopic examination, 72 samples were infected, from which, 10 and 62 cases pertained to cattle and sheep samples respectively. Based on RFLP, the PCR products restricted by the Ava II restriction enzyme produced 529 bp fragments only. According to the positive controls, all restriction patterns were related to Fasciola hepatica, while no restriction patterns were linked to F. gigantica. Conclusion: Based on PCR-RFLP, F. hepatica was dominant species in animals of the studied areas and no evidence of F. gigantica was observed. Therefore, further field studies to verify these results are suggested. PMID:28761485

Diseases and parasites in wolves of the Riding Mountain National Park region, Manitoba, Canada.

PubMed

Stronen, Astrid V; Sallows, Tim; Forbes, Graham J; Wagner, Brent; Paquet, Paul C

2011-01-01

We examined wolf (Canis lupus) blood and fecal samples from the Riding Mountain National Park (RMNP) region of Manitoba, Canada. In 601 fecal samples collected during two study periods in RMNP and the Duck Mountain Provincial Park and Forest (DMPPF) we found gastrointestinal helminth eggs from Alaria sp. (15.5%), Capillaria sp. (1.0%), taeniid tapeworms (30.8%), Toxascaris sp. (1.7%), Toxocara sp. (0.2%), Trichuris sp. (2.2%), and Moniezia sp. (0.5%). In addition, we found Demodex sp. (0.2%) and the protozoal cysts/oocysts of Sarcocystis sp. (37.3%), Cryptosporidium sp. (1.2%), coccidia (Isospora sp. or Eimeria sp.) (1.7%), and Giardia sp. (29.5%). No fecal shedding of canine parvovirus (CPV, n=387) was detected. All 18 blood samples collected in RMNP showed CPV exposure and eight of 18 blood samples indicated canine distemper virus (CDV) exposure. One wolf died from CDV. Our results are consistent with previous findings on pathogens affecting wolves and with high Giardia sp. prevalence in wolves inhabiting agricultural regions.

Elevation and vegetation determine Cryptosporidium oocyst shedding by yellow-bellied marmots (Marmota flaviventris) in the Sierra Nevada Mountains.

PubMed

Montecino-Latorre, Diego; Li, Xunde; Xiao, Chengling; Atwill, Edward R

2015-08-01

Wildlife are increasingly recognized as important biological reservoirs of zoonotic species of Cryptosporidium that might contaminate water and cause human exposure to this protozoal parasite. The habitat range of the yellow-bellied marmot (Marmota flaviventris) overlaps extensively with the watershed boundaries of municipal water supplies for California communities along the foothills of the Sierra Nevada. We conducted a cross-sectional epidemiological study to estimate the fecal shedding of Cryptosporidium oocysts by yellow-bellied marmots and to quantify the environmental loading rate and determine risk factors for Cryptosporidium fecal shedding in this montane wildlife species. The observed proportion of Cryptosporidium positive fecal samples was 14.7% (33/224, positive number relative to total number samples) and the environmental loading rate was estimated to be 10,693 oocysts animal(-1) day(-1). Fecal shedding was associated with the elevation and vegetation status of their habitat. Based on a portion of the 18s rRNA gene sequence of 2 isolates, the Cryptosporidium found in Marmota flaviventris were 99.88%-100% match to multiple isolates of C. parvum in the GenBank.

Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi).

PubMed

Kylie, Jennifer; Weese, J Scott; Turner, Patricia V

2018-04-27

Rabbits are cecotrophic, hindgut-fermenters that rely heavily on their gastrointestinal microbiota for optimal digestion of plant-based diets. Dysbiosis, caused by disruption of the gastrointestinal microbiota, is known to predispose rabbits to rabbit enteritis complex (REC), a major cause of morbidity and mortality. The objectives of this study were to describe the fecal microbiota of domestic rabbits from a variety of settings (commercial meat, companion, laboratory, and shelter) and to identify how factors such as age, season, and routine antimicrobial use affect the fecal microbiota composition. A total of 86 pooled commercial meat, 54 companion, 14 pooled laboratory, and 14 shelter rabbit fecal samples were evaluated using 16S rRNA gene sequencing of the V4 region. In all sample types, the predominant bacterial phylum was Firmicutes. Other commonly identified phyla (composing ≥ 1% of the total microbiota composition) were Verrucomicrobia, Proteobacteria, and Bacteroidetes. Significant differences in composition were noted between commercial, companion, laboratory, and shelter rabbit samples for proportions of Verrucomicrobia (P < 0.01), Proteobacteria (P < 0.01), and Lentisphaerae (P = 0.01) within the total microbiota. Within the commercial meat rabbit samples, significant differences between the microbiota composition of growers (n = 42) and does (n = 44) were limited to one unclassified Firmicutes (P = 0.03) and no differences were identified at the phylum level. Significant differences were present between fecal samples taken from rabbits during the summer (n = 44) compared to the winter (n = 42), with Firmicutes (P = 0.04), Verrucomicrobia (P = 0.03), Proteobacteria (P = 0.02), Deinococcus-Thermus (P = 0.04), Armatimonadates (P = 0.003), and Actinobacteria (P = 0.03) forming significantly different proportions of the microbiota. The only significant difference in composition between those farms that routinely reported antimicrobial use and those that did not was in one unclassified Bacteroidetes (P < 0.05) and no differences were identified at the phylum level. Rabbit husbandry and diet, in addition to season, significantly influence the fecal microbiota composition of domestic rabbits, while age of the rabbit post-weaning has minimal impact.

Duplex quantitative real-time PCR assay for the detection and discrimination of the eggs of Toxocara canis and Toxocara cati (Nematoda, Ascaridoidea) in soil and fecal samples

PubMed Central

2012-01-01

Background Toxocarosis is a zoonotic disease caused by Toxocara canis (T. canis) and/or Toxocara cati (T. cati), two worldwide distributed roundworms which are parasites of canids and felids, respectively. Infections of humans occur through ingestion of embryonated eggs of T. canis or T. cati, when playing with soils contaminated with dogs or cats feces. Accordingly, the assessment of potential contamination of these areas with these roundworms eggs is paramount. Methods A duplex quantitative real-time PCR (2qPCR) targeting the ribosomal RNA gene internal transcribed spacer (ITS2) has been developed and used for rapid and specific identification of T. canis and T. cati eggs in fecal and soil samples. The assay was set up on DNA samples extracted from 53 adult worms including T. canis, T. cati, T. leonina, Ascaris suum (A. suum) and Parascaris equorum (P. equorum). The assay was used to assess the presence of T. cati eggs in several samples, including 12 clean soil samples spiked with eggs of either T. cati or A. suum, 10 actual soil samples randomly collected from playgrounds in Brussels, and fecal samples from cats, dogs, and other animals. 2qPCR results on dogs and cats fecal samples were compared with results from microscopic examination. Results 2qPCR assay allowed specific detection of T. canis and T. cati, whether adult worms, eggs spiked in soil or fecal samples. The 2qPCR limit of detection (LOD) in spiked soil samples was 2 eggs per g of soil for a turnaround time of 3 hours. A perfect concordance was observed between 2qPCR assay and microscopic examination on dogs and cats feces. Conclusion The newly developed 2qPCR assay can be useful for high throughput prospective or retrospective detection of T.canis and/or T. cati eggs in fecal samples as well as in soil samples from playgrounds, parks and sandpits. PMID:23216873

Sample handling factors affecting the enumeration of lactobacilli and cellulolytic bacteria in equine feces

USDA-ARS?s Scientific Manuscript database

The objectives were to compare media types and evaluate the effects of fecal storage time and temperature on the enumeration of cellulolytic bacteria and lactobacilli from horses. Fecal samples were collected from horses (n = 3) and transported to the lab (CO2, 37 ºC, 0.5 h). The samples were assign...

Novel and canine genotypes of Giardia duodenalis in harbor seals ( Phoca vitulina richardsi).

PubMed

Gaydos, J K; Miller, W A; Johnson, C; Zornetzer, H; Melli, A; Packham, A; Jeffries, S J; Lance, M M; Conrad, P A

2008-12-01

Feces of harbor seals (Phoca vitulina richardsi) and hybrid glaucous-winged/western gulls (Larus glaucescens / occidentalis) from Washington State's inland marine waters were examined for Giardia and Cryptosporidium spp. to determine if genotypes carried by these wildlife species were the same genotypes that commonly infect humans and domestic animals. Using immunomagnetic separation followed by direct fluorescent antibody detection, Giardia spp. cysts were detected in 42% of seal fecal samples (41/97). Giardia-positive samples came from 90% of the sites (9/10) and the prevalence of positive seal fecal samples differed significantly among study sites. Fecal samples collected from seal haulout sites with over 400 animals were 4.7 times more likely to have Giardia spp. cysts than samples collected at smaller haulout sites. In gulls, a single Giardia sp. cyst was detected in 4% of fecal samples (3/78). Cryptosporidium spp. oocysts were not detected in any of the seals or gulls tested. Sequence analysis of a 398 bp segment of G. duodenalis DNA at the glutamate dehydrogenase locus suggested that 11 isolates originating from seals throughout the region were a novel genotype and 3 isolates obtained from a single site in south Puget Sound were the G. duodenalis canine genotype D. Real-time TaqMan PCR amplification and subsequent sequencing of a 52 bp small subunit ribosomal DNA region from novel harbor seal genotype isolates showed sequence homology to canine genotypes C and D. Sequence analysis of the 52 bp small subunit ribosomal DNA products from the 3 canine genotype isolates from seals produced mixed sequences at could not be evaluated.

The effect of clinical outbreaks of salmonellosis on the prevalence of fecal Salmonella shedding among dairy cattle in New York.

PubMed

Cummings, Kevin J; Warnick, Lorin D; Elton, Mara; Gröhn, Yrjo T; McDonough, Patrick L; Siler, Julie D

2010-07-01

The objective of this study was to determine if the within-herd prevalence of fecal Salmonella shedding is higher in dairy herds with clinical outbreaks of disease, as compared to herds with subclinical infections only. Data were collected prospectively from dairy herds throughout New York that had at least 150 lactating cows and that received clinical service from participating veterinarians. After enrollment, Salmonella surveillance consisted of both environmental screening and disease monitoring within the herd. Herds positive by either environmental or fecal culture were sampled during three visits to estimate the within-herd prevalence of Salmonella. We characterized isolates by serovar and antimicrobial resistance pattern. Among 57 enrolled herds, 44 (77%) yielded Salmonella-positive samples during the study period; 27 (61%) of the positive herds had Salmonella isolated from environmental samples only, and 17 (39%) had one or more laboratory-confirmed clinical cases. The within-herd prevalence of fecal Salmonella shedding ranged from 0 to 53%. Salmonella Cerro was the predominant serovar, accounting for 56% of all isolates. Antimicrobial resistance ranged from zero to nine drugs, and 14 (32%) of the positive farms generated multidrug-resistant isolates. Herds with laboratory-confirmed clinical cases had a higher prevalence of fecal Salmonella shedding than herds that only generated positive environmental samples, as estimated by a Poisson regression model (prevalence ratio, 2.7; p = 0.01). An association between dairy herd outbreaks of salmonellosis and a higher prevalence of asymptomatic shedding should help guide strategies for reducing the public health threat of Salmonella, as the ability to recognize high-risk herds by clinical laboratory submissions presents an obvious opportunity to maximize food safety at the preharvest level. This is in contrast with other foodborne zoonotic pathogens, such as Campylobacter jejuni and Escherichia coli O157:H7, which occur widely in adult cattle without accompanying clinical disease.

The Effect of Clinical Outbreaks of Salmonellosis on the Prevalence of Fecal Salmonella Shedding Among Dairy Cattle in New York

PubMed Central

Warnick, Lorin D.; Elton, Mara; Gröhn, Yrjo T.; McDonough, Patrick L.; Siler, Julie D.

2010-01-01

Abstract The objective of this study was to determine if the within-herd prevalence of fecal Salmonella shedding is higher in dairy herds with clinical outbreaks of disease, as compared to herds with subclinical infections only. Data were collected prospectively from dairy herds throughout New York that had at least 150 lactating cows and that received clinical service from participating veterinarians. After enrollment, Salmonella surveillance consisted of both environmental screening and disease monitoring within the herd. Herds positive by either environmental or fecal culture were sampled during three visits to estimate the within-herd prevalence of Salmonella. We characterized isolates by serovar and antimicrobial resistance pattern. Among 57 enrolled herds, 44 (77%) yielded Salmonella-positive samples during the study period; 27 (61%) of the positive herds had Salmonella isolated from environmental samples only, and 17 (39%) had one or more laboratory-confirmed clinical cases. The within-herd prevalence of fecal Salmonella shedding ranged from 0 to 53%. Salmonella Cerro was the predominant serovar, accounting for 56% of all isolates. Antimicrobial resistance ranged from zero to nine drugs, and 14 (32%) of the positive farms generated multidrug-resistant isolates. Herds with laboratory-confirmed clinical cases had a higher prevalence of fecal Salmonella shedding than herds that only generated positive environmental samples, as estimated by a Poisson regression model (prevalence ratio, 2.7; p = 0.01). An association between dairy herd outbreaks of salmonellosis and a higher prevalence of asymptomatic shedding should help guide strategies for reducing the public health threat of Salmonella, as the ability to recognize high-risk herds by clinical laboratory submissions presents an obvious opportunity to maximize food safety at the preharvest level. This is in contrast with other foodborne zoonotic pathogens, such as Campylobacter jejuni and Escherichia coli O157:H7, which occur widely in adult cattle without accompanying clinical disease. PMID:20353290

Quantification of Human and Animal Viruses to Differentiate the Origin of the Fecal Contamination Present in Environmental Samples

PubMed Central

Bofill-Mas, Sílvia; Rusiñol, Marta; Fernandez-Cassi, Xavier; Carratalà, Anna; Hundesa, Ayalkibet

2013-01-01

Many different viruses are excreted by humans and animals and are frequently detected in fecal contaminated waters causing public health concerns. Classical bacterial indicator such as E. coli and enterococci could fail to predict the risk for waterborne pathogens such as viruses. Moreover, the presence and levels of bacterial indicators do not always correlate with the presence and concentration of viruses, especially when these indicators are present in low concentrations. Our research group has proposed new viral indicators and methodologies for determining the presence of fecal pollution in environmental samples as well as for tracing the origin of this fecal contamination (microbial source tracking). In this paper, we examine to what extent have these indicators been applied by the scientific community. Recently, quantitative assays for quantification of poultry and ovine viruses have also been described. Overall, quantification by qPCR of human adenoviruses and human polyomavirus JC, porcine adenoviruses, bovine polyomaviruses, chicken/turkey parvoviruses, and ovine polyomaviruses is suggested as a toolbox for the identification of human, porcine, bovine, poultry, and ovine fecal pollution in environmental samples. PMID:23762826

DETECTION OF INTRINSIC VANCOMYCIN RESISTANT ENTEROCOCCI IN ANIMAL AND HUMAN FECES

EPA Science Inventory

A survey was conducted to determine the occurrence of vancomycin resistant enterococci (VRE) in animal and human fecal samples. Fecal samples from 14 animal species and humans were analyzed by quantitative culture for enterococci and VRE. Over 800 VRE isolates were characterize...

Seasonal variation of fecal contamination in drinking water sources in developing countries: a systematic review.

PubMed

Kostyla, Caroline; Bain, Rob; Cronk, Ryan; Bartram, Jamie

2015-05-01

Accounting for fecal contamination of drinking water sources is an important step in improving monitoring of global access to safe drinking water. Fecal contamination varies with time while its monitoring is often infrequent. We sought to understand seasonal trends in fecal contamination to guide best practices to capture seasonal variation and ascertain the extent to which the results of a single sample may overestimate compliance with health guidelines. The findings from 22 studies from developing countries written in English and identified through a systematic review were analyzed. Fecal contamination in improved drinking water sources was shown to follow a statistically significant seasonal trend of greater contamination during the wet season (p<0.001). This trend was consistent across fecal indicator bacteria, five source types, twelve Köppen-Geiger climate zones, and across both rural and urban areas. Guidance on seasonally representative water quality monitoring by the World Health Organization and national water quality agencies could lead to improved assessments of access to safe drinking water. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of the Multiple-sample means with composite sample results for fecal indicator bacteria by quantitative PCR and culture

EPA Science Inventory

ABSTRACT: Few studies have addressed the efficacy of composite sampling for measurement of indicator bacteria by QPCR. In this study, composite results were compared to single sample results for culture- and QPCR-based water quality monitoring. Composite results for both methods ...

The impact of ecological variability on the reproductive endocrinology of wild female African elephants.

PubMed

Wittemyer, George; Ganswindt, André; Hodges, Keith

2007-03-01

Non-invasive endocrine methods enable investigation of the relationship between ecological variation and ovarian activity and how this impacts on demographic processes. The underlying physiological factors driving high variation in inter-calving intervals among multi-parous African elephants offer an interesting system for such an investigation. This study investigates the relationship between Normalized Differential Vegetation Index (NDVI), an ecosystem surrogate measure of primary productivity, and fecal progestin concentrations among wild female elephants. Matched fecal samples and behavioral data on reproductive activity were collected from 37 focal individuals during the two-year study. Linear mixed models were used to explore the relationship between fecal 5alpha-pregnane-3-ol-20-one concentrations and the independent variables of NDVI, calf sex, female age, gestation day, and time since last parturition. Among both non-pregnant and pregnant females, fecal 5alpha-pregnane-3-ol-20-one concentrations were significantly correlated with time-specific NDVI indicating a strong relationship between ecological conditions and endocrine activity regulating reproduction. In addition, the age of a female and time since her last parturition impacted hormone concentrations. These results indicate that the identification of an individual's reproductive status from a single hormone sample is possible, but difficult to achieve in practice since numerous independent factors, particularly season, impact fecal hormone concentrations. Regardless of season, however, fecal 5alpha-pregnane-3-ol-20-one concentrations below 1 microg/g were exclusively collected from non-pregnant females, which could be used as a threshold value to identify non-pregnant individuals. Collectively the information generated contributes to a better understanding of environmental regulation of reproductive endocrinology in wild elephant populations, information salient to the management and manipulation of population dynamics in this species.

Fecal coliform and Escherichia coli bacteria in the St. Croix National Scenic Riverway, Summer 1999

USGS Publications Warehouse

Kroening, Sharon E.

1999-01-01

Fecal coliform and Escherichia coli (E. coli) concentrations were determined in the St. Croix National Scenic Riverway to assess whether pathogenic organisms pose a potential problem for recreational use. Samples were collected from May through September 1999 at 22 locations on the St. Croix and Namekagon Rivers. No concentrations exceeded water-quality criteria or standards set by the U.S. Environmental Protection Agency or the states of Minnesota and Wisconsin. Maximum fecal coliform and E. coli concentrations were measured in the St. Croix River at St. Croix Falls, Wisconsin. Median fecal coliform and E. coli concentrations were greater in the St. Croix River near Woodland Corner, Wisconsin, and at Marine on St. Croix, Minnesota than at other locations sampled. There were no consistent short-term variations in fecal coliform or E. coli concentrations during the summer period or any significant relations between concentrations and stream discharge, based on these results.

Fecal Microbiome and Food Allergy in Pediatric Atopic Dermatitis: A Cross-Sectional Pilot Study.

PubMed

Fieten, Karin B; Totté, Joan E E; Levin, Evgeni; Reyman, Marta; Meijer, Yolanda; Knulst, André; Schuren, Frank; Pasmans, Suzanne G M A

2018-01-01

Exposure to microbes may be important in the development of atopic disease. Atopic diseases have been associated with specific characteristics of the intestinal microbiome. The link between intestinal microbiota and food allergy has rarely been studied, and the gold standard for diagnosing food allergy (double-blind placebo-controlled food challenge [DBPCFC]) has seldom been used. We aimed to distinguish fecal microbial signatures for food allergy in children with atopic dermatitis (AD). Pediatric patients with AD, with and without food allergy, were included in this cross-sectional observational pilot study. AD was diagnosed according to the UK Working Party criteria. Food allergy was defined as a positive DBPCFC or a convincing clinical history, in combination with sensitization to the relevant food allergen. Fecal samples were analyzed using 16S rRNA microbial analysis. Microbial signature species, discriminating between the presence and absence food allergy, were selected by elastic net regression. Eighty-two children with AD (39 girls) with a median age of 2.5 years, and 20 of whom were diagnosed with food allergy, provided fecal samples. Food allergy to peanut and cow's milk was the most common. Six bacterial species from the fecal microbiome were identified, that, when combined, distinguished between children with and without food allergy: Bifidobacterium breve, Bifidobacterium pseudocatenulatum, Bifidobacterium adolescentis, Escherichia coli, Faecalibacterium prausnitzii, and Akkermansia muciniphila (AUC 0.83, sensitivity 0.77, specificity 0.80). In this pilot study, we identified a microbial signature in children with AD that discriminates between the absence and presence of food allergy. Future studies are needed to confirm our findings. © 2018 The Author(s) Published by S. Karger AG, Basel.

Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

PubMed Central

Shanks, Orin C.; Newton, Ryan J.; Kelty, Catherine A.; Huse, Susan M.; Sogin, Mitchell L.

2013-01-01

Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States. PMID:23435885

Quantification of Human Fecal Bifidobacterium Species by Use of Quantitative Real-Time PCR Analysis Targeting the groEL Gene

PubMed Central

Junick, Jana

2012-01-01

Quantitative real-time PCR assays targeting the groEL gene for the specific enumeration of 12 human fecal Bifidobacterium species were developed. The housekeeping gene groEL (HSP60 in eukaryotes) was used as a discriminative marker for the differentiation of Bifidobacterium adolescentis, B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. gallicum, B. longum, B. pseudocatenulatum, B. pseudolongum, and B. thermophilum. The bifidobacterial chromosome contains a single copy of the groEL gene, allowing the determination of the cell number by quantification of the groEL copy number. Real-time PCR assays were validated by comparing fecal samples spiked with known numbers of a given Bifidobacterium species. Independent of the Bifidobacterium species tested, the proportion of groEL copies recovered from fecal samples spiked with 5 to 9 log10 cells/g feces was approximately 50%. The quantification limit was 5 to 6 log10 groEL copies/g feces. The interassay variability was less than 10%, and variability between different DNA extractions was less than 23%. The method developed was applied to fecal samples from healthy adults and full-term breast-fed infants. Bifidobacterial diversity in both adults and infants was low, with mostly ≤3 Bifidobacterium species and B. longum frequently detected. The predominant species in infant and adult fecal samples were B. breve and B. adolescentis, respectively. It was possible to distinguish B. catenulatum and B. pseudocatenulatum. We conclude that the groEL gene is a suitable molecular marker for the specific and accurate quantification of human fecal Bifidobacterium species by real-time PCR. PMID:22307308

Selection and Evaluation of Chemical Indicators for Waste Stream Identification

NASA Astrophysics Data System (ADS)

DeVita, W. M.; Hall, J.

2015-12-01

Human and animal wastes pose a threat to the quality of groundwater, surface water and drinking water. This is especially of concern for private and public water supplies in agricultural areas of Wisconsin where land spreading of livestock waste occurs on thin soils overlaying fractured bedrock. Current microbial source tracking (MST) methods for source identification requires the use of polymerase chain reaction (PCR) techniques. Due to cost, these tests are often not an option for homeowners, municipalities or state agencies with limited resources. The Water and Environmental Analysis Laboratory sought to develop chemical methods to provide lower cost processes to determine sources of fecal waste using fecal sterols, pharmaceuticals (human and veterinary) and human care/use products in ground and surface waters using solid phase extraction combined with triple quadrupole mass spectrometry. The two separate techniques allow for the detection of fecal sterol and other chemical markers in the sub part per billion-range. Fecal sterol ratios from published sources were used to evaluate drinking water samples and wastewater from onsite waste treatment systems and municipal wastewater treatment plants. Pharmaceuticals and personal care products indicative of human waste included: acetaminophen, caffeine, carbamazepine, cotinine, paraxanthine, sulfamethoxazole, and the artificial sweeteners; acesulfame, saccharin, and sucralose. The bovine antibiotic sulfamethazine was also targeted. Well water samples with suspected fecal contamination were analyzed for fecal sterols and PPCPs. Results were compared to traditional MST results from the Wisconsin State Laboratory of Hygiene. Chemical indicators were found in 6 of 11 drinking water samples, and 5 of 11 were in support of MST results. Lack of detection of chemical indicators in samples contaminated with fecal waste supports the need for confirmatory methods and advancement of chemical indicator detection technologies.

Evaluation of a Rapid Fecal PCR Test for Detection of Mycobacterium avium subsp. paratuberculosis in Dairy Cattle▿

PubMed Central

Wells, Scott J.; Collins, Michael T.; Faaberg, Kay S.; Wees, Carrie; Tavornpanich, Saraya; Petrini, Kristine R.; Collins, James E.; Cernicchiaro, Natalia; Whitlock, Robert H.

2006-01-01

A high-throughput TaqMan PCR assay for detection of bovine paratuberculosis was evaluated by using fecal samples from 1,808 dairy cattle in seven naturally infected herds and 347 dairy cattle in seven herds considered free of paratuberculosis. Fecal, blood, and milk samples were submitted to laboratories where the PCR-based assay, three different fecal culture procedures for Mycobacterium avium subsp. paratuberculosis (centrifugation, sedimentation, and the BACTEC filter concentration method), two serologic enzyme-linked immunosorbent assays (ELISAs), and one milk ELISA were performed. Results from testing of dairy cattle in herds free of M. avium subsp. paratuberculosis showed that the PCR assay's specificity was 99.7%. Twenty-three percent of the dairy cows that were fecal culture positive by at least one of the three methods were positive by the PCR assay. By Bayesian non-“gold standard” analysis methods, the TaqMan PCR assay had a higher specificity than the serum ELISAs (99.3%; 95% confidence interval [CI] = 98.6 to 99.7%) and a test sensitivity similar to that of the serum ELISAs (29%; 95% CI = 24 to 35%). By classical methods, the estimated relative sensitivity of the fecal PCR assay was 4% for light and moderate fecal shedders (compared to 12 to 13% for the ELISAs) and 76% for heavy fecal shedders (compared to 67% for the milk ELISA). The PCR assay has higher sensitivity for detection of heavy fecal shedders than the evaluated milk ELISA but lower sensitivity than a serum or milk ELISA for detection of light and moderate fecal shedders. This assay can be used as a quick test for detection of cattle with heavy fecal shedding, those cattle with the highest risk of transmitting infection to susceptible cattle. PMID:16928884

Effects of receiving-water quality and wastewater treatment on injury, survival, and regrowth of fecal-indicator bacteria and implications for assessment of recreational water quality

USGS Publications Warehouse

Francy, D.S.; Hart, T.L.; Virosteck, C.M.

1996-01-01

Bacterial injury, survival, and regrowth were investigated by use of replicate flow-through incubation chambers placed in the Cuyahoga River or Lake Erie in the greater Cleveland metropolitan area during seven 4-day field studies. The chambers contained wastewater or combined-sewer-overflow (CSO) effluents treated three ways-unchlorinated, chlorinated, and dechlorinated. At timestep intervals, the chamber contents were analyzed for concentrations of injured and healthy fecal coliforms by use of standard selective and enhanced-recovery membrane-filtration methods. Mean percent injuries and survivals were calculated from the fecal-coliform concentration data for each field study. The results of analysis of variance (ANOVA) indicated that treatment affected mean percent injury and survival, whereas site did not. In the warm-weather Lake Erie field study, but not in the warm-weather Cuyahoga River studies, the results of ANOVA indicated that dechlorination enhanced the repair of injuries and regrowth of chlorine-injured fecal coliforms on culture media over chlorination alone. The results of ANOVA on the percent injury from CSO effluent field studies indicated that dechlorination reduced the ability of organisms to recover and regrow on culture media over chlorination alone. However, because of atypical patterns of concentration increases and decreases in some CSO effluent samples, more work needs to be done before the effect of dechlorination and chlorination on reducing fecal-coliform concentrations in CSO effluents can be confirmed. The results of ANOVA on percent survivals found statistically significant differences among the three treatment methods for all but one study. Dechlorination was found to be less effective than chlorination alone in reducing the survival of fecal coliforms in wastewater effluent, but not in CSO effluent. If the concentration of fecal coliforms determined by use of the enhanced-recovery method can be predicted accurately from the concentration found by use of the standard method, then increased monitoring and expense to detect chlorine-injured organisms would be unnecessary. The results of linear regression analysis, however, indicated that the relation between enhanced-recovery and standard-method concentrations was best represented when the data were grouped by treatment. The model generated from linear regression of the unchlorinated data set provided an accurate estimate of enhanced-recovery concentrations from standard-method concentrations, whereas the models generated from the chlorinated and dechlorinated data sets did not. In addition, evaluation of fecal-coliform concentrations found in field studies in terms of Ohio recreational water-quality standards showed that concentrations obtained by standard and enhanced-recovery methods were not comparable. Sample treatment and analysis methods were found to affect the percentage of samples meeting and exceeding Ohio's bathing-water, primary-contact, and secondary-contact standards. Therefore, determining the health risk of swimming in receiving waters was often difficult without information on enhanced-recovery method concentrations and was especially difficult in waters receiving high proportions of chlorinated or dechlorinated effluents.

Presence of avian influenza viruses in waterfowl and wetlands during summer 2010 in California: Are resident birds a potential reservoir?

USGS Publications Warehouse

Henaux, V.; Samuel, M.D.; Dusek, Robert J.; Fleskes, J.P.; Ip, Hon S.

2012-01-01

Although wild waterfowl are the main reservoir for low pathogenic avian influenza viruses (LPAIv), the environment plays a critical role for the circulation and persistence of AIv. LPAIv may persist for extended periods in cold environments, suggesting that waterfowl breeding areas in the northern hemisphere may be an important reservoir for AIv in contrast to the warmer southern wintering areas. We evaluated whether southern wetlands, with relatively small populations (thousands) of resident waterfowl, maintain AIv in the summer, prior to the arrival of millions of migratory birds. We collected water and fecal samples at ten wetlands in two regions (Yolo Bypass and Sacramento Valley) of the California Central Valley during three bi-weekly intervals beginning in late July, 2010. We detected AIv in 29/367 fecal samples (7.9%) and 12/597 water samples (2.0%) by matrix real time Reverse Transcription Polymerase Chain Reaction (rRT-PCR). We isolated two H3N8, two H2N3, and one H4N8 among rRT-PCR positive fecal samples but no live virus from water samples. Detection of AIv RNA in fecal samples was higher from wetlands in the Sacramento Valley (11.9%) than in the Yolo Bypass (0.0%), but no difference was found for water samples (2.7 vs. 1.7%, respectively). Our study showed that low densities of hosts and unfavorable environmental conditions did not prevent LPAIv circulation during summer in California wetlands. Our findings justify further investigations to understand AIv dynamics in resident waterfowl populations, compare AIv subtypes between migratory and resident waterfowl, and assess the importance of local AIv as a source of infection for migratory birds.

Surface Sampling Collection and Culture Methods for Escherichia coli in Household Environments with High Fecal Contamination

PubMed Central

Kosek, Margaret N.; Schwab, Kellogg J.

2017-01-01

Empiric quantification of environmental fecal contamination is an important step toward understanding the impact that water, sanitation, and hygiene interventions have on reducing enteric infections. There is a need to standardize the methods used for surface sampling in field studies that examine fecal contamination in low-income settings. The dry cloth method presented in this manuscript improves upon the more commonly used swabbing technique that has been shown in the literature to have a low sampling efficiency. The recovery efficiency of a dry electrostatic cloth sampling method was evaluated using Escherichia coli and then applied to household surfaces in Iquitos, Peru, where there is high fecal contamination and enteric infection. Side-by-side measurements were taken from various floor locations within a household at the same time over a three-month period to compare for consistency of quantification of E. coli bacteria. The dry cloth sampling method in the laboratory setting showed 105% (95% Confidence Interval: 98%, 113%) E. coli recovery efficiency off of the cloths. The field application demonstrated strong agreement of side-by-side results (Pearson correlation coefficient for dirt surfaces was 0.83 (p < 0.0001) and 0.91 (p < 0.0001) for cement surfaces) and moderate agreement for results between entrance and kitchen samples (Pearson (0.53, p < 0.0001) and weighted Kappa statistic (0.54, p < 0.0001)). Our findings suggest that this method can be utilized in households with high bacterial loads using either continuous (quantitative) or categorical (semi-quantitative) data. The standardization of this low-cost, dry electrostatic cloth sampling method can be used to measure differences between households in intervention and non-intervention arms of randomized trials. PMID:28829392

Surface Sampling Collection and Culture Methods for Escherichia coli in Household Environments with High Fecal Contamination.

PubMed

Exum, Natalie G; Kosek, Margaret N; Davis, Meghan F; Schwab, Kellogg J

2017-08-22

Empiric quantification of environmental fecal contamination is an important step toward understanding the impact that water, sanitation, and hygiene interventions have on reducing enteric infections. There is a need to standardize the methods used for surface sampling in field studies that examine fecal contamination in low-income settings. The dry cloth method presented in this manuscript improves upon the more commonly used swabbing technique that has been shown in the literature to have a low sampling efficiency. The recovery efficiency of a dry electrostatic cloth sampling method was evaluated using Escherichia coli and then applied to household surfaces in Iquitos, Peru, where there is high fecal contamination and enteric infection. Side-by-side measurements were taken from various floor locations within a household at the same time over a three-month period to compare for consistency of quantification of E. coli bacteria. The dry cloth sampling method in the laboratory setting showed 105% (95% Confidence Interval: 98%, 113%) E. coli recovery efficiency off of the cloths. The field application demonstrated strong agreement of side-by-side results (Pearson correlation coefficient for dirt surfaces was 0.83 ( p < 0.0001) and 0.91 ( p < 0.0001) for cement surfaces) and moderate agreement for results between entrance and kitchen samples (Pearson (0.53, p < 0.0001) and weighted Kappa statistic (0.54, p < 0.0001)). Our findings suggest that this method can be utilized in households with high bacterial loads using either continuous (quantitative) or categorical (semi-quantitative) data. The standardization of this low-cost, dry electrostatic cloth sampling method can be used to measure differences between households in intervention and non-intervention arms of randomized trials.

Antibiotic-Resistant Genes and Pathogens Shed by Wild Deer Correlate with Land Application of Residuals.

PubMed

Rogers, Shane W; Shaffer, Carrie E; Langen, Tom A; Jahne, Michael; Welsh, Rick

2018-03-09

The purpose of this study was to investigate genetic biomarkers of zoonotic enteric pathogens and antibiotic-resistant genes (ARGs) in the feces of white-tailed deer (Odocoileus virginianus) as related to proximity of deer to land that receives livestock manure or human waste biosolid fertilizers. Deer feces were collected in the St. Lawrence River Valley and Adirondack State Park of New York. Campylobacter spp. 16S rDNA was detected in 12 of 232 fecal samples (8 of 33 sites). Salmonellae were cultivated from 2 of 182 fecal samples (2 of 29 sites). Genetic virulence markers for Shiga-like toxin I (stx 1 ) and enterohemolysin (hylA) were each detected in one isolate of Escherichia coli; E. coli O157 was not detected in any of 295 fecal samples. ARGs detected in deer feces included ermB (erythromycin-resistant gene; 9 of 295 fecal samples, 5 of 38 sites), vanA (vancomycin-resistant gene; 93 of 284 samples, 33 of 38 sites), tetQ (tetracycline-resistant gene; 93 of 295 samples, 25 of 38 sites), and sul(I) (sulfonamide-resistant gene; 113 of 292 samples, 28 of 38 sites). Genetic markers of pathogens and ARGs in deer feces were spatially associated with collection near concentrated animal feeding operations (CAFOs; Campylobacter spp., tetQ, and ermB) and land-applied biosolids (tetQ). These results indicate that contact with human waste biosolids or animal manure may be an important method of pathogen and ARG transmission and that deer in proximity to land-applied manure and human waste biosolids pose increased risk to nearby produce and water quality.

A cross-sectional study of Tritrichomonas foetus infection in feral and shelter cats in Prince Edward Island, Canada.

PubMed

Raab, Oriana; Greenwood, Spencer; Vanderstichel, Raphael; Gelens, Hans

2016-03-01

A cross-sectional study examined the occurrence of Tritrichomonas foetus, and other intestinal parasites, in feral and shelter cats in Prince Edward Island (PEI). Fecal samples were collected from 100 feral cats, 100 cats from the PEI Humane Society, and 5 cats from a private residence. The occurrence of T. foetus, based on fecal culture, was 0% in feral and shelter cats. A single positive sample was obtained from an owned Abyssinian cat that was imported to PEI. Intestinal parasites were identified via fecal flotation in 76% of feral cats and 39% of cats from the humane society. Feral cats had a higher incidence of Toxocara cati than cats from the humane society (P < 0.001), conversely, shelter cats had a higher incidence of Cystoisospora spp. (P < 0.001). These results suggest that while T. foetus is not of importance in feral and shelter cats in PEI, imported cats could serve as reservoirs.

A cross-sectional study of Tritrichomonas foetus infection in feral and shelter cats in Prince Edward Island, Canada

PubMed Central

Raab, Oriana; Greenwood, Spencer; Vanderstichel, Raphael; Gelens, Hans

2016-01-01

A cross-sectional study examined the occurrence of Tritrichomonas foetus, and other intestinal parasites, in feral and shelter cats in Prince Edward Island (PEI). Fecal samples were collected from 100 feral cats, 100 cats from the PEI Humane Society, and 5 cats from a private residence. The occurrence of T. foetus, based on fecal culture, was 0% in feral and shelter cats. A single positive sample was obtained from an owned Abyssinian cat that was imported to PEI. Intestinal parasites were identified via fecal flotation in 76% of feral cats and 39% of cats from the humane society. Feral cats had a higher incidence of Toxocara cati than cats from the humane society (P < 0.001), conversely, shelter cats had a higher incidence of Cystoisospora spp. (P < 0.001). These results suggest that while T. foetus is not of importance in feral and shelter cats in PEI, imported cats could serve as reservoirs. PMID:26933262

A comparison of fecal percent dry matter and number of Cryptosporidium parvum oocysts shed to observational fecal consistency scoring in dairy calves.

PubMed

Bellosa, Mary L; Nydam, Daryl V; Liotta, Janice L; Zambriski, Jennifer A; Linden, Thomas C; Bowman, Dwight D

2011-04-01

Evaluation of dairy calf feces is often used in research and for clinical decision making to assess severity of diarrhea. However, this has not been validated for agreement between dry matter content and observed fecal consistency. Therefore, a comparison of observed fecal consistency score to fecal percent dry matter and Cryptosporidium parvum oocyst shedding was performed to assess the accuracy of observational scoring as a measure of diarrhea and its association with number of oocysts shed. Fecal samples from 20 dairy calves experimentally infected with C. parvum oocysts were collected daily post-infection and scored on a scale from 1 to 4, with 1 being normal feces to 4 being severe diarrhea. An aliquot of each sample was analyzed for percent dry matter and Cryptosporidium oocyst counts by using immunofluorescent microscopy. Fecal consistency scores of 1, 2, 3, and 4 had median percent dry matter of 20.9, 16.3, 9.6, and 5.8, respectively. Using percent dry matter assessed by fecal consistency scoring were significantly different from each other (P < 0.001). A higher fecal consistency score also was associated with a greater number of Cryptosporidium oocysts shed (P < 0 .0001). Scores of 1, 2, 3, and 4 had median oocyst counts of 0, 0, 1.3 × 10⁶, and 2.8 × 10⁶, respectively. These results suggest that observational scoring is a useful proxy to assess diarrhea in dairy calves.

Inactivation of fecal bacteria in drinking water by solar heating.

PubMed

Joyce, T M; McGuigan, K G; Elmore-Meegan, M; Conroy, R M

1996-02-01

We report simulations of the thermal effect of strong equatorial sunshine on water samples contaminated with high populations of fecal coliforms. Water samples, heavily contaminated with a wild-type strain of Escherichia coli (starting population = 20 x 10(5) CFU/ml), are heated to those temperatures recorded for 2-liter samples stored in transparent plastic bottles and exposed to full Kenyan sunshine (maximum water temperature, 55 degrees C). The samples are completely disinfected within 7 h, and no viable E. coli organisms are detected at either the end of the experiment or a further 12 h later, showing that no bacterial recovery has occurred. The feasibility of employing solar disinfection for highly turbid, fecally contaminated water is discussed.

Mechanisms of antimicrobial resistant Salmonella enterica transmission associated with starling-livestock interactions.

