Patterns of Extragenital Chlamydia and Gonorrhea in Women and Men Who Have Sex With Men Reporting a History of Receptive Anal Intercourse.

PubMed

Danby, Claire S; Cosentino, Lisa A; Rabe, Lorna K; Priest, Carol L; Damare, Khrystine C; Macio, Ingrid S; Meyn, Leslie A; Wiesenfeld, Harold C; Hillier, Sharon L

2016-02-01

Screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in men who have sex with men is risk based. Despite high frequencies of oral and receptive anal intercourse (RAI) among women, extragenital screening is not recommended. Women (n = 175) and men who have sex with men (n = 224) primarily recruited from a sexually transmitted infection clinic reporting a lifetime history of RAI completed a structured questionnaire and clinician-collected swab samples from the rectum, pharynx, vagina (women), and urine (men). CT and GC were detected using 2 commercial nucleic acid amplification tests (Aptima Combo 2; Hologic, Inc, Bedford, MA; Xpert CT/NG, Cepheid Innovation, Sunnyvale, CA). The median age of the population was 26 years, 62% were white, and 88% were enrolled from a sexually transmitted disease clinic. Men were more likely than women to have GC (22.8% vs. 3.4%) and CT (21.9% vs. 12.6%). In men versus women, GC was detected in 16.5% versus 2.3% of pharyngeal swabs, 11.6% versus 2.3% of rectal swabs, and 5.4% versus 2.9% of urine samples or vaginal swabs. C. trachomatis was detected in 2.2% versus 1.7% of pharyngeal swabs, 17.4% versus 11.4% of rectal swabs, and 4.5% versus 10.3% for urogenital sites in men versus women. Overall 79.6% of CT and 76.5% of GC in men and 18.2% of CT and 16.7% of GC in women were detected only in the pharynx or rectum. Reliance on urogenital screening alone misses most of GC and CT in men and more than 15% of infections in women reporting RAI.

Syndromic Surveillance: Adapting Innovations to Developing Settings

DTIC Science & Technology

2008-03-01

outbreak investigation was initiated, including rectal swab sampling of patients with watery diarrhea. Culture tests identified Vibrio cholerae in 44...GF, Kulldorff M, Madigan D, et al. (2007) Issues in applied statistics for public health bioterrorism Technical considerations • Harvesting data

The prevalence of lymphogranuloma venereum infection in men who have sex with men: results of a multicentre case finding study

PubMed Central

Ward, H; Alexander, S; Carder, C; Dean, G; French, P; Ivens, D; Ling, C; Paul, J; Tong, W; White, J; Ison, C A

2009-01-01

Objective: To determine the prevalence of lymphogranuloma venereum (LGV) and non-LGV associated serovars of urethral and rectal Chlamydia trachomatis (CT) infection in men who have sex with men (MSM). Design: Multicentre cross-sectional survey. Setting: Four genitourinary medicine clinics in the United Kingdom from 2006–7. Subjects: 4825 urethral and 6778 rectal samples from consecutive MSM attending for sexual health screening. Methods: Urethral swabs or urine and rectal swabs were tested for CT using standard nucleic acid amplification tests. Chlamydia-positive specimens were sent to the reference laboratory for serovar determination. Main outcome: Positivity for both LGV and non-LGV associated CT serovars; proportion of cases that were symptomatic. Results: The positivity (with 95% confidence intervals) in rectal samples was 6.06% (5.51% to 6.66%) for non-LGV CT and 0.90% (0.69% to 1.16%) for LGV; for urethral samples 3.21% (2.74% to 3.76%) for non-LGV CT and 0.04% (0.01% to 0.16%) for LGV. The majority of LGV was symptomatic (95% of rectal, one of two urethral cases); non-LGV chlamydia was mostly symptomatic in the urethra (68%) but not in the rectum (16%). Conclusions: Chlamydial infections are common in MSM attending for sexual health screening, and the majority are non-LGV associated serovars. We did not identify a large reservoir of asymptomatic LGV in the rectum or urethra. Testing for chlamydia from the rectum and urethra should be included for MSM requesting a sexual health screen, but serovar-typing is not indicated in the absence of symptoms. We have yet to identify the source of most cases of LGV in the UK. PMID:19221105

Evaluation of Presto(plus) assay and LightMix kit Trichomonas vaginalis assay for detection of Trichomonas vaginalis in dry vaginal swabs.

PubMed

de Waaij, Dewi J; Ouburg, Sander; Dubbink, Jan Henk; Peters, Remco P H; Morré, Servaas A

2016-08-01

This is an evaluation study of the Presto(plus) Assay for T. vaginalis by comparing to the TIB MOLBIOL LightMix Kit Trichomonas vaginalis Assay using 615 dry collected vaginal and rectal swabs. Discordant samples were analyzed by the Qiagen® Microbial DNA qPCR for TV Assay. Both assays showed comparable performances (McNemar p>0.05). Copyright © 2016 Elsevier B.V. All rights reserved.

Cholera Outbreaks in Urban Bangladesh In 2011

PubMed Central

Haque, Farhana; Hossain, M. Jahangir; Kundu, Subodh Kumar; Naser, Abu Mohd.; Rahman, Mahmudur; Luby, Stephen P.

2015-01-01

Background In 2011, a multidisciplinary team investigated two diarrhoea outbreaks affecting urban Bangladeshi communities from the districts of Bogra and Kishorganj to identify etiology, pathways of transmission, and factors contributing to these outbreaks. Methods We defined case-patients with severe diarrhoea as residents from affected communities admitted with ≥3 loose stools per day. We listed case-patients, interviewed and examined them, and collected rectal swabs. We visited the affected communities to explore the water and sanitation infrastructure. We tested the microbial load of water samples from selected case household taps, tube wells, and pump stations. We conducted anthropological investigations to understand community perceptions regarding the outbreaks. Results We identified 21 case-patients from Bogra and 84 from Kishorganj. The median age in Bogra was 23 years, and 21 years in Kishorganj. There were no reported deaths. We isolated Vibrio in 29% (5/17) of rectal swabs from Bogra and in 40% (8/20) from Kishorganj. We found Vibrio in 1/8 tap water samples from Bogra and in both of the samples from Kishorganj. We did not find Vibrio in water samples from pumps or tube wells in either outbreak. Ground water extracted through deep tube wells was supplied intermittently through interconnected pipes without treatment in both areas. We found leakages in the water pipes in Bogra, and in Kishorganj water pipes passed through open sewers. Conclusion The rapid onset of severe diarrhoea predominantly affecting adults and the isolation of cholera in rectal swabs confirmed that these outbreaks were caused by Vibrio cholerae. The detection of Vibrio in water samples organisms from taps but not from pumps or tube wells, suggested contamination within the pipes. Safe water provision is difficult in municipalities where supply is intermittent, and where pipes commonly leak. Research to develop and evaluate water purification strategies could identify appropriate approaches for ensuring safe drinking water in resource-poor cities. PMID:26702366

Cholera Outbreaks in Urban Bangladesh In 2011.

PubMed

Haque, Farhana; Hossain, M Jahangir; Kundu, Subodh Kumar; Naser, Abu Mohd; Rahman, Mahmudur; Luby, Stephen P

In 2011, a multidisciplinary team investigated two diarrhoea outbreaks affecting urban Bangladeshi communities from the districts of Bogra and Kishorganj to identify etiology, pathways of transmission, and factors contributing to these outbreaks. We defined case-patients with severe diarrhoea as residents from affected communities admitted with ≥3 loose stools per day. We listed case-patients, interviewed and examined them, and collected rectal swabs. We visited the affected communities to explore the water and sanitation infrastructure. We tested the microbial load of water samples from selected case household taps, tube wells, and pump stations. We conducted anthropological investigations to understand community perceptions regarding the outbreaks. We identified 21 case-patients from Bogra and 84 from Kishorganj. The median age in Bogra was 23 years, and 21 years in Kishorganj. There were no reported deaths. We isolated Vibrio in 29% (5/17) of rectal swabs from Bogra and in 40% (8/20) from Kishorganj. We found Vibrio in 1/8 tap water samples from Bogra and in both of the samples from Kishorganj. We did not find Vibrio in water samples from pumps or tube wells in either outbreak. Ground water extracted through deep tube wells was supplied intermittently through interconnected pipes without treatment in both areas. We found leakages in the water pipes in Bogra, and in Kishorganj water pipes passed through open sewers. The rapid onset of severe diarrhoea predominantly affecting adults and the isolation of cholera in rectal swabs confirmed that these outbreaks were caused by Vibrio cholerae . The detection of Vibrio in water samples organisms from taps but not from pumps or tube wells, suggested contamination within the pipes. Safe water provision is difficult in municipalities where supply is intermittent, and where pipes commonly leak. Research to develop and evaluate water purification strategies could identify appropriate approaches for ensuring safe drinking water in resource-poor cities.

[Surveillance on severe acute respiratory syndrome associated coronavirus in animals at a live animal market of Guangzhou in 2004].

PubMed

Wang, Ming; Jing, Huai-qi; Xu, Hui-fang; Jiang, Xiu-gao; Kan, Biao; Liu, Qi-yong; Wan, Kang-lin; Cui, Bu-yun; Zheng, Han; Cui, Zhi-gang; Yan, Mei-ying; Liang, Wei-li; Wang, Hong-xia; Qi, Xiao-bao; Li, Zhen-jun; Li, Ma-chao; Chen, Kai; Zhang, En-min; Zhang, Shou-yin; Hai, Rong; Yu, Dong-zheng; Xu, Jian-guo

2005-02-01

To study the prevalence of severe acute respiratory syndrome coronavirus (SARS-CoV) like virus in animals at a live animal market of Guanzhou in 2004 before and after culling of wild animal action taken by the local authority, in order to predict the re-emerging of SARS from animal originals in this region. Animals at live animal market were sampled for rectal and throat swabs in triplicate. A single step realtime reverse transcription-polymerase chain reaction (RT-PCR) diagnostic kit was performed for screening SARS-CoV like virus, the manual nested RT- PCR and DNA sequencing were performed for confirmation. Only specimens which tested positive for both of the N and P genes by nested RT-PCR were scored as positive. In 31 animals sampled in January 5 2004 before culling of wild animals at Guangdong Province, including 20 cats (Felis catus), 5 red fox (Vulpes vulpes) and 6 Lesser rice field rats (Rattus losea), 8 (25.8%) animals were tested positive for SARS-CoV like virus by RT-PCR methods, of which 4 cats, 3 red fox and one Lesser rice field rats were included. However, two weeks after culling of animals and disinfection of the market were implemented, in 119 animals sampled in January 20 2004, including 6 rabbits (Oryctolagus cuniculus), 13 cats, 46 red jungle fowl (Gallus gallus), 13 spotbill duck (Anas platyrhynchos), 10 greylag goose (Anser anser), 31 Chinese francolin (Franclinus pintadeanus), only rectal swab from one greylag goose was tested positive for SARS-CoV like virus. Furthermore, in 102 animals that including 14 greylag gooses, 3 cats, 5 rabbits, 9 spotbill duck (Anaspoecilorhyncha), 2 Chinese francolin (Franclinus pintadeanus), 8 common pheasant (Phasianus colchicus), 6 pigeons, 9 Chinese muntjac (Muntiacus reevesi), 19 wild boar (Sus scrofa), 16 Lesser rice field rats, 5 dogs, 1 mink (Mustela vison), 3 goats, 2 green peafowl (Pavo muticus) sampled in April, May, June, July, August and November, only rectal swab from one pig was tested positive. However, of 12 and 10 palm civets sampled in November and December including five of which had been at the live animals market for 2 days, none of them was tested positive. This findings revealed that animals being sampled in April, May, June, July, August and November of 2004, only one rectal swab from a pig was tested positive as SARS-CoV like virus, much lower than the results from the previous year, suggesting that the possibility of re-emerging of human infection from animal origins is low for the winter of 2004-2005.

Effects of Sampling Conditions and Environmental Factors on Fecal Volatile Organic Compound Analysis by an Electronic Nose Device

PubMed Central

Berkhout, Daniel J. C.; Benninga, Marc A.; van Stein, Ruby M.; Brinkman, Paul; Niemarkt, Hendrik J.; de Boer, Nanne K. H.; de Meij, Tim G. J.

2016-01-01

Prior to implementation of volatile organic compound (VOC) analysis in clinical practice, substantial challenges, including methodological, biological and analytical difficulties are faced. The aim of this study was to evaluate the influence of several sampling conditions and environmental factors on fecal VOC profiles, analyzed by an electronic nose (eNose). Effects of fecal sample mass, water content, duration of storage at room temperature, fecal sample temperature, number of freeze–thaw cycles and effect of sampling method (rectal swabs vs. fecal samples) on VOC profiles were assessed by analysis of totally 725 fecal samples by means of an eNose (Cyranose320®). Furthermore, fecal VOC profiles of totally 1285 fecal samples from 71 infants born at three different hospitals were compared to assess the influence of center of origin on VOC outcome. We observed that all analyzed variables significantly influenced fecal VOC composition. It was feasible to capture a VOC profile using rectal swabs, although this differed significantly from fecal VOC profiles of similar subjects. In addition, 1285 fecal VOC-profiles could significantly be discriminated based on center of birth. In conclusion, standardization of methodology is necessary before fecal VOC analysis can live up to its potential as diagnostic tool in clinical practice. PMID:27886068

Carriage of group B streptococcus in pregnant women from Oxford, UK

PubMed Central

Jones, N; Oliver, K; Jones, Y; Haines, A; Crook, D

2006-01-01

Objective To investigate asymptomatic vagino‐rectal carriage of group B streptococcus (GBS) in pregnant women. Methods Women in the final trimester of pregnancy were recruited. A single vagino‐rectal swab was taken, with consent, for culture of GBS. Two microbiological methods for isolation of GBS from vagino‐ractal swabs were compared. The distribution of capsular serotypes of the GBS identified was determined. Epidemiological data for a subset (n = 167) of the pregnant women participating were examined. Results 21.3% were colonised vagino‐rectally with GBS. Risk factors for neonatal GBS disease (maternal fever, prolonged rupture of membranes, and preterm delivery) were present in 34 of 167 women (20.4%), and the presence of these factors correlated poorly with GBS carriage. Capsular serotypes III (26.4%), IA (25.8%), V (18.9%), and IB (15.7%) were prevalent in the GBS isolates. Selective broth culture of vagino‐rectal swabs was superior to selective plate culture, but the combination of both methods was associated with increased detection of GBS (7.5%). An algorithm for the identification of GBS from vagino‐rectal swabs was developed. Conclusions GBS carriage is prevalent in pregnant women in Oxfordshire, UK. The poor correlation between risk factors and GBS carriage requires further investigation in larger groups, given that the identification of these surrogate markers is recommended to guide administration of intrapartum antibiotic prophylaxis by the Royal College of Obstetricians of the UK. A selective broth culture detected more GBS carriers than a selective plate culture. PMID:16473927

Detection of Campylobacter jejuni in rectal swab samples from Rousettus amplexicaudatus in the Philippines.

PubMed

Hatta, Yuki; Omatsu, Tsutomu; Tsuchiaka, Shinobu; Katayama, Yukie; Taniguchi, Satoshi; Masangkay, Joseph S; Puentespina, Roberto; Eres, Eduardo; Cosico, Edison; Une, Yumi; Yoshikawa, Yasuhiro; Maeda, Ken; Kyuwa, Shigeru; Mizutani, Tetsuya

2016-09-01

Bats are the second diversity species of mammals and widely distributed in the world. They are thought to be reservoir and vectors of zoonotic pathogens. However, there is scarce report of the evidence of pathogenic bacteria kept in bats. The precise knowledge of the pathogenic bacteria in bat microbiota is important for zoonosis control. Thus, metagenomic analysis targeting the V3-V4 region of the 16S rRNA of the rectal microbiota in Rousettus amplexicaudatus was performed using high throughput sequencing. The results revealed that 103 genera of bacteria including Camplyobacter were detected. Campylobacter was second predominant genus, and Campylobacter coli and Campylobacter jejuni were identified in microbiome of R. amplexicaudatus. Campylobacteriosis is one of the serious bacterial diarrhea in human, and the most often implicated species as the causative agent of campylobacteriosis is C. jejuni. Therefore, we investigated the prevalence of C. jejuni in 91 wild bats with PCR. As a result of PCR assay targeted on 16S-23S intergenic spacer, partial genome of C. jejuni was detected only in five R. amplexicaudatus. This is the first report that C. jejuni was detected in bat rectal swab samples. C. jejuni is the most common cause of campylobacteriosis in humans, transmitted through water and contact with livestock animals. This result indicated that R. amplexicaudatus may be a carrier of C. jejuni.

Self-Collected versus Clinician-Collected Sampling for Chlamydia and Gonorrhea Screening: A Systemic Review and Meta-Analysis

PubMed Central

Lunny, Carole; Taylor, Darlene; Hoang, Linda; Wong, Tom; Gilbert, Mark; Lester, Richard; Krajden, Mel; Ogilvie, Gina

2015-01-01

Background The increases in STI rates since the late 1990s in Canada have occurred despite widespread primary care and targeted public health programs and in the setting of universal health care. More innovative interventions are required that would eliminate barriers to STI testing such as internet-based or mail-in home and community service testing for patients that are hard to reach, who refuse to go for clinician-based testing, or who decline an examination. Jurisdictions such as New Zealand and some American states currently use self-collected sampling, but without the required evidence to determine whether self-collected specimens are as accurate as clinician-collected specimens in terms of chlamydia and gonorrhea diagnostic accuracy. The objective of the review is to compare self-collected vaginal, urine, pharyngeal and rectal samples to our reference standard - clinician-collected cervical, urethral, pharyngeal and rectal sampling techniques to identify a positive specimen using nucleic acid amplification test assays. Methods The hierarchical summary receiver operating characteristic and the fixed effect models were used to assess the accuracy of comparable specimens that were collected by patients compared to clinicians. Sensitivity and specificity estimates with 95% confidence intervals (CI) were reported as our main outcome measures. Findings We included 21 studies based on over 6100 paired samples. Fourteen included studies examined chlamydia only, 6 compared both gonorrhea and chlamydia separately in the same study, and one examined gonorrhea. The six chlamydia studies comparing self-collection by vaginal swab to a clinician-collected cervical swab had the highest sensitivity (92%, 95% CI 87-95) and specificity (98%, 95% CI 97-99), compared to other specimen-types (urine/urethra or urine/cervix). Six studies compared urine self-samples to urethra clinician-collected samples in males and produced a sensitivity of 88% (95% CI 83-93) and a specificity of 99% (95% CI 0.94-0.99). Taking into account that urine samples may be less sensitive than cervical samples, eight chlamydia studies that compared urine self-collected verses clinician-collected cervical samples had a sensitivity of 87% (95% CI 81-91) and high specificity of 99% (95% CI 0.98-1.00). For gonorrhea testing, self-collected urine samples compared to clinician-collected urethra samples in males produced a sensitivity of 92% (95% CI 83-97) and specificity of 99% (95% CI 0.98-1.00). Conclusion The sensitivity and specificity of vaginal self-collected swabs compared to swabs collected by clinicians supports the use of vaginal swab as the recommended specimen of choice in home-based screening for chlamydia and gonorrhea. Urine samples for gonorrhea collected by men had comparably high sensitivity and specificity, so could be recommended as they can be left at room temperature for several days, allowing for the possibility of mail-in home-based testing. In populations that may not go for testing at all, do not have the option of clinical testing, or who refuse a clinical examination, self-collected screening would be a good alternative. We recommend that guidelines on how to self-collect gonorrhea and chlamydia urine, vaginal, rectal and pharyngeal specimens be published. PMID:26168051

Rectal Chlamydia in heterosexual women: more questions than answers.

PubMed

Ding, Alvin; Challenor, Rachel

2014-07-01

The aim of this study was to observe the proportion of concurrent rectal Chlamydia (RCt) infection in women who have cervical Chlamydia (CCt) and to observe whether there was any correlation with receptive anal intercourse (RAI). Untreated CCt-positive women were invited to take part. Women chose either to have a physician-collected or self-taken rectal swab. Treatment was then commenced. 17 samples were physician-collected and 80 were self-collected. 75/97 (77.3%, 95% Confidence Interval [95%CI] 69.0-85.7%) were RCt positive. 25/97 (25.8%, 95%CI 17.1-34.5%) reported RAI. There was no difference in the positivity rate whether RAI was reported (80%) or not (76%) (P = 0.71); or whether swabs were physician-collected (65%) or self-taken (80%) (P = 0.17). Only one of those with RCt reported rectal symptoms. One woman had concurrent gonococcal infection. 34/97 (35%) had a history of past sexually transmitted infections. Verified contact attendance was 0.52 and 72% of verified contacts were Chlamydia positive. Reported RAI may not be helpful in guiding RCt testing. RCt infection in women may be more prevalent than previously thought. We do not know whether RCt infections are clinically significant or whether they may act as a reservoir for re-infection. RCt infections in women require further study. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Comparison of different sampling techniques and of different culture methods for detection of group B streptococcus carriage in pregnant women.

PubMed

El Aila, Nabil A; Tency, Inge; Claeys, Geert; Saerens, Bart; Cools, Piet; Verstraelen, Hans; Temmerman, Marleen; Verhelst, Rita; Vaneechoutte, Mario

2010-09-29

Streptococcus agalactiae (group B streptococcus; GBS) is a significant cause of perinatal and neonatal infections worldwide. To detect GBS colonization in pregnant women, the CDC recommends isolation of the bacterium from vaginal and anorectal swab samples by growth in a selective enrichment medium, such as Lim broth (Todd-Hewitt broth supplemented with selective antibiotics), followed by subculture on sheep blood agar. However, this procedure may require 48 h to complete. We compared different sampling and culture techniques for the detection of GBS. A total of 300 swabs was taken from 100 pregnant women at 35-37 weeks of gestation. For each subject, one rectovaginal, one vaginal and one rectal ESwab were collected. Plating onto Columbia CNA agar (CNA), group B streptococcus differential agar (GBSDA) (Granada Medium) and chromID Strepto B agar (CA), with and without Lim broth enrichment, were compared. The isolates were confirmed as S. agalactiae using the CAMP test on blood agar and by molecular identification with tDNA-PCR or by 16S rRNA gene sequence determination. The overall GBS colonization rate was 22%. GBS positivity for rectovaginal sampling (100%) was significantly higher than detection on the basis of vaginal sampling (50%), but not significantly higher than for rectal sampling (82%). Direct plating of the rectovaginal swab on CNA, GBSDA and CA resulted in detection of 59, 91 and 95% of the carriers, respectively, whereas subculturing of Lim broth yielded 77, 95 and 100% positivity, respectively. Lim broth enrichment enabled the detection of only one additional GBS positive subject. There was no significant difference between GBSDA and CA, whereas both were more sensitive than CNA. Direct culture onto GBSDA or CA (91 and 95%) detected more carriers than Lim broth enrichment and subculture onto CNA (77%). One false negative isolate was observed on GBSDA, and three false positives on CA. In conclusion, rectovaginal sampling increased the number GBS positive women detected, compared to vaginal and/or rectal sampling. Direct plating on CA and/or GBSDA provided rapid detection of GBS that was at least as sensitive and specific as the CDC recommended method of Lim broth subcultured onto non chromogenic agar.

Discovery of a novel Parvovirinae virus, porcine parvovirus 7, by metagenomic sequencing of porcine rectal swabs.

PubMed

Palinski, Rachel M; Mitra, Namita; Hause, Ben M

2016-08-01

Parvoviruses are a diverse group of viruses containing some of the smallest known species that are capable of infecting a wide range of animals. Metagenomic sequencing of pooled rectal swabs from adult pigs identified a 4103-bp contig consisting of two major open reading frames encoding proteins of 672 and 469 amino acids (aa) in length. BLASTP analysis of the 672-aa protein found 42.4 % identity to fruit bat (Eidolon helvum) parvovirus 2 (EhPV2) and 37.9 % to turkey parvovirus (TuPV) TP1-2012/HUN NS1 proteins. The 469-aa protein had no significant similarity to known proteins. Genetic and phylogenetic analyses suggest that PPV7, EhPV2, and TuPV represent a novel genus in the family Parvoviridae. Quantitative PCR screening of 182 porcine diagnostic samples found a total of 16 positives (8.6 %). Together, these data suggest that PPV7 is a highly divergent novel parvovirus prevalent within the US swine.

Molecular and serological surveillance of canine enteric viruses in stray dogs from Vila do Maio, Cape Verde

PubMed Central

2014-01-01

Background Infections caused by canine parvovirus, canine distemper virus and canine coronavirus are an important cause of mortality and morbidity in dogs worldwide. Prior to this study, no information was available concerning the incidence and prevalence of these viruses in Cape Verde archipelago. Results To provide information regarding the health status of the canine population in Vila do Maio, Maio Island, Cape Verde, 53 rectal swabs were collected from 53 stray dogs during 2010 and 93 rectal swabs and 88 blood samples were collected from 125 stray dogs in 2011. All rectal swabs (2010 n = 53; 2011 n = 93) were analysed for the presence of canine parvovirus, canine distemper virus and canine coronavirus nucleic acids by quantitative PCR methods. Specific antibodies against canine distemper virus and canine parvovirus were also assessed (2011 n = 88). From the 2010 sampling, 43.3% (23/53) were positive for canine parvovirus DNA, 11.3% (6/53) for canine distemper virus RNA and 1.9% (1/53) for canine coronavirus RNA. In 2011, the prevalence values for canine parvovirus and canine coronavirus were quite similar to those from the previous year, respectively 44.1% (41/93), and 1.1% (1/93), but canine distemper virus was not detected in any of the samples analysed (0%, 0/93). Antibodies against canine parvovirus were detected in 71.6% (63/88) blood samples and the seroprevalence found for canine distemper virus was 51.1% (45/88). Conclusions This study discloses the data obtained in a molecular and serological epidemiological surveillance carried out in urban populations of stray and domestic animals. Virus transmission and spreading occurs easily in large dog populations leading to high mortality rates particularly in unvaccinated susceptible animals. In addition, these animals can act as disease reservoirs for wild animal populations by occasional contact. Identification of susceptible wildlife of Maio Island is of upmost importance to evaluate the risk of pathogen spill over from domestic to wild animals in Cape Verde and to evaluate the associated threat to the wild susceptible species. PMID:24755118

Molecular and serological surveillance of canine enteric viruses in stray dogs from Vila do Maio, Cape Verde.

PubMed

Castanheira, Pedro; Duarte, Ana; Gil, Solange; Cartaxeiro, Clara; Malta, Manuel; Vieira, Sara; Tavares, Luis

2014-04-23

Infections caused by canine parvovirus, canine distemper virus and canine coronavirus are an important cause of mortality and morbidity in dogs worldwide. Prior to this study, no information was available concerning the incidence and prevalence of these viruses in Cape Verde archipelago. To provide information regarding the health status of the canine population in Vila do Maio, Maio Island, Cape Verde, 53 rectal swabs were collected from 53 stray dogs during 2010 and 93 rectal swabs and 88 blood samples were collected from 125 stray dogs in 2011. All rectal swabs (2010 n = 53; 2011 n = 93) were analysed for the presence of canine parvovirus, canine distemper virus and canine coronavirus nucleic acids by quantitative PCR methods. Specific antibodies against canine distemper virus and canine parvovirus were also assessed (2011 n = 88).From the 2010 sampling, 43.3% (23/53) were positive for canine parvovirus DNA, 11.3% (6/53) for canine distemper virus RNA and 1.9% (1/53) for canine coronavirus RNA. In 2011, the prevalence values for canine parvovirus and canine coronavirus were quite similar to those from the previous year, respectively 44.1% (41/93), and 1.1% (1/93), but canine distemper virus was not detected in any of the samples analysed (0%, 0/93). Antibodies against canine parvovirus were detected in 71.6% (63/88) blood samples and the seroprevalence found for canine distemper virus was 51.1% (45/88). This study discloses the data obtained in a molecular and serological epidemiological surveillance carried out in urban populations of stray and domestic animals. Virus transmission and spreading occurs easily in large dog populations leading to high mortality rates particularly in unvaccinated susceptible animals. In addition, these animals can act as disease reservoirs for wild animal populations by occasional contact. Identification of susceptible wildlife of Maio Island is of upmost importance to evaluate the risk of pathogen spill over from domestic to wild animals in Cape Verde and to evaluate the associated threat to the wild susceptible species.

Canis lupus familiaris involved in the transmission of pathogenic Yersinia spp. in China.

PubMed

Wang, Xin; Liang, Junrong; Xi, Jinxiao; Yang, Jinchuan; Wang, Mingliu; Tian, Kecheng; Li, Jicheng; Qiu, Haiyan; Xiao, Yuchun; Duan, Ran; Yang, Haoshu; Li, Kewei; Cui, Zhigang; Qi, Meiying; Jing, Huaiqi

2014-08-06

To investigate canines carrying pathogens associated with human illness, we studied their roles in transmitting and maintaining pathogenic Yersinia spp. We examined different ecological landscapes in China for the distribution of pathogenic Yersinia spp. in Canis lupus familiaris, the domestic dog. The highest number of pathogenic Yersinia enterocolitica was shown from the tonsils (6.30%), followed by rectal swabs (3.63%) and feces (1.23%). Strains isolated from plague free areas for C. lupus familiaris, local pig and diarrhea patients shared the same pulsed-field gel electrophoresis (PFGE) pattern, indicating they may be from the same clone and the close transmission source of pathogenic Y. enterocolitica infections in these areas. Among 226 dogs serum samples collected from natural plague areas of Yersinia pestis in Gansu and Qinghai Provinces, 49 were positive for F1 antibody, while the serum samples collected from plague free areas were all negative, suggested a potential public health risk following exposure to dogs. No Y. enterocolitica or Yersinia pseudotuberculosis was isolated from canine rectal swabs in natural plague areas. Therefore, pathogenic Yersinia spp. may be regionally distributed in China. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular analysis of partial VP-2 gene amplified from rectal swab samples of diarrheic dogs in Pakistan confirms the circulation of canine parvovirus genetic variant CPV-2a and detects sequences of feline panleukopenia virus (FPV).

PubMed

Ahmed, Nisar; Riaz, Adeel; Zubair, Zahra; Saqib, Muhammad; Ijaz, Sehrish; Nawaz-Ul-Rehman, Muhammad Shah; Al-Qahtani, Ahmed; Mubin, Muhammad

2018-03-15

The infection in dogs due to canine parvovirus (CPV), is a highly contagious one with high mortality rate. The present study was undertaken for a detailed genetic analysis of partial VP2 gene i.e., 630 bp isolated from rectal swab samples of infected domestic and stray dogs from all areas of district Faisalabad. Monitoring of viruses is important, as continuous prevalence of viral infection might be associated with emergence of new virulent strains. In the present study, 40 rectal swab samples were collected from diarrheic dogs from different areas of district Faisalabad, Pakistan, in 2014-15 and screened for the presence of CPV by immunochromatography. Most of these dogs were stray dogs showing symptoms of diarrhea. Viral DNA was isolated and partial VP2 gene was amplified using gene specific primer pair Hfor/Hrev through PCR. Amplified fragments were cloned in pTZ57R/T (Fermentas) and completely sequenced. Sequences were analyzed and assembled by the Lasergene DNA analysis package (v8; DNAStar Inc., Madison, WI, USA). The results with immunochromatography showed that 33/40 (82%) of dogs were positive for CPV. We were able to amplify a fragment of 630 bp from 25 samples. In 25 samples the sequences of CPV-2a were detected showing the amino acid substitution Ser297Ala and presence of amino acid (426-Asn) in partial VP2 protein. Interestingly the BLAST analysis showed the of feline panleukopenia virus (FPV) sequences in 3 samples which were already positive for new CPV-2a, with 99% sequence homology to other FPV sequences present in GenBank. Phylogenetic analysis showed clustering of partial CPV-VP-2 gene with viruses from China, India, Japan and Uruguay identifying a new variant, whereas the 3 FPV sequences showed immediate ancestral relationship with viruses from Portugal, South Africa and USA. Interesting observation was that CPV are clustering away from the commercial vaccine strains. In this work we provide a better understanding of CPV prevailing in Pakistan at molecular level. The detection of FPV could be a case of real co-infection or a case of dual presence, due to ingestion of contaminated food.

Prevalence of fluoroquinolone-resistant rectal flora in patients undergoing transrectal ultrasound-guided prostate needle biopsy: A prospective multicenter study.

PubMed

Chung, Ho Seok; Hwang, Eu Chang; Yu, Ho Song; Jung, Seung Il; Lee, Sun Ju; Lim, Dong Hoon; Cho, Won Jin; Choe, Hyun Sop; Lee, Seung-Ju; Park, Sung Woon

2018-03-01

To estimate the prevalence of fluoroquinolone-resistant rectal flora in patients undergoing transrectal ultrasound-guided prostate needle biopsy and to identify the high-risk groups. From January 2015 to March 2016, rectal swabs of 557 men who underwent transrectal ultrasound-guided prostate needle biopsy were obtained from five institutions. Clinical variables, including demographics, rectal swab culture results and infectious complications, were evaluated. Univariable and multivariable analyses were used to identify the risk factors for fluoroquinolone resistance of rectal flora and infectious complications. The incidence of fluoroquinolone-resistant and extended-spectrum beta-lactamase production was 48.1 and 11.8%, respectively. The most common fluoroquinolone-resistant bacteria was Escherichia coli (81% of total fluoroquinolone-resistant bacteria, 39% of total rectal flora), and 16 (2.9%) patients had infectious complications. Univariable and multivariable analysis of clinical parameters affecting fluoroquinolone resistance showed no factor associated with fluoroquinolone resistance of rectal flora. The clinical parameter related to infectious complications after prostate biopsy was a history of operation within 6 months (relative risk 6.60; 95% confidence interval 1.99-21.8, P = 0.002). These findings suggest that a risk-based approach by history taking cannot predict antibiotic resistance of rectal flora, and physicians should consider targeted antibiotic prophylaxis or extended antibiotic prophylaxis for Korean patients undergoing transrectal ultrasound-guided prostate biopsy because of high antibiotic resistance of rectal flora. © 2017 The Japanese Urological Association.

Lymphogranuloma venereum proctitis

PubMed Central

Harrison, Tucker; Stroup, Jeff

2016-01-01

We describe a 60-year-old man who presented with rectal pain and bleeding of a month's duration. His presentation was highly suggestive of lymphogranuloma venereum (LGV) proctitis. Nucleic acid amplification for chlamydia and gonorrhea via rectal swab revealed evidence supportive of anorectal chlamydia. Treatment with doxycycline resulted in complete resolution of his symptoms. PMID:27695183

Trial Comparing a Combined Regimen of Amikacin and Ciprofloxacin to Ciprofloxacin Alone as Transrectal Prostate Biopsy Prophylaxis in the Era of High Fluoroquinolone-Resistant Rectal Flora.

PubMed

Son, Kyung Chul; Chung, Ho Seok; Jung, Seung Il; Kim, Myung Soo; Hwang, Eu Chang; Kim, Jin Woong; Kwon, Dong Deuk

2018-04-09

To investigate whether addition of amikacin to fluoroquinolone (FQ) antimicrobial prophylaxis reduces infections after transrectal ultrasound-guided prostate biopsy (TRUSPB). A total of 503 patients undergoing rectal swab were divided into three groups. Patients with FQ-sensitive rectal flora (group 1, n = 248) were administered ciprofloxacin before TRUSPB, and patients with FQ-resistant rectal flora were either administered ciprofloxacin (group 2, n = 97) or amikacin and ciprofloxacin (group 3, n = 158) before TRUSPB. Based on the rectal swab, FQ resistance was 54.9%, and extended-spectrum β-lactamase (ESBL) positivity was 17.2%. The incidence of infectious complication in group 1 was 1.6%. Groups 2 and 3, with FQ-resistant rectal flora, tended to have increased infectious complications (5.2% and 4.4%, respectively) but the difference between those results is not statistically significant. The most common pathogens of infectious complications in patients with FQ-resistant rectal flora were FQ-resistant and ESBL-producing Escherichia coli. E. coli pathogens isolated in Group 3 were amikacin-susceptible species. The operation history and ESBL positivity of rectal flora increased the incidence of infectious complications (odds ratio [OR] = 3.68; P = 0.035 and OR = 4.02; P = 0.008, respectively). DM and antibiotics exposure were risk factors for FQ resistance (OR = 2.19; P = 0.002) and ESBL positivity of rectal flora (OR = 2.96; P = 0.005), respectively. Addition of amikacin to ciprofloxacin prophylaxis could not reduce infectious complications in patients with FQ-resistant rectal flora. Despite the amikacin sensitivity of infectious complications, single-dose amikacin addition to ciprofloxacin prophylaxis has limitations. © 2018 The Korean Academy of Medical Sciences.

Evaluation of BBL CHROMagar VanRE for detection of vancomycin-resistant Enterococci in rectal swab specimens.

PubMed

Stamper, Paul D; Shulder, Stephanie; Bekalo, Pearl; Manandhar, Deepika; Ross, Tracy L; Speser, Sharon; Kingery, Julie; Carroll, Karen C

2010-11-01

A study was performed on 517 surveillance rectal swabs to evaluate a selective and differential chromogenic medium, the BBL CHROMagar VanRE (CVRE), which enables recovery and identification of VanA- and VanB-containing Enterococcus faecium (ENFM) and Enterococcus faecalis (ENFS) isolates. Compared to BBL Enterococcosel agar, a bile-esculin-azide-vancomycin (BEAV) agar, the initial overall sensitivity, specificity, and positive and negative predictive values of CVRE for the detection of vancomycin-resistant ENFM and ENFS were 99.1% and 94.8% and 84.2% and 99.7%, respectively. Among our patient population, more vancomycin-resistant enterococci (VRE) were recovered with CVRE than BEAV.

Evaluation of BBL CHROMagar VanRE for Detection of Vancomycin-Resistant Enterococci in Rectal Swab Specimens▿

PubMed Central

Stamper, Paul D.; Shulder, Stephanie; Bekalo, Pearl; Manandhar, Deepika; Ross, Tracy L.; Speser, Sharon; Kingery, Julie; Carroll, Karen C.

2010-01-01

A study was performed on 517 surveillance rectal swabs to evaluate a selective and differential chromogenic medium, the BBL CHROMagar VanRE (CVRE), which enables recovery and identification of VanA- and VanB-containing Enterococcus faecium (ENFM) and Enterococcus faecalis (ENFS) isolates. Compared to BBL Enterococcosel agar, a bile-esculin-azide-vancomycin (BEAV) agar, the initial overall sensitivity, specificity, and positive and negative predictive values of CVRE for the detection of vancomycin-resistant ENFM and ENFS were 99.1% and 94.8% and 84.2% and 99.7%, respectively. Among our patient population, more vancomycin-resistant enterococci (VRE) were recovered with CVRE than BEAV. PMID:20739492

Prevalence of Trichomonas vaginalis infection and protozoan load in South African women: a cross-sectional study.

PubMed

de Waaij, Dewi J; Dubbink, Jan Henk; Ouburg, Sander; Peters, Remco P H; Morré, Servaas A

2017-10-08

Trichomonas vaginalis is thought to be the most common non-viral sexually transmitted infection worldwide. We investigated the prevalence, risk factors and protozoan load of T. vaginalis infection in South African women. A cross-sectional study of 604 women was conducted at 25 primary healthcare facilities in rural South Africa (Mopani district). T. vaginalis DNA was detected in vaginal and rectal swabs. In univariate and multivariate analyses, the T. vaginalis infection was investigated in relation to demographic characteristics, medical history and behavioural factors. The T. vaginalis load was determined as the logarithm of DNA copies per microlitre sample solution. Collected vaginal and rectal swabs were tested for T. vaginalis DNA. Prevalence of vaginal T. vaginalis was 20% (95% CI 17.0% to 23.4%) and rectal 1.2% (95% CI 0.6% to 2.4%). Most women (66%) with a vaginal infection were asymptomatic. Factors associated with T. vaginalis infection were a relationship status of single (OR 2.4; 95% CI 1.5 to 4.0; p<0.001) and HIV positive infection (OR 1.6; 95% CI 1.0 to 2.6; p=0.041). Women with vaginal T. vaginalis infection were more likely to have concurrent Chlamydia trachomatis rectal infection than those without vaginal infection (12%vs3%; p<0.001; OR 4.1). A higher median T. vaginalis load was observed among women with observed vaginal discharge compared with those without vaginal discharge (p=0.025). Vaginal trichomoniasis is highly prevalent in rural South Africa, especially among single women and those with HIV infection, and often presents without symptoms. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Prevalence of Trichomonas vaginalis infection and protozoan load in South African women: a cross-sectional study

PubMed Central

de Waaij, Dewi J

2017-01-01

Objectives Trichomonas vaginalis is thought to be the most common non-viral sexually transmitted infection worldwide. We investigated the prevalence, risk factors and protozoan load of T. vaginalis infection in South African women. Methods A cross-sectional study of 604 women was conducted at 25 primary healthcare facilities in rural South Africa (Mopani district). T. vaginalis DNA was detected in vaginal and rectal swabs. In univariate and multivariate analyses, the T. vaginalis infection was investigated in relation to demographic characteristics, medical history and behavioural factors. The T. vaginalis load was determined as the logarithm of DNA copies per microlitre sample solution. Results Collected vaginal and rectal swabs were tested for T. vaginalis DNA. Prevalence of vaginal T. vaginalis was 20% (95% CI 17.0% to 23.4%) and rectal 1.2% (95% CI 0.6% to 2.4%). Most women (66%) with a vaginal infection were asymptomatic. Factors associated with T. vaginalis infection were a relationship status of single (OR 2.4; 95% CI 1.5 to 4.0; p<0.001) and HIV positive infection (OR 1.6; 95% CI 1.0 to 2.6; p=0.041). Women with vaginal T. vaginalis infection were more likely to have concurrent Chlamydia trachomatis rectal infection than those without vaginal infection (12%vs3%; p<0.001; OR 4.1). A higher median T. vaginalis load was observed among women with observed vaginal discharge compared with those without vaginal discharge (p=0.025). Conclusions Vaginal trichomoniasis is highly prevalent in rural South Africa, especially among single women and those with HIV infection, and often presents without symptoms. PMID:28993385

Case report: lymphogranuloma venereum proctitis-from rapid screening to molecular confirmation of a masked sexually transmitted disease.

PubMed

Markowicz, Mateusz; Grilnberger, Evelyn; Huber, Florian; Leibl, Gabriele; Abrahamian, Heidemarie; Gartner, Manfred; Huber, Monika; Chott, Andreas; Reiter, Michael; Stanek, Gerold

2013-08-01

Proctitis caused by Chlamydia trachomatis L2b can manifest with very mild, nonspecific symptoms, and appropriate diagnostic evaluation is crucial. The case report demonstrates that rapid screening test, detection of specific antibodies in serum, and direct pathogen identification by PCR performed on tissue sample or rectal swab allow successful diagnosis of the still emerging sexually transmitted disease among homosexual patients. Copyright © 2013 Elsevier Inc. All rights reserved.

Emergence and spread of tetracycline resistant Vibrio cholerae O1 El Tor variant during 2010 cholera epidemic in the tribal areas of Odisha, India.

PubMed

Kar, Santanu Kumar; Pal, Bibhuti Bhusan; Khuntia, Hemanta Kumar; Achary, K Gopinath; Khuntia, Chinmaye Priyadarshini

2015-04-01

The epidemics of cholera were reported in the Kashipur, K.singhpur, B cuttack blocks of Rayagada district and Mohana block of Gajapati district of Odisha during 2010. The present study was carried out to isolate the bacterial pathogen, its drug sensitivity pattern and to describe the spread of the disease in those areas. A total of 68 rectal swabs collected from patients with severe diarrhea, admitted to different health centers and diarrhea affected villages were bacteriologically analyzed. Similarly 22 water samples collected from different villages from nala, chua, etc were tested for the presence of V cholerae. Out of 68 rectal swabs tested 35 (51.5%) were V cholerae O1 Ogawa and 14(20.6%) were E coli; which might be commensals. All water samples were negative for V cholerae. The V cholerae strains were sensitive to gentamicin, norfloxacin, ciprofloxacin, azithromycin and ofloxacin; but were resistant to ampicillin, tetracycline, nalidixic acid, furazolidone, streptomycin, erythromycin, co-trimoxazole, neomycin and chloramphenicol. All V cholerae strains were 100% resistant to tetracycline and they were El Tor variants harboring ctxB gene of classical strain. The present study indicated the emergence and spread of tetracycline resistant V cholerae O1 El Tor variant in the tribal areas which needs close monitoring. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

PCR ribotyping and arbitrarily primed PCR for typing strains of Clostridium difficile from a Polish maternity hospital.

PubMed

Martirosian, G; Kuipers, S; Verbrugh, H; van Belkum, A; Meisel-Mikolajczyk, F

1995-08-01

Detection of the source of Clostridium difficile strains is of importance for the control of the nosocomial spread of this microorganism. For this purpose, vaginal and rectal swabs from 183 mothers, duplicate fecal samples (taken on days 1 and 4 after birth) from 183 neonates, and 94 environmental samples were cultured for C. difficile. The microorganism was never detected in the meconium obtained on day 1 after birth. On the other hand, an incidence of 17% C. difficile positivity was noted in the fecal samples obtained on day 4 after birth. Forty-two percent of the 31 colonized neonates had been delivered with complications. The bacteria were never encountered in the rectal swabs of the mothers, and C. difficile was identified in only one vaginal swab. In contrast, 13% of the environmental samples were positive for C. difficile. No major difference was encountered between patient and environmental isolates with respect to toxigenicity (58 to 65% toxigenic isolates). All strains were subsequently typed by PCR amplification of the 16S-23S ribosomal intergenic spacer regions and by arbitrarily primed PCR (AP-PCR) with different primers and combinations thereof. All environmental isolates and 11 of 31 neonatal strains were of a single type. The vaginal strain was unique, and among the maternity ward- and neonate-related isolates, only two additional AP-PCR types were identified. When a collection of C. difficile strains from patients hospitalized in other institutions and suffering from antibiotic-associated diarrhea or pseudomembranous colitis was analyzed in a similar manner, it appeared that the strain from the maternity ward was unique. The other strain commonly encountered among the neonates was also identified frequently among the isolates from patients with antibiotic-associated diarrhea or pseudomembranous colitis, indicating its general occurrence. On the basis of both epidemiological studies and PCR-mediated genotyping, it was shown that the environment and not the birth canal is the major source of C. difficile acquisition by neonates in this maternity hospital setting. Furthermore, AP-PCR appears to be a fast and useful method for epidemiologically relevant typing of C. difficile isolates.

Evaluation of the Granada agar plate for detection of vaginal and rectal group B streptococci in pregnant women.

PubMed

Gil, E G; Rodríguez, M C; Bartolomé, R; Berjano, B; Cabero, L; Andreu, A

1999-08-01

Granada medium was evaluated for the detection of group B streptococci (GBS) in vaginal and rectal swabs compared with selective Columbia blood agar and selective Lim broth. From May 1996 to March 1998, 702 pregnant women (35 to 37 weeks of gestation) participated in this three-phase study; 103 (14.7%) of these women carried GBS. In the first phase of the experiment (n = 273 women), vaginorectal specimens were collected on the same swab; the sensitivities of Granada tube, selective Columbia blood agar, and Lim broth were 31.4, 94.3, and 74.3%, respectively. In the second and third phases (n = 429 women), vaginal and rectal specimens were collected separately; the sensitivities of Granada plate, selective Columbia blood agar, and Lim broth (subcultured at 4 h on selective Columbia agar in the second phase and at 18 to 24 h in Granada plate in the third phase) were 91.1, 83.9, and 75%, respectively, in the second phase and 88.5, 90.4, and 63.5%, respectively, in the third phase. There were no statistically significant differences in GBS recovery between the Granada agar plate and selective Columbia blood agar, but the Granada plate provided a clear advantage; the characteristic red-orange colonies produced overnight by GBS can be identified by the naked eye and is so specific that further identification is unnecessary. The use of the Granada tube and Lim broth did not result in increased isolation of GBS. In conclusion, the Granada agar plate is highly sensitive for detecting GBS in vaginal and rectal swabs from pregnant women and can provide results in 18 to 24 h.

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.

A community-based gastroenteritis outbreak after Typhoon Haiyan, Leyte, Philippines, 2013.

PubMed

Ventura, Ray Justin; Muhi, Edzel; de los Reyes, Vikki Carr; Sucaldito, Ma Nemia; Tayag, Enrique

2015-01-01

Three weeks after Typhoon Haiyan, an increasing number of acute gastroenteritis cases were reported in Kananga, Leyte, an area where evacuated residents had returned home two days after the disaster. An outbreak investigation was conducted to identify the source and risk factors associated with the increase of gastroenteritis. A case was defined as any person in Kananga who developed acute diarrhoea (≥ 3 times/24 hours) and any of the following symptoms: fever, nausea, vomiting or abdominal pain from 11 November 2013 to 10 December 2013. Active case finding was conducted by reviewing medical records, and a case-control study was conducted. Rectal swabs and water samples were tested for bacteriological examination. One hundred and five cases were identified. Multivariate analysis revealed that consumption of untreated drinking-water was associated with illness (adjusted odds ratio: 18.2). Both rectal swabs and municipal water samples tested positive for Aeromonas hydrophila. On inspection of the municipal water system, breaks in the distribution pipes were found with some submerged in river water. This acute gastroenteritis outbreak was most likely caused by Aeromonas hydrophila and transmitted through a contaminated water source. This study highlights that areas less damaged by a disaster that do not require ongoing evacuation centres can still have acute gastroenteritis outbreaks. All affected areas should be monitored during a disaster response, not just those with evacuation centres. Boiling or chlorinating of water should also be recommended for all areas affected by disaster.

Amoebiasis among patrons visiting gay saunas in Taiwan.

PubMed

Hung, C-C; Ko, N-Y; Ko, W-C; Lee, H-C; Ji, D-D; Liu, W-C; Chang, S-C

2008-10-01

This study aimed to assess the prevalence of amoebiasis among patrons visiting gay saunas in Taiwan. A cross-sectional survey was conducted using questionnaire interview and indirect hemagglutination assays and specific Entamoeba histolytica antigen assays of blood and rectal swab specimens, respectively, among patrons visiting 10 gay saunas between September 2006 and December 2006. During the three-month study period, 208 blood and 120 rectal swab specimens were tested for E. histolytica infection. Amoebiasis was detected among 3.8% and 3.3% of the patrons by serologies and antigen assays, respectively. During the latest sexual encounter, more than 70% of the patrons had oral-anogenital sex, and only 20% used condoms during oral-anogenital contact. Our findings suggest that there is a potential risk of E. histolytica transmission among the patrons visiting gay saunas who do not practise safe sex consistently in Taiwan.

Performance Characteristics of the Cepheid Xpert vanA Assay for Rapid Identification of Patients at High Risk for Carriage of Vancomycin-Resistant Enterococci

PubMed Central

Gilhuley, Kathleen; Cianciminio-Bordelon, Diane; Tang, Yi-Wei

2012-01-01

We compared the performance characteristics of culture and the Cepheid Xpert vanA assay for routine surveillance of vancomycin-resistant enterococci (VRE) from rectal swabs in patients at high risk for VRE carriage. The Cepheid Xpert vanA assay had a limit of detection of 100 CFU/ml and correctly detected 101 well-characterized clinical VRE isolates with no cross-reactivity in 27 non-VRE and related culture isolates. The clinical sensitivity, specificity, positive predictive value, and negative predictive value of the Xpert vanA PCR assay were 100%, 96.9%, 91.3%, and 100%, respectively, when tested on 300 consecutively collected rectal swabs. This assay provides excellent predictive values for prompt identification of VRE-colonized patients in hospitals with relatively high rates of VRE carriage. PMID:22972822

Prevalence and predictors of Lymphogranuloma venereum in a high risk population attending a STD outpatients clinic in Italy.

PubMed

Foschi, Claudio; Marangoni, Antonella; D'Antuono, Antonietta; Nardini, Paola; Compri, Monica; Bellavista, Sara; Filippini, Andrea; Bacchi Reggiani, Maria Letizia; Cevenini, Roberto

2014-04-09

We evaluated LGV prevalence and predictors in a high risk population attending a STI Outpatients Clinic in the North of Italy. A total of 108 patients (99 MSM and 9 women), with a history of unsafe anal sexual intercourses, were enrolled. Anorectal swabs and urine samples were tested for Chlamydia trachomatis (CT) DNA detection by Versant CT/GC DNA 1.0 Assay (Siemens Healthcare Diagnostics Terrytown, USA). RFLP analysis was used for CT molecular typing. L2 CT genotype was identified in 13/108 (12%) rectal swabs. All LGV cases were from MSM, declaring high-risk sexual behaviour and complaining anorectal symptoms. Patients first attending the STI Outpatient Clinic received a significant earlier LGV diagnosis than those first seeking care from general practitioners or gastroenterologists (P = 0.0046). LGV prevalence and characteristics found in our population are in agreement with international reports. Statistical analysis showed that LGV positive patients were older (P = 0.0008) and presented more STIs (P = 0.0023) than LGV negative ones, in particular due to syphilis (P < 0.001), HIV (P < 0.001) and HBV (P = 0.001).Multivariate logistic regression analysis revealed that HIV and syphilis infections are strong risk factors for LGV presence (respectively, P = 0.001 and P = 0.010). Even if our results do not provide sufficient evidence to recommend routine screening of anorectal swabs in high-risk population, they strongly suggest to perform CT NAAT tests and genotyping on rectal specimens in presence of ulcerative proctitis in HIV and/or syphilis-positive MSM. In this context, CT DNA detection by Versant CT/GC DNA 1.0 Assay, followed by RFLP analysis for molecular typing demonstrated to be an excellent diagnostic algorithm for LGV identification.

A Novel Protocol Obviates Endoscope Sampling for Carbapenem-Resistant Enterobacteriaceae: Experience of a Center with a Prior Outbreak.

PubMed

Smith, Zachary L; Dua, Arshish; Saeian, Kia; Ledeboer, Nathan A; Graham, Mary Beth; Aburajab, Murad; Ballard, Darren D; Khan, Abdul H; Dua, Kulwinder S

2017-11-01

Numerous published outbreaks, including one from our institution, have described endoscope-associated transmission of multidrug-resistant organisms (MDROs). Individual centers have adopted their own protocols to address this issue, including endoscope culture and sequestration. Endoscope culturing has drawbacks and may allow residual bacteria, including MDROs, to go undetected after high-level disinfection. To report the outcome of our novel protocol, which does not utilize endoscope culturing, to address our outbreak. All patients undergoing procedures with elevator-containing endoscopes were asked to permit performance of a rectal swab. All endoscopes underwent high-level disinfection according to updated manufacturer's guidance. Additionally, ethylene oxide (EtO) sterilization was done in the high-risk settings of (1) positive response to a pre-procedure risk stratification questionnaire, (2) positive or indeterminate CRE polymerase chain reaction (PCR) from rectal swab, (3) refusal to consent for PCR or questionnaire, (4) purulent cholangitis or infected pancreatic fluid collections. Two endoscopes per weekend were sterilized on a rotational basis. From September 1, 2015 to April 30, 2016, 556 endoscopy sessions were performed using elevator-containing endoscopes. Prompted EtO sterilization was done on 46 (8.3%) instances, 3 from positive/indeterminate PCR tests out of 530 samples (0.6%). No CRE transmission was observed during the study period. Damage or altered performance of endoscopes related to EtO was not observed. In this pilot study, prompted EtO sterilization in high-risk patients has thus far eliminated endoscope-associated MDRO transmission, although no CRE infections were noted throughout the institution during the study period. Further studies and a larger patient sample will be required to validate these findings.

Detection and differentiation of field and vaccine strains of canine distemper virus using reverse transcription followed by nested real time PCR (RT-nqPCR) and RFLP analysis.

PubMed

Fischer, Cristine Dossin Bastos; Ikuta, Nilo; Canal, Cláudio Wageck; Makiejczuk, Aline; Allgayer, Mariangela da Costa; Cardoso, Cristine Hoffmeister; Lehmann, Fernanda Kieling; Fonseca, André Salvador Kazantzi; Lunge, Vagner Ricardo

2013-12-01

Canine distemper virus (CDV) is the cause of a severe and highly contagious disease in dogs. Practical diagnosis of canine distemper based on clinical signs and laboratory tests are required to confirm CDV infection. The present study aimed to develop a molecular assay to detect and differentiate field and vaccine CDV strains. Reverse transcription followed by nested real time polymerase chain reaction (RT-nqPCR) was developed, which exhibited analytical specificity (all the samples from healthy dogs and other canine infectious agents were not incorrectly detected) and sensitivity (all replicates of a vaccine strain were positive up to the 3125-fold dilution - 10(0.7) TCID50). RT-nqPCR was validated for CDV detection on different clinical samples (blood, urine, rectal and conjunctival swabs) of 103 animals suspected to have distemper. A total of 53 animals were found to be positive based on RT-nqPCR in at least one clinical sample. Blood resulted in more positive samples (50 out of 53, 94.3%), followed by urine (44/53, 83.0%), rectal (38/53, 71%) and conjunctival (27/53, 50.9%) swabs. A commercial immunochromatography (IC) assay had detected CDV in only 30 conjunctival samples of these positive dogs. Nucleoprotein (NC) gene sequencing of 25 samples demonstrated that 23 of them were closer to other Brazilian field strains and the remaining two to vaccine strains. A single nucleotide sequences difference, which creates an Msp I restriction enzyme digestion, was used to differentiate between field and vaccine CDV strains by restriction fragment length polymorphism (RFLP) analysis. The complete assay was more sensitive than was IC for the detection of CDV. Blood was the more frequently positive specimen and the addition of a restriction enzyme step allowed the differentiation of vaccine and Brazilian field strains. Copyright © 2013 Elsevier B.V. All rights reserved.

Disruption of the microbiota across multiple body sites in critically ill children.

PubMed

Rogers, Matthew B; Firek, Brian; Shi, Min; Yeh, Andrew; Brower-Sinning, Rachel; Aveson, Victoria; Kohl, Brittany L; Fabio, Anthony; Carcillo, Joseph A; Morowitz, Michael J

2016-12-29

Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets. Bacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs. The mean age of the PICU patients was 2.9 years (range 1-9 years), and many were chronically ill children that had previously been hospitalized in the PICU. Relative to healthy adults and children, alpha diversity was decreased in PICU GI and tongue but not skin samples. Measures of beta diversity indicated differences in community membership at each body site between PICU, adult, and pediatric groups. Taxonomic alterations in the PICU included enrichment of gut pathogens such as Enterococcus and Staphylococcus at multiple body sites and depletion of commensals such as Faecalibacterium and Ruminococcus from GI samples. Alpha and beta diversity were unstable over time in patients followed longitudinally. We observed the frequent presence of "dominant" pathogens in PICU samples at relative abundance >50%. PICU samples were characterized by loss of site specificity, with individual taxa commonly present simultaneously at three sample sites on a single individual. Some pathogens identified by culture of tracheal aspirates were commonly observed in skin samples from the same patient. We conclude that the microbiota in critically ill children differs sharply from the microbiota of healthy children and adults. Acknowledgement of dysbiosis associated with critical illness could provide opportunities to modulate the microbiota with precision and thereby improve patient outcomes.

A Multiplex Microsphere-Based Immunoassay Increases the Sensitivity of SIV-Specific Antibody Detection in Serum Samples and Mucosal Specimens Collected from Rhesus Macaques Infected with SIVmac239.

PubMed

Powell, Rebecca L R; Ouellette, Ian; Lindsay, Ross W; Parks, Christopher L; King, C Richter; McDermott, Adrian B; Morrow, Gavin

2013-06-01

Results from recent HIV-1 vaccine studies have indicated that high serum antibody (Ab) titers may not be necessary for Ab-mediated protection, and that Abs localized to mucosal sites might be critical for preventing infection. Enzyme-linked immunosorbent assay (ELISA) has been used for decades as the gold standard for Ab measurement, though recently, highly sensitive microsphere-based assays have become available, with potential utility for improved detection of Abs. In this study, we assessed the Bio-Plex(®) Suspension Array System for the detection of simian immunodeficiency virus (SIV)-specific Abs in rhesus macaques (RMs) chronically infected with SIV, whose serum or mucosal SIV-specific Ab titers were negative by ELISA. We developed a SIVmac239-specific 4-plex bead array for the simultaneous detection of Abs binding to Env, Gag, Pol, and Nef. The 4-plex assay was used to quantify SIV-specific serum IgG and rectal swab IgA titers from control (SIV-naive) and SIVmac239-infected RMs. The Bio-Plex assay specifically detected anti-SIV Abs in specimens from SIV-infected animals for all four analytes when compared to SIV-naive control samples (p≤0.04). Furthermore, in 70% of Env and 79% of Gag ELISA-negative serum samples, specific Ab was detected using the Bio-Plex assay. Similarly, 71% of Env and 48% of Gag ELISA-negative rectal swab samples were identified as positive using the Bio-Plex assay. Importantly, assay specificity (i.e., probability of true positives) was comparable to ELISA (94%-100%). The results reported here indicate that microsphere-based methods provide a substantial improvement over ELISA for the detection of Ab responses, aid in detecting specific Abs when analyzing samples containing low levels of Abs, such as during the early stages of a vaccine trial, and may be valuable in attempts to link protective efficacy of vaccines with induced Ab responses.

Prevalence and molecular identification of Chlamydia abortus in commercial dairy goat farms in a hot region in Mexico.

PubMed

Campos-Hernández, Eleuterio; Vázquez-Chagoyán, Juan Carlos; Salem, Abdelfattah Z M; Saltijeral-Oaxaca, Jorge Antonio; Escalante-Ochoa, Cristina; López-Heydeck, Sandra M; de Oca-Jiménez, Roberto Montes

2014-08-01

The aim of this study was to determine the seroprevalence and presence of Chlamydia abortus in Saanen breed female goats from commercial dairy goat farms under intensive production in the municipality of Guanajuato, Mexico. Sera were collected to determine the prevalence of anti-C. abortus IgG antibodies using recombinant enzyme-linked immunosorbent assay (rELISA) and cell culture. Polymerase chain reaction (PCR) was used to prove the presence of the pathogen in swab samples collected from the vagina and rectum of selected animals. Additionally, foetal tissue samples from a sudden abortion were collected. C. abortus prevalence in female goats of commercial milking farms sampled in Guanajuato, Mexico, was 4.87% (n = 246). Seropositive animals were found in six out of nine (66.6%) dairy goat farms sampled, and prevalence among animals in individual farms ranged between 3.44 and 13.51%. C. abortus was detected using PCR in spleen tissue from the aborted foetus. PCR-based detection, as well as isolation from vaginal and rectal swabs, was not possible in the present study. Isolation through cell culture was also unsuccessful from aborted foetal tissue samples. In conclusion, the results from rELISA and PCR show that C. abortus is present in dairy goat farms in the state of Guanajuato, Mexico.

Aerobic bacteria from mucous membranes, ear canals, and skin wounds of feral cats in Grenada, and the antimicrobial drug susceptibility of major isolates.

PubMed

Hariharan, Harry; Matthew, Vanessa; Fountain, Jacqueline; Snell, Alicia; Doherty, Devin; King, Brittany; Shemer, Eran; Oliveira, Simone; Sharma, Ravindra N

2011-03-01

In a 2-year period 54 feral cats were captured in Grenada, West Indies, and a total of 383 samples consisting of swabs from rectum, vagina, ears, eyes, mouth, nose and wounds/abscesses, were cultured for aerobic bacteria and campylobacters. A total of 251 bacterial isolates were obtained, of which 205 were identified to species level and 46 to genus level. A commercial bacterial identification system (API/Biomerieux), was used for this purpose. The most common species was Escherichia coli (N=60), followed by Staphylococcus felis/simulans (40), S. hominis (16), S. haemolyticus (12), Streptococcus canis (9), Proteus mirabilis (8), Pasteurella multocida (7), Streptococcus mitis (7), Staphylococcus xylosus (7), S. capitis (6), S. chromogenes (4), S. sciuri (3), S. auricularis (2), S. lentus (2), S. hyicus (2), Streptococcus suis (2) and Pseudomonas argentinensis (2). Sixteen other isolates were identified to species level. A molecular method using 16S rRNA sequencing was used to confirm/identify 22 isolates. Salmonella or campylobacters were not isolated from rectal swabs. E. coli and S. felis/simulans together constituted 50% of isolates from vagina. S. felis/simulans was the most common species from culture positive ear and eye samples. P. multocida was isolated from 15% of mouth samples. Coagulase-negative staphylococci were the most common isolates from nose and wound swabs. Staphylococcus aureus, or S. intemedius/S. pseudintermedius were not isolated from any sample. Antimicrobial drug resistance was minimal, most isolates being susceptible to all drugs tested against, including tetracycline. Copyright © 2010 Elsevier Ltd. All rights reserved.

Overweight and the feline gut microbiome - a pilot study.

PubMed

Kieler, I N; Mølbak, L; Hansen, L L; Hermann-Bank, M L; Bjornvad, C R

2016-06-01

Compared with lean humans, the gut microbiota is altered in the obese. Whether these changes are due to an obesogenic diet, and whether the microbiota contributes to adiposity is currently discussed. In the cat population, where obesity is also prevalent, gut microbiome changes associated with obesity have not been studied. Consequently, the aim of this study was to compare the gut microbiota of lean cats, with that of overweight and obese cats. Seventy-seven rescue-shelter cats housed for ≥3 consecutive days were included in the study. Faecal samples were obtained by rectal swab and, when available, by a paired litter box sample. Body condition was assessed using a 9-point scoring system. DNA was extracted, and the 16S rRNA gene was amplified with a high-throughput quantitative real-time PCR chip. Overweight and obese cats had a significantly different gut microbiota compared to lean cats (p < 0.05), but this finding could not be linked to differences in specific bacterial groups. The rectal samples obtained higher DNA concentration than litter box samples (p < 0.0001). In conclusion, overweight and obese cats seem to have an altered gut microbiome as compared to lean cats. Journal of Animal Physiology and Animal Nutrition © 2015 Blackwell Verlag GmbH.

Self-collected versus clinician-collected sampling for sexually transmitted infections: a systematic review and meta-analysis protocol.

PubMed

Taylor, Darlene; Lunny, Carole; Wong, Tom; Gilbert, Mark; Li, Neville; Lester, Richard; Krajden, Mel; Hoang, Linda; Ogilvie, Gina

2013-10-10

Three meta-analyses and one systematic review have been conducted on the question of whether self-collected specimens are as accurate as clinician-collected specimens for STI screening. However, these reviews predate 2007 and did not analyze rectal or pharyngeal collection sites. Currently, there is no consensus on which sampling method is the most effective for the diagnosis of genital chlamydia (CT), gonorrhea (GC) or human papillomavirus (HPV) infection. Our meta-analysis aims to be comprehensive in that it will examine the evidence of whether self-collected vaginal, urine, pharyngeal and rectal specimens provide as accurate a clinical diagnosis as clinician-collected samples (reference standard). Eligible studies include both randomized and non-randomized controlled trials, pre- and post-test designs, and controlled observational studies. The databases that will be searched include the Cochrane Database of Systematic Reviews, Web of Science, Database of Abstracts of Reviews of Effects (DARE), EMBASE and PubMed/Medline. Data will be abstracted independently by two reviewers using a standardized pre-tested data abstraction form. Heterogeneity will be assessed using the Q2 test. Sensitivity and specificity estimates with 95% confidence intervals as well as negative and positive likelihood ratios will be pooled and weighted using random effects meta-analysis, if appropriate. A hierarchical summary receiver operating characteristics curve for self-collected specimens will be generated. This synthesis involves a meta-analysis of self-collected samples (urine, vaginal, pharyngeal and rectal swabs) versus clinician-collected samples for the diagnosis of CT, GC and HPV, the most prevalent STIs. Our systematic review will allow patients, clinicians and researchers to determine the diagnostic accuracy of specimens collected by patients compared to those collected by clinicians in the detection of chlamydia, gonorrhea and HPV.

The "3 in 1" Study: Pooling Self-Taken Pharyngeal, Urethral, and Rectal Samples into a Single Sample for Analysis for Detection of Neisseria gonorrhoeae and Chlamydia trachomatis in Men Who Have Sex with Men.

PubMed

Sultan, B; White, J A; Fish, R; Carrick, G; Brima, N; Copas, A; Robinson, A; Gilson, R; Mercey, D; Benn, P

2016-03-01

Triple-site testing (using pharyngeal, rectal, and urethral/first-void urine samples) for Neisseria gonorrhoeae and Chlamydia trachomatis using nucleic acid amplification tests detects greater numbers of infections among men who have sex with men (MSM). However, triple-site testing represents a cost pressure for services. MSM over 18 years of age were eligible if they requested testing for sexually transmitted infections (STIs), reported recent sexual contact with either C. trachomatis or N. gonorrhoeae, or had symptoms of an STI. Each patient underwent standard-of-care (SOC) triple-site testing, and swabs were taken to form a pooled sample (PS) (pharyngeal, rectal, and urine specimens). The PS was created using two methods during different periods at one clinic, but we analyzed the data in combination because the sensitivity of the two methods did not differ significantly for C. trachomatis (P = 0.774) or N. gonorrhoeae (P = 0.163). The sensitivity of PS testing (92%) was slightly lower than that of SOC testing (96%) for detecting C. trachomatis (P = 0.167). For N. gonorrhoeae, the sensitivity of PS testing (90%) was significantly lower than that of SOC testing (99%) (P < 0.001). When pharynx-only infections were excluded, the sensitivity of PS testing to detect N. gonorrhoeae infections increased to 94%. Our findings show that pooling of self-taken samples could be an effective and cost-saving method, with high negative predictive values. (Interim results of this study were presented at the BASHH 2013 summer meeting.). Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Experimental inoculation study indicates swine as a potential host for Hendra virus

PubMed Central

Li, Mingyi; Embury-Hyatt, Carissa; Weingartl, Hana M.

2010-01-01

Hendra virus (HeV) is a zoonotic virus from the family Paramyxoviridae causing fatal disease in humans and horses. Five-week-old Landrace pigs and 5-month-old Gottingen minipigs were inoculated with approximately 107 plaque forming units per animal. In addition to fever and depression exhibited in all infected pigs, one of the two Landrace pigs developed respiratory signs at 5 days post-inoculation (dpi) and one of the Gottingen minipigs developed respiratory signs at 5 dpi and mild neurological signs at 7 dpi. Virus was detected in all infected pigs at 2–5 dpi from oral, nasal, and rectal swabs and at 3–5 dpi from ocular swabs by real-time RT-PCR targeting the HeV M gene. Virus titers in nasal swab samples were as high as 104.6 TCID50/mL. The viral RNA was mainly distributed in tissues from respiratory and lymphoid systems at an early stage of infection and the presence of virus was confirmed by virus isolation. Pathological changes and immunohistochemical staining for viral antigen were consistent with the tissue distribution of the virus. This new finding indicates that pigs are susceptible to HeV infections and could potentially play a role as an intermediate host in transmission to humans. PMID:20167195

Validation of High Resolution Melting Analysis (HRM) of the Amplified ITS2 Region for the Detection and Identification of Yeasts from Clinical Samples: Comparison with Culture and MALDI-TOF Based Identification.

PubMed

Duyvejonck, Hans; Cools, Piet; Decruyenaere, Johan; Roelens, Kristien; Noens, Lucien; Vermeulen, Stefan; Claeys, Geert; Decat, Ellen; Van Mechelen, Els; Vaneechoutte, Mario

2015-01-01

Candida species are known as opportunistic pathogens, and a possible cause of invasive infections. Because of their species-specific antimycotic resistance patterns, reliable techniques for their detection, quantification and identification are needed. We validated a DNA amplification method for direct detection of Candida spp. from clinical samples, namely the ITS2-High Resolution Melting Analysis (direct method), by comparing it with a culture and MALDI-TOF Mass Spectrometry based method (indirect method) to establish the presence of Candida species in three different types of clinical samples. A total of 347 clinical samples, i.e. throat swabs, rectal swabs and vaginal swabs, were collected from the gynaecology/obstetrics, intensive care and haematology wards at the Ghent University Hospital, Belgium. For the direct method, ITS2-HRM was preceded by NucliSENS easyMAG DNA extraction, directly on the clinical samples. For the indirect method, clinical samples were cultured on Candida ID and individual colonies were identified by MALDI-TOF. For 83.9% of the samples there was complete concordance between both techniques, i.e. the same Candida species were detected in 31.1% of the samples or no Candida species were detected in 52.8% of the samples. In 16.1% of the clinical samples, discrepant results were obtained, of which only 6.01% were considered as major discrepancies. Discrepancies occurred mostly when overall numbers of Candida cells in the samples were low and/or when multiple species were present in the sample. Most of the discrepancies could be decided in the advantage of the direct method. This is due to samples in which no yeast could be cultured whereas low amounts could be detected by the direct method and to samples in which high quantities of Candida robusta according to ITS2-HRM were missed by culture on Candida ID agar. It remains to be decided whether the diagnostic advantages of the direct method compensate for its disadvantages.

Prevalence of Salmonella spp. and thermophilic Campylobacter spp. in the small Asian mongoose (Herpestes javanicus) in Barbados, West Indies.

PubMed

Rhynd, Kamara J R; Leighton, Patrick A; Elcock, David A; Whitehall, Pamela J; Rycroft, Andrew; Macgregor, Shaheed K

2014-12-01

From April to July 2005, rectal swabs were collected from 48 free-ranging small Asian mongooses (Herpestes javanicus) on the east and south coasts of Barbados and analyzed for Salmonella and Campylobacter spp. Salmonella was recovered in 21.12% (7/33) of mongooses at the east-coast site and 26.67% (4/15) at the south-coast site. Four serotypes were isolated: Salmonella enterica serovar Rubislaw, Kentucky, Javiana, and Panama. One east-coast sample of 11 tested for Campylobacter was positive (9.09%). These results indicate that mongooses in Barbados are carriers and shedders of Salmonella and Campylobacter spp. and are a potential wildlife reservoir for these enteropathogens.

Virological and serological findings in dogs with naturally occurring distemper.

PubMed

Elia, Gabriella; Camero, Michele; Losurdo, Michele; Lucente, Maria Stella; Larocca, Vittorio; Martella, Vito; Decaro, Nicola; Buonavoglia, Canio

2015-03-01

Canine distemper virus (CDV) is the cause of a severe and highly contagious disease in dogs. The unpredictable and variable course of CDV-related disease may hamper correct diagnosis of infection and makes it crucial the collection of samples suitable for laboratory confirmation. In the present study we were able to follow the disease in two dogs infected naturally, collecting different biological matrices during the entire period of infection. By real time RT-PCR, viral RNA was detected and quantified, suggesting that urine and rectal swabs would be useful for ante-mortem diagnosis of distemper in dogs, regardless of the clinical stage and form of the illness. Copyright © 2015 Elsevier B.V. All rights reserved.

Risk factors for HIV and STI diagnosis in a community-based HIV/STI testing and counselling site for men having sex with men (MSM) in a large German city in 2011-2012.

PubMed

Marcus, Ulrich; Ort, Jasmin; Grenz, Marc; Eckstein, Kai; Wirtz, Karin; Wille, Andreas

2015-01-13

In recent years community-based voluntary counselling and testing sites (CB-VCT) for men having sex with men (MSM) have been established in larger cities in Germany to offer more opportunities for HIV testing. Increasingly, CB-VCTs also offer testing for other bacterial sexually transmitted infections. In Hamburg, tests in CB-VCTs are offered free and anonymously. Data on demographics and sexual risk behaviours are collected with a paper questionnaire. Questionnaire data from the MSM CB-VCT in Hamburg were linked with serological test results for HIV and syphilis, and with rectal and pharyngeal swab results for gonorrhoea and chlamydia. MSM were defined as males reporting male sex partners. CB-VCT clients were characterized demographically, and associations between sexual behaviour variables and diagnosis of HIV and sexually transmitted infections (STI) were analysed by bivariate and multivariate logistic regression analysis. Among the male clients of the CB-VCT in 2011-2012 who were tested for HIV or any STI 1476 reported male sex partners. Unprotected anal intercourse (UAI) was reported as reason for testing by 61% of the clients. Forty-one of 1413 clients testing for HIV were tested positive (2.9%). Twenty-four of 1380 clients testing for syphilis required treatment (1.7%). Tests for simultaneous detection of N. gonorrhoea and Chlamydia trachomatis were conducted on 882 pharyngeal and 642 rectal swabs, revealing 58 (=6.6%) pharyngeal and 71 (=11.1%) rectal infections with one or both pathogens. In multivariate logistic regression analysis number of partners, UAI (OR=2.42) and relying on visual impression when selecting sex partners (OR = 2.92) were associated with increased risks for diagnosis of syphilis or a rectal STI. Syphilis or rectal STI diagnosis (OR=4.52) were associated with increased risk for HIV diagnosis. The MSM CB-VCT in Hamburg reaches clients at high risk for HIV and STIs. The diagnosis of syphilis or a rectal STI was associated with increased odds of testing positive for HIV. Due to the high prevalence of curable bacterial STI among clients and because syphilis and rectal bacterial STI may facilitate HIV transmission, MSM asking for HIV tests in CB-VCTs should also be offered tests for other bacterial STIs.

Virulence profiles of Shiga Toxin-Producing Escherichia coli and other potentially diarrheagenic E.coli of bovine origin, in Mendoza, Argentina.

PubMed

Pizarro, M A; Orozco, J H; Degarbo, S M; Calderón, A E; Nardello, A L; Laciar, A; Rüttler, M E

2013-12-01

This study described a group of strains obtained from a slaughter house in Mendoza, in terms of their pathogenic factors, serotype, antibiotype and molecular profile. Ninety one rectal swabs and one hundred eight plating samples taken from carcasses of healthy cattle intended for meat consumption were analyzed. Both the swab and the plate samples were processed to analyze the samples for the presence of virulence genes by PCR: stx1, stx2, eae and astA. The Stx positive strains were confirmed by citotoxicity assay in Vero cells. The isolates were subsequently investigated for their O:H serotype, antimicrobial susceptibility and molecular profile by Random Amplification of Polymorphic DNA (RAPD). Twelve E.coli strains were identified by their pathogenicity. Nine were from fecal origin and three from carcasses. Three strains carried the stx1 gene, three the stx2 gene, two carried eae and four the astA gene. The detected serotypes were: O172:H-; O150:H8; O91:H21; O178:H19 and O2:H5. The strains showed a similarity around 70% by RAPD. Some of the E.coli strains belonged to serogroups known for certain life-threatening diseases in humans. Their presence in carcasses indicates the high probability of bacterial spread during slaughter and processing.

Lymphogranuloma venereum in an Italian MSM: concurrent pharyngeal and rectal infection.

PubMed

Foschi, Claudio; Filippini, Andrea; D'Antuono, Antonietta; Compri, Monica; Macca, Francesca; Banzola, Nicoletta; Marangoni, Antonella

2014-07-01

An Italian HIV-positive man having sex with men (MSM) attended the STIs Outpatients Clinic of Sant'Orsola Hospital in Bologna complaining of anal pain and constipation. According to patient's sexual history and repertoires, NAAT testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) was performed. Pharyngeal and anal swabs resulted positive for CT DNA detection and the following molecular genotyping identified a L2 serovar, coming to the final diagnosis of pharyngeal and rectal lymphogranuloma venereum (LGV) infection. After an antibiotic therapy with doxycycline 100 mg twice a day for 3 weeks, the patient completely recovered and the test of cure was negative for LGV infection.

A fifteen month study of Escherichia coli O157:H7 in a dairy herd.

PubMed Central

Mechie, S. C.; Chapman, P. A.; Siddons, C. A.

1997-01-01

A dairy herd associated with Escherichia coli O157 infection in humans was studied for the 15 months following the outbreak to examine seasonal, age and management factors affecting faecal excretion of the organism and to determine the mode and frequency of milk contamination with the organism. Between May 1993 and July 1994, 28 visits were made to the farm to collect a total of 3593 rectal swabs from cows, heifers and calves and 329 milk samples. E. coli O157:H7 was isolated from 153 (4.3%) of 3593 bovine rectal swabs. The maximum prevalence at any one visit was 14% in lactating cows, 40% in non-lactating cows, 56% in calves and 68% in heifers. The prevalence in lactating cows, which was significantly lower than in the other groups, peaked during May-July 1993 and again briefly after the cattle were housed during November 1993 and then again during May 1994. Excretion rates of E. coli O157:H7 in lactating cows were highest during the first month after calving, falling during lactation and rising to another peak at 7 months postpartum. Between November 1993 and May 1994 there was no evidence of excretion in any group. Eighty-seven (74%) of the animals which excreted E. coli O157:H7 did so on only one occasion but 23 (32%) of 73 cows and heifers and 7 (16%) of 44 calves which excreted the organism did so on more than one occasion. E. coli O157:H7 was not isolated from milk taken from the bulk tank but it was isolated from individual milk samples (one milk jar and one fore-milk) from two animals previously shown to be faecal excretors of the organism. All isolates of E. coli O157:H7 obtained were of the same phage type, toxin genotype and plasmid profile. PMID:9042031

The Correlation Between Candida Colonization of Distinct Body Sites and Invasive Candidiasis in Emergency Intensive Care Units: Statistical and Molecular Biological Analysis.

PubMed

Li, Zhen; Jiang, Cen; Dong, Danfeng; Zhang, Lihua; Tian, Yuan; Ni, Qi; Mao, Enqiang; Peng, Yibing

2016-08-01

Both statistical and molecular biological methods were used to evaluate the association between Candida colonization of different body sites and invasive candidiasis (IC) and analyse the potential infection sources of IC. Candida surveillance cultures from the urine, sputum, rectum and skin were performed on patients admitted to an emergency intensive care units (EICU) of a tertiary care hospital in Shanghai, China, from February 2014 to January 2015. Specimens were collected once a week at admission and thereafter. The patients' clinical data were collected, and Candida isolates were genotyped using polymorphic microsatellite markers. A total of 111 patients were enrolled. Patients with positive urine (23.3 vs. 2.5 %, p = 0.001) and rectal swab (13.6 vs. 0 %, p = 0.010) cultures were more likely to develop IC. However, the risk for IC was not significantly different among patients with and without respiratory (10.0 vs. 5.8 %, p = 0.503) and skin (33.3 vs. 6.5 %, p = 0.056) colonization. Gene microevolution frequently occurred at rectal swab and urine sites, and IC with possible source of infection was caused by rectal isolates (2/7), urine isolates (4/7) and sputum isolate (1/7).The colonization of gut and urinary tract maybe more relevant indicators of IC, which should be taken into consideration when selecting practical body sites for Candida surveillance cultures.

Molecular characterization of canine parvovirus strains in Argentina: Detection of the pathogenic variant CPV2c in vaccinated dogs.

PubMed

Calderon, Marina Gallo; Mattion, Nora; Bucafusco, Danilo; Fogel, Fernando; Remorini, Patricia; La Torre, Jose

2009-08-01

PCR amplification with sequence-specific primers was used to detect canine parvovirus (CPV) DNA in 38 rectal swabs from Argentine domestic dogs with symptoms compatible with parvovirus disease. Twenty-seven out of 38 samples analyzed were CPV positive. The classical CPV2 strain was not detected in any of the samples, but nine samples were identified as CPV2a variant and 18 samples as CPV2b variant. Further sequence analysis revealed a mutation at amino acid 426 of the VP2 gene (Asp426Glu), characteristic of the CPV2c variant, in 14 out of 18 of the samples identified initially by PCR as CPV2b. The appearance of CPV2c variant in Argentina might be dated at least to the year 2003. Three different pathogenic CPV variants circulating currently in the Argentine domestic dog population were identified, with CPV2c being the only variant affecting vaccinated and unvaccinated dogs during the year 2008.

Clinical and Virological Factors Associated with Viremia in Pandemic Influenza A/H1N1/2009 Virus Infection

PubMed Central

Tse, Herman; To, Kelvin K. W.; Wen, Xi; Chen, Honglin; Chan, Kwok-Hung; Tsoi, Hoi-Wah; Li, Iris W. S.; Yuen, Kwok-Yung

2011-01-01

Background Positive detection of viral RNA in blood and other non-respiratory specimens occurs in severe human influenza A/H5N1 viral infection but is not known to occur commonly in seasonal human influenza infection. Recently, viral RNA was detected in the blood of patients suffering from severe pandemic influenza A/H1N1/2009 viral infection, although the significance of viremia had not been previously studied. Our study aims to explore the clinical and virological factors associated with pandemic influenza A/H1N1/2009 viremia and to determine its clinical significance. Methodology/Principal Findings Clinical data of patients admitted to hospitals in Hong Kong between May 2009 and April 2010 and tested positive for pandemic influenza A/H1N1/2009 was collected. Viral RNA was detected by reverse-transcription polymerase chain reactions (RT-PCR) targeting the matrix (M) and HA genes of pandemic influenza A/H1N1/2009 virus from the following specimens: nasopharyngeal aspirate (NPA), endotracheal aspirate (ETA), blood, stool and rectal swab. Stool and/ or rectal swab was obtained only if the patient complained of any gastrointestinal symptoms. A total of 139 patients were included in the study, with viral RNA being detected in the blood of 14 patients by RT-PCR. The occurrence of viremia was strongly associated with a severe clinical presentation and a higher mortality rate, although the latter association was not statistically significant. D222G/N quasispecies were observed in 90% of the blood samples. Conclusion Presence of pandemic influenza A/H1N1/2009 viremia is an indicator of disease severity and strongly associated with D222G/N mutation in the viral hemagglutinin protein. PMID:21980333

Streptococcus agalactiae: prevalence of antimicrobial resistance in vaginal and rectal swabs in Italian pregnant women.