PubMed

Carlson, James C; Hyatt, Doreene R; Ellis, Jeremy W; Pipkin, David R; Mangan, Anna M; Russell, Michael; Bolte, Denise S; Engeman, Richard M; DeLiberto, Thomas J; Linz, George M

2015-08-31

Bird-livestock interactions have been implicated as potential sources for bacteria within concentrated animal feeding operations (CAFO). European starlings (Sturnus vulgaris) in particular are known to contaminate cattle feed and water with Salmonella enterica through their fecal waste. We propose that fecal waste is not the only mechanisms through which starlings introduce S. enterica to CAFO. The goal of this study was to assess if starlings can mechanically move S. enterica. We define mechanical movement as the transportation of media containing S. enterica, on the exterior of starlings within CAFO. We collected 100 starlings and obtained external wash and gastrointestinal tract (GI) samples. We also collected 100 samples from animal pens. Within each pen we collected one cattle fecal, feed, and water trough sample. Isolates from all S. enterica positive samples were subjected to antimicrobial susceptibility testing. All sample types, including 17% of external starling wash samples, contained S. enterica. All sample types had at least one antimicrobial resistant (AMR) isolate and starling GI samples harbored multidrug resistant S. enterica. The serotypes isolated from the starling external wash samples were all found in the farm environment and 11.8% (2/17) of isolates from positive starling external wash samples were resistant to at least one class of antibiotics. This study provides evidence of a potential mechanism of wildlife introduced microbial contamination in CAFO. Mechanical movement of microbiological hazards, by starlings, should be considered a potential source of bacteria that is of concern to veterinary, environmental and public health. Published by Elsevier B.V.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

USGS Publications Warehouse

Keiter, David A.; Cunningham, Fred L.; Rhodes, Olin E.; Irwin, Brian J.; Beasley, James

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Optimization of Scat Detection Methods for a Social Ungulate, the Wild Pig, and Experimental Evaluation of Factors Affecting Detection of Scat.

PubMed

Keiter, David A; Cunningham, Fred L; Rhodes, Olin E; Irwin, Brian J; Beasley, James C

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

DOE PAGES

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.; ...

2016-05-25

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Fecal corticoid monitoring in whooping cranes (Grus americana) undergoing reintroduction

USGS Publications Warehouse

Hartup, Barry K.; Olsen, Glenn H.; Czekala, Nancy M.

2005-01-01

We used radioimmunoassay to determine fecal corticoid concentrations and assess potential stress in 10 endangered whooping cranes (Grus americana) undergoing reintroduction to the wild. Fecal samples were collected shortly after hatching at a captive facility in Maryland, during field training in Wisconsin, and throughout a human-led migration to Florida. After a 14-day decline following hatching, fecal corticoid concentrations stabilized at baseline levels for the duration of the captive period, despite exposure to potentially stressful stimuli. Shipment of the cranes to the field training site was correlated with an eight- to 34-fold increase in fecal corticoid concentrations, which returned to baseline levels within 1 week. Increases were positively correlated with age but not body weight at the time of shipping. Fecal corticoid concentrations during the training period increased slightly and exhibited greater variation than levels observed at the captive facility, but were well within expected norms based on previous studies. Fecal corticoid concentrations increased twofold following premigration physical examinations and placement of radiotransmitters, and persisted for up to 4 days before they returned to baseline levels. Though fecal corticoid concentrations and variation during the migration period were similar to training levels, there was an overall decline in fecal corticoid concentrations during the artificial migration. Acute stressors, such as capture, restraint, and severe storms, were associated with stress responses by the cranes that varied in accordance with lasting physical or psychological stimuli. The overall reintroduction process of costume-rearing, ultralight aircraft habituation, training, and artificial migration was not associated with elevations in fecal corticoid concentrations suggestive of chronic stress.

Multipathway Quantitative Assessment of Exposure to Fecal Contamination for Young Children in Low-Income Urban Environments in Accra, Ghana: The SaniPath Analytical Approach

PubMed Central

Wang, Yuke; Moe, Christine L.; Null, Clair; Raj, Suraja J.; Baker, Kelly K.; Robb, Katharine A.; Yakubu, Habib; Ampofo, Joseph A.; Wellington, Nii; Freeman, Matthew C.; Armah, George; Reese, Heather E.; Peprah, Dorothy; Teunis, Peter F. M.

2017-01-01

Abstract. Lack of adequate sanitation results in fecal contamination of the environment and poses a risk of disease transmission via multiple exposure pathways. To better understand how eight different sources contribute to overall exposure to fecal contamination, we quantified exposure through multiple pathways for children under 5 years old in four high-density, low-income, urban neighborhoods in Accra, Ghana. We collected more than 500 hours of structured observation of behaviors of 156 children, 800 household surveys, and 1,855 environmental samples. Data were analyzed using Bayesian models, estimating the environmental and behavioral factors associated with exposure to fecal contamination. These estimates were applied in exposure models simulating sequences of behaviors and transfers of fecal indicators. This approach allows us to identify the contribution of any sources of fecal contamination in the environment to child exposure and use dynamic fecal microbe transfer networks to track fecal indicators from the environment to oral ingestion. The contributions of different sources to exposure were categorized into four types (high/low by dose and frequency), as a basis for ranking pathways by the potential to reduce exposure. Although we observed variation in estimated exposure (108–1016 CFU/day for Escherichia coli) between different age groups and neighborhoods, the greatest contribution was consistently from food (contributing > 99.9% to total exposure). Hands played a pivotal role in fecal microbe transfer, linking environmental sources to oral ingestion. The fecal microbe transfer network constructed here provides a systematic approach to study the complex interaction between contaminated environment and human behavior on exposure to fecal contamination. PMID:29031283

Predicting Fecal Indicator Bacteria Fate and Removal in Urban Stormwater at the Watershed Scale

NASA Astrophysics Data System (ADS)

Wolfand, J.; Hogue, T. S.; Luthy, R. G.

2016-12-01

Urban stormwater is a major cause of water quality impairment, resulting in surface waters that fail to meet water quality standards and support their designated uses. Of the many stormwater pollutants, fecal indicator bacteria are particularly important to track because they are directly linked to pathogens which jeopardize public health; yet, their fate and transport in urban stormwater is poorly understood. Monitoring fecal bacteria in stormwater is possible, but due to the high variability of fecal indicators both spatially and temporally, single grab or composite samples do not fully capture fecal indicator loading. Models have been developed to predict fecal indicator bacteria at the watershed scale, but they are often limited to agricultural areas, or areas that receive frequent rainfall. Further, it is unclear whether best management practices (BMPs), such as bioretention or engineered wetlands, are able to reduce bacteria to meet water quality standards at watershed outlets. This research seeks to develop a model to predict fecal indicator bacteria in urban stormwater in a semi-arid climate at the watershed scale. Using the highly developed Ballona Creek watershed (89 mi2) located in Los Angeles County as a case study, several existing mechanistic models are coupled with a hydrologic model to predict fecal indicator concentrations (E. coli, enterococci, fecal coliform, and total coliform) at the outfall of Ballona Creek watershed, Santa Monica Bay. The hydrologic model was developed using InfoSWMM Sustain, calibrated for flow from WY 1998-2006 (NSE = 0.94; R2 = 0.95), and validated from WY 2007-2015 (NSE = 0.93; R2 = 0.95). The developed coupled model is being used to predict fecal indicator fate and transport and evaluate how BMPs can be optimized to reduce fecal indicator loading to surface waters and recreational beaches.

Rapid detection of Opisthorchis viverrini and Strongyloides stercoralis in human fecal samples using a duplex real-time PCR and melting curve analysis.

PubMed

Janwan, Penchom; Intapan, Pewpan M; Thanchomnang, Tongjit; Lulitanond, Viraphong; Anamnart, Witthaya; Maleewong, Wanchai

2011-12-01

Human opisthorchiasis caused by the liver fluke Opisthorchis viverrini is an endemic disease in Southeast Asian countries including the Lao People's Democratic Republic, Cambodia, Vietnam, and Thailand. Infection with the soil-transmitted roundworm Strongyloides stercoralis is an important problem worldwide. In some areas, both parasitic infections are reported as co-infections. A duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis was developed for the rapid detection of O. viverrini and S. stercoralis in human fecal samples. Duplex real-time FRET PCR is based on fluorescence melting curve analysis of a hybrid of amplicons generated from two genera of DNA elements: the 162 bp pOV-A6 DNA sequence specific to O. viverrini and the 244 bp 18S rRNA sequence specific to S. stercoralis, and two pairs of specific fluorophore-labeled probes. Both O. viverrini and S. stercoralis can be differentially detected in infected human fecal samples by this process through their different fluorescence channels and melting temperatures. Detection limit of the method was as little as two O. viverrini eggs and four S. stercoralis larvae in 100 mg of fecal sample. The assay could distinguish the DNA of both parasites from the DNA of negative fecal samples and fecal samples with other parasite materials, as well as from the DNA of human leukocytes and other control parasites. The technique showed 100% sensitivity and specificity. The introduced duplex real-time FRET PCR can reduce labor time and reagent costs and is not prone to carry over contamination. The method is important for simultaneous detection especially in areas where both parasites overlap incidence and is useful as the screening tool in the returning travelers and immigrants to industrialized countries where number of samples in the diagnostic units will become increasing.

Ovarian cycle approach by rectal temperature and fecal progesterone in a female killer whale, Orcinus orca.

PubMed

Kusuda, Satoshi; Kakizoe, Yuka; Kanda, Koji; Sengoku, Tomoko; Fukumoto, Yohei; Adachi, Itsuki; Watanabe, Yoko; Doi, Osamu

2011-01-01

This study aimed to validate the measurements of body temperature and fecal progesterone concentrations as minimally invasive techniques for assessing ovarian cycle in a single sexually mature female killer whale. Rectal temperature data, fecal and blood samples were collected in the dorsal position using routine husbandry training on a voluntary basis. The correlations between rectal temperature and plasma progesterone concentration and between fecal and plasma progesterone concentrations were investigated. Fecal progesterone metabolites were identified by a combination of high-performance liquid chromatography and enzyme immunoassay. Plasma progesterone concentrations (range: 0.2-18.6 ng/ml) and rectal temperature (range: 35.3-35.9°C) changed cyclically, and cycle lengths were an average (±SD) of 44.9±4.0 days (nine cycles) and 44.6±5.9 days (nine cycles), respectively. Rectal temperature positively correlated with the plasma progesterone concentrations (r=0.641, P<0.01). There was a visual trend for fecal progesterone profiles to be similar to circulating plasma progesterone profiles. Fecal immunoreactive progestagen analysis resulted in a marked immunoreactive peak of progesterone. The data from the single killer whale indicate that the measurement of rectal temperature is suitable for minimally invasive assessment of the estrous cycle and monitoring the fecal progesterone concentration is useful to assess ovarian luteal activity. © 2010 Wiley-Liss, Inc.

Longitudinal fecal hormone analysis for monitoring reproductive activity in the female polar bear (Ursus maritimus).

PubMed

Stoops, M A; MacKinnon, K M; Roth, T L

2012-12-01

The objective was to identify suitable enzyme immunoassays to monitor gonadal and placental function in the female polar bear. Immunoreactive progesterone, progesterone metabolite (PdG), estrogen, and androgen metabolite (T) concentrations were measured in fecal samples collected over 24 mo from captive female bears (N = 20). Whereas fecal extracts produced displacement curves parallel to the standard curve for each respective steroid, T and PdG more accurately reflected reproductive events. Concentrations of fecal T increased (P < 0.05) during the breeding season, and brief spikes were associated with estrus and mating. A postovulatory increase in PdG was not always detected, but sustained baseline T after mating appeared consistent with ovulation. Parturient bears excreted higher PdG concentrations (P < 0.05) during expected time of embryo implantation in Fall, and a late gestational rise in fecal T occurred 30 days prepartum. Many nonparturient bears also had a PdG rise in the Fall, suggesting they experienced either pregnancy loss or a pseudopregnancy. Differentiating pregnant and pseudopregnant states was not achieved using fecal PdG alone, but when combined with fecal T, comprehensive diagnoses could be made. Nonparturient bears demonstrated elevated (P < 0.05) fecal T during summer months, whereas parturient bears did not. In summary, noninvasive hormone monitoring techniques were established for the female polar bear. Although this study was directed at facilitating management and breeding efforts of captive polar bears, the methods could be applied to studies of reproductive function in wild populations. Copyright © 2012 Elsevier Inc. All rights reserved.

Assessment of possible sources of microbiological contamination and water-quality characteristics of the Jacks Fork, Ozark National Scenic Riverways, Missouri; phase II

USGS Publications Warehouse

Davis, Jerri V.; Richards, Joseph M.

2002-01-01

In 1998, an 8-mile reach of the Jacks Fork was included on Missouri?s list of impaired waters as required by Section 303(d) of the Federal Clean Water Act. The identified pollutant on the Jacks Fork was fecal coliform bacteria. Potential sources of fecal contamination to the Jacks Fork include a wastewater treatment plant; campground pit-toilet or septic-system effluent; a large commercial, cross-country horseback trail riding facility; canoeists, boaters, and tubers; and cows.The U.S. Geological Survey, in cooperation with the National Park Service, conducted a study to better understand the extent and sources of microbiological contamination within the Jacks Fork from Alley Spring to the mouth, which includes the 8-mile 303(d) reach. Identification of the sources would provide the National Park Service and the State of Missouri with the information needed to craft a solution of abatement, regulation, prevention, and mitigation with the end result being the removal of the Jacks Fork from the 303(d) list. Fifteen sites were sampled from November 1999 through December 2000. An additional site was sampled one time. Samples were collected mostly during base-flow conditions during a variety of nonrecreational and recreational season river uses. Samples were analyzed for selected fecal indicator bacteria, physical properties, nutrients, and wastewater organic compounds. During the sampling period, the whole-body-contact recreation standard for fecal coliform (200 colonies per 100 milliliters of sample) was exceeded at three sites on August 10, 2000, and also at one site on May 11, June 7, and October 3, 2000. Fecal coliform densities and instantaneous loads generally increased from background concentrations at the Eminence site, peaked about 2 river miles downstream, and then decreased until the most downstream site sampled. Generally, the largest densities and loads at sites downstream from Eminence not related to wet-weather flow were observed during a trail ride held August 6 to12, 2000. A 24-hour sample collection effort was conducted the weekend of July 15 and 16, 2000, to investigate the effect that large numbers of swimmers, canoeists, and tubers had on fecal coliform densities in the Jacks Fork. Five or six samples were collected at six sites between Saturday morning and the following Sunday afternoon. No fecal coliform density at any of the sites sampled exceeded the whole-body-contact recreation standard. Because bacteria survive longer in stream-bed sediments than in water, a source of bacteria in the water column could be from resuspension of accumulated bacteria from streambed sediments. Water and streambed-sediment samples were collected at three sites on August 3, 2000, 1 week before a trail ride and again at three sites on 2 Assessment of Possible Sources of Microbiological Contamination of the Jacks Fork, Missouri?Phase II August 8, 2000, during a trail ride. Results indicate that fecal coliform bacteria densities increased substantially in the streambed sediment and the water column during the trail ride.Sixty-five Escherichia coli isolates obtained from water samples collected at 9 sites and 23 Escherichia coli isolates obtained from stream-bed-sediment samples collected at 5 sites were submitted for ribotyping analysis. Samples were collected in 2000 during a variety of nonrecreational and recreational season river uses, including trail rides, canoeing, tubing, and swimming. Of the 65 isolates from water samples, 40 percent were identified as originating from sewage, 29 percent from horse, 11 percent from cow, and 20 percent from an unknown source. Of the 23 isolates from streambed-sediment samples, 39 percent were identified as originating from sewage, 35 percent from horse, 13 percent from cow, and 13 percent from unknown sources.Analysis of physical property (dissolved oxygen, pH, specific conductance, and temperature) and nutrient (dissolved nitrite plus nitrate and total phosphorus) data

Effects of abomasal oligofructose on blood and feces of Holstein steers.

PubMed

Mainardi, S R; Hengst, B A; Nebzydoski, S J; Nemec, L M; Gressley, T F

2011-08-01

Subacute ruminal acidosis can result in increased flow of fermentable substrates to the hindgut, which can negatively affect animal health and productivity. However, animal responses to increased hindgut fermentation independent of subacute ruminal acidosis have rarely been evaluated. This study determined the impact of abomasal dosage of a fermentable carbohydrate on animal performance and blood and fecal variables. Six ruminally cannulated Holstein steers fed a lactating dairy cow ration were used in a crossover design study with 14-d periods. On d 13 of each period, steers were infused abomasally with a pulse dose of 0 (control) or 1 (Oligo) g of oligofructose/kg of BW. Blood samples collected at 0, 3, 6, 9, 12, and 24 h after abomasal oligofructose dose were evaluated for metabolites (blood urea N, β-hydroxybutyric acid, and NEFA) and systemic inflammatory markers (Cu, serum amyloid A, and haptoglobin). Fecal samples, rectal temperature, heart rate, and respiratory rate were taken at 0, 3, 6, 9, 12, 24, and 48 h after abomasal dosage. Fecal samples were assayed for pH, DM percentage, consistency score (1=liquid to 5=coarse), and organic acid concentrations. Data were evaluated using a model including the fixed effects of treatment, time after dosage, and their interaction. Effects of treatment or treatment × time were not significant for DMI, blood variables, rectal temperature, or respiratory rate. Fecal pH was slightly reduced for Oligo compared with control steers (6.76 vs. 7.02; P=0.04). A treatment × time interaction occurred for fecal DM (P < 0.001). Compared with control steers, DM content of feces was reduced in Oligo steers at 6 h (12.6 vs. 15.2%) but increased at 9 h (16.3 vs. 15.0%) and 12 h (16.5 vs. 15.0). Fecal consistency score was reduced by the Oligo treatment at 6 h (1.44 vs. 2.83; P < 0.001) and 9 h (1.83 vs. 2.67; P=0.005). A treatment × time interaction was detected for fecal concentrations of lactate and acetate (P < 0.05) and tended to occur for propionate and butyrate (P < 0.10). The greatest difference for all organic acids occurred at 12 h, when fecal concentrations of lactate, acetate, propionate, and butyrate were 0.5, 47, 11, and 4.0 mM in control steers and 5.3, 76, 15, and 6.8 mM in Oligo steers, respectively. In summary, abomasal dosage of 1 g of oligofructose/kg of BW increased fecal excretion of microbial fermentation products in steers without causing metabolic acidosis, metabolic disruption, or inflammation. © 2011 American Society of Animal Science. All rights reserved.

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G.

Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Usingmore » NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites- caprate, nicotinate, glutamine, thymine, and aspartate- may potentially function as a biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. Despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.« less

The Adrenocortical Response of Greater Sage Grouse (Centrocercus urophasianus) to Capture, ACTH Injection, and Confinement, as Measured in Fecal Samples

PubMed Central

Jankowski, M. D.; Wittwer, D. J.; Heisey, D. M.; Franson, J. C.; Hofmeister, E. K.

2009-01-01

Investigators of wildlife populations often utilize demographic indicators to understand the relationship between habitat characteristics and population viability. Assessments of corticosterone may enable earlier detection of populations at risk of decline because physiological adjustments to habitat disturbance occur before reproductive diminutions. Noninvasive methods to accomplish these assesments are important in species of concern, such as the greater sage grouse (GRSG). Therefore, we validated a radioimmunoassay that measures immunoreactive corticosterone metabolites (ICM) in fecal samples and used it to characterize the adrenocortical response of 15 GRSG exposed to capture, intravenous injection of 50 IU/kg adrenocorticotrophic hormone (ACTH) or saline, and 22 h of confinement. Those animals injected with ACTH exhibited a more sustained (P = 0.0139) and less variable (P = 0.0012) response than those injected with saline, indicating different levels of adrenocortical activity. We also found that potential field-collection protocols of fecal samples did not alter ICM concentrations: samples held at 4°C for up to 16 h contained similar levels of ICM as those frozen (−20°C) immediately. This study demonstrates a multiphasic adrenocortical response that varied with the level of stimulation and indicates that the assay used to measure this phenomenon is applicable for studies of wild GRSG. PMID:19199814

The adrenocortical response of greater sage grouse (Centrocercus urophasianus) to capture, ACTH injection, and confinement, as measured in fecal samples

USGS Publications Warehouse

Jankowski, M.D.; Wittwer, D.J.; Heisey, D.M.; Franson, J. Christian; Hofmeister, Erik K.

2009-01-01

Investigators of wildlife populations often utilize demographic indicators to understand the relationship between habitat characteristics and population viability. Assessments of corticosterone may enable earlier detection of populations at risk of decline because physiological adjustments to habitat disturbance occur before reproductive diminutions. Noninvasive methods to accomplish these assesments are important in species of concern, such as the greater sage grouse (GRSG). Therefore, we validated a radioimmunoassay that measures immunoreactive corticosterone metabolites (ICM) in fecal samples and used it to characterize the adrenocortical response of 15 GRSG exposed to capture, intravenous injection of 50 IU/kg adrenocorticotrophic hormone (ACTH) or saline, and 22 h of confinement. Those animals injected with ACTH exhibited a more sustained (P = 0.0139) and less variable (P = 0.0012) response than those injected with saline, indicating different levels of adrenocortical activity. We also found that potential field-collection protocols of fecal samples did not alter ICM concentrations: samples held at 4??C for up to 16 h contained similar levels of ICM as those frozen (-20??C) immediately. This study demonstrates a multiphasic adrenocortical response that varied with the level of stimulation and indicates that the assay used to measure this phenomenon is applicable for studies of wild GRSG. ?? 2009 by The University of Chicago. All rights reserved.

Spatial and Temporal Dynamics of Fecal Coliform and Associated with Suspended Solids and Water within Five Northern California Estuaries.

PubMed

Lewis, David J; Atwill, Edward R; Pereira, Maria das Graças C; Bond, Ronald

2013-01-01

Fecal coliform and associated with suspended solids (SS) and water in five northern California estuaries were studied to document process influences and water quality monitoring biases affecting indicator bacteria concentrations. We collected and analyzed 2371 samples during 10 sampling events for the five studied estuaries. Concentrations during wet-season stormflow conditions were greater than during wet-season base flow and dry-season base flow conditions. Results also document concentration gradients across the length of the studied estuaries and with depth of sample collection. Highest concentrations were associated with shallow samples collected furthest inland. Corresponding decreases occurred the deeper and closer to the estuary mouth a sample was collected. Results also identify direct relationships of wind speed and discharge velocity and indirect relationship of tide stage to indicator bacteria concentrations. Bacteria associated with suspended solids (SS), after conversion to the same units of measurement (mass), were three orders of magnitude greater than in the water fraction. However, the mean proportion contributed by SS to composite water sample concentrations was 8% (SE 0.3) for fecal coliform and 7% (SE 0.3) for . Bacteria from the SS proportion is related to seasonality, tide stage, and discharge velocity that are consistent with mechanisms for entrainment, transport of SS, and reduced particle settling. These results are important for both managing and monitoring these systems by improving sample spatial and temporal context and corresponding bacteria concentration values across the freshwater-saltwater interface. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Direct typing of Canine parvovirus (CPV) from infected dog faeces by rapid mini sequencing technique.

PubMed

V, Pavana Jyothi; S, Akila; Selvan, Malini K; Naidu, Hariprasad; Raghunathan, Shwethaa; Kota, Sathish; Sundaram, R C Raja; Rana, Samir Kumar; Raj, G Dhinakar; Srinivasan, V A; Mohana Subramanian, B

2016-12-01

Canine parvovirus (CPV) is a non-enveloped single stranded DNA virus with an icosahedral capsid. Mini-sequencing based CPV typing was developed earlier to detect and differentiate all the CPV types and FPV in a single reaction. This technique was further evaluated in the present study by performing the mini-sequencing directly from fecal samples which avoided tedious virus isolation steps by cell culture system. Fecal swab samples were collected from 84 dogs with enteritis symptoms, suggestive of parvoviral infection from different locations across India. Seventy six of these samples were positive by PCR; the subsequent mini-sequencing reaction typed 74 of them as type 2a virus, and 2 samples as type 2b. Additionally, 25 of the positive samples were typed by cycle sequencing of PCR products. Direct CPV typing from fecal samples using mini-sequencing showed 100% correlation with CPV typing by cycle sequencing. Moreover, CPV typing was achieved by mini-sequencing even with faintly positive PCR amplicons which was not possible by cycle sequencing. Therefore, the mini-sequencing technique is recommended for regular epidemiological follow up of CPV types, since the technique is rapid, highly sensitive and high capacity method for CPV typing. Copyright © 2016. Published by Elsevier B.V.

Field-based evaluation of a male-specific (F+) RNA coliphage ...

EPA Pesticide Factsheets

Fecal contamination of water poses a significant risk to public health due to the potential presence of pathogens, including enteric viruses. Thus, sensitive, reliable and easy to use methods for the detection of microorganisms are needed to evaluate water quality. In this study, we performed a field evaluation of an anion-exchange resin based platform to concentrate F-RNA coliphages (fecal/enteric virus indicators) from diverse fecally impacted environmental waters. In this platform, F-RNA coliphages are adsorbed to anion-exchange resin and direct nucleic acid isolation is performed, yielding a sample amenable to real-time reverse transcriptase PCR detection. Matrix-dependent inhibition was evaluated using known quantities of spiked F-RNA coliphage genogroups GI, GII, GII and GIV. Detection was successful in 97%, 72%, 85% and 98% of the samples for spiked F-RNA coliphage GI, GII, GIII and GIV, respectively, and was differentially affected by inhibitory properties specific to each water sample. No association between inhibition and the water samples’ physicochemical properties was apparent. Parallel evaluations of the spiked samples with internal amplification control (IAC) reactions (a widely used control to assess inhibition) demonstrated that IAC reaction inhibition was not agreement with that observed for spiked samples, suggesting that testing of spiked samples allows for better assessments of matrix-dependent inhibition. Additionally, the anion-

A comparison of three fecal steroid metabolites for pregnancy detection used with single sampling in bighorn sheep (Ovis canadensis)

USGS Publications Warehouse

Schoenecker, K.A.; Lyda, R.O.; Kirkpatrick, J.

2004-01-01

We compared three fecal steroid metabolite assays for their usefulness in detecting pregnancy among free-ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) from Bighorn Canyon National Recreation Area, Wyoming and Montana (USA) and captive bighorn ewes at ZooMontana in Billings, Montana. Fecal samples were collected from 11 free-ranging, radio-collared bighorn ewes in late January–May 2001 and from 20 free-ranging, radio-collared ewes in late March to mid-May 2002. Free-ranging ewes were monitored the following spring to determine whether or not they lambed. In addition, two captive ewes were studied at Zoo-Montana. With three exceptions, free-ranging bighorn ewes that produced lambs had nonspecific progesterone metabolite (iPdG) levels of >1,800 ng/g feces and iPdG levels >7,000 ng/gm feces when samples were collected between early March and mid-May Samples collected earlier in the year were inconclusive. One false negative was suspected to be the result of sample collection error. Of the captive ewes, nonspecific pregnanediol-3α–glucuronide (PdG) and iPdG followed a predictable curve over the course of the 180-day pregnancies. We conclude that estrone conjugates are not useful in diagnosing pregnancy; however, fecal steroid analysis of PdG and iPdG can be used to accurately determine pregnancy and reproductive function in bighorn sheep. This holds great potential as a noninvasive technique for understanding the role of reproductive disease in wild bighorn sheep.

Salmonella detection in poultry samples. Comparison of two commercial real-time PCR systems with culture methods for the detection of Salmonella spp. in environmental and fecal samples of poultry.

PubMed

Sommer, D; Enderlein, D; Antakli, A; Schönenbrücher, H; Slaghuis, J; Redmann, T; Lierz, M

2012-01-01

The efficiency of two commercial PCR methods based on real-time technology, the foodproof® Salmonella detection system and the BAX® PCR Assay Salmonella system was compared to standardized culture methods (EN ISO 6579:2002 - Annex D) for the detection of Salmonella spp. in poultry samples. Four sample matrices (feed, dust, boot swabs, feces) obtained directly from poultry flocks, as well as artificially spiked samples of the same matrices, were used. All samples were tested for Salmonella spp. using culture methods first as the gold standard. In addition samples spiked with Salmonella Enteridis were tested to evaluate the sensitivity of both PCR methods. Furthermore all methods were evaluated in an annual ring-trial of the National Salmonella Reference Laboratory of Germany. Salmonella detection in the matrices feed, dust and boot swabs were comparable in both PCR systems whereas the results from feces differed markedly. The quality, especially the freshness, of the fecal samples had an influence on the sensitivity of the real-time PCR and the results of the culture methods. In fresh fecal samples an initial spiking level of 100cfu/25g Salmonella Enteritidis was detected. Two-days-dried fecal samples allowed the detection of 14cfu/25g. Both real- time PCR protocols appear to be suitable for the detection of Salmonella spp. in all four matrices. The foodproof® system detected eight samples more to be positive compared to the BAX® system, but had a potential false positive result in one case. In 7-days-dried samples none of the methods was able to detect Salmonella likely through letal cell damage. In general the advantage of PCR analyses over the culture method is the reduction of working time from 4-5 days to only 2 days. However, especially for the analysis of fecal samples official validation should be conducted according to the requirement of EN ISO6579:2002 - Annex D.

Longitudinal relationship between fecal culture, fecal quantitative PCR, and milk ELISA in Mycobacterium avium ssp. paratuberculosis-infected cows from low-prevalence dairy herds.

PubMed

Beaver, A; Sweeney, R W; Hovingh, E; Wolfgang, D R; Gröhn, Y T; Schukken, Y H

2017-09-01

Mycobacterium avium ssp. paratuberculosis (MAP), the causative agent of ruminant Johne's disease, presents a particular challenge with regard to infection mitigation on dairy farms. Diagnostic testing strategies to identify and quantify MAP and associated antibodies are imperfect, and certain facets of the relationship between diagnostic tests remain to be explored. Additional repeated-measures data from known infected animals are needed to complement the body of cross-sectional research on Johne's disease-testing methods. Statistical models that accurately account for multiple diagnostic results while adjusting for the effects of individual animals and herds over time can provide a more detailed understanding of the interplay between diagnostic outcomes. Further, test results may be considered as continuous wherever possible so as to avoid the information loss associated with dichotomization. To achieve a broader understanding of the relationship between diagnostic tests, we collected a large number of repeated fecal and milk samples from 14 infected cows, in addition to bulk milk samples, from 2 low-prevalence dairy herds in the northeast United States. Predominately through the use of mixed linear modeling, we identified strong associations between milk ELISA optical density, fecal quantitative PCR, and fecal culture in individual animals while concurrently adjusting for variables that could alter these relationships. Notably, we uncovered subtleties in the predictive abilities of fecal shedding level on milk ELISA results, with animals categorized as disease progressors reaching higher ELISA optical density levels. Moreover, we observed that spikes in fecal shedding could predict subsequent high ELISA values up to 2 mo later. We also investigated the presence of MAP in individual milk samples via PCR and noted an association between poor udder hygiene and MAP positivity in milk, suggesting some level of environmental contamination. The paucity of positive milk samples and the complete absence of detectable MAP in the bulk tank throughout the study period indicate that contamination of milk with MAP may not be of chief concern in low-prevalence herds. An enhanced understanding of the interrelationships between diagnostic tests can only benefit the development of testing strategies and objectives, which in turn may lessen MAP infection prevalence in dairy herds. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents

PubMed Central

2018-01-01

Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750–4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log10 7.2–8.0 marker equivalents (ME) 100 mL–1) and biologically treated wastewater samples (median log10 4.6–6.0 ME 100 mL–1) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe. PMID:29570973

Impact of sequencing depth on the characterization of the microbiome and resistome.

PubMed

Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E; Morley, Paul S; McAllister, Tim A

2018-04-12

Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

Impact of Some Ecological Factors on Fecal Contamination of Drinking Water by Diarrheagenic Antibiotic-Resistant Escherichia coli in Zagazig City, Egypt

PubMed Central

Gohar, Maha Kamal; Atta, Amal Hassan

2016-01-01

Fecal contamination of drinking water is a major health problem which accounts for many cases of diarrhea mainly in infants and foreigners. This contamination is a complex interaction of many parameters. Antibiotic resistance among bacterial isolates complicates the problem. The study was done to identify fecal contamination of drinking water by Diarrheagenic Antibiotic-Resistant Escherichia coli in Zagazig city and to trace reasons for such contamination, three hundred potable water samples were investigated for E. coli existence. Locations of E. coli positive samples were investigated in relation to population density, water source, and type of water pipe. Sixteen E. coli strains were isolated. Antibiotic sensitivity was done and enterotoxigenic, enteropathogenic, and enterohaemorrhagic virulence genes were investigated by PCR. Probability of fecal contamination correlated with higher population density, with increased distance from Zagazig water plant, and with asbestos cement water pipes. Resistance to at least one antimicrobial drug was found in all isolates. Virulence genes were detected in a rate of 26.27%, 13.13%, 20%, 6.67%, and 33.33% for LT, ST, stx1, stx2, and eae genes, respectively. This relatively high frequency of fecal contamination points towards the high risk of developing diarrhea by antibiotic resistant DEC in low socioeconomic communities particularly with old fashion distribution systems. PMID:27725834

Floors and Toilets: Association of Floors and Sanitation Practices with Fecal Contamination in Peruvian Amazon Peri-Urban Households.

PubMed

Exum, Natalie G; Olórtegui, Maribel Paredes; Yori, Pablo Peñataro; Davis, Meghan F; Heaney, Christopher D; Kosek, Margaret; Schwab, Kellogg J

2016-07-19

Over two billion people worldwide lack access to an improved sanitation facility that adequately retains or treats feces. This results in the potential for fecal material containing enteric pathogens to contaminate the environment, including household floors. This study aimed to assess how floor type and sanitation practices impacted the concentration of fecal contamination on household floors. We sampled 189 floor surfaces within 63 households in a peri-urban community in Iquitos, Peru. All samples were analyzed for colony forming units (CFUs) of E. coli, and households were evaluated for their water, sanitation, and hygiene characteristics. Results of multivariate linear regression indicated that households with improved sanitation and cement floors in the kitchen area had reduced fecal contamination to those with unimproved sanitation and dirt floors (Beta: -1.18 log10 E. coli CFU/900 cm(2); 95% confidence interval [CI]: -1.77, -0.60). Households that did not versus did share their sanitation facility also had less contaminated kitchen floors (Beta: -0.65 log10 E. coli CFU/900 cm(2); 95% CI: -1.15, -0.16). These findings suggest that the sanitation facilities of a home may impact the microbial load found on floors, contributing to the potential for household floors to serve as an indirect route of fecal pathogen transmission to children.

Contribution of Colonic Fermentation and Fecal Water Toxicity to the Pathophysiology of Lactose-Intolerance

PubMed Central

Windey, Karen; Houben, Els; Deroover, Lise; Verbeke, Kristin

2015-01-01

Whether or not abdominal symptoms occur in subjects with small intestinal lactose malabsorption might depend on differences in colonic fermentation. To evaluate this hypothesis, we collected fecal samples from subjects with lactose malabsorption with abdominal complaints (LM-IT, n = 11) and without abdominal complaints (LM-T, n = 8) and subjects with normal lactose digestion (NLD, n = 15). Lactose malabsorption was diagnosed using a 13C-lactose breath test. Colonic fermentation was characterized in fecal samples at baseline and after incubation with lactose for 3 h, 6 h and 24 h through a metabolomics approach using gas chromatography-mass spectrometry (GC-MS). Fecal water cytotoxicity was analyzed using a colorimetric assay. Fecal water cytotoxicity was not different between the three groups (Kruskall-Wallis p = 0.164). Cluster analysis of the metabolite patterns revealed separate clusters for NLD, LM-T and LM-IT samples at baseline and after 24 h incubation with lactose. Levels of 5-methyl-2-furancarboxaldehyde were significantly higher in LM-IT and LM-T compared to NLD whereas those of an unidentified aldehyde were significantly higher in LM-IT compared to LM-T and NLD. Incubation with lactose increased short chain fatty acid (SCFA) concentrations more in LM-IT and LM-T compared to NLD. In conclusion, fermentation patterns were clearly different in NLD, LM-IT and LM-T, but not related to differences in fecal water cytotoxicity. PMID:26371036

Contribution of Colonic Fermentation and Fecal Water Toxicity to the Pathophysiology of Lactose-Intolerance.

PubMed

Windey, Karen; Houben, Els; Deroover, Lise; Verbeke, Kristin

2015-09-08

Whether or not abdominal symptoms occur in subjects with small intestinal lactose malabsorption might depend on differences in colonic fermentation. To evaluate this hypothesis, we collected fecal samples from subjects with lactose malabsorption with abdominal complaints (LM-IT, n = 11) and without abdominal complaints (LM-T, n = 8) and subjects with normal lactose digestion (NLD, n = 15). Lactose malabsorption was diagnosed using a (13)C-lactose breath test. Colonic fermentation was characterized in fecal samples at baseline and after incubation with lactose for 3 h, 6 h and 24 h through a metabolomics approach using gas chromatography-mass spectrometry (GC-MS). Fecal water cytotoxicity was analyzed using a colorimetric assay. Fecal water cytotoxicity was not different between the three groups (Kruskall-Wallis p = 0.164). Cluster analysis of the metabolite patterns revealed separate clusters for NLD, LM-T and LM-IT samples at baseline and after 24 h incubation with lactose. Levels of 5-methyl-2-furancarboxaldehyde were significantly higher in LM-IT and LM-T compared to NLD whereas those of an unidentified aldehyde were significantly higher in LM-IT compared to LM-T and NLD. Incubation with lactose increased short chain fatty acid (SCFA) concentrations more in LM-IT and LM-T compared to NLD. In conclusion, fermentation patterns were clearly different in NLD, LM-IT and LM-T, but not related to differences in fecal water cytotoxicity.

Diagnostic stages of the parasites of the Florida manatee, Trichechus manatus latirostris.

PubMed

Bando, Monica; Larkin, Iskande V; Wright, Scott D; Greiner, Ellis C

2014-02-01

Limited information is available on diagnostic stages of parasites in Florida manatees (Trichechus manatus latirostris). We examined 67 fecal samples from captive and wild manatees to define the diagnostic stages of the parasite fauna known to occur in Florida manatees. Parasite eggs were freshly extracted ex utero from identified mature helminths and subsequently characterized, illustrated, and matched to those isolated from fecal samples. In addition, coccidian oocysts in the fecal samples were identified. These diagnostic stages included eggs from 5 species of trematodes (Chiorchis fabaceus, Chiorchis groschafti, Pulmonicola cochleotrema, Moniligerum blairi, and Nudacotyle undicola), 1 nematode (Heterocheilus tunicatus), and oocysts of 2 coccidians (Eimeria manatus and Eimeria nodulosa).

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel.

PubMed

Ohad, Shoshanit; Ben-Dor, Shifra; Prilusky, Jaime; Kravitz, Valeria; Dassa, Bareket; Chalifa-Caspi, Vered; Kashi, Yechezkel; Rorman, Efrat

2016-01-01

The emerging microbial source tracking (MST) methodologies aim to identify fecal contamination originating from domestic and wild animals, and from humans. Avian MST is especially challenging, primarily because the Aves class includes both domesticated and wild species with highly diverse habitats and dietary characteristics. The quest for specific fecal bacterial MST markers can be difficult with respect to attaining sufficient assay sensitivity and specificity. The present study utilizes high throughput sequencing (HTS) to screen bacterial 16S rRNA genes from fecal samples collected from both domestic and wild avian species. Operational taxonomic unit (OTU) analysis was then performed, from which sequences were retained for downstream quantitative polymerase chain reaction (qPCR) marker development. Identification of unique avian host DNA sequences, absent in non-avian hosts, was then carried out using a dedicated database of bacterial 16S rRNA gene taken from the Ribosomal Database Project. Six qPCR assays were developed targeting the 16S rRNA gene of Lactobacillus, Gallibacterium, Firmicutes, Fusobacteriaceae, and other bacteria. Two assays (Av4143 and Av163) identified most of the avian fecal samples and demonstrated sensitivity values of 91 and 70%, respectively. The Av43 assay only identified droppings from battery hens and poultry, whereas each of the other three assays (Av24, Av13, and Av216) identified waterfowl species with lower sensitivities values. The development of an MST assay-panel, which includes both domestic and wild avian species, expands the currently known MST analysis capabilities for decoding fecal contamination.

Male-specific coliphages for source tracking fecal contamination in surface waters and prevalence of Shiga-toxigenic Escherichia coli in a major produce production region of the Central Coast of California.

PubMed

Ravva, Subbarao V; Sarreal, Chester Z; Cooley, Michael B

2015-07-01

To provide data for traditional trace-back studies from fork to farm, it is necessary to determine the environmental sources for Shiga-toxigenic Escherichia coli. We developed SYBR green based reverse-transcriptase PCR methods to determine the prevalence of F+ RNA coliphages (FRNA) as indicators of fecal contamination. Male-specific coliphages, determined using a single-agar overlay method, were prevalent in all surface waters sampled for 8 months. F+ DNA coliphages (FDNA) were predominant compared to FRNA in water samples from majority of sampling locations. Most (90%) of the FRNA were sourced to humans and originated from human-impacted sites. Members of genogroup III represented 77% of FRNA originated from human sources. Furthermore, 93% of FRNA sourced to animals were also detected in water samples from human-impacted sites. Eighty percent of all FRNA were isolated during the winter months indicating seasonality in prevalence. In contrast, FDNA were more prevalent during summer months. E. coli O157:H7 and Shiga-toxigenic E. coli were detected in water samples from locations predominantly influenced by agriculture. Owing to their scarcity, their numbers could not be correlated with the prevalence of FRNA or FDNA in water samples. Both coliform bacteria and generic E. coli from agricultural or human-impacted sites were similar in numbers and thus could not be used to determine the sources of fecal contamination. Data on the prevalence of male-specific coliphages may be invaluable for predicting the sources of fecal contamination and aid in developing methods to prevent enteric pathogen contamination from likely sources during produce production.

Plasma Septin9 versus fecal immunochemical testing for colorectal cancer screening: a prospective multicenter study.