PubMed

Matani, Chiara; Trezzi, Michele; Matteini, Alice; Catalani, Carlotta; Messeri, Daniela; Catalani, Corrado

2016-09-01

Intrapartum antibiotic prophylaxis (IAP) reduces both the vertical transmission of Streptococcus agalactiae or Group B Streptococcus (GBS) and the early onset of neonatal sepsis. However, existing guidelines do not recommend that antimicrobial susceptibility testing (AST) be routinely performed. Penicillin or ampicillin are indicated as first-choice antibiotics, cefazolin being an alternative in the case of history of mild allergic reactions, and vancomycin or clindamycin an alternative in the event of severe reactions. We performed a cross-sectional analysis to identify the presence of any bacterial resistance towards the antibiotics most frequently used for IAP in pregnant women with GBS positive vaginal-rectal swabs, in the Pistoia area of central Italy. Of the 255 tested samples, 65 (25.5%) were positive for GBS. Sensitivity to glycopeptides was over 90%, but lower to ampicillin and penicillin (87.10% and 87.93% respectively). Resistance towards clindamycin and erythromycin was as high as 43.75% and 32.20%. All tested GBS proved susceptible to moxifloxacin, linezolid and tigecycline. Our observed prevalence is aligned or slightly higher than data reported in other series. The less than full effectiveness and low percentages of ampicillin and penicillin sensitivity observed give cause for concern. We confirmed the increase in clindamycin and erythromycin resistance. Glycopeptides can be used as second-line antibiotics, but the complete AST of GBS should always be performed before IAP. Given that gentamicin is used synergically with penicillin when treating chorioamnionitis, it needs to be always included in the AST. This is the first study on the GBS sensitivity profile in Tuscany. Further investigation on a larger scale is required prior to implementing any changes in the current guidelines.

Genomic attributes of extended-spectrum β-lactamase-producing Escherichia coli isolated from patients in Lebanon.

PubMed

Tokajian, Sima; Salloum, Tamara; Eisen, Jonathan A; Jospin, Guillaume; Farra, Anna; Mokhbat, Jacques E; Coil, David A

2017-03-01

Extended-spectrum β-lactamase-producing (ESBL) Escherichia coli are a public threat worldwide. This study aimed at analyzing the genomic and functional attributes of nine ESBLs taken from rectal swabs. Samples were isolated from patients admitted for gastrointestinal and urological procedures at the University Medical Center-Rizk Hospital (UMCRH) in Lebanon. Illumina paired-end libraries were prepared and sequenced. The isolates were distributed into five lineages: ST131, ST648, ST405, ST73 and ST38, and harbored bla OXA-1 , bla TEM-1B , bla TEM-1C and aac(6')Ib-cr. ST131 isolates were carriers of stx2 converting I phage. This is the first comprehensive genomic analysis performed on ESBLs in Lebanon.

Epidemiological investigation of Middle East respiratory syndrome coronavirus in dromedary camel farms linked with human infection in Abu Dhabi Emirate, United Arab Emirates.

PubMed

Muhairi, Salama Al; Hosani, Farida Al; Eltahir, Yassir M; Mulla, Mariam Al; Yusof, Mohammed F; Serhan, Wissam S; Hashem, Farouq M; Elsayed, Elsaeid A; Marzoug, Bahaaeldin A; Abdelazim, Assem S

2016-12-01

The objective of this research was to investigate the prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) infection primarily in dromedary camel farms and the relationship of those infections with infections in humans in the Emirate of Abu Dhabi. Nasal swabs from 1113 dromedary camels (39 farms) and 34 sheep (1 farm) and sputum samples from 2 MERS-CoV-infected camel farm owners and 1 MERS-CoV-infected sheep farm owner were collected. Samples from camels and humans underwent real-time reverse-transcription quantitative PCR screening to detect MERS-CoV. In addition, sequencing and phylogenetic analysis of partially characterized MERS-CoV genome fragments obtained from camels were performed. Among the 40 farms, 6 camel farms were positive for MERS-CoV; the virus was not detected in the single sheep farm. The maximum duration of viral shedding from infected camels was 2 weeks after the first positive test result as detected in nasal swabs and in rectal swabs obtained from infected calves. Three partial camel sequences characterized in this study (open reading frames 1a and 1ab, Spike1, Spike2, and ORF4b) together with the corresponding regions of previously reported MERS-CoV sequence obtained from one farm owner were clustering together within the larger MERS-CoV sequences cluster containing human and camel isolates reported for the Arabian Peninsula. Data provided further evidence of the zoonotic potential of MERS-CoV infection and strongly suggested that camels may have a role in the transmission of the virus to humans.

Molecular characterization of canine parvovirus in Vientiane, Laos.

PubMed

Vannamahaxay, Soulasack; Vongkhamchanh, Souliya; Intanon, Montira; Tangtrongsup, Sahatchai; Tiwananthagorn, Saruda; Pringproa, Kidsadagon; Chuammitri, Phongsakorn

2017-05-01

The global emergence of canine parvovirus type 2c (CPV-2c) has been well documented. In the present study, 139 rectal swab samples collected from diarrheic dogs living in Vientiane, Laos, in 2016 were tested for the presence of the canine parvovirus (CPV) VP2 gene by PCR. The results showed that 82.73% (115/139) of dogs were CPV positive by PCR. The partial VP2 gene was sequenced in 94 of the positive samples; 91 samples belonged to CPV-2c (426Glu) subtype, while 3 samples belonged to the CPV-2a (426Asn) subtype. Notably, phylogenetic analysis of amino acid sequences revealed a close relationship between Laotian isolates and novel Chinese CPV-2c isolates. In Laotian CPV isolates, aligned protein sequences indicated a high rate of residue substitutions at positions 305, 324, 345, 370, 375, and 426 in the GH loop. The mutation at residue 370 (Q370R), a single mutation, was characterized as a unique mutant residue specific to the Laotian CPV-2c variant.

Cross-sectional surveillance of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels and other mammals in Egypt, August 2015 to January 2016

PubMed Central

Ali, Mohamed; El-Shesheny, Rabeh; Kandeil, Ahmed; Shehata, Mahmoud; Elsokary, Basma; Gomaa, Mokhtar; Hassan, Naglaa; El Sayed, Ahmed; El-Taweel, Ahmed; Sobhy, Heba; Oludayo, Fasina Folorunso; Dauphin, Gwenaelle; El Masry, Ihab; Wolde, Abebe Wossene; Daszak, Peter; Miller, Maureen; VonDobschuetz, Sophie; Gardner, Emma; Morzaria, Subhash; Lubroth, Juan; Makonnen, Yilma Jobre

2017-01-01

A cross-sectional study was conducted in Egypt to determine the prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in imported and resident camels and bats, as well as to assess possible transmission of the virus to domestic ruminants and equines. A total of 1,031 sera, 1,078 nasal swabs, 13 rectal swabs, and 38 milk samples were collected from 1,078 camels in different types of sites. In addition, 145 domestic animals and 109 bats were sampled. Overall, of 1,031 serologically-tested camels, 871 (84.5%) had MERS-CoV neutralising antibodies. Seroprevalence was significantly higher in imported (614/692; 88.7%) than resident camels (257/339; 5.8%) (p < 0.05). Camels from Sudan (543/594; 91.4%) had a higher seroprevalence than those from East Africa (71/98; 72.4%) (p < 0.05). Sampling site and age were also associated with MERS-CoV seroprevalence (p < 0.05). All tested samples from domestic animals and bats were negative for MERS-CoV antibodies except one sheep sample which showed a 1:640 titre. Of 1,078 camels, 41 (3.8%) were positive for MERS-CoV genetic material. Sequences obtained were not found to cluster with clade A or B MERS-CoV sequences and were genetically diverse. The presence of neutralising antibodies in one sheep apparently in contact with seropositive camels calls for further studies on domestic animals in contact with camels. PMID:28333616

Swab or biopsy samples for bioburden testing of allograft musculoskeletal tissue?

PubMed

Varettas, Kerry

2014-12-01

Swab and biopsy samples of allograft musculoskeletal tissue are most commonly collected by tissue banks for bacterial and fungal bioburden testing. An in vitro study was performed using the National Committee for Clinical Laboratory Standards standard 'Quality control of microbiological transport systems' (2003) to validate and evaluate the recovery of six challenge organisms from swab and biopsy samples of allograft musculoskeletal tissue. On average, 8.4 to >100 and 7.2 to >100 % of the inoculum was recovered from swab and biopsy samples respectively. A retrospective review of donor episodes was also performed, consisting of paired swab and biopsy samples received in this laboratory during the period 2001-2012. Samples of allograft femoral heads were collected from living donors during hip operations. From the 3,859 donor episodes received, 21 paired swab and biopsy samples each recovered an isolate, 247 swab samples only and 79 biopsy samples only were culture positive. Low numbers of challenge organisms were recovered from inoculated swab and biopsy samples in the in vitro study and validated their use for bioburden testing of allograft musculoskeletal tissue. Skin commensals were the most common group of organisms isolated during a 12-year retrospective review of paired swab and biopsy samples from living donor allograft femoral heads. Paired swab and biopsy samples are a suitable representative sample of allograft musculoskeletal tissue for bioburden testing.

Decolonization of intestinal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae with oral colistin and neomycin: a randomized, double-blind, placebo-controlled trial.

PubMed

Huttner, Benedikt; Haustein, Thomas; Uçkay, Ilker; Renzi, Gesuele; Stewardson, Andrew; Schaerrer, Danièle; Agostinho, Americo; Andremont, Antoine; Schrenzel, Jacques; Pittet, Didier; Harbarth, Stephan

2013-10-01

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are an increasingly frequent cause of infections in the community and the healthcare setting. In this study, we aimed to investigate whether intestinal carriage of ESBL-E can be eradicated. We conducted a double-blind, randomized, placebo-controlled, single-centre trial to assess the efficacy of an oral decolonization regimen on intestinal ESBL-E carriage in adult patients with an ESBL-E-positive rectal swab. Fifty-eight patients were allocated 1 : 1 to either placebo or colistin sulphate (50 mg 4×/day) and neomycin sulphate (250 mg 4×/day) for 10 days plus nitrofurantoin (100 mg 3×/day) for 5 days in the presence of ESBL-E bacteriuria. The primary outcome was detection of ESBL-E by rectal swab 28 ± 7 days after the end of treatment. Missing primary outcome data were imputed based on the last available observation. Additional cultures (rectal, inguinal and urine) were taken on day 6 of treatment and on days 1 and 7 post-treatment. The study protocol has been registered with ClinicalTrials.gov (NCT00826670). Among 54 patients (27 in each group) included in the primary analysis, there was no statistically significant difference between the groups with regard to the primary outcome [14/27 (52%) versus 10/27 (37%), P = 0.27]. During treatment and shortly afterwards, there was significantly lower rectal ESBL-E carriage in the treatment group: 9/26 versus 19/22 on day 6 of treatment (P < 0.001) and 8/25 versus 20/26 on day 1 post-treatment (P = 0.001). This effect had disappeared by day 7 post-treatment (18/27 versus 17/25, P = 0.92). Liquid stools were more common in the treatment group (7/27 versus 2/29, P = 0.05). The regimen used in this study temporarily suppressed ESBL-E carriage, but had no long-term effect.

High Prevalence of Rectal Gonorrhea and Chlamydia Infection in Women Attending a Sexually Transmitted Disease Clinic

PubMed Central

Reese, Patricia Carr; Esber, Allahna; Lahey, Samantha; Ervin, Melissa; Davis, John A.; Fields, Karen; Turner, Abigail Norris

2015-01-01

Abstract Background: Testing women for urogenital Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) is common in sexually transmitted disease (STD) clinics. However, women may not be routinely tested for rectal GC/CT. This may lead to missed infections in women reporting anal intercourse (AI). Methods: This was a retrospective review of all women who underwent rectal GC/CT testing from August 2012 to June 2013 at an STD clinic in Columbus, Ohio. All women who reported AI in the last year had a rectal swab collected for GC/CT nucleic acid amplification testing (n=331). Using log-binomial regression models, we computed unadjusted and adjusted associations for demographic and behavioral factors associated with rectal GC/CT infection. Results: Participants (n=331) were 47% African-American, with median age of 29 years. Prevalence of rectal GC was 6%, rectal CT was 13%, and either rectal infection was 19%. Prevalence of urogenital GC and CT was 7% and 13% respectively. Among women with rectal GC, 14% tested negative for urogenital GC. Similarly, 14% of women with rectal CT tested negative for urogenital CT. In unadjusted analyses, there was increased rectal GC prevalence among women reporting sex in the last year with an injection drug user, with a person exchanging sex for drugs or money, with anonymous partners, and while intoxicated/high on alcohol or illicit drugs. After multivariable adjustment, no significant associations persisted, but a trend of increased rectal GC prevalence was observed for women <26 years of age (p=0.06) and those reporting sex while intoxicated/high on alcohol or drugs (p=0.05). For rectal CT, only age <26 years was associated with prevalent infection in unadjusted models; this association strengthened after multivariable adjustment (prevalence ratio: 6.03; 95% confidence interval: 2.29–15.90). Conclusion: Nearly one in five women who reported AI in the last year had rectal GC or CT infection. Urogenital testing alone would have missed 14% of rectal infections. Standardized guidelines would increase rectal GC/CT testing in women and help detect missed infections. PMID:25692800

Evaluation of two types of swabs for sampling allograft musculoskeletal tissue.

PubMed

Varettas, Kerry

2015-01-01

Allograft musculoskeletal tissue is commonly sampled by a swab for bioburden screening. To determine if bioburden recovery could be improved at the pre-analytical stage, two swab systems were evaluated: the Amies gel swab and the ESwab. In vitro studies were performed to determine the recovery of each swab system with <100 colony-forming unit of challenge organisms using inoculated swabs and by sampling inoculated femoral heads. The standard culture protocol used in this laboratory was also evaluated after sampling of inoculated femoral heads. A prospective study was performed with both swab systems used in parallel to sample cadaveric allograft musculoskeletal tissue. The challenge organisms could be recovered from the in vitro inoculated studies. The standard culture protocol in this laboratory recovered all challenge organisms from both swab systems. One hundred and six paired Amies and ESwabs were collected from eight cadaveric donors with skin commensals the predominant isolates. The sampling of an inoculated femoral head was included to reflect routine swab sampling practice as was the inclusion of the standard method used in this laboratory. This appears to be the first study to compare Amies gel swabs with ESwabs to sample allograft femoral heads and in a prospective study with cadaveric allograft musculoskeletal tissue. Other comparative studies of swab systems have used a much higher inoculum to mimic an infection; however, sepsis is an exclusion criterion for allograft donors. It was found that the Amies gel swab and ESwab are both suitable sampling devices for bioburden testing of allograft musculoskeletal tissue. © 2014 Royal Australasian College of Surgeons.

Efficacy of a Sonicating Swab for Removal and Capture of Listeria monocytogenes in Biofilms on Stainless Steel

PubMed Central

Branck, Tobyn A.; Hurley, Matthew J.; Prata, Gianna N.; Crivello, Christina A.

2017-01-01

ABSTRACT Listeria monocytogenes is of great concern in food processing facilities because it persists in biofilms, facilitating biotransfer. Stainless steel is commonly used for food contact surfaces and transport containers. L. monocytogenes biofilms on stainless steel served as a model system for surface sampling, to test the performance of a sonicating swab in comparison with a standard cotton swab. Swab performance and consistency were determined using total viable counts. Stainless steel coupons sampled with both types of swabs were examined using scanning electron microscopy, to visualize biofilms and surface structures (i.e., polishing grooves and scratches). Laser scanning confocal microscopy was used to image and to quantitate the biofilms remaining after sampling with each swab type. The total viable counts were significantly higher (P ≤ 0.05) with the sonicating swab than with the standard swab in each trial. The sonicating swab was more consistent in cell recovery than was the standard swab, with coefficients of variation ranging from 8.9% to 12.3% and from 7.1% to 37.6%, respectively. Scanning electron microscopic imaging showed that biofilms remained in the polished grooves of the coupons sampled with the standard swab but were noticeably absent with the sonicating swab. Percent area measurements of biofilms remaining on the stainless steel coupons showed significantly (P ≤ 0.05) less biofilm remaining when the sonicating swab was used (median, 1.1%), compared with the standard swab (median, 70.4%). The sonicating swab provided greater recovery of cells, with more consistency, than did the standard swab, and it is employs sonication, suction, and scrubbing. IMPORTANCE Inadequate surface sampling can result in foodborne illness outbreaks from biotransfer, since verification of sanitization protocols relies on surface sampling and recovery of microorganisms for detection and enumeration. Swabbing is a standard method for microbiological sampling of surfaces. Although swabbing offers portability and ease of use, there are limitations, such as high user variability and low recovery rates, which can be attributed to many different causes. This study demonstrates some benefits that a sonicating swab has over a standard swab for removal and collection of microbiological samples from a surface, to provide better verification of surface cleanliness and to help decrease the potential for biotransfer of pathogens into foods. PMID:28314729

Efficacy of a Sonicating Swab for Removal and Capture of Listeria monocytogenes in Biofilms on Stainless Steel.

PubMed

Branck, Tobyn A; Hurley, Matthew J; Prata, Gianna N; Crivello, Christina A; Marek, Patrick J

2017-06-01

Listeria monocytogenes is of great concern in food processing facilities because it persists in biofilms, facilitating biotransfer. Stainless steel is commonly used for food contact surfaces and transport containers. L. monocytogenes biofilms on stainless steel served as a model system for surface sampling, to test the performance of a sonicating swab in comparison with a standard cotton swab. Swab performance and consistency were determined using total viable counts. Stainless steel coupons sampled with both types of swabs were examined using scanning electron microscopy, to visualize biofilms and surface structures (i.e., polishing grooves and scratches). Laser scanning confocal microscopy was used to image and to quantitate the biofilms remaining after sampling with each swab type. The total viable counts were significantly higher ( P ≤ 0.05) with the sonicating swab than with the standard swab in each trial. The sonicating swab was more consistent in cell recovery than was the standard swab, with coefficients of variation ranging from 8.9% to 12.3% and from 7.1% to 37.6%, respectively. Scanning electron microscopic imaging showed that biofilms remained in the polished grooves of the coupons sampled with the standard swab but were noticeably absent with the sonicating swab. Percent area measurements of biofilms remaining on the stainless steel coupons showed significantly ( P ≤ 0.05) less biofilm remaining when the sonicating swab was used (median, 1.1%), compared with the standard swab (median, 70.4%). The sonicating swab provided greater recovery of cells, with more consistency, than did the standard swab, and it is employs sonication, suction, and scrubbing. IMPORTANCE Inadequate surface sampling can result in foodborne illness outbreaks from biotransfer, since verification of sanitization protocols relies on surface sampling and recovery of microorganisms for detection and enumeration. Swabbing is a standard method for microbiological sampling of surfaces. Although swabbing offers portability and ease of use, there are limitations, such as high user variability and low recovery rates, which can be attributed to many different causes. This study demonstrates some benefits that a sonicating swab has over a standard swab for removal and collection of microbiological samples from a surface, to provide better verification of surface cleanliness and to help decrease the potential for biotransfer of pathogens into foods. Copyright © 2017 American Society for Microbiology.

First evaluation of automated specimen inoculation for wound swab samples by use of the Previ Isola system compared to manual inoculation in a routine laboratory: finding a cost-effective and accurate approach.

PubMed

Mischnik, Alexander; Mieth, Markus; Busch, Cornelius J; Hofer, Stefan; Zimmermann, Stefan

2012-08-01

Automation of plate streaking is ongoing in clinical microbiological laboratories, but evaluation for routine use is mostly open. In the present study, the recovery of microorganisms from the Previ Isola system plated polyurethane (PU) swab samples is compared to manually plated control viscose swab samples from wounds according to the CLSI procedure M40-A (quality control of microbiological transport systems). One hundred twelve paired samples (224 swabs) were analyzed. In 80/112 samples (71%), concordant culture results were obtained with the two methods. In 32/112 samples (29%), CFU recovery of microorganisms from the two methods was discordant. In 24 (75%) of the 32 paired samples with a discordant result, Previ Isola plated PU swabs were superior. In 8 (25%) of the 32 paired samples with a discordant result, control viscose swabs were superior. The quality of colony growth on culture media for further investigations was superior with Previ Isola inoculated plates compared to manual plating techniques. Gram stain results were concordant between the two methods in 62/112 samples (55%). In 50/112 samples (45%), the results of Gram staining were discordant between the two methods. In 34 (68%) of the 50 paired samples with discordant results, Gram staining of PU swabs was superior to that of control viscose swabs. In 16 (32%) of the 50 paired samples, Gram staining of control viscose swabs was superior to that of PU swabs. We report the first clinical evaluation of Previ Isola automated specimen inoculation for wound swab samples. This study suggests that use of an automated specimen inoculation system has good results with regard to CFU recovery, quality of Gram staining, and accuracy of diagnosis.

First Evaluation of Automated Specimen Inoculation for Wound Swab Samples by Use of the Previ Isola System Compared to Manual Inoculation in a Routine Laboratory: Finding a Cost-Effective and Accurate Approach

PubMed Central

Mieth, Markus; Busch, Cornelius J.; Hofer, Stefan; Zimmermann, Stefan

2012-01-01

Automation of plate streaking is ongoing in clinical microbiological laboratories, but evaluation for routine use is mostly open. In the present study, the recovery of microorganisms from the Previ Isola system plated polyurethane (PU) swab samples is compared to manually plated control viscose swab samples from wounds according to the CLSI procedure M40-A (quality control of microbiological transport systems). One hundred twelve paired samples (224 swabs) were analyzed. In 80/112 samples (71%), concordant culture results were obtained with the two methods. In 32/112 samples (29%), CFU recovery of microorganisms from the two methods was discordant. In 24 (75%) of the 32 paired samples with a discordant result, Previ Isola plated PU swabs were superior. In 8 (25%) of the 32 paired samples with a discordant result, control viscose swabs were superior. The quality of colony growth on culture media for further investigations was superior with Previ Isola inoculated plates compared to manual plating techniques. Gram stain results were concordant between the two methods in 62/112 samples (55%). In 50/112 samples (45%), the results of Gram staining were discordant between the two methods. In 34 (68%) of the 50 paired samples with discordant results, Gram staining of PU swabs was superior to that of control viscose swabs. In 16 (32%) of the 50 paired samples, Gram staining of control viscose swabs was superior to that of PU swabs. We report the first clinical evaluation of Previ Isola automated specimen inoculation for wound swab samples. This study suggests that use of an automated specimen inoculation system has good results with regard to CFU recovery, quality of Gram staining, and accuracy of diagnosis. PMID:22692745

Laboratory evaluation of sample collection methods (organs vs swabs) for Tasmanian salmon reovirus detection in farmed Atlantic salmon, Salmo salar L.

PubMed

Zainathan, S C; Carson, J; Crane, M St J; Nowak, B F

2013-04-01

The use of swabs relative to organs as a sample collection method for the detection of Tasmanian salmon reovirus (TSRV) in farmed Tasmanian Atlantic salmon, Salmo salar L., was evaluated by RT-qPCR. Evaluation of individual and pooled sample collection (organs vs swabs) was carried out to determine the sensitivity of the collection methods and the effect of pooling of samples for the detection of TSRV. Detection of TSRV in individual samples was as sensitive when organs were sampled compared to swabs, and in pooled samples, organs demonstrated a sensitivity of one 10-fold dilution higher than sampling of pooled swabs. Storage of swabs at 4 °C for t = 24 h demonstrated results similar to those at t = 0. Advantages of using swabs as a preferred sample collection method for the detection of TSRV compared to organ samples are evident from these experimental trials. © 2012 Blackwell Publishing Ltd.

Prevalence of ESBL-positive bacteria in the community in the Czech Republic.

PubMed

Cekanová, Luboslava; Kolár, Milan; Chromá, Magdalena; Sauer, Pavel; Sedlácková, Michaela; Koukalová, Dagmar

2009-07-01

Problematic bacteria in the community include enterobacteria which produce extended-spectrum beta-lactamases. As yet there is no description of the prevalence of these bacteria in persons in the community in the Czech Republic. Therefore the main goal of this study was to determine the prevalence of ESBL-positive enterobacteria in the gastrointestinal tracts of subjects in the community in the Czech Republic. Rectal swabs from the investigated subjects were inoculated onto chromID ESBL selective medium and enterobacteria were identified by the Vitek2 automated system. ESBL were detected using a modified DDST test. The results were confirmed by PCR and direct sequencing of CTX-M-positive amplicons. A total of 579 rectal swabs from subjects in the community were analyzed and ESBL production was both phenotypically and genotypically confirmed in 7 isolates. Thus the prevalence of ESBL-positive bacteria in the gastrointestinal tracts of the persons in the community was 1.2%. All the cases were Escherichia coli strains producing the CTX-M-type ESBL. CTX-M-15 was the most prevalent type in this group of isolates. The presented results are in accord with other authors' studies and suggest that the epidemiologic profile of ESBL-positive enterobacteria in the Czech Republic is comparable to that in other European countries.

Comparison between Indirect Immunofluorescence Assay and Shell Vial Culture for Detection of Mumps Virus from Clinical Samples

PubMed Central

Reina, Jordi; Ballesteros, Francisca; Ruiz de Gopegui, Enrique; Munar, Maria; Mari, Margarita

2003-01-01

We report a prospective comparison of the efficacies of an indirect immunofluorescence assay (IFA) and shell vial culture (SVC) of throat swab and urine samples from patients with mumps. Throat swab samples were used for the IFA; the urine samples and throat swabs were inoculated into vials of Vero cells. We studied 62 patients by using 62 throat swabs and 50 urine samples (50 patients with both samples). Sixty (96.7%) throat samples were positive in the SVC, and 61 (98.3%) were positive in the IFA. For the 50 patients from whom both samples were available, the IFA was positive in 50 (100%) cases, the urine sample was positive in 49 (98%) cases, and the throat swab was positive in 48 (96%) cases (P > 0.05). This comparison of throat swabs and urine samples has shown that the two clinical samples are similar in efficacy. PMID:14605158

An integratable microfluidic cartridge for forensic swab samples lysis.

PubMed

Yang, Jianing; Brooks, Carla; Estes, Matthew D; Hurth, Cedric M; Zenhausern, Frederic

2014-01-01

Fully automated rapid forensic DNA analysis requires integrating several multistep processes onto a single microfluidic platform, including substrate lysis, extraction of DNA from the released lysate solution, multiplexed PCR amplification of STR loci, separation of PCR products by capillary electrophoresis, and analysis for allelic peak calling. Over the past several years, most of the rapid DNA analysis systems developed started with the reference swab sample lysate and involved an off-chip lysis of collected substrates. As a result of advancement in technology and chemistry, addition of a microfluidic module for swab sample lysis has been achieved in a few of the rapid DNA analysis systems. However, recent reports on integrated rapid DNA analysis systems with swab-in and answer-out capability lack any quantitative and qualitative characterization of the swab-in sample lysis module, which is important for downstream forensic sample processing. Maximal collection and subsequent recovery of the biological material from the crime scene is one of the first and critical steps in forensic DNA technology. Herein we present the design, fabrication and characterization of an integratable swab lysis cartridge module and the test results obtained from different types of commonly used forensic swab samples, including buccal, saliva, and blood swab samples, demonstrating the compatibility with different downstream DNA extraction chemistries. This swab lysis cartridge module is easy to operate, compatible with both forensic and microfluidic requirements, and ready to be integrated with our existing automated rapid forensic DNA analysis system. Following the characterization of the swab lysis module, an integrated run from buccal swab sample-in to the microchip CE electropherogram-out was demonstrated on the integrated prototype instrument. Therefore, in this study, we demonstrate that this swab lysis cartridge module is: (1) functionally, comparable with routine benchtop lysis, (2) compatible with various types of swab samples and chemistries, and (3) integratable to achieve a micro total analysis system (μTAS) for rapid DNA analysis. Copyright © 2013 Elsevier Ireland 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.

Apparatus for microbiological sampling. [including automatic swabbing

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Mills, S. M. (Inventor)

1974-01-01

An automatic apparatus is described for microbiologically sampling surface using a cotton swab which eliminates human error. The apparatus includes a self-powered transport device, such as a motor-driven wheeled cart, which mounts a swabbing motor drive for a crank arm which supports a swab in the free end thereof. The swabbing motor is pivotably mounted and an actuator rod movable responsive to the cart traveling a predetermined distance provides lifting of the swab from the surface being sampled and reversal of the direction of travel of the cart.

Comparison of four sampling methods for the detection of Salmonella in broiler litter.

PubMed

Buhr, R J; Richardson, L J; Cason, J A; Cox, N A; Fairchild, B D

2007-01-01

Experiments were conducted to compare litter sampling methods for the detection of Salmonella. In experiment 1, chicks were challenged orally with a suspension of naladixic acid-resistant Salmonella and wing banded, and additional nonchallenged chicks were placed into each of 2 challenge pens. Nonchallenged chicks were placed into each nonchallenge pen located adjacent to the challenge pens. At 7, 8, 10, and 11 wk of age the litter was sampled using 4 methods: fecal droppings, litter grab, drag swab, and sock. For the challenge pens, Salmonella-positive samples were detected in 3 of 16 fecal samples, 6 of 16 litter grab samples, 7 of 16 drag swabs samples, and 7 of 16 sock samples. Samples from the nonchallenge pens were Salmonella positive in 2 of 16 litter grab samples, 9 of 16 drag swab samples, and 9 of 16 sock samples. In experiment 2, chicks were challenged with Salmonella, and the litter in the challenge and adjacent nonchallenge pens were sampled at 4, 6, and 8 wk of age with broilers remaining in all pens. For the challenge pens, Salmonella was detected in 10 of 36 fecal samples, 20 of 36 litter grab samples, 14 of 36 drag swab samples, and 26 of 36 sock samples. Samples from the adjacent nonchallenge pens were positive for Salmonella in 6 of 36 fecal droppings samples, 4 of 36 litter grab samples, 7 of 36 drag swab samples, and 19 of 36 sock samples. Sock samples had the highest rates of Salmonella detection. In experiment 3, the litter from a Salmonella-challenged flock was sampled at 7, 8, and 9 wk by socks and drag swabs. In addition, comparisons with drag swabs that were stepped on during sampling were made. Both socks (24 of 36, 67%) and drag swabs that were stepped on (25 of 36, 69%) showed significantly more Salmonella-positive samples than the traditional drag swab method (16 of 36, 44%). Drag swabs that were stepped on had comparable Salmonella detection level to that for socks. Litter sampling methods that incorporate stepping on the sample material while in contact with the litter appear to detect Salmonella in greater incidence than traditional sampling methods of dragging swabs over the litter surface.

No effect of preoperative selective gut decontamination on endotoxemia and cytokine activation during cardiopulmonary bypass: a randomized, placebo-controlled study.

PubMed

Bouter, Hens; Schippers, Emile F; Luelmo, Saskia A C; Versteegh, Michael I M; Ros, Peter; Guiot, Henri F L; Frölich, Marijke; van Dissel, Jaap T

2002-01-01

Cardiopulmonary bypass predisposes the splanchnic region to inadequate perfusion and increases in gut permeability. Related to these changes, circulating endotoxin has been shown to rise during cardiac surgery, and may contribute to cytokine activation, high oxygen consumption, and fever ("postperfusion syndrome"). To a large extent, free endotoxin in the gut is a product of the proliferation of aerobic gram-negative bacteria and may be reduced by nonabsorbable antibiotics. To evaluate the effect of preoperative selective gut decontamination (SGD) on the incidence of endotoxemia and cytokine activation in patients undergoing open heart surgery. Prospective, randomized, placebo-controlled double-blind trial. Tertiary-care university teaching hospital. Preoperative administration for 5 to 7 days of oral nonabsorbable antibiotics (polymyxin B and neomycin) vs. placebo. The efficacy of SGD was assessed by culture of rectal swabs. Forty-four patients (median age 65 yrs, 29 males) were included in a pilot study to establish the sampling points of perioperative measurements. Seventy-eight consecutive patients (median age 65 yrs, 55 males) were enrolled for the prospective study; of these, 51 were randomly allocated to take SGD (n = 24) or placebo (n = 27); 27 were included in a control group (no medication). SGD but not placebo effectively reduced the number of rectal swabs that grew aerobic gram-negative bacteria (27% vs. 93%, respectively; p < .001). SGD did not affect the occurrence of perioperative endotoxemia, nor did it reduce the tumor necrosis factor-alpha, interleukin-10, or interleukin-6 concentrations (p > .20), as determined before surgery, upon aorta declamping, 30 mins into reperfusion, or 2 hrs after surgery. Also, SGD did not alter the incidence of postoperative fever or clinical outcome measures such as duration of artificial ventilation and intensive care unit and hospital stay. SGD effectively reduces the aerobic gram-negative bowel flora in cardiac surgery patients but fails to affect the incidence of perioperative endotoxemia and cytokine activation during cardiopulmonary bypass and the occurrence of a postperfusion syndrome.

Multidrug resistance in Clostridium perfringens isolated from diarrheal neonatal piglets in Thailand.

PubMed

Ngamwongsatit, Bhinyada; Tanomsridachchai, Wimonrat; Suthienkul, Orasa; Urairong, Supanee; Navasakuljinda, Wichian; Janvilisri, Tavan

2016-04-01

Clostridium perfringens causes diarrhea in neonatal piglets, thereby affecting commercial swine farming. The objective of this study was to determine the prevalence and characterize antimicrobial resistance in C. perfringens isolated from diarrheal neonatal piglets in Thailand. A total of 260 rectal swab samples were collected from 13 farms and were subjected to C. perfringens isolation. A total of 148 samples were PCR-positive for C. perfringens toxin genes, from which 122 were recovered. All isolates were cpb2-encoding C. perfringens type A and enterotoxin gene negative. Most of the isolates were susceptible to ampicillin, bacitracin, chlorotetracycline, doxycycline, and oxytetracycline with MIC50 values ranging from 0.32 to 8 μg/ml. The high resistance rates were observed for ceftiofur, enrofloxacin, erythromycin, lincomycin, and tylosin. Among resistant isolates, 82% were resistant to more than one type of antibiotics. The distinct pattern of multiple drug resistance in C. perfringens was observed in different regions, potentially reflecting the farm specific usage of these agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolution of canine parvovirus in Argentina between years 2003 and 2010: CPV2c has become the predominant variant affecting the domestic dog population.

PubMed

Calderón, Marina Gallo; Romanutti, Carina; D' Antuono, Alejandra; Keller, Leticia; Mattion, Nora; La Torre, Jose

2011-04-01

The current frequency of Canine Parvovirus variants (CPV2a, CPV2b and CPV2c) in the Argentine dog population was investigated by PCR amplification of a 583 bp fragment in the VP2 gene. From a total of 79 rectal swab samples that have been submitted to our laboratory since 2008, 55 (69.6%) resulted positive and were further analyzed by direct DNA sequencing. Fifty positives samples (91%) were characterized as CPV2c variant, which appeared in Argentina in the year 2003 and has been the prevalent type since 2008, whereas CPV2a and CPV2b, still found in Argentine dogs, were represented in 3.6% and 5.4% of the population, respectively. Considering that CPV2c is spreading worldwide, and that this variant is also affecting vaccinated dogs, efforts should be made towards the development of new matched CPV vaccines. Copyright © 2011 Elsevier B.V. All rights reserved.

Longitudinal Comparison of the Microbiota During Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae (KPC-Kp) Acquisition in Long-Term Acute Care Hospital (LTACH) patients

PubMed Central

Seekatz, Anna; Bassis, Christine M; Lolans, Karen; Yelin, Rachel D; Moore, Nicholas M; Okamoto, Koh; Rhee, Yoona; Bell, Pamela; Dangana, Thelma; Sidimirova, Galina; Weinstein, Robert A; Fogg, Louis; Lin, Michael Y; Young, Vincent B; Hayden, Mary K

2017-01-01

Abstract Background Colonization with KPC-Kp precedes infection and represents a potential target for intervention. To identify microbial signatures associated with KPC-Kp acquisition, we conducted a prospective, longitudinal study of the fecal microbiota in LTACH patients at risk of acquiring KPC-Kp. Methods We collected admission and weekly rectal swab samples from patients admitted to one LTACH from May 2015 to May 2016. Patients were screened for KPC-Kp by PCR at each sampling time. KPC acquisition was confirmed by culture of KPC-Kp. To assess changes in the microbiota related to acquisition, we sequenced the 16S rRNA gene (V4 region) from collected rectal swabs. Diversity, intra-individual changes, and the relative abundance of the operational taxonomic unit (OTU) that contains KPC-Kp were compared in patients who were KPC-Kp negative upon admission and who had at least one additional swab sample collected. Results 318 patients (1247 samples) were eligible for analysis; 3.7 samples (mean) were collected per patient. Sixty-two patients (19.5%) acquired KPC-Kp (cases) and 256 patients remained negative for all carbapenem-resistant Enterobacteriaceae throughout their stay (controls). Median length of stay before KPC-Kp detection was 14.5 days. At time of KPC-Kp acquisition, levels of an Enterobacteriaceae OTU increased significantly compared with pre-acquisition samples and to samples from control patients (Wilcoxon test, P < 0.0001). Similarly, we observed a decrease in total diversity of the fecal microbiota at time of acquisition in cases (P < 0.01). Compared with controls, cases exhibited decreased intra-individual fecal microbiota similarity immediately prior to acquisition of KPC-Kp (P < 0.01). Comparison of microbial features at time of admission using random forest revealed a higher abundance of Enterococcus and Escherichia OTUs in controls vs cases. Conclusion We observed intra-individual changes in the fecal microbiota of case patients prior to acquisition of KPC-Kp. Compared with patients who did not acquire KPC-Kp, cases exhibited significant changes in microbiota diversity and increased abundance of potential KPC-Kp at acquisition. Our results suggest that shifts in the microbiota may precede colonization by KPC-Kp. Disclosures N. M. Moore, Cepheid: Research Contractor, Funded and provided reagents for associated research projects; R. A. Weinstein, OpGen: Receipt of donated laboratory services for project, Research support; CLorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; M. Y. Lin, Sage, Inc.: receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; OpGen, Inc.: receipt of in-kind laboratory services, Conducting studies in healthcare facilities that are receiving contributed product; M. K. Hayden, OpGen, Inc.: Receipt of donated laboratory services for project, Research support; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product.

Prevalence and Characterization of Carbapenem-Resistant Enterobacteriaceae Isolated from Mulago National Referral Hospital, Uganda

PubMed Central

Okoche, Deogratius; Asiimwe, Benon B.; Katabazi, Fred Ashaba; Kato, Laban; Najjuka, Christine F.

2015-01-01

Introduction Carbapenemases have increasingly been reported in enterobacteriaceae worldwide. Most carbapenemases are plasmid encoded hence resistance can easily spread. Carbapenem-resistant enterobacteriaceae are reported to cause mortality in up to 50% of patients who acquire bloodstream infections. We set out to determine the burden of carbapenem resistance as well as establish genes encoding for carbapenemases in enterobacteriaceae clinical isolates obtained from Mulago National Referral Hospital, Uganda. Methods This was a cross-sectional study with a total of 196 clinical isolates previously collected from pus swabs, urine, blood, sputum, tracheal aspirates, cervical swabs, endomentrial aspirates, rectal swabs, Vaginal swabs, ear swabs, products of conception, wound biopsy and amniotic fluid. All isolates were subjected to phenotypic carbapenemase screening using Boronic acid-based inhibition, Modified Hodge and EDTA double combined disk test. In addition, all the isolates were subjected to PCR assay to confirm presence of carbapenemase encoding genes. Results The study found carbapenemase prevalence of 22.4% (44/196) in the isolates using phenotypic tests, with the genotypic prevalence slightly higher at 28.6% (56/196). Over all, the most prevalent gene was blaVIM (21,10.7%), followed by blaOXA-48 (19, 9.7%), blaIMP (12, 6.1%), blaKPC (10, 5.1%) and blaNDM-1 (5, 2.6%). Among 56 isolates positive for 67 carbapenemase encoding genes, Klebsiella pneumonia was the species with the highest number (52.2%). Most 32/67(47.7%) of these resistance genes were in bacteria isolated from pus swabs. Conclusion There is a high prevalence of carbapenemases and carbapenem-resistance encoding genes among third generation cephalosporins resistant Enterobacteriaceae in Uganda, indicating a danger of limited treatment options in this setting in the near future. PMID:26284519

Shedding of Hepatitis C Virus Into the Rectum of HIV-infected Men Who Have Sex With Men.

PubMed

Foster, Andrew L; Gaisa, Michael M; Hijdra, Rosanne M; Turner, Samuel S; Morey, Tristan J; Jacobson, Karen B; Fierer, Daniel S

2017-02-01

For over a decade we have known of an epidemic of sexually transmitted hepatitis C virus (HCV) infection among human immunodeficiency virus (HIV)-infected men who have sex with men (MSM), but there still remains significant controversy over which bodily fluid(s) are responsible for HCV transmission in these men. We enrolled HIV-infected MSM with recent and chronic HCV infection and quantified HCV from rectal fluid obtained by blind swab. We compared the rectal HCV viral load (VL) with paired blood HCV VL. We found rectal HCV shedding in 20 (47%) of 43 men, only one (2%) of whom had visible bleeding. Detection of rectal HCV shedding was associated with blood VL > 5 log 10 IU/mL (p = .01), and 85% with blood VL > 5 log 10 IU/mL had rectal shedding. The HCV VL of the rectal fluid ranged from 2.6 to 5.5 log 10 IU/mL. Based on the median rectal fluid VL, the surface of an average human penis would be exposed to at least 2,300 IU of HCV for the duration of anal intercourse. This study provides the first direct evidence to our knowledge that a sufficient quantity of HCV is shed into the rectum in HIV-infected men with HCV infection to directly infect an inserted penis or be passed indirectly through fomite-like transmission to the rectum of sex partner. We must develop an appropriate public health campaign to educate MSM about these routes of HCV infection to reverse the HCV epidemic among HIV-infected MSM. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

9 CFR 147.12 - Procedures for collection, isolation, and identification of Salmonella from environmental samples...

Code of Federal Regulations, 2011 CFR

2011-01-01

..., and identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and... identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and meconium samples... chickens, waterfowl, exhibition poultry, and game birds. All samples and swabs described in this paragraph...

9 CFR 147.12 - Procedures for collection, isolation, and identification of Salmonella from environmental samples...

Code of Federal Regulations, 2012 CFR

2012-01-01

..., and identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and... identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and meconium samples... chickens, waterfowl, exhibition poultry, and game birds. All samples and swabs described in this paragraph...

9 CFR 147.12 - Procedures for collection, isolation, and identification of Salmonella from environmental samples...

Code of Federal Regulations, 2013 CFR

2013-01-01

..., and identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and... identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and meconium samples... chickens, waterfowl, exhibition poultry, and game birds. All samples and swabs described in this paragraph...

9 CFR 147.12 - Procedures for collection, isolation, and identification of Salmonella from environmental samples...

Code of Federal Regulations, 2014 CFR

2014-01-01

..., and identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and... identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and meconium samples... chickens, waterfowl, exhibition poultry, and game birds. All samples and swabs described in this paragraph...

9 CFR 147.12 - Procedures for collection, isolation, and identification of Salmonella from environmental samples...

Code of Federal Regulations, 2010 CFR

2010-01-01

..., and identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and... identification of Salmonella from environmental samples, cloacal swabs, chick box papers, and meconium samples... chickens, waterfowl, exhibition poultry, and game birds. All samples and swabs described in this paragraph...

Development of an ELISA for evaluation of swab recovery efficiencies of bovine serum albumin.

PubMed

Sparding, Nadja; Slotved, Hans-Christian; Nicolaisen, Gert M; Giese, Steen B; Elmlund, Jón; Steenhard, Nina R

2014-01-01

After a potential biological incident the sampling strategy and sample analysis are crucial for the outcome of the investigation and identification. In this study, we have developed a simple sandwich ELISA based on commercial components to quantify BSA (used as a surrogate for ricin) with a detection range of 1.32-80 ng/mL. We used the ELISA to evaluate different protein swabbing procedures (swabbing techniques and after-swabbing treatments) for two swab types: a cotton gauze swab and a flocked nylon swab. The optimal swabbing procedure for each swab type was used to obtain recovery efficiencies from different surface materials. The surface recoveries using the optimal swabbing procedure ranged from 0-60% and were significantly higher from nonporous surfaces compared to porous surfaces. In conclusion, this study presents a swabbing procedure evaluation and a simple BSA ELISA based on commercial components, which are easy to perform in a laboratory with basic facilities. The data indicate that different swabbing procedures were optimal for each of the tested swab types, and the particular swab preference depends on the surface material to be swabbed.

Comparison of the CT OligoGen kit with cobas 4800 assay for detection of Chlamydia trachomatis.

PubMed

Parra-Sánchez, Manuel; Marcuello-López, Ana; García-Rey, Silvia; Zakariya-Yousef, Ismail; Sivianes-Valdecantos, Nieves; Sierra-Atienza, Celestina; Bernal-Martínez, Samuel; Pueyo-Rodrígez, Isabel; Martín-Mazuelos, Estrella; Palomares-Folía, José Carlos

2015-12-01

A prospective study was designed to assess the performance of the new CT OligoGen kit and the cobas 4800 assay for detection of Chlamydia trachomatis. A set of samples that included urine samples (n=212), endocervical (n=167), rectal (n=53), pharyngeal (n=7) and urethral swabs (n=3). The samples were sent from a regional sexually transmitted diseases (STD) clinic in Seville, Spain, and were collected from 261 men and 181 women. Discordant results were re-analyzed and clinical data and other tests were reviewed in order to resolve them. Sensitivity, specificity, positive predicative value (PPV), negative predictive value (NPV) and kappa value for C. trachomatis detection using the CT OligoGen kit were 98.5%, 100%, 100%, 95.4% and 0.97, respectively. This new kit had a high sensitivity, specificity, PPV and NPV for C. trachomatis, therefore the performance profile confirms the usefulness and reliable results of this new assay. Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

A simplified field protocol for genetic sampling of birds using buccal swabs

USGS Publications Warehouse

Vilstrup, Julia T.; Mullins, Thomas D.; Miller, Mark P.; McDearman, Will; Walters, Jeffrey R.; Haig, Susan M.

2018-01-01

DNA sampling is an essential prerequisite for conducting population genetic studies. For many years, blood sampling has been the preferred method for obtaining DNA in birds because of their nucleated red blood cells. Nonetheless, use of buccal swabs has been gaining favor because they are less invasive yet still yield adequate amounts of DNA for amplifying mitochondrial and nuclear markers; however, buccal swab protocols often include steps (e.g., extended air-drying and storage under frozen conditions) not easily adapted to field settings. Furthermore, commercial extraction kits and swabs for buccal sampling can be expensive for large population studies. We therefore developed an efficient, cost-effective, and field-friendly protocol for sampling wild birds after comparing DNA yield among 3 inexpensive buccal swab types (2 with foam tips and 1 with a cotton tip). Extraction and amplification success was high (100% and 97.2% respectively) using inexpensive generic swabs. We found foam-tipped swabs provided higher DNA yields than cotton-tipped swabs. We further determined that omitting a drying step and storing swabs in Longmire buffer increased efficiency in the field while still yielding sufficient amounts of DNA for detailed population genetic studies using mitochondrial and nuclear markers. This new field protocol allows time- and cost-effective DNA sampling of juveniles or small-bodied birds for which drawing blood may cause excessive stress to birds and technicians alike.

Evaluation of rayon swab surface sample collection method for Bacillus spores from nonporous surfaces.

PubMed

Brown, G S; Betty, R G; Brockmann, J E; Lucero, D A; Souza, C A; Walsh, K S; Boucher, R M; Tezak, M S; Wilson, M C; Rudolph, T; Lindquist, H D A; Martinez, K F

2007-10-01

To evaluate US Centers for Disease Control and Prevention recommended swab surface sample collection method for recovery efficiency and limit of detection for powdered Bacillus spores from nonporous surfaces. Stainless steel and painted wallboard surface coupons were seeded with dry aerosolized Bacillus atrophaeus spores and surface concentrations determined. The observed mean rayon swab recovery efficiency from stainless steel was 0.41 with a standard deviation (SD) of +/-0.17 and for painted wallboard was 0.41 with an SD of +/-0.23. Evaluation of a sonication extraction method for the rayon swabs produced a mean extraction efficiency of 0.76 with an SD of +/-0.12. Swab recovery quantitative limits of detection were estimated at 25 colony forming units (CFU) per sample area for both stainless steel and painted wallboard. The swab sample collection method may be appropriate for small area sampling (10 -25 cm2) with a high agent concentration, but has limited value for large surface areas with a low agent concentration. The results of this study provide information necessary for the interpretation of swab environmental sample collection data, that is, positive swab samples are indicative of high surface concentrations and may imply a potential for exposure, whereas negative swab samples do not assure that organisms are absent from the surfaces sampled and may not assure the absence of the potential for exposure. It is critical from a public health perspective that the information obtained is accurate and reproducible. The consequence of an inappropriate public health response founded on information gathered using an ineffective or unreliable sample collection method has the potential for undesired social and economic impact.

Screening haematology patients for carbapenem-resistant Klebsiella pneumoniae

PubMed Central

Kilgour, Elizabeth; Dunn, Caroline; Thomas, Linda; Fox, Richard; Mitchell, Lindsay; Paterson, Pamela

2013-01-01

Following a cluster of haematology patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) septicaemia, we initiated screening for rectal carriage of CRKP and multidrug-resistant K. pneumoniae (MDRKP) in this patient group. Haematology inpatients submit a rectal swab once weekly. When plated onto chromogenic Brilliance™ UTI Agar (Oxoid), and incubated overnight with a 10 µg ertapenem disc (Oxoid), K. pneumoniae is identified and semi-automated antibiotic susceptibility testing is performed using the Vitek 2 analyser (Biomerieux). When no zone of inhibition occurs, immediate intervention through patient isolation and enhanced environmental cleaning can be instigated to control further spread while empirical antibiotic prescribing is adapted to take account of identified resistances. Over 2 years, six patients with CRKP and 20 patients with MDRKP were identified. These isolates were resistant to first-line empirical treatment choices for neutropenic sepsis and presented a clinical risk of treatment failure for sepsis post cytotoxic chemotherapy. We describe how this rectal screening methodology was developed and how the results influenced appropriate antibiotic prescribing, patient placement in single rooms and the cleaning of the ward environment to prevent person-to-person transmission of MDRKP and CRKP. PMID:28989355

Prevalence and characteristics of gastrointestinal infections in men who have sex with men diagnosed with rectal chlamydia infection in the UK: an 'unlinked anonymous' cross-sectional study.

PubMed

Hughes, Gwenda; Silalang, Panida; Were, John; Patel, Hemanti; Childs, Tristan; Alexander, Sarah; Duffell, Stephen; Saxon, Cara; Ison, Cathy; Mitchell, Holly; Field, Nigel; Jenkins, Claire

2017-03-30

Gastrointestinal infections (GII) can cause serious ill health and morbidity. Although primarily transmitted through faecal contamination of food or water, transmission through sexual activity is well described, especially among men who have sex with men (MSM). We investigated the prevalence of GIIs among a convenience sample of MSM who were consecutively diagnosed with rectal Chlamydia trachomatis (CT) at 12 UK genitourinary medicine clinics during 10 weeks in 2012. Residual rectal swabs were coded, anonymised and tested for Shigella , Campylobacter , Salmonella , shiga toxin-producing Escherichia coli and enteroaggregative E. coli (EAEC) using a real-time PCR. Results were linked to respective coded and anonymised clinical and demographic data. Associations were investigated using Fisher's exact tests. Of 444 specimens tested, overall GII prevalence was 8.6% (95% CI 6.3% to 11.6%): 1.8% (0.9% to 3.6%) tested positive for Shigella , 1.8% (0.9% to 3.6%) for Campylobacter and 5.2% (3.5% to 7.7%) for EAEC. No specimens tested positive for Salmonella or other diarrhoeagenic E. coli pathotypes. Among those with any GII, 14/30 were asymptomatic (2/7 with Shigella, 3/6 with Campylobacter and 9/17 with EAEC). Shigella prevalence was higher in MSM who were HIV-positive (4.7% (2.1% to 10.2%) vs 0.5%(0.1% to 3.2%) in HIV-negative MSM; p=0.01). In this small feasibility study, MSM with rectal CT appeared to be at appreciable risk of GII. Asymptomatic carriage may play a role in sexual transmission of GII. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

The rectal microbiota of cats infected with feline immunodeficiency virus infection and uninfected controls.

PubMed

Weese, J S; Nichols, J; Jalali, M; Litster, A

2015-10-22

Rectal swabs were collected from 31 cats, 16 with FIV infection and 15 uninfected controls, to evaluate and compare the rectal bacterial microbiota in cats with feline immunodeficiency virus (FIV) infection and uninfected controls. The rectal microbiota was characterized via next generation sequencing of 16S rRNA gene (V4 region) polymerase chain reaction products. Eighteen different phyla were identified. Firmicutes dominated in both groups, followed by Proteobacteria and Actinobacteria, but there were no significant differences between groups. When predominant orders are compared, FIV-infected cats had significant higher median relative abundances of Bifidobacteriales (P=0.022), Lactobacillales (P=0.022) and Aeromonadales (P=0.043). No differences were identified in the 50 most common genera when adjusted for false discovery rate. There were significant differences in community membership (Jaccard index, unifrac P=0.008, AMOVA P<0.001) and community structure (Yue&Clayton index, unifrac P=0.03, AMOVA P=0.005) between groups. However, only one metacommunity (enterotype) was identified. The rectal microbiota differed between cats with FIV infection and uninfected controls. Some of the changes that were noted have been associated with 'dysbiosis' and proinflammatory states in other species, so it is possible that subclinical alteration in the intestinal microbiota could influence the health of FIV-infected cats. Evaluation of the reasons for microbiota alteration and the potential impact on cat health is required. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantification of loosely associated and tightly associated bacteria on broiler carcass skin using swabbing, stomaching, and grinding methods.

PubMed

Singh, P; Lee, H C; Chin, K B; Ha, S D; Kang, I

2015-12-01

This research was conducted to quantify bacterial populations after swabbing or stomaching, followed by grinding the swabbed or stomached broiler skins. For each of 3 replications, 3 eviscerated broilers were randomly taken from a processing line in a local broiler processing plant. Ten swabs and 10 stomachs per bird were conducted on the left- and the right-side skins (10×7 cm), respectively, which were then finally ground. Results indicated that mesophilic aerobic bacteria (MAB) in the first swabbed sample were significantly lower than those in the first stomached sample (P<0.05), with no difference seen for the remaining sampling times (P>0.05). During 10 swabbings followed by final grinding, 8, 9, and 83% of MAB were detected after the first swabbing, after the second through 10th swabbings, and after final grinding of the skin, respectively. During 10 stomachings followed by the final grinding, 17, 18, and 65% of MAB were detected after the first stomaching, after the second through 10th stomachings, and after final grinding of the skin, respectively. Escherichia coli (E. coli) and coliforms were significantly higher in the first stomaching than those in the first swabbing (P<0.05), with no difference seen between the 2 sampling methods for the rest sampling times (P>0.05). Populations of E. coli and coliforms decreased step-wisely from the highest after grinding to the intermediate after first and second sampling, and to the least after 10th sampling (P<0.05), regardless of swabbing or grinding. In this study, less than 35% of MAB seemed loosely associated in the skin of eviscerated broiler, whereas more than 65% of MAB looked tightly associated, which were not recovered by stomaching or swabbing even 10 times but were recovered by grinding the skin. © 2015 Poultry Science Association Inc.

Treatment efficacy of azithromycin 1 g single dose versus doxycycline 100 mg twice daily for 7 days for the treatment of rectal chlamydia among men who have sex with men - a double-blind randomised controlled trial protocol.

PubMed

Lau, Andrew; Kong, Fabian; Fairley, Christopher K; Donovan, Basil; Chen, Marcus; Bradshaw, Catriona; Boyd, Mark; Amin, Janaki; Timms, Peter; Tabrizi, Sepehr; Regan, David G; Lewis, David A; McNulty, Anna; Hocking, Jane S

2017-01-06

Rectal infection with Chlamydia trachomatis is one of the most common bacterial sexually transmissible infections among men who have sex with men (MSM) with diagnosis rates continuing to rise. Current treatment guidelines recommend either azithromycin 1 g single dose or doxycycline 100 mg twice daily for 7 days. However, there are increasing concerns about treatment failure with azithromycin. We are conducting the first randomised controlled trial (RCT) to compare treatment efficacy of azithromycin versus doxycycline for the treatment of rectal chlamydia in MSM. The Rectal Treatment Study will recruit 700 MSM attending Australian sexual health clinics for the treatment of rectal chlamydia. Participants will be asked to provide rectal swabs and will be randomised to either azithromycin 1 g single dose or doxycycline 100 mg twice daily for 7 days. Participants will be asked to complete questionnaires about adverse drug reactions, sexual behaviour and drug adherence via short message service and online survey. The primary outcome is the treatment efficacy as determined by a negative chlamydia nucleic acid amplification test at 4 weeks post treatment. Secondary outcomes will utilise whole genome sequencing and mRNA assay to differentiate between treatment failure, reinfection or false positive results. Rectal chlamydia is an increasing public health concern as use of pre-exposure prophylaxis against HIV becomes commonplace. Optimal, evidence-based treatment is critical to halting ongoing transmission. This study will provide the first RCT evidence comparing azithromycin and doxycycline for the treatment of rectal chlamydia. The results of this trial will establish which treatment is more efficacious and inform international management guidelines. Australian New Zealand Clinical Trials Registry ACTRN12614001125617.

Ease, Comfort, and Performance of the HerSwab Vaginal Self-Sampling Device for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

PubMed

Arias, Manuel; Jang, Dan; Gilchrist, Jodi; Luinstra, Kathy; Li, Jenny; Smieja, Marek; Chernesky, Max A

2016-02-01

Many sexually transmitted diseases are asymptomatic in the lower genital tract and can cause upper tract complications if left untreated. Self-collected vaginal (SCV) swabs enable the accurate detection of many sexually transmitted infections and give women the option of collecting their own samples while providing them with privacy and convenience. We compared SCV samples collected and transported dry using the HerSwab device to physician-collected vaginal (PCV) Aptima swabs for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), and measured patients' ease and comfort with self-collection. A total of 189 women aged 16 to 41 years were consented into the study and answered a standardized anonymized questionnaire regarding self-collection with the HerSwab device. Women reported self-collection with HerSwab to be easy (97.1%) and comfortable (88.3%). They preferred self-collection over physician collection (80.9%) and would consider using HerSwab for self-collection at home (79.7%). Samples of SCV and PCV showed an overall agreement of 94.7% (κ = 0.64) for CT and of 98.4% (κ = 0.56) for NG, and HerSwab collection detected 7 more positive patients than PCV collection. The overall prevalence of infection was 10.6% for CT and 2.6% for NG. HerSwab SCV samples are suitable for the diagnosis of CT and NG.

A bovine botulism outbreak associated with a suspected cross-contamination from a poultry farm.

PubMed

Souillard, R; Le Maréchal, C; Ballan, V; Mahé, F; Chemaly, M; Le Bouquin, S

2017-09-01

In October 2014, an outbreak of botulism type D/C occurred on two cattle farms in close proximity. A poultry farm located nearby with no history of botulism had transferred poultry manure to both bovine farms before the beginning of the outbreak. Given this context, epidemiological investigation was conducted to determine if the poultry farm was a reservoir of C. botulinum type D/C and to identify the source of contamination on the cattle farms. Environmental samples were collected at three houses on the poultry farm (boot swabs from the surroundings, swabs from the ventilation system, boot swabs from the poultry litter and darkling beetles samples), and on the two cattle farms (silage samples, boot swabs from the cattle stalls, boot swabs from the cattle pasture and poultry manure samples). These samples were analyzed using real-time PCR after an enrichment step to detect C. botulinum type D/C. On the poultry farm, three boot swabs from the surroundings, two swabs from the ventilation system, one boot swab from the litter and one sample of darkling beetles were detected positive. On one cattle farm, C. botulinum type D/C was identified in a sample of silage made from grass grown on a field on which the poultry manure had previously been stored and in a boot swab from a pasture. On the other cattle farm, C. botulinum type D/C was detected in a sample of poultry manure stored on the cattle farm and in a boot swab from a pasture. This investigation shows that the healthy poultry farm might have been the reservoir of C. botulinum type D/C and that cross-contamination between poultry and cattle likely occurred, resulting in the botulism outbreak on the two cattle farms. Copyright © 2017 Elsevier B.V. All rights reserved.

Broth versus solid agar culture of swab samples of cadaveric allograft musculoskeletal tissue.

PubMed

Varettas, Kerry

2013-12-01

As part of the donor assessment protocol, bioburden assessment must be performed on allograft musculoskeletal tissue samples collected at the time of tissue retrieval. Swab samples of musculoskeletal tissue allografts from cadaveric donors are received at the microbiology department of the South Eastern Area Laboratory Services (Australia) to determine the presence of bacteria and fungi. This study will review the isolation rate of organisms from solid agar and broth culture of swab samples of cadaveric allograft musculoskeletal tissue over a 6-year period, 2006-2011. Swabs were inoculated onto horse blood agar (anaerobic, 35 °C) and chocolate agar (CO2, 35 °C) and then placed into a cooked meat broth (aerobic, 35 °C). A total of 1,912 swabs from 389 donors were received during the study period. 557 (29.1 %) swabs were culture positive with the isolation of 713 organisms, 249 (34.9 %) from solid agar culture and an additional 464 (65.1 %) from broth culture only. This study has shown that the broth culture of cadaveric allograft musculoskeletal swab samples recovered a greater amount of organisms than solid agar culture. Isolates such as Clostridium species and Staphylococcus aureus would not have been isolated from solid agar culture alone. Broth culture is an essential part of the bioburden assessment protocol of swab samples of cadaveric allograft musculoskeletal tissue in this laboratory.

Sentinel surveillance for human enterovirus 71 in Sarawak, Malaysia: lessons from the first 7 years.

PubMed

Podin, Yuwana; Gias, Edna L M; Ong, Flora; Leong, Yee-Wei; Yee, Siew-Fung; Yusof, Mohd Apandi; Perera, David; Teo, Bibiana; Wee, Thian-Yew; Yao, Sik-Chi; Yao, Sik-King; Kiyu, Andrew; Arif, Mohd Taha; Cardosa, Mary Jane

2006-07-07

A major outbreak of human enterovirus 71-associated hand, foot and mouth disease in Sarawak in 1997 marked the beginning of a series of outbreaks in the Asia Pacific region. Some of these outbreaks had unusually high numbers of fatalities and this generated much fear and anxiety in the region. We established a sentinel surveillance programme for hand, foot and mouth disease in Sarawak, Malaysia, in March 1998, and the observations of the first 7 years are described here. Virus isolation, serotyping and genotyping were performed on throat, rectal, vesicle and other swabs. During this period Sarawak had two outbreaks of human enterovirus 71, in 2000 and 2003. The predominant strains circulating in the outbreaks of 1997, 2000 and 2003 were all from genogroup B, but the strains isolated during each outbreak were genetically distinct from each other. Human enterovirus 71 outbreaks occurred in a cyclical pattern every three years and Coxsackievirus A16 co-circulated with human enterovirus 71. Although vesicles were most likely to yield an isolate, this sample was not generally available from most cases and obtaining throat swabs was thus found to be the most efficient way to obtain virological information. Knowledge of the epidemiology of human enterovirus 71 transmission will allow public health personnel to predict when outbreaks might occur and to plan interventions in an effective manner in order to reduce the burden of disease.

Variable efficacy of a vaccine and direct-fed microbial for controlling Escherichia coli O157:H7 in feces and on hides of feedlot cattle.

PubMed

Stanford, Kim; Hannon, Sherry; Booker, Calvin W; Jim, G Kee

2014-05-01

To evaluate the efficacy of a type-III secreted proteins vaccine and a Lactobacillus-acidophilus-based direct-fed microbial (DFM) for controlling Escherichia coli O157:H7, cattle (n=864) were allocated to the following groups: DFM, finishing diets containing 10(9) colony-forming units (CFU)/animal/day L. acidophilus and Propionibacterium freudenreichii; VAC, finishing diets and 2 mL intramuscular injection of vaccine at allocation and 28 days later; or CON, finishing diets only. Cattle within replicates were stratified by initial levels of E. coli O157:H7 and randomized to experimental groups, with 30 pens allocated on June 15, 2011 (AS1), 18 pens allocated on June 28, 2011 (AS2), and 18 cattle per pen. Rectal fecal samples and perineal swabs were collected at 28-day intervals until shipment to slaughter (103-145 days on trial). Numbers of cattle with enumerable E. coli O157:H7 (≥1.6 CFU/g feces) were reduced in AS1 and AS2 by VAC (p=0.008), although interventions had no impact on numbers of E. coli O157:H7 shed. For AS1, VAC reduced prevalence of E. coli O157:H7 in feces (p=0.03) and perineal swabs (p=0.04) in the feeding period but not at shipment to slaughter. For AS2, prevalence of E. coli O157:H7 was not reduced in either feces or perineal swabs by VAC at any time. For AS1, DFM reduced prevalence of E. coli O157:H7 in perineal swabs (p=0.01) during the feeding period. For AS2, DFM increased E. coli O157:H7 detection in feces (p=0.03) and perineal swabs (p=0.01) at shipment to slaughter. Seventy-five percent of AS1 E. coli O157:H7 isolates had only stx1, while 87% of AS2 isolates had stx1 and stx2 genes. Of the two interventions, VAC shows the most potential for pre-harvest control of E. coli O157:H7, but due to variable efficacy of both DFM and VAC, additional product development is necessary to ensure more consistent pre-harvest control of E. coli O157:H7.

Asymptomatic lymphogranuloma venereum among Nigerian men who have sex with men.

PubMed

Crowell, Trevor A; Hardick, Justin; Lombardi, Kara; Parker, Zahra; Kokogho, Afoke; Amusu, Senate; Odeyemi, Sunday; Ivo, Andrew; Baral, Stefan D; Nowak, Rebecca G; Adebajo, Sylvia; Charurat, Manhattan E; Ake, Julie; Gaydos, Charlotte A

2018-01-29

Recent outbreaks of anorectal lymphogranuloma venereum (LGV) among men who have sex with men (MSM) have been characterised by proctocolitis requiring extended antibiotic treatment compared with infections caused by other serovars of Chlamydia trachomatis (CT). We describe the prevalence and clinical features of LGV among Nigerian MSM diagnosed with anorectal CT. MSM were recruited for this observational cohort in Lagos, Nigeria, using respondent-driven sampling and screened for HIV and bacterial STIs every three months for up to 18 months. Nucleic acid amplification tests for CT were performed on rectal swab specimens. Prevalent and incident cases of anorectal CT underwent additional testing to identify LGV using novel real-time PCR assays specific for the L-serovars of CT. From April 2014 to July 2016, 420 MSM underwent testing for rectal STIs, of whom 66 (15.7%) had prevalent anorectal CT. Among those without prevalent disease, 68 developed incident infections during 208 person-years of follow-up. Of 134 prevalent and incident cases of anorectal CT, 7 (5.2%) were identified as LGV. None of the seven participants with LGV reported any symptoms. Two of the participants with LGV were simultaneously coinfected with rectal gonorrhoea. HIV coinfection was common among participants with both LGV (n=5, 71%) and non-LGV (n=98, 77%) serovars of CT (P=0.66). Anorectal LGV was uncommon but present among Nigerian MSM in this study. Consistent screening for L-serovars of CT, or presumptive treatment for LGV in cases with a high suspicion for this diagnosis, could potentially improve patient outcomes and decrease transmission. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Evaluation of a real-time PCR assay for rectal screening of OXA-48-producing Enterobacteriaceae in a general intensive care unit of an endemic hospital.

PubMed

Fernández, J; Cunningham, S A; Fernández-Verdugo, A; Viña-Soria, L; Martín, L; Rodicio, M R; Escudero, D; Vazquez, F; Mandrekar, J N; Patel, R

2017-07-01

Carbapenemase-producing Enterobacteriaceae are increasing worldwide. Rectal screening for these bacteria can inform the management of infected and colonized patients, especially those admitted to intensive care units (ICUs). A laboratory developed, qualitative duplex real-time polymerase chain reaction assay for rapid detection of OXA-48-like and VIM producing Enterobacteriaceae, performed on rectal swabs, was designed and evaluated in an intensive care unit with endemic presence of OXA-48. During analytical assay validation, no cross-reactivity was observed and 100% sensitivity and specificity were obtained for both bla OXA-48-like and bla VIM in all spiked clinical samples. During the clinical part of the study, the global sensitivity and specificity of the real-time PCR assay for OXA-48 detection were 95.7% and 100% (P=0.1250), respectively, in comparison with culture; no VIM-producing Enterobacteriaceae were detected. Clinical features of patients in the ICU who were colonized or infected with OXA-48 producing Enterobacteriaceae, including outcome, were analyzed. Most had severe underlying conditions, and had risk factors for colonization with carbapenemase-producing Enterobacteriaceae before or during ICU admission, such as receiving previous antimicrobial therapy, prior healthcare exposure (including long-term care), chronic disease, immunosuppression and/or the presence of an intravascular catheter and/or mechanical ventilation device. The described real-time PCR assay is fast (~2-3hours, if DNA extraction is included), simple to perform and results are easy to interpret, features which make it applicable in the routine of clinical microbiology laboratories. Implementation in endemic hospitals could contribute to early detection of patients colonized by OXA-48 producing Enterobacteriaceae and prevention of their spread. Copyright © 2017 Elsevier Inc. All rights reserved.

HIV-1, sexually transmitted infections, and sexual behavior trends among men who have sex with men in Lima, Peru.

PubMed

Sanchez, Jorge; Lama, Javier R; Kusunoki, Lourdes; Manrique, Hugo; Goicochea, Pedro; Lucchetti, Aldo; Rouillon, Manuel; Pun, Monica; Suarez, Luis; Montano, Silvia; Sanchez, Jose L; Tabet, Stephen; Hughes, James P; Celum, Connie

2007-04-15

To assess and estimate trends in HIV, sexually transmitted infections (STIs), and sexual behavior among men who have sex with men (MSM) in Lima, Peru. Second-generation HIV sentinel surveillance surveys conducted in 1996, 1998, 2000, and 2002. Adult men reporting sex with at least 1 man during the previous year were eligible to participate. Sexual behavior and serum HIV-1 and syphilis antibodies were assessed. HIV seroincidence was estimated by a sensitive/less-sensitive enzyme immunoassay strategy. Rectal and pharyngeal swabs for Neisseria gonorrhoeae culture and a first-void urine sample for urethral leukocytes for presumptive diagnosis of urethritis were obtained. Herpes simplex virus 2 (HSV-2) antibodies were measured in 2002. Although HIV prevalence increased from 18.5% to 22.3% from 1996 through 2002, bacterial prevalence declined significantly for syphilis (16.0% to 12.4%), early syphilis (8.6% to 3.4%), and rectal gonorrhea (5.1% to 0.2%). High HIV seroincidence was estimated, with the lowest (4.8%) incidence in 1998. In 2002, HSV-2 seroprevalence was 51.0%. After adjustment for age, education, and self-reported sexual identity, our data suggest that a yearly increase by 6% in the prevalence of HIV occurred among MSM in Lima, with a corresponding decline in syphilis (by 9%), early syphilis (by 18%), and rectal gonorrhea (by 64%). Condom use during last sexual intercourse increased by 26% each year with the most recent male steady partner and, among non-sex workers, by 11% with the most recent casual partner. HIV continued to spread among MSM in Lima even when a decline in bacterial STIs and increase in condom use were estimated to occur. Intensification of medical and behavior prevention interventions is warranted for MSM in Peru.

Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard.

PubMed

Glad, Trine; Bernhardsen, Pål; Nielsen, Kaare M; Brusetti, Lorenzo; Andersen, Magnus; Aars, Jon; Sundset, Monica A

2010-01-14

Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81 degrees N, 10-33 degrees E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 x 10(4) to 1.6 x 10(6) colony forming units (cfu)/ml for the rectum swabs and 4.0 x 10(3) to 1.0 x 10(5) cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic beta-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.

Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard

PubMed Central

2010-01-01

Background Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81°N, 10-33°E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. Results A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 × 104 to 1.6 × 106 colony forming units (cfu)/ml for the rectum swabs and 4.0 × 103 to 1.0 × 105 cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic β-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. Conclusion The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations. PMID:20074323

Use of swabs for sampling epithelial cells for molecular genetics analyses in Enteroctopus

USGS Publications Warehouse

Hollenback, Nathan; Scheel, David; Gravley, Megan C.; Sage, George K.; Toussaint, Rebecca K.; Talbot, Sandra L.

2017-01-01

We evaluated the efficacy of using swabs to collect cells from the epidermis of octopus as a non-invasive DNA source for classical genetic studies, and demonstrated value of the technique by incorporating it into an effort to determine, within a day, the lineage of captured, live Enteroctopus (E. dofleini or a cryptic lineage). The cryptic lineage was targeted for captive behavioral and morphological studies, while once genetically identified, the non-target lineage could be more rapidly released back to the wild. We used commercially available sterile foamtipped swabs and a high-salt preservation buffer to collect and store paired swab and muscle (arm tip) tissue sampled from live Enteroctopus collected from Prince William Sound, Alaska. We performed a one-day extraction of DNA from epithelial swab samples and amplification of two diagnostic microsatellite loci to determine the lineage of each of the 21 individuals. Following this rapid lineage assessment, which allowed us to release non-target individuals within a day of laboratory work, we compared paired swab and muscle tissue samples from each individual to assess quantity of DNA yields and consistency of genotyping results, followed by assessment of locus-by-locus reliability of DNA extracts from swabs. Epithelial swabs yielded, on average, lower quantities of DNA (170.32 ± 74.72 (SD) ng/μL) relative to DNA obtained from tissues collected using invasive or destructive techniques (310.95 ± 147.37 (SD) ng/μL. We observed some decrease in yields of DNA from extractions of swab samples conducted 19 and 31 months after initial extractions when samples were stored at room temperature in lysis buffer. All extractions yielded quantities of DNA sufficient to amplify and score all loci, which included fragment data from 10 microsatellite loci (nine polymorphic loci and monomorphic locus EdoμA106), and nucleotide sequence data from a 528 base pair portion of the nuclear octopine dehydrogenase gene. All results from genotyping and sequencing using paired swab and muscle tissue extracts were concordant, and experimental reliability levels for multilocus genotypes generated from swab samples exceeded 97%. This technique is useful for studies in which invasive sampling is not optimal, and in remote field situations since samples can be stored at ambient temperatures for at least 31 months. The use of epithelial swabs is thus a noninvasive technique appropriate for sampling genetic material from live octopuses for use in classical genetic studies as well as supporting experimental and behavioral studies.

Chlamydial Proctitis in a Young Man Who Has Sex with Men: Misdiagnosed as Inflammatory Bowel Disease.

PubMed

Lee, Kyung Jin; Kim, Jaeyeon; Shin, Dong Hwan; Jung, Jun Oh; Koh, Seokyoung; Kim, Ka Young; Lee, Jae Min

2015-12-01

We report the case of a 20-year-old man with a 2-month history of anal pain and bloody rectal discharge. He was referred to our clinic of gastroenterology for suspected inflammatory bowel disease (IBD). The colonoscopy showed mucosal nodularities on the rectum and an anal tag. Because the colonoscopic findings were not consistent with the typical manifestations of IBD, we took an additional sexual history and performed studies for infectious proctitis, including serologic tests for Chlamydia trachomatis, Neisseria gonorrhoeae, and Treponema pallidum. He had homosexual experience, and the serologic tests and PCR of a rectal swab were positive for C. trachomatis infection. Finally he was diagnosed as having chlamydial proctitis and was treated with intramuscular ceftriaxone 250 mg in a single dose and doxycycline 100 mg orally twice daily for 7 days. After 2 months, he had no lower abdominal symptoms and his endoscopic findings were improved.

Nasal, oral and rectal microbiota of Black lion tamarins (Leontopithecus chrysopygus)

PubMed Central

Carvalho, Vania M.; Vanstreels, Ralph E.T.; Paula, Cátia D.; Kolesnikovas, Cristiane K.M.; Ramos, Maria Christina C.; Coutinho, Selene D.; Martins, Cristiana S.; Pissinatti, Alcides; Catão-Dias, José L.

2014-01-01

Black lion tamarins (Leontopithecus chrysopygus) are endangered callithrichids. Their conservation may require future translocations or reintroductions; however these approaches involve risks of pathogen introduction in the environment and stress-related opportunistic infections in these animals. In order to screen for opportunistic and potential pathogenic bacterial and fungal microbiota, ten free-ranging and ten captive Black lion tamarins were studied and the results compared. Nasal, oral and rectal swabs were collected and cultured for aerobic and facultative anaerobic bacteria and fungi, and a total 203 bacterial and 84 fungal isolates were obtained. Overall, the most frequent organisms were Staphylococcus spp., Bacillus spp., Candida spp. and Aspergillus spp. Microbiota of free-ranging and captive animals were similar in composition. A number of potentially pathogenic organisms were identified, emphasizing the importance of microbiological screening in future translocation or reintroduction conservation management programs. PMID:25763064

[The Investigation of Acanthamoeba and Other Free Living Amoeba in Swab Samples Obtained from Conjunctiva and Eye Lid].

PubMed

Yünlü, Önder; Özçelik, Semra; Arıcı, Mustafa Kemal

2015-09-01

In the study, it is aimed to determine the prevalence of Acanthamoeba and other free-living amoeba (FLA) species in the swab samples obtained from conjunctiva and lower eye lid. For this purpose, swab samples from the 500 patients'eye lid and conjunctiva were obtained who admitted to Cumhuriyet University, Research and Application Hospital, Department of Ophthalmology with variety of reasons. Swab samples were carried out using sterile cotton swab in steril tubes. The swab samples were inoculated onto non-nutrient agar (NNA). Live Escherichia coli was used as food source for the growth of the FLA. The NNA plates were incubated at 300C and examined daily using ligth microscope for two weeks. For morphotyping of the trophozoites and cysts of the FLA were used taxonomic keys. Two of the 500 swab samples (0.4%) were positive for FLA. One of them (0.2%) were identified as Acanthamoeba spp. and other was identified as Hartmannella spp. However, these patients did not reveal any complaints yet. FLA both themselves and bacteria carrying in their body as reservoirs are potential pathogen. The rapid spread of Acanthamoeba keratitis in recent years reveal that these microorganisms are in contact with the eyes.

CODIFI (Concordance in Diabetic Foot Ulcer Infection): a cross-sectional study of wound swab versus tissue sampling in infected diabetic foot ulcers in England.

PubMed

Nelson, Andrea; Wright-Hughes, Alexandra; Backhouse, Michael Ross; Lipsky, Benjamin A; Nixon, Jane; Bhogal, Moninder S; Reynolds, Catherine; Brown, Sarah

2018-01-31

To determine the extent of agreement and patterns of disagreement between wound swab and tissue samples in patients with an infected diabetic foot ulcer (DFU). Multicentre, prospective, cross-sectional study. Primary and secondary care foot ulcer/diabetic outpatient clinics and hospital wards across England. Inclusion criteria: consenting patients aged ≥18 years; diabetes mellitus; suspected infected DFU. clinically inappropriate to take either sample. Wound swab obtained using Levine's technique; tissue samples collected using a sterile dermal curette or scalpel. Coprimary: reported presence, and number, of pathogens per sample; prevalence of resistance to antimicrobials among likely pathogens. Secondary: recommended change in antibiotic therapy based on blinded clinical review; adverse events; sampling costs. 400 consenting patients (79% male) from 25 centres.Most prevalent reported pathogens were Staphylococcus aureus (43.8%), Streptococcus (16.7%) and other aerobic Gram-positive cocci (70.6%). At least one potential pathogen was reported from 70.1% of wound swab and 86.1% of tissue samples. Pathogen results differed between sampling methods in 58% of patients, with more pathogens and fewer contaminants reported from tissue specimens.The majority of pathogens were reported significantly more frequently in tissue than wound swab samples (P<0.01), with equal disagreement for S. aureus and Pseudomonas aeruginosa. Blinded clinicians more often recommended a change in antibiotic regimen based on tissue compared with wound swab results (increase of 8.9%, 95% CI 2.65% to 15.3%). Ulcer pain and bleeding occurred more often after tissue collection versus wound swabs (pain: 9.3%, 1.3%; bleeding: 6.8%, 1.5%, respectively). Reports of tissue samples more frequently identified pathogens, and less frequently identified non-pathogens compared with wound swab samples. Blinded clinicians more often recommended changes in antibiotic therapy based on tissue compared with wound swab specimens. Further research is needed to determine the effect of the additional information provided by tissue samples. ISRCTN52608451. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Estimation of the sensitivity of various environmental sampling methods for detection of Salmonella in duck flocks.

PubMed

Arnold, Mark E; Mueller-Doblies, Doris; Gosling, Rebecca J; Martelli, Francesca; Davies, Robert H

2015-01-01

Reports of Salmonella in ducks in the UK currently rely upon voluntary submissions from the industry, and as there is no harmonized statutory monitoring and control programme, it is difficult to compare data from different years in order to evaluate any trends in Salmonella prevalence in relation to sampling methodology. Therefore, the aim of this project was to assess the sensitivity of a selection of environmental sampling methods, including the sampling of faeces, dust and water troughs or bowls for the detection of Salmonella in duck flocks, and a range of sampling methods were applied to 67 duck flocks. Bayesian methods in the absence of a gold standard were used to provide estimates of the sensitivity of each of the sampling methods relative to the within-flock prevalence. There was a large influence of the within-flock prevalence on the sensitivity of all sample types, with sensitivity reducing as the within-flock prevalence reduced. Boot swabs (individual and pool of four), swabs of faecally contaminated areas and whole house hand-held fabric swabs showed the overall highest sensitivity for low-prevalence flocks and are recommended for use to detect Salmonella in duck flocks. The sample type with the highest proportion positive was a pool of four hair nets used as boot swabs, but this was not the most sensitive sample for low-prevalence flocks. All the environmental sampling types (faeces swabs, litter pinches, drag swabs, water trough samples and dust) had higher sensitivity than individual faeces sampling. None of the methods consistently identified all the positive flocks, and at least 10 samples would be required for even the most sensitive method (pool of four boot swabs) to detect a 5% prevalence. The sampling of dust had a low sensitivity and is not recommended for ducks.

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

USGS Publications Warehouse

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.

PubMed

Kellogg, Christina A; Piceno, Yvette M; Tom, Lauren M; DeSantis, Todd Z; Zawada, David G; Andersen, Gary L

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease. Published by Elsevier B.V.

Evaluation of a New Environmental Sampling Protocol for Detection of Human Norovirus on Inanimate Surfaces

PubMed Central

Lee, David; Treffiletti, Aimee; Hrsak, Mario; Shugart, Jill; Vinjé, Jan

2015-01-01

Inanimate surfaces are regarded as key vehicles for the spread of human norovirus during outbreaks. ISO method 15216 involves the use of cotton swabs for environmental sampling from food surfaces and fomites for the detection of norovirus genogroup I (GI) and GII. We evaluated the effects of the virus drying time (1, 8, 24, or 48 h), swab material (cotton, polyester, rayon, macrofoam, or an antistatic wipe), surface (stainless steel or a toilet seat), and area of the swabbed surface (25.8 cm2 to 645.0 cm2) on the recovery of human norovirus. Macrofoam swabs produced the highest rate of recovery of norovirus from surfaces as large as 645 cm2. The rates of recovery ranged from 2.2 to 36.0% for virus seeded on stainless-steel coupons (645.0 cm2) to 1.2 to 33.6% for toilet seat surfaces (700 cm2), with detection limits of 3.5 log10 and 4.0 log10 RNA copies. We used macrofoam swabs to collect environmental samples from several case cabins and common areas of a cruise ship where passengers had reported viral gastroenteritis symptoms. Seventeen (18.5%) of 92 samples tested positive for norovirus GII, and 4 samples could be sequenced and had identical GII.1 sequences. The viral loads of the swab samples from the cabins of the sick passengers ranged from 80 to 31,217 RNA copies, compared with 16 to 113 RNA copies for swab samples from public spaces. In conclusion, our swab protocol for norovirus may be a useful tool for outbreak investigations when no clinical samples are available to confirm the etiology. PMID:26116675

The effect of swab sample choice on the detection of avian influenza in apparently healthy wild ducks

USGS Publications Warehouse

Ip, Hon S.; Dusek, Robert J.; Heisey, Dennis M.