PubMed

Johnson, David A; Barclay, Robert L; Mergener, Klaus; Weiss, Gunter; König, Thomas; Beck, Jürgen; Potter, Nicholas T

2014-01-01

Screening improves outcomes related to colorectal cancer (CRC); however, suboptimal participation for available screening tests limits the full benefits of screening. Non-invasive screening using a blood based assay may potentially help reach the unscreened population. To compare the performance of a new Septin9 DNA methylation based blood test with a fecal immunochemical test (FIT) for CRC screening. In this trial, fecal and blood samples were obtained from enrolled patients. To compare test sensitivity for CRC, patients with screening identified colorectal cancer (n = 102) were enrolled and provided samples prior to surgery. To compare test specificity patients were enrolled prospectively (n = 199) and provided samples prior to bowel preparation for screening colonoscopy. Plasma and fecal samples were analyzed using the Epi proColon and OC Fit-Check tests respectively. For all samples, sensitivity for CRC detection was 73.3% (95% CI 63.9-80.9%) and 68.0% (95% CI 58.2-76.5%) for Septin9 and FIT, respectively. Specificity of the Epi proColon test was 81.5% (95% CI 75.5-86.3%) compared with 97.4% (95% CI 94.1-98.9%) for FIT. For paired samples, the sensitivity of the Epi proColon test (72.2% -95% CI 62.5-80.1%) was shown to be statistically non-inferior to FIT (68.0%-95% CI 58.2-76.5%). When test results for Epi proColon and FIT were combined, CRC detection was 88.7% at a specificity of 78.8%. At a sensitivity of 72%, the Epi proColon test is non- inferior to FIT for CRC detection, although at a lower specificity. With negative predictive values of 99.8%, both methods are identical in confirming the absence of CRC. ClinicalTrials.gov NCT01580540.

Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces.

PubMed

Shridhar, P B; Noll, L W; Shi, X; An, B; Cernicchiaro, N; Renter, D G; Nagaraja, T G; Bai, J

2016-01-01

Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture-spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P > 0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.

Combining Land Use Information and Small Stream Sampling with PCR-Based Methods for Better Characterization of Diffuse Sources of Human Fecal Pollution

EPA Science Inventory

Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between...

Impact of zoo visitors on the fecal cortisol levels and behavior of an endangered species: Indian blackbuck (Antelope cervicapra L.).

PubMed

Rajagopal, Thangavel; Archunan, Govindaraju; Sekar, Mahadevan

2011-01-01

This study investigated behavioral activities (resting, moving, aggressive, social, and reproductive behavior) and fecal cortisol levels in 8 individually identified adult male blackbucks during periods of varying levels of zoo visitors (zero, low, high, and extremely high zoo visitor density). This study also elucidated whether zoo visitor density could disturb nonhuman animal welfare. This study analyzed fecal cortisol from the samples of blackbuck by radioimmunoassay and found significant differences (p < .05) for time the animals devoted to moving, resting, aggressive, reproductive, and social behavior on days with high and extremely high levels of zoo visitors. The ANOVA with Duncan's Multiple Range Test test showed that the fecal cortisol concentration was higher (p < .05) during the extremely high (137.30 ± 5.88 ng/g dry feces) and high (113.51 ± 3.70 ng/g dry feces) levels of zoo visitor density. The results of the study suggest that zoo visitor density affected behavior and adrenocortical secretion in Indian Blackbuck, and this may indicate an animal welfare problem.

Dynamics of Escherichia coli Virulence Factors in Dairy Herds and Farm Environments in a Longitudinal Study in the United States

PubMed Central

Lambertini, Elisabetta; Karns, Jeffrey S.; Van Kessel, Jo Ann S.; Cao, Huilin; Schukken, Ynte H.; Wolfgang, David R.; Smith, Julia M.

2015-01-01

Pathogenic Escherichia coli or its associated virulence factors have been frequently detected in dairy cow manure, milk, and dairy farm environments. However, it is unclear what the long-term dynamics of E. coli virulence factors are and which farm compartments act as reservoirs. This study assessed the occurrence and dynamics of four E. coli virulence factors (eae, stx1, stx2, and the gamma allele of the tir gene [γ-tir]) on three U.S. dairy farms. Fecal, manure, water, feed, milk, and milk filter samples were collected from 2004 to 2012. Virulence factors were measured by postenrichment quantitative PCR (qPCR). All factors were detected in most compartments on all farms. Fecal and manure samples showed the highest prevalence, up to 53% for stx and 21% for γ-tir in fecal samples and up to 84% for stx and 44% for γ-tir in manure. Prevalence was low in milk (up to 1.9% for stx and 0.7% for γ-tir). However, 35% of milk filters were positive for stx and 20% were positive for γ-tir. All factors were detected in feed and water. Factor prevalence and levels, expressed as qPCR cycle threshold categories, fluctuated significantly over time, with no clear seasonal signal independent from year-to-year variability. Levels were correlated between fecal and manure samples, and in some cases autocorrelated, but not between manure and milk filters. Shiga toxins were nearly ubiquitous, and 10 to 18% of the lactating cows were potential shedders of E. coli O157 at least once during their time in the herds. E. coli virulence factors appear to persist in many areas of the farms and therefore contribute to transmission dynamics. PMID:25911478

Longitudinal Study of Fecal Shedding of Escherichia coli O157:H7 in Feedlot Cattle: Predominance and Persistence of Specific Clonal Types despite Massive Cattle Population Turnover

PubMed Central

LeJeune, J. T.; Besser, T. E.; Rice, D. H.; Berg, J. L.; Stilborn, R. P.; Hancock, D. D.

2004-01-01

Identification of the sources and methods of transmission of Escherichia coli O157:H7 in feedlot cattle may facilitate the development of on-farm control measures for this important food-borne pathogen. The prevalence of E. coli O157:H7 in fecal samples of commercial feedlot cattle in 20 feedlot pens between April and September 2000 was determined throughout the finishing feeding period prior to slaughter. Using immunomagnetic separation, E. coli O157:H7 was isolated from 636 of 4,790 (13%) fecal samples in this study, with highest prevalence earliest in the feeding period. No differences were observed in the fecal or water trough sediment prevalence values of E. coli O157:H7 in 10 pens supplied with chlorinated drinking water supplies compared with nonchlorinated water pens. Pulsed-field gel electrophoresis of XbaI-digested bacterial DNA of the 230 isolates obtained from eight of the pens revealed 56 unique restriction endonuclease digestion patterns (REDPs), although nearly 60% of the isolates belonged to a group of four closely related genetic subtypes that were present in each of the pens and throughout the sampling period. The other REDPs were typically transiently detected, often in single pens and on single sample dates, and in many cases were also closely related to the four predominant REDPs. The persistence and predominance of a few REDPs observed over the entire feeding period on this livestock operation highlight the importance of the farm environment, and not necessarily the incoming cattle, as a potential source or reservoir of E. coli O157:H7 on farms. PMID:14711666

PCR Inhibition of a Quantitative PCR for Detection of Mycobacterium avium Subspecies Paratuberculosis DNA in Feces: Diagnostic Implications and Potential Solutions

PubMed Central

Acharya, Kamal R.; Dhand, Navneet K.; Whittington, Richard J.; Plain, Karren M.

2017-01-01

Molecular tests such as polymerase chain reaction (PCR) are increasingly being applied for the diagnosis of Johne’s disease, a chronic intestinal infection of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Feces, as the primary test sample, presents challenges in terms of effective DNA isolation, with potential for PCR inhibition and ultimately for reduced analytical and diagnostic sensitivity. However, limited evidence is available regarding the magnitude and diagnostic implications of PCR inhibition for the detection of MAP in feces. This study aimed to investigate the presence and diagnostic implications of PCR inhibition in a quantitative PCR assay for MAP (High-throughput Johne’s test) to investigate the characteristics of samples prone to inhibition and to identify measures that can be taken to overcome this. In a study of fecal samples derived from a high prevalence, endemically infected cattle herd, 19.94% of fecal DNA extracts showed some evidence of inhibition. Relief of inhibition by a five-fold dilution of the DNA extract led to an average increase in quantification of DNA by 3.3-fold that consequently increased test sensitivity of the qPCR from 55 to 80% compared to fecal culture. DNA extracts with higher DNA and protein content had 19.33 and 10.94 times higher odds of showing inhibition, respectively. The results suggest that the current test protocol is sensitive for herd level diagnosis of Johne’s disease but that test sensitivity and individual level diagnosis could be enhanced by relief of PCR inhibition, achieved by five-fold dilution of the DNA extract. Furthermore, qualitative and quantitative parameters derived from absorbance measures of DNA extracts could be useful for prediction of inhibitory fecal samples. PMID:28210245

Dysbiosis of the Fecal Microbiota in Cattle Infected with Mycobacterium avium subsp. paratuberculosis

PubMed Central

Vecchiarelli, Bonnie; Indugu, Nagaraju; Kumar, Sanjay; Gallagher, Susan C.; Fyock, Terry L.; Sweeney, Raymond W.

2016-01-01

Johne's disease (JD) is a chronic, intestinal infection of cattle, caused by Mycobacterium avium subsp. paratuberculosis (MAP). It results in granulomatous inflammation of the intestinal lining, leading to malabsorption, diarrhea, and weight loss. Crohn’s disease (CD), a chronic, inflammatory gastrointestinal disease of humans, has many clinical and pathologic similarities to JD. Dysbiosis of the enteric microbiota has been demonstrated in CD patients. It is speculated that this dysbiosis may contribute to the intestinal inflammation observed in those patients. The purpose of this study was to investigate the diversity patterns of fecal bacterial populations in cattle infected with MAP, compared to those of uninfected control cattle, using phylogenomic analysis. Fecal samples were selected to include samples from 20 MAP-positive cows; 25 MAP-negative herdmates; and 25 MAP-negative cows from a MAP-free herd. The genomic DNA was extracted; PCR amplified sequenced on a 454 Roche platform, and analyzed using QIIME. Approximately 199,077 reads were analyzed from 70 bacterial communities (average of 2,843 reads/sample). The composition of bacterial communities differed between the 3 treatment groups (P < 0.001; Permanova test). Taxonomic assignment of the operational taxonomic units (OTUs) identified 17 bacterial phyla across all samples. Bacteroidetes and Firmicutes constituted more than 95% of the bacterial population in the negative and exposed groups. In the positive group, lineages of Actinobacteria and Proteobacteria increased and those of Bacteroidetes and Firmicutes decreased (P < 0.001). Actinobacteria was highly abundant (30% of the total bacteria) in the positive group compared to exposed and negative groups (0.1–0.2%). Notably, the genus Arthrobacter was found to predominate Actinobacteria in the positive group. This study indicates that MAP-infected cattle have a different composition of their fecal microbiota than MAP-negative cattle. PMID:27494144

Dysbiosis of the Fecal Microbiota in Cattle Infected with Mycobacterium avium subsp. paratuberculosis.

PubMed

Fecteau, Marie-Eve; Pitta, Dipti W; Vecchiarelli, Bonnie; Indugu, Nagaraju; Kumar, Sanjay; Gallagher, Susan C; Fyock, Terry L; Sweeney, Raymond W

2016-01-01

Johne's disease (JD) is a chronic, intestinal infection of cattle, caused by Mycobacterium avium subsp. paratuberculosis (MAP). It results in granulomatous inflammation of the intestinal lining, leading to malabsorption, diarrhea, and weight loss. Crohn's disease (CD), a chronic, inflammatory gastrointestinal disease of humans, has many clinical and pathologic similarities to JD. Dysbiosis of the enteric microbiota has been demonstrated in CD patients. It is speculated that this dysbiosis may contribute to the intestinal inflammation observed in those patients. The purpose of this study was to investigate the diversity patterns of fecal bacterial populations in cattle infected with MAP, compared to those of uninfected control cattle, using phylogenomic analysis. Fecal samples were selected to include samples from 20 MAP-positive cows; 25 MAP-negative herdmates; and 25 MAP-negative cows from a MAP-free herd. The genomic DNA was extracted; PCR amplified sequenced on a 454 Roche platform, and analyzed using QIIME. Approximately 199,077 reads were analyzed from 70 bacterial communities (average of 2,843 reads/sample). The composition of bacterial communities differed between the 3 treatment groups (P < 0.001; Permanova test). Taxonomic assignment of the operational taxonomic units (OTUs) identified 17 bacterial phyla across all samples. Bacteroidetes and Firmicutes constituted more than 95% of the bacterial population in the negative and exposed groups. In the positive group, lineages of Actinobacteria and Proteobacteria increased and those of Bacteroidetes and Firmicutes decreased (P < 0.001). Actinobacteria was highly abundant (30% of the total bacteria) in the positive group compared to exposed and negative groups (0.1-0.2%). Notably, the genus Arthrobacter was found to predominate Actinobacteria in the positive group. This study indicates that MAP-infected cattle have a different composition of their fecal microbiota than MAP-negative cattle.

Identifying fecal sources in a selected catchment reach using multiple source-tracking tools

USGS Publications Warehouse

Vogel, J.R.; Stoeckel, D.M.; Lamendella, R.; Zelt, R.B.; Santo, Domingo J.W.; Walker, S.R.; Oerther, D.B.

2007-01-01

Given known limitations of current microbial source-tracking (MST) tools, emphasis on small, simple study areas may enhance interpretations of fecal contamination sources in streams. In this study, three MST tools - Escherichia coli repetitive element polymerase chain reaction (rep-PCR), coliphage typing, and Bacteroidales 16S rDNA host-associated markers - were evaluated in a selected reach of Plum Creek in sooth-central Nebraska. Water-quality samples were collected from six sites. One reach was selected for MST evaluation based on observed patterns of E. coli contamination. Despite high E. coli concentrations, coliphages were detected only once among water samples, precluding their use as a MST tool in this setting. Rep-PCR classification of E. coli isolates from both water and sediment samples supported the hypothesis that cattle and wildlife were dominant sources of fecal contamination, with minor contributions by horses and humans. Conversely, neither ruminant nor human sources were detected by Bacteroidales markers in most water samples. In bed sediment, ruminant- and human-associated Bacteroidales markers were detected throughout the interval from 0 to 0.3 m, with detections independent of E. coli concentrations in the sediment. Although results by E. coli-based and Bacteroidales-based MST methods led to similar interpretations, detection of Bacteroidales markers in sediment more commonly than in water indicates that different tools to track fecal contamination (in this case, tools based on Bacteroidales DNA and E. coli isolates) may have varying relevance to the more specific goal of tracking the sources of E. coli in watersheds. This is the first report of simultaneous, toolbox approach application of a library-based and marker-based MST analyses to lowing surface water. ?? ASA, CSSA, SSSA.

Preliminary survey of antibiotic-resistant fecal indicator bacteria and pathogenic Escherichia coli from river-water samples collected in Oakland County, Michigan, 2003

USGS Publications Warehouse

Fogarty, Lisa R.; Duris, Joseph W.; Aichele, Stephen S.

2005-01-01

A preliminary study was done in Oakland County, Michigan, to determine the concentration of fecal indicator bacteria (fecal coliform bacteria and enterococci), antibiotic resistance patterns of these two groups, and the presence of potentially pathogenic Escherichia coli (E. coli). For selected sites, specific members of these groups [E. coli, Enterococcus faecium (E. faecium) and Enterococcus faecalis (E. faecalis)] were isolated and tested for levels of resistance to specific antibiotics used to treat human infections by pathogens in these groups and for their potential to transfer these resistances. In addition, water samples from all sites were tested for indicators of potentially pathogenic E. coli by three assays: a growth-based assay for sorbitol-negative E. coli, an immunological assay for E. coli O157, and a molecular assay for three virulence and two serotype genes. Samples were also collected from two non-urbanized sites outside of Oakland County. Results from the urbanized Oakland County area were compared to those from these two non-urbanized sites. Fecal indicator bacteria concentrations exceeded State of Michigan recreational water-quality standards and (or) recommended U.S. Environmental Protection Agency (USEPA) standards in samples from all but two Oakland County sites. Multiple-antibiotic-resistant fecal coliform bacteria were found at all sites, including two reference sites from outside the county. Two sites (Stony Creek and Paint Creek) yielded fecal coliform isolates resistant to all tested antibiotics. Patterns indicative of extended-spectrum-β-lactamase (ESBL)- producing fecal coliform bacteria were found at eight sites in Oakland County and E. coli resistant to clinically significant antibiotics were recovered from the River Rouge, Clinton River, and Paint Creek. Vancomycin-resistant presumptive enterococci were found at six sites in Oakland County and were not found at the reference sites. Evidence of acquired antibiotic resistances was detected in bacteria from multiple sites in Oakland County but not detected in bacteria from the reference sites. Integrons capable of transferring resistance were detected in isolates from the River Rouge and Clinton River. E. faecium and E. faecalis identified in samples collected from Kearsley Creek and Evans Ditch were resistant to high levels of vancomycin and carried transferable genes responsible for resistance. Several sites in Oakland County had indicators of pathogenic E. coli in August and (or) September 2003. Two samples from the Clinton River in August tested positive for all three E. coli O157 tests. Both the August and September samples from one River Rouge site were positive for the immunological and molecular assay for E. coli O157. A combination of virulence genes commonly associated with human illness was detected at five sites in August and seven sites in September. Antibiotic-resistance profiles of clinical concern along with genes capable of transferring the resistance were found at several sites throughout Oakland County; samples from many of these sites also contained potentially pathogenic E. coli.

Seasonal variation of fecal indicator bacteria in storm events within the US stormwater database.

PubMed

Pan, Xubin; Jones, Kim D

2012-01-01

Bacteria are one of the major causes of surface water impairments in the USA. Over the past several years, best management practices, including detention basins, manufactured devices, grass swales, filters and bioretention cells have been used to remove bacteria and other pollutants from stormwater runoff. However, there are data gaps in the comprehensive studies of bacteria concentrations in stormwater runoff. In this paper, the event mean concentration (EMC) of fecal indicator bacteria (Enterococcus, Escherichia coli, fecal Streptococcus group bacteria, and fecal coliform) across the USA was retrieved from the international stormwater best management practices database to analyze the seasonal variations of inflow and outflow event mean concentrations and removal efficiencies. The Kruskal-Wallis test was employed to determine the seasonal variations of bacteria indicator concentrations and removals, and the two-sample Kolmogorov-Smirnov test was used for comparing different seasonal outcomes. The results indicate that all the inflow EMC of FIB in stormwater runoff is above the water quality criteria. The seasonal differences of fecal Streptococcus group bacteria and fecal coliform are significant. Summer has the potential to increase the bacteria EMC and illustrate the seasonal differences.

Antibiotic-resistant fecal bacteria, antibiotics, and mercury in surface waters of Oakland County, Michigan, 2005-2006

USGS Publications Warehouse

Fogarty, Lisa R.; Duris, Joseph W.; Crowley, Suzanne L.; Hardigan, Nicole

2007-01-01

Water samples collected from 20 stream sites in Oakland and Macomb Counties, Mich., were analyzed to learn more about the occurrence of cephalosporin-resistant Escherichia coli (E. coli) and vancomycin-resistant enterococci (VRE) and the co-occurrence of antibiotics and mercury in area streams. Fecal indicator bacteria concentrations exceeded the Michigan recreational water-quality standard of 300 E. coli colony forming units (CFU) per 100 milliliters of water in 19 of 35 stream-water samples collected in Oakland County. A gene commonly associated with enterococci from humans was detected in samples from Paint Creek at Rochester and Evans Ditch at Southfield, indicating that human fecal waste is a possible source of fecal contamination at these sites. E. coli resistant to the cephalosporin antibiotics (cefoxitin and/ or ceftriaxone) were found at all sites on at least one occasion. The highest percentages of E. coli isolates resistant to cefoxitin and ceftriaxone were 71 percent (Clinton River at Auburn Hills) and 19 percent (Sashabaw Creek near Drayton Plains), respectively. Cephalosporin-resistant E. coli was detected more frequently in samples from intensively urbanized or industrialized areas than in samples from less urbanized areas. VRE were not detected in any sample collected in this study. Multiple antibiotics (azithromycin, erythromycin, ofloxacin, sulfamethoxazole, and trimethoprim) were detected in water samples from the Clinton River at Auburn Hills, and tylosin (an antibiotic used in veterinary medicine and livestock production that belongs to the macrolide group, along with erythromycin) was detected in one water sample from Paint Creek at Rochester. Concentrations of total mercury were as high as 19.8 nanograms per liter (Evans Ditch at Southfield). There was no relation among percentage of antibiotic-resistant bacteria and measured concentrations of antibiotics or mercury in the water. Genetic elements capable of exchanging multiple antibiotic-resistance genes (class I integrons) were detected in several samples, indicating that the resistance carried by these organisms may be transferable to other bacteria, including disease-causing bacteria.

Elevation and vegetation determine Cryptosporidium oocyst shedding by yellow-bellied marmots (Marmota flaviventris) in the Sierra Nevada Mountains

PubMed Central

Montecino-Latorre, Diego; Li, Xunde; Xiao, Chengling; Atwill, Edward R.

2015-01-01

Wildlife are increasingly recognized as important biological reservoirs of zoonotic species of Cryptosporidium that might contaminate water and cause human exposure to this protozoal parasite. The habitat range of the yellow-bellied marmot (Marmota flaviventris) overlaps extensively with the watershed boundaries of municipal water supplies for California communities along the foothills of the Sierra Nevada. We conducted a cross-sectional epidemiological study to estimate the fecal shedding of Cryptosporidium oocysts by yellow-bellied marmots and to quantify the environmental loading rate and determine risk factors for Cryptosporidium fecal shedding in this montane wildlife species. The observed proportion of Cryptosporidium positive fecal samples was 14.7% (33/224, positive number relative to total number samples) and the environmental loading rate was estimated to be 10,693 oocysts animal-1 day-1. Fecal shedding was associated with the elevation and vegetation status of their habitat. Based on a portion of the 18s rRNA gene sequence of 2 isolates, the Cryptosporidium found in Marmota flaviventris were 99.88%–100% match to multiple isolates of C. parvum in the GenBank. PMID:25834788

Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

PubMed

Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

2016-01-01

Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

The Fecal Microbiota Profile and Bronchiolitis in Infants

PubMed Central

Linnemann, Rachel W.; Mansbach, Jonathan M.; Ajami, Nadim J.; Espinola, Janice A.; Petrosino, Joseph F.; Piedra, Pedro A.; Stevenson, Michelle D.; Sullivan, Ashley F.; Thompson, Amy D.; Camargo, Carlos A.

2016-01-01

BACKGROUND: Little is known about the association of gut microbiota, a potentially modifiable factor, with bronchiolitis in infants. We aimed to determine the association of fecal microbiota with bronchiolitis in infants. METHODS: We conducted a case–control study. As a part of multicenter prospective study, we collected stool samples from 40 infants hospitalized with bronchiolitis. We concurrently enrolled 115 age-matched healthy controls. By applying 16S rRNA gene sequencing and an unbiased clustering approach to these 155 fecal samples, we identified microbiota profiles and determined the association of microbiota profiles with likelihood of bronchiolitis. RESULTS: Overall, the median age was 3 months, 55% were male, and 54% were non-Hispanic white. Unbiased clustering of fecal microbiota identified 4 distinct profiles: Escherichia-dominant profile (30%), Bifidobacterium-dominant profile (21%), Enterobacter/Veillonella-dominant profile (22%), and Bacteroides-dominant profile (28%). The proportion of bronchiolitis was lowest in infants with the Enterobacter/Veillonella-dominant profile (15%) and highest in the Bacteroides-dominant profile (44%), corresponding to an odds ratio of 4.59 (95% confidence interval, 1.58–15.5; P = .008). In the multivariable model, the significant association between the Bacteroides-dominant profile and a greater likelihood of bronchiolitis persisted (odds ratio for comparison with the Enterobacter/Veillonella-dominant profile, 4.24; 95% confidence interval, 1.56–12.0; P = .005). In contrast, the likelihood of bronchiolitis in infants with the Escherichia-dominant or Bifidobacterium-dominant profile was not significantly different compared with those with the Enterobacter/Veillonella-dominant profile. CONCLUSIONS: In this case–control study, we identified 4 distinct fecal microbiota profiles in infants. The Bacteroides-dominant profile was associated with a higher likelihood of bronchiolitis. PMID:27354456

The associations between culling due to clinical Johne's disease or the detection of Mycobacterium avium subsp. paratuberculosis fecal shedding and the diagnosis of clinical or subclinical diseases in two dairy herds in Minnesota, USA.

PubMed

Raizman, Eran A; Wells, Scott J; Godden, Sandra M; Fetrow, John; Oakes, J Michael

2007-07-16

Our objectives were to identify associations between clinical or subclinical diseases and subsequent culling because of clinical Johne's disease (JD) or the detection of fecal shedding of Mycobacterium paratuberculosis (Map) after 305 days in milk (DIM). A total of 1297 cows from two Minnesota dairies were enrolled in the study. From study cows, fecal samples were obtained prior to calving (close-up period) and after at least 305 DIM or at the time of leaving the herd (sold/dead). Between 3 and 21 DIM, blood samples were obtained for serum betahydroxybutyrate (BHB) and serum total-protein testing. Body-condition score (BCS) was evaluated during the close-up period, between 3 and 21 DIM, and at the end of lactation. The diagnosis time (DIM) of clinical disease events (culling because of JD clinical signs, ketosis, lameness, mastitis, displacement abomasum, injury, metritis, milk fever, pneumonia, and retained placenta) was recorded. Sixty-six cows were culled because of JD clinical signs (CCDJ) with average DIM of 209. CCDJ was associated with event of pneumonia (n=131) (OR=3.0, 95% CI=1.0-6.0) and level of fecal shedding (light: OR=13.0, 95% CI=5.3-30.0; moderate: OR=34.0, 95% CI=13.0-89.0; heavy: OR=66.0, 95% CI=26.0-171.0). Detection of fecal shedding at the end of the lactation (n=79) was associated only with event of pneumonia (OR=2.0, 95% CI=1.0-4.0).

Kefir consumption does not alter plasma lipid levels or cholesterol fractional synthesis rates relative to milk in hyperlipidemic men: a randomized controlled trial [ISRCTN10820810

PubMed Central

St-Onge, Marie-Pierre; Farnworth, Edward R; Savard, Tony; Chabot, Denise; Mafu, Akier; Jones, Peter JH

2002-01-01

Background Fermented milk products have been shown to affect serum cholesterol concentrations in humans. Kefir, a fermented milk product, has been traditionally consumed for its potential health benefits but has to date not been studied for its hypocholesterolemic properties. Methods Thirteen healthy mildly hypercholesterolemic male subjects consumed a dairy supplement in randomized crossover trial for 2 periods of 4 wk each. Subjects were blinded to the dairy supplement consumed. Blood samples were collected at baseline and after 4 wk of supplementation for measurement of plasma total, low-density lipoprotein, and high-density lipoprotein cholesterol and triglyceride concentrations, as well as fatty acid profile and cholesterol synthesis rate. Fecal samples were collected at baseline and after 2 and 4 wk of supplementation for determination of fecal short chain fatty acid level and bacterial content. Results Kefir had no effect on total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglyceride concentrations nor on cholesterol fractional synthesis rates after 4 wk of supplementation. No significant change on plasma fatty acid levels was observed with diet. However, both kefir and milk increased (p < 0.05) fecal isobutyric, isovaleric and propionic acids as well as the total amount of fecal short chain fatty acids. Kefir supplementation resulted in increased fecal bacterial content in the majority of the subjects. Conclusions Since kefir consumption did not result in lowered plasma lipid concentrations, the results of this study do not support consumption of kefir as a cholesterol-lowering agent. PMID:11825344

Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations

PubMed Central

Lamendella, Regina; Li, Kent C.; Oerther, Daniel

2013-01-01

Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental waters. In order to address this, we studied the diversity of 9,340 partial (>600 bp in length) Bacteroidales 16S rRNA gene sequences from 13 fecal sources and nine feces-contaminated watersheds. The compositions of major Bacteroidales populations were analyzed to determine which host and environmental sequences were contributing to each group. This information allowed us to identify populations which were both exclusive to swine fecal sources and detected in swine-contaminated waters. Phylogenetic and diversity analyses revealed that some markers previously believed to be highly specific to swine populations are shared by multiple hosts, potentially explaining the cross-amplification signals obtained with nontargeted hosts. These data suggest that while many Bacteroidales populations are cosmopolitan, others exhibit a preferential host distribution and may be able to survive different environmental conditions. This study further demonstrates the importance of elucidating the diversity patterns of targeted bacterial groups to develop more inclusive fecal source tracking applications. PMID:23160126

Rectal nitric oxide and fecal calprotectin in inflammatory bowel disease.

PubMed

Reinders, Claudia A; Jonkers, Daisy; Janson, Emmellie A; Stockbrügger, Reinhold W; Stobberingh, Ellen E; Hellström, Per M; Lundberg, Jon O

2007-10-01

The assessment of intestinal inflammation in patients with inflammatory bowel disease (IBD) remains a difficult challenge. Both rectal nitric oxide (NO) and fecal calprotectin can be measured using non-invasive methods and are emerging as promising inflammatory markers in IBD. In this study the aim was to compare calprotectin and NO levels in IBD patients. Rectal NO was measured tonometrically in 23 healthy volunteers and 32 patients with IBD. In addition, we collected stool samples from all subjects for measurement of fecal calprotectin and nitrate/nitrite (NO metabolites). Patients with IBD had greatly increased NO and calprotectin levels compared to healthy volunteers (p <0.001). In addition, the nitrate levels were slightly increased in IBD patients. A weak correlation was found between rectal NO levels, disease activity and number of loose stools in IBD patients (Spearman's rho 0.37 and 0.51, respectively; p <0.05). Fecal calprotectin correlated only with age (Spearman's rho 0.51; p <0.01). However, no correlation was found between NO and calprotectin. Both rectal NO and fecal calprotectin are greatly increased during bowel inflammation, but they may reflect different parts of the inflammatory process. Future studies will elucidate the clinical usefulness of these two markers.

Zoonotic pathogens isolated from wild animals and environmental samples at two California wildlife hospitals.

PubMed

Siembieda, Jennifer L; Miller, Woutrina A; Byrne, Barbara A; Ziccardi, Michael H; Anderson, Nancy; Chouicha, Nadira; Sandrock, Christian E; Johnson, Christine K

2011-03-15

To determine types and estimate prevalence of potentially zoonotic enteric pathogens shed by wild animals admitted to either of 2 wildlife hospitals and to characterize distribution of these pathogens and of aerobic bacteria in a hospital environment. Cross-sectional study. Fecal samples from 338 animals in 2 wildlife hospitals and environmental samples from 1 wildlife hospital. Fecal samples were collected within 24 hours of hospital admission. Environmental samples were collected from air and surfaces. Samples were tested for zoonotic pathogens via culture techniques and biochemical analyses. Prevalence of pathogen shedding was compared among species groups, ages, sexes, and seasons. Bacterial counts were determined for environmental samples. Campylobacter spp, Vibrio spp, Salmonella spp, Giardia spp, and Cryptosporidium spp (alone or in combination) were detected in 105 of 338 (31%) fecal samples. Campylobacter spp were isolated only from birds. Juvenile passerines were more likely to shed Campylobacter spp than were adults; prevalence increased among juvenile passerines during summer. Non-O1 serotypes of Vibrio cholerae were isolated from birds; during an oil-spill response, 9 of 10 seabirds screened were shedding this pathogen, which was also detected in environmental samples. Salmonella spp and Giardia spp were isolated from birds and mammals; Cryptosporidium spp were isolated from mammals only. Floors of animal rooms had higher bacterial counts than did floors with only human traffic. Potentially zoonotic enteric pathogens were identified in samples from several species admitted to wildlife hospitals, indicating potential for transmission if prevention is not practiced.

Comparison of spectrofluorometric and HPLC methods for the characterization of fecal porphyrins in river otters.

PubMed

Taylor, C; Duffy, L K; Plumley, F G; Bowyer, R T

2000-09-01

A spectrofluorometric method (B. Grandchamp et al., 1980, Biochem. Biophys. Acta 629, 577-586) developed for the determination of amounts of uroporphyrin I (Uro I), coproporphyrin III (Copro III), and protoporphyrin IX (Proto IX) in skin fibroblasts was compared with a high-performance liquid chromatography (HPLC) method for the analysis of porphyrins in fecal samples of river otters (Lutra canadensis). Heptacarboxylate porphyrin I and coproporphyrin I, two porphyrins determined to be critical in defining the porphyrin profile in fecal samples of river otters with the HPLC method, contributed substantially to the calculation of the concentrations of Uro I and Copro III, respectively, in standard solutions of porphyrins with the spectrofluorometric method. Fluorescent components of the fecal matrix complicated the determination of the concentrations of Uro I, Copro III, and Proto IX with the spectrofluorometric method and resulted in erroneous values for the concentrations of these porphyrins compared with values determined with the HPLC method. These results indicate that the complexity of the sample, particularly with regard to the potential presence of interfering fluorescent compounds, as well as porphyrins additional to Uro I, Copro III, and Proto IX, should be considered prior to the application of the spectrofluorometric method. An alternative HPLC method developed for the rapid characterization of porphyrin profiles in fecal samples of river otters is described. Copyright 2000 Academic Press.

Determination of actinides in urine and fecal samples

DOEpatents

McKibbin, Terry T.

1993-01-01

A method of determining the radioactivity of specific actinides that are carried in urine or fecal sample material is disclosed. The samples are ashed in a muffle furnace, dissolved in an acid, and then treated in a series of steps of reduction, oxidation, dissolution, and precipitation, including a unique step of passing a solution through a chloride form anion exchange resin for separation of uranium and plutonium from americium.

Effects of Holding Time, Storage, and the Preservation of Samples on Sample Integrity for the Detection of Fecal Indicator Bacteria by Quantitative Polymerase Chain Reaction (qPCR)-based assays.

EPA Science Inventory

The purpose of this project was to answer questions related to storage of samples to be analyzed by the quantitative polymerase chain reaction (qPCR)-based assays for fecal indicator bacteria. The project was divided into two parts. The first part was to determine if filters th...

Determination of actinides in urine and fecal samples

DOEpatents

McKibbin, T.T.

1993-03-02

A method of determining the radioactivity of specific actinides that are carried in urine or fecal sample material is disclosed. The samples are ashed in a muffle furnace, dissolved in an acid, and then treated in a series of steps of reduction, oxidation, dissolution, and precipitation, including a unique step of passing a solution through a chloride form anion exchange resin for separation of uranium and plutonium from americium.

Quality of Life Is Related to Fecal Calprotectin Concentrations in Colonic Crohn Disease and Ulcerative Colitis, but not in Ileal Crohn Disease

PubMed Central

Gauss, Annika; Geib, Thomas; Hinz, Ulf; Schaefert, Rainer; Zwickel, Philipp; Zawierucha, Anna; Stremmel, Wolfgang; Klute, Lukas

2016-01-01

Abstract To formulate therapy goals, we aimed to define the relationship between fecal calprotectin and health-related quality of life in inflammatory bowel diseases (IBDs). This retrospective single-center cross-sectional study included ambulatory IBD patients who had completed standardized questionnaires comprising items of health-related quality of life (Short Inflammatory Bowel Disease Questionnaire) and clinical disease activity scores, and who had provided stool samples for calprotectin determination within 30 days of questionnaire completion. Correlation analyses were performed between the indicated parameters. Post hoc analysis was conducted, taking into account only data from patients with fecal calprotectin concentrations measured within 3 days of questionnaire completion. One hundred ninety-seven patients with Crohn disease and 111 patients with ulcerative colitis were enrolled in the study. Lower fecal calprotectin concentrations were associated with better health-related quality of life. The correlations were weak, but stronger if only fecal calprotectin concentrations measured within 3 days of questionnaire completion were included (results for 3 days; Crohn disease: n = 86, rS = −0.419, P < 0.001; ulcerative colitis: n = 43, rS = −0.432, P = 0.004). In Crohn disease, a significant correlation between fecal calprotectin concentration and health-related quality of life was found in patients with colonic involvement (n = 59, rS = −0.470, P < 0.001), but not in patients with purely ileal disease (n = 27, rS = −0.268, P = 0.18). Correlations between fecal calprotectin concentrations and clinical disease activity were also only weak to moderate. Owing to its moderate correlation with fecal calprotectin concentrations in IBD patients with colonic involvement, health-related quality of life should be used in combination with other markers for IBD management. This is even more important in isolated ileal Crohn disease, where no significant correlation between fecal calprotectin concentration and health-related quality of life was found. Especially for use in research studies, care should be taken to keep the time between clinical evaluation of IBD patients and the determination of fecal calprotectin concentrations as short as possible. PMID:27100452

Quality of Life Is Related to Fecal Calprotectin Concentrations in Colonic Crohn Disease and Ulcerative Colitis, but not in Ileal Crohn Disease.

PubMed

Gauss, Annika; Geib, Thomas; Hinz, Ulf; Schaefert, Rainer; Zwickel, Philipp; Zawierucha, Anna; Stremmel, Wolfgang; Klute, Lukas

2016-04-01

To formulate therapy goals, we aimed to define the relationship between fecal calprotectin and health-related quality of life in inflammatory bowel diseases (IBDs). This retrospective single-center cross-sectional study included ambulatory IBD patients who had completed standardized questionnaires comprising items of health-related quality of life (Short Inflammatory Bowel Disease Questionnaire) and clinical disease activity scores, and who had provided stool samples for calprotectin determination within 30 days of questionnaire completion. Correlation analyses were performed between the indicated parameters. Post hoc analysis was conducted, taking into account only data from patients with fecal calprotectin concentrations measured within 3 days of questionnaire completion. One hundred ninety-seven patients with Crohn disease and 111 patients with ulcerative colitis were enrolled in the study. Lower fecal calprotectin concentrations were associated with better health-related quality of life. The correlations were weak, but stronger if only fecal calprotectin concentrations measured within 3 days of questionnaire completion were included (results for 3 days; Crohn disease: n = 86, rS = -0.419, P < 0.001; ulcerative colitis: n = 43, rS = -0.432, P = 0.004). In Crohn disease, a significant correlation between fecal calprotectin concentration and health-related quality of life was found in patients with colonic involvement (n = 59, rS = -0.470, P < 0.001), but not in patients with purely ileal disease (n = 27, rS = -0.268, P = 0.18). Correlations between fecal calprotectin concentrations and clinical disease activity were also only weak to moderate. Owing to its moderate correlation with fecal calprotectin concentrations in IBD patients with colonic involvement, health-related quality of life should be used in combination with other markers for IBD management. This is even more important in isolated ileal Crohn disease, where no significant correlation between fecal calprotectin concentration and health-related quality of life was found. Especially for use in research studies, care should be taken to keep the time between clinical evaluation of IBD patients and the determination of fecal calprotectin concentrations as short as possible.

Gut Microbiota and Energy Expenditure in Health and Obesity.

PubMed

Bakker, Guido J; Zhao, Jing; Herrema, Hilde; Nieuwdorp, Max

2015-01-01

The contribution of intestinal bacterial strains (gut microbiota) to the development of obesity and obesity-related disorders is increasingly recognized as a potential diagnostic and pharmacologic target. Alterations in the intestinal bacterial composition have been associated with presence of chronic low-grade inflammation, a known feature of insulin resistance and type 2 diabetes mellitus. However, causality still needs to be proven. Fecal transplantation studies in germ-free mice have provided crucial insight into the causality of gut microbiota in development of obesity and obesity-related disorders. Moreover, fecal transplantation studies in conjunction with fecal sampling in prospectively followed cohorts will help identify causally involved intestinal bacterial strains in human obesity. Results from these studies will lead to characterization of novel diagnostic markers as well as therapeutic strategies that aim to treat obesity and obesity-related disorders.

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii

PubMed Central

Caffaro-Filho, Roberto A.; Wong, Mayee; Harwood, Valerie J.; Moravcik, Philip; Fujioka, Roger S.

2016-01-01

ABSTRACT Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. IMPORTANCE This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and Escherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers. PMID:27613686

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome.

PubMed

Tap, Julien; Derrien, Muriel; Törnblom, Hans; Brazeilles, Rémi; Cools-Portier, Stéphanie; Doré, Joël; Störsrud, Stine; Le Nevé, Boris; Öhman, Lena; Simrén, Magnus

2017-01-01

We have limited knowledge about the association between the composition of the intestinal microbiota and clinical features of irritable bowel syndrome (IBS). We collected information on the fecal and mucosa-associated microbiota of patients with IBS and evaluated whether these were associated with symptoms. We collected fecal and mucosal samples from adult patients who met the Rome III criteria for IBS at a secondary/tertiary care outpatient clinics in Sweden, as well as from healthy subjects. The exploratory set comprised 149 subjects (110 with IBS and 39 healthy subjects); 232 fecal samples and 59 mucosal biopsy samples were collected and analyzed by 16S ribosomal RNA targeted pyrosequencing. The validation set comprised 46 subjects (29 with IBS and 17 healthy subjects); 46 fecal samples, but no mucosal samples, were collected and analyzed. For each subject, we measured exhaled H 2 and CH 4 , oro-anal transit time, and the severity of psychological and gastrointestinal symptoms. Fecal methanogens were measured by quantitative polymerase chain reaction. Numerical ecology analyses and a machine learning procedure were used to analyze the data. Fecal microbiota showed covariation with mucosal adherent microbiota. By using classic approaches, we found no differences in fecal microbiota abundance or composition between patients with IBS vs healthy patients. A machine learning procedure, a computational statistical technique, allowed us to reduce the 16S ribosomal RNA data complexity into a microbial signature for severe IBS, consisting of 90 bacterial operational taxonomic units. We confirmed the robustness of the intestinal microbial signature for severe IBS in the validation set. The signature was able to discriminate between patients with severe symptoms, patients with mild/moderate symptoms, and healthy subjects. By using this intestinal microbiota signature, we found IBS symptom severity to be associated negatively with microbial richness, exhaled CH 4 , presence of methanogens, and enterotypes enriched with Clostridiales or Prevotella species. This microbiota signature could not be explained by differences in diet or use of medications. In analyzing fecal and mucosal microbiota from patients with IBS and healthy individuals, we identified an intestinal microbiota profile that is associated with the severity of IBS symptoms. NCT01252550. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Excreta Sampling as an Alternative to In Vivo Measurements at the Hanford Site.

PubMed

Carbaugh, Eugene H; Antonio, Cheryl L; Lynch, Timothy P

2015-08-01

The capabilities of indirect radiobioassay by urine and fecal sample analysis were compared with the direct radiobioassay methods of whole body counting and lung counting for the most common radionuclides and inhalation exposure scenarios encountered by Hanford workers. Radionuclides addressed by in vivo measurement included 137Cs, 60Co, 154Eu, and 241Am as an indicator for plutonium mixtures. The same radionuclides were addressed using gamma energy analysis of urine samples, augmented by radiochemistry and alpha spectrometry methods for plutonium in urine and fecal samples. It was concluded that in vivo whole body counting and lung counting capability should be maintained at the Hanford Site for the foreseeable future, however, urine and fecal sample analysis could provide adequate, though degraded, monitoring capability for workers as a short-term alternative, should in vivo capability be lost due to planned or unplanned circumstances.

Evaluation of microbiological accumulation capability of the commercial sponge Spongia officinalis var. adriatica (Schmidt) (Porifera, Demospongiae).

PubMed

Stabili, Loredana; Licciano, Margherita; Longo, Caterina; Corriero, Giuseppe; Mercurio, Maria

2008-05-01

This study was carried out to evaluate the microbiological accumulation capability of the demosponge Spongia officinalis var. adriatica. Six microbiological parameters were researched in two sampling periods in the water and in reared sponge samples coming from sites with different degrees of microbial contamination: an off-shore fish farm displaced off the Apulian coast (Southern Adriatic Sea) and a no-impacted area displaced into the Marine Protected Area of Porto Cesareo (Apulian coast-Ionian Sea). We detected the density of culturable heterotrophic bacteria by spread plate on marine agar, total culturable bacteria at 37 degrees C on Plate Count Agar and vibrios on thiosulphate-citrate-bile-sucrose-salt (TCBS) agar. Total and fecal coliforms as well as fecal streptococci concentrations were detected by the MPN method. Bacterial densities were always higher in the sponge homogenates compared with the corresponding seawater in the sampling points and in both sampling periods. As regard vibrios, total culturable bacteria at 37 degrees C and fecal streptococci concentrations, the highest values were observed in the sponge samples coming from the off-shore fish farm during the summer period. The ability of Spongia officinalis var. adriatica to accumulate the microbial pollution indicators suggests that this species can be employed as a bioindicator for monitoring water quality.

A DNA pooling based system to detect Escherichia coli virulence factors in fecal and wastewater samples

PubMed Central

Luz María Chacón, J; Lizeth Taylor, C; Carmen Valiente, A; Irene Alvarado, P; Ximena Cortés, B

2012-01-01

The availability of a useful tool for simple and timely detection of the most important virulent varieties of Escherichia coli is indispensable. To this end, bacterial DNA pools which had previously been categorized were obtained from isolated colonies as well as selected in terms of utilized phenotype; the pools were assessed by two PCR Multiplex for the detection of virulent E. coli eaeA, bfpA, stx1, stx2, ipaH, ST, LT, and aatA genes, with the 16S gene used as DNA control. The system was validated with 66 fecal samples and 44 wastewater samples. At least one positive isolate was detected by a virulent gene among the 20 that were screened. The analysis of fecal samples from children younger than 6 years of age detected frequencies of 25% LT positive strains, 8.3% eae, 8.3% bfpA, 16.7% ipaH, as well as 12.5 % aatA and ST. On the other hand, wastewater samples revealed frequencies of 25.7% eaeA positive, 30.3% stx1, 15.1% LT and 19.7% aatA. This study is an initial step toward carrying out epidemiological field research that will reveal the presence of these bacterial varieties. PMID:24031959

The Influence of Household- and Community-Level Sanitation and Fecal Sludge Management on Urban Fecal Contamination in Households and Drains and Enteric Infection in Children

PubMed Central

Berendes, David; Kirby, Amy; Clennon, Julie A.; Raj, Suraja; Yakubu, Habib; Leon, Juan; Robb, Katharine; Kartikeyan, Arun; Hemavathy, Priya; Gunasekaran, Annai; Ghale, Ben; Kumar, J. Senthil; Mohan, Venkata Raghava; Kang, Gagandeep; Moe, Christine

2017-01-01

Urban sanitation necessitates management of fecal sludge inside and outside the household. This study examined associations between household sanitation, fecal contamination, and enteric infection in two low-income neighborhoods in Vellore, India. Surveys and spatial analysis assessed the presence and clustering of toilets and fecal sludge management (FSM) practices in 200 households. Fecal contamination was measured in environmental samples from 50 households and household drains. Enteric infection was assessed from stool specimens from children under 5 years of age in these households. The two neighborhoods differed significantly in toilet coverage (78% versus 33%) and spatial clustering. Overall, 49% of toilets discharged directly into open drains (“poor FSM”). Children in households with poor FSM had 3.78 times higher prevalence of enteric infection when compared with children in other households, even those without toilets. In the neighborhood with high coverage of household toilets, children in households with poor FSM had 10 times higher prevalence of enteric infection than other children in the neighborhood and drains in poor FSM clusters who had significantly higher concentrations of genogroup II norovirus. Conversely, children in households with a toilet that contained excreta in a tank onsite had 55% lower prevalence of enteric infection compared with the rest of the study area. Notably, households with a toilet in the neighborhood with low toilet coverage had more fecal contamination on floors where children played compared with those without a toilet. Overall, both toilet coverage levels and FSM were associated with environmental fecal contamination and, subsequently, enteric infection prevalence in this urban setting. PMID:28719269

The utility of fecal calprotectin in predicting the need for escalation of therapy in inflammatory bowel disease.

PubMed

Kwapisz, Lukasz; Gregor, Jamie; Chande, Nilesh; Yan, Brian; Ponich, Terry; Mosli, Mahmoud

2017-08-01

Fecal calprotectin is an important biomarker used in the evaluation of inflammatory bowel disease. It has proven to be an effective tool in initial screening as well monitoring response to therapy. The aim of this study is to examine the utility of fecal calprotectin both as a predictor for the escalation of therapy in established inflammatory bowel disease and as a predictor of de novo diagnosis. Patients with signs and symptoms concerning for inflammatory bowel disease presenting to outpatient clinics were recruited to provide fecal calprotectin stool samples prior to endoscopic evaluation. Patients were followed up for at least one year and monitored clinically for any change in symptomatology, escalation of therapy or development of IBD, confirmed endoscopically. A total of 126 patients, of whom 72 were known to have underlying inflammatory bowel disease, were included in the final analysis. Among the patients with elevated fecal calprotectin levels and known inflammatory bowel disease, 66% (33/50) went on to have escalation of therapy within 12 months compared to 18% (4/22) if the fecal calprotectin levels were in the normal range (p < .0001). For the remaining patients who at baseline did not have inflammatory bowel disease and a normal endoscopic evaluation, elevated fecal calprotectin resulted in no cases (0/17) of a new diagnosis in the next 12 months. Fecal calprotectin is a useful test for predicting escalation of therapy in established inflammatory bowel disease.

Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation

PubMed Central

Parthasarathy, Gopanandan; Chen, Jun; Chen, Xianfeng; Chia, Nicholas; O'Connor, Helen M.; Wolf, Patricia G.; Gaskins, H. Rex; Bharucha, Adil E.

2015-01-01

Background & Aims In fecal samples from patients with chronic constipation, the microbiota differs from that of healthy subjects. However, the profiles of fecal microbiota only partially replicate those of the mucosal microbiota. It is not clear whether these differences are caused by variations in diet or colonic transit, or are associated with methane production (measured by breath tests). We compared the colonic mucosal and fecal microbiota in patients with chronic constipation and in healthy subjects to investigate the relationships between microbiota and other parameters. Methods Sigmoid colonic mucosal and fecal microbiota samples were collected from 25 healthy women (controls) and 25 women with chronic constipation and evaluated by 16S ribosomal RNA gene sequencing (average of 49,186 reads/sample). We assessed associations between microbiota (overall composition and operational taxonomic units) and demographic variables, diet, constipation status, colonic transit, and methane production (measured in breath samples after oral lactulose intake). Results Fourteen patients with chronic constipation had slow colonic transit. The profile of the colonic mucosal microbiota differed between constipated patients and controls (P<.05). The overall composition of the colonic mucosal microbiota was associated with constipation, independent of colonic transit (P<.05) and discriminated between patients with constipation and controls with 94% accuracy. Genera from Bacteroidetes were more abundant in the colonic mucosal microbiota of patients with constipation. The profile of the fecal microbiota was associated with colonic transit before adjusting for constipation, age, body mass index, and diet; genera from Firmicutes (Faecalibacterium, Lactococcus, and Roseburia) correlated with faster colonic transit. Methane production was associated with the composition of the fecal microbiota, but not with constipation or colonic transit. Conclusions After adjusting for diet and colonic transit, the profile of the microbiota in the colonic mucosa could discriminate patients with constipation from healthy individuals. The profile of the fecal microbiota was associated with colonic transit and methane production (measured in breath), but not constipation. PMID:26460205

Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation.

PubMed

Parthasarathy, Gopanandan; Chen, Jun; Chen, Xianfeng; Chia, Nicholas; O'Connor, Helen M; Wolf, Patricia G; Gaskins, H Rex; Bharucha, Adil E

2016-02-01

In fecal samples from patients with chronic constipation, the microbiota differs from that of healthy subjects. However, the profiles of fecal microbiota only partially replicate those of the mucosal microbiota. It is not clear whether these differences are caused by variations in diet or colonic transit, or are associated with methane production (measured by breath tests). We compared the colonic mucosal and fecal microbiota in patients with chronic constipation and in healthy subjects to investigate the relationships between microbiota and other parameters. Sigmoid colonic mucosal and fecal microbiota samples were collected from 25 healthy women (controls) and 25 women with chronic constipation and evaluated by 16S ribosomal RNA gene sequencing (average, 49,186 reads/sample). We assessed associations between microbiota (overall composition and operational taxonomic units) and demographic variables, diet, constipation status, colonic transit, and methane production (measured in breath samples after oral lactulose intake). Fourteen patients with chronic constipation had slow colonic transit. The profile of the colonic mucosal microbiota differed between constipated patients and controls (P < .05). The overall composition of the colonic mucosal microbiota was associated with constipation, independent of colonic transit (P < .05), and discriminated between patients with constipation and controls with 94% accuracy. Genera from Bacteroidetes were more abundant in the colonic mucosal microbiota of patients with constipation. The profile of the fecal microbiota was associated with colonic transit before adjusting for constipation, age, body mass index, and diet; genera from Firmicutes (Faecalibacterium, Lactococcus, and Roseburia) correlated with faster colonic transit. Methane production was associated with the composition of the fecal microbiota, but not with constipation or colonic transit. After adjusting for diet and colonic transit, the profile of the microbiota in the colonic mucosa could discriminate patients with constipation from healthy individuals. The profile of the fecal microbiota was associated with colonic transit and methane production (measured in breath), but not constipation. Copyright © 2016 AGA Institute. Published by Elsevier Inc. All rights reserved.

Analysis of selected water-quality data for surface water in St. Tammany Parish, Louisiana, April-August 1995

USGS Publications Warehouse

Demcheck, Dennis K.

1996-01-01

Physical and chemical-related properties, concentrations of chemical constituents, which included major ions and nutrients, and concentrations of fecal-coliform bacteria were determined for 17 sites on 11 streams in St. Tammany Parish, Louisiana, during the period April-August 1995. The streams were sampled to assess the effects of different streamflow conditions on the concentrations of water-quality constituents. The streams included in the study were Tchefuncte River, Bogue Falaya, Abita River, Bayou Chinchouba, Bayou Castine, Cane Bayou, Bayou Lacombe, Bayou Liberty, Bayou Bonfouca, Bogue Chitto, and West Pearl River. Water-quality samples were collected under several hydrologic conditions. These conditions included a period of wet weather and sustained high river stages; a period of local storms several days apart and river stages typical of that situation; and a period of dry weather and low river stages. The concentrations of inorganic chemical constituents in water from the upstream sites generally were low. Concentrations from the downstream sites varied and were higher. Nutrient and fecal-coliform bacteria concentrations varied and indicated that degraded water-quality conditions that typically occur during storms persisted less than 1-3 days. In general, the larger the drainage basin, the longer it takes for the stream to recover. Fecal-coliform concen- trations reflected the effects of small, isolated storms in the area. Bayou Castine, sampled immediately after a storm, had a fecal-coliform concentration of 26,000 colonies per 100 milliliters. The stream was resampled 24 hours later, and the fecal-coliform concentration had decreased to 1,700 colonies per 100 milliliters. This is an indication of the rapid water-quality changes that typically occur in small streams.

Microbial Source Tracking in Adjacent Karst Springs.

PubMed

Ohad, Shoshanit; Vaizel-Ohayon, Dalit; Rom, Meir; Guttman, Joseph; Berger, Diego; Kravitz, Valeria; Pilo, Shlomo; Huberman, Zohar; Kashi, Yechezkel; Rorman, Efrat

2015-08-01

Modern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. Microbial source tracking (MST) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. This study was intended to assess karst spring susceptibilities to different fecal sources using MST quantitative PCR (qPCR) assays targeting human, bovine, and swine markers. It involved a dual-time monitoring frame: (i) monthly throughout the calendar year and (ii) daily during a rainfall event. Data integration was taken from both monthly and daily MST profile monitoring and improved identification of spring susceptibility to host fecal contamination; three springs located in close geographic proximity revealed different MST profiles. The Giach spring showed moderate fluctuations of MST marker quantities amid wet and dry samplings, while the Zuf spring had the highest rise of the GenBac3 marker during the wet event, which was mirrored in other markers as well. The revelation of human fecal contamination during the dry season not connected to incidents of raining leachates suggests a continuous and direct exposure to septic systems. Pigpens were identified in the watersheds of Zuf, Shefa, and Giach springs and on the border of the Gaaton spring watershed. Their impact was correlated with partial detection of the Pig-2-Bac marker in Gaaton spring, which was lower than detection levels in all three of the other springs. Ruminant and swine markers were detected intermittently, and their contamination potential during the wet samplings was exposed. These results emphasized the importance of sampling design to utilize the MST approach to delineate subtleties of fecal contamination in the environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Occurrence of male-specific bacteriophage in feral and domestic animal wastes, human feces, and human-associated wastewaters.

PubMed

Calci, K R; Burkhardt, W; Watkins, W D; Rippey, S R

1998-12-01

Male-specific bacteriophage (MSB) densities were determined in animal and human fecal wastes to assess their potential impact on aquatic environments. Fecal samples (1,031) from cattle, chickens, dairy cows, dogs, ducks, geese, goats, hogs, horses, seagulls, sheep, and humans as well as 64 sewerage samples were examined for MSB. All animal species were found to harbor MSB, although the great majority excreted these viruses at very low levels. The results from this study demonstrate that in areas affected by both human and animal wastes, wastewater treatment plants are the principal contributors of MSB to fresh, estuarine, and marine waters.

Occurrence of Male-Specific Bacteriophage in Feral and Domestic Animal Wastes, Human Feces, and Human-Associated Wastewaters

PubMed Central

Calci, Kevin R.; Burkhardt, William; Watkins, William D.; Rippey, Scott R.

1998-01-01

Male-specific bacteriophage (MSB) densities were determined in animal and human fecal wastes to assess their potential impact on aquatic environments. Fecal samples (1,031) from cattle, chickens, dairy cows, dogs, ducks, geese, goats, hogs, horses, seagulls, sheep, and humans as well as 64 sewerage samples were examined for MSB. All animal species were found to harbor MSB, although the great majority excreted these viruses at very low levels. The results from this study demonstrate that in areas affected by both human and animal wastes, wastewater treatment plants are the principal contributors of MSB to fresh, estuarine, and marine waters. PMID:9835602

Bacteriophages carrying antibiotic resistance genes in fecal waste from cattle, pigs, and poultry.

PubMed

Colomer-Lluch, Marta; Imamovic, Lejla; Jofre, Juan; Muniesa, Maite

2011-10-01

This study evaluates the occurrence of bacteriophages carrying antibiotic resistance genes in animal environments. bla(TEM), bla(CTX-M) (clusters 1 and 9), and mecA were quantified by quantitative PCR in 71 phage DNA samples from pigs, poultry, and cattle fecal wastes. Densities of 3 to 4 log(10) gene copies (GC) of bla(TEM), 2 to 3 log(10) GC of bla(CTX-M), and 1 to 3 log(10) GC of mecA per milliliter or gram of sample were detected, suggesting that bacteriophages can be environmental vectors for the horizontal transfer of antibiotic resistance genes.

Influences of sample interference and interference controls on quantification of enterococci fecal indicator bacteria in surface water samples by the qPCR method

EPA Science Inventory

A quantitative polymerase chain reaction (qPCR) method for the detection of entercocci fecal indicator bacteria has been shown to be generally applicable for the analysis of temperate fresh (Great Lakes) and marine coastal waters and for providing risk-based determinations of wat...

A microhistological technique for analysis of food habits of mycophagous rodents.

Treesearch

Patrick W. McIntire; Andrew B. Carey

1989-01-01

We present a technique, based on microhistological analysis of fecal pellets, for quantifying the diets of forest rodents. This technique provides for the simultaneous recording of fungal spores and vascular plant material. Fecal samples should be freeze dried, weighed, and rehydrated with distilled water. We recommend a minimum sampling intensity of 50 fields of view...

Effects of DNA Extraction Procedures on Bacteroides Profiles in Fecal Samples From Various Animals Determined by Terminal Restriction Fragment Length Polymorphism Analysis

EPA Science Inventory

A major assumption in microbial source tracking is that some fecal bacteria are specific to a host animal, and thus provide unique microbial fingerprints that can be used to differentiate hosts. However, the DNA information obtained from a particular sample may be biased dependi...

[Virus detection, clinical signs, and laboratory findings in dogs with acute hemorrhagic diarrhea: a retrospective study of 935 cases].

PubMed

Kempf, C; Schulz, B S; Strauch, C; Sauter-Louis, C; Truyen, U; Hartmann, K

2010-01-01

The study evaluated which viruses can be detected in dogs with acute hemorrhagic diarrhea and compared signalment, clinical signs, and laboratory abnormalities among groups of dogs infected with different viruses and those that tested virus-negative. Fecal samples from 935 dogs with acute hemorrhagic diarrhea were examined by electron microscopy. The medical records of these patients were retrospectively evaluated for clinical and laboratory parameters. Virus was detected in 44.2% of the dogs presented with acute bloody diarrhea. The highest prevalence for a virus infection was demonstrated for canine parvovirus (19.9%), followed by coronavirus (17.3%), and paramyxovirus (13.9%). More than one virus species was detected in 6.5% of all fecal samples. Dogs with a virus-positive fecal sample were significantly younger than dogs that tested negative on electron microscopy. Among virus-positive dogs, dogs with parvovirus infection were significantly younger when compared to dogs infected with other enteric viruses. Parvovirus-infected patients also showed significantly lower leukocyte and erythrocyte counts as well as hematocrit, total protein, and albumin levels compared to all other groups. No significant differences were seen when evaluating sex, clinical parameters, character of diarrhea or vomiting among all groups. Young dogs are more likely to suffer from viral enteritis. Based on clinical parameters it is not possible to differentiate a virus-positive from a virus-negative dog or to diagnose a certain virus species. Besides the young age, parvovirus infection is associated with typical changes in laboratory parameters, but not with specific clinical signs. A virologic fecal examination is always indicated.

Endangered Right Whales Enhance Primary Productivity in the Bay of Fundy

PubMed Central

Roman, Joe; Nevins, John; Altabet, Mark; Koopman, Heather; McCarthy, James

2016-01-01

Marine mammals have recently been documented as important facilitators of rapid and efficient nutrient recycling in coastal and offshore waters. Whales enhance phytoplankton nutrition by releasing fecal plumes near the surface after feeding and by migrating from highly productive, high-latitude feeding areas to low-latitude nutrient-poor calving areas. In this study, we measured NH4+ and PO43- release rates from the feces of North Atlantic right whales (Eubalaena glacialis), a highly endangered baleen whale. Samples for this species were primarily collected by locating aggregations of whales in surface-active groups (SAGs), which typically consist of a central female surrounded by males competing for sexual activity. When freshly collected feces were incubated in seawater, high initial rates of N release were generally observed, which decreased to near zero within 24 hours of sampling, a pattern that is consistent with the active role of gut microflora on fecal particles. We estimate that at least 10% of particulate N in whale feces becomes available as NH4+ within 24 hours of defecation. Phosphorous was also abundant in fecal samples: initial release rates of PO43- were higher than for NH4+, yielding low N/P nutrient ratios over the course of our experiments. The rate of PO43- release was thus more than sufficient to preclude the possibility that nitrogenous nutrients supplied by whales would lead to phytoplankton production limited by P availability. Phytoplankton growth experiments indicated that NH4+ released from whale feces enhance productivity, as would be expected, with no evidence that fecal metabolites suppress growth. Although North Atlantic right whales are currently rare (approximately 450 individuals), they once numbered about 14,000 and likely played a substantial role in recycling nutrients in areas where they gathered to feed and mate. Even though the NH4+ released from fresh whale fecal material is a small fraction of total whale fecal nitrogen, and recognizing the fact that the additional nitrogen released in whale urine would be difficult to measure in a field study, the results of this study support the idea that the distinctive isotopic signature of the released NH4+ could be used to provide a conservative estimate of the contribution of the whale pump to primary productivity in coastal regions where whales congregate. PMID:27331902

Endangered Right Whales Enhance Primary Productivity in the Bay of Fundy.

PubMed

Roman, Joe; Nevins, John; Altabet, Mark; Koopman, Heather; McCarthy, James

2016-01-01

Marine mammals have recently been documented as important facilitators of rapid and efficient nutrient recycling in coastal and offshore waters. Whales enhance phytoplankton nutrition by releasing fecal plumes near the surface after feeding and by migrating from highly productive, high-latitude feeding areas to low-latitude nutrient-poor calving areas. In this study, we measured NH4+ and PO43- release rates from the feces of North Atlantic right whales (Eubalaena glacialis), a highly endangered baleen whale. Samples for this species were primarily collected by locating aggregations of whales in surface-active groups (SAGs), which typically consist of a central female surrounded by males competing for sexual activity. When freshly collected feces were incubated in seawater, high initial rates of N release were generally observed, which decreased to near zero within 24 hours of sampling, a pattern that is consistent with the active role of gut microflora on fecal particles. We estimate that at least 10% of particulate N in whale feces becomes available as NH4+ within 24 hours of defecation. Phosphorous was also abundant in fecal samples: initial release rates of PO43- were higher than for NH4+, yielding low N/P nutrient ratios over the course of our experiments. The rate of PO43- release was thus more than sufficient to preclude the possibility that nitrogenous nutrients supplied by whales would lead to phytoplankton production limited by P availability. Phytoplankton growth experiments indicated that NH4+ released from whale feces enhance productivity, as would be expected, with no evidence that fecal metabolites suppress growth. Although North Atlantic right whales are currently rare (approximately 450 individuals), they once numbered about 14,000 and likely played a substantial role in recycling nutrients in areas where they gathered to feed and mate. Even though the NH4+ released from fresh whale fecal material is a small fraction of total whale fecal nitrogen, and recognizing the fact that the additional nitrogen released in whale urine would be difficult to measure in a field study, the results of this study support the idea that the distinctive isotopic signature of the released NH4+ could be used to provide a conservative estimate of the contribution of the whale pump to primary productivity in coastal regions where whales congregate.

Deep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens

PubMed Central

Deusch, Oliver; O’Flynn, Ciaran; Colyer, Alison; Morris, Penelope; Allaway, David; Jones, Paul G.; Swanson, Kelly S.

2014-01-01

Background Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome. Methodology & Principal Findings Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high–protein, low–carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC) were collected at 8, 12 and 16 weeks of age (n = 6 per group). A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified) demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007) between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022) enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome. Conclusions These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary protein:carbohydrate ratio and highlight the impact of diet early in life. PMID:25010839

Effect of housing arrangement on fecal-oral transmission of avian hepatitis E virus in chicken flocks.

PubMed

Liu, Baoyuan; Sun, Yani; Chen, Yiyang; Du, Taofeng; Nan, Yuchen; Wang, Xinjie; Li, Huixia; Huang, Baicheng; Zhang, Gaiping; Zhou, En-Min; Zhao, Qin

2017-09-07

Avian hepatitis E virus (HEV) infection is common in chicken flocks in China, as currently no measures exist to prevent the spread of the disease. In this study, we analyzed the effect of caged versus cage-free housing arrangements on avian HEV transmission. First, 127 serum and 110 clinical fecal samples were collected from 4 chicken flocks including the two arrangements in Shaanxi Province, China and tested for HEV antibodies and/or virus. Concurrently, 36 specific-pathogen-free chickens were divided equally into four experimental living arrangement groups, designated cage-free (Inoculated), caged (Inoculated), cage-free (Negative) and caged (Negative) groups. In caged groups, three cages contained 3 chickens each. Three chickens each from cage-free (Inoculated) and caged (Inoculated) groups (one chicken of each cage) were inoculated by cutaneous ulnar vein with the same dose of avian HEV, respectively. The cage-free (Negative) and caged (Negative) groups served as negative control. Serum and fecal samples were collected at 1 to 7 weeks post-inoculation (wpi) and liver lesions were scored at 7 wpi. The results of serology showed that the avian HEV infection rate (54.10%) of the cage-free chickens was significantly higher than the one (12.12%) for caged chickens (P < 0.05). Also, the rate of detection of avian HEV RNA in the clinical fecal samples was significantly higher in the cage-free (22.80%, 13/57) than caged birds (5.66%, 3/53). Moreover, under experimental conditions, the infected number of uninoculated cage-free chickens (6) was significantly higher than the one for the uninoculated caged birds (2), as evidenced by seroconversion, fecal virus shedding, viremia and gross and microscopic liver lesions. These results suggest that reduction of contact with feces as seen in the caged arrangement of housing chickens can reduce avian HEV transmission. This study provides insights for prevention and control of avian HEV infection in chicken flocks.

Impact assessment of on-site sanitation system on groundwater quality in alluvial settings: A case study from Lucknow city in North India.

PubMed

Jangam, Chandrakant; Ramya Sanam, S; Chaturvedi, M K; Padmakar, C; Pujari, Paras R; Labhasetwar, Pawan K

2015-10-01

The present case study has been undertaken to investigate the impact of on-site sanitation on groundwater quality in alluvial settings in Lucknow City in India. The groundwater samples have been collected in the areas of Lucknow City where the on-site sanitation systems have been implemented. The groundwater samples have been analyzed for the major physicochemical parameters and fecal coliform. The results of analysis reveal that none of the groundwater samples exceeded the Bureau of Indian Standards (BIS) limits for all the parameters. Fecal coliform was not found in majority of the samples including those samples which were very close to the septic tank. The study area has a thick alluvium cover as a top layer which acts as a natural barrier for groundwater contamination from the on-site sanitation system. The t test has been performed to assess the seasonal effect on groundwater quality. The statistical t test implies that there is a significant effect of season on groundwater quality in the study area.

Helminth Fauna in Captive European Gray Wolves (Canis lupus lupus) in Germany.

PubMed

Bindke, Johanna Daniela; Springer, Andrea; Böer, Michael; Strube, Christina

2017-01-01

Captive as well as free-ranging wolves, which are currently recolonizing Germany, may harbor a variety of gastrointestinal parasites. This study investigated endoparasites in captive European gray wolves ( Canis lupus lupus ) using coproscopical methods. Fecal samples were collected monthly between October 2012 and November 2013 from 18 wolf enclosures in 14 German zoological gardens, representing 72 individual wolves. In total, 1,041 fecal samples including 26 bulk samples were analyzed by the sedimentation and flotation method. The most frequently detected egg morphotypes included five nematodes [Ancylostomatidae ( Ancylostoma or Uncinaria spp.), Toxocara canis, Toxascaris leonina, Trichuris vulpis , and Capillaria / Eucoleus spp.], one cestode (Taeniidae) and one trematode ( Alaria alata ). 44.76% of all samples were positive for at least one of these egg morphotypes. Overall, Ancylostomatidae showed the highest frequency (30.84% of all samples), followed by Capillaria/Eucoleus spp. (19.88%), Toxocara canis (5.19%), taeniids (3.75%), Trichuris vulpis and Alaria alata (3.65% each), and Toxascaris leonina (1.25%). As fecal samples were collected from the environment and could not be assigned to individual wolves, sample results were combined per zoo and month. General linear mixed models were employed to analyze the effect of season and management factors on the occurrence of Ancylostomatidae, Capillaria/Eucoleus spp., Toxocara canis and taeniids. No statistically significant effect of season was found, whereas anthelmintic treatment negatively affected Ancylostomatidae egg excretion. Detected parasites and their prevalences are comparable to previous studies on wolf parasitism conducted elsewhere in Europe. As many of the most prevalent helminths are of zoonotic importance, routine anthelmintic treatment of captive wolves should be recommended.

Recovery and Enumeration of Cryptosporidium parvum from Animal Fecal Matrices

PubMed Central

Davies, Cheryl M.; Kaucner, Christine; Deere, Daniel; Ashbolt, Nicholas J.

2003-01-01

Accurate quantification of Cryptosporidium parvum oocysts in animal fecal deposits on land is an essential starting point for estimating watershed C. parvum loads. Due to the general poor performance and variable recovery efficiency of existing enumeration methods, protocols were devised based on initial dispersion of oocysts from feces by vortexing in 2 mM tetrasodium pyrophosphate, followed by immunomagnetic separation. The protocols were validated by using an internal control seed preparation to determine the levels of oocyst recovery for a range of fecal types. The levels of recovery of 102 oocysts from cattle feces (0.5 g of processed feces) ranged from 31 to 46%, and the levels of recovery from sheep feces (0.25 g of processed feces) ranged from 21% to 35%. The within-sample coefficients of variation for the percentages of recovery from five replicates ranged from 10 to 50%. The ranges for levels of recovery of oocysts from cattle, kangaroo, pig, and sheep feces (juveniles and adults) collected in a subsequent watershed animal fecal survey were far wider than the ranges predicted by the validation data. Based on the use of an internal control added to each fecal sample, the levels of recovery ranged from 0 to 83% for cattle, from 4 to 62% for sheep, from 1 to 42% for pigs, and from 40 to 73% for kangaroos. Given the variation in the levels of recovery of oocysts from different fecal matrices, it is recommended that an internal control be added to at least one replicate of every fecal sample analyzed to determine the percentage of recovery. Depending on the animal type and based on the lowest approximate percentages of recovery, between 10 and 100 oocysts g of feces−1 must be present to be detected. PMID:12732556

Diagnostic strategies to reveal covert infections with intestinal helminths in dogs.

PubMed

Adolph, Chris; Barnett, Sharon; Beall, Melissa; Drake, Jason; Elsemore, David; Thomas, Jennifer; Little, Susan

2017-11-30

Intestinal helminths are common in dogs in the United States, particularly non-treated dogs in animal shelters, but surveys by fecal flotation may underestimate their prevalence. To determine the prevalence of intestinal helminths and evaluate the ability of fecal flotation and detection of nematode antigen to identify those infections, contents of the entire gastrointestinal tract of 97 adult (>1year) dogs previously identified for humane euthanasia at two animal control shelters in northeastern Oklahoma, USA, were screened. All helminths recovered were washed in saline and fixed prior to enumeration and identification to genus and species. Fecal samples from each dog were examined by passive sodium nitrate (SG 1.33) and centrifugal sugar solution (SG 1.25) flotation. Fecal antigen detection assays were used to confirm the presence of nematode antigen in frozen fecal samples from 92 dogs. Necropsy examination revealed Ancylostoma caninum in 45/97 (46.4%), Toxocara canis in 11/97 (11.3%), Trichuris vulpis in 38/97 (39.2%), Dipylidium caninum in 48/97 (49.5%), and Taenia sp. in 7/97 (7.2%) dogs. Passive fecal flotation identified 38/45 (84.4%) A. caninum, 6/11 (54.5%) T. canis, 26/38 (68.4%) T. vulpis, 2/48 (4.2%) D. caninum, and 1/7 (14.3%) Taenia sp. infections, while centrifugal flotation combined with antigen detection assays identified A. caninum in 97.7% (43/44), T. canis in 77.8% (7/9), and T. vulpis in 83.3% (30/36) of infected dogs based on necropsy recovery of nematodes. Taken together, these data indicate that detection of nematode antigen is a useful adjunct to microscopic examination of fecal samples for parasite eggs, and that this approach can improve diagnostic sensitivity for intestinal nematode infections in dogs. Copyright © 2017 Elsevier B.V. All rights reserved.

The detection of Giardia muris and Giardia lamblia cysts by immunofluorescence in animal tissues and fecal samples subjected to cycles of freezing and thawing.

PubMed

Erlandsen, S L; Sherlock, L A; Bemrick, W J

1990-04-01

The effects of freezing and thawing on the detection of selected Giardia spp. cysts were investigated using immunofluorescence, bright field microscopy, and low voltage scanning electron microscopy (SEM). Giardia muris cysts were obtained from either animal carcasses, fecal pellets, or isolated cyst preparations, whereas Giardia lamblia cysts were isolated from fecal samples. These samples were stained using an immunofluorescence technique after 1-3 freezing (-16 C) and thawing (20 C) cycles. Cysts were detected successfully by immunofluorescence in all samples. However, in those samples subjected to freeze-thawing, the cyst walls often became distorted and then were not detectable by bright field microscopy. Low voltage SEM demonstrated that the filaments in the distorted cyst wall underwent rearrangements of interfilament spacing. Quantitation of cyst recovery after freezing and thawing demonstrated that a substantial loss occurred after 1 cycle of alternating temperature when low concentrations of cysts were used, but not with high concentrations of cysts. Cyst recovery, after 3 freezing and thawing cycles, was dramatically lowered irrespective of the initial cyst concentration. These results demonstrated that immunofluorescence was an effective technique for the detection of Giardia spp. cysts in frozen samples and would suggest that freezing and thawing of fecal samples could prevent the detection of cysts when only bright field microscopy was employed.

Water quality, weather and environmental factors associated with fecal indicator organism density in beach sand at two recreational marine beaches.

PubMed

Heaney, Christopher D; Exum, Natalie G; Dufour, Alfred P; Brenner, Kristen P; Haugland, Richard A; Chern, Eunice; Schwab, Kellogg J; Love, David C; Serre, Marc L; Noble, Rachel; Wade, Timothy J

2014-11-01

Recent studies showing an association between fecal indicator organisms (FIOs) in sand and gastrointestinal (GI) illness among beachgoers with sand contact have important public health implications because of the large numbers of people who recreate at beaches and engage in sand contact activities. Yet, factors that influence fecal pollution in beach sand remain unclear. During the 2007 National Epidemiological and Environmental Assessment of Recreational (NEEAR) Water Study, sand samples were collected at three locations (60 m apart) on weekend days (Sat, Sun) and holidays between June and September at two marine beaches - Fairhope Beach, AL and Goddard Beach, RI - with nearby publicly-owned treatment works (POTWs) outfalls. F(+) coliphage, enterococci, Bacteroidales, fecal Bacteroides spp., and Clostridium spp. were measured in sand using culture and qPCR-based calibrator-cell equivalent methods. Water samples were also collected on the same days, times and transects as the 144 sand samples and were assayed using the same FIO measurements. Weather and environmental data were collected at the time of sample collection. Mean FIO concentrations in sand varied over time, but not space. Enterococci CFU and CCE densities in sand were not correlated, although other FIOs in sand were. The strongest correlation between FIO density in sand and water was fecal Bacteroides CCE, followed by enterococci CFU, Clostridium spp. CCE, and Bacteroidales CCE. Overall, the factors associated with FIO concentrations in sand were related to the sand-water interface (i.e., sand-wetting) and included daily average densities of FIOs in water, rainfall, and wave height. Targeted monitoring that focuses on daily trends of sand FIO variability, combined with information about specific water quality, weather, and environmental factors may inform beach monitoring and management decisions to reduce microbial burdens in beach sand. The views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency. Copyright © 2014 Elsevier B.V. All rights reserved.

Factors affecting isolation and identification of Mycobacterium avium subsp. paratuberculosis from fecal and tissue samples in a liquid culture system.

PubMed

Whittington, Richard J

2009-03-01

Culture of Mycobacterium avium subsp. paratuberculosis is the definitive diagnostic test for Johne's disease, a chronic granulomatous enteropathy of animals. Compared to solid media, the identification of all strains of the organism in liquid media can be more difficult because the appearance of colonies and mycobactin dependence are not observable, and the growth of other organisms needs to be distinguished, commonly by PCR. Factors affecting the isolation rate of S strains and the contamination rate in modified Middlebrook 7H9 broth (Bactec 12B) and 7H10 agar were studied using 11,598 fecal samples and 2,577 tissue samples from sheep from 1,421 farms over 10 years. Minimization of contamination in Bactec cultures required the avoidance of the carryover of fecal particles from the first sedimentation step in the double-incubation centrifugation method, and contamination was reduced significantly by incubating the sample in a solution containing vancomycin, amphotericin B, and nalidixic acid for 3 days compared to 2 days. The growth of irrelevant microorganisms confounded the identification of M. avium subsp. paratuberculosis in liquid culture by inhibiting IS900 PCR and in solid medium culture by inhibiting the growth of M. avium subsp. paratuberculosis or obscuring colonies. The contamination of samples was clustered in certain laboratory submissions and was reduced by including ampicillin in Bactec medium without affecting the odds of isolation of M. avium subsp. paratuberculosis. The long-term contamination rate for fecal cultures was about 7%, and that for tissue cultures was <0.2%. Liquid medium was more sensitive than solid medium culture for M. avium subsp. paratuberculosis. The applicability of these findings for C strains is discussed.

Monitoring ovarian cycles, pregnancy and post-partum in captive marsh deer (Blastocerus dichotomus) by measuring fecal steroids

PubMed Central

Polegato, Bruna Furlan; Duarte, José Maurício Barbanti

2018-01-01

Abstract The marsh deer is an endangered species from the marshlands of central South America. This study aimed to characterize certain aspects of the reproductive physiology of marsh deer hinds, including the duration and fecal progestins profile of the estrous cycle, pregnancy and post-partum periods, and evaluate the effect of cloprostenol administration on this species. The experimental group consisted of six females and one fertile male marsh deer. During monitoring of the estrous cycle, the fresh fecal samples were collected daily and, during pregnancy, they were collected twice weekly. The hormonal profile obtained from daily fecal samples indicated that the mean duration of the estrous cycle was 21.3 ± 1.3 days (6.4 days inter-luteal phase and 14.8 days luteal phase; n = 16 estrous cycles). The mean concentration of fecal progestins in the inter-luteal phase was 834 ± 311 ng g−1, in the luteal phase was 3979 ± 1611 ng g−1, value between them was 1457 ng g−1. No significant difference in fecal estrogen concentrations was determined during the estrous cycle. The corpora luteum was not responsive to cloprostenol until Day 6 of the estrous cycle, the period previously described as the inter-luteal phase. Half the females became pregnant following treatment with cloprostenol and two others were fertilized in their natural estrous cycle. Four females delivered fawns, and the mean duration of pregnancy was 253 ± 4 days. Fecal progestin concentrations were similar to those of the estrous cycle during the first 11 weeks of pregnancy and increased significantly ( > 15250 ng g−1) thereafter, providing a presumptive diagnosis guideline. Within 60 days of post-partum analyses, 75% of the deer exhibited behavioural estrus and/or ovarian activity. This study generated a broader understanding of the marsh deer species concerning the production of consistent data related to its reproduction. This knowledge can be used to assist the reproductive management of this species and, consequently, to promote its conservation. PMID:29383254

Extent of Fecal Contamination of Household Drinking Water in Nepal: Further Analysis of Nepal Multiple Indicator Cluster Survey 2014.

PubMed

Kandel, Pragya; Kunwar, Ritu; Lamichhane, Prabhat; Karki, Surendra

2017-02-08

Water sources classified as "improved" may not necessarily provide safe drinking water for householders. We analyzed data from Nepal Multiple Indicator Cluster Survey 2014 to explore the extent of fecal contamination of household drinking water. Fecal contamination was detected in 81.2% (95% confidence interval [CI]: 77.9-84.2) household drinking water from improved sources and 89.6% (95% CI: 80.4-94.7) in water samples from unimproved sources. In adjusted analysis, there was no difference in odds of fecal contamination of household drinking water between improved and unimproved sources. We observed significantly lower odds of fecal contamination of drinking water in households in higher wealth quintiles, where soap and water were available for handwashing and in households employing water treatment. The extent of contamination of drinking water as observed in this study highlights the huge amount of effort required to ensure the provision of safely managed water in Nepal by 2030 as aimed in sustainable development goals. © The American Society of Tropical Medicine and Hygiene.