2012-01-01

Historically, avian influenza viruses have been isolated from cloacal swab specimens, but recent data suggest that the highly pathogenic avian influenza (HPAI) H5N1 virus can be better detected from respiratory tract specimens. To better understand how swab sample type affects the detection ability of low pathogenic avian influenza (LPAI) viruses we collected and tested four swab types: oropharyngeal swabs (OS), cloacal swabs (CS), the two swab types combined in the laboratory (LCS), and the two swab types combined in the field (FCS). A total of 1968 wild waterfowl were sampled by each of these four methods and tested for avian influenza virus using matrix gene reverse-transcription (RT)-PCR. The highest detection rate occurred with the FCS (4.3%) followed by the CS (4.0%). Although this difference did not achieve traditional statistical significance, Bayesian analysis indicated that FCS was superior to CS with an 82% probability. The detection rates for both the LCS (2.4%) and the OS (0.4%) were significantly different from the FCS. In addition, every swab type that was matrix RT-PCR positive was also tested for recovery of viable influenza virus. This protocol reduced the detection rate, but the ordering of swab types remained the same: 1.73% FCS, 1.42% CS, 0.81% LCS, and 0% OS. Our data suggest that the FCS performed at least as well as any other swab type for detecting LPAI viruses in the wild ducks tested. When considering recent studies showing that HPAI H5N1 can be better detected in the respiratory tract, the FCS is the most appropriate sample to collect for HPAI H5N1 surveillance while not compromising LPAI studies.

Usefulness of a novel multiplex real-time PCR assay for the diagnosis of sexually-transmitted infections.

PubMed

Fernández, Gema; Martró, Elisa; González, Victoria; Saludes, Verónica; Bascuñana, Elisabet; Marcó, Clara; Rivaya, Belén; López, Evelin; Coll, Pep; Matas, Lurdes; Ausina, Vicente

2016-10-01

Sexually transmitted infections (STI) are currently on the increase worldwide. New molecular tools have been developed in the past few years in order to improve their diagnosis. An evaluation was carried out using a new commercially available real-time PCR assay, Anyplex™ II STI-7 (Seegene, Seoul, Korea), which detects seven major pathogens in a single reaction - Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Ureaplasma parvum - and compared with conventional methods performed in our laboratory. Two different populations were included, and 267 specimens from different sites of infection (urines, endocervical swabs, rectal swabs, vaginal swabs, urethral swabs and one inguinal adenopathy) were processed for both methods. The parameters of clinical performance were calculated for C. trachomatis, N. gonorrhoeae, and T. vaginalis, and the assay achieved sensitivities (SE) from 93.94% to 100%, and specificities (SP) from 96.55% to 100%, with negative predictive values (NPV) from 93.33% to 98.85%, and positive predictive values (PPV) from 96.88% to 100%, with a very good agreement (kappa index from 0.88 to 1). Anyplex™ II STI-7 is a good tool for the reliable diagnosis of STI. Its ease of use and processing allows it to be incorporated into the day to day laboratory work. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Povidone Iodine Rectal Preparation at Time of Prostate Needle Biopsy is a Simple and Reproducible Means to Reduce Risk of Procedural Infection.

PubMed

Raman, Jay D; Lehman, Kathleen K; Dewan, Kalyan; Kirimanjeswara, Girish

2015-09-21

Single institution and population-based studies highlight that infectious complications following transrectal ultrasound guided prostate needle biopsy (TRUS PNB) are increasing. Such infections are largely attributable to quinolone resistant microorganisms which colonize the rectal vault and are translocated into the bloodstream during the biopsy procedure. A povidone iodine rectal preparation (PIRP) at time of biopsy is a simple, reproducible method to reduce rectal microorganism colony counts and therefore resultant infections following TRUS PNB. All patients are administered three days of oral antibiotic therapy prior to biopsy. The PIRP technique involves initially positioning the patient in the standard manner for a TRUS PNB. Following digital rectal examination, 15 ml of a 10% solution of commercially available povidone iodine is mixed with 5 ml of 1% lidocaine jelly to create slurry. A 4 cmx4 cm sterile gauze is soaked in this slurry and then inserted into the rectal vault for 2 min after which it is removed. Thereafter, a disposable cotton gynecologic swab is used to paint both the perianal area and the rectal vault to a distance of 3 cm from the anus. The povidone iodine solution is then allowed to dry for 2-3 min prior to proceeding with standard transrectal ultrasonography and subsequent biopsy. This PIRP technique has been in practice at our institution since March of 2012 with an associated reduction of post-biopsy infections from 4.3% to 0.6% (p=0.02). The principal advantage of this prophylaxis regimen is its simplicity and reproducibility with use of an easily available, inexpensive agent to reduce infections. Furthermore, the technique avoids exposing patients to additional systemic antibiotics with potential further propagation of multi-drug resistant organisms. Usage of PIRP at TRUS PNB, however, is not applicable for patients with iodine or shellfish allergies.

Evaluation of Copan FLOQSwab for the molecular detection of Chlamydia trachomatis by Abbott RealTime CT PCR.

PubMed

Coorevits, L; Vanscheeuwijck, C; Traen, A; Bingé, L; Ryckaert, I; Padalko, E

2015-12-01

We evaluated Copan FLOQSwabs next to Abbott swabs for the detection of Chlamydia trachomatis (CT) by Abbott RealTime PCR. We collected 1062 paired swabs from female sex workers. The study was divided in two arms, according to the order of swab collection. If the Abbott swab was collected first, 501 couples were concordant and two discordant (Abbott negative and Copan positive). If the Copan swab was collected first, 537 couples were concordant and 10 discordant (eight Abbott negative and Copan positive and two Abbott positive and Copan negative). All discordant samples contained low levels of C. trachomatis. Technical issues lead to retesting of 64 Copan and 21 Abbott swabs. Our results show that Copan FLOQSwabs can be used interchangeably with Abbott swabs. While appearing to have an advantage in detecting more positive samples, the use of Copan swabs led to a higher retesting rate due to technical errors.

Comparison of DRY and WET vaginal swabs with cervical specimens in Roche Cobas 4800 HPV and Abbott RealTime High Risk HPV tests.

PubMed

Jun, Jae Kwan; Lim, Myong Cheol; Hwang, Sang-Hyun; Shin, Hye Young; Hwang, Na Rae; Kim, Yeon-Jin; Yoo, Chong Woo; Lee, Dong Ock; Joo, Jungnam; Park, Sang-Yoon; Lee, Do-Hoon

2016-06-01

Self-collected vaginal swab samples have been proposed as an alternative specimen collection method for human papillomavirus (HPV) DNA detection. Two vaginal swabs (a cone-shaped flocked swab (DRY) and a L-shape FLOQSwab with 2mL eNAT transport medium (WET)) were compared to standard cervical samples for HPV DNA testing. Additionally, they were also compared by using Roche Cobas 4800 HPV (Roche_HPV) and Abbott Real-time High Risk HPV (Abbott_HPV) tests. Ninety-six women were prospectively enrolled from the National Cancer Center in Korea between June and August 2015. WET and DRY vaginal swabs and cervical specimens were collected. Roche_HPV and Abbott_HPV tests were performed. The Roche_HPV test on cervical specimens was used as reference. The observed agreements (kappa) of Roche_HPV and Abbott_HPV between WET and DRY swabs were 89.6% (0.790, 95% confidence interval (95% CI): 0.667-0.913) and 91.7% (0.833, 95%CI: 0.723-0.943), respectively. No statistical difference was observed between WET and DRY swabs (p>0.05 for all comparisons). For HPV16/18, the sensitivity/specificity of Roche_HPV on the DRY and WET samples presented 93.8%/96.3% and 87.5%/97.5%, respectively. For other High Risk HPV (hrHPV), the sensitivity/specificity of Roche_HPV on the DRY and WET swabs presented 91.9%/91.5% and 97.3%/98.3, respectively. The sensitivity/specificity of the Abbott_HPV on the DRY and WET swabs were 93.8%/98.8%, 87.5%/98.8% for HPV16/18, and 91.9%/93.2%, 100.0%/93.2% for other hrHPV, respectively. HPV tests performed similarly when using vaginal DRY and WET swab samples. Using DRY and WET swabs to collect vaginal specimens could be an alternative to collecting cervical samples for HPV DNA testing. Copyright © 2016 Elsevier B.V. All rights reserved.

Veterinary Forensic Pathology of Animal Sexual Abuse.

PubMed

Stern, A W; Smith-Blackmore, M

2016-09-01

Animal sexual abuse (ASA) involves harm inflicted on animals for the purposes of human sexual gratification and includes such terms as bestiality, zoophilia, zoosadism, animal sexual assault, and others. The prevalence of ASA is not known, although it may be more common than is currently perceived. Veterinarians have the skills required to identify and document cases of ASA. This article reviews the terminology, legal definitions and forms of ASA, and its social and psychological context. An investigative approach is outlined, including an alternate light source examination; collection of swabs for DNA analysis; sampling vaginal washes, rectal washes, and toenails for trace evidence and biologic analyses; radiographic studies; and a complete forensic necropsy, including histopathology. Gross lesions identified in ASA victims include injuries to the anus, rectum, penis, scrotum, nipples, and vagina; the presence of foreign bodies; and abrasions, bruising, and other evidence of nonaccidental injury. Specialized procedures, including examination using alternate light sources and screening tests to identify human seminal fluid within samples from ASA victims, are of potential value but have not been validated for use in animals. © The Author(s) 2016.

Meatal Swabs Contain Less Cellular Material and Are Associated with a Decrease in Gram Stain Smear Quality Compared to Urethral Swabs in Men.

PubMed

Jordan, Stephen J; Schwebke, Jane R; Aaron, Kristal J; Van Der Pol, Barbara; Hook, Edward W

2017-07-01

Urethral swabs are the samples of choice for point-of-care Gram stain testing to diagnose Neisseria gonorrhoeae infection and nongonococcal urethritis (NGU) in men. As an alternative to urethral swabs, meatal swabs have been recommended for the collection of urethral discharge to diagnose N. gonorrhoeae and Chlamydia trachomatis infection in certain populations by nucleic acid amplification testing (NAAT), as they involve a less invasive collection method. However, as meatal swabs could be sampling a reduced surface area and result in fewer collected epithelial cells compared to urethral swabs, the adequacy of meatal swab specimens to collect sufficient cellular material for Gram stain testing remains unknown. We enrolled 66 men who underwent either urethral or meatal swabbing and compared the cellular content and Gram stain failure rate. We measured the difference in swab cellular content using the Cepheid Xpert CT/NG sample adequacy control crossing threshold (SAC CT ) and determined the failure rate of Gram stain smears (GSS) due to insufficient cellular material. In the absence of discharge, meatal smears were associated with a significant reduction in cellular content ( P = 0.0118), which corresponded with a GSS failure rate significantly higher than that for urethral swabs (45% versus 3%, respectively; P < 0.0001). When discharge was present, there was no difference among results from urethral and meatal swabs. Therefore, if GSS testing is being considered for point-of-care diagnosis of N. gonorrhoeae infection or NGU in men, meatal swabs should be avoided in the absence of a visible discharge. Copyright © 2017 American Society for Microbiology.

Microbiological sampling of swine carcasses: a comparison of data obtained by swabbing with medical gauze and data collected routinely by excision at Swedish abattoirs.

PubMed

Lindblad, M

2007-09-15

Swab sample data from a 13-month microbiological baseline study of swine carcasses at Swedish abattoirs were combined with excision sample data collected routinely at five abattoirs. The aim was to compare the numbers of total aerobic counts, Enterobacteriaceae, and Escherichia coli, recovered by swabbing four carcass sites with gauze (total area 400 cm2) with those obtained by excision at equivalent sites (total area 20 cm2). The results are considered in relation to the process hygiene criteria that are stated in Commission Regulation (EC) No 2073/2005. These criteria apply only to destructive sampling of total aerobic counts and Enterobacteriaceae, but alternative sampling schemes, as well as alternative indicator organisms such as E. coli, are allowed if equivalent guarantees of food safety can be provided. Swab sampling resulted in higher mean log numbers of total aerobic counts at four of the five abattoirs, compared with excision, and lower or equal standard deviations at all abattoirs. The percentage of swab and excision samples positive for Enterobacteriaceae at the different abattoirs ranged from 68 to 100% and 15 to 24%, respectively. Similarly, the percentages of swab samples that were positive for E. coli were higher than the percentages of positive excision samples (range 52 to 84% and 3 to 14%, respectively). Due to the low percentage of positive excision results, the mean log numbers of Enterobacteriaceae and E. coli were only compared at two and one abattoirs, respectively, using log probability regression to substitute censored observations. Higher mean log numbers of Enterobacteriaceae were recovered by swabbing compared with excision at one abattoir, whereas the numbers of Enterobacteriaceae and E. coli did not differ significantly between sampling methods at one abattoir. This study suggests that the same process hygiene criteria as those stipulated for excision can be used for swabbing with gauze without compromising food safety. For monitoring of low numbers of Enterobacteriaceae and E. coli, like those found on swine carcasses at Swedish abattoirs, the results also show that swabbing of a relatively large area is superior to excision of a smaller area.

Experimental infection of nontarget species of rodents and birds with Brucella abortus strain RB51 vaccine

USGS Publications Warehouse

Januszewski, M.C.; Olsen, S.C.; McLean, R.G.; Clark, L.; Rhyan, Jack C.

2001-01-01

The Brucella abortus vaccine strain RB51 (SRB51) is being considered for use in the management of bnucellosis in wild bison (Bison bison) and elk (Cervus elaphus) populations in the Greater Yellowstone Area (USA). Evaluation of the vaccines safety in non-target species was considered necessary prior to field use. Between June 1998 and December 1999, ground squirrels (Spermophilus richardsonii, n = 21), deer mice (Peromyscus maniculatus, n = 14), prairie voles (Microtus ochrogaster, n = 21), and ravens (Corvus corax, n = 13) were orally inoculated with SRB51 or physiologic saline. Oral and rectal swabs and blood samples were collected for bacteriologic evaluation. Rodents were necropsied at 8 to 10 wk and 12 to 21 wk post inoculation (PI), and ravens at 7 and 11 wk PI. Spleen, liver and reproductive tissues were collected for bacteriologic and histopathologic evaluation. No differences in clinical signs, appetite, weight loss or gain, or activity were observed between saline- and SRB51-inoculated animals in all four species. Oral and rectal swabs from all species were negative throughout the study. In tissues obtained from SRB51-inoculated animals, the organism was isolated from six of seven (86%) ground squirrels, one of six (17%) deer mice, none of seven voles, and one of five (20%) ravens necropsied at 8, 8, 10, and 7 wk PI, respectively. Tissues from four of seven (57%) SRB51-inoculated ground squirrels were culture positive for the organism 12 wk PI; SRB51 was not recovered from deer mice, voles. or ravens necropsied 12, 21, or 11 wk, respectively, PI. SRB51 was not recovered from saline-inoculated ground squirrels, deer mice, or voles at any time but was recovered from one saline-inoculated raven at necropsy, 7 wk PI, likely attributable to contact with SRB51-inoculated ravens in an adjacent aviary room. Spleen was time primary tissue site of colonization in ground squirrels, followed by the liver and reproductive organs. The results indicate oral exposure to SRB51 does not produce morbidity or mortality in ravens, ground squirrels, deer mice, or prairie voles.

Molecular Characterization of the Circulating Strains of Vibrio cholerae during 2010 Cholera Outbreak in Nigeria

PubMed Central

Oyedeji, Kolawole S.; Niemogha, Mary-Theresa; Nwaokorie, Francisca O.; Bamidele, Tajudeen A.; Ochoga, Michael; Akinsinde, Kehinde A.; Brai, Bartholomew I.; Oladele, David; Omonigbehin, Emmanuel A.; Bamidele, Moses; Fesobi, Toun W.; Musa, Adesola Z.; Adeneye, Adeniyi K.; Ujah, Innocent A.

2013-01-01

This study aimed at characterizing the phenotypic and toxigenic status of circulating strains of cholera during outbreaks in Nigeria, employing molecular typing techniques. Two hundred and one samples of rectal swabs, stool, vomitus, water (from the well, borehole, sachet, stream, and tap) and disinfectants (sodium hypochlorite) were collected from three states in the country. The samples were inoculated on thiosulphate-citrate bile salt-sucrose (TCBS), Cary-Blair transport medium and smeared on glass slides for direct examination. The Vibrio cholerae isolates were serotyped, biotyped, and characterized using PCR of the cytotoxin gene A (ctxA), wbeO1, and wbfO139 gene primer. Of the 201 samples screened, 96 were positive for V. cholerae O1 (48%), with 69 (72%) positive for ctxA gene. The results from this study showed that the circulating strains of cholera in Nigeria were of Ogawa serotype, also observed in other outbreaks in Nigeria (1991, 1992, and 1996). However, the strains were of the Classical biotype and were mainly (72%) ctxA gene-positive. This current investigation has confirmed the production of cholera toxin by the circulating strains, and this could be harnessed for possible cholera vaccine production in Nigeria. PMID:23930335

HPV strain distribution in patients with genital warts in a female population sample.

PubMed

Boda, Daniel; Neagu, Monica; Constantin, Carolina; Voinescu, Razvan Nicolae; Caruntu, Constantin; Zurac, Sabina; Spandidos, Demetrios A; Drakoulis, Nikolaos; Tsoukalas, Dimitrios; Tsatsakis, Aristides M

2016-09-01

The incidence of human papillomavirus (HPV) in the human cancer domain is still a subject of intensive study. In this study, we examined cervical swab samples from 713 females with genital warts, and tested the samples for high- and low-risk genital HPV. HPV genotyping was assessed using a Genotyping test that detects HPV by the amplification of target DNA using polymerase chain reaction and nucleic acid hybridization. In total, we detected 37 anogenital HPV DNA genotypes [6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 45, 51, 52, 53, 54, 55, 56, 58, 59, 61, 62, 64, 66, 67, 68, 69, 70, 71, 72, 73 (MM9), 81, 82 (MM4), 83 (MM7), 84 (MM8), IS39 and CP6108] and investigated the incidence of these genotypes in the patients with genital warts. We found differences in the distribution of high-/low-risk strains and the incidence of high-risk strains was found to occur mainly in females under 35 years of age. The data from our study suggest that a detailed oral, rectal and genital identification of high-risk strains should be performed to visualize the entire pattern of possible triggers of carcinogenesis.

[An epidemiological investigation on a food-born outbreak of noroviru caused by Sydney 2012 G II.4 strain].

PubMed

Cai, Wen-Feng; Xie, Hua-Ping; Liu, Yu-Fei; Yuan, Jun; Xiao, Xin-Cai; Ding, Peng; Chen, Chun; Zhang, Du; Chen, Jian-Dong; Ma, Xiao-Wei; Geng, Jin-Mei; Lin, Dong-Ming; Lian, Gui-Xiong; Yang, Zhi-Cong

2013-08-01

To identify the source of infection, route of transmission and risk factors related to a cluster of acute gastroenteritis cases in a university of Guangzhou. Cases were identified according to the definition. Descriptive epidemiological approaches and case-control study designs were employed in the analysis. All the samples were tested for norovirus by RT-PCR. Positive samples were subjected to both nucleotide sequence and homology analysis. A total of 141 cases related to norovirus gastroenteritis were identified in January 8 to 21, 2013, with the attack rate as 8.5 per thousand (141/16,600). The peak in morbidity was seen on January 8 to 9. No clustering was found in different classes or dormitories. Results from the case-control study revealed that early cases were infected in Restaurant A (OR = 3.46, 95% CI: 1.07-11.16) and the cold shredded chicken set meal (OR = 17.82, 95% CI: 4.46-78.17) served at lunch (OR = 4.34, 95% CI: 1.18 -17.37) on January 7 was under suspicion. A total of 266 samples, including rectal swabs from the patients and kitchen wokers, leftover food and environmental swabs, were collected. Twenty-one samples (collected from 17 persons) were positive for norovirus by RT-PCR. About 29.6% (8/27) of the kitchen workers in the Restaurant A were tested positive for the virus. The pathogen was identified as the new norovirus genotype II.4 variant, termed Sydney 2012. The virus strains isolated from the patients among student and staff and the kitchen workers were 100% identical in their nucleotide sequence. This was the first reported acute gastroenteritis outbreak caused by the new norovirus genotype II.4 variant, Sydney 2012, which showed that the food was contaminated by the asymptomatic kitchen workers who carried the virus.

Alberta Provincial Pediatric EnTeric Infection TEam (APPETITE): epidemiology, emerging organisms, and economics.

PubMed

Freedman, Stephen B; Lee, Bonita E; Louie, Marie; Pang, Xiao-Li; Ali, Samina; Chuck, Andy; Chui, Linda; Currie, Gillian R; Dickinson, James; Drews, Steven J; Eltorki, Mohamed; Graham, Tim; Jiang, Xi; Johnson, David W; Kellner, James; Lavoie, Martin; MacDonald, Judy; MacDonald, Shannon; Svenson, Lawrence W; Talbot, James; Tarr, Phillip; Tellier, Raymond; Vanderkooi, Otto G

2015-07-31

Each year in Canada there are 5 million episodes of acute gastroenteritis (AGE) with up to 70% attributed to an unidentified pathogen. Moreover, 90% of individuals with AGE do not seek care when ill, thus, burden of disease estimates are limited by under-diagnosing and under-reporting. Further, little is known about the pathogens causing AGE as the majority of episodes are attributed to an "unidentified" etiology. Our team has two main objectives: 1) to improve health through enhanced enteric pathogen identification; 2) to develop economic models incorporating pathogen burden and societal preferences to inform enteric vaccine decision making. This project involves multiple stages: 1) Molecular microbiology experts will participate in a modified Delphi process designed to define criteria to aid in interpreting positive molecular enteric pathogen test results. 2) Clinical data and specimens will be collected from children aged 0-18 years, with vomiting and/or diarrhea who seek medical care in emergency departments, primary care clinics and from those who contact a provincial medical advice line but who do not seek care. Samples to be collected will include stool, rectal swabs (N = 2), and an oral swab. Specimens will be tested employing 1) stool culture; 2) in-house multiplex (N = 5) viral polymerase chain reaction (PCR) panel; and 3) multi-target (N = 15) PCR commercially available array. All participants will have follow-up data collected 14 days later to enable calculation of a Modified Vesikari Scale score and a Burden of Disease Index. Specimens will also be collected from asymptomatic children during their well child vaccination visits to a provincial public health clinic. Following the completion of the initial phases, discrete choice experiments will be conducted to enable a better understanding of societal preferences for diagnostic testing and vaccine policy. All of the results obtained will be integrated into economic models. This study is collecting novel samples (e.g., oral swabs) from previously untested groups of children (e.g., those not seeking medical care) which are then undergoing extensive molecular testing to shed a new perspective on the epidemiology of AGE. The knowledge gained will provide the broadest understanding of the epidemiology of vomiting and diarrhea of children to date.

Comparison of culture versus quantitative real-time polymerase chain reaction for the detection of Taylorella equigenitalis in field samples from naturally infected horses in Canada and Germany.

PubMed

Nadin-Davis, Susan; Knowles, Margaret K; Burke, Teresa; Böse, Reinhard; Devenish, John

2015-07-01

A quantitative real-time polymerase chain reaction method (qPCR) was developed and tested for the detection of Taylorella equigenitalis. It was shown to have an analytical sensitivity of 5 colony-forming units (CFU) of T. equigenitalis when applied to the testing of culture swabs that mimicked field samples, and a high analytical specificity in not reacting to 8 other commensal bacterial species associated with horses. As designed, it could also differentiate specifically between T. equigenitalis and T. asinigenitalis. The qPCR was compared to standard culture in a study that included 45 swab samples from 6 horses (1 stallion, 5 mares) naturally infected with T. equigenitalis in Canada, 39 swab samples from 5 naturally infected stallions in Germany, and 311 swab samples from 87 culture negative horses in Canada. When the comparison was conducted on an individual sample swab basis, the qPCR had a statistical sensitivity and specificity of 100% and 96.4%, respectively, and 100% and 99.1% when the comparison was conducted on a sample set basis. A comparison was also made on 203 sample swabs from the 5 German stallions taken over a span of 4 to 9 mo following antibiotic treatment. The qPCR was found to be highly sensitive and at least as good as culture in detecting the presence of T. equigenitalis in post-treatment samples. The work demonstrates that the qPCR assay described here can potentially be used to detect the presence of T. equigenitalis directly from submitted sample swabs taken from infected horses and also for determining T. equigenitalis freedom following treatment.

Comparison of culture versus quantitative real-time polymerase chain reaction for the detection of Taylorella equigenitalis in field samples from naturally infected horses in Canada and Germany

PubMed Central

Nadin-Davis, Susan; Knowles, Margaret K.; Burke, Teresa; Böse, Reinhard; Devenish, John

2015-01-01

A quantitative real-time polymerase chain reaction method (qPCR) was developed and tested for the detection of Taylorella equigenitalis. It was shown to have an analytical sensitivity of 5 colony-forming units (CFU) of T. equigenitalis when applied to the testing of culture swabs that mimicked field samples, and a high analytical specificity in not reacting to 8 other commensal bacterial species associated with horses. As designed, it could also differentiate specifically between T. equigenitalis and T. asinigenitalis. The qPCR was compared to standard culture in a study that included 45 swab samples from 6 horses (1 stallion, 5 mares) naturally infected with T. equigenitalis in Canada, 39 swab samples from 5 naturally infected stallions in Germany, and 311 swab samples from 87 culture negative horses in Canada. When the comparison was conducted on an individual sample swab basis, the qPCR had a statistical sensitivity and specificity of 100% and 96.4%, respectively, and 100% and 99.1% when the comparison was conducted on a sample set basis. A comparison was also made on 203 sample swabs from the 5 German stallions taken over a span of 4 to 9 mo following antibiotic treatment. The qPCR was found to be highly sensitive and at least as good as culture in detecting the presence of T. equigenitalis in post-treatment samples. The work demonstrates that the qPCR assay described here can potentially be used to detect the presence of T. equigenitalis directly from submitted sample swabs taken from infected horses and also for determining T. equigenitalis freedom following treatment. PMID:26130847

A comparative evaluation of feathers, oropharyngeal swabs, and cloacal swabs for the detection of H5N1 highly pathogenic avian influenza virus infection in experimentally infected chickens and ducks.

PubMed

Nuradji, Harimurti; Bingham, John; Lowther, Sue; Wibawa, Hendra; Colling, Axel; Long, Ngo Thanh; Meers, Joanne

2015-11-01

Oropharyngeal and cloacal swabs have been widely used for the detection of H5N1 highly pathogenic avian Influenza A virus (HPAI virus) in birds. Previous studies have shown that the feather calamus is a site of H5N1 virus replication and therefore has potential for diagnosis of avian influenza. However, studies characterizing the value of feathers for this purpose are not available, to our knowledge; herein we present a study investigating feathers for detection of H5N1 virus. Ducks and chickens were experimentally infected with H5N1 HPAI virus belonging to 1 of 3 clades (Indonesian clades 2.1.1 and 2.1.3, Vietnamese clade 1). Different types of feathers and oropharyngeal and cloacal swab samples were compared by virus isolation. In chickens, virus was detected from all sample types: oral and cloacal swabs, and immature pectorosternal, flight, and tail feathers. During clinical disease, the viral titers were higher in feathers than swabs. In ducks, the proportion of virus-positive samples was variable depending on viral strain and time from challenge; cloacal swabs and mature pectorosternal feathers were clearly inferior to oral swabs and immature pectorosternal, tail, and flight feathers. In ducks infected with Indonesian strains, in which most birds did not develop clinical signs, all sampling methods gave intermittent positive results; 3-23% of immature pectorosternal feathers were positive during the acute infection period; oropharyngeal swabs had slightly higher positivity during early infection, while feathers performed better during late infection. Our results indicate that immature feathers are an alternative sample for the diagnosis of HPAI in chickens and ducks. © 2015 The Author(s).

Assessment of self taken swabs versus clinician taken swab cultures for diagnosing gonorrhoea in women: single centre, diagnostic accuracy study.

PubMed

Stewart, Catherine M W; Schoeman, Sarah A; Booth, Russell A; Smith, Susan D; Wilcox, Mark H; Wilson, Janet D

2012-12-12

To compare gonorrhoea detection by self taken vulvovaginal swabs (tested with nucleic acid amplification tests) with the culture of urethral and endocervical samples taken by clinicians. Prospective study of diagnostic accuracy. 1 sexual health clinic in an urban setting (Leeds Centre for Sexual Health, United Kingdom), between March 2009 and January 2010. Women aged 16 years or older, attending the clinic for sexually transmitted infection (STI) testing and consenting to perform a vulvovaginal swab themselves before routine examination. During examination, clinicians took urethral and endocervical samples for culture and an endocervical swab for nucleic acid amplification testing. Urethra and endocervix samples were analysed by gonococcal culture. Vulvovaginal swabs and endocervical swabs were analysed by the Aptima Combo 2 (AC2) assay; positive results from this assay were confirmed with a second nucleic acid amplification test. Positive confirmation of gonorrhoea. Of 3859 women with complete data and test results, 96 (2.5%) were infected with gonorrhoea (overall test sensitivities: culture 81%, endocervical swabs with AC2 96%, vulvovaginal swabs with AC2 99%). The AC2 assays were more sensitive than culture (P<0.001), but the endocervical and vulvovaginal assays did not differ significantly (P=0.375). Specificity of all Aptima Combo 2 tests was 100%. Of 1625 women who had symptoms suggestive of a bacterial STI, 56 (3.4%) had gonorrhoea (culture 84%, endocervical AC2 100%, vulvovaginal AC2 100%). The AC2 assays were more sensitive than culture (P=0.004), and the endocervical and vulvovaginal assays were equivalent to each other. Of 2234 women who did not have symptoms suggesting a bacterial STI, 40 (1.8%) had gonorrhoea (culture 78%, endocervical AC2 90%, vulvovaginal AC2 98%). The vulvovaginal swab was more sensitive than culture (P=0.008), but there was no difference between the endocervical and vulvovaginal AC2 assays (P=0.375) or between the endocervical AC2 assay and culture (P=0.125). The endocervical swab assay performed less well in women without symptoms of a bacterial STI than in those with symptoms (90% v 100%, P=0.028), whereas the vulvovaginal swab assay performed similarly (98% v 100%, P=0.42). Self taken vulvovaginal swabs analysed by nucleic acid amplification tests are significantly more sensitive at detecting gonorrhoea than culture of clinician taken urethral and endocervical samples, and are equivalent to endocervical swabs analysed by nucleic acid amplification tests. Self taken vulvovaginal swabs are the sample of choice in women without symptoms and have the advantage of being non-invasive. In women who need a clinical examination, either a clinician taken or self taken vulvovaginal swab is recommended.

Enterovirus serotypes in patients with central nervous system and respiratory infections in Viet Nam 1997-2010.

PubMed

B'Krong, Nguyen Thi Thuy Chinh; Minh, Ngo Ngoc Quang; Qui, Phan Tu; Chau, Tran Thi Hong; Nghia, Ho Dang Trung; Do, Lien Anh Ha; Nhung, Nguyen Ngoc; Van Vinh Chau, Nguyen; Thwaites, Guy; Van Tan, Le; van Doorn, H Rogier; Thanh, Tran Tan

2018-04-12

Enteroviruses are the most common causative agents of human illness. Enteroviruses have been associated with regional and global epidemics, recently, including with severe disease (Enterovirus A71 and D68), and are of interest as emerging viruses. Here, we typed Enterovirus A-D (EV) from central nervous system (CNS) and respiratory infections in Viet Nam. Data and specimens from prospective observational clinical studies conducted between 1997 and 2010 were used. Species and serotypes were determined using type-specific RT-PCR and viral protein 1 or 4 (VP1, VP4) sequencing. Samples from patients with CNS infection (51 children - 10 CSF and 41 respiratory/rectal swabs) and 28 adults (28 CSF) and respiratory infection (124 children - 124 respiratory swabs) were analysed. Twenty-six different serotypes of the four Enterovirus species (A-D) were identified, including EV-A71 and EV-D68. Enterovirus B was associated with viral meningitis in children and adults. Hand, foot and mouth disease associated Enteroviruses A (EV-A71 and Coxsackievirus [CV] A10) were detected in children with encephalitis. Diverse serotypes of all four Enterovirus species were found in respiratory samples, including 2 polio-vaccine viruses, but also 8 CV-A24 and 8 EV-D68. With the exception of EV-D68, the relevance of these viruses in respiratory infection remains unknown. We describe the diverse spectrum of enteroviruses from patients with CNS and respiratory infections in Viet Nam between 1997 and 2010. These data confirm the global circulation of Enterovirus genera and their associations and are important for clinical diagnostics, patient management, and outbreak response.

Longitudinal Survey of Microbiota in Hospitalized Preterm Very Low Birth Weight Infants

PubMed Central

Patel, Aloka L.; Mutlu, Ece A.; Sun, Yan; Koenig, Lars; Green, Stefan; Jakubowicz, Andrew; Mryan, Janet; Engen, Phillip; Fogg, Louis; Chen, Andrea L.; Pombar, Xavier; Meier, Paula P.; Keshavarzian, Ali

2015-01-01

Objectives To examine the changes in bacteria in hospitalized preterm infants over the first month of life. Methods Rectal swabs were collected daily from 12 preterm infants. DNA was extracted from swabs from day of birth and weekly thereafter. Bacterial taxa were identified with next generation sequencing using universal bacterial primers targeted at the 16S rDNA on a 454 Roche titanium platform. Sequences were clustered into operational taxonomic units (OTUs), and taxonomy was assigned against the Greengenes databank using Qiime1.4. Quantitative PCR was used to determine the abundance of Bifidobacterium spp. Functional assessment of the microbiome was performed with PICRUSt. Results Average birth weight and gestational age were 1055g and 28 weeks, respectively. There were 6-35 different bacterial families identified in the day of birth samples, unrelated to mode of delivery. Richness decreased over hospitalization (week 1: 16.9±7.7 vs. weeks 3-5: 10.7±3.4, p<0.001). The Shannon diversity index demonstrated lowest diversity at birth, an increase at week 2, followed by a rapid decline at weeks 3-5, suggesting development of a more uniform microbiota composition after 2 weeks of NICU stay. Enterobacteriaceae, Staphylococcaceae, and Enterococcaceae constituted the majority of the bacterial families. Bifidobacterium spp. were infrequently detected at very low levels. PICRUSt analysis revealed enhancement of peroxisome, PPAR and adipocytokine signaling; plant-pathogen interaction; and aminobenzoate degradation pathways in week 1 samples. Conclusions Our results suggest that while preterm infants have individualized microbiota that are detectable at birth, the differences decrease during the neonatal intensive care unit hospitalization with increasing prominence of pathogenic microbiota. PMID:26230901

Sensitive diagnosis of cutaneous leishmaniasis by lesion swab sampling coupled to qPCR

PubMed Central

ADAMS, EMILY R.; GOMEZ, MARIA ADELAIDA; SCHESKE, LAURA; RIOS, RUBY; MARQUEZ, RICARDO; COSSIO, ALEXANDRA; ALBERTINI, AUDREY; SCHALLIG, HENK; SARAVIA, NANCY GORE

2015-01-01

SUMMARY Variation in clinical accuracy of molecular diagnostic methods for cutaneous leishmaniasis (CL) is commonly observed depending on the sample source, the method of DNA recovery and the molecular test. Few attempts have been made to compare these variables. Two swab and aspirate samples from lesions of patients with suspected CL (n = 105) were evaluated alongside standard diagnosis by microscopic detection of amastigotes or culture of parasites from lesion material. Three DNA extraction methods were compared: Qiagen on swab and aspirate specimens, Isohelix on swabs and Boil/Spin of lesion aspirates. Recovery of Leishmania DNA was evaluated for each sample type by real-time polymerase chain reaction detection of parasitic 18S rDNA, and the diagnostic accuracy of the molecular method determined. Swab sampling combined with Qiagen DNA extraction was the most efficient recovery method for Leishmania DNA, and was the most sensitive (98%; 95% CI: 91–100%) and specific (84%; 95% CI: 64–95%) approach. Aspirated material was less sensitive at 80% (95% CI: 70–88%) and 61% (95% CI: 50–72%) when coupled to Qiagen or Boil-Spin DNA extraction, respectively. Swab sampling of lesions was painless, simple to perform and coupled with standardized DNA extraction enhances the feasibility of molecular diagnosis of CL. PMID:25111885

Concordance in diabetic foot ulceration: a cross-sectional study of agreement between wound swabbing and tissue sampling in infected ulcers.

PubMed

Nelson, E Andrea; Wright-Hughes, Alexandra; Brown, Sarah; Lipsky, Benjamin A; Backhouse, Michael; Bhogal, Moninder; Ndosi, Mwidimi; Reynolds, Catherine; Sykes, Gill; Dowson, Christopher; Edmonds, Michael; Vowden, Peter; Jude, Edward B; Dickie, Tom; Nixon, Jane

2016-11-01

There is inadequate evidence to advise clinicians on the relative merits of swabbing versus tissue sampling of infected diabetic foot ulcers (DFUs). To determine (1) concordance between culture results from wound swabs and tissue samples from the same ulcer; (2) whether or not differences in bacterial profiles from swabs and tissue samples are clinically relevant; (3) concordance between results from conventional culture versus polymerase chain reaction (PCR); and (4) prognosis for patients with an infected DFU at 12 months' follow-up. This was a cross-sectional, multicentre study involving patients with diabetes and a foot ulcer that was deemed to be infected by their clinician. Microbiology specimens for culture were taken contemporaneously by swab and by tissue sampling from the same wound. In a substudy, specimens were also processed by PCR. A virtual 'blinded' clinical review compared the appropriateness of patients' initial antibiotic regimens based on the results of swab and tissue specimens. Patients' case notes were reviewed at 12 months to assess prognosis. The main study recruited 400 patients, with 247 patients in the clinical review. There were 12 patients in the PCR study and 299 patients in the prognosis study. Patients' median age was 63 years (range 26-99 years), their diabetes duration was 15 years (range 2 weeks-57 years), and their index ulcer duration was 1.8 months (range 3 days-12 years). Half of the ulcers were neuropathic and the remainder were ischaemic/neuroischaemic. Tissue results reported more than one pathogen in significantly more specimens than swabs {86.1% vs. 70.1% of patients, 15.9% difference [95% confidence interval (CI) 11.8% to 20.1%], McNemar's p -value < 0.0001}. The two sampling techniques reported a difference in the identity of pathogens for 58% of patients. The number of pathogens differed in 50.4% of patients. In the clinical review study, clinicians agreed on the need for a change in therapy for 73.3% of patients (considering swab and tissue results separately), but significantly more tissue than swab samples required a change in therapy. Compared with traditional culture, the PCR technique reported additional pathogens for both swab and tissue samples in six (50%) patients and reported the same pathogens in four (33.3%) patients and different pathogens in two (16.7%) patients. The estimated healing rate was 44.5% (95% CI 38.9% to 50.1%). At 12 months post sampling, 45 (15.1%) patients had died, 52 (17.4%) patients had a lower-extremity ipsilateral amputation and 18 (6.0%) patients had revascularisation surgery. We did not investigate the potential impact of microbiological information on care. We cannot determine if the improved information yield from tissue sampling is attributable to sample collection, sample handling, processing or reporting. Tissue sampling reported both more pathogens and more organisms overall than swabbing. Both techniques missed some organisms, with tissue sampling missing fewer than swabbing. Results from tissue sampling more frequently led to a (virtual) recommended change in therapy. Long-term prognosis for patients with an infected foot ulcer was poor. Research is needed to determine the effect of sampling/processing techniques on clinical outcomes and antibiotic stewardship. The National Institute for Health Research Health Technology Assessment programme.

Apparatus for Sampling Surface Contamination

NASA Technical Reports Server (NTRS)

Wells, Mark

2008-01-01

An apparatus denoted a swab device has been developed as a convenient means of acquiring samples of contaminants from surfaces and suspending the samples in liquids. (Thereafter, the liquids can be dispensed, in controlled volumes, into scientific instruments for analysis of the contaminants.) The swab device is designed so as not to introduce additional contamination and to facilitate, simplify, and systematize the dispensing of controlled volumes of liquid into analytical instruments. The swab device is a single apparatus into which are combined all the equipment and materials needed for sampling surface contamination. The swab device contains disposable components stacked together on a nondisposable dispensing head. One of the disposable components is a supply cartridge holding a sufficient volume of liquid for one complete set of samples. (The liquid could be clean water or another suitable solvent, depending on the application.) This supply of liquid is sealed by Luer valves. At the beginning of a sampling process, the user tears open a sealed bag containing the supply cartridge. A tip on the nondisposable dispensing head is engaged with a Luer valve on one end of the supply cartridge and rotated, locking the supply cartridge on the dispensing head and opening the valve. The swab tip includes a fabric swab that is wiped across the surface of interest to acquire a sample. A sealed bag containing a disposable dispensing tip is then opened, and the swab tip is pushed into the dispensing tip until seated. The dispensing head contains a piston that passes through a spring-loaded lip seal. The air volume displaced by this piston forces the liquid out of the supply cartridge, over the swab, and into the dispensing tip. The piston is manually cycled to enforce oscillation of the air volume and thereby to cause water to flow to wash contaminants from the swab and cause the resulting liquid suspension of contaminants to flow into the dispensing tip. After several cycles to ensure adequate mixing, liquid containing the suspended contaminant sample is dispensed. The disposable components are then removed from the dispensing head, which may then be reused with a fresh set of disposable components.

Prevalence and Risk Factors for Rectal and Urethral Sexually Transmitted Infections From Self-Collected Samples Among Young Men Who Have Sex With Men Participating in the Keep It Up! 2.0 Randomized Controlled Trial.

PubMed

Mustanski, Brian; Feinstein, Brian A; Madkins, Krystal; Sullivan, Patrick; Swann, Gregory

2017-08-01

Despite recommendations that sexually active men who have sex with men be regularly tested for sexually transmitted infections (STIs) and that testing reflect anatomical sites of potential exposure, regular testing is not widely performed, especially for rectal STIs. As such, little is known about the prevalence of rectal and urethral STIs among young men who have sex with men (YMSM). The current study examined the prevalence and risk factors for rectal and urethral chlamydia and gonorrhea in a sample of 1113 YMSM ages 18 to 29 years (mean, 24.07 years). Before participating in a randomized controlled trial for an online human immunodeficiency virus prevention program (Keep It Up! 2.0), participants completed self-report measures and self-collected urine and rectal samples. Participants mailed samples to a laboratory for nucleic acid amplification testing. Viability of self-collected samples was examined as a potential method to increase STI screening for MSM without access to STI testing clinics. Results indicated that 15.1% of participants tested positive for an STI, 13.0% for a rectal STI, 3.4% for a urethral STI, and 1.2% for both rectal and urethral STIs. Rectal chlamydia was significantly more common (8.8%) than rectal gonorrhea (5.0%). Rectal STIs were higher among black YMSM compared with white YMSM. Additionally, rectal STIs were positively associated with condomless receptive anal sex with casual partners. Findings call attention to the need for health care providers to test YMSM for rectal STIs. This study also demonstrates the viability of including self-collected samples for STI testing in an eHealth program.

Alternative sampling strategies for passive classical and African swine fever surveillance in wild boar.

PubMed

Petrov, Anja; Schotte, Ulrich; Pietschmann, Jana; Dräger, Carolin; Beer, Martin; Anheyer-Behmenburg, Helena; Goller, Katja V; Blome, Sandra

2014-10-10

In view of the fact that African swine fever (ASF) was recently introduced into the wild boar population of the European Union and that classical swine fever (CSF) keeps reoccurring, targeted surveillance is of utmost importance for early detection. Introduction of both diseases is usually accompanied by an increased occurrence of animals found dead. Thus, fallen wild boar are the main target for passive surveillance. However, encouraging reporting by hunters and sampling of these animals is difficult. Partly, these problems could be solved by providing a pragmatic sampling approach. For this reason, we assessed the applicability of three different dry/semi-dry blood swabs, namely a cotton swab, a flocked swab, and a forensic livestock swab, for molecular swine fever diagnosis. After nucleic acid extraction using manual and automated systems, routine quantitative real-time polymerase chain reactions (qPCR) were carried out. Results obtained from swabs or their fragments were compared to results generated from EDTA blood. It was shown that reliable detection of both pathogens was possible by qPCR. Shifts in genome copy numbers were observed, but they did not change the qualitative results. In general, all swabs were suitable, but the forensic swab showed slight advantages, especially in terms of cutting and further storage. Robustness of the method was confirmed by the fact that different extraction methods and protocols as well as storage at room temperature did not have an influence on the final outcome. Taken together, swab samples could be recommended as a pragmatic approach to sample fallen wild boar. Copyright © 2014 Elsevier B.V. All rights reserved.

Genetic Mutations in Blood and Tissue Samples in Predicting Response to Treatment in Patients With Locally Advanced Rectal Cancer Undergoing Chemoradiation

ClinicalTrials.gov

2017-09-08

Mucinous Adenocarcinoma of the Rectum; Recurrent Rectal Cancer; Signet Ring Adenocarcinoma of the Rectum; Stage IIA Rectal Cancer; Stage IIB Rectal Cancer; Stage IIC Rectal Cancer; Stage IIIA Rectal Cancer; Stage IIIB Rectal Cancer; Stage IIIC Rectal Cancer

Design of Microstructured Conducting Polymer Films for Enhanced Trace Explosives Detection

NASA Astrophysics Data System (ADS)

Laster, Jennifer S.

The detection of trace amounts of explosive material is critical to national security. Ion mobility spectrometer (IMS)-based contact sampling continues to be a common method employed for the detection of explosives in high security checkpoint applications, such as airport security. In this process a surface of interest, such as a passenger's hands or luggage, is probed by a swab or particle trap to collect and transfer residue to an IMS for analysis. The collection of residue on a sampling swab has been shown to be a limiting step in this detection process. As such, there is significant need to develop new materials with increased adhesion to explosive analytes and with superior particle removal abilities. Here, the design of novel sampling swabs is presented for the enhanced collection of trace explosive residue from surfaces. First, the influence of the swab microstructure on the ability to remove particles from representative substrates is demonstrated. Free-standing microstructured polypyrrole (PPy) films of a variety of dimensions and form factors are fabricated using a templated electropolymerization process. The removal of polystyrene fluorescent particles from an aluminum substrate of varying surface roughness is examined as a function of the polymer microstructure. PPy microstructured films display enhanced particle removal abilities compared to PPy non-structured and current commercial films. This increase in particle removal is attributed to the increased particle-swab contact from the microstructured films. Next, the influence of the surface chemistry of sampling swabs on the collection of a representative explosive analyte, trinitrotoluene (TNT) is explored. The surface chemistry of PPy films is modified by electropolymerizaton of an N-substituted pyrrole monomer. The surface chemistries examined include a methyl, carboxylic acid, and amino-phenyl functionality. The vapor deposition of TNT on the surface of the functionalized PPy films is quantified through ultraviolet-visible (UV-vis) absorption and compared to commercial swabbing materials of varying chemistry and surface roughness. The PPy modified films with potential sites for hydrogen bonding display the highest deposition of TNT, while the Teflon coated commercial films display the lowest interaction with TNT. Finally, the desorption and release of TNT from sampling swabs is studied as an effect of temperature and of applied bias. For successful analyte detection within an IMS, the residue collected on a sampling swab must be released from the swab, typically through a thermal desorption process. In this work the release of TNT from sampling swabs is determined through solid-phase microextraction-gas chromatography mass spectrometry (SPME-GCMS). The results of this thesis provide important information on the design considerations for the development of novel particle sampling swabs with increased performance.

Evaluation of Methods to Improve the Extraction and Recovery of DNA from Cotton Swabs for Forensic Analysis

PubMed Central

Adamowicz, Michael S.; Stasulli, Dominique M.; Sobestanovich, Emily M.; Bille, Todd W.

2014-01-01

Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C) as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol’s incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations. PMID:25549111

Sentinel surveillance for human enterovirus 71 in Sarawak, Malaysia: lessons from the first 7 years

PubMed Central

Podin, Yuwana; Gias, Edna LM; Ong, Flora; Leong, Yee-Wei; Yee, Siew-Fung; Yusof, Mohd Apandi; Perera, David; Teo, Bibiana; Wee, Thian-Yew; Yao, Sik-Chi; Yao, Sik-King; Kiyu, Andrew; Arif, Mohd Taha; Cardosa, Mary Jane

2006-01-01

Background A major outbreak of human enterovirus 71-associated hand, foot and mouth disease in Sarawak in 1997 marked the beginning of a series of outbreaks in the Asia Pacific region. Some of these outbreaks had unusually high numbers of fatalities and this generated much fear and anxiety in the region. Methods We established a sentinel surveillance programme for hand, foot and mouth disease in Sarawak, Malaysia, in March 1998, and the observations of the first 7 years are described here. Virus isolation, serotyping and genotyping were performed on throat, rectal, vesicle and other swabs. Results During this period Sarawak had two outbreaks of human enterovirus 71, in 2000 and 2003. The predominant strains circulating in the outbreaks of 1997, 2000 and 2003 were all from genogroup B, but the strains isolated during each outbreak were genetically distinct from each other. Human enterovirus 71 outbreaks occurred in a cyclical pattern every three years and Coxsackievirus A16 co-circulated with human enterovirus 71. Although vesicles were most likely to yield an isolate, this sample was not generally available from most cases and obtaining throat swabs was thus found to be the most efficient way to obtain virological information. Conclusion Knowledge of the epidemiology of human enterovirus 71 transmission will allow public health personnel to predict when outbreaks might occur and to plan interventions in an effective manner in order to reduce the burden of disease. PMID:16827926

Rates of gastrointestinal tract colonization of carbapenem-resistant Enterobacteriaceae and Pseudomonas aeruginosa in hospitals in Saudi Arabia

PubMed Central

Abdalhamid, B.; Elhadi, N.; Alabdulqader, N.; Alsamman, K.; Aljindan, R.

2016-01-01

Carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem-resistant Pseudomonas aeruginosa (CRPAE) are globally a major medical issue, especially in intensive care units. The digestive tract is the main reservoir for these isolates; therefore, rectal swab surveillance is highly recommended. The purpose of this study was to detect the prevalence of gastrointestinal tract colonization of CRE and CRPAE in patients admitted to intensive care units in Saudi Arabia. This project also aimed to characterize carbapenem-hydrolyzing enzyme production in these isolates. From February to May 2015, 200 rectal swab specimens were screened by CHROMagar KPC. Organism identification and susceptibility testing were performed using the Vitek 2 system. One CRE and 13 CRPAE strains were identified, for a prevalence of 0.5% (1/200) and 6.5% (13/200) respectively. Strains showed high genetic diversity using enterobacterial repetitive intergenic consensus sequence-based PCR. NDM type and VIM type were detected by PCR in four and one CRPAE isolates respectively. ampC overexpression was detected in eight CRPAE isolates using Mueller-Hinton agar containing 1000 μg/mL cloxacillin. CTX-M-15 type was detected in 1 CRE by PCR. The prevalence of CRE strain colonization was lower than that of CRPAE isolates. The detection of NDM and VIM in the colonizing CRPAE strains is a major infection control concern. To our knowledge, this is the first study in Saudi Arabia and the gulf region focusing on digestive tract colonization of CRE and CRPAE organisms and characterizing the mechanisms of carbapenem resistance. PMID:26933499

Quantitation of the cellular content of saliva and buccal swab samples.

PubMed

Theda, Christiane; Hwang, Seo Hye; Czajko, Anna; Loke, Yuk Jing; Leong, Pamela; Craig, Jeffrey M

2018-05-02

Buccal swabs and saliva are the two most common oral sampling methods used for medical research. Often, these samples are used interchangeably, despite previous evidence that both contain buccal cells and blood leukocytes in different proportions. For some research, such as epigenetic studies, the cell types contributing to the analysis are highly relevant. We collected such samples from twelve children and twenty adults and, using Papanicolaou staining, measured the proportions of epithelial cells and leukocytes through microscopy. To our knowledge, no studies have compared cellular heterogeneity in buccal swab and saliva samples from adults and children. We confirmed that buccal swabs contained a higher proportion of epithelial cells than saliva and that children have a greater proportion of such cells in saliva compared to adults. At this level of resolution, buccal swabs and saliva contained similar epithelial cell subtypes. Gingivitis in children was associated with a higher proportion of leukocytes in saliva samples but not in buccal swabs. Compared to more detailed and costly methods such as flow cytometry or deconvolution methods used in epigenomic analysis, the procedure described here can serve as a simple and low-cost method to characterize buccal and saliva samples. Microscopy provides a low-cost tool to alert researchers to the presence of oral inflammation which may affect a subset of their samples. This knowledge might be highly relevant to their specific research questions, may assist with sample selection and thus might be crucial information despite the ability of data deconvolution methods to correct for cellular heterogeneity.

Concordance of human papillomavirus types detected on the surface and in the tissue of genital lesions in men.

PubMed

Anic, Gabriella M; Messina, Jane L; Stoler, Mark H; Rollison, Dana E; Stockwell, Heather; Villa, Luisa L; Lazcano-Ponce, Eduardo; Gage, Christine; Silva, Roberto Jose C; Baggio, Maria L; Salmerón, Jorge; Giuliano, Anna R

2013-09-01

Swabbing the surface of a genital lesion to obtain a sample for HPV DNA testing is less invasive than a biopsy, but may not represent HPV types present in the lesion tissue. The objective of this study was to examine the concordance of HPV types detected in swab and biopsy samples from 165 genital lesions from men ages 18-70. Lesions included 90 condyloma, 10 penile intraepithelial neoplasia (PeIN), 23 non-condyloma with a known histology, and 42 lesions with an undetermined histology. All lesions were sampled by swabbing the surface of the lesion with a pre-wetted Dacron swab and taking a shave biopsy. HPV genotyping was performed using Linear Array for swab samples and INNO-LiPA for biopsy samples. The kappa and McNemar statistics were used to compare the concordance of detecting HPV types in swab and biopsy samples. Both sampling methods had high agreement for detection of HPV DNA in condyloma (87.8% agreement) and PeIN (100% agreement). There was also high concordance for detection of HPV16 (kappa = 1.00) and HPV18 (kappa = 1.00) in PeIN, however, agreement was low to moderate for detecting HPV6 (kappa = 0.31) and HPV11 (kappa = 0.56) in condyloma. Low to moderate agreement was also observed between sampling methods for detecting individual HPV types in the non-condyloma and lesions with an indefinite histology. The results suggest that obtaining a biopsy in addition to swabbing the surface of a lesion may provide additional information about specific HVP types associated with male genital lesions. Copyright © 2013 Wiley Periodicals, Inc.

[Effect of oral administration of probiotics on intestinal colonization with drug-resistant bacteria in preterm infants].

PubMed

Hua, Xin-Tian; Tang, Jun; Mu, De-Zhi

2014-06-01

To evaluate the effect of oral administration of probiotics on intestinal colonization with drug-resistant bacteria among preterm infants in the neonatal intensive care unit (NICU). A double-blind, randomized, placebo-controlled trial was carried out in the preterm infants who were transferred to the NICU immediately after birth. These infants were stratified by whether they were breastfed and then randomized into test group and control group. The test group was given probiotics from the day when enteral feeding began, while the control group was treated conventionally without probiotics. The two groups were compared in terms of the colonization with extended-spectrum beta-lactamase-producing bacteria, as assessed by rectal swabs on days 1, 3, 7, and 14 after birth, and the incidence of diseases. Rectal colonization with drug-resistant bacteria was found in the test group (n=119) and control group (n=138) on days 1, 3, 7, and 14 after birth. There were no significant differences in the incidence of late-onset sepsis and necrotizing enterocolitis between the two groups (P>0.05). Among non-breastfed infants, the test group had significantly decreased rectal colonization with drug-resistant bacteria compared with the control group on day 14 after birth (71.1% vs 88.9%; P=0.04). No probiotic-related adverse events were observed in the study. Oral administration of probiotics may reduce rectal colonization with drug-resistant bacteria in preterm infants under certain conditions and shows good safety.

Cost-effectiveness of culture-guided antimicrobial prophylaxis for the prevention of infections after prostate biopsy.

PubMed

Li, Chi-Kong; Tong, Brian C Y; You, Joyce H S

2016-02-01

Clinical findings suggest that the use of rectal culture-guided antibiotic prophylaxis reduces the infection rate following transrectal ultrasound-guided prostate biopsy (TRUSBx). A decision-analytic model was designed to compare the outcomes of TRUSBx performed with (rectal culture-guided group) and without (standard ciprofloxacin prophylaxis) rectal swab culture-guided antimicrobial prophylaxis in Hong Kong. The post-biopsy infection rate, infection-related costs, quality-adjusted life years (QALYs) lost for infection, and incremental cost per QALY saved (ICER) were assessed. Model inputs were retrieved from local epidemiology data and the medical literature. A sensitivity analysis was performed to test the robustness of the model results. Base-case analysis showed that the infection rate in the culture-guided group was reduced from 2.42% to 0.23% and saved 0.0002 QALYs, with a lower cost (USD 31.4 versus USD 55.6) (USD 1=HKD 7.8). The number needed to screen to prevent an infection episode was 45.7. The hospital days avoided per 100 patients using culture-guided prophylaxis was 7.08 days. The relative effectiveness of culture-guided antimicrobial prophylaxis versus standard prophylaxis in carriers and non-carriers of FQ-resistant rectal flora were identified as potential influencing factors. In 10000 Monte Carlo simulations, ICERs of the culture-guided group were below the willingness-to-pay threshold 99.12% of the time. Using rectal culture-guided antimicrobial prophylaxis for men undergoing TRUSBx appears to be a cost-saving strategy to avert post-biopsy infection and QALY loss in Hong Kong. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Epidemic Outbreak Surveillance (EOS)

DTIC Science & Technology

2006-07-01

Experiment to Test Integrity of2003 Nasal Wash and Throat Swab Samples Stored at -80°C. September 2005 (Sue WorthyLuke Daum) Seven matched pairs of...Nasal Wash and Throat Swab samples, previously tested in September 2004 for Influenza A, were pulled from the -80°C storage freezer for re-testing...January 2006 a detailed vrocess was completed to inventorv and organize the sample storage freezers for all Nasal wash, Throat swab and PAXgene

The acceptability and validity of self-collected nasal swabs for detection of influenza virus infection among older adults in Thailand.

PubMed

Goyal, Sonal; Prasert, Kriengkrai; Praphasiri, Prabda; Chittaganpitch, Malinee; Waicharoen, Sunthareeya; Ditsungnoen, Darunee; Jaichuang, Siriluk; Lindblade, Kim A

2017-09-01

Self-collection of nasal swabs could improve the timeliness of influenza virus detection in older adults. Measure the acceptability, adequacy, timeliness, and validity of self-collected nasal swabs among adults >65 years in Thailand. Our evaluation consisted of two parts: a one-month study among randomly selected, community-dwelling older adults to simulate community-based surveillance for acute respiratory infections (ARI); and a clinic study of older adults with ARI to evaluate the sensitivity and specificity of self-collected nasal swabs for influenza virus infection compared with healthcare worker (HCW)-collected nasal and nasopharyngeal swabs. In the community study, 24% of participants experienced an ARI during the observation period. All (100%) participants with an ARI self-collected nasal swabs within 72 hours of symptom onset of which 92% were considered adequate samples. In the clinic study, 45% of patients with ARI presented within 72 hours of symptom onset. The sensitivity of self-collected nasal swabs for detection of influenza virus infection was 78% (95% CI 40-97) compared to nasopharyngeal and 88% (95% CI 47-100) compared to nasal swabs collected by HCWs. Specificity was 100% (95% CI 97-100) compared to both methods. Self-collection of nasal swabs was found acceptable by 99% of participants in both studies. Self-collection of nasal swabs was acceptable to older adults in Thailand who were able to take adequate samples. Self-collection of nasal swabs may improve the timeliness of sample collection but lower sensitivity will need to be considered. © 2017 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

The role of drinking water in the transmission of antimicrobial-resistant E. coli.

PubMed

Coleman, B L; Salvadori, M I; McGeer, A J; Sibley, K A; Neumann, N F; Bondy, S J; Gutmanis, I A; McEwen, S A; Lavoie, M; Strong, D; Johnson, I; Jamieson, F B; Louie, M

2012-04-01

To determine whether drinking water contaminated with antimicrobial-resistant E. coli is associated with the carriage of resistant E. coli, selected households sending water samples to Ontario and Alberta laboratories in 2005-2006 were asked to participate in a cross-sectional study. Household members aged ≥12 years were asked to complete a questionnaire and to submit a rectal swab. In 878 individuals, 41% carried a resistant strain of E. coli and 28% carried a multidrug-resistant strain. The risk of carriage of resistant E. coli was 1·26 times higher for users of water contaminated with resistant E. coli. Other risk factors included international travel [prevalence ratio (PR) 1·33], having a child in nappies (PR 1·33), being male (PR 1·33), and frequent handling of raw red meats (PR 1·10). Protecting private water sources (e.g. by improving systems to test and treat them) may help slow the emergence of antimicrobial resistance in E. coli.

Characterization of Tn3000, a Transposon Responsible for blaNDM-1 Dissemination among Enterobacteriaceae in Brazil, Nepal, Morocco, and India.

PubMed

Campos, Juliana Coutinho; da Silva, Maria José Félix; dos Santos, Paulo Roberto Nascimento; Barros, Elaine Menezes; Pereira, Mayne de Oliveira; Seco, Bruna Mara Silva; Magagnin, Cibele Massotti; Leiroz, Leonardo Kalab; de Oliveira, Théo Gremen Mimary; de Faria-Júnior, Célio; Cerdeira, Louise Teixeira; Barth, Afonso Luís; Sampaio, Suely Carlos Ferreira; Zavascki, Alexandre Prehn; Poirel, Laurent; Sampaio, Jorge Luiz Mello

2015-12-01

In Enterobacteriaceae, the blaNDM genes have been found in many different genetic contexts, and a wide diversity of plasmid scaffolds bearing those genes has been found. In August 2013, we identified NDM-1-producing Escherichia coli and Enterobacter hormaechei strains from a single rectal swab sample from a patient hospitalized in Rio de Janeiro, Brazil, who had no history of travel abroad. Complete DNA sequencing using the Illumina platform and annotation of the two plasmids harboring the blaNDM-1 gene, one from each strain, showed that they belonged to incompatibility groups IncFIIK and IncX3 and harbored a novel transposon named Tn3000. Similar genetic structures have been identified among other isolates in Brazil but also on plasmids from other continents. Our findings suggest that the blaNDM-1 gene may be transmitted by Tn3000 in different parts of the world. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Surveillance of feral cats for influenza A virus in north central Florida.

PubMed

Gordy, James T; Jones, Cheryl A; Rue, Joanne; Crawford, Patti Cynda; Levy, Julie K; Stallknecht, David E; Tripp, Ralph A; Tompkins, Stephen M

2012-09-01

Transmission of highly pathogenic avian influenza and the recent pandemic H1N1 viruses to domestic cats and other felids creates concern because of the morbidity and mortality associated with human infections as well as disease in the infected animals. Experimental infections have demonstrated transmission of influenza viruses in cats. An epidemiologic survey of feral cats was conducted to determine their exposure to influenza A virus. Feral cat sera and oropharyngeal and rectal swabs were collected from November 2008 through July 2010 in Alachua County, FL and were tested for evidence of influenza A virus infection by virus isolation, PCR, and serological assay. No virus was isolated from any of 927 cats examined using MDCK cell or embryonated chicken egg culture methods, nor was viral RNA detected by RT-PCR in 200 samples tested. However, 0.43% of cats tested antibody positive for influenza A by commercial ELISA. These results suggest feral cats in this region are at minimal risk for influenza A virus infection. © 2011 Blackwell Publishing Ltd.

The paralytic poliomyelitis epidemic of 1978 in Jordan: epidemiological implications

PubMed Central

Khuri-Bulos, Najwa; Melnick, Joseph L.; Hatch, Milford H.; Dawod, Saleh T.

1984-01-01

Poliomyelitis is endemic in Jordan, but until 1978 there were no epidemics. In that year, 66 children were admitted to the Jordan University Hospital with a paralytic illness, compared with 13 in 1979 and 11 in 1980. The epidemic reached a peak in the summer and fall of 1978. While 54% of the patients had not received any vaccine, 19% had received 3 doses of oral poliovaccine; 82% of the cases were in children less than 2 years of age, and all belonged to the lower socioeconomic group. There were 28 deaths with complications of the disease. Poliovirus was isolated from 10 out of 14 rectal swab samples examined (9 with poliovirus 1, 1 with poliovirus 2), and from 4 out of 13 throat specimens from the same patients. It is concluded that as a result of improving living standards in Jordan and neighbouring countries, more epidemics may occur unless immunization efforts against poliomyelitis are intensified. PMID:6609022

Comparison of two non-invasive methods of microbial analysis in surgery practice: incision swabbing and the indirect imprint technique.

PubMed

Chovanec, Zdenek; Veverkova, Lenka; Votava, Miroslav; Svoboda, Jiri; Jedlicka, Vaclav; Capov, Ivan

2014-12-01

A variety of methods exist to take samples from surgical site infections for cultivation; however, an unambiguous and suitable method has not yet been defined. The aim of our retrospective non-randomized study was to compare two non-invasive techniques of sampling material for microbiologic analysis in surgical practice. We compared bacteria cultured from samples obtained with the use of the swab technique, defined in our study as the gold standard, with the indirect imprint technique. A cotton-tipped swab (Copan, Brescia, Italy) was used; the imprints were taken using Whatman no. 4 filter paper (Macherey-Nagal, Duren, Germany) cut into 5×5 cm pieces placed on blood agar in a Petri dish. To culture the microorganisms in the microbiology laboratory, we used blood agar, UriSelect 4 medium (Bio-Rad, Marnes-la-Coquette, France), and a medium with sodium chloride (blood agar with salt). After careful debridement, a sample was taken from the incision surface by swab and subsequently the same area of the surface was imprinted onto filter paper. The samples were analyzed in the microbiology laboratory under standard safety precautions. The cultivation results of the two techniques were processed statistically using contingency tables and the McNemar test. Those samples that were simultaneously cultivation-positive by imprint and -negative by swabbing were processed in greater detail. Over the period between October 2008 and March 2013, 177 samples from 70 patients were analyzed. Sampling was carried out from 42 males and 28 females. One hundred forty-six samples were from incisions after operations (21 samples from six patients after operation on the thoracic cavity, 73 samples from 35 patients after operation on the abdominal cavity combined with the gastrointestinal tract, 52 samples from 19 patients with other surgical site infections not included above) and 31 samples from 11 patients with no post-operative infection. One patient had a sample taken both from a post-operative and a non-post-operative site. Coincidently, the most frequent cultivation finding with both techniques was a sterile one (imprint, 62; swab, 50). The microorganism cultivated most frequently after swabbing was Pseudomonas aeruginosa (22 cases), compared with Escherichia coli when the filter paper (imprint) was used (31 cases). The imprint technique was evaluated as more sensitive compared with swabbing (p=0.0001). The κ statistic used to evaluate the concordance between the two techniques was 0.302. Of the 177 samples there were 53 samples simultaneously sterile using the swab and positive in the imprint. In three samples colony- forming units (CFU) were not counted; 22 samples were within the limit of 0-25×10(1) CFU/cm(2), 20 samples within the limit of 25×10(1)-25×10(2) CFU/cm(2), five within the limit of 25×10(2)-25×10(3) CFU/cm(2), and three of more than 25×10(4) CFU/cm(2). The hypothesis of swabbing as a more precise technique was not confirmed. In our study the imprint technique was more sensitive than swabbing; the strength of agreement was fair. We obtained information not only on the type of the microorganism cultured, but also on the number of viable colonies, expressed in CFU/cm(2).

Comparison of direct selective versus nonselective agar media plus LIM broth enrichment for determination of group B streptococcus colonization status in pregnant women.

PubMed

Elsayed, Sameer; Gregson, Daniel B; Church, Deirdre L

2003-06-01

Group B streptococcus (GBS) is the most common cause of early-onset neonatal sepsis in developed countries, and determination of the GBS colonization status in pregnant patients near term is essential for the provision of prophylactic measures to prevent early-onset disease. To determine if GBS recovery rates and/or result turnaround times for vaginal or combined vaginal/rectal swab specimens from pregnant patients near term are enhanced if swabs are inoculated initially onto selective versus nonselective agar media, in addition to the standard Centers for Disease Control and Prevention method. Prospective laboratory analysis. Urban health region/centralized diagnostic microbiology laboratory. Pregnant women presenting for routine obstetrical care and collection of vaginal or combined vaginal/rectal swab specimens for GBS testing at 35 to 37 weeks' gestation. Culture of specimens directly onto selective (5% sheep blood with colistin and nalidixic acid) or nonselective (5% sheep blood) agar media, in addition to LIM broth enrichment and terminal subculture. Group B streptococcus recovery rate and culture result turnaround time. A total of 639 specimens were tested, with 128 (20%) positive for GBS. Sixty-three isolates were recovered on direct agar media at 24 hours, of which 16 (12.5%) were isolated on selective plates only. An additional 38 isolates were recovered at 48 hours from direct plates. Twenty-seven (21.1%) isolates that failed to grow on direct plates were recovered from the LIM broth subculture only. Three (2.3%) isolates not recovered from LIM broths were detected at 48 hours on the direct selective (2 isolates) and nonselective (1 isolate) agar plates. A 24-hour result turnaround time was achieved for 63 (49.2%) and 47 (36.7%) of the 128 culture-positive specimens for direct selective and nonselective plates, respectively (chi2 = 76.63, P <.001). Use of direct selective agar media, in addition to LIM broth enrichment, for the determination of the GBS colonization status in pregnant patients near term results in decreased turnaround time for reporting positive results.

Comparison of sampling methods for the detection of human rhinovirus RNA.

PubMed

Waris, Matti; Österback, Riikka; Lahti, Elina; Vuorinen, Tytti; Ruuskanen, Olli; Peltola, Ville

2013-09-01

Obtaining a nasal swab (NS) from a child for human rhinovirus (HRV) RNA detection is simple and well tolerated even for repeated sampling, but only few studies have compared them qualitatively and quantitatively with other sampling methods. Real-time PCR was used to study the stability of HRV genomes in swabs, and to compare different swabs and induced sputum specimens with nasopharyngeal aspirates (NPAs). Replicate swabs in a dry test tube were stored at room temperature or mailed to the laboratory before freezing, and compared to freshly frozen specimens. To compare sampling methods, paediatric patients had NPA, NS and throat swab collected. In paired sputum and NPA specimens, viral load was correlated to the amount of β-actin mRNA. Specimens were stable at room temperature for at least 4 days and survived mailing without loss of HRV detectability. As compared to NPA, NS had an equal diagnostic sensitivity, with no significant quantitative difference using flocked nylon swabs and a 2.2-fold drop in the average copy number using cotton swabs. The diagnostic sensitivity of cotton swab-collected throat specimens was 97%, with a 26-fold lower mean copy number. Sputum specimens had higher HRV RNA (2.3-fold) and β-actin mRNA (1.6-fold) copy numbers than NPAs, but there was a poor correlation between HRV RNA and β-actin mRNA. HRV remains well detectable by PCR in specimens mailed to the laboratory. The diagnostic efficacy of NPA can be obtained with NS, quantitative comparison and patient comfort favouring flocked nylon-tipped over cotton-tipped swabs. Copyright © 2013 Elsevier B.V. All rights reserved.

Validation of Performance of the Gen-Probe Human Immunodeficiency Virus Type 1 Viral Load Assay with Genital Swabs and Breast Milk Samples

PubMed Central

DeVange Panteleeff, Dana; Emery, Sandra; Richardson, Barbra A.; Rousseau, Christine; Benki, Sarah; Bodrug, Sharon; Kreiss, Joan K.; Overbaugh, Julie

2002-01-01

Human immunodeficiency type 1 (HIV-1) continues to spread at an alarming rate. The virus may be transmitted through blood, genital secretions, and breast milk, and higher levels of systemic virus in the index case, as measured by plasma RNA viral load, have been shown to correlate with increased risk of transmitting HIV-1 both vertically and sexually. Less is known about the correlation between transmission and HIV-1 levels in breast milk or genital secretions, in part because reliable quantitative assays to detect HIV-1 in these fluids are not available. Here we show that the Gen-Probe HIV-1 viral load assay can be used to accurately quantify viral load in expressed breast milk and in cervical and vaginal samples collected on swabs. Virus could be quantified from breast milk and swab samples spiked with known amounts of virus, including HIV-1 subtypes A, C, and D. As few as 10 copies of HIV-1 RNA could be detected above background threshold levels in ≥77% of assays performed with spiked breast milk supernatants and mock swabs. In genital swab samples from HIV-1-infected women, similar levels of HIV-1 RNA were consistently detected in duplicate swabs taken from the same woman on the same clinic visit, suggesting that the RNA values from a single swab sample can be used to measure genital viral load. PMID:12409354

Comparison of sampling sites and laboratory diagnostic tests for S. equi subsp. equi in horses from confirmed strangles outbreaks.

PubMed

Lindahl, S; Båverud, V; Egenvall, A; Aspán, A; Pringle, J

2013-01-01

Strangles is a contagious equine-specific disease caused by Streptococcus equi subsp. equi. Unfortunately, detection of S. equi can fail in up to 40% of horses with strangles. Whereas recent molecular biologic methods and sampling techniques have improved recovery of S. equi optimal sampling methods and laboratory analyses remain ill-defined. To determine the yield of S. equi from horses with acute strangles in confirmed outbreaks by field-sampling methods subjected to culture and biochemical identification, and real-time PCR directly and after culture. Fifty-seven horses of varying breeds and ages from 8 strangles outbreaks. Prospective study. Culture with biochemical identification and real-time PCR directly, and from culture, were performed on nasal swabs, nasopharyngeal swabs, and nasopharyngeal lavages. Real-time PCR directly from samples identified the highest number of infected horses, with 45/57 nasal swabs, 41/57 nasopharyngeal swabs, and 48/57 nasopharyngeal lavages S. equi positive. Biochemical identification (highest positives 22/57) was inferior to real-time PCR for S. equi recovery regardless of sampling method. Real-time PCR of nasopharyngeal lavage directly and after culture yielded 52/57 positives whereas direct real-time PCR of nasopharyngeal lavage combined with either nasopharyngeal swabs or nasal swabs yielded 53/57 positives. Three horses were negative on all samples. Nasopharyngeal lavage analyzed by a combination of real-time PCR directly and after culture or, alternatively, real-time PCR directly on a nasopharyngeal lavage and a nasal/nasopharyngeal swab can identify S. equi in over 90% of acute strangles cases. Copyright © 2013 by the American College of Veterinary Internal Medicine.

Culture-Independent Evaluation of the Appendix and Rectum Microbiomes in Children with and without Appendicitis

PubMed Central

Davenport, Katherine P.; Fraser, Claire M.; Sandler, Anthony D.; Zeichner, Steven L.

2014-01-01

Purpose The function of the appendix is largely unknown, but its microbiota likely contributes to function. Alterations in microbiota may contribute to appendicitis, but conventional culture studies have not yielded conclusive information. We conducted a pilot, culture-independent 16S rRNA-based microbiota study of paired appendix and rectal samples. Methods We collected appendix and rectal swabs from 21 children undergoing appendectomy, six with normal appendices and fifteen with appendicitis (nine perforated). After DNA extraction, we amplified and sequenced 16S rRNA genes and analyzed sequences using CLoVR. We identified organisms differing in relative abundance using ANOVA (p<0.05) by location (appendix vs. rectum), disease (appendicitis vs. normal), and disease severity (perforated vs. non-perforated). Results We identified 290 taxa in the study's samples. Three taxa were significantly increased in normal appendices vs. normal rectal samples: Fusibacter (p = 0.009), Selenomonas (p = 0.026), and Peptostreptococcus (p = 0.049). Five taxa were increased in abundance in normal vs. diseased appendices: Paenibacillaceae (p = 0.005), Acidobacteriaceae GP4 (p = 0.019), Pseudonocardinae (p = 0.019), Bergeyella (p = 0.019) and Rhizobium (p = 0.045). Twelve taxa were increased in the appendices of appendicitis patients vs. normal appendix: Peptostreptococcus (p = 0.0003), Bilophila (p = 0.0004), Bulleidia (p = 0.012), Fusobacterium (p = 0.018), Parvimonas (p = 0.003), Mogibacterium (p = 0.012), Aminobacterium (p = 0.019), Proteus (p = 0.028), Actinomycineae (p = 0.028), Anaerovorax (p = 0.041), Anaerofilum (p = 0.045), Porphyromonas (p = 0.010). Five taxa were increased in appendices in patients with perforated vs. nonperforated appendicitis: Bulleidia (p = 0.004), Fusibacter (p = 0.005), Prevotella (p = 0.021), Porphyromonas (p = 0.030), Dialister (p = 0.035). Three taxa were increased in rectum samples of patients with appendicitis compared to the normal patients: Bulleidia (p = 0.034), Dialister (p = 0.003), and Porphyromonas (p = 0.026). Conclusion Specific taxa are more abundant in normal appendices compared to the rectum, suggesting that a distinctive appendix microbiota exists. Taxa with altered abundance in diseased and severely diseased (perforated) samples may contribute to appendicitis pathogenesis, and may provide microbial signatures in the rectum useful for guiding both treatment and diagnosis of appendicitis. PMID:24759879

Nipah Virus Contamination of Hospital Surfaces during Outbreaks, Bangladesh, 2013–2014

PubMed Central

Sazzad, Hossain M.S.; Luby, Stephen P.; Sturm-Ramirez, Katharine; Bhuiyan, Mejbah Uddin; Rahman, Mohammed Ziaur; Islam, Md Muzahidul; Ströher, Ute; Sultana, Sharmin; Kafi, Mohammad Abdullah Heel; Daszak, Peter; Rahman, Mahmudur; Gurley, Emily S.

2018-01-01

Nipah virus (NiV) has been transmitted from patient to caregivers in Bangladesh presumably through oral secretions. We aimed to detect whether NiV-infected patients contaminate hospital surfaces with the virus. During December 2013–April 2014, we collected 1 swab sample from 5 surfaces near NiV-infected patients and tested surface and oral swab samples by real-time reverse transcription PCR for NiV RNA. We identified 16 Nipah patients; 12 cases were laboratory-confirmed and 4 probable. Of the 12 laboratory-confirmed cases, 10 showed NiV RNA in oral swab specimens. We obtained surface swab samples for 6 Nipah patients; 5 had evidence of NiV RNA on >1 surface: 4 patients contaminated towels, 3 bed sheets, and 1 the bed rail. Patients with NiV RNA in oral swab samples were significantly more likely than other Nipah patients to die. To reduce the risk for fomite transmission of NiV, infection control should target hospital surfaces. PMID:29260663

Nipah Virus Contamination of Hospital Surfaces during Outbreaks, Bangladesh, 2013-2014.

PubMed

Hassan, Md Zakiul; Sazzad, Hossain M S; Luby, Stephen P; Sturm-Ramirez, Katharine; Bhuiyan, Mejbah Uddin; Rahman, Mohammed Ziaur; Islam, Md Muzahidul; Ströher, Ute; Sultana, Sharmin; Kafi, Mohammad Abdullah Heel; Daszak, Peter; Rahman, Mahmudur; Gurley, Emily S

2018-01-01

Nipah virus (NiV) has been transmitted from patient to caregivers in Bangladesh presumably through oral secretions. We aimed to detect whether NiV-infected patients contaminate hospital surfaces with the virus. During December 2013-April 2014, we collected 1 swab sample from 5 surfaces near NiV-infected patients and tested surface and oral swab samples by real-time reverse transcription PCR for NiV RNA. We identified 16 Nipah patients; 12 cases were laboratory-confirmed and 4 probable. Of the 12 laboratory-confirmed cases, 10 showed NiV RNA in oral swab specimens. We obtained surface swab samples for 6 Nipah patients; 5 had evidence of NiV RNA on >1 surface: 4 patients contaminated towels, 3 bed sheets, and 1 the bed rail. Patients with NiV RNA in oral swab samples were significantly more likely than other Nipah patients to die. To reduce the risk for fomite transmission of NiV, infection control should target hospital surfaces.

The Extraction and Recovery Efficiency of Pure DNA for Different Types of Swabs.

PubMed

Bruijns, Brigitte B; Tiggelaar, Roald M; Gardeniers, Han

2018-06-11

The extraction and recovery efficiency of swabs used to collect evidence at crime scenes is relatively low (typically <50%) for bacterial spores and body fluids. Cell-free deoxyribonucleic acid (DNA) is an interesting alternative compared to whole cells as a source for forensic analysis, but extraction and recovery from swabs has not been tested before using pure DNA. In this study cotton, foam, nylon flocked, polyester and rayon swabs are investigated in order to collect pure DNA isolated from saliva samples. The morphology and absorption capacity of swabs is studied. Extraction and recovery efficiencies are determined and compared to the maximum theoretical efficiency. The results indicate that a substantial part of DNA is not extracted from the swab and some types of swab seem to bind effectively with DNA. The efficiency of the different types of swab never exceeds 50%. The nylon flocked 4N6FLOQSwab used for buccal sampling performs the best. © 2018 The Authors. Journal of Forensic Sciences published by Wiley Periodicals, Inc. on behalf of American Academy of Forensic Sciences.

Environmental swabs as a tool in norovirus outbreak investigation, including outbreaks on cruise ships.

PubMed

Boxman, Ingeborg L A; Dijkman, Remco; te Loeke, Nathalie A J M; Hägele, Geke; Tilburg, Jeroen J H C; Vennema, Harry; Koopmans, Marion

2009-01-01

In this study, we investigated whether environmental swabs can be used to demonstrate the presence of norovirus in outbreak settings. First, a procedure was set up based on viral RNA extraction using guanidium isothiocyanate buffer and binding of nucleic acids to silica. Subsequently, environmental swabs were taken at 23 Dutch restaurants and four cruise ships involved in outbreaks of gastroenteritis. Outbreaks were selected based on clinical symptoms consistent with viral gastroenteritis and time between consumption of suspected food and onset of clinical symptoms (>12 h). Norovirus RNA was demonstrated by real-time reverse transcriptase PCR in 51 of 86 (59%) clinical specimens from 12 of 14 outbreaks (86%), in 13 of 90 (14%) food specimens from 4 of 18 outbreaks (22%), and in 48 of 119 (40%) swab specimens taken from 14 of 27 outbreaks (52%). Positive swab samples agreed with positive clinical samples in seven outbreaks, showing identical sequences. Furthermore, norovirus was detected on swabs taken from kitchen and bathroom surfaces in five outbreaks in which no clinical samples were collected and two outbreaks with negative fecal samples. The detection rate was highest for outbreaks associated with catered meals and lowest for restaurant-associated outbreaks. The use of environmental swabs may be a useful tool in addition to testing of food and clinical specimens, particularlywhen viral RNA is detected on surfaces used for food preparation.

Protocol for the Meningococcal Control Programme - Canadian Forces Base Cornwallis and Canadian Forces Base St. Jean 1980/81,

DTIC Science & Technology

1980-11-01

hours, then overnight in a refrigerator or cold room at 40C. Fol- lowing clot retraction , the serum may be decanted and spun, or the whole sample spun...Drogram. The SIMP programme may involve one or all of the following: collection of post nasal swabs, blood sera samples, air samples and surface samples...outlined in para 16. 16. Culturing of Swabs Swabs shall be placed on Columbia Blood Agar (4 or 5% sheep RBC’s) supplemented with IsoVitalex (Baltimore

Development of a Real-Time PCR Protocol Requiring Minimal Handling for Detection of Vancomycin-Resistant Enterococci with the Fully Automated BD Max System.

PubMed

Dalpke, Alexander H; Hofko, Marjeta; Zimmermann, Stefan

2016-09-01

Vancomycin-resistant enterococci (VRE) are an important cause of health care-associated infections, resulting in significant mortality and a significant economic burden in hospitals. Active surveillance for at-risk populations contributes to the prevention of infections with VRE. The availability of a combination of automation and molecular detection procedures for rapid screening would be beneficial. Here, we report on the development of a laboratory-developed PCR for detection of VRE which runs on the fully automated Becton Dickinson (BD) Max platform, which combines DNA extraction, PCR setup, and real-time PCR amplification. We evaluated two protocols: one using a liquid master mix and the other employing commercially ordered dry-down reagents. The BD Max VRE PCR was evaluated in two rounds with 86 and 61 rectal elution swab (eSwab) samples, and the results were compared to the culture results. The sensitivities of the different PCR formats were 84 to 100% for vanA and 83.7 to 100% for vanB; specificities were 96.8 to 100% for vanA and 81.8 to 97% for vanB The use of dry-down reagents and the ExK DNA-2 kit for extraction showed that the samples were less inhibited (3.3%) than they were by the use of the liquid master mix (14.8%). Adoption of a cutoff threshold cycle of 35 for discrimination of vanB-positive samples allowed an increase of specificity to 87.9%. The performance of the BD Max VRE assay equaled that of the BD GeneOhm VanR assay, which was run in parallel. The use of dry-down reagents simplifies the assay and omits any need to handle liquid PCR reagents. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Validation of Single and Pooled Manure Drag Swabs for the Detection of Salmonella Serovar Enteritidis in Commercial Poultry Houses.