Potential of fecal microbiota for early-stage detection of colorectal cancer

PubMed Central

Zeller, Georg; Tap, Julien; Voigt, Anita Y; Sunagawa, Shinichi; Kultima, Jens Roat; Costea, Paul I; Amiot, Aurélien; Böhm, Jürgen; Brunetti, Francesco; Habermann, Nina; Hercog, Rajna; Koch, Moritz; Luciani, Alain; Mende, Daniel R; Schneider, Martin A; Schrotz-King, Petra; Tournigand, Christophe; Tran Van Nhieu, Jeanne; Yamada, Takuji; Zimmermann, Jürgen; Benes, Vladimir; Kloor, Matthias; Ulrich, Cornelia M; von Knebel Doeberitz, Magnus; Sobhani, Iradj; Bork, Peer

2014-01-01

Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host–microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism. PMID:25432777

Extent of Fecal Contamination of Household Drinking Water in Nepal: Further Analysis of Nepal Multiple Indicator Cluster Survey 2014

PubMed Central

Kandel, Pragya; Kunwar, Ritu; Lamichhane, Prabhat; Karki, Surendra

2017-01-01

Water sources classified as “improved” may not necessarily provide safe drinking water for householders. We analyzed data from Nepal Multiple Indicator Cluster Survey 2014 to explore the extent of fecal contamination of household drinking water. Fecal contamination was detected in 81.2% (95% confidence interval [CI]: 77.9–84.2) household drinking water from improved sources and 89.6% (95% CI: 80.4–94.7) in water samples from unimproved sources. In adjusted analysis, there was no difference in odds of fecal contamination of household drinking water between improved and unimproved sources. We observed significantly lower odds of fecal contamination of drinking water in households in higher wealth quintiles, where soap and water were available for handwashing and in households employing water treatment. The extent of contamination of drinking water as observed in this study highlights the huge amount of effort required to ensure the provision of safely managed water in Nepal by 2030 as aimed in sustainable development goals. PMID:27821687

Prevalence and mechanisms of extended-spectrum cephalosporin resistance in clinical and fecal Enterobacteriaceae isolates from dogs in Ontario, Canada.

PubMed

Zhang, Pauline L C; Shen, Xiao; Chalmers, Gabhan; Reid-Smith, Richard J; Slavic, Durda; Dick, Hani; Boerlin, Patrick

2018-01-01

There is little information on the genetic basis of resistance to the critically important extended-spectrum cephalosporins (ESCs) in Enterobacteriaceae from dogs in Canada. This study assessed the frequency of ESC resistance in Enterobacteriaceae isolated from dogs in Ontario and the distribution of major ESC resistance genes in these bacteria. A total of 542 Enterobacteriaceae were isolated from 506 clinical samples from two diagnostic laboratories in Ontario. Eighty-eight ESC-resistant Enterobacteriaceae and 217 Escherichia coli were isolated from 234 fecal samples from dogs collected at leash-free dog parks. These fecal isolates were tested for ESC resistance along with the clinical isolates. Isolates with reduced ESC susceptibility were screened for bla CMY , bla CTX-M , and bla SHV , and all CTX-M-positive isolates underwent whole-genome sequencing. The prevalence of ESC resistance in clinical Enterobacteriaceae was 10.4%. The average frequency of fecal carriage of ESC-resistant Enterobacteriaceae in healthy dogs was 26.5%. The majority of ESC-resistant isolates were E. coli and the other major Enterobacteriaceae carrying ESC resistance genes were Klebsiella pneumoniae and Proteus mirabilis. The results show that the same ESC resistance genes can be found in clinical and fecal Enterobacteriaceae in dogs. The identified E. coli sequence types (including ST131 and ST648) and CTX-M variants (including CTX-M-14, -15, and -27) support the hypothesis of transfer of resistant bacteria between humans and dogs. CTX-M-1 was frequently found in canine fecal Enterobacteriaceae, while it is still rare in human Enterobacteriaceae in Canada, thus suggesting transfer of resistant bacteria to dogs from food animals or other sources. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Development of a swine-specific fecal pollution marker based on host differences in methanogen mcrA genes.

PubMed

Ufnar, Jennifer A; Ufnar, David F; Wang, Shiao Y; Ellender, R D

2007-08-01

The goal of this study was to evaluate methanogen diversity in animal hosts to develop a swine-specific archaeal molecular marker for fecal source tracking in surface waters. Phylogenetic analysis of swine mcrA sequences compared to mcrA sequences from the feces of five animals (cow, deer, sheep, horse, and chicken) and sewage showed four distinct swine clusters, with three swine-specific clades. From this analysis, six sequences were chosen for molecular marker development and initial testing. Only one mcrA sequence (P23-2) showed specificity for swine and therefore was used for environmental testing. PCR primers for the P23-2 clone mcrA sequence were developed and evaluated for swine specificity. The P23-2 primers amplified products in P23-2 plasmid DNA (100%), pig feces (84%), and swine waste lagoon surface water samples (100%) but did not amplify a product in 47 bacterial and archaeal stock cultures and 477 environmental bacterial isolates and sewage and water samples from a bovine waste lagoon and a polluted creek. Amplification was observed in only one sheep sample out of 260 human and nonswine animal fecal samples. Sequencing of PCR products from pig feces demonstrated 100% similarity to pig mcrA sequence from clone P23-2. The minimal amount of DNA required for the detection was 1 pg for P23-2 plasmid, 1 ng for pig feces, 50 ng for swine waste lagoon surface water, 1 ng for sow waste influent, and 10 ng for lagoon sludge samples. Lower detection limits of 10(-6) g of wet pig feces in 500 ml of phosphate-buffered saline and 10(-4) g of lagoon waste in estuarine water were established for the P23-2 marker. This study was the first to utilize methanogens for the development of a swine-specific fecal contamination marker.

Development of a Swine-Specific Fecal Pollution Marker Based on Host Differences in Methanogen mcrA Genes▿

PubMed Central

Ufnar, Jennifer A.; Ufnar, David F.; Wang, Shiao Y.; Ellender, R. D.

2007-01-01

The goal of this study was to evaluate methanogen diversity in animal hosts to develop a swine-specific archaeal molecular marker for fecal source tracking in surface waters. Phylogenetic analysis of swine mcrA sequences compared to mcrA sequences from the feces of five animals (cow, deer, sheep, horse, and chicken) and sewage showed four distinct swine clusters, with three swine-specific clades. From this analysis, six sequences were chosen for molecular marker development and initial testing. Only one mcrA sequence (P23-2) showed specificity for swine and therefore was used for environmental testing. PCR primers for the P23-2 clone mcrA sequence were developed and evaluated for swine specificity. The P23-2 primers amplified products in P23-2 plasmid DNA (100%), pig feces (84%), and swine waste lagoon surface water samples (100%) but did not amplify a product in 47 bacterial and archaeal stock cultures and 477 environmental bacterial isolates and sewage and water samples from a bovine waste lagoon and a polluted creek. Amplification was observed in only one sheep sample out of 260 human and nonswine animal fecal samples. Sequencing of PCR products from pig feces demonstrated 100% similarity to pig mcrA sequence from clone P23-2. The minimal amount of DNA required for the detection was 1 pg for P23-2 plasmid, 1 ng for pig feces, 50 ng for swine waste lagoon surface water, 1 ng for sow waste influent, and 10 ng for lagoon sludge samples. Lower detection limits of 10−6 g of wet pig feces in 500 ml of phosphate-buffered saline and 10−4 g of lagoon waste in estuarine water were established for the P23-2 marker. This study was the first to utilize methanogens for the development of a swine-specific fecal contamination marker. PMID:17586669

Prevalence of antimicrobial resistance in fecal Escherichia coli and Salmonella enterica in Canadian commercial meat, companion, laboratory, and shelter rabbits (Oryctolagus cuniculus) and its association with routine antimicrobial use in commercial meat rabbits.

PubMed

Kylie, Jennifer; McEwen, Scott A; Boerlin, Patrick; Reid-Smith, Richard J; Weese, J Scott; Turner, Patricia V

2017-11-01

Antimicrobial resistance (AMR) in zoonotic (e.g. Salmonella spp.), pathogenic, and opportunistic (e.g. E. coli) bacteria in animals represents a potential reservoir of antimicrobial resistant bacteria and resistance genes to bacteria infecting humans and other animals. This study evaluated the prevalence of E. coli and Salmonella enterica, and the presence of associated AMR in commercial meat, companion, research, and shelter rabbits in Canada. Associations between antimicrobial usage and prevalence of AMR in bacterial isolates were also examined in commercial meat rabbits. Culture and susceptibility testing was conducted on pooled fecal samples from weanling and adult commercial meat rabbits taken during both summer and winter months (n=100, 27 farms), and from pooled laboratory (n=14, 8 laboratory facilities), companion (n=53), and shelter (n=15, 4 shelters) rabbit fecal samples. At the facility level, E. coli was identified in samples from each commercial rabbit farm, laboratory facility, and 3 of 4 shelters, and in 6 of 53 companion rabbit fecal samples. Seventy-nine of 314 (25.2%; CI: 20.7-30.2%) E. coli isolates demonstrated resistance to >1 antimicrobial agent. At least one E. coli isolate resistant to at least one antimicrobial agent was present in samples from 55.6% of commercial farms, and from 25% of each laboratory and shelter facilities, with resistance to tetracycline being most common; no resistance was identified in companion animal samples. Salmonella enterica subsp. was identified exclusively in pooled fecal samples from commercial rabbit farms; Salmonella enterica serovar London from one farm and Salmonella enterica serovar Kentucky from another. The S. Kentucky isolate was resistant to amoxicillin/clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, streptomycin, and tetracycline, whereas the S. London isolate was pansusceptible. Routine use of antimicrobials on commercial meat rabbit farms was not significantly associated with the presence of antimicrobial resistant E. coli or S. enterica on farms; trends towards resistance were present when resistance to specific antimicrobial classes was examined. E. coli was widely prevalent in many Canadian domestic rabbit populations, while S. enterica was rare. The prevalence of AMR in isolated bacteria was variable and most common in isolates from commercial meat rabbits (96% of the AMR isolates were from commercial meat rabbit fecal samples). Our results highlight that domestic rabbits, and particularly meat rabbits, may be carriers of phenotypically antimicrobial-resistant bacteria and AMR genes, possibly contributing to transmission of these bacteria and their genes to bacteria in humans through food or direct contact, as well as to other co-housed animal species. Copyright © 2017 Elsevier B.V. All rights reserved.

Fecal contamination of drinking water supplies in and around Chandigarh and correlation with acute gastroenteritis.

PubMed

Neelam, Taneja; Malkit, Singh; Pooja, Rao; Manisha, Biswal; Shiva, Priya; Ram, Chander; Meera, Sharma

2012-12-01

Acute gastroenteritis due to Vibrio cholerae and Enterotoxigenic E. coli is a common problem faced in the hot and humid summer months in north India. The study was undertaken to evaluate drinking water supplies for fecal coliforms, V. cholerae and Enterotoxigenic E. coli in urban, semiurban and rural areas in and around Chandigarh and correlate with occurrence of acute gastroenteritis occurring from the same region. Drinking water sample were collected from various sources from April to October 2004 from a defined area. Samples were tested for fecal coliforms and E. coli count. E. coli were screened for heat labile toxin (LT) also. Stool samples from cases of acute gastroenteritis from the same region and time were collected and processed for V. cholerae, Enterotoxigenic E. coli (ETEC) and others like Salmonella, Shigella and Aeromonas spp. A total of 364 water samples were collected, (251 semi urban, 41 rural and 72 from urban areas). 116 (31.8%) samples were contaminated with fecal coliforms (58.5% rural, 33.4% semiurban and 11.1% of samples from urban areas). E. coli were grown from 58 samples. Ninety two isolates of E. coli were tested for enterotoxins of which 8 and 24 were positive for LT and ST respectively. V. cholerae were isolated from 2 samples during the outbreak investigation. Stored water samples showed a significantly higher level of contamination and most of Enterotoxigenic E. coli were isolated from stored water samples. A total of 780 acute gastroenteritis cases occurred; 445 from semiurban, 265 rural and 70 from urban areas. Out of 189 stool samples submitted, ETEC were the commonest (30%) followed by V. cholerae (19%), Shigellae (8.4%), Salmonellae (2.1%) and Aeromonas (2.6%). ST-ETEC (40/57) were commoner than LT-ETEC (17/57). In the present study, high levels of contamination of drinking water supplies (32.1%) correlated well with cases of acute gastroenteritis. Majority of cases of acute gastroenteritis occurred in the semi urban corresponding with high level of contamination (33.4%). The highest level of water contamination was seen in rural areas (58.5%) but the number of acute gastroenteritis cases were lesser (33.9%) as ponds were infrequently used for drinking purpose. Safer household water storage and treatment is recommended to prevent acute gastroenteritis, together with point-of-use water quality monitoring.

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.

PubMed

Holscher, Hannah D; Caporaso, J Gregory; Hooda, Seema; Brulc, Jennifer M; Fahey, George C; Swanson, Kelly S

2015-01-01

In our published randomized, double-blind, placebo-controlled, 3-period crossover trial, healthy adult men (n = 21) consumed bars containing no supplemental fiber (placebo; NFC), polydextrose (21 g/d), and soluble corn fiber (SCF; 21 g/d) for 21 d each. Fecal specimens were collected between days 16 and 21 for fermentative end-product analysis and 16S ribosomal RNA bacterial gene amplification for bacterial taxa identification. Fiber supplementation decreased fecal putrefaction compounds and shifted abundances of several bacterial taxa. The objective was to perform whole-genome shotgun 454 pyrosequencing on the same fecal specimens collected in that clinical trial to obtain comprehensive fecal bacterial genome sequencing coverage and explore the full range of bacterial genetic information in the fecal microbiome, thereby using a systematic approach to study the impact of dietary fiber supplementation on fecal metabolites, bacterial taxa, and bacterial metagenomes. Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing to identify both fecal bacterial populations present and their functional genetic capacity. Whole-genome shotgun sequencing results revealed that fiber consumption shifted the Bacteroidetes:Firmicutes ratio, increasing the relative abundance of Bacteroidetes 12 ± 2% and 13 ± 2% with polydextrose and SCF, respectively, compared with NFC. Bivariate correlations showed a positive correlation between the Bacteroidetes:Firmicutes ratio and total dietary fiber intake but not body mass index. Principal coordinates analysis of Bray-Curtis distances indicated that bacterial gene composition was more similar in participants consuming fibers (polydextrose and SCF combined) in comparison with NFC. Shifts in bacterial gene abundances after polydextrose and SCF supplementation included genes associated with carbohydrate, amino acid, and lipid metabolism, as well as metabolism of cofactors and vitamins. This study conveys novel information about the impact of dietary fiber supplementation on the phylogenetic structure and functional capacity of the fecal microbiome of healthy adults. © 2015 American Society for Nutrition.

Classification of Antibiotic Resistance Patterns of Indicator Bacteria by Discriminant Analysis: Use in Predicting the Source of Fecal Contamination in Subtropical Waters

PubMed Central

Harwood, Valerie J.; Whitlock, John; Withington, Victoria

2000-01-01

The antibiotic resistance patterns of fecal streptococci and fecal coliforms isolated from domestic wastewater and animal feces were determined using a battery of antibiotics (amoxicillin, ampicillin, cephalothin, chlortetracycline, oxytetracycline, tetracycline, erythromycin, streptomycin, and vancomycin) at four concentrations each. The sources of animal feces included wild birds, cattle, chickens, dogs, pigs, and raccoons. Antibiotic resistance patterns of fecal streptococci and fecal coliforms from known sources were grouped into two separate databases, and discriminant analysis of these patterns was used to establish the relationship between the antibiotic resistance patterns and the bacterial source. The fecal streptococcus and fecal coliform databases classified isolates from known sources with similar accuracies. The average rate of correct classification for the fecal streptococcus database was 62.3%, and that for the fecal coliform database was 63.9%. The sources of fecal streptococci and fecal coliforms isolated from surface waters were identified by discriminant analysis of their antibiotic resistance patterns. Both databases identified the source of indicator bacteria isolated from surface waters directly impacted by septic tank discharges as human. At sample sites selected for relatively low anthropogenic impact, the dominant sources of indicator bacteria were identified as various animals. The antibiotic resistance analysis technique promises to be a useful tool in assessing sources of fecal contamination in subtropical waters, such as those in Florida. PMID:10966379

[Rapid Detection of Adenovirus in Fecal Samples by Capillary Electrophoresis-laser Induced Fluorescence and Microchip Capillary Electrophoresis-laser Induced Fluorescence].

PubMed

Ruan, Jia; Ren, Dong-xia; Yang, Dan-ni; Long, Pin-pin; Zhao, Hong-yue; Wang, Yi-qi; Li, Yong-xin

2015-07-01

To establish a rapid and sensitive method based on polymerase chain reaction (PCR) combined with capillary electrophoresis-laser induced fluorescence (CE-LIF) and microchip capillary electrophoresis-laser induced fluorescence (MCE-LIF) for detecting adenoviruses in fecal samples. The DNA of adenovirus in fecal samples were extracted by the commercial kits and the conserved region of hexon gene was selected as the target gene and amplified by PCR reaction. After labeling highly sensitive nucleic acid fluorescent dye SYBR Gold and SYBR Orange respectively, PCR amplification products were separated by CE and MCE under the optimized condition and detected by LIF detector. PCR amplification products could be detected within 9 min by CE-LIF and 6 min by MCE-LIF under the optimized separation condition. The sequenced PCR product showed good specificity in comparison with the prototype sequences from NCBI. The intraday and inter-day relative standard deviation (RSD) of the size (bp) of the target DNA was in the range of 1.14%-1.34% and 1.27%- 2.76%, respectively, for CE-LIF, and 1.18%-1.48% and 2.85%-4.06%, respectively, for MCE-LIF. The detection limits was 2.33 x 10(2) copies/mL for CE-LIF and 2.33 x 10(3) copies/mL for MCE-LIF. The two proposed methods were applied to detect fecal samples, both showing high accuracy. The two proposed methods of PCR-CE-LIF and PCR-MCE-LIF can detect adenovirus in fecal samples rapidly, sensitively and specifically.

FECAL COLIFORM INCREASE AFTER CENTRIFUGATION

EPA Science Inventory

The Water Environment Research Foundation (WERF) recently published a report titled Examination of Reactivation and Regrowth of Fecal Coliforms in Anaerobically Digested Sludges. Seven full-scale publicly owned treatment facilities were sampled several times to determine if bacte...

Lack of infectivity of HBV in feces from patients with chronic hepatitis B virus infection, and infection using chimeric mice.

PubMed

Komatsu, Haruki; Inui, Ayano; Murano, Takeyoshi; Tsunoda, Tomoyuki; Sogo, Tsuyoshi; Fujisawa, Tomoo

2015-08-20

Body fluids such as saliva and tears from patients with hepatitis B virus (HBV) infection are known as infectious agents. The infectivity of feces from patients with HBV infection has not been established. The aim of this study was to determine whether feces from HBV carriers can be a source of HBV infection. Thirty-three children and 17 adults (ages 0-49 years, median age 13 years) who were chronically infected with HBV were enrolled. The levels of HBV DNA in the feces from these patients were quantified by real-time PCR, and the levels of fecal HBsAg were measured. Isolated human hepatocytes from chimeric mice with humanized livers were co-cultured with serum, tears and feces from the HBV carriers. Four chimeric mice were inoculated intravenously with sterilized feces from HBV carriers. HBV DNA was detected in the feces of 37 (74%) of the 50 patients. The fecal HBV DNA levels ranged from 2.8 to 8.4 log copies/mL (mean ± SD  =  5.6 ± 1.2 log copies/mL). A significant correlation was observed in the levels of HBV DNA between serum and feces (r  =  0.54, p < 0.05). Of the 13 HBV carries, 7 (54%) were positive for fecal HBsAg. The fecal HBsAg levels ranged from 0.06 to 1.0 IU/mL (median 0.28 IU/mL). Immunogold electron microscopy showed Dane particles in feces. HBV DNA was detected in the human hepatocytes co-cultured with serum and tears, but not in those co-cultured with feces. HBV DNA was not detected in the serum of the chimeric mice after oral or intravenous inoculation with sterilized fecal samples, which contained 5 log copies/mL of HBV DNA levels. Although the positive rate of fecal HBV DNA was high, the fecal HBsAg levels were extremely low. The chimeric mice were not infected with HBV after oral or intravenous inoculation with sterilized fecal samples. Therefore, feces from HBV carriers seem not to serve as an infectious vehicle for the transmission of HBV.

Linking fecal bacteria in rivers to landscape, geochemical, and hydrologic factors and sources at the basin scale

PubMed Central

Verhougstraete, Marc P.; Martin, Sherry L.; Kendall, Anthony D.; Hyndman, David W.; Rose, Joan B.

2015-01-01

Linking fecal indicator bacteria concentrations in large mixed-use watersheds back to diffuse human sources, such as septic systems, has met limited success. In this study, 64 rivers that drain 84% of Michigan’s Lower Peninsula were sampled under baseflow conditions for Escherichia coli, Bacteroides thetaiotaomicron (a human source-tracking marker), landscape characteristics, and geochemical and hydrologic variables. E. coli and B. thetaiotaomicron were routinely detected in sampled rivers and an E. coli reference level was defined (1.4 log10 most probable number⋅100 mL−1). Using classification and regression tree analysis and demographic estimates of wastewater treatments per watershed, septic systems seem to be the primary driver of fecal bacteria levels. In particular, watersheds with more than 1,621 septic systems exhibited significantly higher concentrations of B. thetaiotaomicron. This information is vital for evaluating water quality and health implications, determining the impacts of septic systems on watersheds, and improving management decisions for locating, constructing, and maintaining on-site wastewater treatment systems. PMID:26240328

Association between thermal environment and Salmonella in fecal samples from dairy cattle in midwestern United States

PubMed Central

Likavec, Tasha; Pires, Alda F.A.; Funk, Julie A.

2016-01-01

The objective of this study was to describe the association between thermal measures in the barn environment (pen temperature and humidity) and fecal shedding of Salmonella in dairy cattle. A repeated cross-sectional study was conducted within a commercial dairy herd located in the midwestern United States. Five pooled fecal samples were collected monthly from each pen for 9 mo and submitted for microbiological culture. Negative binomial regression methods were used to test the association [incidence rate ratio (IRR)] between Salmonella pen status (the count of Salmonella-positive pools) and thermal environmental parameters [average temperature and temperature humidity index (THI)] for 3 time periods (48 h, 72 h, and 1 wk) before fecal sampling. Salmonella was cultured from 10.8% [39/360; 95% confidence interval (CI): 7.8% to 14.5%] of pooled samples. The highest proportion of positive pools occurred in August. The IRR ranged from 1.26 (95% CI: 1.15 to 1.39, THI 1 wk) to 4.5 (95% CI: 2.13 to 9.51, heat exposure 1 wk) across all thermal parameters and lag time periods measured. For example, the incidence rate of Salmonella-positive pools increased by 54% for every 5°C increment in average temperature (IRR = 1.54; 95% CI: 1.29 to 1.85) and 29% for every 5-unit increase in THI (IRR = 1.29; 95% CI: 1.16 to 1.42) during the 72 h before sampling. The incidence rate ratio for pens exposed to higher temperatures (> 25°C) was 4.5 times (95% CI: 2.13 to 9.51) the incidence rate ratio for pens exposed to temperatures < 25°C in the 72 h before sampling. Likewise, the incidence rate ratio for pens exposed to THI > 70 was 4.23 times greater (95% CI: 2.1 to 8.28) than when the THI was < 70 in the 72 h before sampling. An association was found between the thermal environment and Salmonella shedding in dairy cattle. Further research is warranted in order to fully understand the component risks associated with the summer season and increased Salmonella shedding. PMID:27408330

40 CFR 141.202 - Tier 1 Public Notice-Form, manner, and frequency of notice.

Code of Federal Regulations, 2010 CFR

2010-07-01

... fecal coliform or E. coli are present in the water distribution system (as specified in § 141.63(b)), or when the water system fails to test for fecal coliforms or E. coli when any repeat sample tests...) Detection of E. coli, enterococci, or coliphage in source water samples as specified in § 141.402(a) and...

40 CFR 141.202 - Tier 1 Public Notice-Form, manner, and frequency of notice.

Code of Federal Regulations, 2011 CFR

2011-07-01

... fecal coliform or E. coli are present in the water distribution system (as specified in § 141.63(b)), or when the water system fails to test for fecal coliforms or E. coli when any repeat sample tests...) Detection of E. coli, enterococci, or coliphage in source water samples as specified in § 141.402(a) and...

Viral metagenomic analysis of feces of wild small carnivores

PubMed Central

2014-01-01

Background Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores. PMID:24886057

Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients.

PubMed

Hamad, Ibrahim; Abou Abdallah, Rita; Ravaux, Isabelle; Mokhtari, Saadia; Tissot-Dupont, Hervé; Michelle, Caroline; Stein, Andreas; Lagier, Jean-Christophe; Raoult, Didier; Bittar, Fadi

2018-01-01

Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples. Our results revealed that recovering eukaryotic components from fecal samples differs significantly among DNA extraction methods. Subsequently, the composition of the intestinal eukaryotic microbiota was evaluated in HIV-infected patients and healthy volunteers through clone sequencing, high-throughput sequencing of nuclear ribosomal internal transcribed spacers 1 (ITS1) and 2 (ITS2) amplicons and real-time PCRs. Our results revealed that not only richness (Chao-1 index) and alpha diversity (Shannon diversity) differ between HIV-infected patients and healthy volunteers, depending on the molecular strategy used, but also the global eukaryotic community composition, with little overlapping taxa found between techniques. Moreover, our results based on cloning libraries and ITS1/ITS2 metabarcoding sequencing showed significant differences in fungal composition between HIV-infected patients and healthy volunteers, but without distinct clusters separating the two groups. Malassezia restricta was significantly more prevalent in fecal samples of HIV-infected patients, according to cloning libraries, whereas operational taxonomic units (OTUs) belonging to Candida albicans and Candida tropicalis were significantly more abundant in fecal samples of HIV-infected patients compared to healthy subjects in both ITS subregions. Finally, real-time PCR showed the presence of Microsporidia, Giardia lamblia, Blastocystis and Hymenolepis diminuta in different proportions in fecal samples from HIV patients as compared to healthy individuals. Our work revealed that the use of different sequencing approaches can impact the perceived eukaryotic diversity results of the human gut. We also provide a more comprehensive view of the eukaryotic community in the gut of HIV-infected patients through the complementarity of the different molecular techniques used. Combining these various methodologies may provide a gold standard for a more complete characterization of the eukaryotic microbiome in future studies.

Occurrence of fecal-indicator bacteria and protocols for identification of fecal-contamination sources in selected reaches of the West Branch Brandywine Creek, Chester County, Pennsylvania

USGS Publications Warehouse

Cinotto, Peter J.

2005-01-01

The presence of fecal-indicator bacteria indicates the potential presence of pathogens originating from the fecal matter of warm-blooded animals. These pathogens are responsible for numerous human diseases ranging from common diarrhea to meningitis and polio. The detection of fecal-indicator bacteria and interpretation of the resultant data are, therefore, of great importance to water-resource managers. Current (2005) techniques used to assess fecal contamination within the fluvial environment primarily assess samples collected from the water column, either as grab samples or as depth- and (or) width-integrated samples. However, current research indicates approximately 99 percent of all bacteria within nature exist as attached, or sessile, bacteria. Because of this condition, most current techniques for the detection of fecal contamination, which utilize bacteria, assess only about 1 percent of the total bacteria within the fluvial system and are, therefore, problematic. Evaluation of the environmental factors affecting the occurrence and distribution of bacteria within the fluvial system, as well as the evaluation and modification of alternative approaches that effectively quantify the larger population of sessile bacteria within fluvial sediments, will present water-resource managers with more effective tools to assess, prevent, and (or) eliminate sources of fecal contamination within pristine and impaired watersheds. Two stream reaches on the West Branch Brandywine Creek in the Coatesville, Pa., region were studied between September 2002 and August 2003. The effects of sediment particle size, climatic conditions, aquatic growth, environmental chemistry, impervious surfaces, sediment and soil filtration, and dams on observed bacteria concentrations were evaluated. Alternative approaches were assessed to better detect geographic sources of fecal contamination including the use of turbidity as a surrogate for bacteria, the modification and implementation of sandbag bacteria samplers, and the use of optical brighteners. For the purposes of this report, sources of bacteria were defined as geographic locations where elevated concentrations of bacteria are observed within, or expected to enter, the main branch of the West Branch Brandywine Creek. Biologic sources (for example, waterfowl) were noted where applicable; however, no specific study of biologic sources (such as bacterial source tracking) was conducted. Data indicated that specific bacterial populations within fluvial sediments could be related to specific particle-size ranges. This relation is likely the result of the reduced porosity and permeability associated with finer sediments and the ability of specific bacteria to tolerate particular environments. Escherichia coli (E. coli) showed a higher median concentration (2,160 colonies per gram of saturated sediment) in the 0.125 to 0.5-millimeter size range of natural sediments than in other ranges, and enterococcus bacteria showed a higher median concentration (61,830 colonies per gram of saturated sediment) in the 0.062 to 0.25-millimeter size range of natural sediments than in other ranges. There were insufficient data to assess the particle-size relation to fecal coliform bacteria and (or) fecal streptococcus bacteria. Climatic conditions were shown to affect bacteria concentrations in both the water column and fluvial sediments. Drought conditions in 2002 resulted in lower overall bacteria concentrations than the more typically wet year of 2003. E. coli concentrations in fluvial sediment along the Coatesville study reach in 2002 had a median concentration of 92 colonies per gram of saturated sediment; in 2003, the median concentration had risen to 4,752 colonies per gram of saturated sediment. Symbiotic relations between bacteria and aquatic growth were likely responsible for increased bacteria concentrations observed within an impoundment area on the Coatesville study reach. This reach showed evidence of

Exploration of Fecal Microbiota Transplantation in the Treatment of Refractory Diarrhea After Renal Transplantation.

PubMed

Gu, B; Bo, G Z; Ke, C

2018-06-01

Exploration of fecal microbiota transplantation in the treatment of refractory diarrhea after renal transplantation. Summarize the etiology of 120 cases with diarrhea after renal transplantation from 2014 to 2017 in our hospital. There were 4 recipients of refractory diarrhea who accepted fecal microbiota transplantation with informed consent, and we collected clinical data of stool and bacterial culture, gut microbiota analysis, graft function, electrolytes, immunosuppressant concentrations of prognostic evaluation of patients with fecal transplantation. The absorption of electrolyte is slightly higher and concentration of tacrolimus and creatinine were not significantly changed compared with before. Fecal microbiota transplantation provides a new choice to refractory diarrhea after renal transplantation as an innovative treatment, but the effectiveness of fecal microbiota transplantation needs long-term observation and further evaluation through large sample data. Copyright © 2018. Published by Elsevier Inc.

Evaluation of microRNA stability in feces from healthy dogs.

PubMed

Cirera, Susanna; Willumsen, Line M; Johansen, Thea T; Nielsen, Lise N

2018-03-01

Gastrointestinal cancer accounts for approximately 8% of all canine malignancies. Early detection of cancer may have a tremendous impact on both treatment options and prognosis. MicroRNAs (miRNAs), a class of noncoding RNAs that can be found stably expressed in body fluids and feces, have been suggested as valuable human cancer biomarkers. The purpose of the study was to investigate the feasibility of detecting miRNAs in canine feces and to determine the miRNA stability in fecal samples stored at different temperatures for different duration. The levels of 4 Canine familiaris (cfa) miRNAs (cfa-miR-16, cfa-miR-20a, cfa-miR-21, and cfa-miR-92a) were investigated by quantitative real-time PCR(qPCR) in fecal samples from 10 healthy dogs. Fecal samples were collected at 3 different time points and samples from the first time point were stored at different temperatures and for a different duration. A statistically significant difference was found in miRNA levels from samples stored at room temperature compared with samples stored at -20°C for cfa-miR-16 and cfa-miR-21. No significant difference was found in the level of the investigated miRNAs over time. Overall, miRNAs are present in dog feces at measurable levels. Some miRNAs seem to be subject to a higher degree of degradation in samples stored at room temperature for 24 hours compared with samples frozen after collection at -20°C. The investigated miRNAs were stably expressed over time. This study provides the basis for further research on miRNA expression profiles as biomarkers for gastrointestinal cancer in dogs. © 2018 American Society for Veterinary Clinical Pathology.

Altered Fecal Microbiota in Paediatric Inflammatory Bowel Disease.

PubMed

Maukonen, Johanna; Kolho, Kaija-Leena; Paasela, Monika; Honkanen, Jarno; Klemetti, Paula; Vaarala, Outi; Saarela, Maria

2015-12-01

Several factors support the view of inflammatory bowel disease [IBD] origin in the host responsiveness to intestinal bacteria, although no single bacterial species has been shown as a causative agent in the pathogenesis. Our aim was to analyse the fecal microbiota of paediatric IBD patients at different stages of the disease. In addition, the characteristics of immune response to the bacterial isolates showing very low abundance in IBD were studied. Fecal samples [1-3 samples/child] were collected from 10 paediatric patients with crohn's disease [CD], and 12 with ulcerative colitis [UC] and from 8 healthy children, for polyphasic microbiological analysis (culture, real-time polymerase chain reaction [PCR], and denaturing gradient gel electrophoresis). In addition, in vitro cytokine responses of peripheral blood mononuclear cells to the bacterial isolates, which showed very low abundance in IBD, were studied. Although predominant bacterial diversity was higher in IBD, the numbers of Lachnospiraceae and Coriobacteriaceae bacteria were lower in IBD patients as compared with control children [p < 0.05]. In addition, Ruminococcaceae population diversity was lower in IBD [p < 0.05] and correlated negatively with fecal calprotectin levels. Both abundance and diversity of bifidobacterial populations were lower in children with IBD [p < 0.05], and particularly low numbers of certain bifidobacterial isolates were detected. In CD, we found enhanced up-regulation of interleukin-6 transcripts and impaired RAR-related orphan receptor C response to bifidobacteria, whereas decreased interferon-gamma response was observed in both CD and UC. We demonstrate altered fecal microbiota in paediatric IBD, particularly low numbers and diversity of bifidobacterial populations. Interestingly, immunological response to bifidobacteria differed between paediatric CD patients and control children. Copyright © 2015 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A comparative analysis of preservation techniques for the optimal molecular detection of hookworm DNA in a human fecal specimen

PubMed Central

Pilotte, Nils; Baumer, Ben; Grant, Jessica; Asbjornsdottir, Kristjana; Schaer, Fabian; Hu, Yan; Aroian, Raffi; Walson, Judd; Williams, Steven A.

2018-01-01

Background Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time. Methodology Quantitative real-time PCR was used in this study as a measure of the effectiveness of seven commercially available products to preserve hookworm DNA over time and at different temperatures. Results were compared against “no preservative” controls and the “gold standard” of rapidly freezing samples at -20°C. The preservation methods were compared at both 4°C and at simulated tropical ambient temperature (32°C) over a period of 60 days. Evaluation of the effectiveness of each preservative was based on quantitative real-time PCR detection of target hookworm DNA. Conclusions At 4°C there were no significant differences in DNA amplification efficiency (as measured by Cq values) regardless of the preservation method utilized over the 60-day period. At 32°C, preservation with FTA cards, potassium dichromate, and a silica bead two-step desiccation process proved most advantageous for minimizing Cq value increases, while RNA later, 95% ethanol and Paxgene also demonstrate some protective effect. These results suggest that fecal samples spiked with known concentrations of hookworm-derived egg material can remain at 4°C for 60 days in the absence of preservative, without significant degradation of the DNA target. Likewise, a variety of preservation methods can provide a measure of protection in the absence of a cold chain. As a result, other factors, such as preservative toxicity, inhibitor resistance, preservative cost, shipping requirements, sample infectivity, and labor costs should be considered when deciding upon an appropriate method for the storage of fecal specimens for subsequent PCR analysis. Balancing logistical factors and the need to preserve the target DNA, we believe that under most circumstances 95% ethanol provides the most pragmatic choice for preserving stool samples in the field. PMID:29346412

Spiral Plating Method To Quantify the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces.

PubMed

Shridhar, Pragathi B; Noll, Lance W; Cull, Charley A; Shi, Xiaorong; Cernicchiaro, Natalia; Renter, David G; Bai, Jianfa; Nagaraja, T G

2017-04-17

Cattle are a major reservoir of the six major Shiga toxin-producing non-O157 Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) responsible for foodborne illnesses in humans. Besides prevalence in feces, the concentrations of STEC in cattle feces play a major role in their transmission dynamics. A subset of cattle, referred to as super shedders, shed E. coli O157 at high concentrations (≥4 log CFU/g of feces). It is not known whether a similar pattern of fecal shedding exists for non-O157. Our objectives were to initially validate the spiral plating method to quantify the six non-O157 E. coli serogroups with pure cultures and culture-spiked fecal samples and then determine the applicability of the method and compare it with multiplex quantitative PCR (mqPCR) assays for the quantification of the six non-O157 E. coli serogroups in cattle fecal samples collected from commercial feedlots. Quantification limits of the spiral plating method were 3 log, 3 to 4 log, and 3 to 5 log CFU/mL or CFU/g for individual cultures, pooled pure cultures, and cattle fecal samples spiked with pooled pure cultures, respectively. Of the 1,152 cattle fecal samples tested from eight commercial feedlots, 122 (10.6%) and 320 (27.8%) harbored concentrations ≥4 log CFU/g of one or more of the six serogroups of non-O157 by spiral plating and mqPCR methods, respectively. A majority of quantifiable samples, detected by either spiral plating (135 of 137, 98.5%) or mqPCR (239 of 320, 74.7%), were shedding only one serogroup. Only one of the quantifiable samples was positive for a serogroup carrying Shiga toxin (stx 1 ) and intimin (eae) genes; 38 samples were positive for serogroups carrying the intimin gene. In conclusion, the spiral plating method can be used to quantify non-O157 serogroups in cattle feces, and our study identified a subset of cattle that was super shedders of non-O157 E. coli . The method has the advantage of quantifying non-O157 STEC, unlike mqPCR that quantifies serogroups only.

Bacteria, viruses, and parasites in an intermittent stream protected from and exposed to pasturing cattle: prevalence, densities, and quantitative microbial risk assessment.

PubMed

Wilkes, G; Brassard, J; Edge, T A; Gannon, V; Jokinen, C C; Jones, T H; Neumann, N; Pintar, K D M; Ruecker, N; Schmidt, P J; Sunohara, M; Topp, E; Lapen, D R

2013-10-15

Over 3500 individual water samples, for 131 sampling times, targeting waterborne pathogens/fecal indicator bacteria were collected during a 7-year period from 4 sites along an intermittent stream running through a small livestock pasture system with and without cattle access-to-stream restriction measures. The study assessed the impact of cattle pasturing/riparian zone protection on: pathogen (bacterial, viral, parasite) occurrence, concentrations of fecal indicators, and quantitative microbial risk assessments (QMRA) of the risk of Cryptosporidium, Giardia and Escherichia coli O157:H7 infection in humans. Methodologies were developed to compute QMRA mean risks on the basis of water samples exhibiting potentially human infectious Cryptosporidium and E. coli based on genotyping Crytosporidium, and E. coli O157:H7 presence/absence information paired with enumerated E. coli. All Giardia spp. were considered infectious. No significant pasturing treatment effects were observed among pathogens, with the exception of Campylobacter spp. and E. coli O157:H7. Campylobacter spp. prevalence significantly decreased downstream through pasture treatments and E. coli O157:H7 was observed in a few instances in the middle of the unrestricted pasture. Densities of total coliform, fecal coliform, and E. coli reduced significantly downstream in the restricted pasture system, but not in the unrestricted system. Seasonal and flow conditions were associated with greater indicator bacteria densities, especially in the summer. Norovirus GII was detected at rates of 7-22% of samples for all monitoring sites, and rotavirus in 0-7% of samples for all monitoring sites; pasture treatment trends were not evident, however. Seasonal and stream flow variables (and their interactions) were relatively more important than pasture treatments for initially stratifying pathogen occurrence and higher fecal indicator bacteria densities. Significant positive associations among fecal indicator bacteria and Campylobacter spp. detection were observed. For QMRA, adjusting for the proportion of Cryptosporidium spp. detected that are infectious for humans reduces downstream risk estimates by roughly one order of magnitude. Using QMRA in this manner provides a more refined estimate of beneficial management practice effects on pathogen exposure risks to humans. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

A flotation/sieving method to detect Echinococcus multilocularis and Toxocara spp. eggs in soil by real-time PCR

PubMed Central

Umhang, Gérald; Bastien, Matthieu; Renault, Camille; Faisse, Marine; Caillot, Christophe; Boucher, Jean-Marc; Hormaz, Vanessa; Poulle, Marie-Lazarine; Boué, Franck

2017-01-01

Soil can be a source of human infection by many zoonotic helminth species including Echinococcus multilocularis and Toxocara spp. The prevention of alveolar echinococcosis could be greatly improved through the identification of at-risk areas. Yet very few data are available about the detection of E. multilocularis in soil, while more studies have been reported for Toxocara spp. Identification of soil contamination by E. multilocularis eggs requires the use of specific methods. This study describes the development of a method for the detection of E. multilocularis in soil samples with the concentration of eggs using a flotation/sieving method and detection by duplex real-time polymerase chain reaction (PCR). Toxocara spp. egg detection was also undertaken due to the widespread presence of this parasite in soil, despite it being considered less pathogenic. Method sensitivity of 100% was reached for the detection of 10 E. multilocularis eggs spiked in 10 g of soil. Concerning Toxocara spp., method sensitivity was lower but assumed to be due to the reduced effectiveness of the DNA extraction protocol. The parasitological status for E. multilocularis and Toxocara spp. of 63 carnivore fecal samples collected in highly endemic rural areas of France and of soil samples collected under and near these fecal samples was compared. The contamination of soil samples collected under positive fecal samples for E. multilocularis (n = 3) or Toxocara spp. (n = 19) confirmed the transfer of eggs from the definitive host to the environment. PMID:28737135

Analysis of the Microbial Diversity in the Fecal Material of Giraffes.

PubMed

Schmidt, Jessica M; Henken, Susan; Dowd, Scot E; McLaughlin, Richard William

2018-03-01

Using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing, the microbiota of the fecal material of seven giraffes living in captivity at the Jacksonville Zoo and Gardens, Jacksonville, FL was investigated. In all samples, the most predominant bacterial phylum was the Firmicutes followed by Bacteroidetes. The most predominant fungi were members of the phylum Ascomycota followed by Neocallimastigomycota in five of seven samples. The reverse was true in the other two samples.

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

DOE PAGES

Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G.; ...

2017-12-22

Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Usingmore » 1H-NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites-caprate, nicotinate, glutamine, thymine, and aspartate-may potentially function as a modest biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of phylotypes most closely related to Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. In conclusion, despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.« less

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G.

Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Usingmore » 1H-NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites-caprate, nicotinate, glutamine, thymine, and aspartate-may potentially function as a modest biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of phylotypes most closely related to Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. In conclusion, despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.« less

Canine scent detection and microbial source tracking of human waste contamination in storm drains.

PubMed

Van De Werfhorst, Laurie C; Murray, Jill L S; Reynolds, Scott; Reynolds, Karen; Holden, Patricia A

2014-06-01

Human fecal contamination of surface waters and drains is difficult to diagnose. DNA-based and chemical analyses of water samples can be used to specifically quantify human waste contamination, but their expense precludes routine use. We evaluated canine scent tracking, using two dogs trained to respond to the scent of municipal wastewater, as a field approach for surveying human fecal contamination. Fecal indicator bacteria, as well as DNA-based and chemical markers of human waste, were analyzed in waters sampled from canine scent-evaluated sites (urban storm drains and creeks). In the field, the dogs responded positively (70% and 100%) at sites for which sampled waters were then confirmed as contaminated with human waste. When both dogs indicated a negative response, human waste markers were absent. Overall, canine scent tracking appears useful for prioritizing sampling sites for which DNA-based and similarly expensive assays can confirm and quantify human waste contamination.

Water quality in three creeks in the backcountry of Grand Teton National Park, USA

USGS Publications Warehouse

Farag, A.M.; Goldstein, J.N.; Woodward, D.F.

2001-01-01

This study was conducted in Grand Teton National Park during the summers of 1996 and 1997 to investigate the water quality in two high human use areas: Garnet Canyon and lower Cascade Canyon. To evaluate the water quality in these creeks, fecal coliform, Giardia lamblia, coccidia, and microparticulates were measured in water samples. No evidence of fecal coliform, Giardia lamblia, or coccidia, was found in Garnet Creek. The water quality and general water chemistry of Garnet Creek was similar to the reference site. No Giardia lamblia or coccidia were found in Cascade Creek, but fecal coliforms were present. The isolated colonies of Escherichia coli from Cascade Creek matched the ribosome patterns of avian, deer, canine, elk, rodent, and human coliforms.

Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo

PubMed Central

Waite, David W.; Eason, Daryl K.

2014-01-01

The critically endangered New Zealand parrot, the kakapo, is subject to an intensive management regime aiming to maintain bird health and boost population size. Newly hatched kakapo chicks are subjected to human intervention and are frequently placed in captivity throughout their formative months. Hand rearing greatly reduces mortality among juveniles, but the potential long-term impact on the kakapo gut microbiota is uncertain. To track development of the kakapo gut microbiota, fecal samples from healthy, prefledged juvenile kakapos, as well as from unrelated adults, were analyzed by using 16S rRNA gene amplicon pyrosequencing. Following the original sampling, juvenile kakapos underwent a period of captivity, so further sampling during and after captivity aimed to elucidate the impact of captivity on the juvenile gut microbiota. Variation in the fecal microbiota over a year was also investigated, with resampling of the original juvenile population. Amplicon pyrosequencing revealed a juvenile fecal microbiota enriched with particular lactic acid bacteria compared to the microbiota of adults, although the overall community structure did not differ significantly among kakapos of different ages. The abundance of key operational taxonomic units (OTUs) was correlated with antibiotic treatment and captivity, although the importance of these factors could not be proven unequivocally within the bounds of this study. Finally, the microbial community structure of juvenile and adult kakapos changed over time, reinforcing the need for continual monitoring of the microbiota as part of regular health screening. PMID:24837385

FECAL COLIFORM INCREASE AFTER CENTRIFUGATION: EPA PERSPECTIVE

EPA Science Inventory

The Water Environment Research Foundation (WERF) recently published a report titled Examination of Reactivation and Regrowth of Fecal Coliforms in Anaerobically Digested Sludges. Seven full-scale publicly owned treatment facilities were sampled several times to determine if bacte...

Levels of fecal corticosterone in sandhill cranes during a human-led migration.

PubMed

Hartup, Barry K; Olsen, Glenn H; Czekala, Nancy M; Paul-Murphy, Joanne; Langenberg, Julia A

2004-04-01

Fourteen captive-reared greater sandhill cranes (Grus canadensis tabida) were conditioned to follow ultralight aircraft to promote migration between Wisconsin and Florida (USA) after release. Fecal samples were collected throughout the training period in Wisconsin and during a l977-km human-led migration to Florida to determine fecal corticosterone (FC) concentrations by radioimmunnoassay. The mean (+/-SE) FC concentration during the training period was 109.5 +/- 7.5 ng/g and was representative of baseline levels recorded previously from sandhill cranes. Fecal corticosterone concentrations increased in early migration compared to concentrations I mo prior to departure (P < 0.01) but were not different from baseline concentrations at tile end of the 6-wk migration period. The variability of FC concentrations in individual samples was greater throughout the migration than the training period. Increases in FC during migration were modest and generally consistent with normal corticosterone elevations observed in migrating birds.

Measurement of fecal glucocorticoids in parrotfishes to assess stress

USGS Publications Warehouse

Turner, J.W.; Nemeth, R.; Rogers, C.

2003-01-01

Coral reefs are in decline worldwide from a combination of natural and human forces. The environmental compromises faced by coral reef habitats and their associated fishes are potentially stressful, and in this study we examined the potential for assessing stress levels in coral reef fish. We determined the feasibility of using fecal casts from parrotfishes for remote assessment of stress-related hormones (cortisol and corticosterone), and the response of these hormones to the stress of restraint and hypoxia. Measurement of these hormones in fecal extracts by high performance liquid chromatography (HPLC) was validated using mass spectrometry, chemical derivitization, and radioactive tracer methods. In aquarium-adapted parrotfish, baseline levels of cortisol and corticosterone averaged 3.4??1.1 and 14.8??2.8ng/g feces, respectively, across 32 days. During 13 days of periodic stress these hormones, respectively, average 10.8-fold and 3.2-fold greater than baseline, with a return to near baseline during a 23-day follow-up. Testosterone was also measured as a reference hormone which is not part of the stress-response axis. Levels of this hormone were similar across the study. These fecal hormones were also measured in a field study of parrotfish in 10 fringing coral reef areas around the Caribbean Island of St. John, US Virgin Islands. Extracts of remotely collected fecal casts of three parrotfish species revealed no difference in respective average hormone levels among these species. Also, there was no difference in respective hormone levels between aquarium and field environments. However, levels of both cortisol and corticosterone, but not testosterone, were elevated in two of the 10 reef sites surveyed. This study demonstrates that parrotfish fecals can be collected in aquarium and field conditions and that steroid hormones in these fecals can be extracted and reliably measured. The study also demonstrates that cortisol and corticosterone in parrotfish fecals can be used as an indicator of the stress-response which is unlikely to be masked by intrinsic variability in the sample source, environment or methodology. ?? 2003 Elsevier Science (USA). All rights reserved.

Community dynamics drive punctuated engraftment of the fecal microbiome following transplantation using freeze-dried, encapsulated fecal microbiota.

PubMed

Staley, Christopher; Vaughn, Byron P; Graiziger, Carolyn T; Singroy, Stephanie; Hamilton, Matthew J; Yao, Dan; Chen, Chi; Khoruts, Alexander; Sadowsky, Michael J

2017-05-04

Fecal microbiota transplantation (FMT) is a highly effective treatment of recurrent and recalcitrant Clostridium difficile infection (rCDI). In a recent study oral-delivery of encapsulated, freeze-dried donor material, resulted in comparable rates of cure to colonoscopic approaches. Here we characterize shifts in the fecal bacterial community structure of patients treated for rCDI using encapsulated donor material. Prior to FMT, patient fecal samples showed declines in diversity and abundance of Firmicutes and Bacteroidetes, with concurrent increases in members of the Proteobacteria, specifically Enterobacteriaceae. Moreover, patients who experienced recurrence of CDI within the 2-month clinical follow-up had greater abundances of Enterobacteriaceae and did not show resolution of dysbioses. Despite resolution of rCDI following oral-administration of encapsulated fecal microbiota, community composition was slow to return to a normal donor-like assemblage. Post-FMT taxa within the Firmicutes showed rapid increases in relative abundance and did not vary significantly over time. Conversely, Bacteroidetes taxa only showed significant increases in abundance after one month post-FMT, corresponding to significant increases in the community attributable to the donors. Changes in the associations among dominant OTUs were observed at days, weeks, and months post-FMT, suggesting shifts in community dynamics may be related to the timing of increases in abundance of specific taxa. Administration of encapsulated, freeze-dried, fecal microbiota to rCDI patients resulted in restoration of bacterial diversity and resolution of dysbiosis. However, shifts in the fecal microbiome were incremental rather than immediate, and may be driven by changes in community dynamics reflecting changes in the host environment.

Fecal excretion of Bifidobacterium infantis 35624 and changes in fecal microbiota after eight weeks of oral supplementation with encapsulated probiotic

PubMed Central

Charbonneau, Duane; Gibb, Roger D.; Quigley, Eamonn M.M.

2013-01-01

Certain randomized, placebo-controlled trials of oral supplementation with B. infantis 35624 have demonstrated the amelioration of symptoms of irritable bowel syndrome. Potential GI colonization by B. infantis 35624 or effects of supplementation on resident GI microbiota may pertain to these clinical observations. In this study, fecal excretion of B. infantis 35624 before, during and after 8 weeks of daily treatment was compared in subjects with IBS who received either the encapsulated oral supplement (n = 39) or placebo (n = 37) and in healthy subjects who received the supplement (n = 41). Secondarily, changes in assessed fecal microbiota and IBS symptoms were determined. Supplementation significantly increased fecal B. infantis 35624 excretion vs. placebo in IBS subjects; excretion in healthy subjects receiving supplement was quantitatively similar. Fecal levels of the probiotic declined and approached baseline once dosing ceased, documenting that colonization is transient. Although supplementation increased numbers of B infantis 35624 within the GI tract, limited changes in 10 other fecal taxa were observed either in healthy subjects or those with IBS. No impact on IBS symptoms was observed. Detection of bacterial DNA in fecal samples suggests that the probiotic is able to survive transit through the GI tract, although strain selective culture techniques were not performed to confirm viability of B. infantis 35624 in the feces. Continuous probiotic administration was necessary to maintain steady-state transit. Given the complex spectrum of GI microbiota, however, monitoring perturbations in selected taxa may not be not a useful indicator of probiotic function. PMID:23549409

Hydrogeology and quality of ground water in the Boone Formation and Cotter Dolomite in karst terrain of northwestern Boone County, Arkansas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leidy, V.A.; Morris, E.E.

1991-01-01

Shallow groundwater flow systems in karst terrain of northwestern Boone County, Arkansas, are particularly susceptible to contamination. The potential for groundwater contamination probably is greater in the northern one-half of the study area where there are more photolineaments and presumably subsurface fractures. Groundwater samples from 17 springs discharging from the Boone Formation and 17 wells completed in the Cotter Dolomite were analyzed to determine ambient groundwater quality and to document water quality variations. The chemical constituents in groundwater generally did not exceed US Environmental Protection Agency primary or secondary maximum contaminant levels. However, fecal coliform and fecal streptococcus bacteria weremore » detected in most springs and in three wells. One spring, located near an abandoned wood-treatment plant (a designated Superfund site), had maximum iron, manganese, lead, and pentachlorophenol concentration that exceeded US Environmental Protection Agency's primary or secondary maximum contamination levels for drinking water. Water samples collected from selected springs emerging from the Boone Formation exhibited an overall decrease in specific conductance and total alkalinity, calcium, magnesium, sodium, and chloride concentrations and an overall increase in nitrate, fecal coliform, and fecal streptococcus bacteria concentrations 3 to 8 hours after a rainstorm.« less

Behavioral and physiologic responses to environmental enrichment in the maned wolf (Chrysocyon brachyurus).

PubMed

Cummings, Dawn; Brown, Janine L; Rodden, Melissa D; Songsasen, Nucharin

2007-09-01

The ex situ population of maned wolves is not self-sustaining due to poor reproduction, caused primarily by parental incompetence. Studies have shown that environmental enrichment can promote natural parental behaviors in zoo animals. The objective of this study was to determine the effects of environmental enrichment on behavioral and physiological responses of maned wolves. During an 8-week experimental period, daily behavior observations and fecal sample collection were conducted on four adult wolves (2.2) individually housed in environments without enrichment. After 2 weeks, the wolves were chronologically provided with 2-week intervals of hiding dead mice around the exhibit, no enrichment, and introduction of boomer balls. Responses of the wolves to enrichment were assessed based on activity levels and exploratory rates, as well as the level of corticoid metabolites in fecal samples collected daily throughout the study period. Providing wolves with environmental enrichment significantly increased exploratory behaviors (P<0.05), especially when mice were hidden in the enclosure. Fecal corticoid concentrations were increased during periods of enrichment in males (P<0.05), but not in females. Overall, there were no correlations between behavioral responses to enrichment and fecal corticoid levels. Behavioral results suggest that environmental enrichment elicits positive effects on the behavior of captive maned wolves. There is evidence suggesting that providing animals with ability to forage for food is a more effective enrichment strategy than introducing objects. There is need for a longer term study to determine the impact of environmental enrichment in this species. Zoo Biol 26:331-343, 2007. (c) 2007 Wiley-Liss, Inc.

Evaluation of procedures for estimating ruminal particle turnover and diet digestibility in ruminant animals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cochran, R.C.

1985-01-01

Procedures used in estimating ruminal particle turnover and diet digestibility were evaluated in a series of independent experiments. Experiment 1 and 2 evaluated the influence of sampling site, mathematical model and intraruminal mixing on estimates of ruminal particle turnover in beef steers grazing crested wheatgrass or offered ad libitum levels of prairie hay once daily, respectively. Particle turnover rate constants were estimated by intraruminal administration (via rumen cannula) of ytterbium (Yb)-labeled forage, followed by serial collection of rumen digesta or fecal samples. Rumen Yb concentrations were transformed to natural logarithms and regressed on time. Influence of sampling site (rectum versusmore » rumen) on turnover estimates was modified by the model used to fit fecal marker excretion curves in the grazing study. In contrast, estimated turnover rate constants from rumen sampling were smaller (P < 0.05) than rectally derived rate constants, regardless of fecal model used, when steers were fed once daily. In Experiment 3, in vitro residues subjected to acid or neutral detergent fiber extraction (IVADF and IVNDF), acid detergent fiber incubated in cellulase (ADFIC) and acid detergent lignin (ADL) were evaluated as internal markers for predicting diet digestibility. Both IVADF and IVNDF displayed variable accuracy for prediction of in vivo digestibility whereas ADL and ADFIC inaccurately predicted digestibility of all diets.« less

Fecal /sup 13/C analysis for the detection and quantitation of intestinal malabsorption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klein, P.D.; MacLean, W.C. Jr.; Watkins, J.B.

Use of /sup 14/CO/sub 2/ breath tests and fecal analyses for the detection and quantitation of intestinal malabsorption has been extensively documented in adult subjects. The use of radioisotopes has extended the range of breath test applications to include pediatric and geriatric subjects. Here we report a fecal /sup 13/C analysis that can be used in conjunction with /sup 14/CO/sub 2/ breath tests. Twenty-four-hour fecal samples were collected before and after the administration of a labeled substrate. Simultaneous cholyglycine /sup 13/CO/sub 2/ breath tests and fecal assays were performed in five children. One child with bacterial overgrowth had an abnormalmore » breath test and a normal fecal test. Of three children with ileal dysfunction, only one had an abnormal breath test, whereas the fecal test was abnormal in all three. Both the breath test and fecal test were abnormal for a child who had undergone an ileal resection. Both tests were normal for a child with ulcerative colitis.« less

Alteration of digestive tract microbiome in neonatal Holstein bull calves by bacitracin methylene disalicylate treatment and scours.

PubMed

Xie, G; Duff, G C; Hall, L W; Allen, J D; Burrows, C D; Bernal-Rigoli, J C; Dowd, S E; Guerriero, V; Yeoman, C J

2013-10-01

The effects of bacitracin methylene disalicylate (BMD) and scours on the fecal microbiome, animal performance, and health were studied in Holstein bull calves. Holstein bull calves (n = 150) were obtained from a single source at 12 to 24 h of age. Bull calves were randomly assigned to 1 of 2 treatments including CON (no BMD; n = 75 calves) and BMD (n = 75 calves). Starting 3 d after arrival, BMD was added into milk replacer (0.5 g/feeding; twice daily) and fed to the calves for 10 consecutive d. No differences (P > 0.10) were observed in ADG for d 0 to 28 and d 0 to 56, DMI for d 0 to 28, d 29 to 56, and d 0 to 56, or G:F for d 0 to 28, d 29 to 56, and d 0 to 56; ADG for d 29 to 56 tended to increase (P < 0.10) for BMD-treated calves compared with controls. Fecal samples were collected from 15 scouring calves and 10 cohorts (nonscouring calves received on the same day and administered the same treatment as the scouring calves). Animal morbidity and fecal score did not vary between the 2 treatments. Mortality was not influenced by the treatments in the BMD administration period or throughout the experiment. Fecal samples were subjected to pyrotagged 454 FLX pyrosequencing of 16S rRNA gene amplicon to examine compositional dynamics of fecal microbes. Escherichia, Enterococcus, and Shigella had greater (P < 0.05) populations in the BMD group whereas Dorea, Roseburia, Fecalibacterium, Papillibacter, Collinsella, Eubacterium, Peptostreptococcus, and Prevotella were decreased (P < 0.05) by BMD treatment. Genus populations were also compared between scouring and nonscouring calves. Streptococcus was the only genus that had notable increase (P < 0.05) in fecal samples from scouring calves whereas populations of Bacteroides, Roseburia, and Eubacterium were markedly (P < 0.05) greater in nonscouring calves. These results show that BMD has the ability to alter the composition of the fecal microbiome but failed to improve performance in Holstein bull calves. Discrepancy of microorganism profiles between scouring and nonscouring calves might be associated with the occurrence of scours and bacterial genera identified might be potential target of treating diarrhea.

Fecal coliforms on environmental surfaces in two day care centers.

PubMed Central

Weniger, B G; Ruttenber, A J; Goodman, R A; Juranek, D D; Wahlquist, S P; Smith, J D

1983-01-01

A survey of environmental surfaces in two Atlanta area day care centers was conducted to determine the prevalence of fecal coliform bacteria, considered a marker for the presence of fecal contamination which might contain pathogenic parasites, bacteria, or viruses. Fecal coliforms were found in 17 (4.3%) of 398 representative samples of building surfaces, furniture, and other objects. These surfaces may be involved in the chain of transmission of enteric diseases among children. Therefore, disinfection of inanimate objects, in addition to good handwashing, may be important in controlling the spread of enteric diseases in day care centers. PMID:6830225

Diet and Environment Shape Fecal Bacterial Microbiota Composition and Enteric Pathogen Load of Grizzly Bears

PubMed Central

Schwab, Clarissa; Cristescu, Bogdan; Northrup, Joseph M.; Stenhouse, Gordon B.; Gänzle, Michael

2011-01-01

Background Diet and environment impact the composition of mammalian intestinal microbiota; dietary or health disturbances trigger alterations in intestinal microbiota composition and render the host susceptible to enteric pathogens. To date no long term monitoring data exist on the fecal microbiota and pathogen load of carnivores either in natural environments or in captivity. This study investigates fecal microbiota composition and the presence of pathogenic Escherichia coli and toxigenic clostridia in wild and captive grizzly bears (Ursus arctos) and relates these to food resources consumed by bears. Methodology/Principal Findings Feces were obtained from animals of two wild populations and from two captive animals during an active bear season. Wild animals consumed a diverse diet composed of plant material, animal prey and insects. Captive animals were fed a regular granulated diet with a supplement of fruits and vegetables. Bacterial populations were analyzed using quantitative PCR. Fecal microbiota composition fluctuated in wild and in captive animals. The abundance of Clostridium clusters I and XI, and of C. perfringens correlated to regular diet protein intake. Enteroaggregative E. coli were consistently present in all populations. The C. sordellii phospholipase C was identified in three samples of wild animals and for the first time in Ursids. Conclusion This is the first longitudinal study monitoring the fecal microbiota of wild carnivores and comparing it to that of captive individuals of the same species. Location and diet affected fecal bacterial populations as well as the presence of enteric pathogens. PMID:22194798

Diet and environment shape fecal bacterial microbiota composition and enteric pathogen load of grizzly bears.

PubMed

Schwab, Clarissa; Cristescu, Bogdan; Northrup, Joseph M; Stenhouse, Gordon B; Gänzle, Michael

2011-01-01

Diet and environment impact the composition of mammalian intestinal microbiota; dietary or health disturbances trigger alterations in intestinal microbiota composition and render the host susceptible to enteric pathogens. To date no long term monitoring data exist on the fecal microbiota and pathogen load of carnivores either in natural environments or in captivity. This study investigates fecal microbiota composition and the presence of pathogenic Escherichia coli and toxigenic clostridia in wild and captive grizzly bears (Ursus arctos) and relates these to food resources consumed by bears. Feces were obtained from animals of two wild populations and from two captive animals during an active bear season. Wild animals consumed a diverse diet composed of plant material, animal prey and insects. Captive animals were fed a regular granulated diet with a supplement of fruits and vegetables. Bacterial populations were analyzed using quantitative PCR. Fecal microbiota composition fluctuated in wild and in captive animals. The abundance of Clostridium clusters I and XI, and of C. perfringens correlated to regular diet protein intake. Enteroaggregative E. coli were consistently present in all populations. The C. sordellii phospholipase C was identified in three samples of wild animals and for the first time in Ursids. This is the first longitudinal study monitoring the fecal microbiota of wild carnivores and comparing it to that of captive individuals of the same species. Location and diet affected fecal bacterial populations as well as the presence of enteric pathogens.

Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California.

PubMed

Steele, Joshua A; Blackwood, A Denene; Griffith, John F; Noble, Rachel T; Schiff, Kenneth C

2018-06-01

Along southern California beaches, the concentrations of fecal indicator bacteria (FIB) used to quantify the potential presence of fecal contamination in coastal recreational waters have been previously documented to be higher during wet weather conditions (typically winter or spring) than those observed during summer dry weather conditions. FIB are used for management of recreational waters because measurement of the bacterial and viral pathogens that are the potential causes of illness in beachgoers exposed to stormwater can be expensive, time-consuming, and technically difficult. Here, we use droplet digital Polymerase Chain Reaction (digital PCR) and digital reverse transcriptase PCR (digital RT-PCR) assays for direct quantification of pathogenic viruses, pathogenic bacteria, and source-specific markers of fecal contamination in the stormwater discharges. We applied these assays across multiple storm events from two different watersheds that discharge to popular surfing beaches in San Diego, CA. Stormwater discharges had higher FIB concentrations as compared to proximal beaches, often by ten-fold or more during wet weather. Multiple lines of evidence indicated that the stormwater discharges contained human fecal contamination, despite the presence of separate storm sewer and sanitary sewer systems in both watersheds. Human fecal source markers (up to 100% of samples, 20-12440 HF183 copies per 100 ml) and human norovirus (up to 96% of samples, 25-495 NoV copies per 100 ml) were routinely detected in stormwater discharge samples. Potential bacterial pathogens were also detected and quantified: Campylobacter spp. (up to 100% of samples, 16-504 gene copies per 100 ml) and Salmonella (up to 25% of samples, 6-86 gene copies per 100 ml). Other viral human pathogens were also measured, but occurred at generally lower concentrations: adenovirus (detected in up to 22% of samples, 14-41 AdV copies per 100 ml); no enterovirus was detected in any stormwater discharge sample. Higher concentrations of avian source markers were noted in the stormwater discharge located immediately downstream of a large bird sanctuary along with increased Campylobacter concentrations and notably different Campylobacter species composition than the watershed that had no bird sanctuary. This study is one of the few to directly measure an array of important bacterial and viral pathogens in stormwater discharges to recreational beaches, and provides context for stormwater-based management of beaches during high risk wet-weather periods. Furthermore, the combination of culture-based and digital PCR-derived data is demonstrated to be valuable for assessing hydrographic relationships, considering delivery mechanisms, and providing foundational exposure information for risk assessment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparison of four-hour and twenty-four-hour refrigerated storage of nonpotable water for fecal coliform analysis.

PubMed Central

Standridge, J H; Lesar, D J

1977-01-01

The problem of extending the storage time of water samples for fecal coliform analysis was addressed. Included in this report is a literature review of the storage problem. Twenty-eight samples were analyzed in replicate to determine the effect of 24-h storage of water samples at 4 degrees C. A new statistical approach to data analysis, coupled with the concept of practical acceptability, is presented. According to our results, many samples can successfully be stored at 4 degrees C for 24 h. PMID:335972

THE EMPACT BEACHES: A CASE STUDY IN RECREATIONAL WATER SAMPLING

EPA Science Inventory

Various chapters describe sample and experimental design, use of a geometric mean or an arithmetic mean, modeling and forecasting, and risk assessment in relation to monitoring recreational waters for fecal indicators. All of these aspects of monitoring are dependent on the spat...

Detection of K-ras gene mutations in feces by magnetic nanoprobe in patients with pancreatic cancer: A preliminary study.

PubMed

Wang, Xiaoguang; Wang, Jingshuai; Chen, Fei; Zhong, Zhengxiang; Qi, Lifeng

2018-01-01

The present study aimed to investigate the feasibility and effectiveness of detecting K-ras mutation by using magnetic nanoparticles in fecal samples of patients with pancreatic cancer at different stages. The novel methodology of K-ras mutation detection was compared to the existing methodology of cancer antigen (CA)19-9 examination. Patients with pancreatic cancer (n=88), pancreatic benign diseases who displayed chronic pancreatitis (n=35), pancreatic mucinous cyst neoplasms (n=10) and pancreatic serous cyst (n=9) admitted to the Department of Surgery, Jiaxing Second Hospital were enrolled in the present study. Fecal samples were collected from all patients, DNA was extracted and magnetic nanoprobe was then used to detect K-ras mutation. The results obtained using the novel magnetic nanoprobe detection technique showed a K-ras mutation rate of 81.8% (72/88) in the patients with pancreatic cancer and 18.5% (10/54) in patients with pancreatic benign diseases. In patients with pancreatic cancer, the K-ras mutation rate was comparable in stages I + IIA and IIB + III + IV (78.9 vs. 84.0%; P>0.05). The sensitivity and specificity of K-ras mutation for detection of pancreatic cancer was 81.8 and 81.5%, respectively. Sixty-eight pancreatic cancer patients had >37 U/ml CA99 with a sensitivity and specificity for pancreatic cancer detection of 77.3 and 77.8%, which was not significantly lower than detection by the fecal K-ras mutations (P>0.05). Combinational detection of fecal K-ras mutations and serum CA19-9 significantly increased the sensitivity regarding pancreatic cancer detection to 97.7% (P<0.05), while the specificity was not enhanced (80.9%; P>0.05) compared with fecal K-ras mutations or CA19-9 alone. The findings showed that the magnetic nanoprobe is able to detect fecal K-ras mutations in different stages of pancreatic cancer, with comparable sensitivity and specificity to CA19-9 examination for differentiating pancreatic cancer. Furthermore, combined detection of CA19-9 and K-ras mutations has enhanced sensitivity compared with CA19-9 alone.

Prevalence and Genotyping of Cryptosporidium Infection in Pet Parrots in North China

PubMed Central

Zhang, Xiao-Xuan; Zhang, Nian-Zhang; Zhao, Guang-Hui; Zhao, Quan; Zhu, Xing-Quan

2015-01-01

Cryptosporidiosis is a worldwide zoonosis caused by Cryptosporidium spp., sometimes leading to severe diarrhea in humans and animals. In the present study, 311 parrots, belonging to four species, namely, Budgerigars (Melopsittacus undulatus), Lovebirds (Agapornis sp.), Alexandrine parakeets (Psittacula eupatria), and Cockatiel (Nymphicus hollandicus), from Beijing and Weifang cities, were examined for Cryptosporidium spp. infection. Blood samples of each bird were examined using enzyme linked immunosorbent assay (ELISA) and fecal samples were examined by Sheather's sugar flotation technique. Prevalence of Cryptosporidium infection were 3.22% (10/311) and 0.64% (2/311) by ELISA and Sheather's sugar flotation technique, respectively. Seroprevalence of Cryptosporidium infection in different breeds varied from 0 to 15.39%. Sequencing analysis showed that both positive samples from fecal samples belonged to Cryptosporidium avian genotype V. This is the first report of Cryptosporidium avian genotype V in Budgerigars. The results of the present study provided foundation-data for prevention and control of cryptosporidiosis in pet birds in China. PMID:26273629

Prevalence and Genotyping of Cryptosporidium Infection in Pet Parrots in North China.

PubMed

Zhang, Xiao-Xuan; Zhang, Nian-Zhang; Zhao, Guang-Hui; Zhao, Quan; Zhu, Xing-Quan

2015-01-01

Cryptosporidiosis is a worldwide zoonosis caused by Cryptosporidium spp., sometimes leading to severe diarrhea in humans and animals. In the present study, 311 parrots, belonging to four species, namely, Budgerigars (Melopsittacus undulatus), Lovebirds (Agapornis sp.), Alexandrine parakeets (Psittacula eupatria), and Cockatiel (Nymphicus hollandicus), from Beijing and Weifang cities, were examined for Cryptosporidium spp. infection. Blood samples of each bird were examined using enzyme linked immunosorbent assay (ELISA) and fecal samples were examined by Sheather's sugar flotation technique. Prevalence of Cryptosporidium infection were 3.22% (10/311) and 0.64% (2/311) by ELISA and Sheather's sugar flotation technique, respectively. Seroprevalence of Cryptosporidium infection in different breeds varied from 0 to 15.39%. Sequencing analysis showed that both positive samples from fecal samples belonged to Cryptosporidium avian genotype V. This is the first report of Cryptosporidium avian genotype V in Budgerigars. The results of the present study provided foundation-data for prevention and control of cryptosporidiosis in pet birds in China.

Occurrence of Salmonella serotype Typhimurium DT104 on a commercial swine farm before, during, and after depopulation and repopulation.

PubMed

Erdman, Matthew M; Harris, Isabel T; Torremorell, Montserrat; Wilt, Vincil M; Harris, D L Hank

2005-08-01

To determine whether depopulation-repopulation could be used to eradicate Salmonella serotype Typhimurium DT104 from a commercial swine farm in the midwestern United States. Observational study A commercial swine farm undergoing depopulation-repopulation to eliminate porcine reproductive and respiratory syndrome virus and Mycoplasma hyopneumoniae. Pooled fecal samples, tissue samples, and serum samples were collected from pigs on the farm before and after depopulation-repopulation. When there were no pigs on the farm, environmental swab specimens were collected for bacterial culture. Serum was analyzed for anti-Salmonella antibodies with an indirect ELISA. Salmonella isolates obtained by bacterial culture of fecal, tissue, and environmental samples were characterized by means of serotyping, phage typing, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing. 167 Salmonella isolates representing 9 serotypes were recovered from the farm. Results of PFGE and antimicrobial susceptibility testing suggested that S. Typhimurium DT104 strain was not eradicated from the farm. However, seroprevalence of anti-Salmonella antibodies and the percentage of pooled fecal samples positive for Salmonella spp were significantly decreased following repopulation. Results suggested that depopulation-repopulation in conjunction with stringent cleaning and disinfection, attention to biosecurity procedures, control of other diseases, and changes in feed management may reduce the occurrence of, but likely will not eliminate, Salmonella spp in commercial swine herds.

Hepatitis E Virus in Pork Production Chain in Czech Republic, Italy, and Spain, 2010

PubMed Central

Di Bartolo, Ilaria; Diez-Valcarce, Marta; Vasickova, Petra; Kralik, Petr; Hernandez, Marta; Angeloni, Giorgia; Ostanello, Fabio; Bouwknegt, Martijn; Rodríguez-Lázaro, David; Pavlik, Ivo

2012-01-01

We evaluated the prevalence of hepatitis E virus (HEV) in the pork production chain in Czech Republic, Italy, and Spain during 2010. A total of 337 fecal, liver, and meat samples from animals at slaughterhouses were tested for HEV by real-time quantitative PCR. Overall, HEV was higher in Italy (53%) and Spain (39%) than in Czech Republic (7.5%). HEV was detected most frequently in feces in Italy (41%) and Spain (39%) and in liver (5%) and meat (2.5%) in Czech Republic. Of 313 sausages sampled at processing and point of sale, HEV was detected only in Spain (6%). HEV sequencing confirmed only g3 HEV strains. Indicator virus (porcine adenovirus) was ubiquitous in fecal samples and absent in liver samples and was detected in 1 slaughterhouse meat sample. At point of sale, we found porcine adenovirus in sausages (1%–2%). The possible dissemination of HEV and other fecal viruses through pork production demands containment measures. PMID:22840221

33 CFR 159.309 - Limitations on discharge of treated sewage or graywater.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30-day period does not exceed 20 fecal coliform/100 milliliters (ml) and not more than 10 percent of the samples exceed 40 fecal coliform/100 ml; (4) Concentrations of total residual chlorine do not...

33 CFR 159.309 - Limitations on discharge of treated sewage or graywater.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30-day period does not exceed 20 fecal coliform/100 milliliters (ml) and not more than 10 percent of the samples exceed 40 fecal coliform/100 ml; (4) Concentrations of total residual chlorine do not...

The Right Tool for the Job: Detection of Soil-Transmitted Helminths in Areas Co-endemic for Other Helminths

PubMed Central

Periago, Maria V.; Diniz, Renata C.; Pinto, Simone A.; Yakovleva, Anna; Correa-Oliveira, Rodrigo; Diemert, David J.; Bethony, Jeffrey M.

2015-01-01

Background Due to the recent increased use of the McMaster (MM) fecal egg counting method for assessing benzimidazole drug efficacy for treating soil-transmitted helminth (STH) infections, the aim of the current study was to determine the operational value of including the MM method alongside the Kato-Katz (KK) fecal thick smear to increase the diagnostic sensitivity when STHs are co-endemic with trematode helminths (e.g., Schistosoma mansoni). Methods A cross-sectional study was conducted in school-aged children aged 4-18 years in the northeastern region of the State of Minas Gerais (Brazil), where Necator americanus, Ascaris lumbricoides, Trichuris trichiura, and S. mansoni are co-endemic. One fecal sample from each participant was collected and transported to the field laboratory for analysis. Coprological diagnosis was performed on each fecal sample by three different methods: Formalin-Ether Sedimentation (FES), KK and the MM technique. The diagnostic sensitivity and negative predictive value (NPV) of each technique was calculated using the combination of all three techniques as the composite standard. In order to determine the agreement between the three techniques Fleiss´ kappa was used. Both the Cure Rate (CR) and the Fecal Egg Count Reduction (FECR) were calculated using the two quantification techniques (i.e., the MM and KK). Results Fecal samples from 1260 children were analyzed. The KK had higher diagnostic sensitivity than the MM for the detection of both A. lumbricoides (KK 97.3%, MM 69.5%) and hookworm (KK 95.1%, MM 80.8%). The CR of a single dose of mebendazole varied significantly between the KK and MM for both A. lumbricoides (p = 0.016) and hookworm (p = 0.000), with lower rates obtained with the KK. On the other hand, the FECR was very similar between both techniques for both A. lumbricoides and hookworm. Conclusion The MM did not add any diagnostic value over the KK in areas where both STHs and trematodes were co-endemic. The lower sensitivity of the MM would have an important impact on the administration of selective school-based treatment in this area since if only the MM were used, 36 (13.9%) children diagnosed with A. lumbricoides would have gone untreated. PMID:26241329

Assessment of microbiological contamination of fresh, minimally processed, and ready-to-eat lettuces (Lactuca sativa), Rio de Janeiro State, Brazil.

PubMed

Brandão, Marcelo L L; Almeida, Davi O; Bispo, Fernanda C P; Bricio, Silvia M L; Marin, Victor A; Miagostovich, Marize P

2014-05-01

This study aimed to assess the microbiological contamination of lettuces commercialized in Rio de Janeiro, Brazil, in order to investigate detection of norovirus genogroup II (NoV GII), Salmonella spp., total and fecal coliforms, such as Escherichia coli. For NoV detection samples were processed using the adsorption-elution concentration method associated to real-time quantitative polymerase chain reaction (qPCR). A total of 90 samples of lettuce including 30 whole fresh lettuces, 30 minimally processed (MP) lettuces, and 30 raw ready-to-eat (RTE) lettuce salads were randomly collected from different supermarkets (fresh and MP lettuce samples), food services, and self-service restaurants (RTE lettuce salads), all located in Rio de Janeiro, Brazil, from October 2010 to December 2011. NoV GII was not detected and PP7 bacteriophage used as internal control process (ICP) was recovered in 40.0%, 86.7%, and 76.7% of those samples, respectively. Salmonella spp. was not detected although fecal contamination has been observed by fecal coliform concentrations higher than 10(2) most probable number/g. E. coli was detected in 70.0%, 6.7%, and 30.0% of fresh, MP, and RTE samples, respectively. This study highlights the need to improve hygiene procedures at all stages of vegetable production and to show PP7 bacteriophage as an ICP for recovering RNA viruses' methods from MP and RTE lettuce samples, encouraging the evaluation of new protocols that facilitate the establishment of methodologies for NoV detection in a greater number of food microbiology laboratories. The PP7 bacteriophage can be used as an internal control process in methods for recovering RNA viruses from minimally processed and ready-to-eat lettuce samples. © 2014 Institute of Food Technologists®

Prevalence and Characterization of Shiga Toxin-Producing Escherichia coli in Swine Feces Recovered in the National Animal Health Monitoring System's Swine 2000 Study

PubMed Central

Fratamico, Pina M.; Bagi, Lori K.; Bush, Eric J.; Solow, Barbara T.

2004-01-01

A study was conducted to determine the prevalence of Shiga toxin-producing Escherichia coli (STEC) in swine feces in the United States as part of the National Animal Health Monitoring System's Swine 2000 study. Fecal samples collected from swine operations from 13 of the top 17 swine-producing states were tested for the presence of STEC. After enrichment of swine fecal samples in tryptic soy broth, the samples were tested for the presence of stx1 and stx2 by use of the TaqMan E. coli STX1 and STX2 PCR assays. Enrichments of samples positive for stx1 and/or stx2 were plated, and colony hybridization was performed using digoxigenin-labeled probes complementary to the stx1 and stx2 genes. Positive colonies were picked and confirmed by PCR for the presence of the stx1, stx2, or stx2e genes, and the isolates were serotyped. Out of 687 fecal samples tested using the TaqMan assays, 70% (484 of 687) were positive for Shiga toxin genes, and 54% (370 of 687), 64% (436 of 687), and 38% (261 of 687) were positive for stx1, stx2, and both toxin genes, respectively. Out of 219 isolates that were characterized, 29 (13%) produced stx1, 14 (6%) produced stx2, and 176 (80%) produced stx2e. Twenty-three fecal samples contained at least two STEC strains that had different serotypes but that had the same toxin genes or included a strain that possessed stx1 in addition to a strain that possessed stx2 or stx2e. The STEC isolates belonged to various serogroups, including O2, O5, O7, O8, O9, OX10, O11, O15, OX18, O20, O57, O65, O68, O69, O78, O91, O96, O100, O101, O120, O121, O152, O159, O160, O163, and O untypeable. It is noteworthy that no isolates of serogroup O157 were recovered. Results of this study indicate that swine in the United States harbor STEC that can potentially cause human illness. PMID:15574914

Minimally processed vegetable salads: microbial quality evaluation.