PubMed

Kinde, Hailu; Goodluck, Helen A; Pitesky, Maurice; Friend, Tom D; Campbell, James A; Hill, Ashley E

2015-12-01

Single swabs (cultured individually) are currently used in the Food and Drug Administration (FDA) official method for sampling the environment of commercial laying hens for the detection of Salmonella enterica ssp. serovar Enteritidis (Salmonella Enteritidis). The FDA has also granted provisional acceptance of the National Poultry Improvement Plan's (NPIP) Salmonella isolation and identification methodology for samples taken from table-egg layer flock environments. The NPIP method, as with the FDA method, requires single-swab culturing for the environmental sampling of laying houses for Salmonella Enteritidis. The FDA culture protocol requires a multistep culture enrichment broth, and it is more labor intensive than the NPIP culture protocol, which requires a single enrichment broth. The main objective of this study was to compare the FDA single-swab culturing protocol with that of the NPIP culturing protocol but using a four-swab pool scheme. Single and multi-laboratory testing of replicate manure drag swab sets (n  =  525 and 672, respectively) collected from a Salmonella Enteritidis-free commercial poultry flock was performed by artificially contaminating swabs with either Salmonella Enteritidis phage type 4, 8, or 13a at one of two inoculation levels: low, x¯  = 2.5 CFU (range 2.5-2.7), or medium, x¯  = 10.0 CFU (range 7.5-12). For each replicate, a single swab (inoculated), sets of two swabs (one inoculated and one uninoculated), and sets of four swabs (one inoculated and three uninoculated), testing was conducted using the FDA or NPIP culture method. For swabs inoculated with phage type 8, the NPIP method was more efficient (P < 0.05) for all swab sets at both inoculation levels than the reference method. The single swabs in the NPIP method were significantly (P < 0.05) better than four-pool swabs in detecting Salmonella Enteritidis at the lower inoculation level. In the collaborative study (n  =  13 labs) using Salmonella Enteritidis phage type 13a inoculated swabs, there was no significant difference (P > 0.05) between the FDA method (single swabs) and the pooled NPIP method (four-pool swabs). The study concludes that the pooled NPIP method is not significantly different from the FDA method for the detection of Salmonella Enteritidis in drag swabs in commercial poultry laying houses. Consequently based on the FDA's Salmonella Enteritidis rule for equivalency of different methods, the pooled NPIP method should be considered equivalent. Furthermore, the pooled NPIP method was more efficient and cost effective.

Comparative study of selective chromogenic (chromID VRE) and bile esculin agars for isolation and identification of vanB-containing vancomycin-resistant enterococci from feces and rectal swabs.

PubMed

Grabsch, E A; Ghaly-Derias, S; Gao, W; Howden, B P

2008-12-01

The new chromogenic agar chromID VRE (cIDVRE; bioMérieux) was compared with bile esculin agar (BD) containing 6 mg/liter vancomycin for the detection of colonization with vanB-containing vancomycin-resistant enterococci (VRE). At 48 h of incubation, the results obtained with both media were comparable. However, cIDVRE detected significantly more VRE at 24 h (39.3% versus 21.3%, P = 0.003), and its use may facilitate the timely implementation of infection control procedures.

HPV-11 variability, persistence and progression to genital warts in men: the HIM study.

PubMed

Flores-Díaz, Ema; Sereday, Karen A; Ferreira, Silvaneide; Sirak, Bradley; Sobrinho, João Simão; Baggio, Maria Luiza; Galan, Lenice; Silva, Roberto C; Lazcano-Ponce, Eduardo; Giuliano, Anna R; Villa, Luisa L; Sichero, Laura

2017-09-01

HPV-11 and HPV-6 are the etiological agents of about 90 % of genital warts (GWs). The intra-typic variability of HPV-11 and its association with infection persistence and GW development remains undetermined. Here, HPV infection in men (HIM) participants who had an HPV-11 genital swab and/or GW, preceded or not by a normal skin genital swab were analysed. Genomic variants were characterized by PCR-sequencing and classified within lineages (A, B) and sublineages (A1, A2, A3, A4). HPV-11 A2 variants were the most frequently detected in the genital swab samples from controls and in both genital swabs and GW samples from cases. The same HPV-11 variant was detected in the GW sample and its preceding genital swab. There was a lack of association between any particular HPV-11 variant and the increased risk for GW development.

Rates of colonization with extended-spectrum β-lactamase-producing Escherichia coli in Canadian travellers returning from South Asia: a cross-sectional assessment

PubMed Central

Peirano, Gisele; Gregson, Daniel B.; Kuhn, Susan; Vanderkooi, Otto G.; Nobrega, Diego B.; Pitout, Johann D.D.

2017-01-01

Background: A previous study in Calgary showed that travel to India was associated with high risk of community-onset infections with extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. We performed a follow-up study to determine the rate of rectal acquisition of ESBL-producing E. coli among travellers to South Asia and to identify the behaviours putting such travellers at high risk for acquiring ESBL-producing E. coli. Methods: The study was performed at a travel clinic in Calgary. Travellers 18 years or older who were planning to visit South Asia for a period of at least 5 days were included. Three rectal swabs were obtained, and 2 questionaires were administered (before and after travel). Results: A total of 149 travellers participated between January 2012 and July 2014; of these, 116 (78%) provided rectal swabs upon return to Calgary and completed both pre- and post-travel questionaires. Of the 109 travellers without colonization with ESBL-producing E. coli upon enrollment, 70 (64%) acquired ESBL-producing E. coli during travel. Of the 90 participants who visited India, 66 (73%) were positive for ESBL-producing E. coli upon their return to Calgary. Most ESBL-producing E. coli specimens were identified as producing the enzyme CTX-M-15. Behaviours associated with a statistically significant risk of acquiring ESBL-producing E. coli included visiting India (odds ratio [OR] 19.9, 95% confidence interval [CI] 4.5-88.8), consuming meals with the local population (OR 6.9, 95% CI 1.2-39.6), taking any type of antibiotic during travel (OR 4.3, 95% CI 1.3-14.3) and travelling for any purpose other than business (OR 12.4, 95% CI 2.8-55.2). Interpretation: In this study, travel to India was associated with the highest risk of acquiring ESBL-producing E. coli relative to travel to other countries in South Asia. Nonbusiness travel, consuming foods with the local population and the use of antibiotics while travelling were associated with an increased risk of acquiring these antibiotic-resistant organisms while in India. Trial registration: ClinicalTrials.gov, no. NCT01296165. PMID:29246886

Isolation of Canine parvovirus with a view to identify the prevalent serotype on the basis of partial sequence analysis.

PubMed

Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P N; Sharma, N S

2015-01-01

The aim of this study was to isolate Canine parvovirus (CPV) from suspected dogs on madin darby canine kidney (MDCK) cell line and its confirmation by polymerase chain reaction (PCR) and nested PCR (NPCR). Further, VP2 gene of the CPV isolates was amplified and sequenced to determine prevailing antigenic type. A total of 60 rectal swabs were collected from dogs showing signs of gastroenteritis, processed and subjected to isolation in MDCK cell line. The samples showing cytopathic effects (CPE) were confirmed by PCR and NPCR. These samples were subjected to PCR for amplification of VP2 gene of CPV, sequenced and analyzed to study the prevailing antigenic types of CPV. Out of the 60 samples subjected to isolation in MDCK cell line five samples showed CPE in the form of rounding of cells, clumping of cells and finally detachment of the cells. When these samples and the two commercially available vaccines were subjected to PCR for amplification of VP2 gene, a 1710 bp product was amplified. The sequence analysis revealed that the vaccines belonged to the CPV-2 type and the samples were of CPV-2b type. It can be concluded from the present study that out of a total of 60 samples 5 samples exhibited CPE as observed in MDCK cell line. Sequence analysis of the VP2 gene among the samples and vaccine strains revealed that samples belonged to CPV-2b type and vaccines belonging to CPV-2.

Frequent Detection of Human Adenovirus from the Lower Gastrointestinal Tract in Men Who Have Sex with Men

PubMed Central

Curlin, Marcel E.; Huang, Meei-Li; Lu, Xiaoyan; Celum, Connie L.; Sanchez, Jorge; Selke, Stacy; Baeten, Jared M.; Zuckerman, Richard A.; Erdman, Dean D.; Corey, Lawrence

2010-01-01

Background The association between baseline seropositivity to human adenovirus (HAdV) type 5 and increased HIV acquisition in the Step HIV Vaccine Study has raised questions concerning frequency of acquired and/or persistent Adenovirus infections among adults at high risk of HIV-1 infection. Methodology To evaluate the frequency and pattern of HAdV shedding from the lower GI tract, we retrospectively tested rectal swabs for HAdVs in a cohort of 20 HSV-2 positive HIV-positive Peruvian men who have sex with men (MSM) undergoing rectal swabbing three times/week for 18 consecutive weeks, in a prospective study of HSV-2 suppression in HIV infection. Viral DNA was extracted and amplified using a sensitive multiplex PCR assay that detects all currently recognized HAdV types. Molecular typing of viruses was performed on selected samples by hexon gene sequencing. Baseline neutralizing antibody titers to HAdVs −5, −26, −35 and −48 were also assessed. Principal Findings 15/20 individuals had HAdV detected during follow up. The median frequency of HAdV detection was 30% of samples (range 2.0% to 64.7%). HAdV shedding typically occurred on consecutive days in clustered episodes lasting a median of 4 days (range 1 to 9 days) separated by periods without shedding, suggesting frequent new infections or reactivation of latent infections over time. 8 of the 15 shedders had more than one type detected in follow-up. 20 HAdV types from species B, C, and D were identified, including HAdV-5, −26 and −48, HAdV types under development as potential vaccine candidates. 14/20 subjects were seropositive for HAdV-5; 15/20 for HAdV-26; 3/20 for HAdV-35; and 2/20 for HAdV-48. HAdV shedding did not correlate with CD4 count, plasma HIV-1 viral load, or titers to HAdV-5 or HAdV-35. The sole individual with HAdV-5 shedding was HAdV-5 seropositive. Conclusions HAdV shedding was highly prevalent and diverse, including types presently under consideration as HIV vaccine vectors. Subclinical HAdV infection of the GI tract is common among MSM in Peru; the prevalence of HAdV in the enteric tract should be evaluated in other populations. The association between ongoing recent enteric HAdV and the immune response to recombinant HAdV vaccines should be evaluated. PMID:20593015

Optimizing Virus Identification in Critically Ill Children Suspected of Having an Acute Severe Viral Infection.

PubMed

Randolph, Adrienne G; Agan, Anna A; Flanagan, Ryan F; Meece, Jennifer K; Fitzgerald, Julie C; Loftis, Laura L; Truemper, Edward J; Li, Simon; Ferdinands, Jill M

2016-04-01

Multiplex rapid viral tests and nasopharyngeal flocked swabs are increasingly used for viral testing in PICUs. This study aimed at evaluating how the sampling site and the type of diagnostic test influence test results in children with suspected severe viral infection. Prospective cohort study. PICUs at 21 tertiary pediatric referral centers in the United States. During the 2010-2011 and 2011-2012 influenza seasons, we enrolled children (6 mo to 17 yr old) who were suspected to have severe viral infection. We collected samples by using a standardized protocol for nasopharyngeal aspirate and nasopharyngeal flocked swabs in nonintubated patients and for endotracheal tube aspirate and nasopharyngeal flocked swabs in intubated patients. Viral testing included a single reverse transcription-polymerase chain reaction influenza test and the GenMark Respiratory Viral Panel (20 viruses). We enrolled 90 endotracheally intubated and 133 nonintubated children. We identified influenza in 45 patients with reverse transcription-polymerase chain reaction testing; the multiplex panel was falsely negative for influenza in two patients (4.4%). Six patients (13.3%) had not been diagnosed with influenza in the PICU. Non-influenza viruses were identified in 172 of 223 children (77.1%). In nonintubated children, the same virus was identified by nasopharyngeal flocked swabs and nasopharyngeal aspirate in 133 of 183 paired samples (72.7%), with +nasopharyngeal aspirate/-nasopharyngeal flocked swabs in 32 of 183 paired samples (17.4%). In intubated children, the same virus was identified by nasopharyngeal flocked swabs and endotracheal tube aspirate in 67 of 94 paired samples (71.3%), with +nasopharyngeal flocked swabs/- endotracheal tube aspirate in 22 of 94 paired samples (23.4%). Most discrepancies were either adenovirus or rhinovirus in both groups. Standardized specimen collection and sensitive diagnostic testing with a reverse transcription-polymerase chain reaction increased the identification of influenza in critically ill children. For most pathogenic viruses identified, results from nasopharyngeal flocked swabs agreed with those from nasopharyngeal or endotracheal aspirates.

Simplifying sampling for African swine fever surveillance: Assessment of antibody and pathogen detection from blood swabs.

PubMed

Carlson, J; Zani, L; Schwaiger, T; Nurmoja, I; Viltrop, A; Vilem, A; Beer, M; Blome, S

2018-02-01

African swine fever (ASF) is a notifiable disease with serious socio-economic consequences that has been present in wild boar in the Baltic States and Poland since 2014. An introduction of ASF is usually accompanied by increased mortality, making fallen wild boar and hunted animals with signs of disease the main target for early warning and passive surveillance. It is difficult, however, to encourage hunters and foresters to report and take samples from these cases. A pragmatic and easy sampling approach with quick-drying swabs could facilitate this. In this study, we further evaluated the use of dry blood swabs for the detection of ASFV antibody and genome with samples from animal trials and diagnostic submissions (blood, bone and organs) from Estonia. Compared to serum samples, dried blood swabs yielded 93.1% (95% confidence interval: [83.3, 98.1]) sensitivity and 100% [95.9, 100.0] specificity in a commercial ASFV antibody ELISA. Similarly, the swabs gave a sensitivity of 98.9% [93.4, 100.0] and a specificity of 98.1% [90.1, 100.0] for genome detection by a standard ASFV p72 qPCR when compared to EDTA blood. The same swabs were tested in a VP72-antibody lateral flow device, with a sensitivity of 94.7% [85.4, 98.9] and specificity of 96.1% [89.0, 99.2] compared to the serum ELISA. When GenoTube samples tested in ELISA and LFD were compared, the sensitivity was 96.3% [87.3, 99.5] and the specificity was 93.8% [86.0, 97.9]. This study demonstrates reliable detection of ASFV antibody and genome from swabs. A field test of the swabs with decomposed wild boar carcasses in an endemic area in Estonia also gave promising results. Thus, this technique is a practical approach for surveillance of ASF in both free and endemic areas. © 2017 Blackwell Verlag GmbH.

Direct PCR amplification of DNA from human bloodstains, saliva, and touch samples collected with microFLOQ® swabs.

PubMed

Ambers, Angie; Wiley, Rachel; Novroski, Nicole; Budowle, Bruce

2018-01-01

Previous studies have shown that nylon flocked swabs outperform traditional fiber swabs in DNA recovery due to their innovative design and lack of internal absorbent core to entrap cellular materials. The microFLOQ ® Direct swab, a miniaturized version of the 4N6 FLOQSwab ® , has a small swab head that is treated with a lysing agent which allows for direct amplification and DNA profiling from sample collection to final result in less than two hours. Additionally, the microFLOQ ® system subsamples only a minute portion of a stain and preserves the vast majority of the sample for subsequent testing or re-analysis, if desired. The efficacy of direct amplification of DNA from dilute bloodstains, saliva stains, and touch samples was evaluated using microFLOQ ® Direct swabs and the GlobalFiler™ Express system. Comparisons were made to traditional methods to assess the robustness of this alternate workflow. Controlled studies with 1:19 and 1:99 dilutions of bloodstains and saliva stains consistently yielded higher STR peak heights than standard methods with 1ng input DNA from the same samples. Touch samples from common items yielded single source and mixed profiles that were consistent with primary users of the objects. With this novel methodology/workflow, no sample loss occurs and therefore more template DNA is available during amplification. This approach may have important implications for analysis of low quantity and/or degraded samples that plague forensic casework. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Development, validation and testing of a skin sampling method for assessment of metal exposure.

PubMed

Erfani, Behnaz; Midander, Klara; Lidén, Carola; Julander, Anneli

2017-07-01

Nickel, cobalt and chromium are frequent skin sensitizers. Skin exposure results in eczema in sensitized individuals, the risk being related to the skin dose. To develop a self-sampling method for quantification of skin exposure to metals, to validate the method, and to assess its feasibility. Defined metal doses (0.01-5 µg) were applied to the fingers of 5 participants. Skin areas (2 cm 2 ) were sampled with 1% HNO 3 , either as 0.1 ml on a swab, or as 0.5 ml on a wipe. Furthermore, 17 participants performed self-sampling by swab after 2 h of leisure activity. Samples were extracted in 1% HNO 3 and analysed by inductively coupled plasma mass spectrometry. The sampling efficiency by swab was 46%, as compared with 93% for acid wipe sampling, for all tested doses. Most metal from the skin dose was detected in the first swab (33-43%). Despite lower sampling efficiency by swab, skin doses of metals following 2 h of leisure activity without hand washing were quantified in all participants, and ranged from 0.0016 to 0.15 µg/cm 2 , from 0.00014 to -0.0020 µg/cm 2 and from 0.00048 to -0.027 µg/cm 2 for nickel, cobalt, and chromium, respectively. The results indicate a future potential of skin sampling by swab to detect and monitor metals on skin by self-sampling. This will contribute to better knowledge of metal skin exposure among dermatitis patients, workers, and the general population. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Assessment of two different types of sample for the early detection and isolation of thermophilic Campylobacter in broiler farms.

PubMed

Urdaneta, Saulo; Dolz, Roser; Cerdà-Cuéllar, Marta

2015-01-01

In order to assess the optimal method for the early detection and isolation of thermophilic Campylobacter in broilers at farm level, two types of samples were compared: caecal contents obtained by necropsy and cloacal swabs transported in charcoal Amies medium. The study was conducted in five batches of broilers from five different farms, where weekly samples (caecal contents and cloacal swabs) from 30 birds were obtained. Samples were plated onto selective agar (modified charcoal cefoperazone desoxycholate agar, mCCDA) for Campylobacter isolation. Four out of five batches were positive for Campylobacter. No marked differences in sensitivity of both sample types were observed. However, a higher percentage of positive birds were detected when cloacal swabs were used. The results show that cloacal swab samples are adequate, and in some cases even better than caecal samples for the early detection of Campylobacter in broiler flocks at farm level. Also, this sample avoids sacrificing birds to test Campylobacter, which not only allows saving time in sample collection, transportation and processing at the laboratory, but also improves bird welfare and cost of sampling.

Surface-sampling and analysis of TATP by swabbing and gas chromatography/mass spectrometry.

PubMed

Romolo, Francesco Saverio; Cassioli, Luigi; Grossi, Silvana; Cinelli, Giuseppe; Russo, Mario Vincenzo

2013-01-10

The method of sample recovery for trace detection and identification of explosives plays a critical role in several criminal investigations. After bombing, there can be difficulties in sending big objects to a laboratory for analysis. Traces can also be searched for on large surfaces, on hands of suspects or on surfaces where the explosive was placed during preparatory phases (e.g. places where an IED was assembled, vehicles used for transportation, etc.). In this work, triacetone triperoxide (TATP) was synthesized from commercial precursors following reported methods. Several portions of about 6mg of TATP were then spread on different surfaces (e.g. floors, tables, etc.) or used in handling tests. Three different swabbing systems were used: a commercial swab, pre-wetted with propan-2-ol (isopropanol) and water (7:3), dry paper swabs, and cotton swabs wetted with propan-2-ol. Paper and commercial swabs were also used to sample a metal plate, where a small charge of about 4g of TATP was detonated. Swabs were sealed in small glass jars with screw caps and Parafilm(®) M and sent to the laboratory for analysis. Swabs were extracted and analysed several weeks later by gas chromatography/mass spectrometry. All the three systems gave positive results, but wetted swabs collected higher amounts of TATP. The developed procedure showed its suitability for use in real cases, allowing TATP detection in several simulations, including a situation in which people wash their hands after handling the explosive. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Comparison of vaginal microbiota sampling techniques: cytobrush versus swab.

PubMed

Mitra, Anita; MacIntyre, David A; Mahajan, Vishakha; Lee, Yun S; Smith, Ann; Marchesi, Julian R; Lyons, Deirdre; Bennett, Phillip R; Kyrgiou, Maria

2017-08-29

Evidence suggests the vaginal microbiota (VM) may influence risk of persistent Human Papillomavirus (HPV) infection and cervical carcinogenesis. Established cytology biobanks, typically collected with a cytobrush, constitute a unique resource to study such associations longitudinally. It is plausible that compared to rayon swabs; the most commonly used sampling devices, cytobrushes may disrupt biofilms leading to variation in VM composition. Cervico-vaginal samples were collected with cytobrush and rayon swabs from 30 women with high-grade cervical precancer. Quantitative PCR was used to compare bacterial load and Illumina MiSeq sequencing of the V1-V3 regions of the 16S rRNA gene used to compare VM composition. Cytobrushes collected a higher total bacterial load. Relative abundance of bacterial species was highly comparable between sampling devices (R 2  = 0.993). However, in women with a Lactobacillus-depleted, high-diversity VM, significantly less correlation in relative species abundance was observed between devices when compared to those with a Lactobacillus species-dominant VM (p = 0.0049). Cytobrush and swab sampling provide a comparable VM composition. In a small proportion of cases the cytobrush was able to detect underlying high-diversity community structure, not realized with swab sampling. This study highlights the need to consider sampling devices as potential confounders when comparing multiple studies and datasets.

Ear drainage culture

MedlinePlus

... needed. Your health care provider will use a cotton swab to collect the sample from inside the ... Using a cotton swab to take a sample of drainage from the outer ear is not painful. However, ear pain may ...

Evaluation of a new amplified enzyme immunoassay (EIA) for the detection of Chlamydia trachomatis in male urine, female endocervical swab, and patient obtained vaginal swab specimens

PubMed Central

Tanaka, M.; Nakayama, H.; Sagiyama, K.; Haraoka, M.; Yoshida, H.; Hagiwara, T.; Akazawa, K.; Naito, S.

2000-01-01

Aims—To compare the performance of a new generation dual amplified enzyme immunoassay (EIA) with a molecular method for the diagnosis of Chlamydia trachomatis, using a range of urogenital samples, and to assess the reliability of testing self collected vaginal specimens compared with clinician collected vaginal specimens. Methods—Two population groups were tested. For the first population group, first void urine samples were collected from 193 male patients with urethritis, and endocervical swabs were collected from 187 high risk commercial sex workers. All urine and endocervical specimens were tested by a conventional assay (IDEIA chlamydia), a new generation amplified immunoassay (IDEIA PCE chlamydia), and the Amplicor polymerase chain reaction (PCR). Discrepant results obtained among the three sample types were confirmed using a nested PCR test with a different plasmid target region. For the second population group, four swab specimens, including one patient obtained vaginal swab, two clinician obtained endocervical swabs, and one clinician obtained vaginal swab, were collected from 91 high risk sex workers. Self collected and clinician collected vaginal swabs were tested by IDEIA PCE chlamydia. Clinician obtained endocervical swabs were assayed by IDEIA PCE chlamydia and Amplicor PCR. Results—The performance of the IDEIA PCE chlamydia test was comparable to that of the Amplicor PCR test when male urine and female endocervical swab specimens were analysed. The relative sensitivities of IDEIA, IDEIA PCE, and Amplicor PCR on male first void urine specimens were 79.3%, 91.4%, and 100%, respectively. The relative sensitivities of the three tests on female endocervical specimens were 85.0%, 95.0%, and 100%, respectively. The positivity rates for patient collected vaginal specimens and clinician collected vaginal specimens by IDEIA PCE were 25.2% and 23.1%, respectively, whereas those for clinician collected endocervical swabs by PCR and IDEIA PCE were both 27.5%. Conclusions—IDEIA PCE chlamydia is a lower cost but sensitive alternative test to PCR for testing male urine samples and female endocervical swabs. In addition, self collected or clinician collected vaginal specimens tested by IDEIA PCE chlamydia are a reliable alternative to analysing endocervical specimens. Key Words: Chlamydia trachomatis • enzyme immunoassay • clinical specimens PMID:10889816

Norovirus in feces and nasopharyngeal swab of children with and without acute gastroenteritis symptoms: First report of GI.5 in Brazil and GI.3 in nasopharyngeal swab.

PubMed

Dábilla, Nathânia; Nunes Vieira Almeida, Tâmera; Carvalho Rebouças Oliveira, Anniely; Kipnis, André; Neres Silva, Thairiny; Souza Fiaccadori, Fabíola; Teixeira de Sousa, Teresinha; de Paula Cardoso, Divina das Dôres; Souza, Menira

2017-02-01

Noroviruses (NoVs) are an important cause of acute gastroenteritis (AGE), worldwide. To evaluate the frequency, viral load and molecular profile of NoV in fecal and nasopharyngeal swab samples from hospitalized children, and to determine children's secretor status. From May 2014 to May 2015, 219 children were included in the study, 96 with gastroenteric symptoms and 123 without gastroenteric symptoms. All fecal and nasopharyngeal swab samples were screened by TaqMan RT-qPCR duplex (GI/GII NoV) and quality samples were characterized by genomic sequencing. Norovirus positivity rate in feces was 15.4% in asymptomatic and 18.8% in the symptomatic group. The median viral loads in feces were 2.69×10 8 GC/g and 4.32×10 7 GC/g from children with or without AGE symptoms, respectively. In nasopharyngeal swab samples, the NoV positivity was 11.4% in symptomatic children, with a median viral load of 2.20×10 7 GC/mL and 6.5% in asymptomatic children, with an average viral load of 1.73×10 6 GC/mL. In only two cases NoV was detected in both samples. A considerable genomic variability was observed in feces, with six genotypes being detected, as follows: GII.4, GII.6, GI.3 and GII.3, GI.2 and GI.5. Two GI.3 was detected in nasopharyngeal swab. Our data reveal considerable NoV frequencies in both nasopharyngeal and fecal samples from symptomatic and asymptomatic children. Higher viral loads were detected in samples from AGE symptomatic children, when compared to asymptomatic children. High genomic variability was observed, with this being the first report of GI.5 NoV in Brazil and of GI.3 in nasopharyngeal swab samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparative analysis between saliva and buccal swabs as source of DNA: lesson from HLA-B*57:01 testing.

PubMed

Cascella, Raffaella; Stocchi, Laura; Strafella, Claudia; Mezzaroma, Ivano; Mannazzu, Marco; Vullo, Vincenzo; Montella, Francesco; Parruti, Giustino; Borgiani, Paola; Sangiuolo, Federica; Novelli, Giuseppe; Pirazzoli, Antonella; Zampatti, Stefania; Giardina, Emiliano

2015-01-01

Our work aimed to designate the optimal DNA source for pharmacogenetic assays, such as the screening for HLA-B*57:01 allele. A saliva and four buccal swab samples were taken from 104 patients. All the samples were stored at different time and temperature conditions and then genotyped for the HLA-B*57:01 allele by SSP-PCR and classical/capillary electrophoresis. The genotyping analysis reported different performance rates depending on the storage conditions of the samples. Given our results, the buccal swab demonstrated to be more resistant and stable in time with respect to the saliva. Our investigation designates the buccal swab as the optimal DNA source for pharmacogenetic assays in terms of resistance, low infectivity, low-invasiveness and easy sampling, and safe transport in centralized medical centers providing specialized pharmacogenetic tests.

Evaluation of non-extracted genital swabs for real-time HSV PCR.

PubMed

Miari, Victoria F; Wall, Gavin R; Clark, Duncan A

2015-01-01

Nucleic acid extraction of clinical samples is accepted as a key requirement in molecular diagnostics. At Barts Health NHS Trust, swabs taken from patients with clinical suspicion of HSV infection were routinely extracted on the Qiagen MDx BioRobot prior to testing with a real-time triplex PCR for HSV1, HSV2, and VZV. The aim of this study was to adapt an existing HSV1/HSV2/VZV real-time PCR by replacing VZV with phocine herpesvirus 1 (PhHV) as an internal control (IC) and evaluate whether this adapted assay required the nucleic acid extraction step for predominantly genital swabs. First 313 non-extracted and extracted swabs were tested in parallel with the existing triplex HSV1/HSV2/VZV real-time PCR. The second stage involved testing 176 non-extracted swabs using a triplex real-time PCR for HSV1, HSV2, and PhHV and comparing the results with the samples extracted and tested by the original triplex assay. The results correlated well when the existing assay was used, with only three non-extracted samples that would have been reported as negative compared to the extracted sample result (Cq s 33, 39, 35-two samples HSV1, one sample HSV2). In the evaluation using the adapted assay containing the IC, two of 176 samples were discordant, where a HSV negative non-extracted sample result would have been reported differently to the extracted sample result (Cq s 32, 33-both HSV1). This study demonstrated that it is feasible to test non-extracted swabs for HSV in a real-time PCR that includes an IC. J. Med. Virol. 87: 125-129, 2015. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

An outbreak of norovirus-associated acute gastroenteritis associated with contaminated barrelled water in many schools in Zhejiang, China

PubMed Central

Sheng, Minyang; Song, Jianqiang; He, Fan; Qiu, Yinwei; Wu, Haocheng; Lu, Qinbao; Feng, Yan; Lin, Junfen; Chen, Enfu; Chai, Chengliang

2017-01-01

Objectives More than 900 students and teachers at many schools in Jiaxing city developed acute gastroenteritis in February 2014. An immediate epidemiological investigation was conducted to identify the pathogen, infection sources and route of transmission. Methods The probable cases and confirmed cases were defined as students or teachers with diarrhoea or vomiting present since the term began in February 2014. An active search was conducted for undiagnosed cases among students and teachers. Details such as demographic characteristics, gastrointestinal symptoms, and drinking water preference and frequency were collected via a uniform epidemiological questionnaire. A case-control study was implemented, and odds ratios (ORs) and 95% confidence intervals were calculated. Rectal swabs from several patients, food handlers and barrelled water factory workers, as well as water and food samples, were collected to test for potential bacteria and viruses. Results A total of 924 cases fit the definition of the probable case, including 8 cases of laboratory-confirmed norovirus infection at 13 schools in Jiaxing city between February 12 and February 21, 2014. The case-control study demonstrated that barrelled water was a risk factor (OR: 20.15, 95% CI: 2.59–156.76) and that bottled water and boiled barrelled water were protective factors (OR: 0.31, 95% CI: 0.13–0.70, and OR: 0.36, 95% CI: 0.16–0.77). A total of 11 rectal samples and 8 barrelled water samples were detected as norovirus-positive, and the genotypes of viral strains were the same (GII). The norovirus that contaminated the barrelled water largely came from the asymptomatic workers. Conclusions This acute gastroenteritis outbreak was caused by barrelled water contaminated by norovirus. The outbreak was controlled after stopping the supply of barrelled water. The barrelled water supply in China represents a potential source of acute gastroenteritis outbreaks due to the lack of surveillance and supervision. Therefore, more attention should be paid to this area. PMID:28170414

An outbreak of norovirus-associated acute gastroenteritis associated with contaminated barrelled water in many schools in Zhejiang, China.

PubMed

Shang, Xiaopeng; Fu, Xiaofei; Zhang, Peng; Sheng, Minyang; Song, Jianqiang; He, Fan; Qiu, Yinwei; Wu, Haocheng; Lu, Qinbao; Feng, Yan; Lin, Junfen; Chen, Enfu; Chai, Chengliang

2017-01-01

More than 900 students and teachers at many schools in Jiaxing city developed acute gastroenteritis in February 2014. An immediate epidemiological investigation was conducted to identify the pathogen, infection sources and route of transmission. The probable cases and confirmed cases were defined as students or teachers with diarrhoea or vomiting present since the term began in February 2014. An active search was conducted for undiagnosed cases among students and teachers. Details such as demographic characteristics, gastrointestinal symptoms, and drinking water preference and frequency were collected via a uniform epidemiological questionnaire. A case-control study was implemented, and odds ratios (ORs) and 95% confidence intervals were calculated. Rectal swabs from several patients, food handlers and barrelled water factory workers, as well as water and food samples, were collected to test for potential bacteria and viruses. A total of 924 cases fit the definition of the probable case, including 8 cases of laboratory-confirmed norovirus infection at 13 schools in Jiaxing city between February 12 and February 21, 2014. The case-control study demonstrated that barrelled water was a risk factor (OR: 20.15, 95% CI: 2.59-156.76) and that bottled water and boiled barrelled water were protective factors (OR: 0.31, 95% CI: 0.13-0.70, and OR: 0.36, 95% CI: 0.16-0.77). A total of 11 rectal samples and 8 barrelled water samples were detected as norovirus-positive, and the genotypes of viral strains were the same (GII). The norovirus that contaminated the barrelled water largely came from the asymptomatic workers. This acute gastroenteritis outbreak was caused by barrelled water contaminated by norovirus. The outbreak was controlled after stopping the supply of barrelled water. The barrelled water supply in China represents a potential source of acute gastroenteritis outbreaks due to the lack of surveillance and supervision. Therefore, more attention should be paid to this area.

Outbreak of Acinetobacter baumannii in a neonatal intensive care unit: antimicrobial susceptibility and genotyping analysis.

PubMed

Touati, Arabella; Achour, Wafa; Cherif, Ahmed; Hmida, Hayet Ben; Afif, Firas Bou; Jabnoun, Sami; Khrouf, Naima; Hassen, Assia Ben

2009-06-01

We describe an outbreak of nosocomial respiratory infection caused by multi-drug resistant Acinetobacter baumannii in a neonatal intensive care unit (NICU) in Tunis and our investigation to determine the source. Between May 2006 and February 2007, 31 infants hospitalized in the NICU of the Centre of Maternity and Neonatology of La Rabta in Tunis developed A. baumannii pneumonia. A case (infected infant) was defined as any patient hospitalized in the NICU during the outbreak period, with clinical signs of pneumonia and isolation of A. baumannii from tracheal aspirate. Ten rectal swabs and 98 environmental specimens were collected for the epidemiological investigation. Thirty-nine A. baumannii isolates were collected: 31 clinical strains from tracheal aspirates (>10(3) colony-forming units [CFU]/mL), 3 environmental strains from incubators, and 5 from rectal swab. For the genotyping method, we used pulsed-field gel electrophoresis using ApaI restriction endonuclease. Thirty-one neonates developed multiple drug-resistant A. baumannii-associated pneumonia with 10 deaths due to A. baumannii infection, 48.4% had very low birth weight (

Carriage of ESBL- and AmpC-positive Enterobacteriaceae in the gastrointestinal tract of community subjects and hospitalized patients in the Czech Republic.

PubMed

Husickova, Vendula; Cekanova, Luboslava; Chroma, Magdalena; Htoutou-Sedlakova, Miroslava; Hricova, Kristyna; Kolar, Milan

2012-12-01

The study aimed at analyzing ESBL- and AmpC-positive Enterobacteriaceae in the gastrointestinal tracts of university hospital inpatients and persons from the Olomouc Region community, and comparing the results with data from 2007. Bacteria were isolated from rectal swabs inoculated onto the ChromID(TM) ESBL selective medium (bioMérieux). Production of ESBL-type beta-lactamases was confirmed by the modified double-disk synergy test and AmpC enzyme production was detected by the AmpC disk test. ESBL- and AmpC-positive isolates were subjected to basic genetic analysis aimed at detecting the bla(TEM), bla(SHV), bla(CTX-M) and bla(AmpC) genes. Over the study period (1 March 2010 - 1 May 2010), a total of 1,279 rectal swabs (70.4% of community subjects) were analyzed on the above medium. The prevalence rates of ESBL-positive Enterobacteriaceae were 8.2% in hospitalized patients and 3.2% in community subjects. Production of the AmpC enzyme was detected in 1.1% of bacterial isolates from the community and in one (0.3%) hospital isolate. Among ESBL, the most frequent genes encoding enzymes were from the CTX-M-1-like genes. Detected AmpC beta-lactamases belonged to the CIT, DHA and EBC groups. When compared with the year 2007, the rates of carriers of ESBL-positive bacteria increased in both hospitalized patients (from 3% to 8%) and community subjects (from 1% to 3%) in 2010. Given the fact that production of extended-spectrum beta-lactamases is clinically significant, knowing the epidemiological situation is very important for selecting adequate antibiotic therapy.

Recent outbreak of aseptic meningitis in Italy due to Echovirus 30 and phylogenetic relationship with other European circulating strains.

PubMed

Milia, Maria Grazia; Cerutti, Francesco; Gregori, Gabriella; Burdino, Elisa; Allice, Tiziano; Ruggiero, Tina; Proia, Maria; De Rosa, Giulia; Enrico, Eugenia; Lipani, Filippo; Di Perri, Giovanni; Ghisetti, Valeria

2013-11-01

Enteroviruses (EVs) are common human viral pathogens, causing a variety of diseases, including aseptic meningitis. Recently, EV aseptic meningitis outbreaks have been reported across Europe, but, in Italy, knowledge of recent EV molecular epidemiology is very limited. We report an outbreak of EV aseptic meningitis in 10 adults in North-Western Italy, from October to November 2012. Patients were parents or close relatives of children <5 years old attending the same class of a nursery school, suffering from a mild febrile upper respiratory disease. Phylogenetic relationship with other European circulating strains was analyzed updating E30 circulation in Italy in recent years. EVs were detected from cerebrospinal fluid (CSF) specimens with a real-time reverse transcription polymerase chain reaction and virus isolation was achieved from rectal and pharyngeal swabs. For cluster definition and phylogenetic studies, viral VP1 region was directly amplified and sequenced from CSF. EVs were identified in CSF from all patients and from rectal and pharyngeal swabs in 7 of them. Direct sequencing of CSF revealed the presence of the same Echovirus 30 (E30) in all patients and phylogenetic analysis identified it as a diverging clade within E30 genotype VII, the most recent strain circulating in UK, Finland and Denmark since 2006. Molecular techniques allowed the rapid identification and typing of E30 from CSF. Phylogenetic analysis revealed that the cluster might be due to a new E30 variant within the genotype VII currently circulating in Europe, thus updating the epidemiology of EV circulation in Italy. Copyright © 2013 Elsevier B.V. All rights reserved.

An optimized work-flow to reduce time-to-detection of carbapenemase-producing Enterobacteriaceae (CPE) using direct testing from rectal swabs.

PubMed

O'Connor, C; Kiernan, M G; Finnegan, C; O'Hara, M; Power, L; O'Connell, N H; Dunne, C P

2017-05-04

Rapid detection of patients with carbapenemase-producing Enterobacteriaceae (CPE) is essential for the prevention of nosocomial cross-transmission, allocation of isolation facilities and to protect patient safety. Here, we aimed to design a new laboratory work-flow, utilizing existing laboratory resources, in order to reduce time-to-diagnosis of CPE. A review of the current CPE testing processes and of the literature was performed to identify a real-time commercial polymerase chain reaction (PCR) assay that could facilitate batch testing of CPE clinical specimens, with adequate CPE gene coverage. Stool specimens (210) were collected; CPE-positive inpatients (n = 10) and anonymized community stool specimens (n = 200). Rectal swabs (eSwab™) were inoculated from collected stool specimens and a manual DNA extraction method (QIAamp® DNA Stool Mini Kit) was employed. Extracted DNA was then processed on the Check-Direct CPE® assay. The three step process of making the eSwab™, extracting DNA manually and running the Check-Direct CPE® assay, took <5 min, 1 h 30 min and 1 h 50 min, respectively. It was time efficient with a result available in under 4 h, comparing favourably with the existing method of CPE screening; average time-to-diagnosis of 48/72 h. Utilizing this CPE work-flow would allow a 'same-day' result. Antimicrobial susceptibility testing results, as is current practice, would remain a 'next-day' result. In conclusion, the Check-Direct CPE® assay was easily integrated into a local laboratory work-flow and could facilitate a large volume of CPE screening specimens in a single batch, making it cost-effective and convenient for daily CPE testing.

Swabs as a tool for monitoring the presence of norovirus on environmental surfaces in the food industry.

PubMed

Rönnqvist, Maria; Rättö, Marjaana; Tuominen, Pirkko; Salo, Satu; Maunula, Leena

2013-08-01

Human norovirus (HuNoV), which causes gastroenteritis, can be transmitted to food and food contact surfaces via viruscontaminated hands. To investigate this transmission in food processing environments, we developed a swabbing protocol for environmental samples, evaluated the stability of HuNoV in the swabs, and applied the method in the food industry. Swabs made of polyester, flocked nylon, cotton wool, and microfiber were moistened in either phosphate-buffered saline (PBS) or glycine buffer (pH 9.5) and used to swab four surfaces (latex, plastic, stainless steel, and cucumber) inoculated with HuNoV. HuNoV was eluted with either PBS or glycine buffer and detected with quantitative reverse transcription PCR. HuNoV recoveries were generally higher with an inoculation dose of 100 PCR units than 1,000 PCR units. The highest recoveries were obtained when surfaces were swabbed with microfiber cloth moistened in and eluted with glycine buffer after a HuNoV inoculation dose of 100 PCR units: 66% ± 18% on latex, 89% ±2% on plastic, and 79% ±10% on stainless steel. The highest recovery for cucumber, 45% ±5%, was obtained when swabbing the surface with microfiber cloth and PBS. The stability of HuNoV was tested in microfiber cloths moistened in PBS or glycine buffer. HuNoV RNA was detected from swabs after 3 days at 4 and 22°C, although the RNA levels decreased more rapidly in swabs moistened with glycine buffer than in those moistened with PBS at 22°C. In the field study, 172 microfiber and 45 cotton wool swab samples were taken from environmental surfaces at three food processing companies. Five (5.6%) of 90 swabs collected in 2010 and 7 (8.5%) of 82 swabs collected in 2012 were positive for HuNoV genogroup II; all positive samples were collected with microfiber swabs. Three positive results were obtained from the production line and nine were obtained from the food workers' break room and restroom areas. Swabbing is a powerful tool for HuNoV RNA detection from environmental surfaces and enables investigation of virus transmission during food processing.

Sinonasal microbiome sampling: a comparison of techniques.

PubMed

Bassiouni, Ahmed; Cleland, Edward John; Psaltis, Alkis James; Vreugde, Sarah; Wormald, Peter-John

2015-01-01

The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample. Cross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package. At a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith's PD_Whole_Tree and Shannon's index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05). We observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies.

Evaluation of the Aircraft Ground Equipment (AGE) at Pacific Air Force (PACAF) Locations

DTIC Science & Technology

2018-01-16

repair • Dash 95: TC-21; Old DRMO, arrived at Kunsan 2001 • 7000 lb Bomb lift; MH10 Arrived at Kunsan 2011; CAT3 and never been painted • C1-12 stand...aluminum Sample taken by swabbing PBS soaked gauze back and forth three times K-MH10 Bomb lift and front of AGE Sample taken by swabbing PBS...soaked gauze back and forth three times Non-corroded area of bomb lift Sample taken by swabbing PBS soaked gauze back and forth three times

Quarterly Performance/Technical Report of the National Marrow Donor Program

DTIC Science & Technology

2008-02-05

HLA-DRB1 High Resolution Typing Closed 9 IIB.1.3 Aim 3 – Evaluate HLA-C Typing of Donors Closed 9 IIB.1.4 Aim 4 – Evaluate Buccal Swabs Open 10 IIB...December 31, 2007 10 of 21 IIB.1.4 Aim 4: Evaluate Buccal Swabs Period 5 Activity: In April of 2006, the NMDP transitioned to the use of... buccal swabs for the collection of DNA samples from newly recruited donors. To support this change in sample type, Quality Control samples for donor

The forensiX evidence collection tube and its impact on DNA preservation and recovery.

PubMed

Garvin, Alex M; Holzinger, Ralf; Berner, Florian; Krebs, Walter; Hostettler, Bernhard; Lardi, Elges; Hertli, Christian; Quartermaine, Roy; Stamm, Christoph

2013-01-01

Biological samples are vulnerable to degradation from the time they are collected until they are analysed at the laboratory. Biological contaminants, such as bacteria, fungi, and enzymes, as well as environmental factors, such as sunlight, heat, and humidity, can increase the rate of DNA degradation. Currently, DNA samples are normally dried or frozen to limit their degradation prior to their arrival at the laboratory. In this study, the effect of the sample drying rate on DNA preservation was investigated, as well as a comparison between drying and freezing methods. The drying performances of two commercially available DNA collection tools (swab and drying tube) with different drying rates were evaluated. The swabs were used to collect human saliva, placed into the drying tubes, and stored in a controlled environment at 25°C and 60% relative humidity, or frozen at -20°C, for 2 weeks. Swabs that were stored in fast sample drying tubes yielded 95% recoverable DNA, whereas swabs stored in tubes with slower sample drying rates yielded only 12% recoverable DNA; saliva stored in a microtube at -20°C was used as a control. Thus, DNA sampling tools that offer rapid drying can significantly improve the preservation of DNA collected on a swab, increasing the quantity of DNA available for subsequent analysis.

Dynamic of Campylobacter Species Contamination Along a Poultry Slaughtering Chain

PubMed Central

Dib, Hussein; Mrad, Rachelle; Chami, Christelle; Jalkh, Rita

2014-01-01

The prevalence of Campylobacters was studied in a poultry farm and along the slaughtering chain. Fifteen swabs from a farm and 75 samples (swabs and rinsates) from its slaughterhouse were collected. All the faecal and cloacal farm swabs were contaminated by Campylobacter jejuni and C. coli against 50% for breast swabs. C. jejuni had a concentration of 6.26, 6.34 and 5.38 Log10 CFU/mL in faecal, cloacal and breast swabs respectively. Rinsates showed an almost constant concentration of Campylobacters (6 Log10 CFU/mL) with a predominance of the presumptive C. jejuni. C. lari was found in 22% of eviscerated samples. Faecal coliforms and E. coli, used as indicators, were detected in all samples (5.46 and 5.15 Log10 CFU/mL, respectively). Final chilling and chlorine (50 ppm) treatments decreased them to acceptable levels, unlike for Campylobacters. Further investigation of the dynamics of Campylobacters and their response to prevention and treatment measures is required. PMID:27800361

Evaluation of swabs and transport media for the recovery of Yersinia pestis.

PubMed

Gilbert, Sarah E; Rose, Laura J; Howard, Michele; Bradley, Meranda D; Shah, Sanjiv; Silvestri, Erin; Schaefer, Frank W; Noble-Wang, Judith

2014-01-01

The Government Accountability Office report investigating the surface sampling methods used during the 2001 mail contamination with Bacillus anthracis brought to light certain knowledge gaps that existed regarding environmental sampling with biothreat agents. Should a contamination event occur that involves non-spore forming biological select agents, such as Yersinia pestis, surface sample collection and processing protocols specific for these organisms will be needed. Two Y. pestis strains (virulent and avirulent), four swab types (polyester, macrofoam, rayon, and cotton), two pre-moistening solutions, six transport media, three temperatures, two levels of organic load, and four processing methods (vortexing, sonicating, combined sonicating and vortexing, no agitation) were evaluated to determine the conditions that would yield the highest percent of cultivable Y. pestis cells after storage. The optimum pre-moistening agent/transport media combination varied with the Y. pestis strain and swab type. Directly inoculated macrofoam swabs released the highest percent of cells into solution (93.9% recovered by culture) and rayon swabs were considered the second best swab option (77.0% recovered by culture). Storage at 4°C was found to be optimum for all storage times and transport media. In a worst case scenario, where the Y. pestis strain is not known and sample processing and analyses could not occur until 72h after sampling, macrofoam swabs pre-moistened with PBS supplemented with 0.05% Triton X-100 (PBSTX), stored at 4°C in neutralizing buffer (NB) as a transport medium (PBSTX/NB) or pre-moistened with NB and stored in PBSTX as a transport medium (NB/PBSTX), then vortexed 3min in the transport medium, performed significantly better than all other conditions for macrofoam swabs, regardless of strain tested (mean 12 - 72h recovery of 85.9-105.1%, p<0.001). In the same scenario, two combinations of pre-moistening medium/transport medium were found to be optimal for rayon swabs stored at 4°C (p<0.001), then sonicated 3min in the transport medium; PBSTX/PBSTX and NB/PBSTX (mean 12-72h recovery of 83.7-110.1%). © 2013.

Williams conducts SWAB Sampling during Expedition 22

NASA Image and Video Library

2010-03-15

ISS022-E-094369 (15 March 2010) --- NASA astronaut Jeffrey Williams, Expedition 22 commander, conducts a Surface, Water and Air Biocharacterization (SWAB) water sampling from the Potable Water Dispenser (PWD) in the Destiny laboratory of the International Space Station. SWAB uses advanced molecular techniques to comprehensively evaluate microbes onboard the space station, including pathogens (organisms that may cause disease). This study will allow an assessment of the risk of microbes to the crew and the spacecraft.

Williams conducts SWAB Sampling during Expedition 22

NASA Image and Video Library

2010-03-15

ISS022-E-094374 (15 March 2010) --- NASA astronaut Jeffrey Williams, Expedition 22 commander, conducts a Surface, Water and Air Biocharacterization (SWAB) water sampling from the Potable Water Dispenser (PWD) in the Destiny laboratory of the International Space Station. SWAB uses advanced molecular techniques to comprehensively evaluate microbes onboard the space station, including pathogens (organisms that may cause disease). This study will allow an assessment of the risk of microbes to the crew and the spacecraft.

Developing Planetary Protection Technology: Microbial Diversity and Radiation Resistance of Microorganisms in a Spacecraft Assembly Facility.

NASA Astrophysics Data System (ADS)

Chen, F.; La Duc, M. T.; Baker, A.; Koukol, R.; Barengoltz, J.; Kern, R.; Venkateswaran, K.

2001-12-01

Europa has attracted much attention as evidence suggests the presence of a liquid ocean beneath this Jupiter moon's frozen crust. Such an environment might be conducive to the origins of life. Since robotic exploration of Europa is being planned, it becomes crucial to prepare for bio-burden reduction of hardware assembled for Europa missions to avoid contamination of Europa's pristine environment. In this study, we examined the microbial diversity of samples collected from two flight-ready circuit boards and their assembly facility. Also, because Jupiter's strong radiation environment may be able to reduce the viable microbial contamination on flight components, we have also studied the effects of radiation on microbial communities found to be associated with the space-flight hardware and/or present in the assembly facility. Surface samples thought to be representative of considerable human contact were collected from two circuit boards and various locations within the assembly facility using polyester swabs (swab samples). Likewise, sterile wipes were used to sample a shelf above the workstation where the circuit boards were assembled and the floor of the facility (wipe samples). The swab and wipe samples were pooled separately and divided into two halves, one of which was irradiated with 1Mrad gamma radiation for 5.5 hours, the other was not irradiated. About 1.2x104 and 6x104 CFUs/m2 cultivable microbes were detected in the swab and wipe samples, respectively. Radiation proved effective in inhibiting the growth of most microbes. Further characterization of the bacterial colonies observed in the irradiated swab and wipe samples is necessary to determine the degree of the radiation resistance. The16S rDNA sequence analysis of the cultivable microbes indicated that the assembly facility consists mostly of the members of actinobacteria, corynebacteria and pseudomonads. However, the swab samples that include the circuit boards were predominantly populated with Bacillus and Staphylococcus. Molecular microbial diversity was also studied by cloning the 16S rDNA PCR fragment from the samples. The non-irradiated swab samples were largely populated by species of Exiguobacter and Bacillus whereas the irradiated swab samples were dominated by Bacillus and E. coli. Radiation damage of microorganisms was also investigated by epifluorescence microscopy. In summary, our study has shown that gamma radiation can inhibit the growth of most of the cultivable microbes, but preliminary results suggest that radiation such as this has little adverse effect on the DNA molecules of these microorganisms.

Surveillance of bacterial contamination in small animal veterinary hospitals with special focus on antimicrobial resistance and virulence traits of enterococci.

PubMed

KuKanich, Kate S; Ghosh, Anuradha; Skarbek, Jennifer V; Lothamer, Kale M; Zurek, Ludek

2012-02-15

To determine the prevalence of bacterial contamination on 4 surfaces of 4 types of standard equipment in small animal veterinary hospitals. Surveillance study. 10 small animal veterinary hospitals. Each hospital was visited 3 times at 4-month intervals; at each visit, a cage door, stethoscope, rectal thermometer, and mouth gag were swabbed. Swab samples were each plated onto media for culture of enterococci and organisms in the family Enterobacteriaceae. Enterococci were identified via a species-specific PCR assay and sodA gene sequencing; species of Enterobacteriaceae were identified with a biochemical test kit. Antimicrobial susceptibility was assessed via the disk diffusion method. Enterococci were screened for virulence traits and genotyped to assess clonality. Among the 10 hospitals, enterococci were isolated from cage doors in 7, from stethoscopes in 7, from thermometers in 6, and from mouth gags in 1; contamination with species of Enterobacteriaceae was rare. Enterococci were mainly represented by Enterococcus faecium (35.4%), Enterococcus faecalis (33.2%), and Enterococcus hirae (28.3%). Antimicrobial resistance was common in E. faecium, whereas virulence traits were present in 99% of E. faecalis isolates but not in E. faecium isolates. Clonal multidrug-resistant E. faecium was isolated from several surfaces at 1 hospital over multiple visits, whereas sporadic nonclonal contamination was detected in other hospitals. Contamination of surfaces in small animal veterinary hospitals with multidrug-resistant enterococci is a potential concern for pets and humans contacting these surfaces. Implementing precautions to minimize enterococcal contamination on these surfaces is recommended.

Evaluation of a novel material, Diomics X-Swab™, for collection of DNA.

PubMed

Marshall, Pamela L; Stoljarova, Monika; Larue, Bobby L; King, Jonathan L; Budowle, Bruce

2014-09-01

Success of DNA typing is related to the amount of target material recovered from an evidentiary item. Generally, the more DNA that is recovered, the better the chance is of obtaining a typing result that will be robust and reliable. One method of collecting stain materials is by swabbing. Recovery of DNA from a number of commercially available swabs is not an efficient process. The X-Swab™ (Diomics Corporation, La Jolla, CA) is a unique bio-specimen collection material with highly absorptive properties and can be dissolved during certain extraction conditions. Therefore, more DNA may be collected from a substrate and be released from the swab matrix than other swabs. The ability to recover DNA from X-Swab material and success in STR typing were compared with the Copan 4N6FLOQSwab™ (Brescia, Italy), a device which utilizes a proprietary flocked-swab technology to maximize DNA collection and elution efficiency. Both types of swabs were impregnated with known amounts of DNA and body fluids and allowed to air dry. In addition, blood was placed onto glass slides, allowed to dry and collected using both types of swabs. DNA recovery was assessed by DNA quantitation and by STR typing. Results suggested that X-Swab material yielded greater DNA recovery, particularly of low quantity samples (defined as diluted neat samples), compared with the 4N6FLOQSwab. Results also indicated that X-Swab material itself enhances yield of PCR products. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

EVA Swab Tool to Support Planetary Protection and Astrobiology Evaluations

NASA Technical Reports Server (NTRS)

Rucker, Michelle A.; Hood, Drew; Walker, Mary; Venkateswaran, Kasthuri J.; Schuerger, Andrew C.

2018-01-01

When we send humans to search for life on other planets, we'll need to know what we brought with us versus what may already be there. To ensure our crewed systems meet planetary protection requirements-and to protect our science from human contamination-we'll need to assess whether microorganisms may be leaking or venting from our spacecraft. Microbial sample collection outside of a pressurized spacecraft is complicated by temperature extremes, low pressures that preclude the use of laboratory standard (wetted) swabs, and operation either in bulky spacesuits or with robotic assistance. Engineers at the National Aeronautics and Space Administration (NASA) recently developed a swab kit for use in collecting microbial samples from the external surfaces of crewed spacecraft, including spacesuits. The Extravehicular Activity (EVA) Swab Kit consists of a single swab tool handle and an eight-canister sample caddy. The design team minimized development cost by re-purposing a heritage Space Shuttle tile repair handle that was designed to quickly snap into different tool attachments by engaging a mating device in each attachment. This allowed the tool handle to snap onto a fresh swab attachment much like popular shaving razor handles can snap onto a disposable blade cartridge. To disengage the handle from a swab, the user performs two independent functions, which can be done with a single hand. This dual operation mitigates the risk that a swab will be inadvertently released and lost in microgravity. Each swab attachment is fitted with commercially available foam swab tips, vendor-certified to be sterile for Deoxyribonucleic Acid (DNA). A microbial filter installed in the bottom of each sample container allows the container to outgas and repressurize without introducing microbial contaminants to internal void spaces. Extensive ground testing, post-test handling, and sample analysis confirmed the design is able to maintain sterile conditions as the canister moves between various pressure environments. To further minimize cost, the design team acquired extensive ground test experience in a relevant flight environment by piggy-backing onto suited crew training runs. These training runs allowed the project to validate tool interfaces with pressurized EVA gloves and collect user feedback on the tool design and function, as well as characterize baseline microbial data for different types of spacesuits. In general, test subjects found the EVA Swab Kit relatively straightforward to operate, but identified a number of design improvements that will be incorporated into the final design. Although originally intended to help characterize human forward contaminants, this tool has other potential applications, such as for collecting and preserving space-exposed materials to support astrobiology experiments.

Magnetic bead-based separation of sperm from buccal epithelial cells using a monoclonal antibody against MOSPD3.

PubMed

Li, Xue-Bo; Wang, Qing-Shan; Feng, Yu; Ning, Shu-Hua; Miao, Yuan-Ying; Wang, Ye-Quan; Li, Hong-Wei

2014-11-01

Forensic DNA analysis of sexual assault evidence requires unambiguous differentiation of DNA profiles in mixed samples. To investigate the feasibility of magnetic bead-based separation of sperm from cell mixtures using a monoclonal antibody against MOSPD3 (motile sperm domain-containing protein 3), 30 cell samples were prepared by mixing 10(4) female buccal epithelial cells with sperm cells of varying densities (10(3), 10(4), or 10(5) cells/mL). Western blot and immunofluorescence assays showed that MOSPD3 was detectable on the membrane of sperm cells, but not in buccal epithelial cells. After biotinylated MOSPD3 antibody was incubated successively with the prepared cell mixtures and avidin-coated magnetic beads, microscopic observation revealed that each sperm cell was bound by two or more magnetic beads, in the head, neck, mid-piece, or flagellum. A full single-source short tandem repeat profile could be obtained in 80% of mixed samples containing 10(3) sperm cells/mL and in all samples containing ≥10(4) sperm cells/mL. For dried vaginal swab specimens, the rate of successful detection was 100% in both flocked and cotton swabs preserved for 1 day, 87.5% in flocked swabs and 40% in cotton swabs preserved for 3 days, and 40% in flocked swabs and 16.67% in cotton swabs preserved for 10 days. Our findings suggest that immunomagnetic bead-based separation is potentially a promising alternative to conventional methods for isolating sperm cells from mixed forensic samples.

Evaluation of a Chlamydia trachomatis-specific, commercial, real-time PCR for use with ocular swabs.

PubMed

Pickering, Harry; Holland, Martin J; Last, Anna R; Burton, Matthew J; Burr, Sarah E

2018-02-20

Trachoma, the leading infectious cause of blindness worldwide, is caused by conjunctival Chlamydia trachomatis infection. Trachoma is diagnosed clinically by observation of conjunctival inflammation and/or scarring; however, there is evidence that monitoring C. trachomatis infection may be required for elimination programmes. There are many commercial and 'in-house' nucleic acid amplification tests for the detection of C. trachomatis DNA, but the majority have not been validated for use with ocular swabs. This study evaluated a commercial assay, the Fast-Track Vaginal swab kit, using conjunctival samples from trachoma-endemic areas. An objective, biostatistical-based method for binary classification of continuous PCR data was developed, to limit potential user-bias in diagnostic settings. The Fast-Track Vaginal swab assay was run on 210 ocular swab samples from Guinea-Bissau and Tanzania. Fit of individual amplification curves to exponential or sigmoid models, derivative and second derivative of the curves and final fluorescence value were examined for utility in thresholding for determining positivity. The results from the Fast-Track Vaginal swab assay were evaluated against a commercial test (Amplicor CT/NG) and a non-commercial test (in-house droplet digital PCR), both of whose performance has previously been evaluated. Significant evidence of exponential amplification (R 2  > 0.99) and final fluorescence > 0.15 were combined for thresholding. This objective approach identified a population of positive samples, however there were a subset of samples that amplified towards the end of the cycling protocol (at or later than 35 cycles), which were less clearly defined. The Fast-Track Vaginal swab assay showed good sensitivity against the commercial (95.71) and non-commercial (97.18) tests. Specificity was lower against both (90.00 and 96.55, respectively). This study defined a simple, automated protocol for binary classification of continuous, real-time qPCR data, for use in an end-point diagnostic test. This method identified a population of positive samples, however, as with manual thresholding, a subset of samples that amplified towards the end of the cycling program were less easily classified. When used with ocular swabs, the Fast-Track Vaginal swab assay had good sensitivity for C. trachomatis detection, but lower specificity than the commercial and non-commercial assays it was evaluated against, possibly leading to false positives.

Assessment of best single sample for finding chlamydia in women with and without symptoms: a diagnostic test study.

PubMed

Schoeman, Sarah A; Stewart, Catherine M W; Booth, Russell A; Smith, Susan D; Wilcox, Mark H; Wilson, Janet D

2012-12-12

To compare vulvovaginal swabs with endocervical swabs as optimal diagnostic sample for detection of Chlamydia trachomatis infection. A diagnostic test study. An urban sexual health centre. 3973 women aged ≥ 16 years requesting testing for sexually transmitted infections. Participants took a vulvovaginal swab before routine examination, and clinicians took an endocervical swab during examination. Diagnosis of chlamydia infection with samples analysed using the Aptima Combo-2 assay; positive results confirmed with the Aptima CT assay. Of the 3973 participants, 410 (10.3%) were infected with C trachomatis. Infected women were significantly younger (22 v 25 years, P<0.0001) and more likely to have symptoms suggestive of a bacterial sexually transmitted infection (53% v 41%, odds ratio 1.63 (95% CI 1.30 to 2.04)), be a contact of someone with a sexually transmitted infection (25% v 5%, odds ratio 6.18 (4.61 to 8.30)), clinically diagnosed with cervicitis (17% v 4%, odds ratio 4.92 (3.50 to 6.91)), and have pelvic inflammatory disease (9% v 3%, odds ratio 2.85 (1.87 to 4.33)). When women co-infected with gonorrhoea were included in the analysis, there was an association with mixed ethnicity (10% v 7%, odds ratio 1.53 (1.07 to 2.17)); but when those with gonorrhoea were removed, women of white ethnicity were significantly more likely to have chlamydia (85% v 80%, odds ratio 1.40 (1.03 to 1.91)). On analysis of complete paired results, vulvovaginal swabs were significantly more sensitive than endocervical swabs (97% (95% CI 95% to 98%) v 88% (85% to 91%), P<0.00001); corresponding specificities were 99.9% and 100%. In women with symptoms suggestive of a bacterial sexually transmitted infection, vulvovaginal swabs were significantly more sensitive than endocervical swabs (97% (93% to 98%) v 88% (83% to 92%), P=0.0008), as they were in women without symptoms (97% (94% to 99%) v 89% (84% to 93%), P=0.002). Vulvovaginal swabs are significantly better than endocervical swabs at detecting chlamydia in women with and without symptoms suggestive of sexually transmitted infections. In those with symptoms, using endocervical samples rather than vulvovaginal swabs would have missed 9% of infections, or 1 in every 11 cases of chlamydia. ISRCTN42867448.

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs.

PubMed

Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus; Morling, Niels

2016-01-01

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates automation of DNA sequencing.

Comparison of culture and a multiplex probe PCR for identifying Mycoplasma species in bovine milk, semen and swab samples

PubMed Central

Parker, Alysia M.; House, John K.; Hazelton, Mark S.; Bosward, Katrina L.; Sheehy, Paul A.

2017-01-01

Mycoplasma spp. are a major cause of mastitis, arthritis and pneumonia in cattle, and have been associated with reproductive disorders in cows. While culture is the traditional method of identification the use of PCR has become more common. Several investigators have developed PCR protocols to detect M. bovis in milk, yet few studies have evaluated other sample types or other important Mycoplasma species. Therefore the objective of this study was to develop a multiplex PCR assay to detect M. bovis, M. californicum and M. bovigenitalium, and evaluate its analytical performance against traditional culture of bovine milk, semen and swab samples. The PCR specificity was determined and the limit of detection evaluated in spiked milk, semen and swabs. The PCR was then compared to culture on 474 field samples from individual milk, bulk tank milk (BTM), semen and swab (vaginal, preputial, nose and eye) samples. Specificity analysis produced appropriate amplification for all M. bovis, M. californicum and M. bovigenitalium isolates. Amplification was not seen for any of the other Mollicutes or eubacterial isolates. The limit of detection of the PCR was best in milk, followed by semen and swabs. When all three Mycoplasma species were present in a sample, the limit of detection increased. When comparing culture and PCR, overall there was no significant difference in the proportion of culture and PCR positive samples. Culture could detect significantly more positive swab samples. No significant differences were identified for semen, individual milk or BTM samples. PCR identified five samples with two species present. Culture followed by 16S-23S rRNA sequencing did not enable identification of more than one species. Therefore, the superior method for identification of M. bovis, M. californicum and M. bovigenitalium may be dependent on the sample type being analysed, and whether the identification of multiple target species is required. PMID:28264012

Evaluation of Three Swabbing Devices for Detection of Listeria monocytogenes on Different Types of Food Contact Surfaces

PubMed Central

Lahou, Evy; Uyttendaele, Mieke

2014-01-01

Listeria monocytogenes can adhere to different types of food contact surfaces within a food processing environment. Therefore, environmental sampling devices should be capable of detecting unacceptable contamination. In this study, a sponge-stick, foam spatula and an environmental swab were evaluated on their ability to detect low concentrations of L. monocytogenes on different types of food contact surfaces. A cocktail of four L. monocytogenes serotypes was inoculated with a concentration of 100 CFU/250 cm2 onto stainless steel (SS), high density polyethylene (HDPE) and rubber surfaces in a 250 cm2 area. Immediately after inoculation and after 1 h exposure, the surfaces were swabbed with the different swabbing devices. The results of the study show only minor differences in the ability of the swabbing devices to detect L. monocytogenes. All devices were capable to detect the contamination immediately after inoculation. However, when the surfaces were allowed to air-dry for 1 h, L. monocytogenes was undetected in 11.1% of the samples (n = 27) with the sponge stick, in 7.4% of the samples (n = 27) with the foam spatula and in 3.7% of the samples (n = 27) with the environmental swab, especially on SS surfaces. The detection ability of the different devices for L. monocytogenes can be concluded to be rather high on different types of food contact surfaces. PMID:24406663

Fast and simple DNA extraction from saliva and sperm cells obtained from the skin or isolated from swabs.

PubMed

von Wurmb-Schwark, Nicole; Mályusz, Victoria; Fremdt, Heike; Koch, Christine; Simeoni, Eva; Schwark, Thorsten

2006-05-01

The forensic scientist often has to cope with problematic samples from the crime scene due to their minute size and thus the low amount of extractable DNA. The retrieval of DNA from swabs taken from the surface of the skin, for example, in cases of strangulation, can be especially difficult. We systematically investigated swabs taken from the skin (to obtain a genetic profile from the victim and also from a possible offender) and from sperm cell containing swabs using two extraction kits: the Invisorb forensic and the Invisorb spin swab kit (both Invitek, Germany). DNA quality and quantity were tested on ethidium bromide containing agarose gels and in a highly sensitive duplex-PCR, which amplifies fragments specific for mitochondrial and nuclear DNA. Absolute quantification was done using real time PCR. Samples, which were positive in the duplex-PCR, were also employed to genetic fingerprinting using the Powerplex ES and the AmpFlSTRIdentifiler(TM) kits. Our study shows that the easy-to-use Invisorb spin swab kit is very suitable for DNA isolation from swabs taken from the skin and also from sperm cells. Retrieval of cells from the skin with swabs moistened in extraction buffer, not in distilled water, led to a significant higher DNA yield.

The Orbiting Primate Experiment (OPE)

NASA Technical Reports Server (NTRS)

Bourne, G. H.; Debourne, M. N. G.; Mcclure, H. M.

1977-01-01

Instrumentation and life support systems are described for an experiment to determine the physiological effects of long term space flight on unrestrained, minimally instrumented rhesus macaques flown in orbit for periods up to six months or one year. On return from orbit, vestibular, cardiovascular, and skeletal muscle function will be tested. Blood chemistry and hematological studies will be conducted as well as tests of the immunological competence of selected animals. Nasal, rectal, and throat swabs will be used for bacterial and viral studies, and histopathological and histochemical investigations will be be made of all organs using light and electron microscopy. The experiment is being considered as a payload for the biomedical experiment scientific satellite.

A survey of canine parvovirus-2 in Albania.

PubMed

Kusi, I

1997-11-01

Observations were made on 97 dogs that had clinical signs of enteritis and on another group of 68 unvaccinated clinically healthy dogs for detecting the prevalence of serum hemagglutination inhibiting antibody to CPV. Canine parvovirus antigens agglutinating cat RBC were detected in feces or rectal swabs from 72 of 97 dogs. An ELISA to detect CPV antigen in feces and virus isolation on cell culture were also performed. Thirty-one of 72 dogs died. Mortality was exclusively observed in the age group of 0- to 6-month old. Canine parvovirus hemagglutination inhibition antibodies were detected in sera from 45 of 68 unvaccinated dogs examined.

Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis.

PubMed

Byrne, Allison Q; Rothstein, Andrew P; Poorten, Thomas J; Erens, Jesse; Settles, Matthew L; Rosenblum, Erica Bree

2017-11-01

One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures have advanced our understanding of Bd phylogenetics, genomic architecture and mechanisms of virulence. However, pure cultures are laborious to obtain and whole-genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus, we still know little about the genetic diversity of Bd in natural systems. The most common noninvasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole-genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, noninvasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations. © 2017 John Wiley & Sons Ltd.

Resurgence of canine parvovirus 2a strain in the domestic dog population from Argentina.

PubMed

Calderón, Marina Gallo; Romanutti, Carina; Wilda, Maximiliano; D' Antuono, Alejandra; Keller, Leticia; Giacomodonato, Mónica N; Mattion, Nora; La Torre, José

2015-09-15

Ninety-three rectal swab samples were taken, from dogs suspected of canine parvovirus (CPV) infection and analyzed by PCR. A fragment of the VP2 gene, was amplified in 41 (44%) of them, resulting CPV positive samples. Sequencing analysis of these PCR products showed that 37 samples (90.2%) belonged to the CPV2c type, whereas four samples (9.8%) were identified as CPV2a, which has not been found since 2008. It was also found that 24 out of 37 CPV2c samples (65%), carried the mutation Thr440Ala, whereas this mutation was absent in the four CPV2a strains reported herein. Using phylogenetic analysis of the full length VP2 gene, which was amplified by PCR in six local samples, it was seen that CPV2a Argentine strains reported in this study, were genetically closer to a previous local CPV2a isolate (year 2003) and to a South African CPV2a strain, than to any of the recently reported Uruguayan CPV2a strains. The results obtained in this work, together with those reported previously in Uruguay strongly suggest that, in spite of the geographical proximity, wild type CPV strains undergo different evolutive pathways in each country, resulting in the prevalence of different strains in related dog populations. Further extensive epidemiological studies are needed in order to improve the understanding of CPV evolution. Copyright © 2015 Elsevier B.V. All rights reserved.

Randomized Comparison of Two Vaginal Self-Sampling Methods for Human Papillomavirus Detection: Dry Swab versus FTA Cartridge

PubMed Central

Catarino, Rosa; Vassilakos, Pierre; Bilancioni, Aline; Vanden Eynde, Mathieu; Meyer-Hamme, Ulrike; Menoud, Pierre-Alain; Guerry, Frédéric; Petignat, Patrick

2015-01-01

Background Human papillomavirus (HPV) self-sampling (self-HPV) is valuable in cervical cancer screening. HPV testing is usually performed on physician-collected cervical smears stored in liquid-based medium. Dry filters and swabs are an alternative. We evaluated the adequacy of self-HPV using two dry storage and transport devices, the FTA cartridge and swab. Methods A total of 130 women performed two consecutive self-HPV samples. Randomization determined which of the two tests was performed first: self-HPV using dry swabs (s-DRY) or vaginal specimen collection using a cytobrush applied to an FTA cartridge (s-FTA). After self-HPV, a physician collected a cervical sample using liquid-based medium (Dr-WET). HPV types were identified by real-time PCR. Agreement between collection methods was measured using the kappa statistic. Results HPV prevalence for high-risk types was 62.3% (95%CI: 53.7–70.2) detected by s-DRY, 56.2% (95%CI: 47.6–64.4) by Dr-WET, and 54.6% (95%CI: 46.1–62.9) by s-FTA. There was overall agreement of 70.8% between s-FTA and s-DRY samples (kappa = 0.34), and of 82.3% between self-HPV and Dr-WET samples (kappa = 0.56). Detection sensitivities for low-grade squamous intraepithelial lesion or worse (LSIL+) were: 64.0% (95%CI: 44.5–79.8) for s-FTA, 84.6% (95%CI: 66.5–93.9) for s-DRY, and 76.9% (95%CI: 58.0–89.0) for Dr-WET. The preferred self-collection method among patients was s-DRY (40.8% vs. 15.4%). Regarding costs, FTA card was five times more expensive than the swab (~5 US dollars (USD)/per card vs. ~1 USD/per swab). Conclusion Self-HPV using dry swabs is sensitive for detecting LSIL+ and less expensive than s-FTA. Trial Registration International Standard Randomized Controlled Trial Number (ISRCTN): 43310942 PMID:26630353

Randomized Comparison of Two Vaginal Self-Sampling Methods for Human Papillomavirus Detection: Dry Swab versus FTA Cartridge.

PubMed

Catarino, Rosa; Vassilakos, Pierre; Bilancioni, Aline; Vanden Eynde, Mathieu; Meyer-Hamme, Ulrike; Menoud, Pierre-Alain; Guerry, Frédéric; Petignat, Patrick

2015-01-01

Human papillomavirus (HPV) self-sampling (self-HPV) is valuable in cervical cancer screening. HPV testing is usually performed on physician-collected cervical smears stored in liquid-based medium. Dry filters and swabs are an alternative. We evaluated the adequacy of self-HPV using two dry storage and transport devices, the FTA cartridge and swab. A total of 130 women performed two consecutive self-HPV samples. Randomization determined which of the two tests was performed first: self-HPV using dry swabs (s-DRY) or vaginal specimen collection using a cytobrush applied to an FTA cartridge (s-FTA). After self-HPV, a physician collected a cervical sample using liquid-based medium (Dr-WET). HPV types were identified by real-time PCR. Agreement between collection methods was measured using the kappa statistic. HPV prevalence for high-risk types was 62.3% (95%CI: 53.7-70.2) detected by s-DRY, 56.2% (95%CI: 47.6-64.4) by Dr-WET, and 54.6% (95%CI: 46.1-62.9) by s-FTA. There was overall agreement of 70.8% between s-FTA and s-DRY samples (kappa = 0.34), and of 82.3% between self-HPV and Dr-WET samples (kappa = 0.56). Detection sensitivities for low-grade squamous intraepithelial lesion or worse (LSIL+) were: 64.0% (95%CI: 44.5-79.8) for s-FTA, 84.6% (95%CI: 66.5-93.9) for s-DRY, and 76.9% (95%CI: 58.0-89.0) for Dr-WET. The preferred self-collection method among patients was s-DRY (40.8% vs. 15.4%). Regarding costs, FTA card was five times more expensive than the swab (~5 US dollars (USD)/per card vs. ~1 USD/per swab). Self-HPV using dry swabs is sensitive for detecting LSIL+ and less expensive than s-FTA. International Standard Randomized Controlled Trial Number (ISRCTN): 43310942.

Evaluation of sampling technique and transport media for the diagnostics of adenoviral eye infections. Adenovirus sampling and transport.

PubMed

Wölfel, Roman; Pfeffer, Martin; Essbauer, Sandra; Nerkelun, Sylke; Dobler, Gerhard

2006-11-01

Human adenoviruses (HAdV) may cause pharyngoconjunctival fever, follicular conjunctivitis or epidemic keratoconjunctivitis (EKC). Especially, outbreaks of the latter may lead to severe economic losses when preventive measures are implemented too late. Thus, a safe sampling method, proper specimen transport conditions and a fast and sensitive diagnostic technique is mandatory. Two commercially available virus transport systems (VTS) were compared with two NaCl-moisturised sampling devices, one of which comprises Dacron-tipped plastic-shafted swabs and the other a cotton-tipped wood-shafted swab, available in most ophthalmologists' offices. Downstream methods for specific detection of HAdV included direct immunofluorescence assay (IFA) of conjunctival swabs, virus isolation by cell culture and quantitative real-time polymerase chain reaction (qPCR). Furthermore, the influence of application of local anaesthetics prior to swabbing on subsequent detection of HAdV was investigated. Application of local anaesthetics had a positive influence on the amount of swabbed cells, thus increasing the chance of obtaining positive results by IFA. Neither isolation of HAdV by cell culture nor by qPCR was negatively influenced by this pretreatment. Surprisingly, both commercially available VTS performed significantly worse than the NaCl-moisturised swabs. This was shown with regard to virus recovery rates in cell culture as well as viral genome copy numbers in the qPCR. Based on our results, the following recommendations are provided to improve sampling, transport and diagnostic techniques regarding conjunctival swabs for diagnosis of human adenovirus infection: (1) application of local anaesthetics, (2) NaCl-moisturised VTS for shipment of specimens, and (3) detection of HAdV by qPCR. The latter method proved to be superior to virus isolation by cell culture, including subsequent identification by IFA, because it is faster, more sensitive and allows simultaneous handling of a number of samples. Hence, countermeasures to prevent further virus spread in an outbreak situation can be implemented earlier, thus reducing the number of subsequent adenoviral infections.

The prevention of early-onset neonatal group B streptococcal disease.

PubMed

Money, Deborah; Allen, Victoria M

2013-10-01

To review the evidence in the literature and to provide recommendations on the management of pregnant women in labour for the prevention of early-onset neonatal group B streptococcal disease. The key revisions in this updated guideline include changed recommendations for regimens for antibiotic prophylaxis, susceptibility testing, and management of women with pre-labour rupture of membranes. Maternal outcomes evaluated included exposure to antibiotics in pregnancy and labour and complications related to antibiotic use. Neonatal outcomes of rates of early-onset group B streptococcal infections are evaluated. Published literature was retrieved through searches of MEDLINE, CINAHL, and The Cochrane Library from January 1980 to July 2012 using appropriate controlled vocabulary and key words (group B streptococcus, antibiotic therapy, infection, prevention). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies. There were no date or language restrictions. Searches were updated on a regular basis and incorporated in the guideline to May 2013. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical specialty societies. The quality of evidence in this document was rated using the criteria described in the Report of the Canadian Task Force on Preventive Health Care (Table 1). The recommendations in this guideline are designed to help clinicians identify and manage pregnancies at risk for neonatal group B streptococcal disease to optimize maternal and perinatal outcomes. No cost-benefit analysis is provided. There is good evidence based on randomized control trial data that in women with pre-labour rupture of membranes at term who are colonized with group B streptococcus, rates of neonatal infection are reduced with induction of labour. (I) There is no evidence to support safe neonatal outcomes with expectant management in this clinical situation. 1. Offer all women screening for colonization with group B streptococcus at 35 to 37 weeks' gestation with culture taken from one swab first to the vagina and then to the rectum (through the anal sphincter). (II-1A) This includes women with planned Caesarean delivery because of their risk of labour or ruptured membranes earlier than the scheduled Caesarean delivery. (II-2B) 2. Because of the association of heavy colonization with early onset neonatal disease, provide intravenous antibiotic prophylaxis for group B streptococcus at the onset of labour or rupture of the membranes to: • any woman positive for group B streptococcus by vaginal/rectal swab culture screening done at 35 to 37 weeks' gestation (II-2B); • any woman with an infant previously infected with group B streptococcus (II-3B); • any woman with documented group B streptococcus bacteriuria (regardless of level of colony-forming units) in the current pregnancy. (II-2A) 3. Manage all women who are < 37 weeks' gestation and in labour or with rupture of membranes with intravenous group B streptococcus antibiotic prophylaxis for a minimum of 48 hours, unless there has been a negative vaginal/rectal swab culture or rapid nucleic acid-based test within the previous 5 weeks. (II-3A) 4. Treat all women with intrapartum fever and signs of chorioamnionitis with broad spectrum intravenous antibiotics targeting chorioamnionitis and including coverage for group B streptococcus, regardless of group B streptococcus status and gestational age. (II-2A) 5. Request antibiotic susceptibility testing on group B streptococcus-positive urine and vaginal/rectal swab cultures in women who are thought to have a significant risk of anaphylaxis from penicillin. (II-1A) 6. If a woman with pre-labour rupture of membranes at ≥ 37 weeks' gestation is positive for group B streptococcus by vaginal/rectal swab culture screening, has had group B streptococcus bacteriuria in the current pregnancy, or has had an infant previously affected by group B streptococcus disease, administer intravenous group B streptococcus antibiotic prophylaxis. Immediate obstetrical delivery (such as induction of labour) is indicated, as described in the Induction of Labour guideline published by the Society of Obstetricians and Gynaecologist in September 2013. (II-2B) 7. At ≥ 37 weeks' gestation, if group B streptococcus colonization status is unknown and the 35- to 37-week culture was not performed or the result is unavailable and the membranes have been ruptured for greater than 18 hours, administer intravenous group B streptococcus antibiotic prophylaxis. (II-2B) 8. If a woman with pre-labour rupture of membranes at < 37 weeks' gestation has an unknown or positive group B streptococcus culture status, administer intravenous group B streptococcus prophylaxis for 48 hours, as well as other antibiotics if indicated, while awaiting spontaneous or obstetrically indicated labour. (II-3B).

Detection of Neisseria gonorrhoeae in the pharynx and saliva: implications for gonorrhoea transmission.

PubMed

Chow, Eric P F; Lee, David; Tabrizi, Sepehr N; Phillips, Samuel; Snow, Anthony; Cook, Stuart; Howden, Benjamin P; Petalotis, Irene; Bradshaw, Catriona S; Chen, Marcus Y; Fairley, Christopher K

2016-08-01

This study aimed to determine the proportion of untreated pharyngeal swabs or saliva samples positive by culture or nucleic acid amplification tests (NAATs) for Neisseria gonorrhoeae up to 14 days after an initial culture-positive pharyngeal swab. Men who have sex with men who tested positive for pharyngeal gonorrhoea at Melbourne Sexual Health Centre (MSHC) and returned to MSHC for treatment within 14 days between 13 October 2014 and 25 March 2015 were included in this study. Pharyngeal swabs and saliva samples were collected for culture and NAAT. Of 33 initially culture-positive pharyngeal swabs, 32 saliva samples and 31 pharyngeal swabs were positive by NAAT and 14 pharyngeal and 6 saliva samples were positive by culture within 14 days. There was a significant decline in the proportion of repeated pharyngeal culture samples positive by culture over time (p<0.001). The rapid decline suggests pharyngeal gonorrhoea is short-lived, and the finding of gonorrhoea commonly in the saliva implicates this body fluid in its transmission without direct throat inoculation. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Bacterial counts on teat skin and in new sand, recycled sand, and recycled manure solids used as bedding in freestalls.

PubMed

Rowbotham, R F; Ruegg, P L

2016-08-01

On modern dairy farms, environmental mastitis pathogens are usually the predominant cause of mastitis, and bedding often serves as a point of exposure to these organisms. The objective of this longitudinal study was to determine bacterial populations of 4 different bedding types [deep-bedded new sand (NES), deep-bedded recycled sand (RS), deep-bedded manure solids (DBMS), and shallow-bedded manure solids over foam core mattresses (SBMS)] and of teat skin swabs of primarily primiparous cows housed in a single facility over all 4 seasons. Samples of bedding were collected weekly (n=49wk) from pens that each contained 32 lactating dairy cows. Throughout the length of the same period, composite swabs of teat skin were collected weekly from all cows before and after premilking teat sanitation. Median numbers of streptococci and streptococci-like organisms (SSLO) were >8.6×10(6) cfu/g and >6.9×10(3) cfu/teat swab for all bedding types and teat swabs, respectively. Numbers of SSLO were greatest in samples of SBMS (2.1×10(8) cfu/g) and least in samples of NES (8.6×10(6) cfu/g), RS (1.3×10(7) cfu/g), and DBMS (1.7×10(7) cfu/g). Numbers of gram-negative bacteria in bedding (5.5×10(4) to 1.2×10(7) cfu/g) were fewer than numbers of SSLO (8.6×10(6) to 2.1×10(8) cfu/g). Numbers of coliform bacteria were greatest in samples of DBMS (2.2×10(6) cfu/g) and least in samples of NES (3.6×10(3) cfu/g). In general, the relative number of bacteria on teat skin corresponded to exposure in bedding. Numbers of gram-negative bacteria recovered from prepreparation teat swabs were greatest for cows bedded with DBMS (1.0×10(4) cfu/swab) and RS (2.5×10(3) cfu/swab) and least for cows bedded with NES (5.8×10(2) cfu/swab). Median numbers of coliform and Klebsiella spp. recovered from prepreparation teat swabs were below the limit of detection for all cows except those bedded with DBMS. Numbers of SSLO recovered from prepreparation teat swabs were least for cows bedded with DBMS (6.9×10(3) cfu/swab) and greatest for cows bedded with RS (5.1×10(4) cfu/swab) or SBMS (1.6×10(5) cfu/swab). The numbers of all types of measured bacteria (total gram-negative, coliforms, Klebsiella spp., SSLO) on postpreparation teat swabs were reduced by up to 2.6 logs from numbers of bacteria on prepreparation swabs, verifying effective preparation procedures. Significant correlations between bacterial counts of bedding samples and teat skin swabs were observed for several types of bacteria. As compared with other bedding types, the least amount of gram-negative bacteria were recovered from NES and may indicate that cows on NES have a reduced risk of exposure to pathogens that are typically a cause of clinical mastitis. In contrast, exposure to large numbers of SSLO was consistent across all bedding types and may indicate that risk of subclinical mastitis typically associated with streptococci is not as influenced by bedding type; however, significantly greater numbers of SSLO were found in SBMS than in other bedding types. These findings indicate that use of different bedding types results in exposure to different distributions of mastitis pathogens that may alter the proportion of etiologies of clinical mastitis, although the incidence rate of clinical mastitis did not differ among bedding types. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Isolation of Canine parvovirus with a view to identify the prevalent serotype on the basis of partial sequence analysis

PubMed Central

Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P. N.; Sharma, N. S.

2015-01-01

Aim: The aim of this study was to isolate Canine parvovirus (CPV) from suspected dogs on madin darby canine kidney (MDCK) cell line and its confirmation by polymerase chain reaction (PCR) and nested PCR (NPCR). Further, VP2 gene of the CPV isolates was amplified and sequenced to determine prevailing antigenic type. Materials and Methods: A total of 60 rectal swabs were collected from dogs showing signs of gastroenteritis, processed and subjected to isolation in MDCK cell line. The samples showing cytopathic effects (CPE) were confirmed by PCR and NPCR. These samples were subjected to PCR for amplification of VP2 gene of CPV, sequenced and analyzed to study the prevailing antigenic types of CPV. Results: Out of the 60 samples subjected to isolation in MDCK cell line five samples showed CPE in the form of rounding of cells, clumping of cells and finally detachment of the cells. When these samples and the two commercially available vaccines were subjected to PCR for amplification of VP2 gene, a 1710 bp product was amplified. The sequence analysis revealed that the vaccines belonged to the CPV-2 type and the samples were of CPV-2b type. Conclusion: It can be concluded from the present study that out of a total of 60 samples 5 samples exhibited CPE as observed in MDCK cell line. Sequence analysis of the VP2 gene among the samples and vaccine strains revealed that samples belonged to CPV-2b type and vaccines belonging to CPV-2. PMID:27046996

Personal exposure to aerosolized red tide toxins (brevetoxins).

PubMed

Cheng, Yung Sung; Zhou, Yue; Naar, Jerome; Irvin, C Mitch; Su, Wei-Chung; Fleming, Lora E; Kirkpatrick, Barbara; Pierce, Richard H; Backer, Lorraine C; Baden, Daniel G

2010-06-01

Florida red tides occur annually in the Gulf of Mexico from blooms of the marine dinoflagellate, Karenia brevis, which produces highly potent natural polyether toxins, brevetoxins. Several epidemiologic studies have demonstrated that human exposure to red tide aerosol could result in increased respiratory symptoms. Environmental monitoring of aerosolized brevetoxins was performed using a high-volume sampler taken hourly at fixed locations on Siesta Beach, Florida. Personal exposure was monitored using personal air samplers and taking nasal swab samples from the subjects who were instructed to spend 1 hr on Sarasota Beach during two sampling periods of an active Florida red tide event in March 2005, and in May 2008 when there was no red tide. Results showed that the aerosolized brevetoxins from the personal sampler were in modest agreement with the environmental concentration taken from a high-volume sampler. Analysis of nasal swab samples for brevetoxins demonstrated 68% positive samples in the March 2005 sampling period when air concentrations of brevetoxins were between 50 to 120 ng/m(3) measured with the high-volume sampler. No swab samples showed detectable levels of brevetoxins in the May 2008 study, when all personal samples were below the limit of detection. However, there were no statistical correlations between the amounts of brevetoxins detected in the swab samples with either the environmental or personal concentration. Results showed that the personal sample might provide an estimate of individual exposure level. Nasal swab samples showed that brevetoxins indeed were inhaled and deposited in the nasal passage during the March 2005 red tide event.

Anorectal Lymphogranuloma Venereum in Madrid: A Persistent Emerging Problem in Men Who Have Sex With Men.

PubMed

Cabello Úbeda, Alfonso; Fernández Roblas, Ricardo; García Delgado, Rosa; Martínez García, Laura; Sterlin, Fabiola; Fernández Guerrero, Manuel L; Górgolas, Miguel

2016-07-01

Since 2003, outbreaks of lymphogranuloma venereum (LGV) with anorectal syndrome have been increasingly recognized in many Western countries. All of them have been classified as LGV serovar L2b, mainly occurring in human immunodeficiency virus (HIV)-infected men who have had sex with men (MSM). We describe a series of 26 diagnosed cases of LGV proctitis in downtown Madrid, Spain, in 2014, after implementing routine diagnostic procedures for this disease in symptomatic MSM. We conducted an observational study of patients with symptomatic proctitis attending an outpatient infectious diseases clinic in Madrid, Spain during calendar year 2014. Clinical, epidemiological, laboratory, and therapeutic data were gathered and analyzed. Twenty-six patients were included in the analysis. All were MSM, and 24 of them were HIV-positive. All patients reported having acute proctitis symptoms including tenesmus (85%), pain (88%), constipation (62%), or anal discharge (96%). Proctoscopy showed mucopurulent exudate (25 patients [96%]), and rectal bleeding, with mucosal erythema and/or oedema in all cases. Rectal swabs were obtained from all patients, and LGV serovar L2 was confirmed in all of them. The cure rate was 100% after standard treatments with doxycycline 100 mg twice per day for 3 weeks. Simultaneous rectal infections with other sexually transmitted pathogens (gonorrhoea, herpes simplex virus, Mycoplasma genitalium) and systemic sexually transmitted diseases (STDs) (syphilis, acute HIV, and hepatitis C infections) were also documented in 12 patients (46%), but these co-infections did not appear to influence the clinical manifestations of LGV. Anorectal LGV is a common cause of acute proctitis and proctocolitis among HIV-infected MSM who practice unprotected anal sex, and it is frequently associated with other rectal STDs. The implementation of routine screening and prompt diagnosis of these rectal infections should be mandatory in all clinical settings attended by HIV and STD patients.

FLOQSwab™: Optimisation of Procedures for the Recovery of Microbiological Samples from Surfaces

PubMed Central

Finazzi, Guido; Losio, Marina Nadia; Varisco, Giorgio

2016-01-01

The FLOQSwab™ is a specimen collection device worldwide recognised for its superior performance in the clinical diagnostics. The aim of this work was to evaluate FLOQSwab™ for the recovery of microbiological samples from surfaces compared to the traditional swab (rayon tipped swab) as per ISO 18593:2004 standard. The FLOQSwab™, thanks to its innovative manufacturing technology, allows improving the efficiency of recovery and release of analyte. The study has been divided into two experiments. In the first experiment the two swabs were evaluated for their capacity to recover and release the analyte (three different bacterial loads of Escherichia coli). In the second experiment, the two swabs were evaluated for their capacity to recover three different bacterial loads of E. coli from two different surface materials (stainless steel and polypropylene). In all experiments the flocked swab demonstrated a higher recovery rate compared to the traditional rayon tipped swab. The data obtained from this preliminary study demonstrated that the FLOQSwab™ could be a good food surfaces collection device, which improves the recovery of the analyte and thus produces accurate results. Based on the outcomes of the study, a larger field study is in progress using the FLOQSwab™ for samples collection to improve both environmental monitoring and the efficacy of the hygiene controls for food safety. PMID:27853708

Methods for quantitative and qualitative evaluation of vaginal microflora during menstruation.

PubMed Central

Onderdonk, A B; Zamarchi, G R; Walsh, J A; Mellor, R D; Muñoz, A; Kass, E H

1986-01-01

The quantitative and qualitative changes in the bacterial flora of the vagina during menstruation have received inadequate study. Similarly, the effect of vaginal tampons on the microbial flora as well as the relationship between the microbial flora of the vagina and that of the tampon has not been adequately evaluated. The purposes of the present study were (i) to develop quantitative methods for studying the vaginal flora and the flora of tampons obtained during menstruation and (ii) to determine whether there were differences between the microflora of the tampon and that of the vaginal vault. Tampon and swab samples were obtained at various times from eight young healthy volunteers for 8 to 10 menstrual cycles. Samples consisted of swabs from women wearing menstrual pads compared with swab and tampon samples taken at various times during the menstrual cycle. Samples were analyzed for total facultative and anaerobic bacterial counts, and the six dominant bacterial species in each culture were identified. Statistical evaluation of the results indicates that total bacterial counts decreased during menstruation and that swab and tampon samples yielded similar total counts per unit weight of sample. The numbers of bacteria in tampons tended to be lower than in swabs taken at the same time. Overall, during menstruation, the concentrations of lactobacilli declined, but otherwise there was little difference among the species found during menstruation compared with those found in intermenstrual samples. Cotton tampons had little discernible effect on the microbial flora. PMID:3954346

Owner-collected swabs of pets: a method fit for the purpose of zoonoses research.

PubMed

Möbius, N; Hille, K; Verspohl, J; Wefstaedt, P; Kreienbrock, L

2013-09-01

As part of the preparation of a large cohort study in the entire German population, this study examined the feasibility of cat and dog owners collecting nasal and oral swabs of their animals at home as a method of assessing exposure to zoonoses. In veterinary clinics in Hannover, Germany, 100 pet owners were recruited. Nasal and oral swabs of pets were taken by a veterinarian at the clinic and owners took swabs at home. Swabs were analysed regarding bacterial growth and compared (owner vs. vet) using Cohen's kappa and McNemar's test. The return rate of kits was 92%, and 77% of owners thought it unnecessary to have veterinarian assistance to swab the mouth. McNemar's test results: oral swabs 78% agreement with Gram-positive bacterial growth, 87% agreement with Gram-negative bacterial growth; with similar results for nasal swabs. Although sample quality differed, this method allowed the receipt of swabs from pets in order to obtain information about colonization with zoonotic pathogens.

Brucella Infection in Asian Sea Otters (Enhydra lutris lutris) on Bering Island, Russia.

PubMed

Burgess, Tristan L; Johnson, Christine Kreuder; Burdin, Alexander; Gill, Verena A; Doroff, Angela M; Tuomi, Pamela; Smith, Woutrina A; Goldstein, Tracey

2017-10-01

Infection with Brucella spp., long known as a cause of abortion, infertility, and reproductive loss in domestic livestock, has increasingly been documented in marine mammals over the past two decades. We report molecular evidence of Brucella infection in Asian sea otters (Enhydra lutris lutris). Brucella DNA was detected in 3 of 78 (4%) rectal swab samples collected between 2004 and 2006 on Bering Island, Russia. These 78 animals had previously been documented to have a Brucella seroprevalence of 28%, markedly higher than the prevalence documented in sea otters (Enhydra lutris) in North America. All of the DNA sequences amplified were identical to one or more previously isolated Brucella spp. including strains from both terrestrial and marine hosts. Phylogenetic analysis of this sequence suggested that one animal was shedding Brucella spp. DNA with a sequence matching a Brucella abortus strain, whereas two animals yielded a sequence matching a group of strains including isolates classified as Brucella pinnipedialis and Brucella melitensis. Our results highlight the diversity of Brucella spp. within a single sea otter population.

EVA Swab Tool to Support Planetary Protection and Astrobiology Evaluations

NASA Technical Reports Server (NTRS)

Rucker, Michelle A.; Hood, Drew; Walker, Mary; Venkateswaran, Kasthuri J.; Schuerger, Andrew C.

2018-01-01

When we send humans to search for life on other planets, we'll need to know what we brought with us versus what may already be there. To ensure our crewed systems meet planetary protection requirements-and to protect our science from human contamination-we'll need to assess whether microorganisms may be leaking or venting from our spacecraft. Microbial sample collection outside of a pressurized spacecraft is complicated by temperature extremes, low pressures that preclude the use of laboratory standard (wetted) swabs, and operation either in bulky spacesuits or with robotic assistance. A team at the National Aeronautics and Space Administration (NASA) recently developed a swab kit for use in collecting microbial samples from the external surfaces of crewed spacecraft, including spacesuits. The Extravehicular Activity (EVA) Swab Kit consists of a single swab tool handle and an eight-canister sample caddy. The design team minimized development cost by re-purposing a heritage Space Shuttle tile repair handle that was designed to quickly snap into different tool attachments by engaging a mating device in each end effector. This allowed the tool handle to snap onto a fresh swab end effector much like popular shaving razor handles can snap onto a disposable blade cartridge. To disengage the handle from a swab, the user performs two independent functions, which can be done with a single hand. This dual operation mitigates the risk that a swab will be inadvertently released and lost in microgravity. Each swab end effector is fitted with commercially available foam swab tips, vendor-certified to be sterile for Deoxyribonucleic Acid (DNA). A microbial filter installed in the bottom of each sample container allows the container to outgas and re-pressurize without introducing microbial contaminants to internal void spaces. Extensive ground testing, post-test handling, and sample analysis confirmed the design is able to maintain sterile conditions as the canister moves between various pressure environments. To further minimize cost, the design team acquired extensive ground test experience in a relevant flight environment by piggy-backing onto suited crew training runs. These training runs allowed the project to validate tool interfaces with pressurized EVA gloves and collect user feedback on the tool design and function, as well as characterize baseline microbial data for different types of spacesuits. In general, test subjects found the EVA Swab Kit relatively straightforward to operate, but identified a number of design improvements that will be incorporated into the final design. Although originally intended to help characterize human forward contaminants, this tool has other potential applications, such as for collecting and preserving space-exposed materials to support astrobiology experiments.

Storage Effects on Sample Integrity of Environmental Surface Sampling Specimens with Bacillus anthracis Spores

PubMed Central

Perry, K. Allison; O’Connell, Heather A.; Rose, Laura J.; Noble-Wang, Judith A.; Arduino, Matthew J.

2016-01-01

The effect of packaging, shipping temperatures and storage times on recovery of Bacillus anthracis. Sterne spores from swabs was investigated. Macrofoam swabs were pre-moistened, inoculated with Bacillus anthracis spores, and packaged in primary containment or secondary containment before storage at −15°C, 5°C, 21°C, or 35°C for 0–7 days. Swabs were processed according to validated Centers for Disease Control/Laboratory Response Network culture protocols, and the percent recovery relative to a reference sample (T0) was determined for each variable. No differences were observed in recovery between swabs held at −15° and 5°C, (p ≥ 0.23). These two temperatures provided significantly better recovery than swabs held at 21°C or 35°C (all 7 days pooled, p ≤ 0.04). The percent recovery at 5°C was not significantly different if processed on days 1, 2 or 4, but was significantly lower on day 7 (day 2 vs. 7, 5°C, 102, p=0.03). Secondary containment provided significantly better percent recovery than primary containment, regardless of storage time (5°C data, p ≤ 0.008). The integrity of environmental swab samples containing Bacillus anthracis spores shipped in secondary containment was maintained when stored at −15°C or 5°C and processed within 4 days to yield the optimum percent recovery of spores. PMID:27213119

Storage Effects on Sample Integrity of Environmental Surface Sampling Specimens with Bacillus anthracis Spores.

PubMed

Perry, K Allison; O'Connell, Heather A; Rose, Laura J; Noble-Wang, Judith A; Arduino, Matthew J

The effect of packaging, shipping temperatures and storage times on recovery of Bacillus anthracis . Sterne spores from swabs was investigated. Macrofoam swabs were pre-moistened, inoculated with Bacillus anthracis spores, and packaged in primary containment or secondary containment before storage at -15°C, 5°C, 21°C, or 35°C for 0-7 days. Swabs were processed according to validated Centers for Disease Control/Laboratory Response Network culture protocols, and the percent recovery relative to a reference sample (T 0 ) was determined for each variable. No differences were observed in recovery between swabs held at -15° and 5°C, (p ≥ 0.23). These two temperatures provided significantly better recovery than swabs held at 21°C or 35°C (all 7 days pooled, p ≤ 0.04). The percent recovery at 5°C was not significantly different if processed on days 1, 2 or 4, but was significantly lower on day 7 (day 2 vs. 7, 5°C, 10 2 , p=0.03). Secondary containment provided significantly better percent recovery than primary containment, regardless of storage time (5°C data, p ≤ 0.008). The integrity of environmental swab samples containing Bacillus anthracis spores shipped in secondary containment was maintained when stored at -15°C or 5°C and processed within 4 days to yield the optimum percent recovery of spores.

Clinical forensic sample collection techniques following consensual intercourse in volunteers - cervical canal brush compared to conventional swabs.

PubMed

Joki-Erkkilä, Minna; Tuomisto, Sari; Seppänen, Mervi; Huhtala, Heini; Ahola, Arja; Rainio, Juha; Karhunen, Pekka J

2014-10-01

The purpose of the research was to evaluate gynecological evidence collection techniques; the benefit of cervical canal brush sample compared to vaginal fornix and cervical swab samples and the time frame for detecting Y-chromosomal material QiAmp DNA Mini Kit(®) and Quantifiler Y Human Male DNA Quantification Kit(®) in adult volunteers following consensual intercourse. Eighty-four adult female volunteers following consensual intercourse were recruited for the study. By combining all sample collecting techniques, 81.0% of the volunteers were Y-DNA positive. Up to 60 h the conventional swab sampling techniques detected more Y-DNA positive samples when compared to the brush technique. However, after 60 h, the cervical canal brush sample technique showed its benefit by detecting 27.3% (6/22) of Y-DNA positive samples, which were Y-DNA negative in both conventional swab sampling techniques. By combining swab and brush techniques, 75% of the volunteers were still Y-DNA positive in 72-144 post-coital hours. The rate of measurable Y-DNA decreased approximately 3% per hour. Despite reported consensual intercourse, 6.8% (3/44) of volunteers were Y-DNA negative within 48 h. Y-DNA was not detected after 144 post-coital hours (6 days). In conclusion, the brush as a forensic evidence collection method may provide additional biological trace evidence from the cervical canal, although the best biological trace evidence collection can be obtained by combining all three sampling techniques. The time frame for gynecological forensic evidence sample collection should be considered to be at least a week if sexual violence is suspected. Copyright © 2014 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Rapid, Automated Determination of Elemental Compositions of Ions in Mass Spectra Obtained with an Open-Air Ion Source (2 of 2)

EPA Science Inventory

An inexpensive autosampler for a DART/TOFMS provides mass spectra from analytes absorbed on 76 cotton swab, wipe samples in 7.5 min. A field sample carrier simplifies sample collection and provides swabs nearly ready for analysis to the lab. Applications of the high throughput pr...

Contamination of turkey carcasses by thermotolerant species of Campylobacter during postslaughter processing.

PubMed

Wysok, B; Uradziński, J

2009-01-01

Ample literature data indicate explicitly that the major source of alimentary infections induced by Campylobacter spp. is poultry meat and its products. The undertaken research was aimed at determining the level of contamination of turkey carcasses during selected stages of postslaughter processing. Analyses were conducted on 200 turkey carcasses that were examined in 10 experimental series. In each series, 5 carcasses were analyzed at the selected stages of processing, i.e.: after defeathering, evisceration, washing and chilling. Swabs were collected from each carcass from 20 cm2 skin surface at the area of neck, steak and wall of the body cavity. Out of 550 samples of swabs from the skin surface and wall of the body cavity, 385 isolates were classified as Campylobacter--positive, which constituted 70% of the samples. Out of 100 analyzed swabs collected from the carcasses after defeathering, 73 (73%) were found to contain Campylobacter species. In turn, the presence of this pathogen was confirmed in 122 (81.33%) out of 150 swabs collected from carcasses after evisceration, in 106 (70.66%) swabs collected after washing and in 84 (56%) swabs collected after chilling.

Stability Study of Cervical Specimens Collected by Swab and Stored Dry Followed by Human Papillomavirus DNA Detection Using the cobas 4800 Test.

PubMed

Lin, Chun-Qing; Zeng, Xi; Cui, Jian-Feng; Liao, Guang-Dong; Wu, Ze-Ni; Gao, Qian-Qian; Zhang, Xun; Yu, Xiu-Zhang; Chen, Wen; Xi, Ming-Rong; Qiao, You-Lin

2017-02-01

Safer, more convenient methods for cervical sample collection and storage are necessary to facilitate human papillomavirus (HPV) DNA testing in low-resource settings. Our study aimed to evaluate the stability of cervical specimens collected with dry swabs and stored dry, compared to liquid-based cytology (LBC) samples, as detected by HPV DNA testing. Women with abnormal cytological findings or HPV-positive results at colposcopy were recruited from the West China Second University Hospital, Sichuan University, between October 2013 and March 2014. From each woman, physicians collected cervical specimens with a swab placed into a Sarstedt tube and a CytoBrush placed into LBC medium. Samples were randomly assigned to be stored at uncontrolled ambient temperature for 2, 7, 14, or 28 days and then were tested for 14 high-risk HPV (HR-HPV) types using the cobas HPV test. The rates of agreement between dry swab and LBC samples for any HR-HPV type, HPV16, HPV18, and the 12 pooled HR-HPV types were 93.8%, 97.8%, 99.4%, and 93.2%, respectively, with kappa values of 0.87 (95% confidence interval [CI], 0.83 to 0.91), 0.94 (95% CI, 0.91 to 0.97), 0.94 (95% CI, 0.87 to 1.00), and 0.86 (95% CI, 0.82 to 0.90). The performance of swab samples for detection of cervical precancerous lesions by means of cobas HPV testing was equal to that of LBC samples, even with stratification by storage time. Dry storage of swab-collected cervical samples can last for 1 month without loss of test performance by cobas HPV testing, compared to LBC samples, which may offer a simple inexpensive approach for cervical cancer screening in low-resource settings. Copyright © 2017 American Society for Microbiology.

Bruised Poultry Tissue as a Possible Source of Staphylococcal Infection

PubMed Central

Roskey, C. T.; Hamdy, M. K.

1972-01-01

Bacteriological analyses were made on 45 swab samples secured from hands of poultry workers on processing line, on 31 bruised and 15 normal poultry tissue samples, and on 15 swabs obtained from infected lacerations and exudates of abcesses on hands, arms, chest, and abdomen of poultry workers. A total of 170 Staphylococcus cultures were isolated from samples examined. These cultures were characterized morphologically and biochemically and then grouped into six distinct patterns. S. aureus was found in 86.6% of swab samples obtained from infected workers, in 40% of swabs from hands of workers who handle bruised birds, and in 38.7% of bruised tissues, and was absent from all samples obtained from hands of workers who do not handle bruised birds. All the coagulase-positive staphylococcal isolates were bacteriophage-typed, and the results showed that the same phage-type S. aureus was found in many poultry bruises and in infected lesions of poultry workers as well as on hands of workers who handle bruised birds. These results indicate that poultry bruises are a source of staphylococcal infection encountered among poultry workers. PMID:4553136

Multiple diagnostic tests to identify cattle with Bovine viral diarrhea virus and duration of positive test results in persistently infected cattle

PubMed Central

Fulton, Robert W.; Hessman, Bill E.; Ridpath, Julia F.; Johnson, Bill J.; Burge, Lurinda J.; Kapil, Sanjay; Braziel, Barbara; Kautz, Kira; Reck, Amy

2009-01-01

Several tests for Bovine viral diarrhea virus (BVDV) were applied to samples collected monthly from December 20, 2005, through November 27, 2006 (day 0 to day 342) from 12 persistently infected (PI) cattle with BVDV subtypes found in US cattle: BVDV-1a, BVDV-1b, and BVDV-2a. The samples included clotted blood for serum, nasal swabs, and fresh and formalin-fixed ear notches. The tests were as follows: titration of infectious virus in serum and nasal swabs; antigen-capture (AC) enzyme-linked immunosorbent assay (ELISA), or ACE, on serum, nasal swabs, and fresh ear notches; gel-based polymerase chain reaction (PCR) testing of serum, nasal swabs, and fresh ear notches; immunohistochemical (IHC) testing of formalin-fixed ear notches; and serologic testing for BVDV antibodies in serum. Of the 12 animals starting the study, 3 died with mucosal disease. The ACE and IHC tests on ear notches had positive results throughout the study, as did the ACE and PCR tests on serum. There was detectable virus in nasal swabs from all the cattle throughout the study except for a few samples that were toxic to cell cultures. The serum had a virus titer ≥ log10 1.60 in all samples from all the cattle except for 3 collections from 1 animal. Although there were several equivocal results, the PCR test most often had positive results. The BVDV antibodies were due to vaccination or exposure to heterologous strains and did not appear to interfere with any BVDV test. These findings illustrate that PI cattle may be identified by several tests, but differentiation of PI cattle from cattle with acute BVDV infection requires additional testing, especially of blood samples and nasal swabs positive on initial testing. Also, calves PI with BVDV are continual shedders of infectious virus, as shown by the infectivity of nasal swabs over the 11-mo study. PMID:19436580

Quantitative assessment of vaginal microflora during use of tampons of various compositions.

PubMed Central

Onderdonk, A B; Zamarchi, G R; Rodriguez, M L; Hirsch, M L; Muñoz, A; Kass, E H

1987-01-01

Although the effect of vaginal tampons on the microbial flora during menstruation has recently been studied by several investigators, quantitative effects attributable to particular tampon fibers have received less attention. The purposes of the present study were (i) to determine and then to compare the effects of polyacrylate rayon tampons and viscose rayon tampons on the normal vaginal flora, (ii) to compare quantitative bacterial counts obtained from these tampons with those obtained from concomitant vaginal swabs, and (iii) to determine whether either of these tampon types alters the vaginal microflora when compared with the microflora in the same women using all-cotton tampons or external catamenial pads. Tampon and swab samples were obtained at predetermined times from 18 women for an average of seven menstrual cycles. Samples consisting of swabs from women wearing menstrual pads were compared with swab and tampon samples taken at predetermined times during the menstrual cycle from women using cotton, polyacrylate rayon, or viscose rayon tampons. Samples were analyzed for total aerobic, facultative, and anaerobic bacterial counts. Statistical evaluation of the results indicated that, on the whole, total bacterial counts decreased during menstruation and that the numbers of bacteria in tampons tended to be lower than those in swab samples taken at the same time. The tampon type had little effect on the vaginal microflora. PMID:3435142

Throat Swabs and Sputum Culture as Predictors of P. aeruginosa or S. aureus Lung Colonization in Adult Cystic Fibrosis Patients.

PubMed

Seidler, Darius; Griffin, Mary; Nymon, Amanda; Koeppen, Katja; Ashare, Alix

2016-01-01

Due to frequent infections in cystic fibrosis (CF) patients, repeated respiratory cultures are obtained to inform treatment. When patients are unable to expectorate sputum, clinicians obtain throat swabs as a surrogate for lower respiratory cultures. There is no clear data in adult subjects demonstrating the adequacy of throat swabs as a surrogate for sputum or BAL. Our study was designed to determine the utility of throat swabs in identifying lung colonization with common organisms in adults with CF. Adult CF subjects (n = 20) underwent bronchoscopy with BAL. Prior to bronchoscopy, a throat swab was obtained. A sputum sample was obtained from subjects who were able to spontaneously expectorate. All samples were sent for standard microbiology culture. Using BAL as the gold standard, we found the positive predictive value for Pseudomonas aeruginosa to be 100% in both sputum and throat swab compared to BAL. However, the negative predictive value for P. aeruginosa was 60% and 50% in sputum and throat swab, respectively. Conversely, the positive predictive value for Staphylococcus aureus was 57% in sputum and only 41% in throat swab and the negative predictive value of S. aureus was 100% in sputum and throat swab compared to BAL. Our data show that positive sputum and throat culture findings of P. aeruginosa reflect results found on BAL fluid analysis, suggesting these are reasonable surrogates to determine lung colonization with P. aeruginosa. However, sputum and throat culture findings of S. aureus do not appear to reflect S. aureus colonization of the lung.

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

PubMed Central

Ingala, Melissa R.; Simmons, Nancy B.; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A.; Perkins, Susan L.

2018-01-01

The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated. PMID:29765359

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution.

PubMed

Ingala, Melissa R; Simmons, Nancy B; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A; Perkins, Susan L

2018-01-01

The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

Expressed prostate secretions in the study of human papillomavirus epidemiology in the male.

PubMed

Smelov, Vitaly; Eklund, Carina; Bzhalava, Davit; Novikov, Andrey; Dillner, Joakim

2013-01-01

Exploring different sampling sites and methods is of interest for studies of the epidemiology of HPV infections in the male. Expressed prostate secretions (EPS) are obtained during digital rectal examination (DRE), a daily routine urological diagnostic procedure, following massage of the prostate. Urethral swabs and EPS samples were obtained from a consecutive sample of 752 men (mean age 32.4 years; median life-time sex partners 34) visiting urology outpatient clinics in St. Petersburg, Russia and tested for HPV DNA by general primer PCR, followed by genotyping using Luminex. Overall, 47.9% (360/752) of men were HPV-positive, with 42.0% (316/752) being positive for high-risk (HR-) HPV and 12.6% (95/752) for multiple HPV types. HPV-positivity in the EPS samples was 32.6% (27.7% HR-HPV) and in the urethral samples 25.9% (24.5% HR-HPV). 10.6% were HPV positive in both EPS and urethral samples. 6.4% had the same HPV-type in both EPS and urethral samples. 10.6% were HPV positive in both EPS and urethral samples. 6.4% had the same HPV-type in both EPS and urethral samples. The concordance between the urethral samples and EPS was 62.5% (470/752), with 80 cases double positive and 390 cases double negative in both sites. The sensitivity of urethral samples for overall HPV detection was 54.2% (195/360). Compared to analysis of urethral samples only, the analysis of EPS increased the HPV prevalence in this population with 26.2%. EPS represent informative sampling material for the study of HPV epidemiology in the male.

Ensuring safety of home-produced eggs to control salmonellosis in Poland: lessons from an outbreak in September 2011.

PubMed

Zielicka-Hardy, A; Zarowna, D; Szych, J; Madajczak, G; Sadkowska-Todys, M

2012-11-22

Implementation of control measures in line with European Commission regulations has led to a decrease in salmonellosis in the European Union since 2004. However, control programmes do not address laying hens whose eggs are produced for personal consumption or local sale. This article reports an investigatxion of a salmonellosis outbreak linked to home-produced eggs following a family event held in a farm in September 2011 near Warsaw, Poland. In the outbreak, 34 people developed gastroenteritis symptoms. Results from a cohort study indicated a cake, prepared from raw home-produced eggs, as the vehicle of the outbreak. Laboratory analysis identified Salmonella enterica serotype Enteritidis (S. Enteritidis) in stool samples or rectal swabs from 18 of 24 people and in two egg samples. As no food items remained, we used phage typing to link the source of the outbreak with the isolated strains. Seven S. Enteritidis strains analysed (five from attendees and two from eggs) were phage type 21c. Our findings resulted in culling of the infected laying hens and symptomatic pigeons housed next to the hens. Salmonella poses as a public health problem in Poland: control measures should not forget home-produced eggs, as there is a risk of infection from their consumption.

Vibrio cholerae O1 Ogawa Strains Carrying the ctxB7 Allele Caused a Large Cholera Outbreak during 2014 in the Tribal Areas of Odisha, India.

PubMed

Pal, Bibhuti Bhusan; Khuntia, Hemant Kumar; Nayak, Smruti Ranjan; Mohanty, Anima; Biswal, Bhagyalaxmi

2017-09-25

The large outbreak of cholera reported during July to September 2014 in the Narla block of Kalahandi district, India, was investigated to determine the causative organism. Rectal swabs collected from patients with diarrhea and environmental water samples were cultured following standard techniques. The causative organism was identified as Vibrio cholerae O1 Ogawa biotype El Tor, and analysis by double mismatch mutation assay PCR confirmed that all strains were the ctxB7 variant of Haitian V. cholerae O1. The environmental water samples were negative for V. cholerae. The V. cholerae O1 strains were sensitive to tetracycline, ciprofloxacin, norfloxacin, ofloxacin, doxycycline, and azithromycin, but were resistant to erythromycin, gentamicin, chloramphenicol, furazolidone, neomycin, cotrimoxazole, nalidixic acid, and ampicillin. In the 2014 cholera outbreak, the early reporting of the pathogen enabled the government authorities to implement adequate control measures in time to curtail the spread of the disease. That was the second large cholera outbreak due to Haitian variants of V. cholerae O1 after the 2010 Haiti cholera outbreak reported from Odisha, India, and other locations globally. Active surveillance is required to track the spread of this strain in the Odisha region.

Norovirus prevention and the prevalence of asymptomatic norovirus infection in kindergartens and primary schools in Changzhou, China: Status of the knowledge, attitudes, behaviors, and requirements.

PubMed

Qi, Rui; Ye, Chao; Chen, Cong; Yao, Ping; Hu, Feifei; Lin, Qin

2015-08-01

We estimated the status of norovirus infection and prevention in kindergartens and primary schools and identified poor areas for which future education is needed. We evaluated the knowledge, attitude, behavior, requirements of outbreak prevention, and rate of asymptomatic carriers. Two self-administered questionnaires were conducted for data collection. Five hundred seventy-four teachers from kindergartens and primary schools and 3,114 students from primary schools in Changzhou city were sampled for questionnaire investigation. In addition, 511 rectal swabs from healthy children were taken for norovirus detection. Twenty-one of 511 children were asymptomatically infected with norovirus. The rate of asymptomatic norovirus infection children in kindergartens was 2.7% and 4.7% in primary schools. Nineteen of 21 positive samples were GII strains, the other 2 were GI strains. In addition, we found that primary schools were less prepared to prevent norovirus outbreaks than kindergartens. Settings in the suburban counties needed more education on norovirus prevention. The results of this study emphasize the need for training of primary schools and suburban schools about norovirus prevention. Asymptomatic norovirus infection should receive more attention. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Random sampling of the Central European bat fauna reveals the existence of numerous hitherto unknown adenoviruses.

PubMed

Vidovszky, Márton; Kohl, Claudia; Boldogh, Sándor; Görföl, Tamás; Wibbelt, Gudrun; Kurth, Andreas; Harrach, Balázs

2015-12-01

From over 1250 extant species of the order Chiroptera, 25 and 28 are known to occur in Germany and Hungary, respectively. Close to 350 samples originating from 28 bat species (17 from Germany, 27 from Hungary) were screened for the presence of adenoviruses (AdVs) using a nested PCR that targets the DNA polymerase gene of AdVs. An additional PCR was designed and applied to amplify a fragment from the gene encoding the IVa2 protein of mastadenoviruses. All German samples originated from organs of bats found moribund or dead. The Hungarian samples were excrements collected from colonies of known bat species, throat or rectal swab samples, taken from live individuals that had been captured for faunistic surveys and migration studies, as well as internal organs of dead specimens. Overall, 51 samples (14.73%) were found positive. We detected 28 seemingly novel and six previously described bat AdVs by sequencing the PCR products. The positivity rate was the highest among the guano samples of bat colonies. In phylogeny reconstructions, the AdVs detected in bats clustered roughly, but not perfectly, according to the hosts' families (Vespertilionidae, Rhinolophidae, Hipposideridae, Phyllostomidae and Pteropodidae). In a few cases, identical sequences were derived from animals of closely related species. On the other hand, some bat species proved to harbour more than one type of AdV. The high prevalence of infection and the large number of chiropteran species worldwide make us hypothesise that hundreds of different yet unknown AdV types might circulate in bats.

Infection dynamics and acute phase response of an Actinobacillus pleuropneumoniae field isolate of moderate virulence in pigs.

PubMed

Gómez-Laguna, Jaime; Islas, Armando; Muñoz, Dennis; Ruiz, Alvaro; Villamil, Aura; Carrasco, Librado; Quezada, Manuel

2014-10-10

Actinobacillus pleuropneumoniae, the causative agent of porcine contagious pleuropneumonia (PCP), causes significant economic losses associated mainly with growth stunting of animals. Although serotypes can be distinguished according to their virulence, most of the studies are focused in A. pleuropneumoniae infections with virulent serotypes. There is little information regarding the role of acute phase proteins (APPs) and proinflammatory cytokines in infections with isolates of mild or moderate virulence. Thus, the present study aims to evaluate the kinetics of infection with an A. pleuropneumoniae serotype 6 (Ap6) field isolate of moderate virulence and the changes in the serum concentration of specific antibodies and different APPs and proinflammatory cytokines. Control animals showed no clinical signs or lesions throughout the study. Infected animals showed increased rectal temperature, respiratory distress and depression from 24hpi, and typical gross and microscopic lesions of PCP from 6hpi onwards. Ap6 was isolated from nasal swabs of four out of five inoculated animals at 24hpi, and from nasal swabs, tonsil and lung samples from all inoculated animals at 72hpi. Specific antibodies against Ap6 or changes in the serum concentration of IL-1β, IL-10 and TNF-α were not detected throughout the study. The serum concentration of IL-6 increased from 6hpi as well as serum A amyloid, C-reactive protein and haptoglobin from 24hpi onwards. Our results highlight the onset of the acute phase response after the infection with a field isolate of A. pleuropneumoniae of moderate virulence from 24hpi onwards which may be of interest in the study of the pathogenesis of this disease. Copyright © 2014 Elsevier B.V. All rights reserved.

Nondestructive Biological Evidence Collection with Alternative Swabs and Adhesive Lifters.

PubMed

Plaza, Dane T; Mealy, Jamia L; Lane, J Nicholas; Parsons, M Neal; Bathrick, Abigail S; Slack, Donia P

2016-03-01

In forensic science, biological material is typically collected from evidence via wet/dry double swabbing with cotton swabs, which is effective but can visibly damage an item's surface. When an item's appearance must be maintained, dry swabbing and tape-lifting may be employed as collection techniques that are visually nondestructive to substrates' surfaces. This study examined the efficacy of alternative swab matrices and adhesive lifters when collecting blood and fingerprints from glass, painted drywall, 100% cotton, and copy paper. Data were evaluated by determining the percent profile and quality score for each STR profile generated. Hydraflock(®) swabs, BVDA Gellifters(®) , and Scenesafe FAST™ tape performed as well as or better than cotton swabs when collecting fingerprints from painted drywall and 100% cotton. Collection success was also dependent on the type of biological material sampled and the substrate on which it was deposited. These results demonstrated that alternative swabs and adhesive lifters can be effective for nondestructive DNA collection from various substrates. © 2015 American Academy of Forensic Sciences.

Detection of canine astrovirus in dogs with diarrhea in Japan.

PubMed

Takano, Tomomi; Takashina, Midori; Doki, Tomoyoshi; Hohdatsu, Tsutomu

2015-06-01

Canine astrovirus (CAstV) is the causative agent of gastroenteritis in dogs. We collected rectal swabs from dogs with or without diarrhea symptoms in Japan and examined the feces for the presence of CAstV by RT-PCR with primers based on a conserved region of the ORF1b gene. The ORF1b gene of CAstV was not detected in the 42 dogs without clinical illness but was present in three pups out of the 31 dogs with diarrhea symptoms. Based on the full-length capsid protein, the CAstV KU-D4-12 strain that we detected in this study shared high homology with the novel virulent CAstV VM-2011 strain.

Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos)

PubMed Central

Wheat, Rachel E.; Allen, Jennifer M.; Miller, Sophie D. L.; Wilmers, Christopher C.; Levi, Taal

2016-01-01

Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species. PMID:27828988

Electrostatic sampling of trace DNA from clothing.

PubMed

Zieger, Martin; Defaux, Priscille Merciani; Utz, Silvia

2016-05-01

During acts of physical aggression, offenders frequently come into contact with clothes of the victim, thereby leaving traces of DNA-bearing biological material on the garments. Since tape-lifting and swabbing, the currently established methods for non-destructive trace DNA sampling from clothing, both have their shortcomings in collection efficiency and handling, we thought about a new collection method for these challenging samples. Testing two readily available electrostatic devices for their potential to sample biological material from garments made of different fabrics, we found one of them, the electrostatic dust print lifter (DPL), to perform comparable to well-established sampling with wet cotton swabs. In simulated aggression scenarios, we had the same success rate for the establishment of single aggressor profiles, suitable for database submission, with both the DPL and wet swabbing. However, we lost a substantial amount of information with electrostatic sampling, since almost no mixed aggressor-victim profiles suitable for database entry could be established, compared to conventional swabbing. This study serves as a proof of principle for electrostatic DNA sampling from items of clothing. The technique still requires optimization before it might be used in real casework. But we are confident that in the future it could be an efficient and convenient contribution to the toolbox of forensic practitioners.

The effectiveness of targeted relative to empiric prophylaxis on infectious complications after transrectal ultrasound-guided prostate biopsy: a meta-analysis.

PubMed

Scott, Susan; Harris, Patrick N; Williamson, Deborah A; Liss, Michael A; Doi, Suhail A R; Roberts, Matthew J

2018-07-01

Rectal culture screening for fluoroquinolone (FQ)-resistant Enterobacteriaceae before transrectal ultrasound guided prostate (TRUSPB) biopsy and targeted antibiotic prophylaxis (TAP) may decrease post-TRUSPB infection rates compared to empiric (EAP) regimens. The objective of this study was to evaluate the effectiveness of targeted relative to empiric prophylaxis regimens on rates of infectious complications after TRUSPB and to determine the baseline prevalence of FQ resistance based on prior rectal swabs. An electronic search within literature databases including EMBASE and Web of Science (all databases) for articles assessing TAP as an approach to TRUSPB prophylaxis was conducted. Quality assessment was performed using the Hoy instrument. Meta-analysis was performed using MetaXL 5.3. From 15 studies (eight retrospective and seven prospective) representing 12,320 participants, infectious complication incidence was 3.4% in EAP and 0.8% in TAP patients. The number needed to treat with TAP to avoid one more infection when compared to the EAP group was 39. Effect sizes were homogeneous. Prevalence of FQ resistance showed low (15%) and high (28%) subgroups, likely due to region of origin (within and outside USA, respectively). Rectal culture prior to TRUSPB and use of TAP adjusts for endemic FQ resistance and is associated with less infectious complications and resulting morbidity when compared to EAP. Overtreatment associated with augmented prophylaxis approaches may be reduced as a result. Further prospective assessment and cost-benefit analyses are required before widespread implementation can be recommended.

Unusual microorganisms and antimicrobial resistances in a group of Syrian migrants: Sentinel surveillance data from an asylum seekers centre in Italy.

PubMed

Angeletti, Silvia; Ceccarelli, Giancarlo; Vita, Serena; Dicuonzo, Giordano; Lopalco, Maurizio; Dedej, Etleva; Blasi, Aletheia; Antonelli, Francesca; Conti, Alessia; De Cesaris, Marina; Farchi, Francesca; Lo Presti, Alessandra; Ciccozzi, Massimo

2016-01-01

Three years of civil war in Syria have caused death and increase of communicable diseases. The suffering population has been forced to migrate creating a fertile condition for epidemic spread of infection within the refugee camps. Forty-eight Syrian migrants, upon their arrival in Italy, were accommodated at the asylum seekers centre of Castelnuovo di Porto. They received a physical examination and were subjected to microbiological surveillance by blood, rectal, pharyngeal and nasal swabs collection and delivering to the Clinical Pathology and Microbiology Laboratory of the University Campus Bio-Medico of Rome. All refugees resulted negative for HBV, HCV and HIV infections. In swabs a large number of unusual gram-negative bacteria species were isolated, such as Pseudomonas putida, Pseudomonas monteilii, Pseudomonas fulva, Pseudomonas moselii, Aeromonas veronii, Aeromonas caviae, Aeromonas hydrophila, Acinteobacter guilloviae, Acinteobacter lowffii; Acinetobacter johnsonii; Acinteobacter tjernbergae; Pantoea agglomerans; Pantoea calida. Among isolates, strains resistant to carbapenems, ESBL producers and methicillin resistant were found. The microbiological surveillance performed represents a useful action to understand refugees health status and to trace unusual microorganisms movement even carriers of antimicrobial resistance during migrants traveling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genotyping and pathobiologic characterization of canine parvovirus circulating in Nanjing, China

PubMed Central

2013-01-01

Background Canine parvovirus (CPV) is an important pathogen that causes acute enteric disease in dogs. It has mutated and spread throughout the world in dog populations. We provide an update on the molecular characterization of CPV that circulated in Nanjing, a provincial capital in China between 2009 and 2012. Results Seventy rectal swab samples were collected from the dogs diagnosed with CPV infection in 8 animal hospitals of Nanjing. Sequence analysis of VP2 genes of 31 samples revealed that 29 viral strains belonged to CPV-2a subtype, while other two strains were classified into CPV-2b. To investigate the pathogenicity of the prevalent virus, we isolated CPV-2a and performed the animal experiment. Nine beagles were inoculated with 105.86 of 50% tissue culture infectious doses (TCID50) of the virus. All the experimentally infected beagles exhibited mild to moderate mucoid or watery diarrhea on day 4 post-infection (p.i.). On day 9 p.i., characteristic histopathological lesions were clearly observed in multiple organs of infected dogs, including liver, spleen, kidney, brain and all segments of the small and large intestines, while viral DNA and antigen staining could be detected in the sampled tissues. It is notable that canine parvovirus was isolated in one from two brain samples processed. Conclusion Our results indicated that CPV-2a is the predominant subtype in Nanjing of China. And this virus caused extensive lesions in a variety of tissues, including the brain. PMID:23988202

Salmonella Weltevreden food poisoning in a tea garden of Assam: An outbreak investigation.

PubMed

Saikia, L; Sharma, A; Nath, R; Choudhury, G; Borah, A K

2015-01-01

Salmonella enterica serovar Weltevreden has been a rare cause of acute gastroenteritis occurring worldwide. Here, we report an outbreak of food poisoning in a tea garden. To determine the aetiological agent and risk factors responsible for the outbreak and to take necessary steps for prevention of future outbreaks. Affected area was visited by a team of microbiologists for collecting stool samples/rectal swabs from affected patients. Samples were processed by culture followed by confirmation of the isolates biochemically, automated bacterial identification system, conventional serotyping and molecular typing. Water samples were also processed for detection of faecal contamination. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion technique according to the Clinical Laboratory Standard Institute guidelines. The isolates were confirmed as S. enterica subspecies enterica serovar Weltevreden. They were found sensitive to ampicillin, amoxycillin-clavulanic acid, ciprofloxacin, ofloxacin, norfloxacin, cefotaxime, ceftriaxone, co-trimoxazole and doxycycline. Water samples showed high-level faecal contamination. Source of outbreak was found to be drinking water contaminated with dead livestock. House to house visit was made for early diagnosis and treatment of the cases, awareness campaigning and chlorination of drinking water. This report emphasises the geographical distribution of this organism in Assam. As S. Weltevreden is widely distributed in domestic animals, people should be made aware of immediate reporting of any unusual death among the livestock and their safe disposal which can significantly reduce the incidence of non-typhoidal salmonellosis in the country.

Genotyping and pathobiologic characterization of canine parvovirus circulating in Nanjing, China.

PubMed

Zhao, Yanbing; Lin, Yan; Zeng, Xujian; Lu, Chengping; Hou, Jiafa

2013-08-29

Canine parvovirus (CPV) is an important pathogen that causes acute enteric disease in dogs. It has mutated and spread throughout the world in dog populations. We provide an update on the molecular characterization of CPV that circulated in Nanjing, a provincial capital in China between 2009 and 2012. Seventy rectal swab samples were collected from the dogs diagnosed with CPV infection in 8 animal hospitals of Nanjing. Sequence analysis of VP2 genes of 31 samples revealed that 29 viral strains belonged to CPV-2a subtype, while other two strains were classified into CPV-2b. To investigate the pathogenicity of the prevalent virus, we isolated CPV-2a and performed the animal experiment. Nine beagles were inoculated with 105.86 of 50% tissue culture infectious doses (TCID50) of the virus. All the experimentally infected beagles exhibited mild to moderate mucoid or watery diarrhea on day 4 post-infection (p.i.). On day 9 p.i., characteristic histopathological lesions were clearly observed in multiple organs of infected dogs, including liver, spleen, kidney, brain and all segments of the small and large intestines, while viral DNA and antigen staining could be detected in the sampled tissues. It is notable that canine parvovirus was isolated in one from two brain samples processed. Our results indicated that CPV-2a is the predominant subtype in Nanjing of China. And this virus caused extensive lesions in a variety of tissues, including the brain.

Sampling methods for microbiological analysis of red meat and poultry carcasses.

PubMed

Capita, Rosa; Prieto, Miguel; Alonso-Calleja, Carlos

2004-06-01

Microbiological analysis of carcasses at slaughterhouses is required in the European Union for evaluating the hygienic performance of carcass production processes as required for effective hazard analysis critical control point implementation. The European Union microbial performance standards refer exclusively to the excision method, even though swabbing using the wet/dry technique is also permitted when correlation between both destructive and nondestructive methods can be established. For practical and economic reasons, the swab technique is the most extensively used carcass surface-sampling method. The main characteristics, advantages, and limitations of the common excision and swabbing methods are described here.

Use of buccal swabs for sampling DNA from nestling and adult birds

USGS Publications Warehouse

Handel, Colleen M.; Pajot, Lisa; Talbot, Sandra L.; Sage, George K.

2006-01-01

We evaluated the feasibility and efficiency of using swabs to collect buccal epithelial cells fromsmall (2‐ to 13‐g) birds as a source of DNA for genetic studies. We used commercially available buccal swab kits to collect samples from 42 adult and 39 nestling (4‐ to 8‐day‐old) black‐capped chickadees (Poecile atricapillus) and from6 4‐day‐old nestling boreal chickadees (P. hudsonica). We compared DNA from buccal epithelial samples to that fromblood samples from the same individuals. We extracted sufficient quantities of DNA for analysis from all buccalsamples, and samples remained viable even after being stored in original plastic sampling tubes at room temperature for up to 18 months. Yields were equivalent whether extracted using the proprietary quick‐extraction solution provided with buccal swab kits or using a salt‐extraction process with inexpensive reagents. Yields of DNA from buccal samples were consistently lower than those from blood samples, but quantities were sufficient for all analyses. Assignment of sex, based on DNA extracted from paired buccal and blood samples, was identical for all 87 birds. We found no difference in the genotypes obtained from buccal and blood samples for 12 individuals tested using 5 microsatellite loci and found perfect concordance in sequencing of an 823‐base‐pair segment within the control region of mitochondrial DNA for 7 individuals tested. Use of buccal swabs is highly recommended as a rapid, noninvasive technique for sampling avian genomic DNA, especially for extremely young altricial nestlings or small‐bodied adults, or for any birds for which blood sampling may be impossible or stressful.

Rationale and design of REACT: a randomised controlled trial assessing the effectiveness of home-collection to increase chlamydia retesting and detect repeat positive tests.

PubMed

Smith, Kirsty S; Hocking, Jane S; Chen, Marcus; Fairley, Christopher K; McNulty, Anna; Read, Phillip; Bradshaw, Catriona S; Tabrizi, Sepehr N; Wand, Handan; Saville, Marion; Rawlinson, William; Garland, Suzanne M; Donovan, Basil; Kaldor, John M; Guy, Rebecca

2014-04-24

Repeat infection with Chlamydia trachomatis is common and increases the risk of sequelae in women and HIV seroconversion in men who have sex with men (MSM). Despite guidelines recommending chlamydia retesting three months after treatment, retesting rates are low. We are conducting the first randomised controlled trial to assess the effectiveness of home collection combined with short message service (SMS) reminders on chlamydia retesting and reinfection rates in three risk groups. The REACT (retest after Chlamydia trachomatis) trial involves 600 patients diagnosed with chlamydia: 200 MSM, 200 women and 200 heterosexual men recruited from two Australian sexual health clinics where SMS reminders for retesting are routine practice. Participants will be randomised to the home group (3-month SMS reminder and home-collection) or the clinic group (3-month SMS reminder to return to the clinic). Participants in the home group will be given the choice of attending the clinic if they prefer. The mailed home-collection kit includes a self-collected vaginal swab (women), UriSWAB (Copan) for urine collection (heterosexual men), and UriSWAB plus rectal swab (MSM). The primary outcome is the retest rate at 1-4 months after a chlamydia diagnosis, and the secondary outcomes are: the repeat positive test rate; the reinfection rate; the acceptability of home testing with SMS reminders; and the cost effectiveness of home testing. Sexual behaviour data collected via an online survey at 4-5 months, and genotyping of repeat infections, will be used to discriminate reinfections from treatment failures. The trial will be conducted over two years. An intention to treat analysis will be conducted. This study will provide evidence about the effectiveness of home-collection combined with SMS reminders on chlamydia retesting, repeat infection and reinfection rates in three risk groups. The trial will determine client acceptability and cost effectiveness of this strategy. Australian and New Zealand Clinical Trials Registry ACTRN12611000968976.

Efficacy of a cold-adapted, intranasal, equine influenza vaccine: challenge trials.

PubMed

Townsend, H G; Penner, S J; Watts, T C; Cook, A; Bogdan, J; Haines, D M; Griffin, S; Chambers, T; Holland, R E; Whitaker-Dowling, P; Youngner, J S; Sebring, R W

2001-11-01

A randomised, controlled, double-blind, influenza virus, aerosol challenge of horses was undertaken to determine the efficacy of a cold-adapted, temperature sensitive, modified-live virus, intranasal, equine influenza vaccine. Ninety 11-month-old influenza-naïve foals were assigned randomly to 3 groups (20 vaccinates and 10 controls per group) and challenged 5 weeks, 6 and 12 months after a single vaccination. Challenges were performed on Day 0 in a plastic-lined chamber. Between Days 1 and 10, animals were examined daily for evidence of clinical signs of influenza. Nasal swabs for virus isolation were obtained on Day 1 and Days 1 to 8 and blood samples for serology were collected on Days 1, 7 and 14. There was no adverse response to vaccination in any animal. Following challenge at 5 weeks and 6 months, vaccinates had significantly lower clinical scores (P = 0.0001 and 0.005, respectively), experienced smaller increases in rectal temperature (P = 0.0008 and 0.0007, respectively) and shed less virus (P<0.0001 and P = 0.03, respectively) over fewer days (P<0.0001 and P = 0.002, respectively) than did the controls. After the 12 month challenge, rectal temperatures (P = 0.006) as well as the duration (P = 0.03) and concentration of virus shed (P = 0.04) were significantly reduced among vaccinated animals. The results of this study showed that 6 months after a single dose of vaccine the duration and severity of clinical signs were markedly reduced amongst vaccinated animals exposed to a severe live-virus challenge. Appropriate use of this vaccine should lead to a marked reduction in the frequency, severity and duration of outbreaks of equine influenza in North America.

Evaluation of Skin Surface as an Alternative Source of Reference DNA Samples: A Pilot Study.

PubMed

Albujja, Mohammed H; Bin Dukhyil, Abdul Aziz; Chaudhary, Abdul Rauf; Kassab, Ahmed Ch; Refaat, Ahmed M; Babu, Saranya Ramesh; Okla, Mohammad K; Kumar, Sachil

2018-01-01

An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2.1 ng/μL). Cotton swabs moistened with ethanol yielded higher quantities of DNA than swabs moistened with salicylic acid, and it gave the highest percentage of full STR profiles (97%). This study supports the use of SSC as a noninvasive sampling technique and as a extremely useful source of DNA reference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable. © 2017 American Academy of Forensic Sciences.

Enhanced Detection of Surface-Associated Bacteria in Indoor Environments by Quantitative PCR

PubMed Central

Buttner, Mark P.; Cruz-Perez, Patricia; Stetzenbach, Linda D.

2001-01-01

Methods for detecting microorganisms on surfaces are needed to locate biocontamination sources and to relate surface and airborne concentrations. Research was conducted in an experimental room to evaluate surface sampling methods and quantitative PCR (QPCR) for enhanced detection of a target biocontaminant present on flooring materials. QPCR and culture analyses were used to quantitate Bacillus subtilis (Bacillus globigii) endospores on vinyl tile, commercial carpet, and new and soiled residential carpet with samples obtained by four surface sampling methods: a swab kit, a sponge swipe, a cotton swab, and a bulk method. The initial data showed that greater overall sensitivity was obtained with the QPCR than with culture analysis; however, the QPCR results for bulk samples from residential carpet were negative. The swab kit and the sponge swipe methods were then tested with two levels of background biological contamination consisting of Penicillium chrysogenum spores. The B. subtilis values obtained by the QPCR method were greater than those obtained by culture analysis. The differences between the QPCR and culture data were significant for the samples obtained with the swab kit for all flooring materials except soiled residential carpet and with the sponge swipe for commercial carpet. The QPCR data showed that there were no significant differences between the swab kit and sponge swipe sampling methods for any of the flooring materials. Inhibition of QPCR due solely to biological contamination of flooring materials was not evident. However, some degree of inhibition was observed with the soiled residential carpet, which may have been caused by the presence of abiotic contaminants, alone or in combination with biological contaminants. The results of this research demonstrate the ability of QPCR to enhance detection and enumeration of biocontaminants on surface materials and provide information concerning the comparability of currently available surface sampling methods. PMID:11375164

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

Comparison of sampling procedures and microbiological and non-microbiological parameters to evaluate cleaning and disinfection in broiler houses.

PubMed

Luyckx, K; Dewulf, J; Van Weyenberg, S; Herman, L; Zoons, J; Vervaet, E; Heyndrickx, M; De Reu, K

2015-04-01

Cleaning and disinfection of the broiler stable environment is an essential part of farm hygiene management. Adequate cleaning and disinfection is essential for prevention and control of animal diseases and zoonoses. The goal of this study was to shed light on the dynamics of microbiological and non-microbiological parameters during the successive steps of cleaning and disinfection and to select the most suitable sampling methods and parameters to evaluate cleaning and disinfection in broiler houses. The effectiveness of cleaning and disinfection protocols was measured in six broiler houses on two farms through visual inspection, adenosine triphosphate hygiene monitoring and microbiological analyses. Samples were taken at three time points: 1) before cleaning, 2) after cleaning, and 3) after disinfection. Before cleaning and after disinfection, air samples were taken in addition to agar contact plates and swab samples taken from various sampling points for enumeration of total aerobic flora, Enterococcus spp., and Escherichia coli and the detection of E. coli and Salmonella. After cleaning, air samples, swab samples, and adenosine triphosphate swabs were taken and a visual score was also assigned for each sampling point. The mean total aerobic flora determined by swab samples decreased from 7.7±1.4 to 5.7±1.2 log CFU/625 cm2 after cleaning and to 4.2±1.6 log CFU/625 cm2 after disinfection. Agar contact plates were used as the standard for evaluating cleaning and disinfection, but in this study they were found to be less suitable than swabs for enumeration. In addition to measuring total aerobic flora, Enterococcus spp. seemed to be a better hygiene indicator to evaluate cleaning and disinfection protocols than E. coli. All stables were Salmonella negative, but the detection of its indicator organism E. coli provided additional information for evaluating cleaning and disinfection protocols. Adenosine triphosphate analyses gave additional information about the hygiene level of the different sampling points. © 2015 Poultry Science Association Inc.

Effect of sampling and short isolation methodologies on the recovery of human pathogenic Yersinia enterocolitica from pig tonsils.

PubMed

Van Damme, Inge; Berkvens, Dirk; De Zutter, Lieven

2012-07-01

The objective of this study was to determine the effect of sampling (swab samples compared to destructive samples) on isolation rates of human pathogenic Yersinia enterocolitica from pig tonsils. Moreover, the relative efficiency of different rapid, routinely applicable isolation methods was evaluated. Therefore, swab and destructive samples from tonsils of 120 pigs at slaughter were analyzed in parallel using direct plating and different enrichment methods. Salmonella-Shigella-desoxycholate-calcium chloride (SSDC) agar, cefsulodin-irgasan-novobiocin (CIN) agar, and Yersinia enterocolitica chromogenic medium (YeCM) were used as selective agar media. For enrichment, irgasan-ticarcillin-potassium chlorate (ITC) broth and peptone-sorbitol-bile (PSB) broth were incubated at 25°C for 48 h. Overall, 55 tonsils (45.8%) were positive for Y. enterocolitica bioserotype 4/O:3. Recovery was significantly higher using the destructive method compared to the swabbing method. Direct plating resulted in 47 and 28 Y. enterocolitica-positive destructive and swab samples, respectively. Alkali treatment of PSB and ITC enrichment broths significantly increased recovery of pathogenic Y. enterocolitica from destructive tonsil samples. The performance of YeCM for qualitative and quantitative isolation of pathogenic Y. enterocolitica from pig tonsils was equal to SSDC and CIN. In conclusion, direct plating and ISO 10273: 2003 with minor modifications are suitable and rapid methods for isolation of pathogenic Y. enterocolitica from destructive tonsil samples.

[Surveillance of Antimicrobial Resistant Esherichia coli by Rectal Swab Method--Annual Change of Prevalence of Quinolone-resistant and ESBL Producing Strains from 2009 to 2013].

PubMed

Nasu, Yoshitsugu; Sako, Shinichi; Yano, Tomofumi; Kosaka, Noriko

2015-09-01

Although most of commonly used antimicrobial agents had been susceptible to Esherichia coli, recently there are a lot of reports concerning about community-acquired infection caused by resistant E. coli. The aim of this study is to define the prevalence of resistant E. coli in normal flora colonization by the rectal swab method. From June 2009 to December 2013, 251 male patients (50-85 year-old, median 68) planned to transrectal prostate biopsy participated in this study. Stools stuck on the glove at the digital examination were provided for culture specimen. Identification of E. coli and determination of MIC was performed by MicroScan WalkAway40plus (Siemens). Isolated E. coli were deemed quinolone-resistant strains when their MIC of levofloxacine was 4 μg/mL or above according to the breakpoint MIC by the CLSI criteria. ESBL producing ability was determined by the double disk method used by CVA contained ESBL definition disc (Eikenkagaku). Of the 251 study patients, 224 patients had positive cultures of E. coli. Twenty-four patients had quinolone-resistant strains and 9 patients had ESBL producing strains. The prevalence of quinolone-resistant strains in 2009, 2010, 2011, 2012 and 2013 were 5.9% (2 out of 34 strains), 13.5% (5 out of 37 strains), 12.5% (4 out of 32 strains), 9.0% (6 out of 67) and 13.0% (7 out of 54 strains), respectively. The prevalence of ESBL producing strains in 2009, 2010, 2011, 2012 and 2013 were 0% (0 out of 34 strains), 5.4% (2 out of 37 strains), 3.1% (1 out of 32 strains), 3.0% (2 out of 67 strains) and 7.4% (4 out of 54 strains), respectively. In 2013, the prevalence of antimicrobial resistant E. coli, both quinolone-resistant and ESBL producing strains, were increasing. We have to pay a close attention to the increase of resistant E. coli.

Non-invasive method to obtain DNA from freshwater mussels (Bivalvia: Unionidae)

USGS Publications Warehouse

Henley, W.F.; Grobler, P.J.; Neves, R.J.

2006-01-01

To determine whether DNA could be isolated from tissues obtained by brush-swabbing the mantle, viscera and foot, mantle-clips and swabbed cells were obtained from eight Quadrula pustulosa (Lea, 1831). DNA yields from clips and swabbings were 447.0 and 975.3 ??g/??L, respectively. Furthermore, comparisons of sequences from the ND-1 mitochondrial gene region showed a 100% sequence agreement of DNA from cells obtained by clips and swabs. To determine the number of swabs needed to obtain adequate yields of DNA for analyses, the visceras and feet of 5 Q. pustulosa each were successively swabbed 2, 4 and 6 times. DNA yields from the 2, 4 and 6 swabbed mussel groups were 399.4, 833.8 and 852.6 ng/??L, respectively. ND-1 sequences from the lowest yield still provided 846-901 bp for the ND-1 region. Nevertheless, to ensure adequate DNA yield from cell samples obtained by swabbing, we recommend that 4 swab-strokes of the viscera and foot be obtained. The use of integumental swabbing for collection of cells for determination of genetic relationships among freshwater mussels is noninvasive, when compared with tissue collection by mantle-clipping. Therefore, its use is recommended for freshwater mussels, especially state-protected or federally listed mussel species.

A misleading false-negative result using Neisseria gonorrhoeae opa MGB multiplex PCR assay in patient's rectal sample due to partial mutations of the opa gene.

PubMed

Vahidnia, Ali; van Empel, Pieter Jan; Costa, Sandra; Oud, Rob T N; van der Straaten, Tahar; Bliekendaal, Harry; Spaargaren, Joke

2015-07-01

A 53-year-old homosexual man presented at his general practitioner (GP) practice with a suspicion of sexually transmitted infection. Initial NAAT screening was performed for Chlamydia trachomatis and Neisseria gonorrhoeae. The patient was positive for Neisseria gonorrhoeae both for his urine and rectal sample. The subsequent confirmation test for Neisseria gonorrhoeae by a second laboratory was only confirmed for the urine sample and the rectal sample was negative. We report a case of a potential false-negative diagnosis of Neisseria gonorrhoeae due to mutations of DNA sequence in the probe region of opa-MGB assay of the rectal sample. The patient did not suffer any discomfort as diagnosis of Neisseria gonorrhoeae in his urine sample had already led to treatment by prescribing the patient with Ceftriaxone 500 mg IV dissolved in 1 ml lidocaine 2% and 4 mL saline. The patient also received a prescription for Azithromycin (2x500 mg).

Sperm Hy-Liter™: an effective tool for the detection of spermatozoa in sexual assault exhibits.

PubMed

De Moors, Anick; Georgalis, Tina; Armstrong, Gail; Modler, Jeff; Frégeau, Chantal J

2013-05-01

A fluorescence-based assay specifically targeting human spermatozoa was tested and optimized for best staining results using a variety of mock sexual assault samples. Swab clippings versus whole swabs were evaluated for best sample preparation and to simplify workflow (direct application versus swab extraction). The practicality and sensitivity of Sperm Hy-Liter™ was compared to our current phase contrast microscopy protocol for searching for the presence of spermatozoa. Sperm Hy-Liter™ was more sensitive than phase contrast microscopy and was able to detect spermatozoa more effectively in actual sexual assault samples (recent [N=240] or 24 years old [N=4]) containing few spermatozoa. Correlations were drawn between the Sperm Hy-Liter™ spermatozoa counts and the AmpFlSTR(®) Profiler(®) Plus male profiles generated from the sperm cell DNA fractions of semen containing swabs and swab clippings. In addition, recovered spermatozoa from Sperm Hy-Liter™-stained slides with greater than 40 spermatozoa produced full STR male profiles in 20.3% of slides tested and partial STR male profiles in 52.8% of slides tested. The adoption of Sperm Hy-Liter™ offers a means to standardize and improve the efficiency of the microscopic screening of sexual assault evidence. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Use of FTA sampling cards for molecular detection of avian influenza virus in wild birds.

PubMed

Keeler, Shamus P; Ferro, Pamela J; Brown, Justin D; Fang, Xingwang; El-Attrache, John; Poulson, Rebecca; Jackwood, Mark W; Stallknecht, David E

2012-03-01

Current avian influenza (AI) virus surveillance programs involving wild birds rely on sample collection methods that require refrigeration or low temperature freezing to maintain sample integrity for virus isolation and/or reverse-transcriptase (RT) PCR. Maintaining the cold chain is critical for the success of these diagnostic assays but is not always possible under field conditions. The aim of this study was to test the utility of Finders Technology Associates (FTA) cards for reliable detection of AI virus from cloacal and oropharyngeal swabs of wild birds. The minimum detectable titer was determined, and the effect of room temperature storage was evaluated experimentally using multiple egg-propagated stock viruses (n = 6). Using real time RT-PCR, we compared results from paired cloacal swab and samples collected on FTA cards from both experimentally infected mallards (Anasplatyrhynchos) and hunter-harvested waterfowl sampled along the Texas Gulf Coast. Based on the laboratory trials, the average minimal detectable viral titer was determined to be 1 x 10(4.7) median embryo infectious dose (EID50)/ml (range: 1 x 10(4.3) to 1 x 10(5.4) EID50/ml), and viral RNA was consistently detectable on the FTA cards for a minimum of 20 days and up to 30 days for most subtypes at room temperature (23 C) storage. Real-time RT-PCR of samples collected using the FTA cards showed fair to good agreement in live birds when compared with both real-time RT-PCR and virus isolation of swabs. AI virus detection rates in samples from several wild bird species were higher when samples were collected using the FTA cards compared with cloacal swabs. These results suggest that FTA cards can be used as an alternative sample collection method when traditional surveillance methods are not possible, especially in avian populations that have historically received limited testing or situations in which field conditions limit the ability to properly store or ship swab samples.

ESDA®-Lite collection of DNA from latent fingerprints on documents.

PubMed

Plaza, Dane T; Mealy, Jamia L; Lane, J Nicholas; Parsons, M Neal; Bathrick, Abigail S; Slack, Donia P

2015-05-01

The ability to detect and non-destructively collect biological samples for DNA processing would benefit the forensic community by preserving the physical integrity of evidentiary items for more thorough evaluations by other forensic disciplines. The Electrostatic Detection Apparatus (ESDA®) was systemically evaluated for its ability to non-destructively collect DNA from latent fingerprints deposited on various paper substrates for short tandem repeat (STR) DNA profiling. Fingerprints were deposited on a variety of paper substrates that included resume paper, cotton paper, magazine paper, currency, copy paper, and newspaper. Three DNA collection techniques were performed: ESDA collection, dry swabbing, and substrate cutting. Efficacy of each collection technique was evaluated by the quantity of DNA present in each sample and the percent profile generated by each sample. Both the ESDA and dry swabbing non-destructive sampling techniques outperformed the destructive methodology of substrate cutting. A greater number of full profiles were generated from samples collected with the non-destructive dry swabbing collection technique than were generated from samples collected with the ESDA; however, the ESDA also allowed the user to visualize the area of interest while non-destructively collecting the biological material. The ability to visualize the biological material made sampling straightforward and eliminated the need for numerous, random swabbings/cuttings. Based on these results, the evaluated non-destructive ESDA collection technique has great potential for real-world forensic implementation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Validation of a new HPV self-sampling device for cervical cancer screening: The Cervical and Self-Sample In Screening (CASSIS) study.

PubMed

El-Zein, Mariam; Bouten, Sheila; Louvanto, Karolina; Gilbert, Lucy; Gotlieb, Walter; Hemmings, Robert; Behr, Marcel A; Franco, Eduardo L

2018-04-17

We compared the self-sampling performance of the newly designed HerSwab™ device with a physician-collected cervical sample and another self-sample using the cobas® PCR Female swab for the detection of cervical intraepithelial neoplasia (CIN) and cancer. Women referred for colposcopy at McGill University affiliated hospital clinics collected two consecutive self-samples, one with HerSwab™ and one with cobas® swab, after receiving instructions. The order of sampling was randomized. The colposcopist then collected a cervical sample and conducted a colposcopic examination. Samples were tested for human papillomavirus (HPV) DNA. Sensitivity and specificity to detect CIN2+ and respective 95% confidence intervals (CI) were calculated to compare sampling approaches. The HPV testing agreement between samples was measured using the Kappa statistic. Of 1217 women enrolled, 1076 had complete results for HPV and cytology; 148 (13.8%) had CIN1, 147 (13.7%) had CIN2/3, and 5 (0.5%) had cancer. There was very good agreement between methods for HPV detection (HerSwab™ versus physician: kappa=0.84; cobas® swabs versus physician: kappa=0.81; HerSwab™ versus cobas® swabs: kappa=0.87). The sensitivity of HPV detection for CIN2+ was 87.6% (95%CI: 79.8-93.2) with self-sampling using HerSwab™, 88.6% (95%CI: 80.9-94.0) with self-sampling using the cobas® swab, and 92.4% (95%CI: 85.5-96.7) with physician sampling. Corresponding estimates of specificity were 58.1% (95%CI: 54.1-62.1), 55.0% (95%CI: 50.9-59.0) and 58.7% (95%CI: 54.6-62.6). Cytology (ASC-US or more severe) done on the physician-collected specimen was 80.2% (95%CI: 70.8-87.6) sensitive and 61.4% (95%CI: 57.2-65.5) specific for CIN2+. The HerSwab™ had good agreement with physician sampling in detecting HPV, and adequate performance in detecting high-grade lesions among women referred to colposcopy for abnormal cytology. Copyright © 2018 Elsevier Inc. All rights reserved.

Low bioavailability of ergotamine tartrate after oral and rectal administration in migraine sufferers.

PubMed Central

Ibraheem, J J; Paalzow, L; Tfelt-Hansen, P

1983-01-01

Fifteen migraine patients were administered 2 mg ergotamine tartrate in a partial cross-over design as a single, oral tablet, rectal suppository and rectal solution. Eight of these patients were in a previous investigation given 0.5 mg ergotamine tartrate intravenously. The blood samples were taken up to 54 h after oral and suppository while it was followed for only 3 h after rectal solution. The chemical analysis was performed by applying h.p.l.c. method with a limit of sensitivity of 0.1 ng/ml ergotamine base in plasma. No ergotamine was detected in the blood samples after the oral route, whereas small and very variable quantities was found in blood after the rectal route. Regular calculation of bioavailability could therefore not be performed. An estimate of the maximal possible bioavailability was found to yield a mean value of 2% (tablets); 5% (suppositories) and 6% (rectal solution). Rectal solution elicited faster absorption and the extent of absorption was significantly higher (P less than 0.05) than for the suppository. PMID:6419759

Isolation of Salmonella Virchow from a fruit bat (Pteropus giganteus).

PubMed

Islam, Ausraful; Mikolon, Andrea; Mikoleit, Matthew; Ahmed, Dilruba; Khan, Salah Udddin; Sharker, M A Yushuf; Hossain, M Jahangir; Islam, Ariful; Epstein, Jonathan H; Zeidner, Nord; Luby, Stephen P

2013-12-01

Detection of zoonotic pathogens carried by bats is important both for understanding disease ecology and for developing preventive measures. Pteropus fruit bats have been identified as potential carriers of Salmonella enterica serotype Typhi. A cross-sectional study was conducted to determine the prevalence of Salmonella Typhi and other Salmonella serotypes in Pteropus giganteus fruit bats in Bangladesh. Rectal swabs were collected from 302 bats and cultured for Salmonella species. The bats were trapped in three districts (Faridpur, Rajbari, and Cox's Bazar). Salmonella Typhi was not found but one juvenile female bat from Faridpur district was positive for Salmonella Virchow. Close associations between frugivorous bats, humans, and livestock in rural Bangladesh make it likely that the bat was infected by consuming contaminated water.

Recurrent Streptococcus pyogenes genital infection in a woman: test and treat the partner!

PubMed

Verkaeren, Emilienne; Epelboin, Loïc; Epelboin, Sylvie; Boddaert, Nathalie; Brossier, Florence; Caumes, Eric

2014-12-01

Group A Streptococcus (GAS) is a well-known cause of vulvovaginitis in prepubescent girls, but it is rarely described in adult women. We describe the case of a 64-year-old woman who presented with endometritis revealed by GAS bacteraemia, followed by recurrent vulvovaginitis due to a wild-type strain of GAS. She relapsed twice despite amoxicillin treatment. Her husband was found to be an asymptomatic carrier after GAS was identified in nasal and rectal swabs. She was cured after eradication of carriage in both herself and her husband with amoxicillin and rifampin. When recurrent Streptococcus pyogenes genital infections occur, test and treat the partner. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Enterotoxigenic Escherichia coli infection in captive black-footed ferrets.

PubMed

Bradley, G A; Orr, K; Reggiardo, C; Glock, R D

2001-07-01

Enterotoxigenic Escherichia coli with genes for heat stabile toxins Sta and STb was isolated from the gastrointestinal tract and multiple visceral organs of three adult and three juvenile black-footed ferrets (Mustela nigripes) that died in a captive breeding colony between 24 May 1998 and 2 July 1998. Similar isolates were obtained from rectal swabs of one adult and one juvenile that were clinically ill. All were fed a diet composed of mink chow, raw rabbit meat, beef liver powder, blood meal and lard. Escherichia coli of the same toxin genotype was isolated from the mixed ration. Clinical signs included sudden death, dehydration, anorexia and diarrhea. Necropsy lesions included acute enteritis with large numbers of rod shaped bacteria microscopically visible on intestinal villi.

Increased recovery of touch DNA evidence using FTA paper compared to conventional collection methods.

PubMed

Kirgiz, Irina A; Calloway, Cassandra

2017-04-01

Tape lifting and FTA paper scraping methods were directly compared to traditional double swabbing for collecting touch DNA from car steering wheels (n = 70 cars). Touch DNA was collected from the left or right side of each steering wheel (randomized) using two sterile cotton swabs, while the other side was sampled using water-soluble tape or FTA paper cards. DNA was extracted and quantified in duplicate using qPCR. Quantifiable amounts of DNA were detected for 100% of the samples (n = 140) collected independent of the method. However, the DNA collection yield was dependent on the collection method. A statistically significant difference in DNA yield was observed between FTA scraping and double swabbing methods (p = 0.0051), with FTA paper collecting a two-fold higher amount. Statistical analysis showed no significant difference in DNA yields between the double swabbing and tape lifting techniques (p = 0.21). Based on the DNA concentration required for 1 ng input, 47% of the samples collected using FTA paper would be expected to yield a short tandem repeat (STR) profile compared to 30% and 23% using double swabbing or tape, respectively. Further, 55% and 77% of the samples collected using double swabbing or tape, respectively, did not yield a high enough DNA concentration for the 0.5 ng of DNA input recommended for conventional STR kits and would be expected to result in a partial or no profile compared to 35% of the samples collected using FTA paper. STR analysis was conducted for a subset of the higher concentrated samples to confirm that the DNA collected from the steering wheel was from the driver. 32 samples were selected with DNA amounts of at least 1 ng total DNA (100 pg/μl when concentrated if required). A mixed STR profile was observed for 26 samples (88%) and the last driver was the major DNA contributor for 29 samples (94%). For one sample, the last driver was the minor DNA contributor. A full STR profile of the last driver was observed for 21 samples (69%) and a partial profile was observed for nine samples (25%); STR analysis failed for two samples collected using tape (6%). In conclusion, we show that the FTA paper scraping method has the potential to collect higher DNA yields from touch DNA evidence deposited on non-porous surfaces often encountered in criminal cases compared to conventional methods. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Isolation and identification of female DNA on postcoital penile swabs.

PubMed

Cina, S J; Collins, K A; Pettenati, M J; Fitts, M

2000-06-01

After sexual assault, cells originating from the assailant may be recovered from the victim. Through polymerase chain reaction (PCR)-based technology, positive scientific identification of the assailant may be made from these cells. Described is a prospective study describing a method for positively identifying cells from a female sex partner obtained from postcoital swabs of the penis of the male sex partner. Swabs were taken from the penis of a man at 1- to 24-hour intervals after coitus. DNA was isolated from each swab through standard organic extraction methods. The presence of female DNA was detected using the gender-specific amelogenin marker. Extracted DNA was amplified for eight different genetic loci using the Promega PowerPlex kit (Promega) and Amplitaq Gold (Perkin Elmer). Amplified samples were electrophoresed on precast sequencing gels (Hitachi) and were analyzed fluorescently using Hitachi's FMBIO 2 fluorescent scanner and software. Each sample obtained from a penile swab or condom was compared to male and female buccal controls. Female DNA was isolated from all postcoital penile swabs as determined by exclusive amplification of the X-chromosome specific 212 base pair amelogenin marker. In all cases, scientific identification of the female DNA from the swabs was determined by coamplification of eight STR loci (PowerPlex) and was compared to female and male control profiles. Cells shed from a female victim during sexual intercourse can be retrieved from the penis of a male offender after sexual intercourse during a 1- to 24-hour postcoital interval. DNA can be extracted from these cells and can be used to scientifically identify the female sexual participant through PCR-based technology. It is suggested that penile swabs be taken from alleged perpetrators of sexual assaults to associate them with a female victim.

Sampling technique is important for optimal isolation of pharyngeal gonorrhoea.

PubMed

Mitchell, M; Rane, V; Fairley, C K; Whiley, D M; Bradshaw, C S; Bissessor, M; Chen, M Y

2013-11-01

Culture is insensitive for the detection of pharyngeal gonorrhoea but isolation is pivotal to antimicrobial resistance surveillance. The aim of this study was to ascertain whether recommendations provided to clinicians (doctors and nurses) on pharyngeal swabbing technique could improve gonorrhoea detection rates and to determine which aspects of swabbing technique are important for optimal isolation. This study was undertaken at the Melbourne Sexual Health Centre, Australia. Detection rates among clinicians for pharyngeal gonorrhoea were compared before (June 2006-May 2009) and after (June 2009-June 2012) recommendations on swabbing technique were provided. Associations between detection rates and reported swabbing technique obtained via a clinician questionnaire were examined. The overall yield from testing before and after provision of the recommendations among 28 clinicians was 1.6% (134/8586) and 1.8% (264/15,046) respectively (p=0.17). Significantly higher detection rates were seen following the recommendations among clinicians who reported a change in their swabbing technique in response to the recommendations (2.1% vs. 1.5%; p=0.004), swabbing a larger surface area (2.0% vs. 1.5%; p=0.02), applying more swab pressure (2.5% vs. 1.5%; p<0.001) and a change in the anatomical sites they swabbed (2.2% vs. 1.5%; p=0.002). The predominant change in sites swabbed was an increase in swabbing of the oropharynx: from a median of 0% to 80% of the time. More thorough swabbing improves the isolation of pharyngeal gonorrhoea using culture. Clinicians should receive training to ensure swabbing is performed with sufficient pressure and that it covers an adequate area that includes the oropharynx.

A novel quantitative real-time polymerase chain reaction method for detecting toxigenic Pasteurella multocida in nasal swabs from swine.

PubMed

Scherrer, Simone; Frei, Daniel; Wittenbrink, Max Michael

2016-12-01

Progressive atrophic rhinitis (PAR) in pigs is caused by toxigenic Pasteurella multocida. In Switzerland, PAR is monitored by selective culture of nasal swabs and subsequent polymerase chain reaction (PCR) screening of bacterial colonies for the P. multocida toxA gene. A panel of 203 nasal swabs from a recent PAR outbreak were used to evaluate a novel quantitative real-time PCR for toxigenic P. multocida in porcine nasal swabs. In comparison to the conventional PCR with a limit of detection of 100 genome equivalents per PCR reaction, the real-time PCR had a limit of detection of 10 genome equivalents. The real-time PCR detected toxA-positive P. multocida in 101 samples (49.8%), whereas the conventional PCR was less sensitive with 90 toxA-positive samples (44.3%). In comparison to the real-time PCR, 5.4% of the toxA-positive samples revealed unevaluable results by conventional PCR. The approach of culture-coupled toxA PCR for the monitoring of PAR in pigs is substantially improved by a novel quantitative real-time PCR.

Evaluation of Two Surface Sampling Methods for Microbiological and Chemical Analyses To Assess the Presence of Biofilms in Food Companies.

PubMed

Maes, Sharon; Huu, Son Nguyen; Heyndrickx, Marc; Weyenberg, Stephanie van; Steenackers, Hans; Verplaetse, Alex; Vackier, Thijs; Sampers, Imca; Raes, Katleen; Reu, Koen De

2017-12-01

Biofilms are an important source of contamination in food companies, yet the composition of biofilms in practice is still mostly unknown. The chemical and microbiological characterization of surface samples taken after cleaning and disinfection is very important to distinguish free-living bacteria from the attached bacteria in biofilms. In this study, sampling methods that are potentially useful for both chemical and microbiological analyses of surface samples were evaluated. In the manufacturing facilities of eight Belgian food companies, surfaces were sampled after cleaning and disinfection using two sampling methods: the scraper-flocked swab method and the sponge stick method. Microbiological and chemical analyses were performed on these samples to evaluate the suitability of the sampling methods for the quantification of extracellular polymeric substance components and microorganisms originating from biofilms in these facilities. The scraper-flocked swab method was most suitable for chemical analyses of the samples because the material in these swabs did not interfere with determination of the chemical components. For microbiological enumerations, the sponge stick method was slightly but not significantly more effective than the scraper-flocked swab method. In all but one of the facilities, at least 20% of the sampled surfaces had more than 10 2 CFU/100 cm 2 . Proteins were found in 20% of the chemically analyzed surface samples, and carbohydrates and uronic acids were found in 15 and 8% of the samples, respectively. When chemical and microbiological results were combined, 17% of the sampled surfaces were contaminated with both microorganisms and at least one of the analyzed chemical components; thus, these surfaces were characterized as carrying biofilm. Overall, microbiological contamination in the food industry is highly variable by food sector and even within a facility at various sampling points and sampling times.

An outbreak of multiple norovirus strains on a cruise ship in China, 2014.

PubMed

Wang, X; Yong, W; Shi, L; Qiao, M; He, M; Zhang, H; Guo, B; Xie, G; Zhang, M; Jin, M; Ding, J

2016-01-01

To determine the cause of an outbreak of acute gastroenteritis that occurred on a cruise ship sailing along the Yangzi River from Chongqing to Nanjing, China. Noroviruses were identified by reverse transcription-PCR (RT-PCR) in rectal swabs from 34 of 54 subjects tested (63·0%). Sequencing and genotyping showed that noroviruses of up to seven different genotypes circulated in this outbreak: noroviruses GI.1, GI.2, GI.3, GI.4, GI.8, GI.9 and an uncommon strain GII.17. Common genotypes were not identified in this event. None of the food or water samples were tested positive for noroviruses. We suspected that it was a point-source infection due to contaminated water or food harvested from contaminated water, taking account of the co-existence of diverse norovirus genotypes. In this study, we presented the molecular investigation of a norovirus outbreak on a cruise in China. We revealed that the outbreak was caused by several different norovirus genotypes and analysed the possible source of infection as well, thus facilitating the evaluation of epidemiological issues regarding noroviruses in this area. © 2015 The Society for Applied Microbiology.