PubMed

Fröder, Hans; Martins, Cecília Geraldes; De Souza, Katia Leani Oliveira; Landgraf, Mariza; Franco, Bernadette D G M; Destro, Maria Teresa

2007-05-01

The increasing demand for fresh fruits and vegetables and for convenience foods is causing an expansion of the market share for minimally processed vegetables. Among the more common pathogenic microorganisms that can be transmitted to humans by these products are Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella. The aim of this study was to evaluate the microbial quality of a selection of minimally processed vegetables. A total of 181 samples of minimally processed leafy salads were collected from retailers in the city of Sao Paulo, Brazil. Counts of total coliforms, fecal coliforms, Enterobacteriaceae, psychrotrophic microorganisms, and Salmonella were conducted for 133 samples. L. monocytogenes was assessed in 181 samples using the BAX System and by plating the enrichment broth onto Palcam and Oxford agars. Suspected Listeria colonies were submitted to classical biochemical tests. Populations of psychrotrophic microorganisms >10(6) CFU/g were found in 51% of the 133 samples, and Enterobacteriaceae populations between 10(5) and 106 CFU/g were found in 42% of the samples. Fecal coliform concentrations higher than 10(2) CFU/g (Brazilian standard) were found in 97 (73%) of the samples, and Salmonella was detected in 4 (3%) of the samples. Two of the Salmonella-positive samples had <10(2) CFU/g concentrations of fecal coliforms. L. monocytogenes was detected in only 1 (0.6%) of the 181 samples examined. This positive sample was simultaneously detected by both methods. The other Listeria species identified by plating were L. welshimeri (one sample of curly lettuce) and L. innocua (2 samples of watercress). The results indicate that minimally processed vegetables had poor microbiological quality, and these products could be a vehicle for pathogens such as Salmonella and L. monocytogenes.

Household siblings and nasal and fecal microbiota in infants.

PubMed

Hasegawa, Kohei; Linnemann, Rachel W; Mansbach, Jonathan M; Ajami, Nadim J; Espinola, Janice A; Fiechtner, Lauren G; Petrosino, Joseph F; Camargo, Carlos A

2017-04-01

Early-life exposure to older siblings is associated with a lower risk of asthma. To date, no study has addressed the impact of having siblings on both the airway and fecal microbiota during infancy. The aim of this study was therefore to profile the nasal airway and fecal microbiota in infants, and to examine the association between having siblings and microbiota profile. We conducted a cross-sectional study of 105 healthy infants (aged <1 year). Using 16S rRNA gene sequencing and an unbiased clustering approach to the nasal airway and fecal samples, we identified microbiota profiles and then determined the association between having siblings and microbiome profile. Overall, the median age was 3.4 months (IQR, 2.0-4.7 months); 43% had siblings in the household. Unbiased clustering of nasal airway microbiota identified three profiles: Moraxella dominant (43%), Corynebacterium/Dolosigranulum dominant (36%), and mixed (21%). Infants with siblings were more likely to have a Moraxella-dominant profile than Corynebacterium/Dolosigranulum-dominant profile (76% vs 18%), while those without siblings had the opposite pattern (18% vs 50%; P < 0.001, multivariable-adjusted). Fecal microbiota consisted of three profiles: Bifidobacterium dominant (39%), Escherichia dominant (31%), and Enterobacter dominant (30%). Infants with siblings were more likely to have a Bifidobacterium-dominant profile than Escherichia-dominant profile (49% vs 24%) while those without siblings had the opposite pattern (32% vs 37%; P = 0.04, multivariable-adjusted). In this cross-sectional study, infants with siblings were more likely to have a Moraxella-dominant nasal microbiota profile and Bifidobacterium-dominant fecal microbiota profile. These findings should facilitate further investigation of the interplay between early-life environmental exposure, the microbiome, and childhood asthma. © 2016 Japan Pediatric Society.

Plasma Septin9 versus Fecal Immunochemical Testing for Colorectal Cancer Screening: A Prospective Multicenter Study

PubMed Central

Johnson, David A.; Barclay, Robert L.; Mergener, Klaus; Weiss, Gunter; König, Thomas; Beck, Jürgen; Potter, Nicholas T.

2014-01-01

Background Screening improves outcomes related to colorectal cancer (CRC); however, suboptimal participation for available screening tests limits the full benefits of screening. Non-invasive screening using a blood based assay may potentially help reach the unscreened population. Objective To compare the performance of a new Septin9 DNA methylation based blood test with a fecal immunochemical test (FIT) for CRC screening. Design: In this trial, fecal and blood samples were obtained from enrolled patients. To compare test sensitivity for CRC, patients with screening identified colorectal cancer (n = 102) were enrolled and provided samples prior to surgery. To compare test specificity patients were enrolled prospectively (n = 199) and provided samples prior to bowel preparation for screening colonoscopy. Measurements Plasma and fecal samples were analyzed using the Epi proColon and OC Fit-Check tests respectively. Results For all samples, sensitivity for CRC detection was 73.3% (95% CI 63.9–80.9%) and 68.0% (95% CI 58.2–76.5%) for Septin9 and FIT, respectively. Specificity of the Epi proColon test was 81.5% (95% CI 75.5–86.3%) compared with 97.4% (95% CI 94.1–98.9%) for FIT. For paired samples, the sensitivity of the Epi proColon test (72.2% –95% CI 62.5–80.1%) was shown to be statistically non-inferior to FIT (68.0%–95% CI 58.2–76.5%). When test results for Epi proColon and FIT were combined, CRC detection was 88.7% at a specificity of 78.8%. Conclusions At a sensitivity of 72%, the Epi proColon test is non- inferior to FIT for CRC detection, although at a lower specificity. With negative predictive values of 99.8%, both methods are identical in confirming the absence of CRC. Trial Registration ClinicalTrials.gov NCT01580540 PMID:24901436

Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent

PubMed Central

McLellan, S.L.; Huse, S.M.; Mueller-Spitz, S.R.; Andreishcheva, E.N.; Sogin, M.L.

2009-01-01

The release of untreated sewage introduces non-indigenous microbial populations of uncertain composition into surface waters. We used massively parallel 454 sequencing of hypervariable regions in rRNA genes to profile microbial communities from eight untreated sewage influent samples of two wastewater treatment plants (WWTP) in metropolitan Milwaukee. The sewage profiles included a discernable human fecal signature made up of several taxonomic groups including multiple Bifidobacteriaceae, Coriobacteriaceae, Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae genera. The fecal signature made up a small fraction of the taxa present in sewage but the relative abundance of these sequence tags mirrored the population structures of human fecal samples. These genera were much more prevalent in the sewage influent than standard indicators species. High-abundance sequences from taxonomic groups within the Beta- and Gammaproteobacteria dominated the sewage samples but occurred at very low levels in fecal and surface water samples, suggesting that these organisms proliferate within the sewer system. Samples from Jones Island (JI – servicing residential plus a combined sewer system) and South Shore (SS – servicing a residential area) WWTPs had very consistent community profiles, with greater similarity between WWTPs on a given collection day than the same plant collected on different days. Rainfall increased influent flows at SS and JI WWTPs, and this corresponded to greater diversity in the community at both plants. Overall, the sewer system appears to be a defined environment with both infiltration of rainwater and stormwater inputs modulating community composition. Microbial sewage communities represent a combination of inputs from human fecal microbes and enrichment of specific microbes from the environment to form a unique population structure. PMID:19840106

Comparison of bacteroides-prevotella 16S rRNA genetic markers for fecal samples from different animal species.

PubMed

Fogarty, Lisa R; Voytek, Mary A

2005-10-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples from Different Animal Species

PubMed Central

Fogarty, Lisa R.; Voytek, Mary A.

2005-01-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment. PMID:16204514

Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species

USGS Publications Warehouse

Fogarty, L.R.; Voytek, M.A.

2005-01-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

Effects of leuprolide acetate on selected blood and fecal sex hormones in Hispaniolan Amazon parrots (Amazona ventrais).

PubMed

Klaphake, Eric; Fecteau, Kellie; DeWit, Martine; Greenacre, Cheryl; Grizzle, Judith; Jones, Michael; Zagaya, Nancy; Abney, L Kim; Oliver, Jack

2009-12-01

The luteinizing hormone-releasing hormone agonist leuprolide acetate is used commonly to anage reproductive problems in pet birds. To determine the effect of leuprolide acetate on plas a and fecal hormone levels in a psittacine species, a single 800 microg/kg dose of the 30-day depot form of leuprolide acetate was administered IM in 11 healthy, nonbreeding adult Hispaniolan Amazon parrots (Amazona ventralis), and plasma and fecal hormone levels were measured before and after leuprolide administration. At pooled baseline to 21 days postleuprolide acetate administration, sample collection day was significantly associated with plasma 17beta-estradiol and androstenedione levels and fecal 17beta-estradiol levels (evaluated in females only). Both plasma androstenedione and plasma 17beta-estradiol levels decreased significantly from baseline to a nadir at 7 days postleuprolide acetate administration but did not differ significantly 14 days later from that nadir or from pooled baseline samples, suggesting that the effect of leuprolide on hormone levels remained about 2 weeks. Fecal 17beta-estradiol levels increased significantly from the nadir at 7 days postleuprolide to 21 days postleuprolide administration, with trends of the level at 21 days postleuprolide being higher than the pooled baseline level and of decreasing levels from pooled baseline to 7 days postleuprolide administration. Plasma luteinizing hormone and fecal testosterone levels did not change significantly from baseline levels after leuprolide administration over the 2-day period. No significant correlations were found between plasma hormone and fecal hormone levels. These results suggest that measurement of plasma androstenedione, plasma 17beta-estradiol, and fecal 17beta-estradiol levels might be useful in assessing the effects of 30-day depot leuprolide acetate in Hispaniolan Amazon parrots.

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii.

PubMed

Kirs, Marek; Caffaro-Filho, Roberto A; Wong, Mayee; Harwood, Valerie J; Moravcik, Philip; Fujioka, Roger S

2016-11-15

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and Escherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Frequency and Duration of Fecal Shedding of Salmonella Enteritidis by Experimentally Infected Laying Hens Housed in Enriched Colony Cages at Different Stocking Densities

PubMed Central

Gast, Richard K.; Guraya, Rupa; Jones, Deana R.; Anderson, Kenneth E.; Karcher, Darrin M.

2017-01-01

Human infections with Salmonella Enteritidis are often attributed to the consumption of contaminated eggs, so the prevalence of this pathogen in egg-laying poultry is an important public health risk factor. Numerous and complex environmental influences on Salmonella persistence and transmission are exerted by management practices and housing facilities used in commercial egg production. In recent years, the animal welfare implications of poultry housing systems have guided the development of alternatives to traditional cage-based housing, but their food safety consequences are not yet fully understood. The present study assessed the effects of different bird stocking densities on the frequency and duration of fecal shedding of S. Enteritidis in groups of experimentally infected laying hens housed in colony cages enriched with perching and nesting areas. In two trials, groups of laying hens were distributed at two stocking densities (648 and 973 cm2/bird) into enriched colony cages and (along with a group housed in conventional cages at 648 cm2/bird) orally inoculated with doses of 1.0 × 108 cfu of S. Enteritidis. At 10 weekly postinoculation intervals, samples of voided feces were collected from beneath each cage and cultured to detect S. Enteritidis. Fecal shedding of S. Enteritidis was detected for up to 10 weeks postinoculation by hens in all three housing treatment groups. The overall frequency of positive fecal cultures was significantly (P < 0.05) greater from conventional cages than from enriched colony cages (at the lower stocking density) for the total of all sampling dates (45.0 vs. 33.3%) and also for samples collected at 4–9 weeks postinfection. Likewise, the frequency of S. Enteritidis isolation from feces from conventional cages was significantly greater than from enriched colony cages (at the higher hen stocking density) for the sum of all samples (45.0 vs. 36.7%) and at 6 weeks postinoculation. Moreover, the frequency of S. Enteritidis fecal recovery from enriched colony cages at the higher hen stocking was significantly greater than from similar cages at the lower stocking density for all 10 sampling dates combined (39.4 vs. 33.3%). These results suggest that stocking density can affect S. Enteritidis intestinal colonization and fecal shedding in laying hens, but some other difference between conventional and enriched colony cage systems appears to exert an additional influence. PMID:28443289

High-Throughput Direct Fecal PCR Assay for Detection of Mycobacterium avium subsp. paratuberculosis in Sheep and Cattle

PubMed Central

Waldron, Anna M.; Galea, Francesca; Whittington, Ann-Michele; Saunders, Vanessa F.; Begg, Douglas J.; de Silva, Kumudika; Purdie, Auriol C.; Whittington, Richard J.

2014-01-01

Johne's disease (JD) is a chronic enteric disease caused by Mycobacterium avium subsp. paratuberculosis that affects ruminants. Transmission occurs by the fecal-oral route. A commonly used antemortem diagnostic test for the detection of M. avium subsp. paratuberculosis in feces is liquid culture; however, a major constraint is the 2- to 3-month incubation period needed for this method. Rapid methods for the detection of M. avium subsp. paratuberculosis based on PCR have been reported, but comprehensive validation data are lacking. We describe here a new test, the high-throughput-Johnes (HT-J), to detect M. avium subsp. paratuberculosis in feces. Its diagnostic accuracy was compared with that of liquid radiometric (Bactec) fecal culture using samples from cattle (1,330 samples from 23 herds) and sheep (596 samples from 16 flocks). The multistage protocol involves the recovery of M. avium subsp. paratuberculosis cells from a fecal suspension, cell rupture by bead beating, extraction of DNA using magnetic beads, and IS900 quantitative PCR. The limit of detection of the assay was 0.0005 pg, and the limit of quantification was 0.005 pg M. avium subsp. paratuberculosis genomic DNA. Only M. avium subsp. paratuberculosis was detected from a panel of 51 mycobacterial isolates, including 10 with IS900-like sequences. Of the 549 culture-negative fecal samples from unexposed herds and flocks, 99% were negative in the HT-J test, while 60% of the bovine- and 84% of the ovine-culture-positive samples were positive in the HT-J test. As similar total numbers of samples from M. avium subsp. paratuberculosis-exposed animals were positive in culture and HT-J tests in both species, and as the results of a McNemar's test were not significant, these methods probably have similar sensitivities, but the true diagnostic sensitivities of these tests are unknown. These validation data meet the consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis and the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (S. A. Bustin et al., Clin. Chem. 55:611–622, 2009, doi:10.1373/clinchem.2008.112797). The HT-J assay has been approved for use in JD control programs in Australia and New Zealand. PMID:24352996

Evaluation of Two Library-Independent Microbial Source Tracking Methods To Identify Sources of Fecal Contamination in French Estuaries▿

PubMed Central

Gourmelon, Michèle; Caprais, Marie Paule; Ségura, Raphaël; Le Mennec, Cécile; Lozach, Solen; Piriou, Jean Yves; Rincé, Alain

2007-01-01

In order to identify the origin of the fecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophage genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, and bird) feces. Two human-specific markers (HF183 and HF134), one ruminant-specific marker (CF193′), and one pig-specific marker (PF163) showed a high level of specificity (>90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep feces and 96% of pig feces. F RNA bacteriophages were detected in only 21% of individual fecal samples tested, in 60% of pig slurries, but in all sewage samples. Most detected F RNA bacteriophages were from genotypes II and III in sewage samples and from genotypes I and IV in bovine, pig, and bird feces and from pig slurries. Both MST methods were applied to 28 water samples collected from three watersheds at different times. Classification of water samples as subject to human, animal, or mixed fecal contamination was more frequent when using Bacteroidales markers (82.1% of water samples) than by bacteriophage genotyping (50%). The ability to classify a water sample increased with increasing Escherichia coli or enterococcus concentration. For the samples that could be classified by bacteriophage genotyping, 78% agreed with the classification obtained from Bacteroidales markers. PMID:17557850

Visual loop-mediated isothermal amplification (LAMP) for the rapid diagnosis of Enterocytozoon hepatopenaei (EHP) infection.

PubMed

T, Sathish Kumar; A, Navaneeth Krishnan; J, Joseph Sahaya Rajan; M, Makesh; K P, Jithendran; S V, Alavandi; K K, Vijayan

2018-05-01

The emerging microsporidian parasite Enterocytozoon hepatopenaei (EHP), the causative agent of hepatopancreatic microsporidiosis, has been widely reported in shrimp-farming countries. EHP infection can be detected by light microscopy observation of spores (1.7 × 1 μm) in stained hepatopancreas (HP) tissue smears, HP tissue sections, and fecal samples. EHP can also be detected by polymerase chain reaction (PCR) targeting the small subunit (SSU) ribosomal RNA (rRNA) gene or the spore wall protein gene (SWP). In this study, a rapid, sensitive, specific, and closed tube visual loop-mediated isothermal amplification (LAMP) protocol combined with FTA cards was developed for the diagnosis of EHP. LAMP primers were designed based on the SSU rRNA gene of EHP. The target sequence of EHP was amplified at constant temperature of 65 °C for 45 min and amplified LAMP products were visually detected in a closed tube system by using SYBR™ green I dye. Detection limit of this LAMP protocol was ten copies. Field and clinical applicability of this assay was evaluated using 162 field samples including 106 HP tissue samples and 56 fecal samples collected from shrimp farms. Out of 162 samples, EHP could be detected in 62 samples (47 HP samples and 15 fecal samples). When compared with SWP-PCR as the gold standard, this EHP LAMP assay had 95.31% sensitivity, 98.98% specificity, and a kappa value of 0.948. This simple, closed tube, clinically evaluated visual LAMP assay has great potential for diagnosing EHP at the farm level, particularly under low-resource circumstances.

Effect of short-term room temperature storage on the microbial community in infant fecal samples.

PubMed

Guo, Yong; Li, Sheng-Hui; Kuang, Ya-Shu; He, Jian-Rong; Lu, Jin-Hua; Luo, Bei-Jun; Jiang, Feng-Ju; Liu, Yao-Zhong; Papasian, Christopher J; Xia, Hui-Min; Deng, Hong-Wen; Qiu, Xiu

2016-05-26

Sample storage conditions are important for unbiased analysis of microbial communities in metagenomic studies. Specifically, for infant gut microbiota studies, stool specimens are often exposed to room temperature (RT) conditions prior to analysis. This could lead to variations in structural and quantitative assessment of bacterial communities. To estimate such effects of RT storage, we collected feces from 29 healthy infants (0-3 months) and partitioned each sample into 5 portions to be stored for different lengths of time at RT before freezing at -80 °C. Alpha diversity did not differ between samples with storage time from 0 to 2 hours. The UniFrac distances and microbial composition analysis showed significant differences by testing among individuals, but not by testing between different time points at RT. Changes in the relative abundance of some specific (less common, minor) taxa were still found during storage at room temperature. Our results support previous studies in children and adults, and provided useful information for accurate characterization of infant gut microbiomes. In particular, our study furnished a solid foundation and justification for using fecal samples exposed to RT for less than 2 hours for comparative analyses between various medical conditions.

Coliphages and Gastrointestinal Illness in Recreational Waters

PubMed Central

Benjamin-Chung, Jade; Arnold, Benjamin F.; Wade, Timothy J.; Schiff, Kenneth; Griffith, John F.; Dufour, Alfred P.; Weisberg, Stephen B.

2017-01-01

Background: Coliphages have been proposed as indicators of fecal contamination in recreational waters because they better mimic the persistence of pathogenic viruses in the environment and wastewater treatment than fecal indicator bacteria. We estimated the association between coliphages and gastrointestinal illness and compared it with the association with culturable enterococci. Methods: We pooled data from six prospective cohort studies that enrolled coastal beachgoers in California, Alabama, and Rhode Island. Water samples were collected and gastrointestinal illness within 10 days of the beach visit was recorded. Samples were tested for enterococci and male-specific and somatic coliphages. We estimated cumulative incidence ratios (CIR) for the association between swimming in water with detectable coliphage and gastrointestinal illness when human fecal pollution was likely present, not likely present, and under all conditions combined. The reference group was unexposed swimmers. We defined continuous and threshold-based exposures (coliphage present/absent, enterococci >35 vs. ≤35 CFU/100 ml). Results: Under all conditions combined, there was no association between gastrointestinal illness and swimming in water with detectable coliphage or enterococci. When human fecal pollution was likely present, coliphage and enterococci were associated with increased gastrointestinal illness, and there was an association between male-specific coliphage level and illness that was somewhat stronger than the association between enterococci and illness. There were no substantial differences between male-specific and somatic coliphage. Conclusions: Somatic coliphage and enterococci had similar associations with gastrointestinal illness; there was some evidence that male-specific coliphage had a stronger association with illness than enterococci in marine waters with human fecal contamination. PMID:28489717

Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease.

PubMed

Robinson, Ainsley M; Gondalia, Shakuntla V; Karpe, Avinash V; Eri, Rajaraman; Beale, David J; Morrison, Paul D; Palombo, Enzo A; Nurgali, Kulmira

2016-12-01

Dysbiosis of the gut microbiota may be involved in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms underlying the role of the intestinal microbiome and metabolome in IBD onset and its alteration during active treatment and recovery remain unknown. Animal models of chronic intestinal inflammation with similar microbial and metabolomic profiles would enable investigation of these mechanisms and development of more effective treatments. Recently, the Winnie mouse model of colitis closely representing the clinical symptoms and characteristics of human IBD has been developed. In this study, we have analyzed fecal microbial and metabolomic profiles in Winnie mice and discussed their relevance to human IBD. The 16S rRNA gene was sequenced from fecal DNA of Winnie and C57BL/6 mice to define operational taxonomic units at ≥97% similarity threshold. Metabolomic profiling of the same fecal samples was performed by gas chromatography-mass spectrometry. Composition of the dominant microbiota was disturbed, and prominent differences were evident at all levels of the intestinal microbiome in fecal samples from Winnie mice, similar to observations in patients with IBD. Metabolomic profiling revealed that chronic colitis in Winnie mice upregulated production of metabolites and altered several metabolic pathways, mostly affecting amino acid synthesis and breakdown of monosaccharides to short chain fatty acids. Significant dysbiosis in the Winnie mouse gut replicates many changes observed in patients with IBD. These results provide justification for the suitability of this model to investigate mechanisms underlying the role of intestinal microbiota and metabolome in the pathophysiology of IBD.

Coliphages and Gastrointestinal Illness in Recreational Waters: Pooled Analysis of Six Coastal Beach Cohorts.

PubMed

Benjamin-Chung, Jade; Arnold, Benjamin F; Wade, Timothy J; Schiff, Kenneth; Griffith, John F; Dufour, Alfred P; Weisberg, Stephen B; Colford, John M

2017-09-01

Coliphages have been proposed as indicators of fecal contamination in recreational waters because they better mimic the persistence of pathogenic viruses in the environment and wastewater treatment than fecal indicator bacteria. We estimated the association between coliphages and gastrointestinal illness and compared it with the association with culturable enterococci. We pooled data from six prospective cohort studies that enrolled coastal beachgoers in California, Alabama, and Rhode Island. Water samples were collected and gastrointestinal illness within 10 days of the beach visit was recorded. Samples were tested for enterococci and male-specific and somatic coliphages. We estimated cumulative incidence ratios (CIR) for the association between swimming in water with detectable coliphage and gastrointestinal illness when human fecal pollution was likely present, not likely present, and under all conditions combined. The reference group was unexposed swimmers. We defined continuous and threshold-based exposures (coliphage present/absent, enterococci >35 vs. ≤35 CFU/100 ml). Under all conditions combined, there was no association between gastrointestinal illness and swimming in water with detectable coliphage or enterococci. When human fecal pollution was likely present, coliphage and enterococci were associated with increased gastrointestinal illness, and there was an association between male-specific coliphage level and illness that was somewhat stronger than the association between enterococci and illness. There were no substantial differences between male-specific and somatic coliphage. Somatic coliphage and enterococci had similar associations with gastrointestinal illness; there was some evidence that male-specific coliphage had a stronger association with illness than enterococci in marine waters with human fecal contamination.

Chapter 11. Community analysis-based methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Y.; Wu, C.H.; Andersen, G.L.

2010-05-01

Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. Inmore » increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.« less

Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson's disease mice: Gut microbiota, glial reaction and TLR4/TNF-α signaling pathway.

PubMed

Sun, Meng-Fei; Zhu, Ying-Li; Zhou, Zhi-Lan; Jia, Xue-Bing; Xu, Yi-Da; Yang, Qin; Cui, Chun; Shen, Yan-Qin

2018-05-01

Parkinson's disease (PD) patients display alterations in gut microbiota composition. However, mechanism between gut microbial dysbiosis and pathogenesis of PD remains unexplored, and no recognized therapies are available to halt or slow progression of PD. Here we identified that gut microbiota from PD mice induced motor impairment and striatal neurotransmitter decrease on normal mice. Sequencing of 16S rRNA revealed that phylum Firmicutes and order Clostridiales decreased, while phylum Proteobacteria, order Turicibacterales and Enterobacteriales increased in fecal samples of PD mice, along with increased fecal short-chain fatty acids (SCFAs). Remarkably, fecal microbiota transplantation (FMT) reduced gut microbial dysbiosis, decreased fecal SCFAs, alleviated physical impairment, and increased striatal DA and 5-HT content of PD mice. Further, FMT reduced the activation of microglia and astrocytes in the substantia nigra, and reduced expression of TLR4/TNF-α signaling pathway components in gut and brain. Our study demonstrates that gut microbial dysbiosis is involved in PD pathogenesis, and FMT can protect PD mice by suppressing neuroinflammation and reducing TLR4/TNF-α signaling. Copyright © 2018 Elsevier Inc. All rights reserved.

Characterization of the Fecal Microbiome from Non-Human Wild Primates Reveals Species Specific Microbial Communities

PubMed Central

Yildirim, Suleyman; Yeoman, Carl J.; Sipos, Maksim; Torralba, Manolito; Wilson, Brenda A.; Goldberg, Tony L.; Stumpf, Rebecca M.; Leigh, Steven R.; White, Bryan A.; Nelson, Karen E.

2010-01-01

Background Host-associated microbes comprise an integral part of animal digestive systems and these interactions have a long evolutionary history. It has been hypothesized that the gastrointestinal microbiome of humans and other non-human primates may have played significant roles in host evolution by facilitating a range of dietary adaptations. We have undertaken a comparative sequencing survey of the gastrointestinal microbiomes of several non-human primate species, with the goal of better understanding how these microbiomes relate to the evolution of non-human primate diversity. Here we present a comparative analysis of gastrointestinal microbial communities from three different species of Old World wild monkeys. Methodology/Principal Findings We analyzed fecal samples from three different wild non-human primate species (black-and-white colobus [Colubus guereza], red colobus [Piliocolobus tephrosceles], and red-tailed guenon [Cercopithecus ascanius]). Three samples from each species were subjected to small subunit rRNA tag pyrosequencing. Firmicutes comprised the vast majority of the phyla in each sample. Other phyla represented were Bacterioidetes, Proteobacteria, Spirochaetes, Actinobacteria, Verrucomicrobia, Lentisphaerae, Tenericutes, Planctomycetes, Fibrobacateres, and TM7. Bray-Curtis similarity analysis of these microbiomes indicated that microbial community composition within the same primate species are more similar to each other than to those of different primate species. Comparison of fecal microbiota from non-human primates with microbiota of human stool samples obtained in previous studies revealed that the gut microbiota of these primates are distinct and reflect host phylogeny. Conclusion/Significance Our analysis provides evidence that the fecal microbiomes of wild primates co-vary with their hosts, and that this is manifested in higher intraspecies similarity among wild primate species, perhaps reflecting species specificity of the microbiome in addition to dietary influences. These results contribute to the limited body of primate microbiome studies and provide a framework for comparative microbiome analysis between human and non-human primates as well as a comparative evolutionary understanding of the human microbiome. PMID:21103066

Development and evaluation of a culture-independent method for source determination of fecal wastes in surface and storm waters using reverse transcriptase-PCR detection of FRNA coliphage genogroup gene sequences.

PubMed

Paar, Jack; Doolittle, Mark M; Varma, Manju; Siefring, Shawn; Oshima, Kevin; Haugland, Richard A

2015-05-01

A method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for detecting interferences in RNA recovery and analysis, was developed for the direct, culture-independent detection of genetic markers from FRNA coliphage genogroups I, II & IV in water samples. Results were obtained from an initial evaluation of the performance of this method in analyses of waste water, ambient surface water and stormwater drain and outfall samples from predominantly urban locations. The evaluation also included a comparison of the occurrence of the FRNA genetic markers with genetic markers from general and human-related bacterial fecal indicators determined by current or pending EPA-validated qPCR methods. Strong associations were observed between the occurrence of the putatively human related FRNA genogroup II marker and the densities of the bacterial markers in the stormwater drain and outfall samples. However fewer samples were positive for FRNA coliphage compared to either the general bacterial fecal indicator or the human-related bacterial fecal indicator markers particularly for ambient water samples. Together, these methods show promise as complementary tools for the identification of contaminated storm water drainage systems as well as the determination of human and non-human sources of contamination. Published by Elsevier B.V.

Water quality in the Withers Swash Basin, with emphasis on enteric bacteria, Myrtle Beach, South Carolina, 1991-93

USGS Publications Warehouse

Guimaraes, W.B.

1995-01-01

Water samples were collected in 1991-93 from Withers Swash and its two tributaries (the Mainstem and KOA Branches) in Myrtle Beach, S.C., and analyzed for physical properties, organic and inorganic constituents, and fecal coliform and streptococcus bacteria. Samples were collected during wet- and dry-weather conditions to assess the water quality of the streams before and after storm runoff. Water samples were analyzed for over 200 separate physical, chemical, and biological constituents. Concentrations of 11 constituents violated State criteria for shellfish harvesting waters, and State Human Health Criteria. The 11 constituents included concentrations of dissolved oxygen, arsenic, lead, cadmium, mercury, chlordane, dieldrin, 1,1,1-trichloroethane, 1,1-dichloroethylene, trichloroethylene, and fecal coliform bacteria. Water samples were examined for the presence of enteric bacteria (fecal coliform and fecal streptococcus) at 46 sites throughout the Withers Swash Basin and 5 sites on the beach and in the Atlantic Ocean. Water samples were collected just upstream from all confluences in order to determine sources of bacterial contamination. Temporally and spatially high concentrations of enteric bacteria were detected throughout the Withers Swash Basin; however, these sporadic bacteria concentrations made it difficult to determine a single source of the contamination. These enteric bacteria concentrations are probably derived from a number of sources in the basin including septic tanks, garbage containers, and the feces of waterfowl and domestic animals.

Genotypic Diversity of Escherichia coli in the Water and Soil of Tropical Watersheds in Hawaii ▿

PubMed Central

Goto, Dustin K.; Yan, Tao

2011-01-01

High levels of Escherichia coli were frequently detected in tropical soils in Hawaii, which present important environmental sources of E. coli to water bodies. This study systematically examined E. coli isolates from water and soil of several watersheds in Hawaii and observed high overall genotypic diversity (35.5% unique genotypes). In the Manoa watershed, fewer than 9.3% of the observed E. coli genotypes in water and 6.6% in soil were shared between different sampling sites, suggesting the lack of dominant fecal sources in the watershed. High temporal variability of E. coli genotypes in soil was also observed, which suggests a dynamic E. coli population corresponding with the frequently observed high concentrations in tropical soils. When E. coli genotypes detected from the same sampling events were compared, limited sharing between the soil and water samples was observed in the majority of comparisons (73.5%). However, several comparisons reported up to 33.3% overlap of E. coli genotypes between soil and water, illustrating the potential for soil-water interactions under favorable environmental conditions. In addition, genotype accumulation curves for E. coli from water and soil indicated that the sampling efforts in the Manoa watershed could not exhaust the overall genotypic diversity. Comparisons of E. coli genotypes from other watersheds on Oahu, Hawaii, identified no apparent grouping according to sampling locations. The results of the present study demonstrate the complexity of using E. coli as a fecal indicator bacterium in tropical watersheds and highlight the need to differentiate environmental sources of E. coli from fecal sources in water quality monitoring. PMID:21515724

Bacteriology of Dehydrated Space Foods 1

PubMed Central

Powers, Edmund M.; Ay, Carl; El-Bisi, Hamed M.; Rowley, Durwood B.

1971-01-01

The initial bacteriological requirement established in 1964 for space foods by the U.S. Army Natick Laboratories are: a total aerobic plate count (≤ 10,000 per g), a total coliform count (≤ 10 per g), fecal coliforms (negative per gram), fecal streptococci (≤ 20 per g), coagulase-positive staphylococci (negative in 5 g) and salmonellae (negative in 10 g). Of the space foods and prototypes tested during 1968 and 1969, 93% complied with the total aerobic plate count, 98% had less than 1 coliform per g, and 99% were negative for fecal coliforms; 88% complied with the streptococci requirement; 100 and 98% were negative for staphylococci and salmonellae, respectively. Nineteen food samples which did not comply (as indicated parenthetically by actual counts per gram) with the requirements were (i) total aerobic plate count: beef soup and gravy base (18,000), chicken soup and gravy base (57,000), spaghetti with meat sauce (12,100 and 14,000), sugared coffee (> 300,000), chocolate ice cream cubes (20,000), and each of four samples of chocolate candy (12,000 to 61,000); (ii) coliforms: two out of three vanilla milk drinks (16 and 127) and one beef hash bar (14); (iii) fecal coliforms: one sample of chicken soup and gravy base positive; (iv) fecal streptococci: two samples of peanut cubes (40 and 108), coconut cubes (75), chicken soup and gravy base (2,650), beef soup and gravy base (33), and five out of six flavored milk drinks (23 to 300); (v) salmonellae: one each of chicken and beef soup and gravy base were positive. Images PMID:4940878

Surveillance for Highly Pathogenic Avian Influenza Virus in Wild Birds during Outbreaks in Domestic Poultry, Minnesota, 2015.

PubMed

Jennelle, Christopher S; Carstensen, Michelle; Hildebrand, Erik C; Cornicelli, Louis; Wolf, Paul; Grear, Daniel A; Ip, Hon S; Vandalen, Kaci K; Minicucci, Larissa A

2016-07-01

In 2015, a major outbreak of highly pathogenic avian influenza virus (HPAIV) infection devastated poultry facilities in Minnesota, USA. To understand the potential role of wild birds, we tested 3,139 waterfowl fecal samples and 104 sick and dead birds during March 9-June 4, 2015. HPAIV was isolated from a Cooper's hawk but not from waterfowl fecal samples.

Notes on the Diet of Reproductively Active Male Rafinesque's Big Eared Bats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Menzel, M.A.; Carter, T.C.; Menzel, J.M.

Diet examination through the use of fecal samples, of five reproductively active male Rafinesque's big-eared bats from the Upper Coastal Plain of South Carolina during August and September 1999. Diets of these individuals in upland pine stands were similar to diets of Rafinesque's big-eared bats in bottomland and upland hardwood habitats. Although fecal samples had three insect orders, the diet consisted primarily of lepidopterans.

Human Parvovirus 4 in Nasal and Fecal Specimens from Children, Ghana

PubMed Central

Drexler, Jan Felix; Reber, Ulrike; Muth, Doreen; Herzog, Petra; Annan, Augustina; Ebach, Fabian; Sarpong, Nimarko; Acquah, Samuel; Adlkofer, Julia; Adu-Sarkodie, Yaw; Panning, Marcus; Tannich, Egbert; May, Jürgen; Drosten, Christian

2012-01-01

Nonparenteral transmission might contribute to human parvovirus 4 (PARV4) infections in sub-Saharan Africa. PARV4 DNA was detected in 8 (0.83%) of 961 nasal samples and 5 (0.53%) of 943 fecal samples from 1,904 children in Ghana. Virus concentrations ≤6–7 log10 copies/mL suggest respiratory or fecal–oral modes of PARV4 transmission. PMID:23018024

Fecal water genotoxicity in healthy free-living young Italian people.

PubMed

Daniela, Erba; Sara, Soldi; Marcella, Malavolti; Giovanni, Aragone; Meynier, Alexandra; Sophie, Vinoy; Cristina, Casiraghi M

2014-02-01

Dietary habit affects the composition of human feces thus determining intestinal environment and exposure of colon mucosa to risk factors. Fecal water (FW) citotoxicity and genotoxicity were investigated in 33 healthy young Italian people, as well as the relationship between genotoxicity and nutrient intake or microflora composition. Two fecal samples were collected at 2 weeks apart and 3-d dietary diary was recorded for each volunteer. Cytotoxicity was measured using the Trypan Blue Dye Exclusion assay and genotoxicity using the Comet Assay (alkaline single-cell electrophoresis). Fecal bifidobacteria, total microbial count and nutrient intakes were also assessed. High intra- and inter-variability in genotoxicity data and in bacteria counts were found. None of the FW samples were citotoxic, but 90% of FW samples were genotoxic. Seventy five percent indicated intermediate and 15% were highly genotoxic. There was a different sex-related distribution. Genotoxicity was positively correlated to the total lipid intake in females and to the bifidobacteria/total bacteria count ratio in male volunteers. These results demonstrate that the majority of FW samples isolated from free-living Italian people show intermediate level of genotoxicity and sustain a relation between this possible non-invasive marker of colorectal cancer risk with both dietary habits and colonic ecosystem. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fecal parasite identification by microscopy and PCR in scimitar-horned oryx, Oryx dammah, managed at two sites.

PubMed

Pauling, Cassandra Dawn; Oller, Anna R; Jackson, Victoria

2016-12-01

The scimitar-horned oryx, Oryx dammah , an endangered species extinct in the wild, is managed in various captive management programs and is the focus of reintroduction efforts. Management variability can contribute to substantial parasite load differences, which can affect deworming programs and potentially transfer parasites to different regions with translocations. Parasite studies in O. dammah are lacking. In this study, we determined fecal egg/oocyst counts of O. dammah in two captive herds, Fossil Rim Wildlife Center (FRWC) and Kansas City Zoo (KCZ). Fecal egg counts (FEC) were performed on O. dammah feces collected seasonally using the modified McMaster method, and microscopy provided additional identification of parasite genera ova and oocysts. To identify parasites to species level, homogenized fecals provided DNA subjected to the polymerase chain reaction (PCR) using genus specific primers. Microscopy and sequencing results indicated the presence of Strongylus (Strongylus vulgaris, Angiostrongylus cantonensis) , Trichostrongylus (Haemonchus contortus, Camelostrongylus mentulatus) , Trichuris (T. leporis, T. ovis, and T. discolor) , Isospora (Isospora gryphoni) and Eimeria (E. zuernii and E. bovis) , with Strongylus being the most common. Nematodirus was identified through microscopy at FRWC. Fecal egg counts were significantly higher in (FRWC) than in (KCZ) in all samplings (P = <0.001). No significant difference was seen between parasite load and seasons (P = 0.103), nor site and season (P = 0.51). Both study sites maintained most animals within commonly accepted FEC levels found in domestic livestock. Individuals with high numbers of EPG or OPG were subordinate males, pregnant females, or neonates. Several significant interactions were found between genera of parasites, age, sex, season, and pregnancy status in the FRWC herd. Sampling limitations prevented further analysis of the KCZ herd. Understanding interactions between parasite loads and physiological, environmental, and regional differences can help determine inter-specific transfer of parasites, and establish appropriate anthelmintic programs for O. dammah herds.

Evaluation of multiplex tandem real-time PCR for detection of Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis in clinical stool samples.

PubMed

Stark, D; Al-Qassab, S E; Barratt, J L N; Stanley, K; Roberts, T; Marriott, D; Harkness, J; Ellis, J T

2011-01-01

The aim of this study was to describe the first development and evaluation of a multiplex tandem PCR (MT-PCR) assay for the detection and identification of 4 common pathogenic protozoan parasites, Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis, from human clinical samples. A total of 472 fecal samples submitted to the Department of Microbiology at St. Vincent's Hospital were included in the study. The MT-PCR assay was compared to four real-time PCR (RT-PCR) assays and microscopy by a traditional modified iron hematoxylin stain. The MT-PCR detected 28 G. intestinalis, 26 D. fragilis, 11 E. histolytica, and 9 Cryptosporidium sp. isolates. Detection and identification of the fecal protozoa by MT-PCR demonstrated 100% correlation with the RT-PCR results, and compared to RT-PCR, MT-PCR exhibited 100% sensitivity and specificity, while traditional microscopy of stained fixed fecal smears exhibited sensitivities and specificities of 56% and 100% for Cryptosporidium spp., 38% and 99% for D. fragilis, 47% and 97% for E. histolytica, and 50% and 100% for G. intestinalis. No cross-reactivity was detected in 100 stool samples containing various other bacterial, viral, and protozoan species. The MT-PCR assay was able to provide rapid, sensitive, and specific simultaneous detection and identification of the four most important diarrhea-causing protozoan parasites that infect humans. This study also highlights the lack of sensitivity demonstrated by microscopy, and thus, molecular methods such as MT-PCR must be considered the diagnostic methods of choice for enteric protozoan parasites.