Antigenic characterization of intermediate adenovirus 14-11 strains associated with upper respiratory illness in a military camp.

PubMed Central

Hierholzer, J C; Pumarola, A

1976-01-01

An unusual variant of adenovirus (AV) 11 was isolated from throat and rectal swabs from six persons with upper respiratory illness in a Spanish military camp in March 1969. The same strain was serologically related to the upper respiratory illness of seven other men among 25 sample cases studied in detail. After strain purification, the virus was grouped as an AV by standard biological tests; it possessed the usual titers of group-specific hexon antigen but only low hemagglutinin titers (1:4 to 1:8) with erythrocytes from selected rhesus monkeys. The virus gave little reaction in hemagglutination inhibition (HI) tests with antisera to AV 1 through 35, but was neutralized to homologous titers by AV 11 antiserum. Reciprocally, rabbit and guinea pig antisera to the isolates possessed high HI antibody titers to prototype AV 14 and high serum neutralization (SN) antibody titers to prototype AV 11. On this basis, the variants were classified as AV 14-11 intermediates. Sequential serum specimens from the patients with and without positive cultures showed diagnostic rises in HI and SN antibody levels to the AV 14-11 intermediate and to prototype AV 11, but little response to AV 14. PMID:177365

Surface, Water and Air Biocharacterization (SWAB)

NASA Image and Video Library

2009-08-18

ISS020-E-031558 (18 Aug. 2009) --- NASA astronaut Michael Barratt, Expedition 20 flight engineer, conducts a Surface, Water and Air Biocharacterization (SWAB) water sampling from the Potable Water Dispenser (PWD) in the Destiny laboratory of the International Space Station. SWAB uses advanced molecular techniques to comprehensively evaluate microbes onboard the space station, including pathogens (organisms that may cause disease). This study will allow an assessment of the risk of microbes to the crew and the spacecraft.

Characteristics Associated With Urethral and Rectal Gonorrhea and Chlamydia Diagnoses in a US National Sample of Gay and Bisexual Men: Results From the One Thousand Strong Panel.

PubMed

Grov, Christian; Cain, Demetria; Rendina, H Jonathan; Ventuneac, Ana; Parsons, Jeffrey T

2016-03-01

Gay and bisexual men are at elevated risk for Neisseria gonorrhoeae and Chlamydia trachomatis (GC/CT). Rectal GC/CT symptoms may be less obvious than urethral, increasing opportunities for undiagnosed rectal GC/CT. A US national sample of 1071 gay and bisexual men completed urethral and rectal GC/CT testing and an online survey. In total, 6.2% were GC/CT positive (5.3% rectal, 1.7% urethral). We calculated adjusted (for education, race, age, relationship status, having health insurance, and income) odds ratios for factors associated with rectal and urethral GC/CT diagnoses. Age was inversely associated with urethral and rectal GC/CT. Compared with white men, Latinos had significantly greater odds of rectal GC/CT. Among men who reported anal sex, those reporting only insertive sex had lower odds of rectal GC/CT than did men who reported both insertive and receptive. There was a positive association between rectal GC/CT and number of male partners (<12 months), the number of anal receptive acts, receptive condomless anal sex (CAS) acts, and insertive CAS acts. Compared with those who had engaged in both insertive and receptive anal sex, those who engaged in only receptive anal sex had lower odds of urethral GC/CT. The number of male partners (<12 months) was associated with increased odds of urethral GC/CT. Rectal GC/CT was more common than urethral and associated with some demographic and behavioral characteristics. Our finding that insertive CAS acts was associated with rectal GC/CT highlights that providers should screen patients for GC/CT via a full range of transmission routes, lest GC/CT go undiagnosed.

A multiplex PCR method for the simultaneous detection of three viruses associated with canine viral enteric infections.

PubMed

Deng, Xiaoyu; Zhang, Jiali; Su, Jiazi; Liu, Hao; Cong, Yanlong; Zhang, Lei; Zhang, Kemeng; Shi, Ning; Lu, Rongguang; Yan, Xijun

2018-04-19

The aim of this study was to establish a multiplex PCR (mPCR) method that can simultaneously detect canine parvovirus (CPV-2), canine coronavirus (CCoV) and canine adenovirus (CAV), thereby eliminating the need to detect these pathogens individually. Based on conserved regions in the genomes of these three viruses, the VP2 gene of CPV-2, the endoribonuclease nsp15 gene of CCoV, and the 52K gene of CAV were selected for primer design. The specificity of the mPCR results showed no amplification of canine distemper virus (CDV), canine parainfluenza virus (CPIV), or pseudorabies virus (PRV), indicating that the method had good specificity. A sensitivity test showed that the detection limit of the mPCR method was 1 × 10 4 viral copies. A total of 63 rectal swabs from dogs with diarrheal symptoms were evaluated using mPCR and routine PCR. The ratio of positive samples to total samples for CPV-2, CCoV, and CAV was 55.6% (35/63) for mPCR and 55.6% (35/63) for routine PCR. Thirty-five positive samples were detected by both methods, for a coincidence ratio of 100%. This mPCR method can simultaneously detect CCoV (CCoV-II), CAV (CAV-1, CAV-2) and CPV-2 (CPV-2a, CPV-2b, CPV-2c), which are associated with viral enteritis, thereby providing an efficient, inexpensive, specific, and accurate new tool for clinical diagnosis and laboratory epidemiological investigations.

Burden and characteristics of HIV infection among female sex workers in Kampala, Uganda - a respondent-driven sampling survey.

PubMed

Hladik, Wolfgang; Baughman, Andrew L; Serwadda, David; Tappero, Jordan W; Kwezi, Rachel; Nakato, Namakula D; Barker, Joseph

2017-06-10

Sex workers in Uganda are at significant risk for HIV infection. We characterized the HIV epidemic among Kampala female sex workers (FSW). We used respondent-driven sampling to sample FSW aged 15+ years who reported having sold sex to men in the preceding 30 days; collected data through audio-computer assisted self-interviews, and tested blood, vaginal and rectal swabs for HIV, syphilis, neisseria gonorrhea, chlamydia trachomatis, and trichomonas vaginalis. A total of 942 FSW were enrolled from June 2008 through April 2009. The overall estimated HIV prevalence was 33% (95% confidence intervals [CI] 30%-37%) and among FSW 25 years or older was 44%. HIV infection is associated with low levels of schooling, having no other work, never having tested for HIV, self-reported genital ulcers or sores, and testing positive for neisseria gonorrhea or any sexually transmitted infections (STI). Two thirds (65%) of commercial sex acts reportedly were protected by condoms; one in five (19%) FSW reported having had anal sex. Gender-based violence was frequent; 34% reported having been raped and 24% reported having been beaten by clients in the preceding 30 days. One in three FSW in Kampala is HIV-infected, suggesting a severe HIV epidemic in this population. Intensified interventions are warranted to increase condom use, HIV testing, STI screening, as well as antiretroviral treatment and pre-exposure prophylaxis along with measures to overcome gender-based violence.

Longitudinal Study of the Persistence of Antimicrobial-Resistant Campylobacter Strains in Distinct Swine Production Systems on Farms, at Slaughter, and in the Environment

PubMed Central

Quintana-Hayashi, Macarena P.

2012-01-01

The objectives of this study were to compare and characterize the prevalence of antimicrobial-resistant (AR) Campylobacter in conventional and antimicrobial-free (ABF) production systems on farms, at slaughter, and in the environment. Fecal and environmental samples were collected from ABF farms (pigs, 1,239; environment, 797) and conventional farms (pigs, 1,650; environment, 1,325). At slaughter, we collected samples from carcasses, including postevisceration swabs, postchill swabs, and mesenteric lymph nodes from ABF systems (postevisceration swabs, 182; postchill swabs, 199; mesenteric lymph nodes, 184) and conventional systems (postevisceration swabs, 272; postchill swabs, 271; mesenteric lymph nodes, 255) at separate processing facilities. We also sampled the processing plant environment, including truck and lairage floor swab samples (ABF, 115; conventional, 90). Overall, a total of 2,908 Campylobacter isolates, including Campylobacter coli (farm, 2,557, 99.8%; slaughter, 341, 98.3%) and Campylobacter jejuni (farm, 4, 0.2%; slaughter, 6, 1.7%), were isolated in the study. There was no significant difference in the prevalence of Campylobacter between ABF and conventionally raised pigs (farrowing, P = 0.20; nursery, P = 0.06; finishing, P = 0.24) and the environment (P = 0.37). At slaughter, Campylobacter was isolated from all of the stages, including postchill. The highest frequencies of resistance were exhibited against tetracycline (ABF, 48.2%; conventional, 88.3%). Ciprofloxacin-resistant C. coli isolates were observed in conventionally raised (17.1%) and ABF (1.2%) pigs (P = 0.11). Antimicrobial use data from conventional farms indicated significant associations between oxytetracycline use and tetracycline resistance in the nursery pigs (P = 0.01), between tiamulin exposure and azithromycin and erythromycin resistance in nursery (P < 0.01) and finishing (P < 0.01) pigs, and between enrofloxacin exposure and ciprofloxacin and nalidixic acid resistance in farrowing (P < 0.01) and nursery (P < 0.01) pigs. Identical antimicrobial resistance profiles were observed in the pigs and their environments on farms and at slaughter. In summary, our results highlight the persistence and dissemination of AR Campylobacter from farm to slaughter in ABF and conventionally raised pigs and their environments. PMID:22307299

National validation study of a swab protocol for the recovery of Bacillus anthracis spores from surfaces.

PubMed

Hodges, Lisa R; Rose, Laura J; O'Connell, Heather; Arduino, Matthew J

2010-05-01

Twelve Laboratory Response Network (LRN) affiliated laboratories participated in a validation study of a macrofoam swab protocol for the recovery, detection, and quantification of viable B. anthracis (BA) Sterne spores from steel surfaces. CDC personnel inoculated steel coupons (26cm(2)) with 1-4 log(10) BA spores and recovered them by sampling with pre-moistened macrofoam swabs. Phase 1 (P1) of the study evaluated swabs containing BA only, while dust and background organisms were added to swabs in Phase 2 (P2) to mimic environmental conditions. Laboratories processed swabs and enumerated spores by culturing eluted swab suspensions and counting colonies with morphology consistent with BA. Processed swabs were placed in enrichment broth, incubated 24h, and cultured by streaking for isolation. Real-time PCR was performed on selected colonies from P2 samples to confirm the identity of BA. Mean percent recovery (%R) of spores from the surface ranged from 15.8 to 31.0% (P1) and from 27.9 to 55.0% (P2). The highest mean percent recovery was 31.0% (sd 10.9%) for P1 (4 log(10) inoculum) and 55.0% (sd 27.6%) for P2 (1 log(10) inoculum). The overall %R was higher for P2 (44.6%) than P1 (24.1%), but the overall reproducibility (between-lab variability) was lower in P2 than in P1 (25.0 vs 16.5%CV, respectively). The overall precision (within-lab variability) was close to identical for P1 and P2 (44.0 and 44.1, respectively), but varied greatly between inoculum levels. The protocol demonstrated linearity in %R over the three inoculum levels and is able to detect between 26 and 5x10(6)spores/26cm(2). Sensitivity as determined by culture was >98.3% for both phases and all inocula, suggesting that the culture method maintains sensitivity in the presence of contaminants. The enrichment broth method alone was less sensitive for sampled swabs (66.4%) during P2, suggesting that the presence of background organisms inhibited growth or isolation of BA from the broth. The addition of real-time PCR testing to the assay increased specificity from >85.4% to >95.0% in P2. Although the precision was low at the 1 log(10) inoculum level in both phases (59.0 and 50.2%), this swab processing protocol, was sensitive, specific, precise, and reproducible at 2-4 log(10)/26cm(2) spore concentrations. Published by Elsevier B.V.

Identification of a Lineage D Betacoronavirus in Cave Nectar Bats (Eonycteris spelaea) in Singapore and an Overview of Lineage D Reservoir Ecology in SE Asian Bats.

PubMed

Mendenhall, I H; Borthwick, S; Neves, E S; Low, D; Linster, M; Liang, B; Skiles, M; Jayakumar, J; Han, H; Gunalan, V; Lee, B P Y-H; Okahara, K; Wang, L-F; Maurer-Stroh, S; Su, Y C F; Smith, G J D

2017-12-01

Coronaviruses are a diverse group of viruses that infect mammals and birds. Bats are reservoirs for several different coronaviruses in the Alphacoronavirus and Betacoronavirus genera. They also appear to be the natural reservoir for the ancestral viruses that generated the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus outbreaks. Here, we detected coronavirus sequences in next-generation sequence data created from Eonycteris spelaea faeces and urine. We also screened by PCR urine samples, faecal samples and rectal swabs collected from six species of bats in Singapore between 2011 and 2014, all of which were negative. The phylogenetic analysis indicates this novel strain is most closely related to lineage D Betacoronaviruses detected in a diverse range of bat species. This is the second time that coronaviruses have been detected in cave nectar bats, but the first coronavirus sequence data generated from this species. Bat species from which this group of coronaviruses has been detected are widely distributed across SE Asia, South Asia and Southern China. They overlap geographically, often share roosting sites and have been witnessed to forage on the same plant. The addition of sequence data from this group of viruses will allow us to better understand coronavirus evolution and host specificity. © 2016 Blackwell Verlag GmbH.

Different methods for volatile sampling in mammals

PubMed Central

Möller, Manfred; Marcillo, Andrea; Einspanier, Almuth; Weiß, Brigitte M.

2017-01-01

Previous studies showed that olfactory cues are important for mammalian communication. However, many specific compounds that convey information between conspecifics are still unknown. To understand mechanisms and functions of olfactory cues, olfactory signals such as volatile compounds emitted from individuals need to be assessed. Sampling of animals with and without scent glands was typically conducted using cotton swabs rubbed over the skin or fur and analysed by gas chromatography-mass spectrometry (GC-MS). However, this method has various drawbacks, including a high level of contaminations. Thus, we adapted two methods of volatile sampling from other research fields and compared them to sampling with cotton swabs. To do so we assessed the body odor of common marmosets (Callithrix jacchus) using cotton swabs, thermal desorption (TD) tubes and, alternatively, a mobile GC-MS device containing a thermal desorption trap. Overall, TD tubes comprised most compounds (N = 113), with half of those compounds being volatile (N = 52). The mobile GC-MS captured the fewest compounds (N = 35), of which all were volatile. Cotton swabs contained an intermediate number of compounds (N = 55), but very few volatiles (N = 10). Almost all compounds found with the mobile GC-MS were also captured with TD tubes (94%). Hence, we recommend TD tubes for state of the art sampling of body odor of mammals or other vertebrates, particularly for field studies, as they can be easily transported, stored and analysed with high performance instruments in the lab. Nevertheless, cotton swabs capture compounds which still may contribute to the body odor, e.g. after bacterial fermentation, while profiles from mobile GC-MS include only the most abundant volatiles of the body odor. PMID:28841690

The use of PCR technique in the identification of Mycobacterium species responsible for bovine tuberculosis in cattle and buffaloes in Pakistan.

PubMed

Akhtar, Farah; Javed, Muhammad Tariq; Aziz-ur-Rehman; Khan, Muhammad Nisar; Akhtar, Pervez; Hussain, Sayed Misdaq; Aslam, Muhammad Sohaib; Kausar, Razia; Qamar, Mehwish; Cagiola, Monica

2015-08-01

Bovine tuberculosis is one of the important diseases of dairy and wild animals. The disease is prevalent all over the world, though developed countries have tremendously reduced the prevalence through eradication campaigns. The prevalence of disease in Pakistan on the basis of tuberculin testing or culture isolation of the organism has been reported previously. It is, however, important to use the latest diagnostic tools, i.e. PCR to confirm the type of Mycobacterium infecting the animals in Pakistan. Therefore, the present study was carried out to assess the utility of direct PCR on milk samples and nasal swabs to confirm the type of Mycobacterium infecting the animals. This study was carried out on 215 cattle and buffaloes of more than 2 years of age present at two livestock farms. The tuberculin results showed 22.5% prevalence at one farm and 25.9% at the other with an overall prevalence of 24.7%. The 92.5% of milk samples and/or nasal swabs showed positive PCR for Mycobacterium genus, 86.8% for Mycobacterium tuberculosis complex and 77.4% for Mycobacterium bovis. The M. bovis by PCR was detected in 13.2% of milk samples, 24.5% of nasal swabs and 39.6% of both milk samples + nasal swabs. The results suggested that there are 60% higher chance for a nasal swab to yield a positive PCR for M. bovis than the milk sample. It can be concluded from the present study that tuberculin testing is a useful method in studying the prevalence of disease as the PCR for Mycobacterium genus was positive in 92.5%, M. tuberculosis complex in 86.8% and Mycobacterium bovis in 77.4% cases.

The Use of Multiplex PCR to Determine the Prevalence of Enterotoxigenic Staphylococcus aureus Isolated from Raw Milk, Feta Cheese, and Hand Swabs.

PubMed

Zeinhom, Mohamed M A; Abdel-Latef, Gihan K; Jordan, Kieran

2015-12-01

Staphylococcus aureus (S. aureus) can cause mastitis in cattle and, therefore, can be present in milk. This study was undertaken to determine the prevalence of coagulase positive S. aureus and its enterotoxin genes sea, seb, and sec in isolates recovered from raw milk, feta cheese, and human hand swabs of milk and cheese handlers in Beni-Suef province, Egypt. A total of 100 samples of raw milk and 50 samples of pasteurized-milk feta cheese were collected. In addition, 50 hand swabs from milk handlers and 25 hand swabs from cheese handlers were examined for the presence of coagulase positive S. aureus. The isolates were characterized by multiplex PCR for detection of sea, seb, and sec genes, and for resistance to 5 classes of commonly used antibiotics. Twelve (12/100), 12 (6/50), and 17% (13/75) of milk, cheese, and hand swab samples, respectively, were positive for coagulase positive S. aureus. One isolate was obtained from each positive sample (31 isolates), and none contained genes for SEA or SEC production. Twenty-five percent, 33%, and 31%, respectively, of the isolates contained the genes for SEB, resulting in 3%, 4%, and 5% of samples being positive for toxin producing coagulase positive S. aureus, respectively. At least one isolate was resistant to each of the antibiotics tested. Despite the low potential for SEB production shown, preventative measures, such as maintenance of the cold-chain and good hygienic practices should be implemented to further reduce the potential risk to public health from SEB, and to reduce the spread of antimicrobial resistance. © 2015 Institute of Food Technologists®

Cytomegalovirus survival and transferability and the effectiveness of common hand-washing agents against cytomegalovirus on live human hands.

PubMed

Stowell, Jennifer D; Forlin-Passoni, Daniela; Radford, Kay; Bate, Sheri L; Dollard, Sheila C; Bialek, Stephanie R; Cannon, Michael J; Schmid, D Scott

2014-01-01

Congenital cytomegalovirus (CMV) transmission can occur when women acquire CMV while pregnant. Infection control guidelines may reduce risk for transmission. We studied the duration of CMV survival after application of bacteria to the hands and after transfer from the hands to surfaces and the effectiveness of cleansing with water, regular and antibacterial soaps, sanitizer, and diaper wipes. Experiments used CMV AD169 in saliva at initial titers of 1 × 10(5) infectious particles/ml. Samples from hands or surfaces (points between 0 and 15 min) were placed in culture and observed for at least 2 weeks. Samples were also tested using CMV real-time PCR. After application of bacteria to the hands, viable CMV was recovered from 17/20 swabs at 0 min, 18/20 swabs at 1 min, 5/20 swabs at 5 min, and 4/20 swabs at 15 min. After transfer, duration of survival was at least 15 min on plastic (1/2 swabs), 5 min on crackers and glass (3/4 swabs), and 1 min or less on metal and cloth (3/4 swabs); no viable virus was collected from wood, rubber, or hands. After cleansing, no viable virus was recovered using water (0/22), plain soap (0/20), antibacterial soap (0/20), or sanitizer (0/22). Viable CMV was recovered from 4/20 hands 10 min after diaper wipe cleansing. CMV remains viable on hands for sufficient times to allow transmission. CMV may be transferred to surfaces with reduced viability. Hand-cleansing methods were effective at eliminating viable CMV from hands.

Cytomegalovirus Survival and Transferability and the Effectiveness of Common Hand-Washing Agents against Cytomegalovirus on Live Human Hands

PubMed Central

Stowell, Jennifer D.; Forlin-Passoni, Daniela; Radford, Kay; Bate, Sheri L.; Dollard, Sheila C.; Bialek, Stephanie R.; Cannon, Michael J.

2014-01-01

Congenital cytomegalovirus (CMV) transmission can occur when women acquire CMV while pregnant. Infection control guidelines may reduce risk for transmission. We studied the duration of CMV survival after application of bacteria to the hands and after transfer from the hands to surfaces and the effectiveness of cleansing with water, regular and antibacterial soaps, sanitizer, and diaper wipes. Experiments used CMV AD169 in saliva at initial titers of 1 × 105 infectious particles/ml. Samples from hands or surfaces (points between 0 and 15 min) were placed in culture and observed for at least 2 weeks. Samples were also tested using CMV real-time PCR. After application of bacteria to the hands, viable CMV was recovered from 17/20 swabs at 0 min, 18/20 swabs at 1 min, 5/20 swabs at 5 min, and 4/20 swabs at 15 min. After transfer, duration of survival was at least 15 min on plastic (1/2 swabs), 5 min on crackers and glass (3/4 swabs), and 1 min or less on metal and cloth (3/4 swabs); no viable virus was collected from wood, rubber, or hands. After cleansing, no viable virus was recovered using water (0/22), plain soap (0/20), antibacterial soap (0/20), or sanitizer (0/22). Viable CMV was recovered from 4/20 hands 10 min after diaper wipe cleansing. CMV remains viable on hands for sufficient times to allow transmission. CMV may be transferred to surfaces with reduced viability. Hand-cleansing methods were effective at eliminating viable CMV from hands. PMID:24185855

Zoonoses research in the German National Cohort : feasibility of parallel sampling of pets and owners.

PubMed

Hille, Katja; Möbius, Nadine; Akmatov, Manas K; Verspohl, Jutta; Rabold, Denise; Hartmann, Maria; Günther, Kathrin; Obi, Nadia; Kreienbrock, Lothar

2014-11-01

Cats and dogs live in more than 20 % of German households and the contact between these pets and their owners can be very close. Therefore, a transmission of zoonotic pathogens may occur. To investigate whether zoonotic research questions can be examined in the context of population-based studies like the German National Cohort (GNC), two studies on different study populations were conducted as part of the feasibility tests of the GNC. The aim of the first study was to quantify the actual exposure of participants of the GNC to cats and dogs. In the second study summarised here the feasibility of the sampling of cats and dogs by their owners was tested. To quantify the exposure of participants of the GNC to cats and dogs 744 study participants of the Pretests of the GNC were asked whether they had contact with animals. Currently 10 % have a dog and 14 % have a cat in their household. These figures confirm that a large proportion of the German population has contact with pets and that there is a need for further zoonoses research. To establish the collection of biological samples from cats and dogs in the context of large-scale population-based studies feasible methods are needed. Therefore, a study was conducted to test whether pet owners can take samples from their cats and dogs and whether the quality of these samples is comparable to samples taken by a qualified veterinarian. A total of 82 dog and 18 cat owners were recruited in two veterinary practices in Hannover and the Clinic for Small Animals at the University of Veterinary Medicine in Hannover. Sampling instructions and sample material for nasal and buccal swabs, faecal samples and, in the case of cat owners, a brush for fur samples, were given to the pet owners. The pet owners were asked to take the samples from their pets at home and to send the samples by surface mail. Swab samples were cultured and bacterial growth was quantified independent of bacterial species. The growth of Gram-positive and Gram-negative bacteria from samples taken by the veterinarian and the pet owners were compared. For Gram-positive bacteria the agreement of laboratory results was 71 % for nasal swabs and 78 % for oral swabs while for Gram-negative bacteria the agreement of laboratory results was 55 % for nasal swabs and 87 % for oral swabs. In conclusion it has been shown that participants of the GNC are exposed to cats and dogs and that the sampling of cats and dogs by their owners is a feasible method which can be a useful tool for zoonoses research in population-based studies.

E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology.

PubMed

Akmatov, Manas K; Krebs, Stephan; Preusse, Matthias; Gatzemeier, Anja; Frischmann, Ursula; Schughart, Klaus; Pessler, Frank

2011-11-01

We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. The study was conducted among a convenience sample of employees (n=53) at a research institution (December 2009-April 2010). Real-time data on the occurrence of acute respiratory symptoms and a nasal self-swab were collected prospectively, with automated weekly e-mails as a reminder mechanism. Reverse transcription polymerase chain reaction (RT-PCR) was used to detect respiratory viral pathogens in the swabs. Fifty-one out of 53 participants completed the study. The study design was well accepted. Thirty (∼57%) participants reported at least one episode of acute respiratory infection and returned the nasal swab during the study period (eight participants reported two episodes). The majority had no difficulties taking the self-swab and preferred this to swabbing by study personnel. Most participants obtained and returned the swabs within the recommended time. Viral respiratory pathogens were detected in 19 of 38 swabs (50%), with coronaviruses 229E/NL63 and OC43 and rhinoviruses A and B constituting 17 positive swabs (89%). Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. Copyright © 2011 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Survey and Experimental Infection of Enteropathogenic Escherichia coli in Common Marmosets (Callithrix jacchus).

PubMed

Hayashimoto, Nobuhito; Inoue, Takashi; Morita, Hanako; Yasuda, Masahiko; Ueno, Masami; Kawai, Kenji; Itoh, Toshio

2016-01-01

Common marmosets (Callithrix jacchus) are frequently used for biomedical research but can be afflicted with diarrhea-a serious and potentially lethal health problem. Enteropathogenic Escherichia coli (EPEC) is thought to be the causative pathogen of hemorrhagic typhlocolitis in common marmosets, but the actual incidence of the disease and the relationship between EPEC and hematochezia are unknown. This study investigated the prevalence of EPEC infection in common marmosets and the association between EPEC and hematochezia. A total of 230 stool or rectal swab samples were collected from 230 common marmosets (98 clinically healthy, 85 diarrhea, and 47 bloody stool samples) and tested by culture-based detection and PCR amplification of VT1, VT2, LT, ST, eae, and bfp genes. Healthy animals were divided into three groups (n = 4 each for high and low concentration groups and n = 2 as negative control), and those in the experimental groups were perorally inoculated with a 2-ml of suspension of EPEC R811 strain adjusted to 5 × 108 (high concentration) and 5 × 104 (low concentration) CFU/ ml. Two animals in each group were examined 3 and 14 days post-inoculation (DPI). EPEC was detected in 10 of 98 clinically healthy samples (10.2%), 17 of 85 diarrhea samples (20%), and all 47 bloody stool samples (100%), with a significant difference detected between presence of EPEC and sample status (P < 0.01). Acute hematochezia was observed in all animals of the high-concentration group but not in other groups at 1 or 2 DPI. A histopathological examination revealed the attachment of gram-negative bacilli to epithelial apical membranes and desquamated epithelial cells in the cecum of animals in the high-concentration group at 3 DPI. These findings suggest that EPEC is a causative agent of hemorrhagic typhlocolitis in common marmosets.

Improved quantitative recovery of Listeria monocytogenes from stainless steel surfaces using a one-ply composite tissue.

PubMed

Vorst, Keith L; Todd, Ewen C D; Rysert, Elliot T

2004-10-01

Four sampling devices, a sterile environmental sponge (ES), a sterile cotton-tipped swab (CS), a sterile calcium alginate fiber-tipped swab (CAS), and a one-ply composite tissue (CT), were evaluated for quantitative recovery of Listeria monocytogenes from a food-grade stainless steel surface. Sterile 304-grade stainless steel plates (6 by 6 cm) were inoculated with approximately 106 CFU/cm2 L. monocytogenes strain Scott A and dried for 1 h. The ES and CT sampling devices were rehydrated in phosphate buffer solution. After plate swabbing, ES and CT were placed in 40 ml of phosphate buffer solution, stomached for 1 min and hand massaged for 30 s. Each CS and CAS device was rehydrated in 0.1% peptone before swabbing. After swabbing, CS and CAS were vortexed in 0.1% peptone for 1 min. Samples were spiral plated on modified Oxford agar with modified Oxford agar Rodac Contact plates used to recover any remaining cells from the stainless steel surface. Potential inhibition from CT was examined in both phosphate buffer solution and in a modified disc-diffusion assay. Recovery was 2.70, 1.34, and 0.62 log greater using CT compared with ES, CS, and CAS, respectively, with these differences statistically significant (P < 0.001) for ES and CT and for CAS, CS, and CT (P < 0.05). Rodac plates were typically overgrown following ES, positive after CS and CAS, and negative after CT sampling. CT was noninhibitory in both phosphate buffer solution and the modified disc-diffusion assay. Using scanning electron microscopy, Listeria cells were observed on stainless steel plates sampled with each sampling device except CT. The CT device, which is inexpensive and easy to use, represents a major improvement over other methods in quantifying L. monocytogenes on stainless steel surfaces and is likely applicable to enrichment of environmental samples.

Culturability and toxicity of sick building syndrome-related fungi over time.

PubMed

Wilson, Stephen C; Carriker, Curtis G; Brasel, Trevor L; Karunasena, Enusha; Douglas, David R; Wu, Chunfa; Andriychuk, Larysa A; Fogle, Matthew R; Martin, Jared M; Straus, David C

2004-08-01

Two experiments were conducted regarding the culturability and toxicity of fungi located on building materials over time and the efficacy of seven laboratory techniques in recovering culturable fungi from sample swabs. In the first experiment, eight sections of drywall were inoculated with Stachybotrys chartarum and stored at 25 +/- 5 degrees Celsius and 20-60% relative humidity (RH) for up to two years. Another eight sections of ceiling tile were stored at 100% RH for 1 year. Six sections of ceiling tile and 15 swabs were also inoculated with Penicillium chrysogenum and S. chartarum respectively and stored under the same conditions for 8 months and 3.3 years. All materials were tested for culturability at the end of the storage period. S. chartarum-inoculated samples were also tested for toxicity. In the second experiment (replicated twice), S. chartarum and Chaetomium globosum were inoculated onto 84 swabs each. Storage was up to 266 days at 25 +/- 5 degrees Celsius and 20-60% RH. Seven techniques were compared regarding the recovery of culturable fungi from the swabs over different time points. Results for Experiment 1 showed that all samples were culturable after the storage period and that the S. chartarum-inoculated drywall samples were toxic. In Experiment 2, all techniques showed high rates of recovery. These data show that despite being without a water source, these organisms can be culturable and toxic after long periods of time under conditions similar to human-occupied dwellings and that a number of preparation techniques are suitable for the recovery of these fungi from inoculated swabs.

The Prevalence and Molecular Epidemiology of Multidrug-Resistant Enterobacteriaceae Colonization in a Pediatric Intensive Care Unit.

PubMed

Suwantarat, Nuntra; Logan, Latania K; Carroll, Karen C; Bonomo, Robert A; Simner, Patricia J; Rudin, Susan D; Milstone, Aaron M; Tekle, Tsigereda; Ross, Tracy; Tamma, Pranita D

2016-05-01

To determine the prevalence and acquisition of extended-spectrum β-lactamases (ESBLs), plasmid-mediated AmpCs (pAmpCs), and carbapenemases ("MDR Enterobacteriaceae") colonizing children admitted to a pediatric intensive care unit (PICU). Prospective study. 40-bed PICU. Admission and weekly thereafter rectal surveillance swabs were collected on all pediatric patients during a 6-month study period. Routine phenotypic identification and antibiotic susceptibility testing were performed. Enterobacteriaceae displaying characteristic resistance profiles underwent further molecular characterization to identify genetic determinants of resistance likely to be transmitted on mobile genetic elements and to evaluate relatedness of strains including DNA microarray, multilocus sequence typing, repetitive sequence-based PCR, and hsp60 sequencing typing. Evaluating 854 swabs from unique children, the overall prevalence of colonization with an MDR Enterobacteriaceae upon admission to the PICU based on β-lactamase gene identification was 4.3% (n=37), including 2.8% ESBLs (n=24), 1.3% pAmpCs (n=11), and 0.2% carbapenemases (n=2). Among 157 pediatric patients contributing 603 subsequent weekly swabs, 6 children (3.8%) acquired an incident MDR Enterobacteriaceae during their PICU stay. One child acquired a pAmpC (E. coli containing bla DHA) related to an isolate from another patient. Approximately 4% of children admitted to a PICU were colonized with MDR Enterobacteriaceae (based on β-lactamase gene identification) and an additional 4% of children who remained in the PICU for at least 1 week acquired 1 of these organisms during their PICU stay. The acquired MDR Enterobacteriaceae were relatively heterogeneous, suggesting that a single source was not responsible for the introduction of these resistance mechanisms into the PICU setting.

The Prevalence and Molecular Epidemiology of Multidrug-Resistant Enterobacteriaceae Colonization in a Pediatric Intensive Care Unit

PubMed Central

Suwantarat, Nuntra; Logan, Latania K.; Carroll, Karen C.; Bonomo, Robert A.; Simner, Patricia J.; Rudin, Susan D.; Milstone, Aaron M.; Tekle, Tsigereda; Ross, Tracy; Tamma, Pranita D.

2016-01-01

OBJECTIVE To determine the prevalence and acquisition of extended-spectrum β-lactamases (ESBLs), plasmid-mediated AmpCs (pAmpCs), and carbapenemases (“MDR Enterobacteriaceae”) colonizing children admitted to a pediatric intensive care unit (PICU). DESIGN Prospective study. SETTING 40-bed PICU. METHODS Admission and weekly thereafter rectal surveillance swabs were collected on all pediatric patients during a 6-month study period. Routine phenotypic identification and antibiotic susceptibility testing were performed. Enterobacteriaceae displaying characteristic resistance profiles underwent further molecular characterization to identify genetic determinants of resistance likely to be transmitted on mobile genetic elements and to evaluate relatedness of strains including DNA microarray, multilocus sequence typing, repetitive sequence-based PCR, and hsp60 sequencing typing. Results Evaluating 854 swabs from unique children, the overall prevalence of colonization with an MDR Enterobacteriaceae upon admission to the PICU based on β-lactamase gene identification was 4.3% (n = 37), including 2.8% ESBLs (n =24), 1.3% pAmpCs (n =11), and 0.2% carbapenemases (n =2). Among 157 pediatric patients contributing 603 subsequent weekly swabs, 6 children (3.8%) acquired an incident MDR Enterobacteriaceae during their PICU stay. One child acquired a pAmpC (E. coli containing blaDHA) related to an isolate from another patient. Conclusions Approximately 4% of children admitted to a PICU were colonized with MDR Enterobacteriaceae (based on β-lactamase gene identification) and an additional 4% of children who remained in the PICU for at least 1 week acquired 1 of these organisms during their PICU stay. The acquired MDR Enterobacteriaceae were relatively heterogeneous, suggesting that a single source was not responsible for the introduction of these resistance mechanisms into the PICU setting. PMID:26856439

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

PubMed Central

Kirk, Michelle R.; Jonker, Arjan; McCulloch, Alan

2015-01-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. PMID:26276109

Evaluation of an autoclave resistant anatomic nose model for the testing of nasal swabs

PubMed Central

Bartolitius, Lennart; Warnke, Philipp; Ottl, Peter; Podbielski, Andreas

2014-01-01

A nose model that allows for the comparison of different modes of sample acquisition as well as of nasal swab systems concerning their suitability to detect defined quantities of intranasal microorganisms, and further for training procedures of medical staff, was evaluated. Based on an imprint of a human nose, a model made of a silicone elastomer was formed. Autoclave stability was assessed. Using an inoculation suspension containing Staphylococcus aureus and Staphylococcus epidermidis, the model was compared with standardized glass plate inoculations. Effects of inoculation time, mode of sampling, and sample storage time were assessed. The model was stable to 20 autoclaving cycles. There were no differences regarding the optimum coverage from the nose and from glass plates. Optimum sampling time was 1 h after inoculation. Storage time after sampling was of minor relevance for the recovery. Rotating the swab around its own axis while circling the nasal cavity resulted in best sampling results. The suitability of the assessed nose model for the comparison of sampling strategies and systems was confirmed. Without disadvantages in comparison with sampling from standardized glass plates, the model allows for the assessment of a correct sampling technique due to its anatomically correct shape. PMID:25215192

Evaluation of an autoclave resistant anatomic nose model for the testing of nasal swabs.

PubMed

Bartolitius, Lennart; Frickmann, Hagen; Warnke, Philipp; Ottl, Peter; Podbielski, Andreas

2014-09-01

A nose model that allows for the comparison of different modes of sample acquisition as well as of nasal swab systems concerning their suitability to detect defined quantities of intranasal microorganisms, and further for training procedures of medical staff, was evaluated. Based on an imprint of a human nose, a model made of a silicone elastomer was formed. Autoclave stability was assessed. Using an inoculation suspension containing Staphylococcus aureus and Staphylococcus epidermidis, the model was compared with standardized glass plate inoculations. Effects of inoculation time, mode of sampling, and sample storage time were assessed. The model was stable to 20 autoclaving cycles. There were no differences regarding the optimum coverage from the nose and from glass plates. Optimum sampling time was 1 h after inoculation. Storage time after sampling was of minor relevance for the recovery. Rotating the swab around its own axis while circling the nasal cavity resulted in best sampling results. The suitability of the assessed nose model for the comparison of sampling strategies and systems was confirmed. Without disadvantages in comparison with sampling from standardized glass plates, the model allows for the assessment of a correct sampling technique due to its anatomically correct shape.

Occurrence of Escherichia coli O157:H7 in cattle feces and contamination of carcass and various contact surfaces in abattoir and butcher shops of Hawassa, Ethiopia.

PubMed

Atnafie, Biruhtesfa; Paulos, Degmawi; Abera, Mesele; Tefera, Genene; Hailu, Dereje; Kasaye, Surafel; Amenu, Kebede

2017-01-25

Despite of the sanitation measures in municipal abattoirs to reduce contamination, Escherichia coli continues to be a health hazard. The present study was conducted on 150 apparently healthy slaughtered cattle at municipal abattoir and in 50 different butcher shops in Hawassa town, Ethiopia. The objectives of the study were investigating the occurrence and antimicrobial resistance of E. coli O157:H7 isolated from fecal samples, carcasses swab, contacts surfaces (swabs of meat handlers hands, knife and clothes of meat transporters) as well as from butcher shops (meat samples, swabs from cutting board swab, butcher men hand and knife surface). E. coli O157:H7 was isolated and identified using bacteriological culture, biochemical tests and Biolog identification system. All E. coli O157:H7 isolates were then checked for their antimicrobial susceptibility pattern using eleven selected antimicrobial discs. Of the entire set of 630 samples, 2.4% (15/630) (95% CI = 1.3-3.9%) were positive for E. coli O157:H7. When disaggregated by the sources of the samples, E. coli O157:H7 were prevalent in 2.8% (11 of 390) of the abattoir samples, of which 4.7% of the fecal sample and 2.7% of the carcass swabs. And E. coli O157:H7 were positive in 1.7% (4 of 240) of butcher shop specimens of which 2% of meat sample and 3.3% of Cutting board swabs. No statistically significant difference in the prevalence of E. coli 0157: H7 between sex, origin, and breed of cattle. The isolated E. coli O157:H7 were found to be100% susceptible to cefotaxime, ceftriaxone, gentamycin, kanamycin and nalidixic acid. This study concludes the occurrence of E. coli O157:H7 and the presence of multiple antibiotic resistance profiles in cattle slaughtered at Hawassa municipal abattoir and retail meat sold at butcher shops. This indicates high risk to public health especially in Ethiopia where many people consume raw or under cooked meat. Regulatory control of antibiotics usage in livestock production and pharmaco-epidemiological surveillance in food animals and animal products is hereby recommended to ensure consumer safety.

Microbiological test results of the environmental control and life support systems vapors compression distillation subsystem recycle tank components following various pretreatment protocols

NASA Technical Reports Server (NTRS)

Huff, Tim

1993-01-01

Microbiological samples were collected from the recycle tank of the vapor compression distillation (VCD) subsystem of the water recovery test at NASA MSFC following a 68-day run. The recycle tank collects rejected urine brine that was pretreated with a commercially available oxidant (Oxone) and sulfuric acid and pumps it back to the processing component of the VCD. Samples collected included a water sample and two swab samples, one from the particulate filter surface and a second from material floating on the surface of the water. No bacteria were recovered from the water sample. Both swab samples contained a spore-forming bacterium, Bacillus insolitus. A filamentous fungus was isolated from the floating material. Approximately 1 month after the pretreatment chemicals were changed to sodium hypochlorite and sulfuric acid, a swab of the particulate filter was again analyzed for microbial content. One fungus was isolated, and spore-forming bacteria were observed. These results indicate the inability of these pretreatments to inhibit surface attachment. The implications of the presence of these organisms are discussed.

Microbiological hazard identification and exposure assessment of street food vending in Johannesburg, South Africa.

PubMed

Mosupye, F M; von Holy, A

2000-11-01

One hundred and thirty-two samples of beef, chicken, salad and gravy were collected from two street vendors over eleven replicate surveys to assess microbiological safety and quality. For each food type samples were collected during preparation and holding. Dish water was also collected and food preparation surfaces swabbed during preparation and display. Standard methods were used to determine aerobic plate counts, Enterobacteriaceae counts, coliform counts and spore counts. Six hundred and seventy-five predominant colonies were isolated from aerobic plate counts of all samples and characterised. The incidence of selected foodborne bacterial pathogens and non-pathogenic E. coli 1 was also determined. In most cases mean bacterial counts of the raw materials were significantly higher (P < 0.05) than those of corresponding cooked foods. No significant differences (P > 0.05) in all count types were observed between food samples collected during cooking and those collected during holding. In addition, no significant differences (P > 0.05) in all count types were observed between prepared salads and their raw materials. Mean bacterial counts of water and swab samples collected from vendor 1 were lower than those of water and swab samples collected from vendor 2.The predominant populations isolated from the aerobic plate counts were Bacillus spp., Staphylococcus spp., Enterobacteriaceae and Alcaligenes spp. Bacillus cereus was detected in 17%, Clostridium perfringens in 1%, Staphylococcus aureus in 3% and Vibrio metchnikovii in 2% of the food samples. Campylobacter jejuni, Listeria monocytogenes, and Escherichia coli O157:H7 were not detected. Non-pathogenic E. coli 1 was detected in 13% of food samples, in 86 and 36% of dish water samples collected from vendors 1 and 2, respectively, and in 36% of surface swab samples from vendor 2.

Swab culture monitoring of automated endoscope reprocessors after high-level disinfection

PubMed Central

Lu, Lung-Sheng; Wu, Keng-Liang; Chiu, Yi-Chun; Lin, Ming-Tzung; Hu, Tsung-Hui; Chiu, King-Wah

2012-01-01

AIM: To conduct a bacterial culture study for monitoring decontamination of automated endoscope reprocessors (AERs) after high-level disinfection (HLD). METHODS: From February 2006 to January 2011, authors conducted randomized consecutive sampling each month for 7 AERs. Authors collected a total of 420 swab cultures, including 300 cultures from 5 gastroscope AERs, and 120 cultures from 2 colonoscope AERs. Swab cultures were obtained from the residual water from the AERs after a full reprocessing cycle. Samples were cultured to test for aerobic bacteria, anaerobic bacteria, and mycobacterium tuberculosis. RESULTS: The positive culture rate of the AERs was 2.0% (6/300) for gastroscope AERs and 0.8% (1/120) for colonoscope AERs. All the positive cultures, including 6 from gastroscope and 1 from colonoscope AERs, showed monofloral colonization. Of the gastroscope AER samples, 50% (3/6) were colonized by aerobic bacterial and 50% (3/6) by fungal contaminations. CONCLUSION: A full reprocessing cycle of an AER with HLD is adequate for disinfection of the machine. Swab culture is a useful method for monitoring AER decontamination after each reprocessing cycle. Fungal contamination of AERs after reprocessing should also be kept in mind. PMID:22529696

Methicillin-Resistant Staphylococcus aureus (MRSA) Detection: Comparison of Two Molecular Methods (IDI-MRSA PCR Assay and GenoType MRSA Direct PCR Assay) with Three Selective MRSA Agars (MRSA ID, MRSASelect, and CHROMagar MRSA) for Use with Infection-Control Swabs▿

PubMed Central

van Hal, S. J.; Stark, D.; Lockwood, B.; Marriott, D.; Harkness, J.

2007-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing problem. Rapid detection of MRSA-colonized patients has the potential to limit spread of the organism. We evaluated the sensitivities and specificities of MRSA detection by two molecular methods (IDI-MRSA PCR assay and GenoType MRSA Direct PCR assay) and three selective MRSA agars (MRSA ID, MRSASelect, and CHROMagar MRSA), using 205 (101 nasal, 52 groin, and 52 axillary samples) samples from consecutive known MRSA-infected and/or -colonized patients. All detection methods had higher MRSA detection rates for nasal swabs than for axillary and groin swabs. Detection of MRSA by IDI-MRSA was the most sensitive method, independent of the site (94% for nasal samples, 80% for nonnasal samples, and 90% overall). The sensitivities of the GenoType MRSA Direct assay and the MRSA ID, MRSASelect, and CHROMagar MRSA agars with nasal swabs were 70%, 72%, 68%, and 75%, respectively. All detection methods had high specificities (95 to 99%), independent of the swab site. Extended incubation for a further 24 h with selective MRSA agars increased the detection of MRSA, with a corresponding decline in specificity secondary to a significant increase in false-positive results. There was a noticeable difference in test performance of the GenoType MRSA Direct assay in detection of MRSA (28/38 samples [74%]) compared with detection of nonmultiresistant MRSA (17/31 samples [55%]) (susceptible to two or more non-β-lactam antibiotics). This was not observed with selective MRSA agar plates or IDI-MRSA. Although it is more expensive, in addition to rapid turnaround times of 2 to 4 h, IDI-MRSA offers greater detection of MRSA colonization, independent of the swab site, than do conventional selective agars and GenoType MRSA Direct. PMID:17537949

Comparing a single-day swabbing regimen with an established 3-day protocol for MRSA decolonization control.

PubMed

Frickmann, H; Schwarz, N G; Hahn, A; Ludyga, A; Warnke, P; Podbielski, A

2018-05-01

Success of methicillin-resistant Staphylococcus aureus (MRSA) decolonization procedures is usually verified by control swabs of the colonized body region. This prospective controlled study compared a single-day regimen with a well-established 3-day scheme for noninferiority and adherence to the testing scheme. Two sampling schemes for screening MRSA patients of a single study cohort at a German tertiary-care hospital 2 days after decolonization were compared regarding their ability to identify MRSA colonization in throat or nose. In each patient, three nose and three throat swabs were taken at 3- to 4-hour intervals during screening day 1, and in the same patients once daily on days 1, 2 and 3. Swabs were analysed using chromogenic agar and broth enrichment. The study aimed to investigate whether the single-day swabbing scheme is not inferior to the 3-day scheme with a 15% noninferiority margin. One hundred sixty patients were included, comprising 105 and 101 patients with results on all three swabs for decolonization screening of the nose and throat, respectively. Noninferiority of the single-day swabbing scheme was confirmed for both pharyngeal and nasal swabs, with 91.8% and 89% agreement, respectively. The absolute difference of positivity rates between the swabbing regimens was 0.025 (-0.082, 0.131) for the nose and 0.006 (-0.102, 0.114) (95% confidence interval) for the pharynx as calculated with McNemar's test for matched or paired data. Compliance with the single-day scheme was better, with 12% lacking second-day swabs and 27% lacking third-day swabs from the nostrils. The better adherence to the single-day screening scheme with noninferiority suggests its implementation as the new gold standard. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

[Preparation and evaluation of coagglutination reagents for the identification of Vibrio cholerae 01. Its trial during a cholera outbreak in Minatitlán, Veracruz].

PubMed

González Bonilla, C; Villanueva Zamudio, A; Bolaños Monrroy, G; Giono Cerezo, S; Valdespino Gómez, J L

1992-01-01

This study was realized in Minatitlán, Veracruz during a cholera outbreak. 169 rectal swabs were taken from hilles and their contacts. They were transfer alkaline peptone water for enrichment to V. cholerae and incubated for 8 hrs to 37 degrees C, 70 were positive for V. cholerae in both techniques. The coagglutination was done with a reagent prepared at the Instituto de Diagnóstico y Referencia Epidemiológicos of México and the culture were also performed in the same Institute. We obtained 100% of sensitivity and specificity of co-agglutination in relation with culture. This results gave the possibility to use this kind or reagents for a rapid presumptive diagnosis of cholera.

Acute seronegative polyarthritis associated with lymphogranuloma venereum infection in a patient with prevalent HIV infection.

PubMed

Kober, C; Richardson, D; Bell, C; Walker-Bone, K

2011-01-01

A 44-year-old man who has sex with men presented with a three-month asymmetrical polyarthropathy. He had a positive HIV-1 antibody test consistent with infection acquired more than six months previously. Lymphogranuloma venereum (LGV)-associated DNA was detected from a rectal swab. Following successful treatment for LGV his arthritis resolved completely. Infection with HIV-1 has been hypothesized to cause reactive arthritis but this has been disputed. The most likely diagnosis in this patient was sexually acquired reactive arthritis secondary to LGV infection. As LGV can be asymptomatic and treatment differs from that of the other serovars, screening should be considered in all men who have sex with men (MSM) presenting with acute arthritis, particularly if they are HIV infected.

Effects of hot water pasteurizing treatments on the microbiological condition of manufacturing beef used for hamburger patty manufacture.

PubMed

Gill, C O; Bryant, J; Badoni, M

2001-02-15

Ten 12-kg lots of manufacturing beef from a single packing plant were obtained from a hamburger patty manufacturing plant. Each lot was divided into two, 6-kg portions, one of which was not treated while the other was treated with water of 85 degrees C. A portion from one lot was treated for 15 s. A portion from each of three lots was treated for 30 s, three portions were treated for 45 s, and three were treated for 60 s. Twenty-five pieces of meat from each portion were swabbed over areas of 100 cm2. Subsequently, each portion was first coarsely ground then finely ground, with twenty-five 100-g samples being taken from each portion at each stage of grinding. Each swab and sample of ground meat was separately processed for the enumeration of total aerobic counts, coliforms and Escherichia coli at levels of detection of 1 cfu/cm2, 1 cfu/100 cm2 and 1 cfu/100 cm2, respectively, for swab samples; and at a level of detection of 1 cfu/g for all three types of bacteria in samples of ground beef. A 250-kg batch of manufacturing beef was treated with water of 85 degrees C for 60 s. The product was processed through commercial equipment for manufacturing frozen hamburger patties. The flavour of patties prepared from the pasteurized product was compared with the flavour of patties prepared during normal commercial operation of the equipment. The weight of the manufacturing beef was not affected by the treatments. Similar total numbers of coliforms or E. coli were recovered per 2500 cm2 from the 25 swab samples or per 25 g from the 25 ground beef samples from each untreated portion. As the ratio of the surface area in cm2 to the weight in g would likely be < or = 1, the similar numbers indicated that swab sampling was inefficient for recovering coliforms and E. coli from the meat. However, coliforms and E. coli were recovered more frequently from swab than from ground beef samples from treated portions. Thus, some swabs from all three portions of beef treated for 30 s yielded coliforms and E. coli, but samples from portions treated for 45 or 60 s yielded few coliforms and no E. coli. The numbers recovered from the treated and untreated portions indicated that treatments for 45 or 60 s reduced both coliform and E. coli numbers by two orders of magnitude. The flavours of cooked patties prepared from the meat pasteurized with water of 85 degrees C for 60 s were not distinguished from the normal commercial product. The data indicate that pasteurizing manufacturing beef with water of 85 degrees C for 45 s could be a practicable treatment for enhancing the microbiological safety of frozen hamburger patties.

Screening of Active Lyssavirus Infection in Wild Bat Populations by Viral RNA Detection on Oropharyngeal Swabs

PubMed Central

Echevarría, Juan E.; Avellón, Ana; Juste, Javier; Vera, Manuel; Ibáñez, Carlos

2001-01-01

Brain analysis cannot be used for the investigation of active lyssavirus infection in healthy bats because most bat species are protected by conservation directives. Consequently, serology remains the only tool for performing virological studies on natural bat populations; however, the presence of antibodies merely reflects past exposure to the virus and is not a valid marker of active infection. This work describes a new nested reverse transcription (RT)-PCR technique specifically designed for the detection of the European bat virus 1 on oropharyngeal swabs obtained from bats but also able to amplify RNA from the remaining rabies-related lyssaviruses in brain samples. The technique was successfully used for surveillance of a serotine bat (Eptesicus serotinus) colony involved in a case of human exposure, in which 15 out of 71 oropharyngeal swabs were positive. Lyssavirus infection was detected on 13 oropharyngeal swabs but in only 5 brains out of the 34 animals from which simultaneous brain and oropharyngeal samples had been taken. The lyssavirus involved could be rapidly identified by automatic sequencing of the RT-PCR products obtained from 14 brains and three bat oropharyngeal swabs. In conclusion, RT-PCR using oropharyngeal swabs will permit screening of wild bat populations for active lyssavirus infection, for research or epidemiological purposes, in line not only with conservation policies but also in a more efficient manner than classical detection techniques used on the brain. PMID:11574590

Filter forensics: microbiota recovery from residential HVAC filters.

PubMed

Maestre, Juan P; Jennings, Wiley; Wylie, Dennis; Horner, Sharon D; Siegel, Jeffrey; Kinney, Kerry A

2018-01-30

Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust samples provides valuable insights into the microbiome present in human-occupied spaces. However, the effect that different sampling methods have on the microbial community recovered from dust samples is not well understood across sample types. Heating, ventilation, and air conditioning (HVAC) filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne microbiome in homes and other climate-controlled spaces. In this study, the effect that dust recovery method (i.e., cut and elution, swabbing, or vacuuming) has on the microbial community structure, membership, and repeatability inferred by Illumina sequencing was evaluated. The results indicate that vacuum samples captured higher quantities of total, bacterial, and fungal DNA than swab or cut samples. Repeated swab and vacuum samples collected from the same filter were less variable than cut samples with respect to both quantitative DNA recovery and bacterial community structure. Vacuum samples captured substantially greater bacterial diversity than the other methods, whereas fungal diversity was similar across all three methods. Vacuum and swab samples of HVAC filter dust were repeatable and generally superior to cut samples. Nevertheless, the contribution of environmental and human sources to the bacterial and fungal communities recovered via each sampling method was generally consistent across the methods investigated. Dust recovery methodologies have been shown to affect the recovery, repeatability, structure, and membership of microbial communities recovered from dust samples in the built environment. The results of this study are directly applicable to indoor microbiota studies utilizing the filter forensics approach. More broadly, this study provides a better understanding of the microbial community variability attributable to sampling methodology and helps inform interpretation of data collected from other types of dust samples collected from indoor environments.

Etiologic predictive value of a rapid immunoassay for the detection of group A Streptococcus antigen from throat swabs in patients presenting with a sore throat.

PubMed

Orda, Ulrich; Gunnarsson, Ronny; Orda, Sabine; Fitzgerald, Mark; Rofe, Geoff; Dargan, Anna

2016-04-01

Clinical reasoning utilizing certain symptoms and scores has not proven to be a reliable decision-making tool to determine whether or not to suspect a group A Streptococcus (GAS) infection in the patient presenting with a sore throat. Culture as the so-called 'gold standard' is impracticable because it takes 1 to 2 days (and even longer in remote locations) for a result, and thus treatment decisions will be made without the result available. Rapid diagnostic antigen tests have demonstrated sufficient sensitivities and specificities in detecting GAS antigens to identify GAS throat infections. Throat swab samples were collected from patients attending the Mount Isa Hospital emergency department for a sore throat; these samples were compared to swab samples collected from healthy controls who did not have a sore throat. Both groups were aged 3-15 years. All swab samples were analyzed with a point-of-care test (Alere Test Pack +Plus with OBC Strep A). The etiologic predictive value (EPV) of the throat swab was calculated. The 95% confidence interval for positive EPV was 88-100% and for negative EPV was 97-99%, depending on assumptions made. This study demonstrates that the point-of-care test Alere Test Pack +Plus Strep A has a high positive predictive value and is able to rule in GAS infection as long as the proportion of carriers is low. Also the negative predictive value for ruling out GAS as the etiologic agent is very high irrespective of the carrier rate. Hence, this test is always useful to rule out GAS infection. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Reiter works with SWAB ASD Filter Kit in the U.S. Laboratory during Expedition 13

NASA Image and Video Library

2006-09-10

ISS013-E-80066 (10 Sept. 2006) --- European Space Agency (ESA) astronaut Thomas Reiter, Expedition 13 flight engineer, works with the surface, water and air biocharacterization (SWAB) air sampling device (ASD) filter kit in the Destiny laboratory of the International Space Station.

Comparison of the diagnostic performance of bacterial culture of nasopharyngeal swab and bronchoalveolar lavage fluid samples obtained from calves with bovine respiratory disease

USDA-ARS?s Scientific Manuscript database

Objective: Examine the culture results, gamithromycin susceptibility, predictive values, and agreement of pooled bilateral nasopharyngeal swabs (NPS) and bronchoalveolar lavages (BAL) for identification of Mannheimia haemolytica genotypes, Pasteurella multocida, and Histophilus somni in calves treat...

Complete Genome Sequence of a Porcine Polyomavirus from Nasal Swabs of Pigs with Respiratory Disease

PubMed Central

Smith, Catherine; Bishop, Brian; Stewart, Chelsea; Simonson, Randy

2018-01-01

ABSTRACT Metagenomic sequencing of pooled nasal swabs from pigs with unexplained respiratory disease identified a large number of reads mapping to a previously uncharacterized porcine polyomavirus. Sus scrofa polyomavirus 2 was most closely related to betapolyomaviruses frequently detected in mammalian respiratory samples. PMID:29700160

Bioavailabilities of rectal and oral methadone in healthy subjects

PubMed Central

Dale, Ola; Sheffels, Pamela; Kharasch, Evan D

2004-01-01

Aims Rectal administration of methadone may be an alternative to intravenous and oral dosing in cancer pain, but the bioavailability of the rectal route is not known. The aim of this study was to compare the absolute rectal bioavailability of methadone with its oral bioavailability in healthy humans. Methods Seven healthy subjects (six males, one female, aged 20–39 years) received 10 mg d5-methadone-HCl rectally (5 ml in 20% glycofurol) together with either d0-methadone intravenously (5 mg) or orally (10 mg) on two separate occasions. Blood samples for the LC-MS analyses of methadone and it's metabolite EDDP were drawn for up to 96 h. Noninvasive infrared pupillometry was peformed at the same time as blood sampling. Results The mean absolute rectal bioavalability of methadone was 0.76 (0.7, 0.81), compared to 0.86 (0.75, 0.97) for oral administration (mean (95% CI)). Rectal absorption of methadone was more rapid than after oral dosing with Tmax values of 1.4 (0.9, 1.8) vs. 2.8 (1.6, 4.0) h. The extent of formation of the metabolite EDDP did not differ between routes of administration. Single doses of methadone had a duration of action of at least 10 h and were well tolerated. Conclusions Rectal administration of methadone results in rapid absorption, a high bioavailability and long duration of action. No evidence of presystemic elimination was seen. Rectal methadone has characteristics that make it a potential alternative to intravenous and oral administration, particularly in cancer pain and palliative care. PMID:15255797

Early Results and Spaceflight Implications of the SWAB Flight Experiment

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Pierson, Duane L.

2007-01-01

Microbial monitoring of spacecraft environments provides key information in the assessment of infectious disease risk to the crew. Monitoring aboard the Mir space station and International Space Station (ISS) has provided a tremendous informational baseline to aid in determining the types and concentrations of microorganisms during a mission. Still, current microbial monitoring hardware utilizes culture-based methodology which may not detect many medically significant organisms, such as Legionella pneumophila. We hypothesize that evaluation of the ISS environment using non-culture-based technologies would reveal microorganisms not previously reported in spacecraft, allowing for a more complete health assessment. To achieve this goal, a spaceflight experiment, operationally designated as SWAB, was designed to evaluate the DNA from environmental samples collected from ISS and vehicles destined for ISS. Results from initial samples indicate that the sample collection and return procedures were successful. Analysis of these samples using denaturing gradient gel electrophoresis and targeted PCR primers for fungal contaminants is underway. The current results of SWAB and their implication for in-flight molecular analysis of environmental samples will be discussed.

Diagnosis of duck plague in waterfowl by polymerase chain reaction

USGS Publications Warehouse

Hansen, W.R.; Nashold, S.W.; Docherty, D.E.; Brown, S.E.; Knudson, D.L.

2000-01-01

A recently developed polymerase chain reaction (PCR) assay was used for diagnosis of duck plague in waterfowl tissues from past and current cases of waterfowl mortality and to identify duck plague virus in combined cloacal/oral-pharyngeal swab samples from healthy mallards (Anas platyrhynchos) after a disease outbreak. The PCR was able to detect viral DNA from all the individual or pooled tissues assayed from 10 waterfowl, including liver and spleen samples from three Muscovy ducks (Cairina moschata domesticus) that did not yield virus isolates. The strong staining intensity of the PCR products from the waterfowl tissues indicated that large amounts of virus were present, even when virus was not isolated. Duck plague DNA was also detected in a cloacal swab sample from a wood duck (Aix sponsa) carcass submitted for diagnosis. The PCR assay identified duck plague DNA in 13 swab samples that produced virus isolates from carrier mallards sampled in 1981 after a duck plague die-off. The duck plague PCR clearly demonstrated the ability to quickly diagnose duck plague in suspect mortality cases and to detect virus shed by carrier waterfowl.

Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen.

PubMed

Kittelmann, Sandra; Kirk, Michelle R; Jonker, Arjan; McCulloch, Alan; Janssen, Peter H

2015-11-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

DETECTION OF ZOONOTIC PATHOGENS IN WILD BIRDS IN THE CROSS-BORDER REGION AUSTRIA - CZECH REPUBLIC.

PubMed

Konicek, Cornelia; Vodrážka, Pavel; Barták, Pavel; Knotek, Zdenek; Hess, Claudia; Račka, Karol; Hess, Michael; Troxler, Salome

2016-10-01

To assess the importance of wild birds as a reservoir of zoonotic pathogens in Austria and the Czech Republic, we sampled 1,325 wild birds representing 13 orders, 32 families, and 81 species. The majority belonged to orders Columbiformes (43%), Passeriformes (25%), and to birds of prey: Accipitriformes, Strigiformes, and Falconiformes (15%). We collected cloacal swabs from 1,191 birds for bacterial culture and 1,214 triple swabs (conjunctiva, choana, cloaca) for DNA and RNA isolation. The cloacal swabs were processed by classical bacteriologic methods for isolation of Escherichia coli , Salmonella spp., methicillin-resistant Staphylococcus aureus (MRSA), and thermophilic Campylobacter spp. Nucleic acids isolated from triple swabs were investigated by PCR for West Nile virus, avian influenza viruses, and Chlamydia spp. We also tested tissue samples from 110 fresh carcasses for Mycobacterium spp. by PCR and we cultured fresh droppings from 114 birds for Cryptococcus spp. The most-frequently detected zoonotic bacteria were thermophilic Campylobacter spp. (12.5%) and Chlamydia spp. (10.3%). From 79.2% of the sampled birds we isolated E. coli , while 8.7% and 0.2% of E. coli isolates possessed the virulence genes for intimin (eaeA) and Shiga toxins (stx 1 and stx 2 ), respectively. Salmonella spp. were rarely found in the sampled birds (2.2%), similar to findings of MRSA (0.3%). None of the samples were positive for Cryptococcus neoformans , Mycobacterium spp., avian influenza viruses, or West Nile virus.

Mild Illness in Avian Influenza A(H7N9) Virus–Infected Poultry Worker, Huzhou, China, April 2013

PubMed Central

Lv, Huakun; Han, Jiankang; Zhang, Peng; Lu, Ye; Wen, Dong; Cai, Jian; Liu, Shelan; Sun, Jimin; Yu, Zhao; Zhang, Heng; Gong, Zhenyu; Chen, Enfu

2013-01-01

During April 2013 in China, mild respiratory symptoms developed in 1/61 workers who had culled influenza A(H7N9) virus–infected poultry. Laboratory testing confirmed A(H7N9) infection in the worker and showed that the virus persisted longer in sputum than pharyngeal swab samples. Pharyngeal swab samples from the other workers were negative for A(H7N9) virus. PMID:24209963

Impact of broad-spectrum antimicrobial treatment on the ecology of intestinal flora.

PubMed

Yang, Jen-Jia; Wang, Jann-Tay; Cheng, Aristine; Chuang, Yu-Chung; Sheng, Wang-Huei

2017-06-28

Suppression of intestinal flora by broad-spectrum antimicrobial agents facilitated risk of colonization or infection with resistant pathogen. We aimed to investigate the changes in bowel carriage of target resistant microorganisms (TRO) among patients treated with three different classes of Pseudomonas-sparing broad-spectrum antimicrobial agents (ertapenem, moxifloxacin and flomoxef) with anaerobic coverage. Risk factors for developing colonization of TRO were also analyzed. We prospectively enrolled the adult hospitalized patients (>20 years old) who were indicated for at least 7-day course with either of ertapenem, moxifloxacin or flomoxef. Rectal swabs were performed for the patients who received at least 1-day course of study antibiotics during the treatment duration. The TROs included Pseudomonas aeruginosa, Enterobacteriaceae, and Acinetobacter baumannii. MacConkey agars with study antibiotics were used to isolate the TROs and evaluate the antimicrobial resistance. The mean age of our study population was 61.6 years, and 58.8% were males. The rates of rectal colonization for Pseudomonas aeruginosa was similar among the study medications (ertapenem 13.2%, flomoxef 20%, moxifloxacin 14.3%, p = 0.809). Compared with ertapenem, flomoxef (odds ratio [OR], 4.30; 95% confidence interval [95% CI], 1.28-14.48, p = 0.019) and moxifloxacin (OR, 6.95; 95% CI, 1.36-35.52, p = 0.019) had higher risk for colonization of ertapenem-resistant Escherichiacoli colonization. The patients who received treatment of ertapenem may have a lower risk of rectal colonization for ertapenem resistant Escherichia coli than those who received flomoxef or moxifloxacin. The rate of Pseudomonas colonization did not differ between the three study Pseudomonas-sparing agents. Copyright © 2017. Published by Elsevier B.V.

Test performance and acceptability of self- versus provider-collected swabs for high-risk HPV DNA testing in female-to-male trans masculine patients.

PubMed

Reisner, Sari L; Deutsch, Madeline B; Peitzmeier, Sarah M; White Hughto, Jaclyn M; Cavanaugh, Timothy P; Pardee, Dana J; McLean, Sarah A; Panther, Lori A; Gelman, Marcy; Mimiaga, Matthew J; Potter, Jennifer E

2018-01-01

High-risk human papillomavirus (hrHPV) causes virtually all cervical cancers. Trans masculine (TM) people (those assigned female at birth who identify with a gender other than female) have low uptake of conventional cervical cancer screening. Self-collected hrHPV DNA testing has high levels of acceptability among cisgender (non-transgender) females and may support increased cervical cancer screening uptake in TM individuals. To assess the test performance and acceptability of self-collected vaginal specimens in comparison to provider-collected cervical swabs for hrHPV DNA detection in TM individuals ages 21-64 years. Between March 2015-September 2016, 150 TM participants with a cervix (mean age = 27.5 years; SD = 5.7) completed a one-time study visit comprised of a self-report survey, self-collected vaginal HPV DNA swab, clinician-administered cervical HPV swab, and brief interview on acceptability of clinical procedures. Participants were randomized to complete either self- or provider-collection first to minimize ordering effects. Self- and provider-collected samples were tested for 13 hrHPV DNA types using a DNA Hybridization Assay. The primary outcome variable was the concordance (kappa statistic) and performance (sensitivity, specificity) of self-collected vaginal HPV DNA specimens versus provider-collected cervical HPV swabs as the gold standard. Of the 131 participants completing both the self- and provider-collected HPV tests, 21 cases of hrHPV were detected by the provider cervical swab (gold standard; 16.0% hrHPV prevalence); 15 of these cases were accurately detected by the self-collected vaginal swab (71.4% concordance) (Kappa = 0.75, 95% Confidence Interval [CI]: 0.59, 0.92; p<0.001). Compared to the provider-collected cervical hrHPV DNA sample (gold standard), the self-collected vaginal hrHPV DNA test demonstrated a sensitivity of 71.4% (95% CI: 0.52, 0.91; p = 0.0495) and specificity of 98.2% (95% CI: 0.96, 1.00; p<0.0001). Over 90% of participants endorsed a preference for the self-collected vaginal swab over provider-collected cervical swab. Self-collected vaginal swabs are highly acceptable to TM as a means to test for hrHPV DNA. Test performance of this self-collection method for hrHPV detection in TM is consistent with previous studies in cisgender females. Self-collected vaginal swab testing for hrHPV DNA represents a reasonable and patient-centered strategy for primary cervical cancer screening in TM patients unwilling to undergo provider collection of specimens via speculum exam.

Response of glutathione S-transferase Pi (GSTP1) to neoadjuvant therapy in rectal adenocarcinoma.

PubMed

Bedford, M R; Anathhanam, S; Saleh, D; Hickson, A; McGregor, A K; Boyle, K; Burke, D

2012-12-01

The response of rectal adenocarcinoma to neoadjuvant therapy is variable. Accurate prediction of response would enable selective administration of therapy. The enzyme glutathione S-transferase Pi (GSTP1) has been shown to influence response to therapy in some solid tumours. Few data are available for rectal cancer. The GSTP1 levels in rectal adenocarcinoma and adjacent normal mucosa were quantified before and after exposure to neoadjuvant therapy. Venous blood samples and biopsies of normal rectal mucosa and tumour were prospectively obtained from patients with primary rectal cancer. Patients were stratified by exposure to neoadjuvant therapy or surgery alone. GSTP1 was quantitatively measured using an enzyme-linked immunosorbent assay. Ninety-two patients (54 men; median age 68 years) were recruited. The median GSTP1 level was significantly higher in rectal adenocarcinoma than in matched normal mucosa [6.59 μg/mg vs 4.57 μg/mg; P < 0.001]. The median tumour GSTP1 level was significantly lower in the therapy group compared with unmatched samples from the no-therapy group [4.47 μg/mg vs 7.76 μg/mg; P < 0.001]. The GSTP1 level is increased in rectal adenocarcinoma compared with adjacent normal mucosa. It decreases following neoadjuvant therapy. Future studies correlating pre-therapy GSTP1 levels with pathological response would be of interest. © 2012 The Authors. Colorectal Disease © 2012 The Association of Coloproctology of Great Britain and Ireland.

EVA-Compatible Microbial Swab Tool

NASA Technical Reports Server (NTRS)

Rucker, Michelle A.

2016-01-01

When we send humans to search for life on Mars, we'll need to know what we brought with us versus what may already be there. To ensure our crewed spacecraft meet planetary protection requirements—and to protect our science from human contamination—we'll need to know whether micro-organisms are leaking/venting from our ships and spacesuits. This is easily done by swabbing external vents and suit surfaces for analysis, but requires a specialized tool for the job. Engineers at the National Aeronautics and Space Administration (NASA) recently developed an Extravehicular Activity (EVA)-compatible swab tool that can be used to sample current space suits and life support systems. Data collected now will influence Mars life support and EVA hardware early in the planning process, before design changes become difficult and expensive.NASA’s EVA swab tool pairs a Space Shuttle-era tool handle with a commercially available swab tip mounted into a custom-designed end effector. A glove-compatible release mechanism allows the handle to quickly switch between swab tips, much like a shaving razor handle can snap onto a disposable blade cartridge. Swab tips are stowed inside individual sterile containers, each fitted with a microbial filter that allows the container to equalize atmospheric pressure, but prevents cabin contaminants from rushing into the container when passing from the EVA environment into a pressurized cabin. A bank of containers arrayed inside a tool caddy allows up to six individual samples to be collected during a given spacewalk.NASA plans to use the tool in 2016 to collect samples from various spacesuits during ground testing to determine what (if any) human-borne microbial contamination leaks from the suit under simulated thermal vacuum conditions. Next, the tool will be used on board the International Space Station to assess the types of microbial contaminants found on external environmental control and life support system vents. Data will support advanced EVA and life support system maturation studies, helping to answer questions such as “how close can an EVA-suited crew member approach an area of scientific interest without compromising the science?”

The prevention of early-onset neonatal group B streptococcal disease.

PubMed

Money, Deborah M; Dobson, Simon

2004-09-01

To review the evidence in the literature and to provide recommendations on the management of pregnant women in labour for the prevention of early-onset neonatal group B streptococcal (GBS) disease. Maternal outcomes evaluated included exposure to antibiotics in pregnancy and labour and complications related to antibiotic use. Neonatal outcomes of rates of early-onset group B streptococcal infections are evaluated. A review of the literature through MEDLINE from January 1980 to December 2003, relating to neonatal group B streptococcal infection and a review of the Centers for Disease Control and Prevention recommendations. The evidence obtained was reviewed and evaluated by the Infectious Diseases Committee of the Society of Obstetricians and Gynaecologists of Canada (SOGC) under the leadership of the principal authors, and recommendations were made according to guidelines developed by the Canadian Task Force on the Periodic Health Exam. 1. Offer all women screening for group B streptococcal disease at 35 to 37 weeks' gestation with culture done from one swab first to the vagina then to the rectal area. (II-1)2. Treat the following women intrapartum at time of labour or rupture of membranes with IV antibiotics: -all women positive by GBS culture screening done at 35 to 37 weeks (II-2) - any women with an infant previously infected with GBS (II-3) - any women with documented GBS bacteriuria (regardless of level of colony-forming units per mL) in this pregnancy (II-2) 3. Treat women at less than 37 weeks' gestation with IV antibiotics unless there has been a negative GBS vaginal/rectal swab culture within 5 weeks. (II-3) 4. Treat women with intrapartum fever with IV antibiotics (i.e., chorioamnionitis must be treated, but broader spectrum antibiotics would be advised). (II-2) 5. If a woman is GBS-positive by culture screening or by history of bacteriuria, with prelabour rupture of membranes at term, treat with GBS antibiotic prophylaxis and initiate induction of labour with IV oxytocin (II-1) 6. If GBS culture result is unknown and the woman has ruptured membranes at term for greater than 18 hours, treat with GBS antibiotic prophylaxis. (II-2)

Surveillance cultures of samples obtained from biopsy channels and automated endoscope reprocessors after high-level disinfection of gastrointestinal endoscopes

PubMed Central

2012-01-01

Background The instrument channels of gastrointestinal (GI) endoscopes may be heavily contaminated with bacteria even after high-level disinfection (HLD). The British Society of Gastroenterology guidelines emphasize the benefits of manually brushing endoscope channels and using automated endoscope reprocessors (AERs) for disinfecting endoscopes. In this study, we aimed to assess the effectiveness of decontamination using reprocessors after HLD by comparing the cultured samples obtained from biopsy channels (BCs) of GI endoscopes and the internal surfaces of AERs. Methods We conducted a 5-year prospective study. Every month random consecutive sampling was carried out after a complete reprocessing cycle; 420 rinse and swabs samples were collected from BCs and internal surface of AERs, respectively. Of the 420 rinse samples collected from the BC of the GI endoscopes, 300 were obtained from the BCs of gastroscopes and 120 from BCs of colonoscopes. Samples were collected by flushing the BCs with sterile distilled water, and swabbing the residual water from the AERs after reprocessing. These samples were cultured to detect the presence of aerobic and anaerobic bacteria and mycobacteria. Results The number of culture-positive samples obtained from BCs (13.6%, 57/420) was significantly higher than that obtained from AERs (1.7%, 7/420). In addition, the number of culture-positive samples obtained from the BCs of gastroscopes (10.7%, 32/300) and colonoscopes (20.8%, 25/120) were significantly higher than that obtained from AER reprocess to gastroscopes (2.0%, 6/300) and AER reprocess to colonoscopes (0.8%, 1/120). Conclusions Culturing rinse samples obtained from BCs provides a better indication of the effectiveness of the decontamination of GI endoscopes after HLD than culturing the swab samples obtained from the inner surfaces of AERs as the swab samples only indicate whether the AERs are free from microbial contamination or not. PMID:22943739

Surveillance cultures of samples obtained from biopsy channels and automated endoscope reprocessors after high-level disinfection of gastrointestinal endoscopes.

PubMed

Chiu, King-Wah; Tsai, Ming-Chao; Wu, Keng-Liang; Chiu, Yi-Chun; Lin, Ming-Tzung; Hu, Tsung-Hui

2012-09-03

The instrument channels of gastrointestinal (GI) endoscopes may be heavily contaminated with bacteria even after high-level disinfection (HLD). The British Society of Gastroenterology guidelines emphasize the benefits of manually brushing endoscope channels and using automated endoscope reprocessors (AERs) for disinfecting endoscopes. In this study, we aimed to assess the effectiveness of decontamination using reprocessors after HLD by comparing the cultured samples obtained from biopsy channels (BCs) of GI endoscopes and the internal surfaces of AERs. We conducted a 5-year prospective study. Every month random consecutive sampling was carried out after a complete reprocessing cycle; 420 rinse and swabs samples were collected from BCs and internal surface of AERs, respectively. Of the 420 rinse samples collected from the BC of the GI endoscopes, 300 were obtained from the BCs of gastroscopes and 120 from BCs of colonoscopes. Samples were collected by flushing the BCs with sterile distilled water, and swabbing the residual water from the AERs after reprocessing. These samples were cultured to detect the presence of aerobic and anaerobic bacteria and mycobacteria. The number of culture-positive samples obtained from BCs (13.6%, 57/420) was significantly higher than that obtained from AERs (1.7%, 7/420). In addition, the number of culture-positive samples obtained from the BCs of gastroscopes (10.7%, 32/300) and colonoscopes (20.8%, 25/120) were significantly higher than that obtained from AER reprocess to gastroscopes (2.0%, 6/300) and AER reprocess to colonoscopes (0.8%, 1/120). Culturing rinse samples obtained from BCs provides a better indication of the effectiveness of the decontamination of GI endoscopes after HLD than culturing the swab samples obtained from the inner surfaces of AERs as the swab samples only indicate whether the AERs are free from microbial contamination or not.

Identification of a Novel Human Papillomavirus, Type HPV199, Isolated from a Nasopharynx and Anal Canal, and Complete Genomic Characterization of Papillomavirus Species Gamma-12

PubMed Central

Oštrbenk, Anja; Kocjan, Boštjan J.; Hošnjak, Lea; Li, Jingjing; Deng, Qiuju; Šterbenc, Anja; Poljak, Mario

2015-01-01

The novel human papillomavirus type 199 (HPV199) was initially identified in a nasopharyngeal swab sample obtained from a 25 year-old immunocompetent male. The complete genome of HPV199 is 7,184 bp in length with a GC content of 36.5%. Comparative genomic characterization of HPV199 and its closest relatives showed the classical genomic organization of Gammapapillomaviruses (Gamma-PVs). HPV199 has seven major open reading frames (ORFs), encoding five early (E1, E2, E4, E6, and E7) and two late (L1 and L2) proteins, while lacking the E5 ORF. The long control region (LCR) of 513 bp is located between the L1 and E6 ORFs. Phylogenetic analysis additionally confirmed that HPV-199 clusters into the Gamma-PV genus, species Gamma-12, additionally containing HPV127, HV132, HPV148, HPV165, and three putative HPV types: KC5, CG2 and CG3. HPV199 is most closely related to HPV127 (nucleotide identity 77%). The complete viral genome sequence of additional HPV199 isolate was determined from anal canal swab sample. Two HPV199 complete viral sequences exhibit 99.4% nucleotide identity. To the best of our knowledge, this is the first member of Gamma-PV with complete nucleotide sequences determined from two independent clinical samples. To evaluate the tissue tropism of the novel HPV type, 916 clinical samples were tested using HPV199 type-specific real-time PCR: HPV199 was detected in 2/76 tissue samples of histologically confirmed common warts, 2/108 samples of eyebrow hair follicles, 2/137 anal canal swabs obtained from individuals with clinically evident anal pathology, 4/184 nasopharyngeal swabs and 3/411 cervical swabs obtained from women with normal cervical cytology. Although HPV199 was found in 1.4% of cutaneous and mucosal samples only, it exhibits dual tissue tropism. According to the results of our study and literature data, dual tropism of all Gamma-12 members is highly possible. PMID:26375679

Canine Skin and Conjunctival Swab Samples for the Detection and Quantification of Leishmania infantum DNA in an Endemic Urban Area in Brazil

PubMed Central

de Almeida Ferreira, Sidney; Leite, Rodrigo Souza; Ituassu, Leonardo Trindade; Almeida, Gregório Guilherme; Souza, Daniel Menezes; Fujiwara, Ricardo Toshio; de Andrade, Antero Silva Ribeiro; Melo, Maria Norma

2012-01-01

Background We evaluated kDNA PCR/hybridization and quantitative real-time PCR (qPCR) targeting the gene of DNA polymerase of Leishmania infantum for CVL diagnosis and assessment of parasite load in clinical samples obtained invasively and non-invasively. Methodology/Principal Findings Eighty naturally infected dogs from an endemic urban area in Brazil were used. Animals were divided into two groups based on the presence or absence of CVL clinical sings. Skin biopsies, bone marrow, blood and conjunctival swabs samples were collected and submitted to L. infantum DNA detection. In addition, anti-Leishmania antibody titers were measured by Immunofluorescence antibody test. The symptomatic dogs had increased titers compared to asymptomatic dogs (P = 0.025). The frequencies of positive results obtained by kDNA PCR/hybridization for asymptomatic and symptomatic dogs, respectively, were as follows: right conjunctiva, 77.5% and 95.0%; left conjunctiva, 75.0% and 87.5%; skin, 45.0% and 75.0%; bone marrow, 50.0% and 77.5%; and blood, 27.5% and 22.5%. In both groups, the parasite load in the skin samples was the highest (P<0.0001). The parasite loads in the conjunctival swab and bone marrow samples were statistically equivalent within each group. The parasite burden in conjunctival swabs was higher in the dogs with clinical signs than in asymptomatic dogs (P = 0.028). This same relationship was also observed in the bone marrow samples (P = 0.002). No differences in amastigotes load in the skin were detected between the groups. Conclusions The conjunctival swab is a suitable clinical sample for qualitative molecular diagnosis of CVL. The highest parasite burdens were detected in skin regardless of the presence of VL-associated clinical signs. The qPCR results emphasized the role of dogs, particularly asymptomatic dogs, as reservoirs for CVL because of the high cutaneous parasite loads. These results may help to explain the maintenance of high transmission rates and numbers of CVL cases in endemic urban regions. PMID:22506084

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

Corvidae feather pulp and West Nile virus detection

USGS Publications Warehouse

Docherty, D.E.; Romaine Long, R.; Griffin, Katie M.; Saito, E.K.

2004-01-01

We evaluated cloacal swab, vascular pulp of flight feather, and kidney and spleen pool samples from carcasses of members of the family Corvidae as sources of West Nile virus (WNV). The cloacal swab, kidney and spleen pool, and feather pulp were the source of WNV in 38%, 43%, and 77%, respectively, of the carcasses.

Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis.

PubMed

Korsak, N; Taminiau, B; Hupperts, C; Delhalle, L; Nezer, C; Delcenserie, V; Daube, G

2017-04-17

The aim of this study was to investigate the influence of the slaughter technique (Halal vs Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological procedures and 16S rDNA metagenetics. The purpose was also to investigate the neck area to identify bacteria originating from the digestive or the respiratory tract. Twenty bovine carcasses (10 from each group) were swabbed at the slaughterhouse, where both slaughtering methods are practiced. Two swabbing areas were chosen: one "legal" zone of 1600cm 2 (composed of zones from rump, flank, brisket and forelimb) and locally on the neck area (200cm 2 ). Samples were submitted to classical microbiology for aerobic Total Viable Counts (TVC) at 30°C and Enterobacteriaceae counts, while metagenetic analysis was performed on the same samples. The classical microbiological results revealed no significant differences between both slaughtering practices; with values between 3.95 and 4.87log CFU/100cm 2 and 0.49 and 1.94log CFU/100cm 2 , for TVC and Enterobacteriaceae respectively. Analysis of pyrosequencing data showed that differences in the bacterial population abundance between slaughtering methods were mainly observed in the "legal" swabbing zone compared to the neck area. Bacterial genera belonging to the Actinobacteria phylum were more abundant in the "legal" swabbing zone in "Halal" samples, while Brevibacterium and Corynebacterium were encountered more in "Halal" samples, in all swabbing areas. This was also the case for Firmicutes bacterial populations (families of Aerococcaceae, Planococcaceae). Except for Planococcoceae, the analysis of Operational Taxonomic Unit (OTU) abundances of bacteria from the digestive or respiratory tract revealed no differences between groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis of taxonomy at the genus level taxonomy highlights differences between swabbing areas. Although not clearly proven in this study, differences in hygiene practices used during both slaughtering protocols could explain the differences in contamination between carcasses from both slaughtering groups. Copyright © 2016 Elsevier B.V. All rights reserved.

Salmonella senftenberg: a new pathogen in the burns ward.

PubMed

Nair, D; Gupta, N; Kabra, S; Ahuja, R B; Prakash, S K

1999-12-01

This is the first report of Salmonella senftenberg serovar outbreak in a burns unit. This unit admits about 2000 patients with major burn injuries annually. Routine sampling from wound swabs in December 1995 revealed S. senftenberg in a few samples following which a study was instituted from January to March 1996. Of 446 burn admissions during this period 80 patients were culture positive for S. senftenberg in wound swabs. The protocol for investigation included wound swabs on admission and then at biweekly interval, blood culture studies on clinically toxic patients, anti-microbial sensitivity studies, environmental sampling and hand swabs and stool cultures from about 50 staff members of the burns ward. No wound swab at the time of admission was positive for S. senftenberg. Environmental study and the study of staff members did not reveal any obvious source of the infection. S. senftenberg strains were sensitive to more than seven of the 11 anti-microbials tested at the beginning of the study but later 96.3% of the strains showed multidrug (more than three drugs) resistance. By April 1996 the isolates became negligible and later disappeared completely. The organism resurfaced again in March 1997 and the same study was instituted again on 413 admissions between March and May 1997. Fifty patients were culture positive for S. senftenberg. This time stool sample from one burn dresser tested positive for S. senftenberg. Interestingly, again at the beginning of the second outbreak the Salmonella strains were sensitive to 9 out of 11 anti-microbials tested, but later 96.11% strains became multidrug resistant. S. senftenberg strains showed maximum resistance to amoxycillin (97.5%) and minimum to chloramphenicol, tetracycline and cotrimoxazole (12%). It was noticed that Salmonella strains surfaced in wound swabs after 3-4 weeks of hospital stay. Forty-five out of 130 patients studied, in both the episodes, died due to septicemia. The majority of the patients who died had sustained > 60% TBSA burns. Blood cultures were done in 34/130 patients and eight yielded growth (2 S. senftenberg, 4 Klebsiella spp., and two Pseudomonas spp.)

Influenza testing trends in sentinel surveillance general practices in Victoria 2007 to 2014.

PubMed

Cowie, Genevieve A; Cowie, Benjamin C; Fielding, James E

2017-03-31

The Victorian Sentinel Practice Influenza Network conducts syndromic surveillance for influenza-like illness (ILI), with testing for laboratory confirmation of a proportion of cases at the discretion of general practitioners. The aim of this study was to evaluate the consistency of sentinel general practitioners' swabbing practice within and between influenza seasons. Aggregated, weekly, non-identified data for May to October each year from 2007 to 2014 were used to calculate the proportion of patients presenting with ILI (defined as cough, fever and fatigue), proportion of ILI patients swabbed and proportion of swabs positive for influenza. Data on the proportion of consultations for ILI and the proportion of ILI patients swabbed were aggregated into time-period quintiles for each year. Analysis of variance was used to compare ILI patients swabbed for each aggregated time-period quintile over all 8 years. Spearman's correlation and Bland-Altman analyses were used to measure association and agreement respectively between ILI proportions of consultations and swabs positive for influenza in time period quintiles within each year. Data were aggregated by year for the rest of the analyses. Between 2007 and 2014 there was a slight decrease in the proportion of positive tests and the proportion of ILI patients was generally a good proxy for influenza test positivity. There was consistency in testing within and between seasons, despite an overall testing increase between 2007 and 2014. There was no evidence for temporal sampling bias in these data despite testing not being performed on a systematic basis. This sampling regimen could also be considered in other similar surveillance systems.

Inference of Antibiotic Resistance and Virulence Among Diverse Group A Streptococcus Strains Using emm Sequencing and Multilocus Genotyping Methods

DTIC Science & Technology

2009-09-04

apparent GAS-associated conditions were sampled by oropharyn- geal swab. Swabs were streaked on blood agar plates using Table 3. Isolate properties by...testing, samples were re-streaked on blood agar plates (5% sheep blood in TSA base) (Hardy Diagnostics, Santa Maria, CA), and incubated at 35–37uC with 5–10...sensitivity (A-disk method, Hardy Diagnostics) and positive GAS latex agglutination reaction (Hardy Diagnostics). Confirmed GAS isolates were then

The pharmacokinetics of a single oral or rectal dose of concurrently administered isoniazid, rifampin, pyrazinamide, and ethambutol in Asian elephants (Elephas maximus).

PubMed

P Brock, A; Isaza, R; Egelund, E F; Hunter, R P; Peloquin, C A

2014-10-01

Tuberculosis, caused by Mycobacterium tuberculosis, is a disease of concern in captive Asian elephants (Elephas maximus). Treatment for tuberculosis in elephants utilizes multidrug protocols combining isoniazid, rifampin, pyrazinamide, and/or ethambutol. In this study, a single, coformulated dose of isoniazid 5 mg/kg, rifampin 10 mg/kg, pyrazinamide 30 mg/kg, and ethambutol 30 mg/kg was administered orally to six Asian elephants, and rectally to five elephants using a cross-over design. Blood samples were collected serially over 24 h. Pyrazinamide and ethambutol concentrations were determined using validated gas chromatography assays. Isoniazid and rifampin concentrations were determined using validated high-performance liquid chromatography assays. Rectal isoniazid produced an earlier Tmax compared with oral administration. Oral isoniazid resulted in a comparatively lower Cmax , but higher AUC values compared with rectal isoniazid. Oral rifampin and oral ethambutol were well absorbed while rectal rifampin was not. Oral pyrazinamide produced comparatively higher Cmax and AUC values compared with rectal pyrazinamide. Results of this study indicate that currently recommended therapeutic monitoring sample collection times for rectal isoniazid and oral rifampin do not provide an accurate assessment of exposure for these drugs. This study demonstrates notable individual variability, indicating that dosing of these medications requires individual monitoring and provides additional information to guide the clinician when treating elephants. © 2014 John Wiley & Sons Ltd.

A microbial survey of the International Space Station (ISS)

PubMed Central

Lang, Jenna M.; Coil, David A.; Neches, Russell Y.; Brown, Wendy E.; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T.; Gilbert, Jack A.

2017-01-01

Background Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the “buildings” in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Results Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. Conclusions While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036–4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain. PMID:29492330

A microbial survey of the International Space Station (ISS).

PubMed

Lang, Jenna M; Coil, David A; Neches, Russell Y; Brown, Wendy E; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T; Gilbert, Jack A; Eisen, Jonathan A

2017-01-01

Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036-4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

Contamination sampling device

NASA Technical Reports Server (NTRS)

Delgado, Felix A. (Inventor); Stern, Susan M. (Inventor)

1998-01-01

A contamination sample collection device has a wooden dowel with a cotton swab at one end, the cotton being covered by a nylon cloth and the wooden dowel being encapsulated by plastic tubing which is heat shrunk onto the dowel and onto a portion of the cotton swab to secure the cotton in place. Another plastic tube is heat shrunk onto the plastic that encapsulates the dowel and a portion of the nylon cloth to secure the nylon cloth in place. The device may thereafter be covered with aluminum foil protector. The device may be used for obtaining samples of contamination in clean room environments.

Surveillance of feral cats for influenza A virus in North Central Florida

PubMed Central

Gordy, James T.; Jones, Cheryl A.; Rue, Joanne; Crawford, Patti Cynda; Levy, Julie K.; Stallknecht, David E.; Tripp, Ralph A.; Tompkins, Stephen M.

2011-01-01

Please cite this paper as: Gordy JT et al. (2012) Surveillance of feral cats for influenza A virus in North Central Florida. Influenza and Other Respiratory Viruses 6(5), 341–347. Background  Transmission of highly pathogenic avian influenza and the recent pandemic H1N1 viruses to domestic cats and other felids creates concern because of the morbidity and mortality associated with human infections as well as disease in the infected animals. Experimental infections have demonstrated transmission of influenza viruses in cats. Objectives  An epidemiologic survey of feral cats was conducted to determine their exposure to influenza A virus. Methods  Feral cat sera and oropharyngeal and rectal swabs were collected from November 2008 through July 2010 in Alachua County, FL and were tested for evidence of influenza A virus infection by virus isolation, PCR, and serological assay. Results and conclusions  No virus was isolated from any of 927 cats examined using MDCK cell or embryonated chicken egg culture methods, nor was viral RNA detected by RT‐PCR in 200 samples tested. However, 0.43% of cats tested antibody positive for influenza A by commercial ELISA. These results suggest feral cats in this region are at minimal risk for influenza A virus infection. PMID:22212818

Pharmacokinetic and pharmacodynamic evaluations of a 10 mg/kg enrofloxacin intramuscular administration in bearded dragons (Pogona vitticeps): a preliminary assessment.

PubMed

Salvadori, M; Vercelli, C; De Vito, V; Dezzutto, D; Bergagna, S; Re, G; Giorgi, M

2017-01-01

Enrofloxacin (E) is commonly used in veterinary medicine. It is necessary to perform pharmacokinetic/dynamic studies to minimize the selection of resistant mutants of bacteria and extend the efficacy of antimicrobial agents. Eight healthy adult Pogona vitticeps were assigned into two groups of equal size and treated with a single intramuscular injection of E at 10 mg/kg. Blood samples were withdrawn at different scheduled times for each group, and rectal swabs were collected. E and ciprofloxacin (active metabolite) blood concentrations were quantified by an HPLC validated method, while the in vitro antimicrobial susceptibility was evaluated by the Kirby-Bauer disc diffusion susceptibility test. The pharmacokinetic profiles of E gave similar pharmacokinetic parameters irrespective of the collection time schedule. Bacteria isolation showed the presence of both E. coli, Salmonella enterica subspecies enterica and subspecies 3a, Proteus spp., and Pseudomonas spp. The majority of isolated colonies were sensitive to E, but the treatment did not reduce the number of bacteria in faeces. Results suggest that E is able to reach blood concentrations high enough to kill susceptible bacteria (MIC < 0.9 μg/mL), but at the same time does not significantly affect intestinal bacteria. © 2016 John Wiley & Sons Ltd.

Colonization with third-generation cephalosporin-resistant Enterobacteriaceae on hospital admission: prevalence and risk factors.

PubMed

Hamprecht, A; Rohde, A M; Behnke, M; Feihl, S; Gastmeier, P; Gebhardt, F; Kern, W V; Knobloch, J K; Mischnik, A; Obermann, B; Querbach, C; Peter, S; Schneider, C; Schröder, W; Schwab, F; Tacconelli, E; Wiese-Posselt, M; Wille, T; Willmann, M; Seifert, H; Zweigner, J

2016-10-01

The objectives of this study were to prospectively assess the rectal carriage rate of third-generation cephalosporin-resistant Enterobacteriaceae (3GCREB) in non-ICU patients on hospital admission and to investigate resistance mechanisms and risk factors for carriage. Adult patients were screened for 3GCREB carriage at six German tertiary care hospitals in 2014 using rectal swabs or stool samples. 3GCREB isolates were characterized by phenotypic and molecular methods. Each patient answered a questionnaire about potential risk factors for colonization with MDR organisms (MDROs). Univariable and multivariable risk factor analyses were performed to identify factors associated with 3GCREB carriage. Of 4376 patients, 416 (9.5%) were 3GCREB carriers. Escherichia coli was the predominant species (79.1%). ESBLs of the CTX-M-1 group (67.3%) and the CTX-M-9 group (16.8%) were the most frequent β-lactamases. Five patients (0.11%) were colonized with carbapenemase-producing Enterobacteriaceae. The following risk factors were significantly associated with 3GCREB colonization in the multivariable analysis (P < 0.05): centre; previous MDRO colonization (OR = 2.12); antibiotic use within the previous 6 months (OR = 2.09); travel outside Europe (OR = 2.24); stay in a long-term care facility (OR = 1.33); and treatment of gastroesophageal reflux disease (GERD) (OR = 1.22). To our knowledge, this is the largest admission prevalence study of 3GCREB in Europe. The observed prevalence of 9.5% 3GCREB carriage was higher than previously reported and differed significantly among centres. In addition to previously identified risk factors, the treatment of GERD proved to be an independent risk factor for 3GCREB colonization. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Physiological effects of stress related to helicopter travel in Federal Emergency Management Agency search-and-rescue canines.

PubMed

Perry, E; Gulson, N; Liu Cross, T-W; Swanson, K S

2017-01-01

Working canines are deployed by the Federal Emergency Management Agency (FEMA), as part of a National Disaster Response Plan. Stress associated with helicopter flight and the resulting physical effects on the dog are unknown. Our objective was to test the hypotheses that (1) helicopter travel affects the physiology and faecal microbiota of working canines, but that (2) physiological consequences of helicopter travel will not negatively affect their work performance. A total of nine FEMA canines were loaded onto helicopters and flown for 30 min in July 2015. Rectal temperature, behavioural stress indicators and saliva swabs (for cortisol) were collected at baseline, loading, mid-flight and post-flight. After flight, canines completed a standardised search exercise to monitor work performance. Faecal samples were collected for microbial DNA extraction and Illumina sequencing. All canines were on a standardised diet (CANIDAE ® Grain Free PURE Land ® ) for 3 weeks prior to the study. Visible indicators of stress were observed at loading and at mid-flight and corresponded with an increase ( P  < 0·05) in salivary cortisol from 5·4 µg/l (baseline) to 6·4 µg/l (loading). Additionally, rectal temperature increased ( P < 0·05) from 38·61°C (baseline) to 39·33°C (mid-flight) and 39·72°C (post-flight). Helicopter travel did not affect search performance ( P  > 0·05). We found that α- and β-diversity measures of faecal microbiota were not affected ( P  > 0·05). Our data suggest that although helicopter travel may cause physiological changes that have been associated with stress in working dogs, it does not make an impact on their search performance or the stability of faecal microbiota.

[Benefit of clinical and laboratory parameters for the diagnosis of endometritis in dairy cows].

PubMed

Hässig, M; Steinmann, B; Wittenbrink, M M

2010-09-01

The goal of this work was to answer the question of whether or not there are significant differences between cows with abnormal vaginal discharge and cows with the diagnosis of puerperal or chronic endometritis, using blood and urine parameters. In addition, cows with and without vaginal discharge were examined for significant bacteriological differences in uterine mucous samples. The question of false positive and false negatives from the diagnosis of endometritis was also investigated. A total of 35 matched-pairs (+/-vaginal discharge) from 27 stables was examined 21 to 63 days post partum. The examination consisted of a rectal and vaginal exam, urine and blood samples as well as vaginal swab from the corpus uteri using a Folmer-Nielsen-Catheter. Based on the history vaginal discharge occurred more frequently in dystocia and retentio secundinarium. Cows with a history of distocia and retentio secundinarium showed significantly more vaginal discharge. Gammaglutamyltransferase (GGT; p=0.01) and cholesterine (p=0.04) were different in cows with endometritis. The bacteriology results showed a statistically significant difference (p<0.01) only for Escherichia coli and Arcanobacterium pyogenes. The Folmer-Nielsen smears/endometritis showed a significant difference between the two groups (p<0.01). In a multivariate analysis with final step-back procedure regarding endometritis Gammaglutamyltransferase (GGT) and Betahydroxybutteracid (BHB) were significant different (p=0.02). The hypothesis vaginal discharge alike endometritis showed that 34 % of the clinical suspicious cases were recorded as false negatives. In the non-suspicious cases 20 % were diagnosed as false negative.

Culture and Real-Time PCR Based Maternal Screening and Antibiotic Susceptibility for Group B Streptococcus: An Iranian Experience.

PubMed

Goudarzi, Gholamreza; Ghafarzadeh, Masoumeh; Shakib, Pegah; Anbari, Khatereh

2015-04-19

Vertical Transmission of group B streptococcus (GBS) from a vagina colonized mother to her infant upon rupture of membranes (ROM) or after the onset of labor can cause life-threatening infections in newborn. Although intrapartum antibiotic prophylaxis (IAP) can significantly decrease neonatal GBS diseases, this issue has potentiated the emergence of antibiotic resistance strains. Our study examined the colonization rate of GBS using real-time PCR and culture methods, and trends in antibiotic resistance of GBS isolates obtained from pregnant women in Khorramabad, Iran. In this cross-sectional study, two vaginal-rectal swabs were collected and analyzed separately from 100 pregnant women at 35-37 weeks of gestation by convenience sampling method. The specimens were subjected to GBS detection using real-time PCR assay and standard culture. Susceptibility pattern of the GBS isolates was examined using the disk diffusion method. GBS carriage rate was 17% and 19% using culture and real-time PCR, respectively. In six samples, the culture was positive and the real-time PCR was negative. Sensitivity and specificity for real-time PCR were 72.7% and 96.1%, respectively using culture as the gold standard. Amongst twenty-two isolates examined, 100% resistance to erythromycin and clindamycin was observed. One isolate (4%) exhibited resistance to penicillin. Considering the relatively high GBS carriage rate in Khorramabad, routine antepartum screening for GBS is recommended. Penicillin can remain the antibiotic of choice for IAP; however, in penicillin-allergic mothers, vancomycin can be an alternative antibiotic.

Risk factors for colonization and infection by Pseudomonas aeruginosa in patients hospitalized in intensive care units in France.

PubMed

Hoang, S; Georget, A; Asselineau, J; Venier, A-G; Leroyer, C; Rogues, A M; Thiébaut, R

2018-01-01

To assess the role of environment, medical care and individual risks factors for P. aeruginosa colonization and infection. A French multicentric prospective study involved ten ICUs for a five months period. Every adult patient newly hospitalized in ICUs with no P. aeruginosa carriage up to 48 hours after admission was included and weekly screened before discharge or death. Screening swabs were either rectal, sputum or oropharyngeal samples. Hydric environment was also sampled each week. Data on patient clinical features, environmental and device exposures, and antibiotics supports were regularly collected. Multivariate analysis was performed with a multistate model. The overall prevalence of P. aeruginosa carriage was 15.3% (201/1314). Risk factors associated with patient colonization were: use of inactive antibiotics against P. aeruginosa (HR = 1.60 [1.15-2.21] p<0.01), tap water contamination at the entry in the room (HR = 1.66 [1.01-2.27] p<0.05) and mechanical invasive ventilation (HR = 4.70 [2.66-8.31] p<0.0001). Active antibiotics prevented from colonization (HR = 0.67 [0.48-0.93] p = 0.02) and from infection (HR = 0.64 [0.41-1.01] p = 0.05). Interaction between hydric environment antibiotics support was not statistically associated with patient colonization. Hydric contamination and antibiotics pressure seem to remain key independent risk factors in P. aeruginosa colonization. These results advocate the need to carry on preventive and targeted interventions toward healthcare associated infections.

Development of a novel real-time RT-PCR assay to detect Seneca Valley virus-1 associated with emerging cases of vesicular disease in pigs.

PubMed

Fowler, Veronica L; Ransburgh, Russell H; Poulsen, Elizabeth G; Wadsworth, Jemma; King, Donald P; Mioulet, Valerie; Knowles, Nick J; Williamson, Susanna; Liu, Xuming; Anderson, Gary A; Fang, Ying; Bai, Jianfa

2017-01-01

Seneca Valley virus 1 (SVV-1) can cause vesicular disease that is clinically indistinguishable from foot-and-mouth disease, vesicular stomatitis and swine vesicular disease. SVV-1-associated disease has been identified in pigs in several countries, namely USA, Canada, Brazil and China. Diagnostic tests are required to reliably detect this emerging virus, and this report describes the development and evaluation of a novel real-time (r) reverse-transcription (RT) PCR assay (rRT-PCR), targeting the viral polymerase gene (3D) of SVV-1. This new assay detected all historical and contemporary SVV-1 isolates examined (n=8), while no cross-reactivity was observed with nucleic acid templates prepared from other vesicular disease viruses or common swine pathogens. The analytical sensitivity of the rRT-PCR was 0.79 TCID 50 /ml and the limit of detection was equivalent using two different rRT-PCR master-mixes. The performance of the test was further evaluated using pig nasal (n=25) and rectal swab samples (n=25), where concordant results compared to virus sequencing were generated for 43/50 samples. The availability of this assay, will enable laboratories to rapidly detect SVV-1 in cases of vesicular disease in pigs, negated for notifiable diseases, and could enable existing knowledge gaps to be investigated surrounding the natural epidemiology of SVV-1. Copyright © 2016 Elsevier B.V. All rights reserved.

Prevalence of O157:H7 and non-O157 E. coli in Iranian domestic sheep.

PubMed

Tahamtan, Yahya; Namavari, Mehdi

2014-01-01

The aim of the present study was the isolation of both E. coli O157 and non-O157 in sheep. Verotoxins (VT) 1, 2 and eae genes were tested for this propose. Sheep faces are an important source of Shiga toxin-producing Escherichia coli (STEC). Escherichia coli O157:H7 is a highly virulent food-borne pathogen and threat to public health. Rectal swab samples from sheep were collected during 2009-2010. Conventional plating and Polymerase Chain Reaction (PCR) were carried out according to virulence factors (Stx1, Stx2 and eaeA).There significant differences between prevalence of STEC and session were observed. It was at highest in spring and late summer. Six (3.92%) sheep carcasses were contaminated by E. coli O157:H7.Only six samples were positive by PCR specific for the VT2 gene and produced verocytotoxin VT2, whereas all isolates were negative for the presence of VT1 and eae virulence genes considered. Geographical variations and season may be influenced in the prevalence rate. The composition of the gastrointestinal flora may be changed by different diet and, therefore O157 STEC rate in sheep and lamb was different. Iranian sheep indicated as a natural host of E. coli O157 strains therefore, may be potentially pathogenic for humans. This is the first report of E. coli O157 detection from sheep in Iran.

Detection of herpes simplex virus and varicella-zoster virus in clinical swabs: frequent inhibition of PCR as determined by internal controls.

PubMed

Bezold, G; Volkenandt, M; Gottlöber, P; Peter, R U

2000-12-01

PCR-based detection of microorganisms is widely used for diagnostic purposes. Most routine PCR applications do not control for inhibition of PCR, thus leading to false-negative results. One hundred eighteen swab samples obtained from skin and mucosa were investigated for the presence of herpes simplex virus (HSV), varicella-zoster virus (VZV), and the control gene betaglobin by internally controlled PCR with purified and unpurified DNA in parallel. With unpurified DNA, inhibition of PCR was detected in 23% of betaglobin PCRs, 25% of VZV PCRs, and 16% of HSV PCRs versus 3% each for purified DNA. Approximately 20% of the samples with positive results for HSV or VZV had negative or inhibited results using unpurified DNA. These results indicate that PCR from clinical swab specimens should be performed exclusively with internal controls because the positive control alone cannot exclude PCR inhibition in individual samples. Purification of DNA will decrease, but not exclude, PCR inhibition.

Experimental Design for a Macrofoam Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

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

Piepel, Gregory F.; Hutchison, Janine R.

2014-04-16

This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (plating/counting and polymerase chain reaction) will be used. Only one previous study has investigated false negative as a function of affecting test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completingmore » gaps in the available information on the performance of macrofoam swab sampling at low concentrations.« less

Experimental Design for a Macrofoam-Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

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

Piepel, Gregory F.; Hutchison, Janine R.

This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam-swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (culture and polymerase chain reaction) will be used. Only one previous study has investigated how the false negative rate depends on test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completing gapsmore » in the available information on the performance of macrofoam-swab sampling at low concentrations.« less

Potential of DNA methylation in rectal cancer as diagnostic and prognostic biomarkers

PubMed Central

Exner, Ruth; Pulverer, Walter; Diem, Martina; Spaller, Lisa; Woltering, Laura; Schreiber, Martin; Wolf, Brigitte; Sonntagbauer, Markus; Schröder, Fabian; Stift, Judith; Wrba, Fritz; Bergmann, Michael; Weinhäusel, Andreas; Egger, Gerda

2015-01-01

Background: Aberrant DNA methylation is more prominent in proximal compared with distal colorectal cancers. Although a number of methylation markers were identified for colon cancer, yet few are available for rectal cancer. Methods: DNA methylation differences were assessed by a targeted DNA microarray for 360 marker candidates between 22 fresh frozen rectal tumour samples and 8 controls and validated by microfluidic high-throughput and methylation-sensitive qPCR in fresh frozen and formalin-fixed paraffin-embedded (FFPE) samples, respectively. The CpG island methylator phenotype (CIMP) was assessed by MethyLight in FFPE material from 78 patients with pT2 and pT3 rectal adenocarcinoma. Results: We identified and confirmed two novel three-gene signatures in fresh frozen samples that can distinguish tumours from adjacent tissue as well as from blood with a high sensitivity and specificity of up to 1 and an AUC of 1. In addition, methylation of individual CIMP markers was associated with specific clinical parameters such as tumour stage, therapy or patients' age. Methylation of CDKN2A was a negative prognostic factor for overall survival of patients. Conclusions: The newly defined methylation markers will be suitable for early disease detection and monitoring of rectal cancer. PMID:26335606

Self-sampling for human papillomavirus DNA detection: a preliminary study of compliance and feasibility in BOLIVIA.

PubMed

Surriabre, Pedro; Allende, Gustavo; Prado, Marcela; Cáceres, Leyddy; Bellot, Diego; Torrico, Andrea; Ustariz, Karina; Rojas, Shirley; Barriga, Jaime; Calle, Pamela; Villarroel, Ligia; Yañez, Rosse Mary; Baay, Marc; Rodriguez, Patricia; Fontaine, Véronique

2017-12-22

Cervical cancer incidence and mortality rates in Bolivia are among the highest in Latin America. This investigation aims to evaluate the possibility of using simple devices, e.g. a cotton swab and a glass slide, for self-sampling in order to detect human papillomavirus (HPV) DNA by PCR in cervico-vaginal cells. In the first phase of our study we evaluated the use of a glass slide as a transport medium for cervical cells. A physician took paired-cervical samples from 235 women. One sample was transported in Easyfix® solution and the other sample was smeared over a glass slide. Both were further analyzed and compared for human DNA recovery and HPV detection. A kappa value was determined to evaluate the agreement between the HPV DNA detection rates. In the second phase of the study, 222 women from the urban, peri-urban and rural regions of Cochabamba were requested to perform self-sampling using the following devices: a cotton swab combined with a glass slide, and a vaginal tampon. Women gave their opinion about the self-sampling technique. Finally, the agreement for high risk-HPV detection between self- and physician-collected samples was performed in 201 samples in order to evaluate the self-sampling technique. Firstly, the comparison between Easyfix® solution and the glass slide to transport clinical samples gave a good agreement for HPV DNA detection (κ = 0.71, 95% CI 0.60-0.81). Secondly, self-sampling, especially with cotton swab combined with glass slide, would generally be preferred over clinician sampling for a screening program based on HPV detection. Finally, we showed a good agreement between self- and physician collected samples for high risk-HPV detection (κ = 0.71, 95% CI 0.55-0.88). Simple devices such as a cotton swab and a glass slide can be used to perform self-sampling and HPV DNA detection. Furthermore, most Bolivian women preferred self-sampling over clinician-sampling for cervical cancer screening.

Two sampling techniques for game meat.

PubMed

van der Merwe, Maretha; Jooste, Piet J; Hoffman, Louw C; Calitz, Frikkie J

2013-03-20

A study was conducted to compare the excision sampling technique used by the export market and the sampling technique preferred by European countries, namely the biotrace cattle and swine test. The measuring unit for the excision sampling was grams (g) and square centimetres (cm2) for the swabbing technique. The two techniques were compared after a pilot test was conducted on spiked approved beef carcasses (n = 12) that statistically proved the two measuring units correlated. The two sampling techniques were conducted on the same game carcasses (n = 13) and analyses performed for aerobic plate count (APC), Escherichia coli and Staphylococcus aureus, for both techniques. A more representative result was obtained by swabbing and no damage was caused to the carcass. Conversely, the excision technique yielded fewer organisms and caused minor damage to the carcass. The recovery ratio from the sampling technique improved 5.4 times for APC, 108.0 times for E. coli and 3.4 times for S. aureus over the results obtained from the excision technique. It was concluded that the sampling methods of excision and swabbing can be used to obtain bacterial profiles from both export and local carcasses and could be used to indicate whether game carcasses intended for the local market are possibly on par with game carcasses intended for the export market and therefore safe for human consumption.

Imperfect pathogen detection from non-invasive skin swabs biases disease inference

USGS Publications Warehouse

DiRenzo, Graziella V.; Grant, Evan H. Campbell; Longo, Ana; Che-Castaldo, Christian; Zamudio, Kelly R.; Lips, Karen

2018-01-01

1. Conservation managers rely on accurate estimates of disease parameters, such as pathogen prevalence and infection intensity, to assess disease status of a host population. However, these disease metrics may be biased if low-level infection intensities are missed by sampling methods or laboratory diagnostic tests. These false negatives underestimate pathogen prevalence and overestimate mean infection intensity of infected individuals. 2. Our objectives were two-fold. First, we quantified false negative error rates of Batrachochytrium dendrobatidis on non-invasive skin swabs collected from an amphibian community in El Copé, Panama. We swabbed amphibians twice in sequence, and we used a recently developed hierarchical Bayesian estimator to assess disease status of the population. Second, we developed a novel hierarchical Bayesian model to simultaneously account for imperfect pathogen detection from field sampling and laboratory diagnostic testing. We evaluated the performance of the model using simulations and varying sampling design to quantify the magnitude of bias in estimates of pathogen prevalence and infection intensity. 3. We show that Bd detection probability from skin swabs was related to host infection intensity, where Bd infections < 10 zoospores have < 95% probability of being detected. If imperfect Bd detection was not considered, then Bd prevalence was underestimated by as much as 16%. In the Bd-amphibian system, this indicates a need to correct for imperfect pathogen detection caused by skin swabs in persisting host communities with low-level infections. More generally, our results have implications for study designs in other disease systems, particularly those with similar objectives, biology, and sampling decisions. 4. Uncertainty in pathogen detection is an inherent property of most sampling protocols and diagnostic tests, where the magnitude of bias depends on the study system, type of infection, and false negative error rates. Given that it may be difficult to know this information in advance, we advocate that the most cautious approach is to assume all errors are possible and to accommodate them by adjusting sampling designs. The modeling framework presented here improves the accuracy in estimating pathogen prevalence and infection intensity.

Rhinitis, Ocular, Throat and Dermal Symptoms, Headache and Tiredness among Students in Schools from Johor Bahru, Malaysia: Associations with Fungal DNA and Mycotoxins in Classroom Dust

PubMed Central

Norbäck, Dan; Hashim, Jamal Hisham; Cai, Gui-Hong; Hashim, Zailina; Ali, Faridah; Bloom, Erica; Larsson, Lennart

2016-01-01

There are few studies on rhinitis and sick building syndrome (SBS) among students in tropical countries. We studied associations between levels of five fungal DNA sequences, two mycotoxins (sterigmatocystin and verrucarol) and cat allergen (Fel d 1) levels in schools and rhinitis and other weekly SBS symptoms in the students. Fungal DNA was measured by quantitative PCR and cat allergen by ELISA. Pupils (N = 462) from eight randomly selected schools in Johor Bahru, Malaysia participated (96%). Dust samples were collected by cotton swabs and Petri dishes exposed for one week. None of the schools had a mechanical ventilation system, but all classrooms had openable windows that were kept open during lectures and indoor CO2 levels were low (mean 492 ppm; range 380–690 ppm). Weekly nasal symptoms (rhinitis) (18.8%), ocular (11.6%), throat (11.1%), dermal symptoms, headache (20.6%) and tiredness (22.1%) were common. Total fungal DNA in swab samples was associated with rhinitis (p = 0.02), ocular symptoms (p = 0.009) and tiredness (p = 0.001). There were positive associations between Aspergillus versicolor DNA in Petri dish samples, ocular symptoms (p = 0.02) and tiredness (p = 0.001). The level of the mycotoxin verrucarol (produced by Stachybotrys chartarum) in swab samples was positively associated with tiredness (p = 0.04). Streptomyces DNA in swab samples (p = 0.03) and Petri dish samples (p = 0.03) were negatively associated with tiredness. In conclusion, total fungal contamination, measured as total fungal DNA) in the classrooms, Aspergillus versicolor and verrucarol can be risk factors for rhinitis and SBS symptoms among students in the tropical country Malaysia. PMID:26829324

Legionella prevalence and risk of legionellosis in Japanese households.

PubMed

Kuroki, T; Watanabe, Y; Teranishi, H; Izumiyama, S; Amemura-Maekawa, J; Kura, F

2017-05-01

This study determined the occurrence of legionellae in private houses for which there were no available data on aquatic environments other than the water supply system. From June 2013 to November 2014, we collected 138 water and 90 swab samples from aquatic environments in 19 houses. Legionella DNA was detected via a loop-mediated isothermal amplification assay in 66 (47·8%) water and 17 (18·9%) swab samples. High Legionella DNA detection rates were observed in water samples from washing machines and aquariums. Legionella spp. was isolated from 9 (6·5%) water and 3 (3·3%) swab samples. Legionella pneumophila SG 1 was detected from the outlet water of a bathtub spout and a bath sponge. Use of amoebic co-culture effectively increased legionellae and Legionella DNA detection rates from all sample types. A logistic regression analysis revealed that the heterotrophic plate count was significantly related to Legionella contamination. Our findings indicate that there is a risk of legionellosis from exposure to Legionella spp. in a variety of aquatic environments in residential houses. Control measures for legionellae in houses should include frequent cleaning and disinfecting to reduce heterotrophic bacteria in water and, where possible, preventing aerosolization from aquatic environments.

Transrectal rigid-hybrid NOTES cholecystectomy can be performed without peritoneal contamination: a controlled porcine survival study.

PubMed

Müller, Philip C; Senft, Jonas D; Gath, Philip; Steinemann, Daniel C; Nickel, Felix; Billeter, Adrian T; Müller-Stich, Beat P; Linke, Georg R

2018-01-01

The risk of infectious complications due to peritoneal contamination is a major concern and inhibits the widespread use of transrectal NOTES. A standardized rectal washout with a reversible colon occlusion device in situ has previously shown potential in reducing peritoneal contamination. The aim of this study was to compare the peritoneal contamination rate and inflammatory reaction for transrectal cholecystectomy after ideal rectal preparation (trCCE) and standard laparoscopic cholecystectomy (lapCCE) in a porcine survival experiment. Twenty pigs were randomized to trCCE (n = 10) or lapCCE (n = 10). Before trCCE, rectal washout was performed with saline solution. A colon occlusion device was then inserted and a second washout with povidone-iodine was performed. The perioperative course and the inflammatory reaction (leukocytes, C-reactive protein) were compared. At necropsy, 14 days after surgery the abdominal cavity was screened for infectious complications and peritoneal swabs were obtained for comparison of peritoneal contamination. Peritoneal contamination was lower after trCCE than after lapCCE (0/10 vs. 6/10; p = 0.003). No infectious complications were found at necropsy in either group and postoperative complications did not differ (p = 1.0). Immediately after the procedure, leukocytes were higher after lapCCE (17.0 ± 2.7 vs. 14.6 ± 2.3; p = 0.047). Leukocytes and C-reactive protein showed no difference in the further postoperative course. Intraoperative complications and total operation time (trCCE 114 ± 32 vs. 111 ± 27 min; p = 0.921) did not differ, but wound closure took longer for trCCE (31.5 ± 19 vs. 13 ± 5 min; p = 0.002). After standardized rectal washout with a colon occlusion device in situ, trCCE was associated without peritoneal contamination and without access-related infectious complications. Based on the findings of this study, a randomized controlled clinical study comparing clinical outcomes of trCCE with lapCCE should be conducted.

Human leukocyte antigen typing using buccal swabs as accurate and non-invasive substitute for venipuncture in children at risk for celiac disease.

PubMed

Adriaanse, Marlou P M; Vreugdenhil, Anita C E; Vastmans, Véronique; Groeneveld, Lisette; Molenbroeck, Stefan; Schott, Dina A; Voorter, Christina E M; Tilanus, Marcel G J

2016-10-01

Human leukocyte antigen (HLA) typing is an important step in the diagnostic algorithm for celiac disease (CD) and is also used for screening purposes. Collection of blood is invasive and accompanied with emotional impact especially in children. Genetic technological progress now enables HLA typing from buccal cell samples. This study evaluated the reliability and feasibility of HLA typing for CD-associated HLA polymorphisms using buccal swabs as routine test in high-risk individuals. Blood and buccal swabs of 77 children and adolescents with high risk for CD were prospectively collected in this cohort study. Buccal swab collection was performed either by the investigator at the outpatient clinic or by the patient or its parents at home. To evaluate the possibility of self-administration, three families performed the test at home. DNA was extracted using an adapted QIAamp method. Quantity, quality, and purity of DNA were recorded. HLA-DRB1, HLA-DQA1, and HLA-DQB1 typing was examined on buccal cell-derived and blood-derived DNA at low and, if necessary, high resolution level, using sequence-specific oligonucleotide and sequence-based typing, respectively. DNA isolation using buccal swabs yielded a good quality and sufficient quantity of DNA to perform HLA-DQ typing in all individuals. HLA typing results on buccal cell-derived DNA were identical to typing on blood-derived DNA, also for the self-administered samples. Introduction of the buccal swab test for HLA typing of CD risk in routine diagnostics can omit the current venipuncture and enables self-administration at home. Therefore, the buccal swab test is beneficial for individuals with a clinical suspicion for CD, as well as for screening purposes in high-risk populations. © 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Test performance and acceptability of self- versus provider-collected swabs for high-risk HPV DNA testing in female-to-male trans masculine patients

PubMed Central

Deutsch, Madeline B.; Peitzmeier, Sarah M.; White Hughto, Jaclyn M.; Cavanaugh, Timothy P.; Pardee, Dana J.; McLean, Sarah A.; Panther, Lori A.; Gelman, Marcy; Mimiaga, Matthew J.; Potter, Jennifer E.

2018-01-01

Background High-risk human papillomavirus (hrHPV) causes virtually all cervical cancers. Trans masculine (TM) people (those assigned female at birth who identify with a gender other than female) have low uptake of conventional cervical cancer screening. Self-collected hrHPV DNA testing has high levels of acceptability among cisgender (non-transgender) females and may support increased cervical cancer screening uptake in TM individuals. Objective To assess the test performance and acceptability of self-collected vaginal specimens in comparison to provider-collected cervical swabs for hrHPV DNA detection in TM individuals ages 21–64 years. Methods Between March 2015-September 2016, 150 TM participants with a cervix (mean age = 27.5 years; SD = 5.7) completed a one-time study visit comprised of a self-report survey, self-collected vaginal HPV DNA swab, clinician-administered cervical HPV swab, and brief interview on acceptability of clinical procedures. Participants were randomized to complete either self- or provider-collection first to minimize ordering effects. Self- and provider-collected samples were tested for 13 hrHPV DNA types using a DNA Hybridization Assay. The primary outcome variable was the concordance (kappa statistic) and performance (sensitivity, specificity) of self-collected vaginal HPV DNA specimens versus provider-collected cervical HPV swabs as the gold standard. Results Of the 131 participants completing both the self- and provider-collected HPV tests, 21 cases of hrHPV were detected by the provider cervical swab (gold standard; 16.0% hrHPV prevalence); 15 of these cases were accurately detected by the self-collected vaginal swab (71.4% concordance) (Kappa = 0.75, 95% Confidence Interval [CI]: 0.59, 0.92; p<0.001). Compared to the provider-collected cervical hrHPV DNA sample (gold standard), the self-collected vaginal hrHPV DNA test demonstrated a sensitivity of 71.4% (95% CI: 0.52, 0.91; p = 0.0495) and specificity of 98.2% (95% CI: 0.96, 1.00; p<0.0001). Over 90% of participants endorsed a preference for the self-collected vaginal swab over provider-collected cervical swab. Conclusion Self-collected vaginal swabs are highly acceptable to TM as a means to test for hrHPV DNA. Test performance of this self-collection method for hrHPV detection in TM is consistent with previous studies in cisgender females. Self-collected vaginal swab testing for hrHPV DNA represents a reasonable and patient-centered strategy for primary cervical cancer screening in TM patients unwilling to undergo provider collection of specimens via speculum exam. PMID:29538411

Comparative performance of contact plates, electrostatic wipes, swabs and a novel sampling device for the detection of Staphylococcus aureus on environmental surfaces.

PubMed

Lutz, J K; Crawford, J; Hoet, A E; Wilkins, J R; Lee, J

2013-07-01

To evaluate the performance of four sampling methods [contact plates, electrostatic wipes (wipe), swabs and a novel roller sampler] for recovery of Staphylococcus aureus from a stainless steel surface. Stainless steel test plates were inoculated with Staph. aureus, dried for 24 h and sampled using each of the four methods. Samples were either incubated directly (roller, contact plate) or processed using elution and membrane filtration (swab, wipe). Performance was assessed by calculating the apparent sampling efficiency (ASE), analytical sensitivity (Sn) and percentage of replications with positive growth. The wipe demonstrated the best performance across all inoculating concentrations (ASE(48 h) = 18%; Sn(48 h) = 7 CFU per 100 cm(2)). The swab performed well when corrected for area actually sampled (ASE(48 h) = 24%; Sn(48 h) = 76 CFU per 100 cm(2)). Of the contact-based methods, the newly developed roller sampler outperformed the contact plate (roller: ASE(48 h) = 10%; Sn(48 h) = 17 CFU per 100 cm(2); contact plate: ASE(48 h) = 0·04%; Sn(48 h) = 1412 CFU per 100 cm(2)); both contact samplers performed better at higher inoculating concentrations (6E3 CFU per 100 cm(2) for the roller and 6E6 CFU per 100 cm(2) for the contact plate). Overall, the electrostatic wipe produced the highest number of replications resulting in positive growth (74%(24 h), 91%(48 h)). This study demonstrates that selection of the sampling method must be carefully considered, given that different methods have varying performance. This is the first study assessing static wipes for sampling and one that uses a more real-world-relevant 24-h drying time. The results help with infection control, and environmental health professionals choose better sampling methodologies. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

Isolation of Campylobacter from Brazilian broiler flocks using different culturing procedures.

PubMed

Vaz, C S L; Voss-Rech, D; Pozza, J S; Coldebella, A; Silva, V S

2014-11-01

Conventional culturing methods enable the detection of Campylobacter in broiler flocks. However, laboratory culture of Campylobacter is laborious because of its fastidious behavior and the presence of competing nontarget bacteria. This study evaluated different protocols to isolate Campylobacter from broiler litter, feces, and cloacal and drag swabs. Samples taken from commercial Brazilian broiler flocks were directly streaked onto Preston agar (PA), Campy-Line agar (CLA), and modified charcoal cefoperazone deoxycholate agar (mCCDA) and also enriched in blood-free Bolton broth (bfBB) for 24 and 48 h followed by plating onto the different selective media. Higher numbers of Campylobacter-positive cloacal and drag swab samples were observed using either direct plating or enrichment for 24 h before plating onto PA, compared with enrichment for 48 h (P < 0.05). Furthermore, direct plating was a more sensitive method to detect Campylobacter in broiler litter and feces samples. Analysis of directly plated samples revealed that higher Campylobacter levels were detected in feces streaked onto PA (88.8%), cloacal swabs plated onto mCCDA (72.2%), drag swabs streaked onto CLA or mCCDA (69.4%), and litter samples inoculated onto PA (63.8%). Preston agar was the best agar to isolate Campylobacter from directly plated litter samples (P < 0.05), but there was no difference in the efficacies of PA, mCCDA, and CLA in detecting Campylobacter in other samples. The isolated Campylobacter strains were phenotypically identified as Campylobacter jejuni or Campylobacter coli. The predominant contaminant observed in the Campylobacter cultures was Proteus mirabilis, which was resistant to the majority of antimicrobial agents in selective media. Together, these data showed that direct plating onto PA and onto either CLA or mCCDA as the second selective agar enabled the reliable isolation of thermophilic Campylobacter species from broiler samples. Finally, Campylobacter was detected in all broiler flocks sampled. ©2014 Poultry Science Association Inc.

Fabrication of SERS swab for direct detection of trace explosives in fingerprints.

PubMed

Gong, Zhengjun; Du, Hongjie; Cheng, Fansheng; Wang, Cong; Wang, Canchen; Fan, Meikun

2014-12-24

Swab sampling is of great importance in surface contamination analysis. A cotton swab (cotton Q-tip) was successfully transformed into surface-enhanced Raman scattering (SERS) substrate (SERS Q-tip) through a bottom-up strategy, where Ag NPs were first self-assembled onto the Q-tip followed by in situ growing. The capability for direct swab detection of Raman probe Nile Blue A (NBA) and a primary explosive marker 2,4-dinitrotoluene (2,4-DNT) using the SERS Q-tip was explored. It was found that at optimum conditions, a femotogram of NBA on glass surface could be swab-detected. The lowest detectable amount for 2,4-DNT is only ∼1.2 ng/cm(2) (total amount of 5 ng) on glass surface, 2 orders of magnitude more sensitive than similar surface analysis achieved with infrared technique, and comparable even with that obtained by ion mobility spectrometry-mass spectrometry. Finally, 2,4-DNT left on fingerprints was also analyzed. It was found that SERS signal of 2,4-DNT from 27th fingerprint after touching 2,4-DNT powder can still be clearly identified by swabbing with the SERS Q-tip. We believe this is the first direct SERS swabbing test of explosives on fingerprint on glass. Considering its relative long shelf life (>30 d), the SERS Q-tip may find great potential in future homeland security applications when combined with portable Raman spectrometers.

Comparison between nasopharyngeal swab and nasal wash, using culture and PCR, in the detection of potential respiratory pathogens.

PubMed

Gritzfeld, Jenna F; Roberts, Paul; Roche, Lorna; El Batrawy, Sherouk; Gordon, Stephen B

2011-04-13

Nasopharyngeal carriage of potential pathogens is important as it is both the major source of transmission and the prerequisite of invasive disease. New methods for detecting carriage could improve comfort, accuracy and laboratory utility. The aims of this study were to compare the sensitivities of a nasopharyngeal swab (NPS) and a nasal wash (NW) in detecting potential respiratory pathogens in healthy adults using microbiological culture and PCR. Healthy volunteers attended for nasal washing and brushing of the posterior nasopharynx. Conventional and real-time PCR were used to detect pneumococcus and meningococcus. Statistical differences between the two nasal sampling methods were determined using a nonparametric Mann-Whitney U test; differences between culture and PCR methods were determined using the McNemar test.Nasal washing was more comfortable for volunteers than swabbing (n = 24). In detection by culture, the NW was significantly more likely to detect pathogens than the NPS (p < 0.00001). Overall, there was a low carriage rate of pathogens in this sample; no significant difference was seen in the detection of bacteria between culture and PCR methods. Nasal washing and PCR may provide effective alternatives to nasopharyngeal swabbing and classical microbiology, respectively.

Most Probable Number Rapid Viability PCR Method to Detect Viable Spores of Bacillus anthracis in Swab Samples

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

Letant, S E; Kane, S R; Murphy, G A

2008-05-30

This note presents a comparison of Most-Probable-Number Rapid Viability (MPN-RV) PCR and traditional culture methods for the quantification of Bacillus anthracis Sterne spores in macrofoam swabs generated by the Centers for Disease Control and Prevention (CDC) for a multi-center validation study aimed at testing environmental swab processing methods for recovery, detection, and quantification of viable B. anthracis spores from surfaces. Results show that spore numbers provided by the MPN RV-PCR method were in statistical agreement with the CDC conventional culture method for all three levels of spores tested (10{sup 4}, 10{sup 2}, and 10 spores) even in the presence ofmore » dirt. In addition to detecting low levels of spores in environmental conditions, the MPN RV-PCR method is specific, and compatible with automated high-throughput sample processing and analysis protocols.« less

A Field Investigation of Bacillus anthracis Contamination of U.S. Department of Agriculture and Other Washington, D.C., Buildings during the Anthrax Attack of October 2001

PubMed Central

Higgins, James A.; Cooper, Mary; Schroeder-Tucker, Linda; Black, Scott; Miller, David; Karns, Jeffrey S.; Manthey, Erlynn; Breeze, Roger; Perdue, Michael L.

2003-01-01

In response to a bioterrorism attack in the Washington, D.C., area in October 2001, a mobile laboratory (ML) was set up in the city to conduct rapid molecular tests on environmental samples for the presence of Bacillus anthracis spores and to route samples for further culture analysis. The ML contained class I laminar-flow hoods, a portable autoclave, two portable real-time PCR devices (Ruggedized Advanced Pathogen Identification Device [RAPID]), and miscellaneous supplies and equipment to process samples. Envelopes and swab and air samples collected from 30 locations in the metropolitan area once every three days were subjected to visual examination and DNA extraction, followed by real-time PCR using freeze-dried, fluorescent-probe-based reagents. Surface swabs and air samples were also cultured for B. anthracis at the National Veterinary Service Laboratory (NVSL) in Ames, Iowa. From 24 October 2001 to 15 September 2002, 2,092 pieces of mail were examined, 405 real-time PCR assays were performed (comprising 4,639 samples), and at the NVSL 6,275 samples were subjected to over 18,000 platings. None of the PCR assays on DNA extracted from swab and air samples were positive, but viable spores were cultured from surface swabs taken from six locations in the metropolitan area in October, November, and December 2001 and February, March, and May 2002. DNA extracted from these suspected B. anthracis colonies was positive by real-time and conventional PCRs for the lethal factor, pXO1, and for capA and vrr genes; sequence analysis of the latter amplicons indicated >99% homology with the Ames, vollum, B6273-93, C93022281, and W-21 strains of B. anthracis, suggesting they arose from cross-contamination during the attack through the mail. The RAPID-based PCR analysis provided fast confirmation of suspect colonies from an overnight incubation on agar plates. PMID:12514046

Dialysis of the rectum for sampling drug concentrations in the luminal extracellular fluid of the gut: technique and precision.

PubMed

Egan, L J; Sandborn, W J; Mays, D C; Tremaine, W J; Lipsky, J J

1998-07-01

It is useful to measure the luminal concentration of drugs which act in the gut. Dialysis of the rectum has not previously been used or validated for this purpose. To determine the precision of rectal dialysis for measuring rectal drug concentrations. To establish the duration of dialysis required to approach equilibrium, the rate of methotrexate diffusion into dialysis bags was first determined in vitro. The precision of rectal dialysis for sampling the methotrexate concentration of colonic lumen extracellular fluid was determined in seven subjects who underwent two consecutive dialysis procedures. Subjects treated with subcutaneous methotrexate for refractory inflammatory bowel disease were studied. Methotrexate crossed the dialysis membrane by a first-order process, and after a 2 h in vitro dialysis, equilibration was 74 +/- 2% (mean +/- s.d.) complete. Rectal dialysis was well tolerated by all subjects. The mean +/- s.e. methotrexate concentration of 3.6 +/- 1.1 nmol/L in the first dialysate was not significantly different from 3.6 +/- 0.9 nmol/L in the second dialysate. P = 0.99 (paired two-tailed t-test). Similar precision was obtained for an endogenous molecule, potassium, secreted by the rectal mucosa. Dialysis of the rectum is a well tolerated and precise technique for sampling the colonic lumen extracellular fluid for quantitative analyses of exogenous and endogenous substances.

Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions

PubMed Central

Stellato, Giuseppina; La Storia, Antonietta; De Filippis, Francesca; Borriello, Giorgia; Villani, Francesco

2016-01-01

ABSTRACT Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The aims of this study were to learn more about the possible influence of the meat processing environment on initial fresh meat contamination and to investigate the differences between small-scale retail distribution (SD) and large-scale retail distribution (LD) facilities. Samples were collected from butcheries (n = 20), including LD (n = 10) and SD (n = 10) facilities, over two sampling campaigns. Samples included fresh beef and pork cuts and swab samples from the knife, the chopping board, and the butcher's hand. The microbiota of both meat samples and environmental swabs were very complex, including more than 800 operational taxonomic units (OTUs) collapsed at the species level. The 16S rRNA sequencing analysis showed that core microbiota were shared by 80% of the samples and included Pseudomonas spp., Streptococcus spp., Brochothrix spp., Psychrobacter spp., and Acinetobacter spp. Hierarchical clustering of the samples based on the microbiota showed a certain separation between meat and environmental samples, with higher levels of Proteobacteria in meat. In particular, levels of Pseudomonas and several Enterobacteriaceae members were significantly higher in meat samples, while Brochothrix, Staphylococcus, lactic acid bacteria, and Psychrobacter prevailed in environmental swab samples. Consistent clustering was also observed when metabolic activities were considered by predictive metagenomic analysis of the samples. An increase in carbohydrate metabolism was predicted for the environmental swabs and was consistently linked to Firmicutes, while increases in pathways related to amino acid and lipid metabolism were predicted for the meat samples and were positively correlated with Proteobacteria. Our results highlighted the importance of the processing environment in contributing to the initial microbial levels of meat and clearly showed that the type of retail facility (LD or SD) did not apparently affect the contamination. IMPORTANCE The study provides an in-depth description of the microbiota of meat and meat processing environments. It highlights the importance of the environment as a contamination source of spoilage bacteria, and it shows that the size of the retail facility does not affect the level and type of contamination. PMID:27129965

Detection of atypical porcine pestivirus in semen from commercial boar studs in the United States.

PubMed

Gatto, I R H; Arruda, P H; Visek, C A; Victoria, J G; Patterson, A R; Krull, A C; Schwartz, K J; de Oliveira, L G; Arruda, B L

2018-04-01

Atypical porcine pestivirus (APPV) has recently been identified as a cause of congenital tremor (CT) in pigs and has been detected in semen and preputial swabs from boars that were known to be clinically affected with CT. Accordingly, the objectives of this study were to 1) detect the presence of APPV in semen, preputial fluids and preputial swabs from adult boars by quantitative reverse transcription PCR (qRT-PCR) and 2) genetically characterize a subset of positive samples to better understand the ecology of APPV in commercial boar studs and the potential risk of transmission of APPV via semen. A total of 597 samples of semen, preputial fluid and preputial swabs each representing a different boar were obtained from four commercial boar studs located in three different states in the United States. Viral RNA was detected by qRT-PCR in 90 samples (15.08%; 90/597), with the greatest per cent positive from preputial swabs (23.81%; 5/21) followed by preputial fluid (22.81%; 26/114) and semen (12.91%; 59/457). The mean cycle quantification (Cq) between sample types was similar while eleven semen samples had Cq values lower than 27.0 corresponding to approximately 2 × 10 6  copies/ml. Based on phylogenetic analysis of the Npro gene, different viral strains can be on the same farm at the same and different times. This is the first report of detection of APPV in semen from commercial boar studs. Studies investigating the role of semen in the transmission of APPV and production of CT are needed. © 2017 Blackwell Verlag GmbH.

In vivo trans-rectal ultrasound coupled trans-rectal near-infrared optical tomography of canine prostate bearing transmissible venereal tumor

NASA Astrophysics Data System (ADS)

Jiang, Zhen; Holyoak, G. Reed; Bartels, Kenneth E.; Ritchey, Jerry W.; Xu, Guan; Bunting, Charles F.; Slobodov, Gennady; Krasinski, Jerzy S.; Piao, Daqing

2009-02-01

In vivo trans-rectal near-infrared (NIR) optical tomography is conducted on a tumor-bearing canine prostate with the assistance of trans-rectal ultrasound (TRUS). The canine prostate tumor model is made possible by a unique round cell neoplasm of dogs, transmissible venereal tumor (TVT) that can be transferred from dog to dog regardless of histocompatibility. A characterized TVT cell line was homogenized and passed twice in subcutaneous tissue of NOD/SCID mice. Following the second passage, the tumor was recovered, homogenized and then inoculated by ultrasound guidance into the prostate gland of a healthy dog. The dog was then imaged with a combined trans-rectal NIR and TRUS imager using an integrated trans-rectal NIR/US applicator. The image was taken by NIR and US modalities concurrently, both in sagittal view. The trans-rectal NIR imager is a continuous-wave system that illuminates 7 source channels sequentially by a fiber switch to deliver sufficient light power to the relatively more absorbing prostate tissue and samples 7 detection channels simultaneously by a gated intensified high-resolution CCD camera. This work tests the feasibility of detecting prostate tumor by trans-rectal NIR optical tomography and the benefit of augmenting TRUS with trans-rectal NIR imaging.

[Performance of Cholera-SMART and Pathogen-Detection-Kit in the quick diagnosis of cholera].

PubMed

Bolaños, Hilda María; Acuña, María Teresa; Serrano, Ana María; Obando, Xinia; Mairena, Hazel; Cháves, Lorena; Sandí, Flor; Rodríguez, Gina; Tamplin, Mark L; Pérez, Enrique; Campos, Elena

2004-10-01

To compare the performance of two rapid systems for the diagnosis of cholera with the culture method, and to propose a strategy for improving the specificity and sensitivity of these systems and reducing the costs involved in making a diagnosis. The following institutions participated in the study: the National Bacteriology Referral Center (Centro Nacional de Referencia en Bacteriologia, CNRB) of the Costa Rican Institute for Research and Teaching in Nutrition and Health (Instituto Costarricense de Investigacion y Ensenanza en Nutricion y Salud, INCIENSA) and various hospitals in the provinces of Alajuela, Guanacaste and San Jose, in Costa Rica. A total of 237 feces samples were used to asses the performance of two tests for the rapid detection of Vibrio cholerae 01: the Pathogen Detection Kit (PDK, Intelligent Monitoring Systems, Gainesville, Florida, USA) and Cholera-SMART (New Horizons Diagnostics Corp., Columbia, Maryland, USA), both when applied directly (direct SMART and direct PDK) and when applied to specimens cultured in broth-enriched medium for 6 hours (SMART-6 and CPK-6) and for 18 hours (SMART-18 and PDK-18) at 37 degrees C in alkaline peptone water. Liquid and partially formed stools were cultured and examined by means of the rapid direct test; when the initial result was negative, the tests were repeated after culture for periods of 6 and 18 hours. Rectal and fecal swabs were obtained from feces cultured in enriched-broth medium for 6 and 18 hours. In addition, we studied the sensitivity of the rapid testing systems by using pure cultures of V. cholerae 01 (strain SOS-833, CNRB, Costa Rica) that were incubated for 18 to 24 hours, and we assessed the usefulness of observing motility under the microscope in order to rationalize the use of rapid methods. The sensitivity of the direct SMART test and of the direct PDK test was 100% when samples obtained from liquid and partially formed stools and from the intestinal contents of dead bodies were used. With these samples, the direct SMART procedure showed a specificity of 100%, whereas the direct PDK procedure showed a specificity that ranged from 85.7% to 77.4%, depending on the type of sample. False positives obtained with the direct PDK method turned out to be negative with PDK-6 and PDK-18. Among the rectal and fecal swabs of persons with and without diarrhea or who had received prior treatment with antibiotics, three results that were negative with the SMART-6 procedure and two that were negative with the PDK-6 procedure turned out to be positive with the SMART-18 and PDK-18 procedures, respectively. Both systems showed excellent concordance (kappa index above 0.9) throughout. Both systems were sensitive to 6 x 10(7) colony-forming units per milliliter (cfu/mL), which was concordant with the microscopic observation of 10 microorganisms or more per field with the type of motility that characterizes vibrios (at 1000 x magnification). Samples having fewer than 10 microorganisms with the motility that characterizes vibrios had concentrations between 6 x 10(3) and 6 x 10(6) cfu/mL and became positive only after incubation in enriched-broth medium for 6 to 18 hours. We propose a strategy for diagnosing the presence of V. cholerae 01 infection in less time than it takes with traditional methods, with positive and negative predictive values of 100%. The SMART and PDK systems make it possible to accurately diagnose cholera quickly, don't require sophisticated equipment or highly qualified technical personnel, and perform satisfactorily in field conditions. Through the proposed strategy, it becomes possible to improve the specificity and sensitivity of these systems and to reduce the cost of making a diagnosis, thus making them suitable for use in cholera surveillance in low-income settings where this disease is a serious public health problem.

Chemoradiotherapy response in recurrent rectal cancer.

PubMed

Yu, Stanley K T; Bhangu, Aneel; Tait, Diana M; Tekkis, Paris; Wotherspoon, Andrew; Brown, Gina

2014-02-01

The efficacy of response to preoperative chemoradiotherapy (CRT) in recurrent versus primary rectal cancer has not been investigated. We compared radiological downsizing between primary and recurrent rectal cancers following CRT and determined the optimal size reduction threshold for response validated by survival outcomes. The proportional change in tumor length for primary and recurrent rectal cancers following CRT was compared using the independent sample t-test. Overall survival (OS) was calculated using the Kaplan-Meier product limit method and differences between survival for tumor size reduction thresholds of 30% (response evaluation criteria in solid tumors [RECIST]), 40%, and 50% after CRT in primary and recurrent rectal cancer groups. A total of 385 patients undergoing CRT were analyzed, 99 with recurrent rectal cancer and 286 with primary rectal cancer. The mean proportional reduction in maximum craniocaudal length was significantly higher for primary rectal tumors (33%) compared with recurrent rectal cancer (11%) (P < 0.01). There was no difference in OS for either primary or recurrent rectal cancer when ≤30% or ≤40% definitions were used. However, for both primary and recurrent tumors, significant differences in median 3-year OS were observed when a RECIST cut-off of 50% was used. OS was 99% versus 77% in primary and 100% versus 42% in recurrent rectal cancer (P = 0.002 and P = 0.03, respectively). Only patients that demonstrated >50% size reduction showed a survival benefit. Recurrent rectal cancer appears radioresistant compared with primary tumors for tumor size after CRT. Further investigation into improving/intensifying chemotherapy and radiotherapy for locally recurrent rectal cancer is justified. © 2013 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Influence of the Environment on Body Temperature of Racing Greyhounds.

PubMed

McNicholl, Jane; Howarth, Gordon S; Hazel, Susan J

2016-01-01

Heat strain is a potential risk factor for racing greyhounds in hot climates. However, there have been limited studies into the incidence of heat strain (when excess heat causes physiological or pathological effects) in racing greyhounds. The aim of this study was to determine if heat strain occurs in racing greyhounds, and, if so, whether environmental factors (e.g., ambient temperature and relative humidity) or dog-related factors (e.g., sex, bodyweight, color) are associated with the risk of heat strain. A total of 229 greyhounds were included in over 46 race meetings and seven different race venues in South Australia, Australia. Rectal temperatures of dogs were measured pre- and postrace and urine samples collected for analysis of myoglobinuria. Ambient temperature at race times ranged between 11.0 and 40.8°C and relative humidity ranged from 17 to 92%. There was a mean increase in greyhound rectal temperature of 2.1°C (range 1.1-3.1°C). A small but significant association was present between ambient temperature and increase in rectal temperature (r (2) = 0.033, P = 0.007). The mean ambient temperature at race time, of dogs with postrace rectal temperature of or exceeding 41.5°C, was significantly greater than at race time of dogs with a postrace rectal temperature ≤41.5°C (31.2 vs. 27.3°C, respectively, P = 0.004). When the ambient temperature reached 38(o)C, over one-third (39%) of dogs had a rectal temperature >41.5°C. Over half of postrace urine samples were positive by Dipstick reading for hemoglobin/myoglobin, and of 77 urine samples positive for Dipstick readings, 95% were positive for myoglobin. However, urinary myoglobin levels were not associated with ambient temperature or postrace rectal temperatures. The mean increase in rectal temperature was greater in dark (black, blue, brindle) than light (fawn and white) colored greyhounds. The results suggest heat strain occurs in racing greyhounds, evidenced by postrace rectal temperatures over 41.5°C and postrace myoglobinuria. Risk of heat strain may be increased in higher ambient temperatures and in darker colored greyhounds. Further research into the incidence of heat strain in racing greyhounds, and longer term physiological responses to heat strain, are warranted.

Influence of the Environment on Body Temperature of Racing Greyhounds

PubMed Central

McNicholl, Jane; Howarth, Gordon S.; Hazel, Susan J.

2016-01-01

Heat strain is a potential risk factor for racing greyhounds in hot climates. However, there have been limited studies into the incidence of heat strain (when excess heat causes physiological or pathological effects) in racing greyhounds. The aim of this study was to determine if heat strain occurs in racing greyhounds, and, if so, whether environmental factors (e.g., ambient temperature and relative humidity) or dog-related factors (e.g., sex, bodyweight, color) are associated with the risk of heat strain. A total of 229 greyhounds were included in over 46 race meetings and seven different race venues in South Australia, Australia. Rectal temperatures of dogs were measured pre- and postrace and urine samples collected for analysis of myoglobinuria. Ambient temperature at race times ranged between 11.0 and 40.8°C and relative humidity ranged from 17 to 92%. There was a mean increase in greyhound rectal temperature of 2.1°C (range 1.1–3.1°C). A small but significant association was present between ambient temperature and increase in rectal temperature (r2 = 0.033, P = 0.007). The mean ambient temperature at race time, of dogs with postrace rectal temperature of or exceeding 41.5°C, was significantly greater than at race time of dogs with a postrace rectal temperature ≤41.5°C (31.2 vs. 27.3°C, respectively, P = 0.004). When the ambient temperature reached 38oC, over one-third (39%) of dogs had a rectal temperature >41.5°C. Over half of postrace urine samples were positive by Dipstick reading for hemoglobin/myoglobin, and of 77 urine samples positive for Dipstick readings, 95% were positive for myoglobin. However, urinary myoglobin levels were not associated with ambient temperature or postrace rectal temperatures. The mean increase in rectal temperature was greater in dark (black, blue, brindle) than light (fawn and white) colored greyhounds. The results suggest heat strain occurs in racing greyhounds, evidenced by postrace rectal temperatures over 41.5°C and postrace myoglobinuria. Risk of heat strain may be increased in higher ambient temperatures and in darker colored greyhounds. Further research into the incidence of heat strain in racing greyhounds, and longer term physiological responses to heat strain, are warranted. PMID:27446941

[NOTES ASSISTED ENDOLUMENAL RECTAL RESECTION AND SPECIMEN EXTRACTION WITHOUT RECTAL STUMP OPENING - OUR EXPERIENCE WITH THIS NOVEL TECHNIQUE IN A PORCINE MODEL].

PubMed

Kvasha, Anton; Rosenthal, Eyal; Khalifa, Muhammad; Waksman, Igor

2017-05-01

Laparoscopic surgery has long been used for colon and rectal resection, and the laparoscopic-assisted approach has prevailed in surgical practice. While this technique includes the fashioning of an intra-corporeal anastomosis, it still requires an abdominal incision for specimen extraction. Elimination of the abdominal incision and its potential complications has been the motivation for the development of natural orifice specimen extraction (NOSE) techniques. Many of these techniques make use of an open rectal stump, which poses as a potential for intra-abdominal contamination. Our group has recently described a novel, NOTES assisted, clean, endoluminal rectal resection utilizing transabdominal and transanal approaches. In this paper we report the combined experience of two study groups: an open approach to the abdominal cavity and a laparoscopic approach to the peritoneal cavity. Ten female pigs were used for this research; 5 in a group using an open approach and 5 using a laparoscopic approach for the abdominal part of the procedure. During the procedure, the rectum was mobilized. An end-to-end circular stapler was used to create a recto-rectal intussusception and pull-through (IPT). The specimen was resected and extracted by making a full thickness incision through 2 bowel walls. The stapler was applied, and a recto-rectal anastomosis created. This was allowed to retract into the abdomen. Peritoneal fluid was sampled for bacteria, the pigs were sacrificed immediately after the experiment and necropsy was performed. All 10 pigs underwent an endoluminal rectal resection utilizing the trans-anal IPT technique. The proximal and distal resection margins remained approximated over the shaft of the anvil after bowel resection in all 10 subjects. A 2- to 4-mm resection margin, distal to the ligatures was accomplished consistently in all 10 subjects. No aerobic or anaerobic bacterial growth was observed in any of the peritoneal fluid samples. Our research demonstrated the feasibility of the described technique in both open and laparoscopic approaches to a clean endoluminal bowel resection and trans-anal specimen extraction without rectal stump opening. The fact that no bacterial growth was found in any of the peritoneal samples supports the initial classification of this novel technique as clean, as opposed to clean contaminated, which classifies all other techniques in use to date.

Beyond the swab: ecosystem sampling to understand the persistence of an amphibian pathogen.

PubMed

Mosher, Brittany A; Huyvaert, Kathryn P; Bailey, Larissa L

2018-06-02

Understanding the ecosystem-level persistence of pathogens is essential for predicting and measuring host-pathogen dynamics. However, this process is often masked, in part due to a reliance on host-based pathogen detection methods. The amphibian pathogens Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) are pathogens of global conservation concern. Despite having free-living life stages, little is known about the distribution and persistence of these pathogens outside of their amphibian hosts. We combine historic amphibian monitoring data with contemporary host- and environment-based pathogen detection data to obtain estimates of Bd occurrence independent of amphibian host distributions. We also evaluate differences in filter- and swab-based detection probability and assess inferential differences arising from using different decision criteria used to classify samples as positive or negative. Water filtration-based detection probabilities were lower than those from swabs but were > 10%, and swab-based detection probabilities varied seasonally, declining in the early fall. The decision criterion used to classify samples as positive or negative was important; using a more liberal criterion yielded higher estimates of Bd occurrence than when a conservative criterion was used. Different covariates were important when using the liberal or conservative criterion in modeling Bd detection. We found evidence of long-term Bd persistence for several years after an amphibian host species of conservation concern, the boreal toad (Anaxyrus boreas boreas), was last detected. Our work provides evidence of long-term Bd persistence in the ecosystem, and underscores the importance of environmental samples for understanding and mitigating disease-related threats to amphibian biodiversity.

How to use: bacterial cultures in diagnosing lower respiratory tract infections in cystic fibrosis.

PubMed

Ahmed, Bushra; Bush, Andrew; Davies, Jane C

2014-10-01

Respiratory infections are the leading cause of morbidity and mortality in cystic fibrosis. Certain bacteria, such as Pseudomonas aeruginosa, are associated with a worse clinical outcome than others, but can be completely eradicated if identified and treated early. The diagnosis of lower respiratory tract infections can be challenging in the non-expectorating patient, in whom upper airway samples, such as cough swabs, are a surrogate for lower airway sampling. However, the results of these often do not fit with the clinical picture, presenting a management dilemma. Frequently, clinicians are faced with a negative culture result in a progressively symptomatic patient and vice versa. When judging the clinical significance of a positive upper airway culture result in an asymptomatic patient, it is important to consider the prognostic significance of the organism cultured. Given that the reported sensitivity of upper airway swabs (which includes throat swabs) is variable, ranging from 35.7% to 71% for Pseudomonas aeruginosa, 50% to 86% for Staphylococcus aureus and 11% to 92% for Haemophilus influenza, upper airway samples may fail to identify lower airway infections. Therefore, in symptomatic children, a repeatedly negative upper airway swab should not be considered as reassuring, and alternative sampling methods, such as induced sputum or bronchoalveolar lavage, should be considered. Here we use some examples of common scenarios to illustrate how best to use bacterial cultures to aid management decisions in cystic fibrosis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Chlamydophila psittaci in free-living Blue-fronted Amazon parrots (Amazona aestiva) and Hyacinth macaws (Anodorhynchus hyacinthinus) in the Pantanal of Mato Grosso do Sul, Brazil.

PubMed

de Freitas Raso, Tânia; Seixas, Gláucia Helena Fernandes; Guedes, Neiva Maria Robaldo; Pinto, Aramis Augusto

2006-10-31

Chlamydophila psittaci (C. psittaci) infection was evaluated in 77 free-living nestlings of Blue-fronted Amazon parrots (Amazona aestiva) and Hyacinth macaws (Anodorhynchus hyacinthinus) in the Pantanal of Mato Grosso do Sul, Brazil. Tracheal and cloacal swab samples from 32 wild parrot and 45 macaw nestlings were submitted to semi-nested PCR, while serum samples were submitted to complement fixation test (CFT). Although all 32 Amazon parrot serum samples were negative by CFT, cloacal swabs from two birds were positive for Chlamydophila DNA by semi-nested PCR (6.3%); these positive birds were 32 and 45 days old. In macaws, tracheal and cloacal swabs were positive in 8.9% and 26.7% of the samples, respectively. Complement-fixing antibodies were detected in 4.8% of the macaw nestlings; macaw nestlings with positive findings were between 33 and 88 days old. These results indicate widespread dissemination of this pathogen in the two evaluated psittacine populations. No birds had clinical signs suggestive of chlamydiosis. To the best of our knowledge, this is the first report on C. psittaci in free-living Blue-fronted Amazon parrots and Hyacinth macaws in Brazil.

Novel Parvovirus Related to Primate Bufaviruses in Dogs.

PubMed

Martella, Vito; Lanave, Gianvito; Mihalov-Kovács, Eszter; Marton, Szilvia; Varga-Kugler, Renáta; Kaszab, Eszter; Di Martino, Barbara; Camero, Michele; Decaro, Nicola; Buonavoglia, Canio; Bányai, Krisztián

2018-06-01

A novel protoparvovirus species, related genetically to human bufaviruses, was identified in dogs with respiratory signs. The canine bufavirus was distantly related to the well-known canine protoparvovirus, canine parvovirus type 2, sharing low amino acid identities in the nonstructural protein 1 (40.6%) and in the capsid protein 1 (33.4%). By screening collections of fecal, nasal, and oropharyngeal samples obtained from juvenile dogs (<1 year of age), canine bufavirus DNA appeared as a common component of canine virome. The virus was common in the stool samples of dogs with or without enteric disease and in the nasal and oropharyngeal swab samples of dogs with respiratory signs. However, the virus was not detected in nasal and oropharyngeal swab samples from animals without clinical signs.

Highly diverse MLVA-ompA genotypes of rectal Chlamydia trachomatis among men who have sex with men in Brighton, UK and evidence for an HIV-related sexual network.

PubMed

Labiran, Clare; Marsh, Peter; Zhou, Judith; Bannister, Alan; Clarke, Ian Nicholas; Goubet, Stephanie; Soni, Suneeta

2016-06-01

In this prospective study, we aimed to determine the distribution of genotypes by multilocus variable number tandem repeat (VNTR) analysis plus analysis of the ompA gene (MLVA-ompA) of rectal Chlamydia trachomatis among men who have sex with men (MSM) attending Brighton Genitourinary Medicine (GUM) Clinic and to examine any correlations with clinical variables, including HIV status, and to isolate rectal C. trachomatis cultures maximising the possibility of obtaining complete genotyping data. Samples were assigned genotypes by PCR and sequencing of the markers of the MLVA-ompA genotyping system. Rectal C. trachomatis was isolated in cell culture using McCoy cells. Data regarding demographics, HIV status, rectal symptoms and history of sexually transmitted infections, including C. trachomatis, were collected. 1809 MSM attending the clinic between October 2011 and January 2013 took part in the study, 112 (6.2%) of whom had rectal samples that tested positive for C. trachomatis. 85/112 (75.9%) C. trachomatis-positive rectal samples were assigned 66 different genotypes. Two distinct genotype subclusters were identified: subcluster 1 consisted of more HIV-negative men than subcluster 2 (p=0.025), and the MLVA-ompA genotypes in these subclusters reflected this. Isolates were successfully cultured from 37 of the 112 specimens, from which 27 otherwise unobtainable (from direct PCR) MLVA-ompA genotypes were gained. The most prevalent genotypes were G, E and D representing some overlap with the heterosexual distribution in UK. Subcluster 1 consisted of more 'heterosexual genotypes' and significantly more HIV-negative men than subcluster 2, associated with 'MSM genotypes'. There was a higher diversity of C. trachomatis strains among MSM in Brighton than observed in other cities. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Dual Intervention to Increase Chlamydia Retesting: A Randomized Controlled Trial in Three Populations.

PubMed

Smith, Kirsty S; Hocking, Jane S; Chen, Marcus Y; Fairley, Christopher K; McNulty, Anna M; Read, Phillip; Bradshaw, Catriona S; Tabrizi, Sepehr N; Wand, Handan; Saville, Marion; Rawlinson, William; Garland, Suzanne M; Donovan, Basil; Kaldor, John M; Guy, Rebecca J

2015-07-01

Chlamydia retesting 3 months after treatment is recommended to detect reinfections, but retesting rates are typically low. The purpose of this study is to determine if the addition of a postal home collection kit to a short message service (SMS) reminder at 3 months increases the percentage of patients retested for chlamydia at 1-4 months, compared to SMS alone. In this unblinded randomized controlled trial, participants were randomized 1:1 to intervention (home arm) or control (clinic arm) status. Participants included 200 each of women, heterosexual men, and men who have sex with men diagnosed and treated for chlamydia at sexual health services. Three months after chlamydia diagnosis, home arm participants received an SMS reminder and postal home collection kit (women, vaginal swab; heterosexual men, Copan UriSwab; men who have sex with men, UriSwab and rectal swab). The main outcome measures were the percentage of participants retested at 1-4 months after chlamydia diagnosis and the percentage in each arm with repeat positive tests, by risk group and overall, analyzed by intention to treat. Data were collected from 2011 to 2013 and analyzed in 2014. The percentage retested within 1-4 months of chlamydia diagnosis was significantly higher in home versus clinic arm participants among women (64% [66/103] vs 39% [38/97], p<0.001); heterosexual men (56% [57/101] vs 34% [34/99], p=0.002); men who have sex with men (62% [61/98] vs 44% [45/102], p=0.010); and overall (61% [184/302] vs 39% [117/298], p<0.001). The percentage in the home versus clinic arm with repeat positive tests was significantly higher among men who have sex with men (16% [16/98] vs 5% [5/102], p=0.021) and overall (10% [31/302] vs 4% [12/298], p=0.006). The addition of a postal home collection kit to routine SMS reminders resulted in substantial improvements in chlamydia retesting rates in all three risk groups and detection of more repeat positive tests, compared with SMS alone. Extending the intervention to other primary care settings with low retesting rates should be considered. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

Salmonella spp. contamination in commercial layer hen farms using different types of samples and detection methods.

PubMed

Soria, M C; Soria, M A; Bueno, D J; Godano, E I; Gómez, S C; ViaButron, I A; Padin, V M; Rogé, A D

2017-08-01

The performance of detection methods (culture methods and polymerase chain reaction assay) and plating media used in the same type of samples were determined as well as the specificity of PCR primers to detected Salmonella spp. contamination in layer hen farms. Also, the association of farm characteristics with Salmonella presence was evaluated. Environmental samples (feces, feed, drinking water, air, boot-swabs) and eggs were taken from 40 layer hen houses. Salmonella spp. was most detected in boot-swabs taken around the houses (30% and 35% by isolation and PCR, respectively) follow by fecal samples (15.2% and 13.6% by isolation and PCR, respectively). Eggs, drinking water, and air samples were negative for Salmonella detection. Salmonella Schwarzengrund and S. Enteritidis were the most isolated serotypes. For plating media, relative specificity was 1, and the relative sensitivity was greater for EF-18 agar than XLDT agar in feed and fecal samples. However, relative sensitivity was greater in XLDT agar than EF-18 agar for boot-swab samples. Agreement was between fair to good depending on the sample, and it was good between isolation and PCR (feces and boot-swabs), without agreement for feed samples. Salmonella spp. PCR was positive for all strains, while S. Typhimurium PCR was negative. Salmonella Enteritidis PCR used was not specific. Based in the multiple logistic regression analyses, categorization by counties was significant for Salmonella spp. presence (P-value = 0.010). This study shows the importance of considering different types of samples, plating media and detection methods during a Salmonella spp. monitoring study. In addition, it is important to incorporate the sampling of floors around the layer hen houses to learn if biosecurity measures should be strengthened to minimize the entry and spread of Salmonella in the houses. Also, the performance of some PCR methods and S. Enteritidis PCR should be improved, and biosecurity measures in hen farms must be reinforced in the region of more concentrated layer hen houses to reduce the probability of Salmonella spp. presence. © 2017 Poultry Science Association Inc.

A proof of concept study to assess the potential of PCR testing to detect natural Mycobacterium bovis infection in South American camelids.

PubMed

Crawshaw, Timothy R; Chanter, Jeremy I; McGoldrick, Adrian; Line, Kirsty

2014-02-07

Cases of Mycobacterium bovis infection South American camelids have been increasing in Great Britain. Current antemortem immunological tests have some limitations. Cases at post mortem examination frequently show extensive pathology. The feasibility of detecting Mycobacterium bovis DNA in clinical samples was investigated. A sensitive extraction methodology was developed and used on nasal swabs and faeces taken post-mortem to assess the potential for a PCR test to detect Mycobacterium bovis in clinical samples. The gross pathology of the studied South American camelids was scored and a significantly greater proportion of South American camelids with more severe pathology were positive in both the nasal swab and faecal PCR tests. A combination of the nasal swab and faecal PCR tests detected 63.9% of all the South American camelids with pathology that were tested. The results suggest that antemortem diagnosis of Mycobacterium bovis in South American camelids may be possible using a PCR test on clinical samples, however more work is required to determine sensitivity and specificity, and the practicalities of applying the test in the field.

Study of the prevalence and association of ocular chlamydial conjunctivitis in women with genital infection by Chlamydia trachomatis, Mycoplasma genitalium and Candida albicans attending outpatient clinic.

PubMed

Khattab, Rania Abdelmonem; Abdelfattah, Maha Mohssen

2016-01-01

To determine the association between chlamydial conjunctivitis and genital infection by Chlamydia trachomatis, Mycoplasma genitalium and Candida albicans, in addition to the possible relationship between cultured bacterial pathogens and oculogenital chlamydial infection. This study was performed on 100 (50 symptomatic and 50 asymptomatic) women attending the Gynecological and Obstetric outpatient clinic of Alzahra hospital, Alazhar University. Simultaneously a conjunctival swab was taken from these patients. Polymerase chain reaction (PCR) was done on DNA extracted from both vaginal and conjunctival swab samples. Culture for both vaginal and conjunctival swabs was also done. Candida albicans was the predominant organism isolated by culture in 20% and 40% of conjunctival and vaginal swabs respectively. By the PCR method, ocular Chlamydia trachomatis was present in 60% of symptomatic women, while genital Chlamydia trachomatis infection was present in 30% of symptomatic women. The results of this method also indicated that 25/50 (50%) vaginal swabs were positive with PCR for Candida albicans versus 15/50 (30%) were PCR positive in conjunctival swab. Mycoplasma genitalium was present in only 10% of vaginal swabs. Concomitant oculogenital PCR positive results for Chlamydia trachomatis and Candida albicans were 30% and 28% respectively. Ocular Chlamydia trachomatis was associated with genital Chlamydia trachomatis in a high percentage of women followed by Candida albicans. Cultured bacterial organisms do not play a role in enhancement of Chlamydia trachomatis infection.

Rapid Detection of Staphylococcus aureus and Methicillin-Resistant S. aureus in Atopic Dermatitis by Using the BD Max StaphSR Assay.

PubMed

Lee, Mi Kyung; Park, Kui Young; Jin, Taewon; Kim, Ju Hee; Seo, Seong Jun

2017-07-01

Eczematous lesions of atopic dermatitis (AD) patients are known to be a source of Staphylococcus aureus (SA) transmission and might be a reservoir for community-associated methicillin-resistant SA (MRSA). The BD Max StaphSR (BD-SR) is a fully automated, multiplex real-time PCR assay for the direct detection and differentiation of SA and MRSA from nasal swab samples. We evaluated the detection rates of SA and MRSA from skin lesions of outpatients with AD using the BD-SR assay, and determined the usefulness of the BD-SR assay. A total of 244 skin swab samples (skin lesions of 213 outpatients with AD and normal skin of 31 healthy controls) were tested directly by using the BD-SR assay. Of the 213 samples from patients with AD, 69 (32.4%) were positive for SA, 6 (8.7%) of which were positive for MRSA. Only 1 (3.2%) of 31 samples from healthy controls was positive for SA. The BD-SR assay is effective for the rapid detection of SA and MRSA from skin swab samples, which can provide important information for managing patients with AD and preventing the spread of MRSA. © The Korean Society for Laboratory Medicine.

Fluoroquinolone-resistant Escherichia coli carriage in long-term care facility.

PubMed

Maslow, Joel N; Lee, Betsy; Lautenbach, Ebbing

2005-06-01

We conducted a cross-sectional study to determine the prevalence of, and risk factors for, colonization with fluoroquinolone (FQ)-resistant Escherichia coli in residents in a long-term care facility. FQ-resistant E. coli were identified from rectal swabs for 25 (51%) of 49 participants at study entry. On multivariable analyses, prior FQ use was the only independent risk factor for FQ-resistant E. coli carriage and was consistent for FQ exposures in the previous 3, 6, 9, or 12 months. Pulsed-field gel electrophoresis of FQ-resistant E. coli identified clonal spread of 1 strain among 16 residents. Loss (6 residents) or acquisition (7 residents) of FQ-resistant E. coli was documented and was associated with de novo colonization with genetically distinct strains. Unlike the case in the hospital setting, FQ-resistant E. coli carriage in long-term care facilities is associated with clonal spread.

Fluoroquinolone-resistant Escherichia coli Carriage in Long-Term Care Facility

PubMed Central

Lee, Betsy; Lautenbach, Ebbing

2005-01-01

We conducted a cross-sectional study to determine the prevalence of, and risk factors for, colonization with fluoroquinolone (FQ)-resistant Escherichia coli in residents in a long-term care facility. FQ-resistant E. coli were identified from rectal swabs for 25 (51%) of 49 participants at study entry. On multivariable analyses, prior FQ use was the only independent risk factor for FQ-resistant E. coli carriage and was consistent for FQ exposures in the previous 3, 6, 9, or 12 months. Pulsed-field gel electrophoresis of FQ-resistant E. coli identified clonal spread of 1 strain among 16 residents. Loss (6 residents) or acquisition (7 residents) of FQ-resistant E. coli was documented and was associated with de novo colonization with genetically distinct strains. Unlike the case in the hospital setting, FQ-resistant E. coli carriage in long-term care facilities is associated with clonal spread. PMID:15963284

Analysis of the VP2 protein gene of canine parvovirus strains from affected dogs in Japan.