Current and future trends in fecal source tracking and deployment in the Lake Taihu Region of China

NASA Astrophysics Data System (ADS)

Hagedorn, Charles; Liang, Xinqiang

The emerging discipline of microbial and/or chemical source tracking (collectively termed fecal source tracking (FST)) is being used to identify origins of fecal contamination in polluted waters in many countries around the world. FST has developed rapidly because standard methods of measuring contamination in water by enumerating fecal indicator bacteria (FIB) such as fecal coliforms and enterococci do not identify the sources of the contamination. FST is an active area of research and development in both the academic and private sectors and includes: Developing and testing new microbial and chemical FST methods. Determining the geographic application and animal host ranges of existing and emerging FST techniques. Conducting experimental comparisons of FST techniques. Combining direct monitoring of human pathogens associated with waterborne outbreaks and zoonotic pathogens responsible for infections among people, wildlife, or domesticated animals with the use of FST techniques. Applying FST to watershed analysis and coastal environments. Designing appropriate statistical and probability analysis of FST data and developing models for mass loadings of host-specific fecal contamination. This paper includes a critical review of FST with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), which methods are applicable to different situations, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper addresses the broader question of whether FST and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many FST methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the “real” answer is not known, so their comparative performance and accuracy cannot be assessed. For FST to be quantitative, stability of ratios between host-specific markers in the environment must be established. In addition, research is needed on the correlation between host-specific markers and pathogens, and survival of markers after waste treatments. As a result of the exclusive emphasis on FIB by regulatory agencies, monitoring and FST development has concentrated on FIB rather than the actual pathogens. A more rational approach to regulating water quality might be to use available epidemiological data to identify pathogens of concern in a particular water body, and then use targeted pathogen monitoring coupled with very specific FST approaches to control the pathogens. Baseline monitoring of FIB would be just one tool among many in this example.

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

PubMed Central

Palumbo, Michelle C.; Xu, Gege; Davis, Jasmine C. C.; Lebrilla, Carlito B.; Freeman, Samara L.; German, J. Bruce; Smilowitz, Jennifer T.

2017-01-01

ABSTRACT Attempts to alter intestinal dysbiosis via administration of probiotics have consistently shown that colonization with the administered microbes is transient. This study sought to determine whether provision of an initial course of Bifidobacterium longum subsp. infantis (B. infantis) would lead to persistent colonization of the probiotic organism in breastfed infants. Mothers intending to breastfeed were recruited and provided with lactation support. One group of mothers fed B. infantis EVC001 to their infants from day 7 to day 28 of life (n = 34), and the second group did not administer any probiotic (n = 32). Fecal samples were collected during the first 60 postnatal days in both groups. Fecal samples were assessed by 16S rRNA gene sequencing, quantitative PCR, mass spectrometry, and endotoxin measurement. B. infantis-fed infants had significantly higher populations of fecal Bifidobacteriaceae, in particular B. infantis, while EVC001 was fed, and this difference persisted more than 30 days after EVC001 supplementation ceased. Fecal milk oligosaccharides were significantly lower in B. infantis EVC001-fed infants, demonstrating higher consumption of human milk oligosaccharides by B. infantis EVC001. Concentrations of acetate and lactate were significantly higher and fecal pH was significantly lower in infants fed EVC001, demonstrating alterations in intestinal fermentation. Infants colonized by Bifidobacteriaceae at high levels had 4-fold-lower fecal endotoxin levels, consistent with observed lower levels of Gram-negative Proteobacteria and Bacteroidetes. IMPORTANCE The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function. PMID:29242832

Cryptosporidium parvum Infection Involving Novel Genotypes in Wildlife from Lower New York State

PubMed Central

Perz, Joseph F.; Le Blancq, Sylvie M.

2001-01-01

Cryptosporidium, an enteric parasite of humans and a wide range of other mammals, presents numerous challenges to the supply of safe drinking water. We performed a wildlife survey, focusing on white-tailed deer and small mammals, to assess whether they may serve as environmental sources of Cryptosporidium. A PCR-based approach that permitted genetic characterization via sequence analysis was applied to wildlife fecal samples (n = 111) collected from September 1996 to July 1998 from three areas in lower New York State. Southern analysis revealed 22 fecal samples containing Cryptosporidium small-subunit (SSU) ribosomal DNA; these included 10 of 91 white-tailed deer (Odocoileus virginianus) samples, 3 of 5 chipmunk (Tamias striatus) samples, 1 of 2 white-footed mouse (Peromyscus leucopus) samples, 1 of 2 striped skunk (Mephitis mephitis) samples, 1 of 5 racoon (Procyon lotor) samples, and 6 of 6 muskrat (Ondatra zibethicus) samples. All of the 15 SSU PCR products sequenced were characterized as Cryptosporidium parvum; two were identical to genotype 2 (bovine), whereas the remainder belonged to two novel SSU sequence groups, designated genotypes 3 and 4. Genotype 3 comprised four deer-derived sequences, whereas genotype 4 included nine sequences from deer, mouse, chipmunk, and muskrat samples. PCR analysis was performed on the SSU-positive fecal samples for three other Cryptosporidium loci (dihydrofolate reductase, polythreonine-rich protein, and beta-tubulin), and 8 of 10 cloned PCR products were consistent with C. parvum genotype 2. These data provide evidence that there is sylvatic transmission of C. parvum involving deer and other small mammals. This study affirmed the importance of wildlife as potential sources of Cryptosporidium in the catchments of public water supplies. PMID:11229905

Cryptosporidium parvum infection involving novel genotypes in wildlife from lower New York State.

PubMed

Perz, J F; Le Blancq, S M

2001-03-01

Cryptosporidium, an enteric parasite of humans and a wide range of other mammals, presents numerous challenges to the supply of safe drinking water. We performed a wildlife survey, focusing on white-tailed deer and small mammals, to assess whether they may serve as environmental sources of Cryptosporidium. A PCR-based approach that permitted genetic characterization via sequence analysis was applied to wildlife fecal samples (n = 111) collected from September 1996 to July 1998 from three areas in lower New York State. Southern analysis revealed 22 fecal samples containing Cryptosporidium small-subunit (SSU) ribosomal DNA; these included 10 of 91 white-tailed deer (Odocoileus virginianus) samples, 3 of 5 chipmunk (Tamias striatus) samples, 1 of 2 white-footed mouse (Peromyscus leucopus) samples, 1 of 2 striped skunk (Mephitis mephitis) samples, 1 of 5 racoon (Procyon lotor) samples, and 6 of 6 muskrat (Ondatra zibethicus) samples. All of the 15 SSU PCR products sequenced were characterized as Cryptosporidium parvum; two were identical to genotype 2 (bovine), whereas the remainder belonged to two novel SSU sequence groups, designated genotypes 3 and 4. Genotype 3 comprised four deer-derived sequences, whereas genotype 4 included nine sequences from deer, mouse, chipmunk, and muskrat samples. PCR analysis was performed on the SSU-positive fecal samples for three other Cryptosporidium loci (dihydrofolate reductase, polythreonine-rich protein, and beta-tubulin), and 8 of 10 cloned PCR products were consistent with C. parvum genotype 2. These data provide evidence that there is sylvatic transmission of C. parvum involving deer and other small mammals. This study affirmed the importance of wildlife as potential sources of Cryptosporidium in the catchments of public water supplies.

Urinary and fecal incontinence in a community-residing older population in Japan.

PubMed

Nakanishi, N; Tatara, K; Naramura, H; Fujiwara, H; Takashima, Y; Fukuda, H

1997-02-01

To estimate the prevalence and risk factors of urinary and fecal incontinence among a community-residing older population in Japan. Population-based cross-sectional study. A randomly selected sample of 1473 people aged 65 years and older living in the City of Settsu, Osaka, in 1992. Data collected via in-home visits were used to estimate the prevalence of urinary and fecal incontinence and to provide information regarding potential risk factors of urinary and fecal incontinence. Data were obtained from 1405 older adults, a response rate of 95.4%. The prevalence of any degree of urinary incontinence was 98/1000 in both sexes, and 87/ 1000 men and 66/1000 women admitted to some degree of fecal incontinence. Daily, 34/1000 and 20/1000 of the population were incontinent of urine and feces, respectively. There was an increasing prevalence of urinary and fecal incontinence with age in both sexes, but the expected greater prevalence in women was not found. By univariate analyses, age older than 75 years, poor general health as measured by Activities of Daily Living, stroke, dementia, no participation in social activities, and lack of life worth living (Ikigai) were associated significantly with both urinary and fecal incontinence. In the multivariate analyses using logistic regression, age older than 75 years, poor general health, and stroke were independent risk factors for any type of incontinence. Diabetes was an independent risk factor for isolated fecal incontinence, and dementia and no participation in social activities were independent risk factors for double incontinence. Incontinence of urine and feces is a prevalent condition among very old people living in the community in Japan and is associated highly with health and psychosocial conditions.

ENHANCED CONCENTRATION AND ISOLATION OF CYCLOSPORA CAYETANENSIS OOCYSTS FROM HUMAN FECAL SAMPLES

EPA Science Inventory

Cyclospora cayetanensis is the causative agent of cyclosporiasis, an emerging infections disease. A new method for the purification of Cycloposra cayetanensis oocysts from fecal matter has been developed, using a modified detachment solution and a Renocal-sucrose gradient sedimen...

Multiple modes of water quality impairment by fecal contamination in a rapidly developing coastal area: southwest Brunswick County, North Carolina.

PubMed

Cahoon, Lawrence B; Hales, Jason C; Carey, Erin S; Loucaides, Socratis; Rowland, Kevin R; Toothman, Byron R

2016-02-01

Fecal contamination of surface waters is a significant problem, particularly in rapidly developing coastal watersheds. Data from a water quality monitoring program in southwest Brunswick County, North Carolina, gathered in support of a regional wastewater and stormwater management program were used to examine likely modes and sources of fecal contamination. Sampling was conducted at 42 locations at 3-4-week intervals between 1996 and 2003, including streams, ponds, and estuarine waters in a variety of land use settings. Expected fecal sources included human wastewater systems (on-site and central), stormwater runoff, and direct deposition by animals. Fecal coliform levels were positively associated with rainfall measures, but frequent high fecal coliform concentrations at times of no rain indicated other modes of contamination as well. Fecal coliform levels were also positively associated with silicate levels, a groundwater source signal, indicating that flux of fecal-contaminated groundwater was a mode of contamination, potentially elevating FC levels in impacted waters independent of stormwater runoff. Fecal contamination by failing septic or sewer systems at many locations was significant and in addition to effects of stormwater runoff. Rainfall was also linked to fecal contamination by central sewage treatment system failures. These results highlight the importance of considering multiple modes of water pollution and different ways in which human activities cause water quality degradation. Management of water quality in coastal regions must therefore recognize diverse drivers of fecal contamination to surface waters.

Fecal calprotectin concentrations in adult dogs with chronic diarrhea.

PubMed

Grellet, Aurélien; Heilmann, Romy M; Lecoindre, Patrick; Feugier, Alexandre; Day, Michael J; Peeters, Dominique; Freiche, Valérie; Hernandez, Juan; Grandjean, Dominique; Suchodolski, Jan S; Steiner, Jorg M

2013-05-01

To evaluate fecal calprotectin concentrations in healthy dogs and dogs with chronic diarrhea, to identify cutoff values for fecal calprotectin concentrations for use in differentiating dogs with chronic diarrhea and a canine chronic enteropathy clinical activity index (CCECAI) < 12 from dogs with chronic diarrhea and a CCECAI ≥ 12, and to evaluate the association between histologic evidence of intestinal mucosal changes and fecal calprotectin concentrations in dogs with chronic diarrhea. Fecal samples from 96 adult dogs (27 dogs with chronic diarrhea and 69 healthy control dogs). Severity of clinical signs was evaluated on the basis of the CCECAI scoring system. Endoscopy was performed in all dogs with chronic diarrhea, and mucosal biopsy specimens were evaluated histologically. Fecal calprotectin concentration was quantified via radioimmunoassay. Fecal calprotectin concentrations were significantly higher in dogs with chronic diarrhea than in healthy control dogs. Fecal calprotectin concentrations were also significantly higher in dogs with a CCECAI ≥ 12, compared with concentrations for dogs with a CCECAI between 4 and 11. Fecal calprotectin concentrations were significantly higher in dogs with chronic diarrhea associated with histologic lesions, compared with concentrations in control dogs, and were significantly correlated with the severity of histologic intestinal lesions. Among dogs with chronic diarrhea, the best cutoff fecal calprotectin concentration for predicting a CCECAI ≥ 12 was 48.9 μg/g (sensitivity, 53.3%; specificity, 91.7%). Fecal calprotectin may be a useful biomarker in dogs with chronic diarrhea, especially dogs with histologic lesions.

The presence and near-shore transport of human fecal pollution in Lake Michigan beaches

USGS Publications Warehouse

Molloy, S.L.; Liu, L.B.; Phanikumar, M.S.; Jenkins, T.M.; Wong, M.V.; Rose, J.B.; Whitman, R.L.; Shively, D.A.; Nevers, M.B.

2005-01-01

The Great Lakes are a source of water for municipal, agricultural and industrial use, and support significant recreation, commercial and sport fishing industries. Every year millions of people visit the 500 plus recreational beaches in the Great Lakes. An increasing public health risk has been suggested with increased evidence of fecal contamination at the shoreline. To investigate the transport and fate of fecal pollution at Great Lakes beaches and the health risk associated with swimming at these beaches, the near-shore waters of Mt Baldy Beach, Lake Michigan and Trail Creek, a tributary discharging into the lake were examined for fecal pollution indicators. A model of surf zone hydrodynamics coupled with a transport model with first-order inactivation of pollutant was used to understand the relative importance of different processes operating in the surf zone (e.g. physical versus biological processes). The Enterococcus human fecal pollution marker, which targets a putative virulence factor, the enterococcal surface protein (esp) in Enterococcus faecium, was detected in 2/28 samples (7%) from the tributaries draining into Lake Michigan and in 6/30 samples (20%) from Lake Michigan beaches. Preliminary analysis suggests that the majority of fecal indicator bactateria variation and water quality changes at the beaches can be explained by inputs from the influential stream and hydrometeorological conditions. Using modeling methods to predict impaired water quality may help reduce potential health threats to recreational visitors.

Intestinal blood loss as an aggravating factor of iron deficiency in infants aged 9 to 12 months fed whole cow's milk.

PubMed

Fernandes, Sandra Maria Rodrigues; de Morais, Mauro Batista; Amancio, Olga Maria Silverio

2008-02-01

To verify the occurrence of occult intestinal blood loss and iron deficiency in infants aged 9 to 12 months. A consecutive sample of 98 infants of the Pediatric Public Health Primary Care Unit in the town of Arapongas, Parana State, Brazil was involved in this cross-sectional study. Dietary history, hemoglobin, serum iron, transferrin saturation, ferritin, and an occult fecal blood loss investigation, by the immune chromatographic method specific for human hemoglobin were performed. Presence of occult intestinal blood occurred in 8/23 of the breast-fed (plus complementary feed) infants and in 30/64 of the infants who were fed with cow's milk (plus complementary feed) (P=0.449). The comparison of body iron indicators in accordance to positive or negative occult fecal blood, did not show any significant difference in the 23 breast-fed infants. Serum ferritin (median=4.2 ng/mL) was significantly lower (P=0.004) in infants who received whole cow's milk and had positive occult fecal blood, than in those infants who received whole cow's milk but were without occult fecal blood (median=12.1 ng/mL). In breast-fed infants with negative occult fecal blood, iron deficiency severity is not greater than in those with positive results. In infants fed whole cow's milk, occult fecal blood loss is an aggravating factor of iron deficiency.

Fecal sterols, seasonal variability, and probable sources along the ring of cenotes, Yucatan, Mexico

NASA Astrophysics Data System (ADS)

Arcega-Cabrera, F.; Velázquez-Tavera, N.; Fargher, L.; Derrien, M.; Noreña-Barroso, E.

2014-11-01

Rapid development in Yucatan has had a dramatic impact on the environment, especially the water supply. Groundwater is the only source of water in Yucatan, since surface water is virtually absent due to the karstic nature of the soil. The ring of cenotes (RC) is a geological feature which functions as a source of water and as nodes in the underground river system that canalizes water towards the coast. Numerous productive and domestic activities take place around the RC in the absence of wastewater treatment or sewage systems. Consequently, a number of researchers have hypothesized that pollutants could migrate from the land surface to the underlying aquifer and, eventually, to the coast. Therefore, the present study investigates the relationship among sources of fecal sterols and their levels in cenotes, using the expected levels of fecal sterols obtained by a spatial analysis of the sources and a Pollution Source Index. Accordingly, expected levels are compared with the detected levels of fecal sterols in 5 areas around the RC. Regarding levels, observed during a sampling campaign carried out along the RC during September 2011 (rainy season) and May 2012 (dry season), varied from low to high concentrations of sterols (0.5-2396.42 μg g- 1) and fecal sterols (0.3-1690.18 μg g- 1). These concentrations showed no relationship between neighboring cenotes, where similar fecal sterol concentrations or gradients were expected. When comparing expected fecal sterols levels with the detected ones, only two of the five analyzed areas concur, suggesting that no clear relationship exists among sources and fecal sterols levels at the regional scale. Multivariate analysis showed that fecal sterols were associated with sterols and fine grain particulates during the rainy season, which suggests co-transport. During the dry season, fecal sterols associated with fine grain particulate and organic matter, which indicates a change to a deposition phenomenon. These findings indicate that defining a relationship among sources and fecal sterols levels is highly difficult and this could be the result of the absorption or migration through an intricate conduit, crack, or fracture karst system. Nevertheless, the “source-levels approach”, used in this study, was consistent for the northeast edge and the middle western part of the RC. New and more extensive research should be done to assess the environmental fate of fecal sterols, especially considering the intricate karstic system and its compound retention capacity.

Fecal sterols, seasonal variability, and probable sources along the ring of cenotes, Yucatan, Mexico.

PubMed

Arcega-Cabrera, F; Velázquez-Tavera, N; Fargher, L; Derrien, M; Noreña-Barroso, E

2014-11-01

Rapid development in Yucatan has had a dramatic impact on the environment, especially the water supply. Groundwater is the only source of water in Yucatan, since surface water is virtually absent due to the karstic nature of the soil. The ring of cenotes (RC) is a geological feature which functions as a source of water and as nodes in the underground river system that canalizes water towards the coast. Numerous productive and domestic activities take place around the RC in the absence of wastewater treatment or sewage systems. Consequently, a number of researchers have hypothesized that pollutants could migrate from the land surface to the underlying aquifer and, eventually, to the coast. Therefore, the present study investigates the relationship among sources of fecal sterols and their levels in cenotes, using the expected levels of fecal sterols obtained by a spatial analysis of the sources and a Pollution Source Index. Accordingly, expected levels are compared with the detected levels of fecal sterols in 5 areas around the RC. Regarding levels, observed during a sampling campaign carried out along the RC during September 2011 (rainy season) and May 2012 (dry season), varied from low to high concentrations of sterols (0.5-2396.42 μg g(-1)) and fecal sterols (0.3-1690.18 μg g(-1)). These concentrations showed no relationship between neighboring cenotes, where similar fecal sterol concentrations or gradients were expected. When comparing expected fecal sterols levels with the detected ones, only two of the five analyzed areas concur, suggesting that no clear relationship exists among sources and fecal sterols levels at the regional scale. Multivariate analysis showed that fecal sterols were associated with sterols and fine grain particulates during the rainy season, which suggests co-transport. During the dry season, fecal sterols associated with fine grain particulate and organic matter, which indicates a change to a deposition phenomenon. These findings indicate that defining a relationship among sources and fecal sterols levels is highly difficult and this could be the result of the absorption or migration through an intricate conduit, crack, or fracture karst system. Nevertheless, the "source-levels approach", used in this study, was consistent for the northeast edge and the middle western part of the RC. New and more extensive research should be done to assess the environmental fate of fecal sterols, especially considering the intricate karstic system and its compound retention capacity. Copyright © 2014 Elsevier B.V. All rights reserved.

Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type.

PubMed

Oki, Kaihei; Toyama, Mutsumi; Banno, Taihei; Chonan, Osamu; Benno, Yoshimi; Watanabe, Koichi

2016-11-28

In Japan, a variety of traditional dietary habits and daily routines have developed in many regions. The effects of these behaviors, and the regional differences in the composition of the gut microbiota, are yet to be sufficiently studied. To characterize the Japanese gut microbiota and identify the factors shaping its composition, we conducted 16S metagenomics analysis of fecal samples collected from healthy Japanese adults residing in various regions of Japan. Each participant also completed a 94-question lifestyle questionnaire. We collected fecal samples from 516 healthy Japanese adults (325 females, 191 males; age, 21-88). Heatmap and biplot analyses based on the bacterial family composition of the fecal microbiota showed that subjects' region of residence or gender were not strongly correlated with the general composition of the fecal microbiota. Although clustering analysis for the whole cohort did not reveal any distinct clusters, two enterotype-like clusters were observed in the male, but not the female, subjects. In the whole subject population, the scores for bowel movement frequency were significantly correlated with the abundances of Christensenellaceae, Mogibacteriaceae, and Rikenellaceae in the fecal microbiota (P < 0.001). These three bacterial families were also significantly more abundant (P < 0.05 or 0.01) in lean subjects (body mass index (BMI) < 25) than in obese subjects (BMI > 30), which is consistent with previously published results. However, a previously reported correlation between BMI and bowel movement frequency was not observed. In addition, the abundances of these three families were positively correlated with each other and comprised a correlative network with 14 other bacterial families. The present study showed that the composition of the fecal microbiota of healthy Japanese adults at the national level was not strongly correlated with subjects' area of residence or gender. In addition, enterotype partitioning was ambiguous in this cohort of healthy Japanese adults. Finally, the results implied that the abundances of Christensenellaceae, Mogibacteriaceae, and Rikenellaceae, along with several other bacterial components that together comprised a correlative network, contributed to a phenotype characterized by a high frequency of bowel movements and a lean body type.

Survival and persistence of fecal host-specific Bacteroidales cells and their DNA assessed by PMA-qPCR

NASA Astrophysics Data System (ADS)

Bae, S.; Bombardelli, F.; Wuertz, S.

2008-12-01

Understanding and managing microbial pollutions in water is one of the foremost challenges of establishing effective managements and remediation strategies to impaired water bodies polluted by uncharacterized fecal sources. Quantitative microbial source tracking (MST) approaches using fecal Bacteroidales and quantitative PCR (qPCR) assays to measure gene copies of host-specific 16S rRNA genetic markers are promising because they can allow for identifying and quantifying fecal loadings from a particular animal host and understanding the fate and transport of host-specific Bacteroidales over a range of conditions in water bodies. Similar to the case of traditional fecal indicator bacteria, a relatively long persistence of target DNA may hamper applied MST studies, if genetic markers cannot be linked to recent fecal pollution in water. We report a successful approach to removing the qPCR signal derived from free DNA and dead host-specific Bacteroidales cells by selectively binding the DNA and consequently inhibiting PCR amplification using light- activated propidium monoazide (PMA). Optimal PMA-qPCR conditions were determined as 100 µM of PMA concentration and a 10-min light exposure time at different solids concentrations in order to mimic a range of water samples. Under these conditions, PMA-qPCR resulted in the selective exclusion of DNA from heat- treated cells of non-culturable Bacteroidales in human feces and wastewater influent and effluent samples. Also, the persistence of feces-derived host-specific Bacteroidales DNA and their cells (determined by universal, human-, cow- and dog-specific Bacteroidales qPCR assays) in seawater was investigated in microcosms at environmental conditions. The average T99 (two log reduction) value for host-specific viable Bacteroidales cells was 28 h, whereas that for total host-specific Bacteroidales DNA was 177 h. Natural sunlight did not have a strong influence on the fate of fecal Bacteroidales cells and their DNA, presumably because the presence of oxygen significantly affected the viability and persistence of these obligate anaerobes. In conclusion, measuring Bacteroidales DNA in viable cells is recommended in applied MST studies because extracellular Bacteroidales DNA persists longer in the environment. The methods and results presented are helpful to improve the accuracy of MST applications, to develop a model of fate and transport of host-specific Bacteroidales, and to implement management practices to protect water quality.

Molecular detection of bovine coronavirus in a diarrhea outbreak in pasture-feeding Nellore steers in southern Brazil.

PubMed

Ribeiro, Juliane; Lorenzetti, Elis; Alfieri, Alice Fernandes; Alfieri, Amauri Alcindo

2016-03-01

Worldwide diarrhea outbreaks in cattle herds are more frequently detected in calves being that diarrhea outbreaks in adult cattle are not common. Winter dysentery (WD) is a bovine coronavirus (BCoV) enteric infection that is more reported in Northern hemisphere. Seasonal outbreaks of WD in adult cattle occur mainly in dairy cows. WD has not been described in beef cattle herds of tropical countries. This study describes the molecular detection of BCoV in a diarrhea outbreak in beef cattle steers (Nellore) raised on pasture in Parana, southern Brazil. During the outbreak, the farm had about 600 fattening steers. Watery and bloody diarrhea unresponsive to systemic broad-spectrum antibiotic therapy reveals a morbidity rate of approximately 15 %. The BCoV N gene was identified in 42.9 % (6/14) of the diarrheic fecal samples evaluated by semi-nested polymerase chain reaction (SN-PCR) technique. Other enteric microorganisms occasionally identified in adult cattle and evaluated in this study such as bovine groups A, B, and C rotavirus, bovine viral diarrhea virus, bovine torovirus, aichivirus B, and Eimeria sp. were not identified in the fecal samples. To the best knowledge of the authors, this is the first description of the BCoV diagnosis in fecal samples collected in a diarrhea outbreak in adult beef cattle grazing in the grass in a tropical country.

Effects of canine parvovirus strain variations on diagnostic test results and clinical management of enteritis in dogs.

PubMed

Markovich, Jessica E; Stucker, Karla M; Carr, Alaina H; Harbison, Carole E; Scarlett, Janet M; Parrish, Colin R

2012-07-01

To estimate the prevalence of canine parvovirus (CPV) strains among dogs with enteritis admitted to a referral hospital in the southwestern United States during an 11-month period and to compare diagnostic test results, disease severity, and patient outcome among CPV strains. Prospective observational study. 72 dogs with histories and clinical signs of parvoviral enteritis. For each dog, a fecal sample or rectal swab specimen was evaluated for CPV antigen via an ELISA. Subsequently, fecal samples (n = 42 dogs) and pharyngeal swab specimens (16) were obtained and tested for CPV antigen via an ELISA and CPV DNA via a PCR assay. For specimens with CPV-positive results via PCR assay, genetic sequencing was performed to identify the CPV strain. 56 dogs tested positive for CPV via ELISA or PCR assay. For 42 fecal samples tested via both ELISA and PCR assay, 27 had positive results via both assays, whereas 6 had positive PCR assay results only. Ten pharyngeal swab specimens yielded positive PCR assay results. Genetic sequencing was performed on 34 fecal or pharyngeal swab specimens that had CPV-positive PCR assay results; 25 (73.5%) were identified as containing CPV type-2c, and 9 (26.5%) were identified as containing CPV type-2b. No association was found between CPV strain and disease severity or clinical outcome. CPV type-2b and CPV type-2c posed similar health risks for dogs; therefore, genetic sequencing of CPV does not appear necessary for clinical management of infected patients. The diagnostic tests used could detect CPV type-2c.

Origin of fecal contamination in waters from contrasted areas: stanols as Microbial Source Tracking markers.

PubMed

Derrien, M; Jardé, E; Gruau, G; Pourcher, A M; Gourmelon, M; Jadas-Hécart, A; Pierson Wickmann, A C

2012-09-01

Improving the microbiological quality of coastal and river waters relies on the development of reliable markers that are capable of determining sources of fecal pollution. Recently, a principal component analysis (PCA) method based on six stanol compounds (i.e. 5β-cholestan-3β-ol (coprostanol), 5β-cholestan-3α-ol (epicoprostanol), 24-methyl-5α-cholestan-3β-ol (campestanol), 24-ethyl-5α-cholestan-3β-ol (sitostanol), 24-ethyl-5β-cholestan-3β-ol (24-ethylcoprostanol) and 24-ethyl-5β-cholestan-3α-ol (24-ethylepicoprostanol)) was shown to be suitable for distinguishing between porcine and bovine feces. In this study, we tested if this PCA method, using the above six stanols, could be used as a tool in "Microbial Source Tracking (MST)" methods in water from areas of intensive agriculture where diffuse fecal contamination is often marked by the co-existence of human and animal sources. In particular, well-defined and stable clusters were found in PCA score plots clustering samples of "pure" human, bovine and porcine feces along with runoff and diluted waters in which the source of contamination is known. A good consistency was also observed between the source assignments made by the 6-stanol-based PCA method and the microbial markers for river waters contaminated by fecal matter of unknown origin. More generally, the tests conducted in this study argue for the addition of the PCA method based on six stanols in the MST toolbox to help identify fecal contamination sources. The data presented in this study show that this addition would improve the determination of fecal contamination sources when the contamination levels are low to moderate. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats

PubMed Central

Rindt, Hansjorg; Grobman, Megan E.; Graham, Amber; Bishop, Kaitlin; Cohn, Leah A.; Reinero, Carol R.

2017-01-01

Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p < 0.001) with no significant difference (p = 0.180) in richness between time points. PCA revealed site-specific microbial communities in the feces, and upper and lower airways. In comparison, blood had an apparent compositional similarity with BALF with regard to a few dominant taxa, but shared more OTUs with feces. Samples clustered more by time than by individual, with OP swabs having subjectively greater variation than other samples. In summary, healthy cats have a rich and distinct lower airway microbiome with dynamic bacterial populations. The microbiome is likely to be altered by factors such as age, environmental influences, and disease states. Further data are necessary to determine how the distinct feline microbiomes from the upper and lower airways, feces and blood are established and evolve. These data are relevant for comparisons between healthy cats and cats with respiratory disease. PMID:28278278

Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats.

PubMed

Vientós-Plotts, Aida I; Ericsson, Aaron C; Rindt, Hansjorg; Grobman, Megan E; Graham, Amber; Bishop, Kaitlin; Cohn, Leah A; Reinero, Carol R

2017-01-01

Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p < 0.001) with no significant difference (p = 0.180) in richness between time points. PCA revealed site-specific microbial communities in the feces, and upper and lower airways. In comparison, blood had an apparent compositional similarity with BALF with regard to a few dominant taxa, but shared more OTUs with feces. Samples clustered more by time than by individual, with OP swabs having subjectively greater variation than other samples. In summary, healthy cats have a rich and distinct lower airway microbiome with dynamic bacterial populations. The microbiome is likely to be altered by factors such as age, environmental influences, and disease states. Further data are necessary to determine how the distinct feline microbiomes from the upper and lower airways, feces and blood are established and evolve. These data are relevant for comparisons between healthy cats and cats with respiratory disease.

Effect of Aging on the Composition of Fecal Microbiota in Donors for FMT and Its Impact on Clinical Outcomes.

PubMed

Anand, Rohit; Song, Yang; Garg, Shashank; Girotra, Mohit; Sinha, Amitasha; Sivaraman, Anita; Phillips, Laila; Dutta, Sudhir K

2017-04-01

Fecal microbiota transplantation (FMT) is emerging as an effective therapy for the treatment of recurrent Clostridium difficile infection (RCDI). Selecting an appropriate donor is vital to the success of FMT. However, the relationship between age of donors and the efficacy of FMT has not been examined to date. The aim of this study was to examine the effect of age of healthy donors on their fecal microbiota and assess the impact of these changes on the clinical efficacy of FMT. This IRB-approved prospective study enrolled donors who were deemed healthy for FMT after careful detailed screening for infectious diseases per institutional protocol. The study was conducted between January 2011 and October 2014. Fecal samples were processed and analyzed using 16S rRNA gene amplicon sequencing. Differences in relative abundance and diversity of the donor fecal microbiota were analyzed in donors above and below 60 years of age. Effect of fecal microbiota from donors of different age groups on the efficacy of FMT was also evaluated. Twenty-eight healthy human subjects from ages 20-82 years were enrolled as donors for FMT. All patients receiving FMT from their respective donors had resolution of RCDI symptoms and had a negative C. difficile toxin test 4-12 weeks after FMT. Genomic analysis showed that the relative abundance of phylum Actinobacteria and family Bifidobacteriaceae was reduced in the donors ≥60 years of age (p < 0.05). However, Bacteroidetes-to-Fermicutes ratio did not demonstrate a significant change between the two groups. Furthermore, microbial diversity did not change significantly with advancing age. These observations suggest that aging in healthy donors is associated with compositional alterations in the fecal microbiome without change in the overall microbial diversity. These changes do not seem to affect the clinical efficacy of FMT in RCDI patients over 12 months.

Hydrology, water quality, and potential alternatives for water-resources development in the Rio Majada and Rio Lapa basins near the Albergue Olimpico, southern Puerto Rico

USGS Publications Warehouse

Ramos-Gines, Orlando

1994-01-01

A water-resources investigation was conducted during 1989 in the Rio Lapa mountain basins in southern Puerto Rico, to define the hydrology, water quality, and to describe alternatives for additional water- resources supply. The total water budget for both surface- and ground-water resources in the study area was estimated to be 7,530 acre-feet per year for 1989. The water budget for the ground-water system, from which water needs are supplied in the study area, was estimated to be 2,760 acre-feet per year for 1989. Concentration of dissolved solids and fecal bacteria increased during the dry season as both streamflow and ground-water levels decreased. Water samples collected at two stream sites exceeded the recommended U.S. Environmental Protection Agency fecal bacteria concentration for natural water of 2,000 colonies per 100 milliliters during June to November 1989. Water samples obtained from a well in the Rio Lapa Valley exceeded the secondary drinking-water standard for dissolved solids of 500 milligrams per liter during four dry months. In addition, fecal bacteria concentrations at this water-supply well exceeded the primary fecal- bacteria drinking-water standard of 1 colony per 100 milliliter during June to October 1989. Existing water resources can probably be developed to meet additional demands of 110 acre-feet per year pro- jected for 1995. Storage of the surface-water runoff during the wet season and its gradual release to the study area could offset ground-water declines during the dry season. Ground-water withdrawals can be increased by the construction and use of low- capacity wells to reduce the amount of water lowing out of the study area.

A Validation of Extraction Methods for Noninvasive Sampling of Glucocorticoids in Free-Living Ground Squirrels

PubMed Central

Mateo, Jill M.; Cavigelli, Sonia A.

2008-01-01

Fecal hormone assays provide a powerful tool for noninvasive monitoring of endocrine status in wild animals. In this study we validated a protocol for extracting and measuring glucocorticoids in free-living and captive Belding’s ground squirrels (Spermophilus beldingi). We first compared two commonly used extraction protocols to determine which performed better with commercially available antibodies. We next verified the preferred extraction method by correlating circulating and fecal glucocorticoid measures from a group of individuals over time. For this comparison, we used both a cortisol and a corticosterone antibody to determine which had greater affinity to the fecal metabolites. Cortisol was the primary circulating glucocorticoid, but both hormones were present in well above detectable concentrations in the blood, which does not occur in other sciurids. In addition, the cortisol antibody showed greater binding with the fecal extracts than did the corticosterone antibody. Finally, we used adrenocorticotropic hormone and dexamethasone challenges to demonstrate that changes in adrenal functioning are reflected in changing fecal corticoid levels. These results suggest that our extraction protocol provides a fast, reliable assay of stress hormones in free-living ground squirrels without the confounding influence of short-term rises in glucocorticoid concentrations caused by handling and restraint stress and that it can facilitate ecological and evolutionary studies of stress in wild species. PMID:16228945

Fiber source and inclusion level affects characteristics of excreta from growing pigs

PubMed Central

Ndou, Saymore Petros; Bakare, Archibold Garikayi

2018-01-01

Objective The objective of the study was to determine the influence of varying fibrous diets on fecal characteristics of growing pigs. Methods A total of 104 pigs (initial weight 18±2.0 kg) were used in the study. They were housed in individual pens and fed on diets containing maize cob, grass hay, lucerne hay, maize stover, and sunflower husk. These fibers were included at 0, 80, 160, 240, 320 and 400 g/kg. Fecal and urine samples were collected. Results Fecal output was largest amongst pigs fed on diets containing grass hay and maize stover (p<0.05). Nitrogen content was highest in feces from pigs fed on sunflower husk (p< 0.05). Pigs fed on diets containing maize stover and maize cobs produced the largest concentrations of short chain fatty acids. Acetate concentration was high in feces of pigs fed maize stover than those fed grass hay and lucerne hay (p<0.05). As the level of fiber inclusion increased, fecal consistency and nitrogen content increased linearly (p<0.05). Urea nitrogen decreased as the inclusion level increased across all the fibers (p<0.05), with maize cobs containing the largest content of urea nitrogen. As dietary fiber content increased, fecal nitrogen content also increased (p<0.05). Conclusion It was concluded that different fiber sources influence fecal characteristics, thereby having different implications on pig waste management. It is vital to monitor fiber inclusion thresholds so as to easily manage environmental pollutants such as butyrate that contribute to odors. PMID:26954189

Occurrence of bacteriophages infecting Aeromonas, Enterobacter, and Klebsiella in water and association with contamination sources in Thailand.

PubMed

Wangkahad, Bencharong; Bosup, Suchada; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

2015-06-01

The co-residence of bacteriophages and their bacterial hosts in humans, animals, and environmental sources directed the use of bacteriophages to track the origins of the pathogenic bacteria that can be found in contaminated water. The objective of this study was to enumerate bacteriophages of Aeromonas caviae (AecaKS148), Enterobacter sp. (EnspKS513), and Klebsiella pneumoniae (KlpnKS648) in water and evaluate their association with contamination sources (human vs. animals). Bacterial host strains were isolated from untreated wastewater in Bangkok, Thailand. A double-layer agar technique was used to detect bacteriophages. All three bacteriophages were detected in polluted canal samples, with likely contamination from human wastewater, whereas none was found in non-polluted river samples. AecaKS148 was found to be associated with human fecal sources, while EnspKS513 and KlpnKS648 seemed to be equally prevalent in both human and animal fecal sources. Both bacteriophages were also present in polluted canals that could receive contamination from other fecal sources or the environment. In conclusion, all three bacteriophages were successfully monitored in Bangkok, Thailand. This study provided an example of bacteriophages for potential use as source identifiers of pathogen contamination. The results from this study will assist in controlling sources of pathogen contamination, especially in developing countries.

Tracing the Temporal and Spatial Variations in the Origin of Fecal Material in Three Oklahoma Watersheds Using Sterol Fingerprints

NASA Astrophysics Data System (ADS)

Lu, Y.; Philp, P. R.

2014-12-01

Organic wastes, in particular fecal material, are qualified as one of the major causes of water quality deterioration. Their accumulation in water bodies may increase algal proliferation and eutrophication and the number of pathogenic organisms, which are responsible for many intestinal diseases especially when the water is used for recreational activities and/or as a supply for drinking water. In order to estimate the risk level associated with primary body contact in recreational water bodies, enumeration of some specific micro-organisms, such as Enterococci and Escherichia coli, are commonly used. Sterol distributions can provide some relevant information on the origin of fecal material in water system, since they are ubiquitous organic compounds and their distributions in many warm-blooded animal feces can be used as evidence for their source. In this study, we monitored fecal material contamination in three Oklahoma watersheds based on sterol fingerprints over a one-year period (2012 ~ 2013). The sterols from sediments and water samples (sterols associated to suspended particles as well as free sterols in water) were recovered using sonication and solid phase extraction (SPE), respectively, using different organic solvents. They were then identified and quantified by gas chromatography - mass spectrometry (GC-MS) using an internal standard. The GC-MS was previously calibrated with a sterol mixture injected at different concentrations. Our primary results show that the concentration of total sterols generally increases from the Upper Canadian < Neosho Grand < Cimarron - Upper Arkansas Basins in Oklahoma. The fecal sterols commonly represent a small proportion (<15%) within the total sterols quantified in these three basins. Their distributions show a significant contribution from herbivore feces. By means of this monitoring, we are able to determine the presence of fecal contamination and provide a better understanding on the ability of using sterol fingerprints to determine the origin of the fecal contamination. Additionally, such a sampling strategy, over a one-year period at regular intervals, enable us to track the water contamination by feces according to the seasonal climatic variations such as drought or heavy rainfall events.

Characterization of Vancomycin-Resistant Enterococcus faecalis and Enterococcus faecium Isolated from Fresh Produces and Human Fecal Samples.

PubMed

Kim, Min-Chan; Cha, Min-Hyeok; Ryu, Jae-Gee; Woo, Gun-Jo

2017-04-01

Increased enterococcal infections in hospitals and multidrug-resistant and vancomycin-resistant enterococci (VRE) isolated from humans, animals, and food sources raised public health concern on the presence of VRE in multiple sources. We performed a comparative analysis of the antimicrobial resistance and genetics of VRE isolates derived from fresh produce and human fecal samples. Of 389 Enterococcus isolates, 8 fecal and 3 produce isolates were resistant to vancomycin and teicoplanin; all harbored vanA gene. The VRE isolates showed multidrug-resistant properties. The isolates from fresh produce in this study showed to have the common shared characteristics with the isolates from humans by the results of antimicrobial resistance, multilocus sequence typing, and Tn 1546 transposon analysis. Therefore, VRE isolates from fresh produce are likely related to VRE derived from humans. The results suggested that VRE may contaminate vegetables through the environment, and the contaminated vegetables could then act as a vehicle for human infections. Ongoing nationwide surveillance of antibiotic resistance and the promotion of the proper use of antibiotics are necessary.