PubMed

Soma, Takehisa; Taharaguchi, Satoshi; Ohinata, Tsuyoshi; Ishii, Hiroshi; Hara, Motonobu

2013-04-01

To clarify the evolution of canine parvovirus 2 (CPV-2) that has recently been epidemic in Japan, VP2 gene sequences at positions 3556-4166 were analyzed in 107 CPV-2 strains obtained from rectal swabs of diarrheic dogs from 2009 to 2011. CPV-2b (95 strains) was more frequently detected than CPV-2a (nine strains), while CPV-2c was not detected. Remaining three strains were identified as the original type CPV-2, which should be derived from vaccines. These findings are similar to the previous results involving Japanese strains, suggesting there has been no great change in the recent CPV-2 epidemic in Japan. This epidemic is the same as that in Taiwan. Furthermore, a 324-lle mutant, which has been reported in Korean and Chinese strains, was detected in 66.7% of CPV-2a strains. Copyright © 2012 Elsevier Ltd. All rights reserved.

Coronavirus infections in horses in Saudi Arabia and Oman.

PubMed

Hemida, M G; Chu, D K W; Perera, R A P M; Ko, R L W; So, R T Y; Ng, B C Y; Chan, S M S; Chu, S; Alnaeem, A A; Alhammadi, M A; Webby, R J; Poon, L L M; Balasuriya, U B R; Peiris, M

2017-12-01

Equine coronaviruses (ECoV) are the only coronavirus known to infect horses. So far, data on ECoV infection in horses remain limited to the USA, France and Japan and its geographic distribution is not well understood. We carried out RT-PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. We document evidence of infection with ECoV and HKU23 coronavirus by RT-PCR. There was no conclusive evidence of Middle East respiratory syndrome coronavirus infection in horses. Serological data suggest that lineage A betacoronavirus infections are commonly infecting horses in Saudi Arabia and Oman but antibody cross-reactivities between these viruses do not permit us to use serological data alone to identify which coronaviruses are causing these infections. © 2017 Blackwell Verlag GmbH.

Antigenic typing of canine parvovirus using differential PCR.

PubMed

Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P N; Sharma, N S

2014-12-01

Canine parvovirus (CPV) is an enteric pathogen causing hemorrhagic enteritis in pups of 3-6 months of age and is mainly transmitted via feco-oral route. In the present study, a total of 85 animals rectal swabs suspected of CPV were tested using a PCR, nested PCR and a newly designed differential PCR. Using PCR 7 (8.23 %) animals were positive whereas 39 (45.88 %) were positive by using nested PCR and 40 (47.05 %) were positive for either one or more than one antigenic types of CPV using differential PCR. Using differential PCR it was found that CPV-2a and CPV-2b were the most prevailing antigenic types. Also it was found that dogs that were vaccinated too yielded positive CPV indicating a possible presence of additional CPV antigenic types. Thus, the primers used in differential PCR can be used in a single PCR reaction to detect various antigenic types of CPV.

Detection of West Nile virus and tick-borne encephalitis virus in birds in Slovakia, using a universal primer set.

PubMed

Csank, Tomáš; Bhide, Katarína; Bencúrová, Elena; Dolinská, Saskia; Drzewnioková, Petra; Major, Peter; Korytár, Ľuboš; Bocková, Eva; Bhide, Mangesh; Pistl, Juraj

2016-06-01

West Nile virus (WNV) is a mosquito-borne neurotropic pathogen that presents a major public health concern. Information on WNV prevalence and circulation in Slovakia is insufficient. Oral and cloacal swabs and bird brain samples were tested for flavivirus RNA by RT-PCR using newly designed generic primers. The species designation was confirmed by sequencing. WNV was detected in swab and brain samples, whereas one brain sample was positive for tick-borne encephalitis virus (TBEV). The WNV sequences clustered with lineages 1 and 2. These results confirm the circulation of WNV in birds in Slovakia and emphasize the risk of infection of humans and horses.

Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach

PubMed Central

2012-01-01

Background Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim’s epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim’s DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim’s fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim’s fraction, and then digest the residual victim’s DNA with a nuclease. Methods The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. Results For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. Conclusions In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods. PMID:23211019

Impact of enzymatic digestion on bacterial community composition in CF airway samples.

PubMed

Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

2017-01-01

Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  < 0.01), Streptococcus ( p  < 0.01), and Rothia ( p  < 0.01). Staphylococcus ( p  < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella ( p  < 0.01), Granulicatella ( p  < 0.01), Prevotella ( p  < 0.01), and Gemella ( p  = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

75 FR 10463 - Marine Mammals; File No. 15126

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-08

... natural and anthropogenic factors for ribbon seals (Phoca fasciata), spotted seals (P. largha), ringed... samples (blood, blubber, muscle, skin, hair, vibrissae, swab samples), attachment of telemetry devices...

Mycoplasmas isolated from stone curlews (Burhinus oedicnemus) used in falconry in the United Arab Emirates.

PubMed

Schmidt, Volker; Spergser, Joachim; Cramer, Kerstin; Di Somma, Antonio; Krautwald-Junghanns, Maria-Elisabeth; Bailey, Tom

2009-06-01

The aim of this study was to evaluate the risk of transmission of Mycoplasma spp. from quarry to hunting falcons in the Middle East. Groups of 17 houbara bustards (Chlamydotis undulata) and 29 stone curlews (Burhinus oedicnemus) kept at three different private collections in Dubai were evaluated for the presence of Mycoplasma. Additionally, 10 falcons used for hunting were investigated for comparison. The falcons showed no clinical signs and were examined within the scope of a routine health check. From all birds, conjunctival and choanal swabs were taken and analyzed via polymerase chain reaction and culture. Although mycoplasmas were not recovered from choanal and conjunctival swabs taken from the houbara bustards, Mycoplasma gypis and M. falconis were isolated from the majority (28/29; 97%) of the stone curlews from choanal and conjunctival swabs. Most of the birds had no associated pathologic findings. Mycoplasma falconis was also detected in samples collected from 2 of the 10 falcons, and M. buteonis was isolated from the majority of falcons (6/10 falcons) from choanal (n = 5) and conjunctival (n = 1) swabs. Mycoplasma gypis could also be isolated from tissue samples (liver, oviduct, syrinx) of one dead stone curlew. This study presents the first isolation of mycoplasmas from stone curlews.

Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa.

PubMed

Koeller, Kerstin; Herlemann, Daniel P R; Schuldt, Tobias; Ovari, Attila; Guder, Ellen; Podbielski, Andreas; Kreikemeyer, Bernd; Olzowy, Bernhard

2018-01-01

The role of bacteria in chronic rhinosinusitis (CRS) is still not well understood. Whole microbiome analysis adds new aspects to our current understanding that is mainly based on isolated bacteria. It is still unclear how the results of microbiome analysis and the classical culture based approaches interrelate. To address this, middle meatus swabs and tissue samples were obtained during sinus surgery in 5 patients with CRS with nasal polyps (CRSwNP), 5 patients with diffuse CRS without nasal polyps (CRSsNP), 5 patients with unilateral purulent maxillary CRS (upm CRS) and 3 patients with healthy sinus mucosa. Swabs were cultured, and associated bacteria were identified. Additionally, parts of each tissue sample also underwent culture approaches, and in parallel DNA was extracted for 16S rRNA gene amplicon-based microbiome analysis. From tissue samples 4.2 ± 1.2 distinct species per patient were cultured, from swabs 5.4 ± 1.6. The most frequently cultured species from the swabs were Propionibacterium acnes, Staphylococcus epidermidis, Corynebacterium spp. and Staphylococcus aureus . The 16S-RNA gene analysis revealed no clear differentiation of the bacterial community of healthy compared to CRS samples of unilateral purulent maxillary CRS and CRSwNP. However, the bacterial community of CRSsNP differed significantly from the healthy controls. In the CRSsNP samples Flavobacterium, Pseudomonas, Pedobacter, Porphyromonas, Stenotrophomonas , and Brevundimonas were significantly enriched compared to the healthy controls. Species isolated from culture did not generally correspond with the most abundant genera in microbiome analysis. Only Fusobacteria, Parvimonas , and Prevotella found in 2 unilateral purulent maxillary CRS samples by the cultivation dependent approach were also found in the cultivation independent approach in high abundance, suggesting a classic infectious pathogenesis of odontogenic origin in these two specific cases. Alterations of the bacterial community might be a more crucial factor for the development of CRSsNP compared to CRSwNP. Further studies are needed to investigate the relation between bacterial community characteristics and the development of CRSsNP.

Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa

PubMed Central

Koeller, Kerstin; Herlemann, Daniel P. R.; Schuldt, Tobias; Ovari, Attila; Guder, Ellen; Podbielski, Andreas; Kreikemeyer, Bernd; Olzowy, Bernhard

2018-01-01

The role of bacteria in chronic rhinosinusitis (CRS) is still not well understood. Whole microbiome analysis adds new aspects to our current understanding that is mainly based on isolated bacteria. It is still unclear how the results of microbiome analysis and the classical culture based approaches interrelate. To address this, middle meatus swabs and tissue samples were obtained during sinus surgery in 5 patients with CRS with nasal polyps (CRSwNP), 5 patients with diffuse CRS without nasal polyps (CRSsNP), 5 patients with unilateral purulent maxillary CRS (upm CRS) and 3 patients with healthy sinus mucosa. Swabs were cultured, and associated bacteria were identified. Additionally, parts of each tissue sample also underwent culture approaches, and in parallel DNA was extracted for 16S rRNA gene amplicon-based microbiome analysis. From tissue samples 4.2 ± 1.2 distinct species per patient were cultured, from swabs 5.4 ± 1.6. The most frequently cultured species from the swabs were Propionibacterium acnes, Staphylococcus epidermidis, Corynebacterium spp. and Staphylococcus aureus. The 16S-RNA gene analysis revealed no clear differentiation of the bacterial community of healthy compared to CRS samples of unilateral purulent maxillary CRS and CRSwNP. However, the bacterial community of CRSsNP differed significantly from the healthy controls. In the CRSsNP samples Flavobacterium, Pseudomonas, Pedobacter, Porphyromonas, Stenotrophomonas, and Brevundimonas were significantly enriched compared to the healthy controls. Species isolated from culture did not generally correspond with the most abundant genera in microbiome analysis. Only Fusobacteria, Parvimonas, and Prevotella found in 2 unilateral purulent maxillary CRS samples by the cultivation dependent approach were also found in the cultivation independent approach in high abundance, suggesting a classic infectious pathogenesis of odontogenic origin in these two specific cases. Alterations of the bacterial community might be a more crucial factor for the development of CRSsNP compared to CRSwNP. Further studies are needed to investigate the relation between bacterial community characteristics and the development of CRSsNP. PMID:29755418

Direct impression on agar surface as a diagnostic sampling procedure for candida balanitis.

PubMed

Lisboa, Carmen; Santos, António; Azevedo, Filomena; Pina-Vaz, Cidália; Rodrigues, Acácio Gonçalves

2010-02-01

The diagnosis of candida balanitis should be based upon both clinical and mycological data. The procedure of material collection is a critical issue to confirm or rule out the clinical diagnosis of candida balanitis. To compare direct impression of the glans on the agar surface of solid culture media with the collection of genital exudates with cotton swab for the diagnosis of candida balanitis. A prospective cross-sectional study was carried out during a 36-month period. Sexually transmitted disease clinic attendees with balanitis and asymptomatic men were included. Specimens for yeast culture were collected from the glans penis and inner preputial layer using the direct impression on CHROMagar candida medium and by swabbing with a sterile cotton swab. Among 478 men enrolled, 189 had balanitis. The prevalence of candida balanitis was 17.8% (85/478) confirmed after culture by direct impression; the swab method detected only 54/85 (63.5%) of these men. Of the 289 asymptomatic men, 36 (12.5%) yielded Candida spp; the swab method detected only 38.9% of these men. The risk of having candida balanitis is 8.9 (IC 95% 2.48 to 32.04) whenever the number of candida colonies recovered by direct impression was greater than 10. Direct impression on CHROMagar candida medium resulted in the highest Candida spp recovery rate. More than 10 colonies yielded by impression culture were statistically associated with candida balanitis. This method shows the ideal profile for sampling the male genital area for yeasts and should be included in the management of balanitis.

Antimicrobial susceptibility pattern of Klebsiella species from Ebonyi State University Teaching Hospital Abakaliki, Nigeria.

PubMed

Akujobi, C N

2005-12-01

Klesiella specie isolated from clinical specimens from Ebonyi State University Teaching Hospital (EBSUTH). Abakakliki were studied to determine the antimicrobial susceptibility pattern. Between January, 2003 and September 2004 a total of 3.600 specimens processed in the routine Medical Microbiology laboratory of EBSUTH, of which 245(6.8%) yielded Klebsiella species, with 84 from out - patients and 161 from in - patients. The number of isolates from various samples were: Urine 126, Sputum 37 Endocervical swab 13, Aspirates 8, High Vaginal Swab 7, Blood 3, Eye Swab, Ear Swab and Cerebrospinal fluid were 2 samples each. Organisms were identified by conventional methods. Antimicrobial susceptibility was done by the disk diffusion methods. The antimicrobial disk used include: Ceftazidime, Cefuroxime, Cefotaxine, Augmentin, Pefloxacin (30ug), Doxycyline (25ug) Genticin (10 ug) Ciprofloacin and Ofloxacin (5ug) each and Erythromycin (15ug). All were Oxoid products. Results were interpreted according to NCCLS criteria. Klebsilla species were isolated mostly from urine specimens (51.4%) followed by wound swabs (18.4%). Antimicrobial susceptibility to various groups drugs used was generally poor. The most sensitive antimicrobial was Ciprofloxacin with 121(49.4%) isolates susceptible to it, followed by Gentamicin with 95 (38.8%) and Ceftazidime with 90(36.7%). Seventeen isolates were multiresistant to all the antimicrobial agents used. The result of this study will help in the empiric therapy of infection caused by Klebsiella species in Ebonyi State University Teaching Hospital, Abakaliki, Nigeria but continuous surverillance of antimicrobial resistance of the organnisn is very necessary in the formulation of a sound antibiotic policy in the hospital.

Longitudinal study of age-specific pattern of coronavirus infection in Lyle's flying fox (Pteropus lylei) in Thailand.

PubMed

Wacharapluesadee, Supaporn; Duengkae, Prateep; Chaiyes, Aingorn; Kaewpom, Thongchai; Rodpan, Apaporn; Yingsakmongkon, Sangchai; Petcharat, Sininat; Phengsakul, Patcharakiti; Maneeorn, Pattarapol; Hemachudha, Thiravat

2018-02-20

Bats are natural reservoirs for several highly pathogenic and novel viruses including coronaviruses (CoVs) (mainly Alphacoronavirus and Betacoronavirus). Lyle's flying fox (Pteropus lylei)'s roosts and foraging sites are usually in the proximity to humans and animals. Knowledge about age-specific pattern of CoV infection in P. lylei, prevalence, and viral shedding at roosts and foraging sites may have an impact on infection-age-structure model to control CoV outbreak. P. lylei bats were captured monthly during January-December 2012 for detection of CoV at three areas in Chonburi province; two human dwellings, S1 and S2, where few fruit trees were located with an open pig farm, 0.6 km and 5.5 km away from the bat roost, S3. Nested RT-PCR of RNA-dependent RNA polymerase (RdRp) gene from rectal swabs was used for CoV detection. The strain of CoV was confirmed by sequencing and phylogenetic analysis. CoV infection was found in both juveniles and adult bats between May and October (January, in adults only and April, in juveniles only). Of total rectal swab positives (68/367, 18.5%), ratio was higher in bats captured at S1 (11/44, 25.0%) and S2 (35/99, 35.4%) foraging sites than at roost (S3) (22/224, 9.8%). Juveniles (forearm length ≤ 136 mm) were found with more CoV infection than adults at all three sites; S1 (9/24, 37.5% vs 2/20, 10%), S2 (22/49, 44.9% vs 13/50, 26.0%), and S3 (10/30, 33.3% vs 12/194, 6.2%). The average BCI of CoV infected bats was significantly lower than uninfected bats. No gender difference related to infection was found at the sites. Phylogenetic analysis of conserved RdRp gene revealed that the detected CoVs belonged to group D betacoronavirus (n = 64) and alphacoronavirus (n = 4). The fact that CoV infection and shedding was found in more juvenile than adult bats may suggest transmission from mother during peripartum period. Whether viral reactivation during parturition period or stress is responsible in maintaining transmission in the bat colony needs to be explored.

Consumption of sweetened, dried cranberries may reduce urinary tract infection incidence in susceptible women – a modified observational study

PubMed Central

2013-01-01

Background Urinary tract infections (UTIs) are one of the most common bacterial infections, and over 50% of women will have a UTI during their lifetimes. Antibiotics are used for prophylaxis of recurrent UTIs but can lead to emergence of drug-resistant bacteria. Therefore, it is reasonable to investigate nutritional strategies for prevention of UTIs. Cranberry juices and supplements have been used for UTI prophylaxis, but with variable efficacy. Because dried cranberries may contain a different spectrum of polyphenolics than juice, consuming berries may or may not be more beneficial than juice in decreasing the incidence of UTIs in susceptible women. The primary objectives of this study were to determine if consumption of sweetened, dried cranberries (SDC) decreases recurrent UTIs and whether this intervention would alter the heterogeneity, virulence factor (VF) profiles, or numbers of intestinal E. coli. Methods Twenty women with recurrent UTIs were enrolled in the trial and consumed one serving of SDC daily for two weeks. Clinical efficacy was determined by two criteria, a decrease in the six-month UTI rates pre- and post-consumption and increased time until the first UTI since beginning the study. Strain heterogeneity and virulence factor profiles of intestinal E. coli isolated from rectal swabs were determined by DNA fingerprinting and muliplex PCR, respectively. The numbers of intestinal E. coli eluted from rectal swabs pre- and post-consumption were also quantified. Results Over one-half of the patients did not experience a UTI within six months of SDC consumption, and the mean UTI rate per six months decreased significantly. Kaplan-Meier analysis of infection incidence in women consuming SDC compared to patients in a previous control group showed a significant reduction in time until first UTI within six months. The heterogeneity, VF profiles, and prevalence of intestinal E. coli strains were not significantly different after cranberry consumption. Conclusions Results of this study indicate a beneficial effect from consuming SDC to reduce the number of UTIs in susceptible women. Because there were no changes in the heterogeneity or VF profiles of E. coli, additional studies are needed to determine the mechanism of action of SDC for reduction of UTIs. PMID:24139545

Nipah virus transmission in a hamster model.

PubMed

de Wit, Emmie; Bushmaker, Trenton; Scott, Dana; Feldmann, Heinz; Munster, Vincent J

2011-12-01

Based on epidemiological data, it is believed that human-to-human transmission plays an important role in Nipah virus outbreaks. No experimental data are currently available on the potential routes of human-to-human transmission of Nipah virus. In a first dose-finding experiment in Syrian hamsters, it was shown that Nipah virus was predominantly shed via the respiratory tract within nasal and oropharyngeal secretions. Although Nipah viral RNA was detected in urogenital and rectal swabs, no infectious virus was recovered from these samples, suggesting no viable virus was shed via these routes. In addition, hamsters inoculated with high doses shed significantly higher amounts of viable Nipah virus particles in comparison with hamsters infected with lower inoculum doses. Using the highest inoculum dose, three potential routes of Nipah virus transmission were investigated in the hamster model: transmission via fomites, transmission via direct contact and transmission via aerosols. It was demonstrated that Nipah virus is transmitted efficiently via direct contact and inefficiently via fomites, but not via aerosols. These findings are in line with epidemiological data which suggest that direct contact with nasal and oropharyngeal secretions of Nipah virus infected individuals resulted in greater risk of Nipah virus infection. The data provide new and much-needed insights into the modes and efficiency of Nipah virus transmission and have important public health implications with regards to the risk assessment and management of future Nipah virus outbreaks.

Nipah Virus Transmission in a Hamster Model

PubMed Central

de Wit, Emmie; Bushmaker, Trenton; Scott, Dana; Feldmann, Heinz; Munster, Vincent J.

2011-01-01

Based on epidemiological data, it is believed that human-to-human transmission plays an important role in Nipah virus outbreaks. No experimental data are currently available on the potential routes of human-to-human transmission of Nipah virus. In a first dose-finding experiment in Syrian hamsters, it was shown that Nipah virus was predominantly shed via the respiratory tract within nasal and oropharyngeal secretions. Although Nipah viral RNA was detected in urogenital and rectal swabs, no infectious virus was recovered from these samples, suggesting no viable virus was shed via these routes. In addition, hamsters inoculated with high doses shed significantly higher amounts of viable Nipah virus particles in comparison with hamsters infected with lower inoculum doses. Using the highest inoculum dose, three potential routes of Nipah virus transmission were investigated in the hamster model: transmission via fomites, transmission via direct contact and transmission via aerosols. It was demonstrated that Nipah virus is transmitted efficiently via direct contact and inefficiently via fomites, but not via aerosols. These findings are in line with epidemiological data which suggest that direct contact with nasal and oropharyngeal secretions of Nipah virus infected individuals resulted in greater risk of Nipah virus infection. The data provide new and much-needed insights into the modes and efficiency of Nipah virus transmission and have important public health implications with regards to the risk assessment and management of future Nipah virus outbreaks. PMID:22180802

The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)

PubMed Central

Carrique-Mas, Juan J.; Tue, Ngo T.; Bryant, Juliet E.; Saylors, Karen; Cuong, Nguyen V.; Hoa, Ngo T.; An, Nguyen N.; Hien, Vo B.; Lao, Pham V.; Tu, Nguyen C.; Chuyen, Nguyen K.; Chuc, Nguyen T.K.; Tan, Dinh V.; Duong, Hoang Van V.; Toan, Tran K.; Chi, Nguyen T.Y.; Campbell, James; Rabaa, Maia A.; Nadjm, Behzad; Woolhouse, Mark; Wertheim, Heiman; Thwaites, Guy; Baker, Stephen

2015-01-01

The Vietnam Initiative for Zoonotic Infections (VIZIONS) includes community-based ‘high-risk sentinel cohort’ (HRSC) studies investigating individuals at risk of zoonotic infection due to occupational or residential exposure to animals. A total of 852 HRSC members were recruited between March 2013 and August 2014 from three provinces (Ha Noi, Dak Lak, and Dong Thap). The most numerous group (72.8%) corresponded to individuals living on farms, followed by slaughterers (16.3%) and animal health workers (8.5%). Nasal/pharyngeal and rectal swabs were collected from HRSC members at recruitment and after notifying illness. Exposure to exotic animals (including wild pigs, porcupine, monkey, civet, bamboo rat and bat) was highest for the Dak Lak cohort (53.7%), followed by Ha Noi (13.7%) and Dong Thap (4.0%). A total of 26.8% of individuals reported consumption of raw blood over the previous year; 33.6% slaughterers reported no use of protective equipment at work. Over 686 person-years of observation, 213 episodes of suspect infectious disease were notified, equivalent of 0.35 reports per person-year. Responsive samples were collected from animals in the farm cohort. There was noticeable time and space clustering of disease episodes suggesting that the VIZIONS set up is also suitable for the formal epidemiological investigation of disease outbreaks. PMID:26659094

Extensive Viable Middle East Respiratory Syndrome (MERS) Coronavirus Contamination in Air and Surrounding Environment in MERS Isolation Wards.

PubMed

Kim, Sung-Han; Chang, So Young; Sung, Minki; Park, Ji Hoon; Bin Kim, Hong; Lee, Heeyoung; Choi, Jae-Phil; Choi, Won Suk; Min, Ji-Young

2016-08-01

The largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) outside the Middle East occurred in South Korea in 2015 and resulted in 186 laboratory-confirmed infections, including 36 (19%) deaths. Some hospitals were considered epicenters of infection and voluntarily shut down most of their operations after nearly half of all transmissions occurred in hospital settings. However, the ways that MERS-CoV is transmitted in healthcare settings are not well defined. We explored the possible contribution of contaminated hospital air and surfaces to MERS transmission by collecting air and swabbing environmental surfaces in 2 hospitals treating MERS-CoV patients. The samples were tested by viral culture with reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescence assay (IFA) using MERS-CoV Spike antibody, and electron microscopy (EM). The presence of MERS-CoV was confirmed by RT-PCR of viral cultures of 4 of 7 air samples from 2 patients' rooms, 1 patient's restroom, and 1 common corridor. In addition, MERS-CoV was detected in 15 of 68 surface swabs by viral cultures. IFA on the cultures of the air and swab samples revealed the presence of MERS-CoV. EM images also revealed intact particles of MERS-CoV in viral cultures of the air and swab samples. These data provide experimental evidence for extensive viable MERS-CoV contamination of the air and surrounding materials in MERS outbreak units. Thus, our findings call for epidemiologic investigation of the possible scenarios for contact and airborne transmission, and raise concern regarding the adequacy of current infection control procedures. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Comparison of sampling methods used for MRSA-classification of herds with breeding pigs.

PubMed

Broens, E M; Graat, E A M; Engel, B; van Oosterom, R A A; van de Giessen, A W; van der Wolf, P J

2011-01-27

Since the first report on methicillin resistant Staphylococcus aureus (MRSA) CC398 in pigs, several countries have determined the prevalence of MRSA-positive pig herds using different sampling and laboratory techniques. The objective of the study was to compare three sampling methods for MRSA-classification of herds. Therefore, nasal swabs of pigs and environmental wipes were collected from 147 herds with breeding pigs. Per herd, laboratory examination was done on 10 pools of 6 nasal swabs (NASAL), 5 single environmental wipes (ENVSINGLE) and one pool of 5 environmental wipes (ENVPOOL). Large differences in apparent prevalence of MRSA-positive herds between methods were found: 19.1% for ENVPOOL, 53.1% for ENVSINGLE, and 70.8% for NASAL. Pairwise comparisons of methods resulted in relative sensitivities of 26.9% (ENVPOOL vs. NASAL), 34.6% (ENVPOOL vs. ENVSINGLE), and 72.1% (ENVSINGLE vs. NASAL) with relative specificities of respectively 100%, 98.6% and 93.0%. Cohen's kappa was respectively 0.18, 0.32 and 0.55, thus varying between very poor and moderate agreement. Examination of environmental wipes is an easy and non-invasive method to classify herds for MRSA. The number of environmental wipes needed depends on e.g. required detection limits and within-herd prevalence. In low prevalent herds (e.g. herds with <3 positive pools of nasal swabs), 25 single environmental wipes are required to be 90% sure that MRSA is detected at a detection limit similar to analyzing 10 pools of nasal swabs. Individual analysis of environmental wipes is highly recommended, as pooling 5 environmental samples resulted in a substantial reduction of the apparent prevalence. Copyright © 2010 Elsevier B.V. All rights reserved.

Reduction of bacterial surface contamination in the hospital environment by application of a new product with persistent effect.

PubMed

Hedin, G; Rynbäck, J; Loré, B

2010-06-01

The benefit of routine surface disinfection in hospitals has been discussed. In this study we have investigated a new product, Appeartex. After application on surfaces a remnant effect is achieved due to the positive charge of the active molecule. We studied the persistent effect of Appeartex one day after application in both an experimental study in the laboratory and a field study in a hospital ward. Surfaces of bedside tables were investigated. In the experimental study, large inocula of >or=10(6)cfu of S. aureus or enterococci were inoculated on to well-defined areas which had been treated/not treated with Appeartex. One hour later, samples were taken with a swab rinse technique. A reduction in the number of viable bacteria in the magnitude 10-10(3) cfu was seen due to the effect of Appeartex. In the field study the effect on naturally occurring low level contamination was studied. Defined surfaces on bedside tables used by patients were treated/not treated with Appeartex. One day later, samples were taken with contact agar plates and with a new swab method using two sequential nylon flocked swabs. Significantly fewer bacteria were found on Appeartex-treated surfaces compared with untreated surfaces. The median counts on Appeartex-treated surfaces were 10 cfu/50 cm(2), and on untreated surfaces 20 cfu/50 cm(2). There was no significant difference in the number of bacteria found by culture of samples taken with the contact agar method compared with samples taken using the nylon flocked swab method. (c) 2010 The Hospital Infection Society. Published by Elsevier Ltd. All rights reserved.

The inability to screen exhibition swine for influenza A virus using body temperature

PubMed Central

Bowman, Andrew S.; Nolting, Jacqueline M.; Workman, Jeffrey D.; Cooper, Maria; Fisher, Aaron E; Marsh, Bret; Forshey, Tony

2015-01-01

Summary Agricultural fairs create an unconventional animal-human interface that has been associated with swine-to-human transmission of influenza A virus (IAV) in recent years. Early detection of IAV-infected pigs at agricultural fairs would allow veterinarians to better protect swine and human health during these swine exhibitions. The present study assessed the use of swine body temperature measurement, recorded by infrared and rectal thermometers, as a practical method to detect IAV-infected swine at agricultural fairs. In our first objective, infrared thermometers were used to record the body surface temperature of 1,092 pigs at the time of IAV nasal swab collection at the end of the exhibition period of 55 agricultural fairs. IAV was recovered from 212 (19.4%) pigs and the difference in mean infrared body temperature measurement of IAV-positive and negative pigs was 0.83°C. In a second objective, snout wipes were collected from 1,948 pigs immediately prior to the unloading of the animals at a single large swine exhibition. Concurrent to the snout wipe collection, owners took the rectal temperatures of his/her pigs. In this case, 47 (2.4%) pigs tested positive for IAV before they entered the swine barn. The mean rectal temperatures differed by only 0.19°C between IAV-positive and negative pigs. The low prevalence of IAV among the pigs upon entry to the fair in the second objective provides evidence that limiting intra-species spread of IAV during the fairs will likely have significant impacts on the zoonotic transmission. However, in both objectives, the high degree of similarity in the body temperature measurements between the IAV-positive and negative pigs made it impossible to set a diagnostically meaningful cut point to differentiate IAV status of the individual animals. Unfortunately, body temperature measurement cannot be used to accurately screen exhibition swine for IAV. PMID:25884907

The Inability to Screen Exhibition Swine for Influenza A Virus Using Body Temperature.

PubMed

Bowman, A S; Nolting, J M; Workman, J D; Cooper, M; Fisher, A E; Marsh, B; Forshey, T

2016-02-01

Agricultural fairs create an unconventional animal-human interface that has been associated with swine-to-human transmission of influenza A virus (IAV) in recent years. Early detection of IAV-infected pigs at agricultural fairs would allow veterinarians to better protect swine and human health during these swine exhibitions. This study assessed the use of swine body temperature measurement, recorded by infrared and rectal thermometers, as a practical method to detect IAV-infected swine at agricultural fairs. In our first objective, infrared thermometers were used to record the body surface temperature of 1,092 pigs at the time of IAV nasal swab collection at the end of the exhibition period of 55 agricultural fairs. IAV was recovered from 212 (19.4%) pigs, and the difference in mean infrared body temperature measurement of IAV-positive and IAV-negative pigs was 0.83°C. In a second objective, snout wipes were collected from 1,948 pigs immediately prior to the unloading of the animals at a single large swine exhibition. Concurrent to the snout wipe collection, owners took the rectal temperatures of his/her pigs. In this case, 47 (2.4%) pigs tested positive for IAV before they entered the swine barn. The mean rectal temperatures differed by only 0.19°C between IAV-positive and IAV-negative pigs. The low prevalence of IAV among the pigs upon entry to the fair in the second objective provides evidence that limiting intraspecies spread of IAV during the fairs will likely have significant impacts on the zoonotic transmission. However, in both objectives, the high degree of similarity in the body temperature measurements between the IAV-positive and IAV-negative pigs made it impossible to set a diagnostically meaningful cut point to differentiate IAV status of the individual animals. Unfortunately, body temperature measurement cannot be used to accurately screen exhibition swine for IAV. © 2015 Blackwell Verlag GmbH.

Expression of SLP-2 gene and CCBE1 are associated with prognosis of rectal cancer.

PubMed

Zhang, L; Liu, F-J

2017-03-01

This study aims to investigate the clinical significance of SLP-2 gene for patients with rectal cancer. To analyze the effect of CCBE1 (Collagen and calcium-binding EGF domain-containing protein 1) on rectal cancer tissue and lymph vessels of para-carcinoma tissue. A total of 50 samples of rectal cancer tissues were enrolled in the experimental group, confirmed by pathological examination. 50 samples of para-carcinoma normal tissues were collected as control group. Protein expression of SLP-2 and CCBE1 was examined with immunohistochemical staining. mRNA expression of SLP-2 was examined with RT-PCR. Lymphatic vessel density (LVD) was evaluated with LYVE-1 immunohistochemical staining. Correlation analysis was performed to assess the relationship between patient survival data and clinical pathological features of rectal cancer. Immunohistochemical staining showed that, compared with the control group, a positive expression rate of SLP-2 in the experimental group was significantly higher (68.0% vs. 24.0%, p<0.05), and mRNA of SLP-2 was also significantly increased (p<0.05). Compared with the control group, protein expression of CCBE1 in the experimental group was significantly higher (p<0.05). Moreover, the expression level of SLP-2 was remarkably associated with TNM classification and lymphatic metastasis. Further analysis demonstrated that a positive expression of CCBE1 was associated with lymphatic metastasis, LVD and Ducks classification, and had a negative correlation with survival rate. Increased expression of SLP-2 promoted the formation of lymph vessels and exacerbated lymphatic metastasis of rectal cancer via up-regulating CCBE1. As a risk factor related to lymphatic metastasis, CCBE1 could be a novel biomarker for diagnosis and prognosis of rectal cancer.

Cell-free DNA levels and correlation to stage and outcome following treatment of locally advanced rectal cancer.

PubMed

Boysen, Anders Kindberg; Wettergren, Yvonne; Sorensen, Boe Sandahl; Taflin, Helena; Gustavson, Bengt; Spindler, Karen-Lise Garm

2017-11-01

Accurate staging of rectal cancer remains essential for optimal patient selection for combined modality treatment, including radiotherapy, chemotherapy and surgery. We aimed at examining the correlation of cell free DNA with the pathologic stage and subsequent risk of recurrence for patients with locally advanced rectal cancer undergoing preoperative chemoradiation. We examined 75 patients with locally advanced rectal cancer receiving preoperative chemoradiation. Blood samples for translational use were drawn prior to rectal surgery. The level of cell free DNA was quantified by digital droplet PCR and expressed as copy number of beta 2 microglobulin. We found a median level of cell free DNA in the AJCC stages I-III of 3100, 8300, and 10,700 copies/mL respectively. For patients with 12 sampled lymph nodes or above, the median level of cell free DNA were 2400 copies/mL and 4400 copies/mL (p = 0.04) for node negative and node positive disease respectively. The median follow-up was 39 months and 11 recurrences were detected (15%). The median level for patients with recurrent disease was 13,000 copies/mL compared to 5200 copies/mL for non-recurrent patients (p = 0.08). We have demonstrated a correlation between the level of total cell free DNA and the pathologic stage and nodal involvement. Furthermore, we have found a trend towards a correlation with the risk of recurrence following resection of localized rectal cancer.

Rapid PCR detection of group A Streptococcus from flocked throat swabs: a retrospective clinical study.

PubMed

Slinger, Robert; Goldfarb, David; Rajakumar, Derek; Moldovan, Ioana; Barrowman, Nicholas; Tam, Ronald; Chan, Francis

2011-09-02

Rapid diagnosis of GAS pharyngitis may improve patient care by ensuring that patients with GAS pharyngitis are treated quickly and also avoiding unnecessary use of antibiotics in those without GAS infection. Very few molecular methods for detection of GAS in clinical throat swab specimens have been described. We performed a study of a laboratory-developed internally-controlled rapid Group A streptococcus (GAS) PCR assay using flocked swab throat specimens. We compared the GAS PCR assay to GAS culture results using a collection of archived throat swab samples obtained during a study comparing the performance of conventional and flocked throat swabs. The sensitivity of the GAS PCR assay as compared to the reference standard was 96.0% (95% CI 90.1% to 98.4%), specificity 98.6% (95% CI 95.8% to 99.5%), positive predictive value (PPV) 96.9% (95% CI 91.4% to 99.0%) and negative predictive value (NPV) of 98.1% (95% CI 95.2% to 99.2%). For conventional swab cultures, sensitivity was 96.0% (95% CI 90.1% to 98.4%), specificity 100% (95% CI 98.2% to 100%), PPV 100%, (95% CI 96.1% to 100%) and NPV 98.1% (95% CI 95.2% to 99.3%) In this retrospective study, the GAS PCR assay appeared to perform as well as conventional throat swab culture, the current standard of practice. Since the GAS PCR assay, including DNA extraction, can be performed in approximately 1 hour, prospective studies of this assay are warranted to evaluate the clinical impact of the assay on management of patients with pharyngitis.

Evaluation of hygiene practices in catering premises at large-scale events in the UK: identifying risks for the Olympics 2012.

PubMed

Willis, C; Elviss, N; Aird, H; Fenelon, D; McLauchlin, J

2012-08-01

To investigate hygiene practices of caterers at large events in order to: support the production of guidance on catering at such events; to compare hygiene standards at weekends with other times in the week; and to learn lessons in preparation for the London Olympics in 2012. UK-wide study of caterers at large events, including questionnaires on hygiene procedures and microbiological examination of food, water and environmental samples. In total, 1364 samples of food, water, surface swabs and cloths were collected at 139 events, by local authority sampling officers, and transported to laboratories for microbiological analysis. Eight percent of food samples were of an unsatisfactory quality, and a further 2% contained potentially hazardous levels of Bacillus spp. A significantly higher proportion of unsatisfactory food samples were taken from vendors without adequate food safety procedures in place. Fifty-two percent of water samples, 38% of swabs and 71% of cloths were also unsatisfactory. The majority of samples (57%) were collected on Saturdays, Sundays or bank holidays. Environmental swab results were significantly poorer at weekends compared with other days of the week. This study reinforces the fact that food hygiene is a continuing cause for concern in mobile vendors, and indicates a need for an ongoing programme of training and monitoring of caterers in preparation for the London Olympics. Copyright © 2012 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Genetic stability of Brucella abortus isolates from an outbreak by multiple-locus variable-number tandem repeat analysis (MLVA16)

PubMed Central

2014-01-01

Background Brucellosis caused by Brucella abortus is one of the most important zoonoses in the world. Multiple-locus variable-number tandem repeat analysis (MLVA16) has been shown be a useful tool to epidemiological traceback studies in B. abortus infection. Thus, the present study aimed (i) to evaluate the genetic diversity of B. abortus isolates from a brucellosis outbreak, and (ii) to investigate the in vivo stability of the MLVA16 markers. Results Three-hundred and seventy-five clinical samples, including 275 vaginal swabs and 100 milk samples, were cultured from a brucellosis outbreak in a cattle herd, which adopted RB51 vaccination and test-and-slaughter policies. Thirty-seven B. abortus isolates were obtained, eight from milk and twenty-nine from post-partum/abortion vaginal swabs, which were submitted to biotyping and genotyping by MLVA16. Twelve B. abortus isolates obtained from vaginal swabs were identified as RB51. Twenty four isolates, seven obtained from milk samples and seventeen from vaginal swabs, were identified as B. abortus biovar 3, while one isolate from vaginal swabs was identified as B. abortus biovar 1. Three distinct genotypes were observed during the brucellosis outbreak: RB observed in all isolates identified as RB51; W observed in all B. abortus biovar 3 isolates; and Z observed in the single B. abortus biovar 1 isolate. Epidemiological and molecular data show that the B. abortus biovar 1 genotype Z strain is not related to the B. abortus biovar 3 genotype W isolates, and represents a new introduction B. abortus during the outbreak. Conclusions The results of the present study on typing of multiple clinical B. abortus isolates from the same outbreak over a sixteen month period indicate the in vivo stability of MLVA16 markers, a low genetic diversity among B. abortus isolates and the usefulness of MLVA16 for epidemiological studies of bovine brucellosis. PMID:25015840

Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection

USGS Publications Warehouse

Zylberberg, Maxine; Van Hemert, Caroline R.; Handel, Colleen M.; DeRisi, Joseph L.

2018-01-01

BackgroundAvian keratin disorder (AKD) is an epizootic of debilitating beak deformities, first documented in black-capped chickadees (Poecile atricapillus) in Alaska during the late 1990s. Similar deformities have now been recorded in dozens of species of birds across multiple continents. Despite this, the etiology of AKD has remained elusive, making it difficult to assess the impacts of this disease on wild populations. We previously identified an association between infection with a novel picornavirus, Poecivirus, and AKD in a small cohort of black-capped chickadees.MethodsTo test if the association between Poecivirus and AKD holds in a larger study population, we used targeted PCR followed by Sanger sequencing to screen 124 symptomatic and asymptomatic black-capped chickadees for Poecivirus infection. We further compared the efficacy of multiple non-terminal field sampling methods (buccal swabs, cloacal swabs, fecal samples, and blood samples) for Poecivirus screening. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to determine if virus is actively replicating in beak tissue.ResultsPoecivirus was detected in 28/28 (100%) individuals with AKD, but only 9/96 (9.4%) asymptomatic individuals with apparently normal beaks (p < 0.0001). We found that cloacal swabs are the most sensitive of these sample types for detecting Poecivirus in birds with AKD, but that buccal swabs should be combined with cloacal swabs in evaluating the infection status of asymptomatic birds. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to provide evidence of active viral replication.ConclusionThe data presented here show a strong, statistically significant relationship between Poecivirus infection and AKD, and provide evidence that Poecivirus is indeed an avian virus, infecting and actively replicating in beak tissue of AKD-affected BCCH. Taken together, these data corroborate and extend the evidence for a potential causal association between Poecivirus and AKD in the black-capped chickadee. Poecivirus continues to warrant further investigation as a candidate agent of AKD.

Molecular characterization of Mycobacterium tuberculosis complex (MTBC) isolated from cattle in northeast and northwest China.

PubMed

Du, Yanfen; Qi, Yingfang; Yu, Lu; Lin, Jingkai; Liu, Siguo; Ni, Hongbo; Pang, Hai; Liu, Huifang; Si, Wei; Zhao, Hailing; Wang, Chunlai

2011-06-01

We studied throat swabs and corresponding serum samples collected from 1067 protein purified derivative (PPD)-tuberculin skin test (TST) positive cattle from different regions of China. The 1067 throat swabs were inoculated onto modified Löwenstein-Jensen medium for the isolation and culture of Mycobacteria. Acid-fast bacilli were identified using traditional biochemical methods, polymerase chain reaction (PCR) amplification and multiplex PCR. They were distinguished as Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) strains. An indirect Enzyme-Linked Immunosorbent Assay (ELISA) was applied to detect specific antibodies against bovine TB (bTB). Correlations among the ELISA, bacteriology and TST were analyzed and compared. Spoligotyping and variable number tandem repeats-mycobacterial interspersed repetitive unit (VNTR-MIRU) analysis were used to genotype the MTBC. In total, 111 strains of Mycobacteria were cultured from the 1067 throat swab samples, including 43 stains of MTBC (14 strains of Mycobacterium bovis and 29 of Mycobacterium tuberculosis) and 68 strains of NTM. Thirty-eight MTBC strains and four NTM strains were isolated from 72 throat swab samples that the ELISA determined were antibody positive; five MTBC strains and 64 NTM strains were isolated from 995 throat swab samples that were antibody negative on the ELISA. The positive isolation rates of MTBC and NTM were 38.7% (43/111) and 61.3% (68/111), respectively. The concordance rate of cultured MTBC with a positive result on the indirect ELISA for antibody was 52.8% (38/72), which was much higher than the positive rate for TST (4.0%; 43/1067). Genotyping of the 43 strains of MTBC isolated, using spoligotyping and VNTR-MIRU, showed that the 43 isolates had 26 genotypes; 16 strains had a unique genotype. Two groups of six strains and two strains, respectively, showed the same spoligotyping pattern, and belonged to the Beijing family and Beijing-like family, respectively. Combined application of spoligotyping and VNTR-MIRU typing would improve the molecular epidemiological investigation and monitoring of the etiology of bTB in China. Copyright © 2010 Elsevier Ltd. All rights reserved.

Development of a rectal sexually transmitted infection (STI) Model in Rhesus macaques using Chlamydia trachomatis serovars E and L2.

PubMed

Henning, Tara R; Morris, Monica; Ellis, Shanon; Kelley, Kristen; Phillips, Christi; Ritter, Jana; Jones, Tara; Nachamkin, Eli; Chen, Cheng Y; Hong, Jaeyoung; Kang, Joseph; Patton, Dorothy; McNicholl, Janet; Papp, John; Kersh, Ellen N

2017-10-01

Rectal STI coinfection models enhance the understanding of rectal HIV transmission risk factors. Rhesus macaques (n=9) were exposed to one of three rectal Chlamydia trachomatis (CT) challenges: C. trachomatis L 2 (CT-L 2 ); C. trachomatis serovar E (CT-E), followed by CT-L 2 ; or CT-E, treatment/clearance, then CT-L 2 . Infections were monitored by PCR. Weekly blood and rectal secretion/lavage samples were collected for cytokine analyzes and/or epithelial sloughing, occult, and overt blood determinations. Chlamydial infections were successfully established in each animal, with varying degrees of persistence. Mucosal IL-1beta was upregulated in animals consecutively infected with CT-E then CT-L 2 (P=.05). Epithelial sloughing was also significantly increased post-infection in this group (P=.0003). This study demonstrates successful rectal infection of rhesus macaques with CT-E and CT-L 2 and describes measures of assessing rectal inflammation and pathology. Different infection strategies yield varying inflammatory and pathologic outcomes, providing well-described models for future SIV/SHIV susceptibility studies. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Development of a multiplex real-time PCR for the simultaneous detection of herpes simplex and varicella zoster viruses in cerebrospinal fluid and lesion swab specimens.

PubMed

Wong, Anita A; Pabbaraju, Kanti; Wong, Sallene; Tellier, Raymond

2016-03-01

Herpes simplex viruses (HSV) and varicella zoster virus (VZV) can have very similar and wide-ranging clinical presentations. Rapid identification is necessary for timely antiviral therapy, especially with infections involving the central nervous system, neonates, and immunocompromised individuals. Detection of HSV-1, HSV-2 and VZV was combined into one real-time PCR reaction utilizing hydrolysis probes. The assay was validated on the LightCycler(®) (Roche) and Applied Biosystems 7500 Real-Time PCR System (Thermo Fisher Scientific Inc.) to detect alphaherpesviruses in cerebral spinal fluid (CSF) and lesion swab specimens, respectively. Validation data on blood and tissue samples are also presented. The multiplex assay showed excellent sensitivity, specificity and reproducibility when compared to two singleplex real-time PCR assays for CSF samples and direct fluorescent antigen/culture for lesion swab samples. Implementation of the multiplex assay has facilitated improved sensitivity and accuracy as well as reduced turn-around-times and costs. The results from a large data set of 16,622 prospective samples tested between August 16, 2012 to February 1, 2014 at the Provincial Laboratory for Public Health (Alberta, Canada) are presented here. Copyright © 2015 Elsevier B.V. All rights reserved.

Physical therapy clinic therapeutic ultrasound equipment as a source for bacterial contamination.

PubMed

Spratt, Henry G; Levine, David; Tillman, Larry

2014-10-01

A procedure commonly used in physical therapy (PT) clinics is therapeutic ultrasound (US). This equipment and associated gel comes in contact with patient skin, potentially serving as a reservoir for bacteria. In this study, we sampled US heads, gel bottle tips and gel from nine outpatient PT clinics in Southeastern Tennessee. Samples were collected using sterile swabs. At the microbiology laboratory, these swabs were used to inoculate mannitol salt agar and CHROM-MRSA agar (for Staphylococcal species) and tryptic soy broth to determine non-specific bacterial contamination. US heads, gel bottle tips and gel had variable levels of contamination. Tips of gel bottles had the highest contamination, with 52.7% positive for non-specific bacterial contamination and 3.6% positive for methicillin-resistant Staphylococcus aureus (MRSA). Contamination of gel by non-specific bacteria was found in 14.5% of bottles sampled. US heads (35.5% of those sampled) had non-specific bacterial contamination, with no MRSA detected. Disinfecting US heads after initial swabbing resulted in removal of 90.9% of non-specific contamination. Gel storage at temperatures below 40 °C was found to encourage the growth of mesophilic bacteria. This study demonstrates the need for better cleaning and storage protocols for US heads and gel bottles in PT clinics.

Recovery Efficiency and Limit of Detection of Aerosolized Bacillus anthracis Sterne from Environmental Surface Samples ▿

PubMed Central

Estill, Cheryl Fairfield; Baron, Paul A.; Beard, Jeremy K.; Hein, Misty J.; Larsen, Lloyd D.; Rose, Laura; Schaefer, Frank W.; Noble-Wang, Judith; Hodges, Lisa; Lindquist, H. D. Alan; Deye, Gregory J.; Arduino, Matthew J.

2009-01-01

After the 2001 anthrax incidents, surface sampling techniques for biological agents were found to be inadequately validated, especially at low surface loadings. We aerosolized Bacillus anthracis Sterne spores within a chamber to achieve very low surface loading (ca. 3, 30, and 200 CFU per 100 cm2). Steel and carpet coupons seeded in the chamber were sampled with swab (103 cm2) or wipe or vacuum (929 cm2) surface sampling methods and analyzed at three laboratories. Agar settle plates (60 cm2) were the reference for determining recovery efficiency (RE). The minimum estimated surface concentrations to achieve a 95% response rate based on probit regression were 190, 15, and 44 CFU/100 cm2 for sampling steel surfaces and 40, 9.2, and 28 CFU/100 cm2 for sampling carpet surfaces with swab, wipe, and vacuum methods, respectively; however, these results should be cautiously interpreted because of high observed variability. Mean REs at the highest surface loading were 5.0%, 18%, and 3.7% on steel and 12%, 23%, and 4.7% on carpet for the swab, wipe, and vacuum methods, respectively. Precision (coefficient of variation) was poor at the lower surface concentrations but improved with increasing surface concentration. The best precision was obtained with wipe samples on carpet, achieving 38% at the highest surface concentration. The wipe sampling method detected B. anthracis at lower estimated surface concentrations and had higher RE and better precision than the other methods. These results may guide investigators to more meaningfully conduct environmental sampling, quantify contamination levels, and conduct risk assessment for humans. PMID:19429546

Association between an outbreak strain causing mycoplasma bovis mastitis and its asymptomatic carriage in the herd: a case study from Idaho, USA.

PubMed

Punyapornwithaya, V; Fox, L K; Hancock, D D; Gay, J M; Alldredge, J R

2010-01-01

The objective of this study was to determine the association between mycoplasma mastitis and colonization of mycoplasma organisms at body sites of asymptomatic carriers. The investigation was done in a dairy herd with a first outbreak of mycoplasma mastitis. Milk and swab solution specimens from accessible mucosal surfaces of body sites from cows and replacements were sampled at quarterly intervals (Herd Samplings 1-4). Samples were cultured and Mycoplasma spp. were isolated, speciated and fingerprinted. During Herd Sampling 1 two cows with mycoplasma bovis mastitis were identified and all swabbing solutions of body site samples from 18 of 84 cows and 36 of 77 replacements were positive to Mycoplasma bovis and fingerprinted as the same strain. A case of clinical M. bovis mastitis developed during Herd Sampling 3. During Herd Samplings 2-4, 4 lactating cows and 12 replacements were positive to M. bovis at various body sites with 4 different strains. Three isolates of Mycoplasma californicum were found from swabbing solutions of three cows during Herd Samplings 3 and 4. Only one strain of M. bovis caused mastitis although four strains were isolated from body sites of animals. Isolation of M. bovis from a body site never preceded mastitis. No lactating cow developed mastitis during Herd Sampling 4 although some animals were colonized with the organism. It appears that during the initial outbreak of M. bovis mastitis colonization of body sites by the outbreak strain may be common. However, the prevalence of colonization subsides and colonization does not appear to precede mastitis.

Recovery efficiency and limit of detection of aerosolized Bacillus anthracis Sterne from environmental surface samples.

PubMed

Estill, Cheryl Fairfield; Baron, Paul A; Beard, Jeremy K; Hein, Misty J; Larsen, Lloyd D; Rose, Laura; Schaefer, Frank W; Noble-Wang, Judith; Hodges, Lisa; Lindquist, H D Alan; Deye, Gregory J; Arduino, Matthew J

2009-07-01

After the 2001 anthrax incidents, surface sampling techniques for biological agents were found to be inadequately validated, especially at low surface loadings. We aerosolized Bacillus anthracis Sterne spores within a chamber to achieve very low surface loading (ca. 3, 30, and 200 CFU per 100 cm(2)). Steel and carpet coupons seeded in the chamber were sampled with swab (103 cm(2)) or wipe or vacuum (929 cm(2)) surface sampling methods and analyzed at three laboratories. Agar settle plates (60 cm(2)) were the reference for determining recovery efficiency (RE). The minimum estimated surface concentrations to achieve a 95% response rate based on probit regression were 190, 15, and 44 CFU/100 cm(2) for sampling steel surfaces and 40, 9.2, and 28 CFU/100 cm(2) for sampling carpet surfaces with swab, wipe, and vacuum methods, respectively; however, these results should be cautiously interpreted because of high observed variability. Mean REs at the highest surface loading were 5.0%, 18%, and 3.7% on steel and 12%, 23%, and 4.7% on carpet for the swab, wipe, and vacuum methods, respectively. Precision (coefficient of variation) was poor at the lower surface concentrations but improved with increasing surface concentration. The best precision was obtained with wipe samples on carpet, achieving 38% at the highest surface concentration. The wipe sampling method detected B. anthracis at lower estimated surface concentrations and had higher RE and better precision than the other methods. These results may guide investigators to more meaningfully conduct environmental sampling, quantify contamination levels, and conduct risk assessment for humans.

Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques (Macaca mulatta).

PubMed

Balasubramaniam, Krishna; Beisner, Brianne; Guan, Jiahui; Vandeleest, Jessica; Fushing, Hsieh; Atwill, Edward; McCowan, Brenda

2018-01-01

In group-living animals, heterogeneity in individuals' social connections may mediate the sharing of microbial infectious agents. In this regard, the genetic relatedness of individuals' commensal gut bacterium Escherichia coli may be ideal to assess the potential for pathogen transmission through animal social networks. Here we use microbial phylogenetics and population genetics approaches, as well as host social network reconstruction, to assess evidence for the contact-mediated sharing of E. coli among three groups of captively housed rhesus macaques ( Macaca mulatta ), at multiple organizational scales. For each group, behavioral data on grooming, huddling, and aggressive interactions collected for a six-week period were used to reconstruct social network communities via the Data Cloud Geometry (DCG) clustering algorithm. Further, an E. coli isolate was biochemically confirmed and genotypically fingerprinted from fecal swabs collected from each macaque. Population genetics approaches revealed that Group Membership, in comparison to intrinsic attributes like age, sex, and/or matriline membership of individuals, accounted for the highest proportion of variance in E. coli genotypic similarity. Social network approaches revealed that such sharing was evident at the community-level rather than the dyadic level. Specifically, although we found no links between dyadic E. coli similarity and social contact frequencies, similarity was significantly greater among macaques within the same social network communities compared to those across different communities. Moreover, tests for one of our study-groups confirmed that E. coli isolated from macaque rectal swabs were more genotypically similar to each other than they were to isolates from environmentally deposited feces. In summary, our results suggest that among frequently interacting, spatially constrained macaques with complex social relationships, microbial sharing via fecal-oral, social contact-mediated routes may depend on both individuals' direct connections and on secondary network pathways that define community structure. They lend support to the hypothesis that social network communities may act as bottlenecks to contain the spread of infectious agents, thereby encouraging disease control strategies to focus on multiple organizational scales. Future directions includeincreasing microbial sampling effort per individual to better-detect dyadic transmission events, and assessments of the co-evolutionary links between sociality, infectious agent risk, and host immune function.

Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions.

PubMed

Stellato, Giuseppina; La Storia, Antonietta; De Filippis, Francesca; Borriello, Giorgia; Villani, Francesco; Ercolini, Danilo

2016-07-01

Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The aims of this study were to learn more about the possible influence of the meat processing environment on initial fresh meat contamination and to investigate the differences between small-scale retail distribution (SD) and large-scale retail distribution (LD) facilities. Samples were collected from butcheries (n = 20), including LD (n = 10) and SD (n = 10) facilities, over two sampling campaigns. Samples included fresh beef and pork cuts and swab samples from the knife, the chopping board, and the butcher's hand. The microbiota of both meat samples and environmental swabs were very complex, including more than 800 operational taxonomic units (OTUs) collapsed at the species level. The 16S rRNA sequencing analysis showed that core microbiota were shared by 80% of the samples and included Pseudomonas spp., Streptococcus spp., Brochothrix spp., Psychrobacter spp., and Acinetobacter spp. Hierarchical clustering of the samples based on the microbiota showed a certain separation between meat and environmental samples, with higher levels of Proteobacteria in meat. In particular, levels of Pseudomonas and several Enterobacteriaceae members were significantly higher in meat samples, while Brochothrix, Staphylococcus, lactic acid bacteria, and Psychrobacter prevailed in environmental swab samples. Consistent clustering was also observed when metabolic activities were considered by predictive metagenomic analysis of the samples. An increase in carbohydrate metabolism was predicted for the environmental swabs and was consistently linked to Firmicutes, while increases in pathways related to amino acid and lipid metabolism were predicted for the meat samples and were positively correlated with Proteobacteria Our results highlighted the importance of the processing environment in contributing to the initial microbial levels of meat and clearly showed that the type of retail facility (LD or SD) did not apparently affect the contamination. The study provides an in-depth description of the microbiota of meat and meat processing environments. It highlights the importance of the environment as a contamination source of spoilage bacteria, and it shows that the size of the retail facility does not affect the level and type of contamination. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Direct PCR Improves the Recovery of DNA from Various Substrates.

PubMed

Templeton, Jennifer E L; Taylor, Duncan; Handt, Oliva; Skuza, Pawel; Linacre, Adrian

2015-11-01

This study reports on the comparison of a standard extraction process with the direct PCR approach of processing low-level DNA swabs typical in forensic investigations. Varying concentrations of control DNA were deposited onto three commonly encountered substrates, brass, plastic, and glass, left to dry, and swabbed using premoistened DNA-free nylon FLOQswabs(™) . Swabs (n = 90) were either processed using the DNA IQ(™) kit or, for direct PCR, swab fibers (~2 mm(2) ) were added directly to the PCR with no prior extraction. A significant increase in the height of the alleles (p < 0.005) was observed when using the direct PCR approach over the extraction methodology when controlling for surface type and mass of DNA deposited. The findings indicate the potential use of direct PCR for increasing the PCR product obtained from low-template DNA samples in addition to minimizing contamination and saving resources. © 2015 American Academy of Forensic Sciences.

Comparison between culture and a multiplex quantitative real-time polymerase chain reaction assay detecting Ureaplasma urealyticum and U. parvum.

PubMed

Frølund, Maria; Björnelius, Eva; Lidbrink, Peter; Ahrens, Peter; Jensen, Jørgen Skov

2014-01-01

A novel multiplex quantitative real-time polymerase chain reaction (qPCR) for simultaneous detection of U. urealyticum and U. parvum was developed and compared with quantitative culture in Shepard's 10 C medium for ureaplasmas in urethral swabs from 129 men and 66 women, and cervical swabs from 61 women. Using culture as the gold standard, the sensitivity of the qPCR was 96% and 95% for female urethral and cervical swabs, respectively. In male urethral swabs the sensitivity was 89%. The corresponding specificities were 100%, 87% and 99%. The qPCR showed a linear increasing DNA copy number with increasing colour-changing units. Although slightly less sensitive than culture, this multiplex qPCR assay detecting U. urealyticum and U. parvum constitutes a simple and fast alternative to the traditional methods for identification of ureaplasmas and allows simultaneous species differentiation and quantitation in clinical samples. Furthermore, specimens overgrown by other bacteria using the culture method can be evaluated in the qPCR.

Enumeration of Escherichia coli in swab samples from pre- and post-chilled pork and lamb carcasses using 3M™ Petrifilm™ Select E. coli and Simplate® Coliforms/E. coli.

PubMed

Hauge, Sigrun J; Østensvik, Øyvin; Monshaugen, Marte; Røtterud, Ole-Johan; Nesbakken, Truls; Alvseike, Ole

2017-08-01

The aim of the study was to compare two analytical methods; 3M Petrifilm™ Select E. coli and SimPlate® Coliforms &E. coli, for detection and enumeration of E. coli using swab samples from naturally contaminated pork and lamb carcasses that were collected before and after chilling. Blast chilling was used for pork carcasses. Swab samples (n=180) were collected from 60 warm and 60 chilled pork carcasses, and 30 warm and 30 chilled lamb carcasses, and analysed in parallel. The concordance correlation coefficient between Petrifilm and SimPlate was 0.89 for pork and 0.81 for lamb carcasses. However, the correlation was higher for warm carcasses (0.90) than chilled carcasses (0.72). For chilled lamb carcasses, the correlation was only 0.50, and SimPlate gave slightly higher results than Petrifilm (P=0.09). Slower chilling gave slightly lesser agreement between methods than for blast chilling, however, both Petrifilm and SimPlate methodologies are suitable and recommended for use in small laboratories in abattoirs. Copyright © 2017 Elsevier Ltd. All rights reserved.

A proof of concept study to assess the potential of PCR testing to detect natural Mycobacterium bovis infection in South American camelids

PubMed Central

2014-01-01

Background Cases of Mycobacterium bovis infection South American camelids have been increasing in Great Britain. Current antemortem immunological tests have some limitations. Cases at post mortem examination frequently show extensive pathology. The feasibility of detecting Mycobacterium bovis DNA in clinical samples was investigated. Findings A sensitive extraction methodology was developed and used on nasal swabs and faeces taken post-mortem to assess the potential for a PCR test to detect Mycobacterium bovis in clinical samples. The gross pathology of the studied South American camelids was scored and a significantly greater proportion of South American camelids with more severe pathology were positive in both the nasal swab and faecal PCR tests. A combination of the nasal swab and faecal PCR tests detected 63.9% of all the South American camelids with pathology that were tested. Conclusions The results suggest that antemortem diagnosis of Mycobacterium bovis in South American camelids may be possible using a PCR test on clinical samples, however more work is required to determine sensitivity and specificity, and the practicalities of applying the test in the field. PMID:24507471

Pharmacokinetics of three formulations of ondansetron hydrochloride in healthy volunteers: 24-mg oral tablet, rectal suppository, and i.v. infusion.

PubMed

VanDenBerg, C M; Kazmi, Y; Stewart, J; Weidler, D J; Tenjarla, S N; Ward, E S; Jann, M W

2000-06-01

The absolute bioavailability and pharmacokinetics of three formulations of ondansetron hydrochloride 24 mg--an oral tablet, an intravenous solution, and an extemporaneous rectal suppository--were studied. Twelve healthy, nonsmoking volunteers (six men and six women) were given ondansetron in a study with a three-way cross-over design. All subjects received each dosage form on the same day in the following order: oral tablet, rectal suppository, and intravenous infusion. Administrations were separated by one week. Blood sampling times varied, depending on the administration route. Mean absolute bioavailability for the oral tablet and the rectal suppository differed significantly. Absorption of ondansetron was prolonged when it was administered as the rectal suppository. Absolute bioavailability for the 24-mg tablet was similar to that for other tablet strengths in previous studies. All subjects completed the study without significant adverse effects. Absorption of ondansetron from the rectal suppository was prolonged compared with the oral tablet and the i.v. infusion. Bioavailability for the 24-mg suppository formulation was considerably lower than for the 24-mg tablet.

Effectiveness of sampling methods employed for Acanthamoeba keratitis diagnosis by culture.

PubMed

Muiño, Laura; Rodrigo, Donoso; Villegas, Rodrigo; Romero, Pablo; Peredo, Daniel E; Vargas, Rafael A; Liempi, Daniela; Osuna, Antonio; Jercic, María Isabel

2018-06-18

This retrospective, observational study was designed to evaluate the effectiveness of the sampling methods commonly used for the collection of corneal scrapes for the diagnosis of Acanthamoeba keratitis (AK) by culture, in terms of their ability to provide a positive result. A total of 553 samples from 380 patients with suspected AK received at the Parasitology Section of the Public Health Institute of Chile, between January 2005 and December 2015, were evaluated. A logistic regression model was used to determine the correlation between the culture outcome (positive or negative) and the method for sample collection. The year of sample collection was also included in the analysis as a confounding variable. Three hundred and sixty-five samples (27%) from 122 patients (32.1%) were positive by culture. The distribution of sample types was as follows: 142 corneal scrapes collected using a modified bezel needle (a novel method developed by a team of Chilean corneologists), 176 corneal scrapes obtained using a scalpel, 50 corneal biopsies, 30 corneal swabs, and 155 non-biological materials including contact lens and its paraphernalia. Biopsy provided the highest likelihood ratio for a positive result by culture (1.89), followed by non-biological materials (1.10) and corneal scrapes obtained using a modified needle (1.00). The lowest likelihood ratio was estimated for corneal scrapes obtained using a scalpel (0.88) and cotton swabs (0.78). Apart from biopsy, optimum corneal samples for the improved diagnosis of AK can be obtained using a modified bezel needle instead of a scalpel, while cotton swabs are not recommended.

The role of environmental contamination with small round structured viruses in a hospital outbreak investigated by reverse-transcriptase polymerase chain reaction assay.

PubMed

Green, J; Wright, P A; Gallimore, C I; Mitchell, O; Morgan-Capner, P; Brown, D W

1998-05-01

In May 1994 an outbreak of vomiting and diarrhoea occurred in a 28-bed long-stay ward for the mentally infirm. The predominant symptoms were vomiting, diarrhoea, malaise and abdominal pain lasting for approximately 12 h in most cases. The attack rate was 62% (13/21) for patients and 46% (16/35) for staff members. Infection control measures were implemented (containment of infectious individuals, hand hygiene among staff and environmental decontamination) and the ward was closed to admissions. Affected staff were excluded from contact with patients and their food until asymptomatic for 72 h. The outbreak lasted for 17 days. Faecal samples from nine symptomatic persons were negative for bacterial enteric pathogens, Giardia, Cryptosporidium and group A rotavirus. Electron microscopy of 12 faecal samples and one sample of vomitus revealed small round structured virus (SRSV) particles in one faecal sample. A further 30 faecal samples and seven vomitus samples were tested by reverse transcription polymerase chain reaction (RT-PCR) for SRSV of which 12 (40%) and 1 (14%) were positive respectively. Twenty-eight throat swabs from symptomatic and asymptomatic patients were collected, three (9.5%) of which were positive for SRSV by RT-PCR. Thirty-six environmental swabs were collected on the affected ward, and 11 (30%) were positive by RT-PCR. Positive swabs were from lockers, curtains and commodes and confined to the immediate environment of symptomatic patients. The distribution of contamination supports the rationale of cohorting sick patients.

Confirmatory analysis of 17beta-boldenone, 17alpha-boldenone and androsta-1,4-diene-3,17-dione in bovine urine, faeces, feed and skin swab samples by liquid chromatography-electrospray ionisation tandem mass spectrometry.

PubMed

Nielen, Michel W F; Rutgers, Paula; van Bennekom, Eric O; Lasaroms, Johan J P; van Rhijn, J A Hans

2004-03-05

The origin, i.e. natural occurrence or illegal treatment, of findings of 17alpha-boldenone (alpha-Bol) and 17beta-boldenone (beta-Bol) in urine and faeces of cattle is under debate within the European Union. A liquid chromatographic positive ion electrospray tandem mass spectrometric method is presented for the confirmatory analysis of 17beta-boldenone, 17alpha-boldenone and an important metabolite/precursor androsta-1,4-diene-3,17-dione (ADD), using deuterium-labelled 17beta-boldenone (beta-Bol-d3) as internal standard. Detailed sample preparation procedures were developed for a variety of sample matrices such as bovine urine, faeces, feed and skin swab samples. The method was validated as a quantitative confirmatory method according to the latest EU guidelines and shows good precision, linearity and accuracy data, and CCalpha and CCbeta values of 0.1-0.3 and 0.4-1.0 ng/ml, respectively. Currently, the method has been successfully applied to suspect urine samples for more than a year, and occasionally to faeces, feed and swab samples as well. Results obtained from untreated and treated animals are given and their impact on the debate about the origin of residues of 17beta-boldenone is critically discussed. Finally, preliminary data about the degree of conjugation of boldenone residues are presented and a simple procedure for discrimination between residues from abuse versus natural origin is proposed.

Comparison of three methods of sampling for endometrial cytology in the mare. Preliminary study.

PubMed

Defontis, M; Vaillancourt, D; Grand, F X

2011-01-01

This prospective study aims to compare three different sampling techniques for the collection of endometrial cytological specimens in the mare: the guarded culture swab, the uterine cytobrush and the low volume uterine flush. The study population consisted of six healthy Standardbred mares in dioestrus. In each mare an acute endometritis was induced by performing a low- volume uterine flush 6days after ovulation using a sterile isotonic solution (lactated Ringer's solution or ViGro™ Complete Flush Solution). Two days after initiating inflammation, samples were collected from each mare using the three compared techniques: the double guarded cotton swab, the uterine cytobrush and the low volume uterine flush. The cytological evaluation of the samples was based on following criteria: the quality and cellularity of the samples and the number of neutrophils recovered. The uterine cytobrush yielded slides of significantly (p=0.02) better quality than the low volume uterine flush. There was no significant difference between the cytobrush and the double guarded swab technique for the quality. There was no difference between techniques in the number of endometrial cells (p=0.55) and neutrophils recovered (p=0.28). Endometrial cytology is a practical method for the diagnosis of acute endometrial inflammation in the mare. Since no difference in the number of neutrophils was found between the three techniques, the choice of the sampling method should be based on other factors such as practicability, costs and disadvantages of each technique.

Pigment identification in artwork using graphite furnace atomic absorption spectrometry.

PubMed

Goltz, D M; Coombs, J; Marion, C; Cloutis, E; Gibson, J; Attas, M; Choo-Smith, L-P; Collins, C

2004-06-17

The use of a sampling technique is described for the identification of metals from inorganic pigments in paint. The sampling technique involves gently contacting a cotton swab with the painted surface to physically remove a minute quantity ( approximately 1-2mug) of pigment. The amount of material removed from the painted surface is invisible to the unaided eye and does not cause any visible effect to the painted surface. The cotton swab was then placed in a 1.5ml polystyrene beaker containing HNO(3) to extract pigment metals prior to analysis using graphite furnace atomic absorption spectrometry (GFAAS). GFAAS is well suited for identifying pigment metals since it requires small samples and many pigments consist of main group elements (e.g. Al) as well as transition metals (e.g. Zn, Fe and Cd). Using Cd (cadmium red) as the test element, the reproducibility of sampling a paint surface with the cotton swab was approximately 13% in either a water or oil medium. To test the feasibility of cotton sampling for pigment identification, samples were obtained from paintings (watercolour and oil) of a local collection. Raman spectra provided complementary information to the GFAAS, which together are essential for positive identification of some pigments. For example, GFAAS indicated the presence of Cu, but the Raman spectra positively identified the modern copper pigment phthalocyanine green (Cu(C(32)Cl(16)N(8)). Both Raman spectroscopy and GFAAS were useful for identifying ZnO as a white pigment.

Aneuploidy-dependent massive deregulation of the cellular transcriptome and apparent divergence of the Wnt/beta-catenin signaling pathway in human rectal carcinomas.

PubMed

Grade, Marian; Ghadimi, B Michael; Varma, Sudhir; Simon, Richard; Wangsa, Danny; Barenboim-Stapleton, Linda; Liersch, Torsten; Becker, Heinz; Ried, Thomas; Difilippantonio, Michael J

2006-01-01

To identify genetic alterations underlying rectal carcinogenesis, we used global gene expression profiling of a series of 17 locally advanced rectal adenocarcinomas and 20 normal rectal mucosa biopsies on oligonucleotide arrays. A total of 351 genes were differentially expressed (P < 1.0e-7) between normal rectal mucosa and rectal carcinomas, 77 genes had a >5-fold difference, and 85 genes always had at least a 2-fold change in all of the matched samples. Twelve genes satisfied all three of these criteria. Altered expression of genes such as PTGS2 (COX-2), WNT1, TGFB1, VEGF, and MYC was confirmed, whereas our data for other genes, like PPARD and LEF1, were inconsistent with previous reports. In addition, we found deregulated expression of many genes whose involvement in rectal carcinogenesis has not been reported. By mapping the genomic imbalances in the tumors using comparative genomic hybridization, we could show that DNA copy number gains of recurrently aneuploid chromosome arms 7p, 8q, 13q, 18q, 20p, and 20q correlated significantly with their average chromosome arm expression profile. Taken together, our results show that both the high-level, significant transcriptional deregulation of specific genes and general modification of the average transcriptional activity of genes residing on aneuploid chromosomes coexist in rectal adenocarcinomas.

Aneuploidy-Dependent Massive Deregulation of the Cellular Transcriptome and Apparent Divergence of the Wnt/β-catenin Signaling Pathway in Human Rectal Carcinomas

PubMed Central

Grade, Marian; Ghadimi, B. Michael; Varma, Sudhir; Simon, Richard; Wangsa, Danny; Barenboim-Stapleton, Linda; Liersch, Torsten; Becker, Heinz; Ried, Thomas; Difilippantonio, Michael J.

2016-01-01

To identify genetic alterations underlying rectal carcinogenesis, we used global gene expression profiling of a series of 17 locally advanced rectal adenocarcinomas and 20 normal rectal mucosa biopsies on oligonucleotide arrays. A total of 351 genes were differentially expressed (P < 1.0e–7) between normal rectal mucosa and rectal carcinomas, 77 genes had a >5-fold difference, and 85 genes always had at least a 2-fold change in all of the matched samples. Twelve genes satisfied all three of these criteria. Altered expression of genes such as PTGS2 (COX-2), WNT1, TGFB1, VEGF, and MYC was confirmed, whereas our data for other genes, like PPARD and LEF1, were inconsistent with previous reports. In addition, we found deregulated expression of many genes whose involvement in rectal carcinogenesis has not been reported. By mapping the genomic imbalances in the tumors using comparative genomic hybridization, we could show that DNA copy number gains of recurrently aneuploid chromosome arms 7p, 8q, 13q, 18q, 20p, and 20q correlated significantly with their average chromosome arm expression profile. Taken together, our results show that both the high-level, significant transcriptional deregulation of specific genes and general modification of the average transcriptional activity of genes residing on aneuploid chromosomes coexist in rectal adenocarcinomas. PMID:16397240

Evaluation of a new T2 Magnetic Resonance assay for rapid detection of emergent fungal pathogen Candida auris on clinical skin swab samples.

PubMed

Sexton, D Joseph; Bentz, Meghan L; Welsh, Rory M; Litvintseva, Anastasia P

2018-06-25

Candida auris is a multidrug-resistant pathogenic yeast whose recent emergence is of increasing public-health concern. C. auris can colonize multiple body sites, including patients' skin, and survive for weeks in the healthcare environment, facilitating patient-to-patient transmission and fueling healthcare-associated outbreaks. Rapid and accurate detection of C. auris colonization is essential for timely implementation of infection control measures and prevent transmission. Currently, axilla/groin composite swabs, used to assess colonization status, are processed using a culture-based method that is sensitive and specific but requires 14 days. This delay limits the opportunity to respond and highlights the need for a faster alternative. The culture-independent T2 Magnetic Resonance (T2MR) system is a rapid diagnostic platform shown to detect target pathogens of interest from unprocessed blood samples in <5 hours. In this study, a new C. auris-specific T2 assay was evaluated for screening of the skin surveillance samples. Inclusivity and limit of detection of the T2 C. auris assay were assessed with spiked samples in a representative skin flora background. The T2 C. auris assay recognized isolates from each of the 4 known clades of C. auris and consistently detected cells at 5 CFU/mL. Finally, 89 clinical axilla/groin swab samples were processed with the T2 C. auris assay. The culture-based diagnostic assay was used as a gold standard to determine performance statistics including sensitivity (0.89) and specificity (0.98). Overall, the T2 C. auris assay performed well as a rapid diagnostic and could help expedite the detection of C. auris in patient skin swabs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Surveillance of Salmonella enteritidis in layer houses: a retrospective comparison of the Food and Drug Administration's egg safety rule (2010-2011) and the California Egg Quality Assurance Program (2007-2011).

PubMed

Pitesky, Maurice; Charlton, Bruce; Bland, Mark; Rolfe, Dan

2013-03-01

Between July 2007 and December 2011, 2660 environmental drag swab samples were collected in total from California layer flocks on behalf of the California Egg Quality Assurance Program (CEQAP), the egg safety rule (21 CFR Parts 16 and 118) of the Food and Drug Administration (FDA), or both. The samples were processed by the California Animal Health and Food Safety Lab, and positive or negative results for Salmonella enterica serovar Enteritidis (SE) were recorded. This study retrospectively compares the differences between the FDA and CEQAP programs with respect to their SE environmental sampling surveillance results. To accomplish this comparison, two different CEQAP (new and old) data sets representing different SE environmental surveillance approaches in the life of the flock were compared against each other and against the FDA's SE environmental testing plan. Significant differences were noted between the CEQAP and FDA programs with respect to the prevalence of SE in the farm environment. Analyses of the prevalence of SE at different stages in the flock's life cycle (chick papers, preproduction, midproduction, postmolt, and premarket) found the highest prevalence of SE in premarket (11.9%), followed by postmolt (3.5%) and midproduction (3.4%), and there was a tie between chick papers and preproduction (2.1%). To assess the main effects of the presence of SE in the farm environment, backwards binary logistic regression was used. Of six independent variables examined (age of flock, year, season, owner, CEQAP membership, and analysis of pooled samples vs. individual swabs), only age of flock, owner, and year were determined to be significant factors in the final model. Although CEQAP membership and pooling vs. individuals swabs were not included in the final model, Pearson chi-square tests did show significantly higher odds of SE for non-CEQAP member farms and higher odds of SE in pooled samples vs. individual swabs.

¹H NMR-based metabolic profiling of human rectal cancer tissue

PubMed Central

2013-01-01

Background Rectal cancer is one of the most prevalent tumor types. Understanding the metabolic profile of rectal cancer is important for developing therapeutic approaches and molecular diagnosis. Methods Here, we report a metabonomics profiling of tissue samples on a large cohort of human rectal cancer subjects (n = 127) and normal controls (n = 43) using 1H nuclear magnetic resonance (1H NMR) based metabonomics assay, which is a highly sensitive and non-destructive method for the biomarker identification in biological systems. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal projection to latent structure with discriminant analysis (OPLS-DA) were applied to analyze the 1H-NMR profiling data to identify the distinguishing metabolites of rectal cancer. Results Excellent separation was obtained and distinguishing metabolites were observed among the different stages of rectal cancer tissues (stage I = 35; stage II = 37; stage III = 37 and stage IV = 18) and normal controls. A total of 38 differential metabolites were identified, 16 of which were closely correlated with the stage of rectal cancer. The up-regulation of 10 metabolites, including lactate, threonine, acetate, glutathione, uracil, succinate, serine, formate, lysine and tyrosine, were detected in the cancer tissues. On the other hand, 6 metabolites, including myo-inositol, taurine, phosphocreatine, creatine, betaine and dimethylglycine were decreased in cancer tissues. These modified metabolites revealed disturbance of energy, amino acids, ketone body and choline metabolism, which may be correlated with the progression of human rectal cancer. Conclusion Our findings firstly identify the distinguishing metabolites in different stages of rectal cancer tissues, indicating possibility of the attribution of metabolites disturbance to the progression of rectal cancer. The altered metabolites may be as potential biomarkers, which would provide a promising molecular diagnostic approach for clinical diagnosis of human rectal cancer. The role and underlying mechanism of metabolites in rectal cancer progression are worth being further investigated. PMID:24138801

A Deep Nasopharyngeal Swab Versus Nonendoscopic Bronchoalveolar Lavage for Isolation of Bacterial Pathogens from Preweaned Calves With Respiratory Disease.

PubMed

Van Driessche, L; Valgaeren, B R; Gille, L; Boyen, F; Ducatelle, R; Haesebrouck, F; Deprez, P; Pardon, B

2017-05-01

Nonendoscopic bronchoalveolar lavage (BAL) is a practical alternative for a deep nasopharyngeal swab (DNS) to sample the airways of a large number of calves in a short period of time. The extent of commensal overgrowth and agreement of BAL with DNS culture results in preweaned calves are unknown. To compare commensal overgrowth and bacterial culture results between DNS and BAL samples. A total of 183 preweaned calves (144 with bovine respiratory disease and 39 healthy animals). Cross-sectional study. Deep nasopharyngeal swab and BAL samples were taken from each calf and cultured to detect Pasteurellaceae and Mycoplasma bovis. Agreement and associations between culture results of DNS and BAL samples were determined by kappa statistics and logistic regression. Bronchoalveolar lavage samples were less often polymicrobial, more frequently negative and yielded more pure cultures compared to DNS, leading to a clinically interpretable culture result in 79.2% of the cases compared to only in 31.2% of the DNS samples. Isolation rates were lower in healthy animals, but not different between DNS and BAL samples. Only Histophilus somni was more likely to be isolated from BAL samples. In clinical cases, a polymicrobial DNS culture result did not increase the probability of a polymicrobial BAL result by ≥30%, nor did it influence the probability of a negative culture. A significant herd effect was noted for all observed relationships. Nonendoscopic BAL samples are far less overgrown by bacteria compared to DNS samples under the conditions of this study, facilitating clinical interpretation and resulting in a higher return on investment in bacteriologic culturing. Copyright © 2017 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

A comparison of salicylic acid levels in normal subjects after rectal versus oral dosing.

PubMed

Maalouf, Roger; Mosley, Mark; James Kallail, K; Kramer, Karen M; Kumar, Gaurav

2009-02-01

The common practice is to use 162 mg of aspirin orally in the emergency department (ED) for patients presenting with myocardial infarction. If the patient cannot take aspirin orally in the authors' facility, then 600 mg of aspirin is given rectally. However, no strong evidence exists as to whether the oral and rectal doses provide equivalent risk protection. The authors hypothesized that the salicylic acid levels for orally and rectally administered aspirin will not be similar, because of the different dosages used and the different routes of administration. The study sample consisted of healthy, nonpregnant, adult volunteers without active illness, who did not take any medication regularly. Each subject served as his or her own control to account for any confounding factors. The study was conducted on 2 days, separated by a 1-week washout period. On the first day, 162 mg of oral aspirin was chewed and swallowed. Salicylic acid levels were obtained at baseline (i.e., before taking the aspirin) and then 30, 60, and 90 minutes after dosing. The 600-mg aspirin suppository was self-administered 1 week later with a sample for laboratory measures again drawn at baseline and then 30, 60, and 90 minutes after dosing. Twenty-four subjects completed the study. The rectal suppository provided significantly more salicylic acid into the blood than the oral tablets over 90 minutes (p < 0.001). No statistical difference was noted between oral and rectal administration from baseline to 30 minutes (p > 0.05). However, mean salicylic acid levels from the rectal suppository were statistically higher than from the oral tablets from 30 to 60 minutes (p < 0.001) and from 60 to 90 minutes (p = 0.002). More than 60% of the subjects had an increasing salicylic acid level response over time to the rectal suppository. The salicylic acid level response to the oral administration was more evenly divided between those subjects whose salicylic acid levels peaked quickly and then fell or held steady (33%), those whose salicylic acid levels increased over time (29%), and those whose salicylic acid levels were measureable only after 60 minutes (25%). Although not statistically significant, these differences in group distributions for the type of salicylic acid level response between oral and rectal doses suggested the possibility of a rectal advantage. Whether the higher salicylic acid levels and faster absorption of the rectal aspirin translate into better clinical outcomes is unknown and cannot be concluded from our study. Previous evidence, however, has shown that 162 mg of aspirin chewed and swallowed provided lower mortality in patients presenting with myocardial infarction. Our results suggested the rectal administration of a 600-mg suppository provides sufficient levels of salicylic acid within 90 minutes to meet or exceed that of oral aspirin.

The application of alkaline lysis and pressure cycling technology in the differential extraction of DNA from sperm and epithelial cells recovered from cotton swabs.

PubMed

Nori, Deepthi V; McCord, Bruce R

2015-09-01

This study reports the development of a two-step protocol using pressure cycling technology (PCT) and alkaline lysis for differential extraction of DNA from mixtures of sperm and vaginal epithelial cells recovered from cotton swabs. In controlled experiments, in which equal quantities of sperm and female epithelial cells were added to cotton swabs, 5 min of pressure pulsing in the presence of 0.4 M NaOH resulted in 104 ± 6% recovery of female epithelial DNA present on the swab. Following the pressure treatment, exposing the swabs to a second 5-min alkaline treatment at 95 °C without pressure resulted in the selective recovery of 69 ± 6% of the sperm DNA. The recovery of the vaginal epithelia and sperm DNA was optimized by examining the effect of sodium hydroxide concentration, incubation temperature, and time. Following the alkaline lysis steps, the samples were neutralized with 2 M Tris (pH 7.5) and purified with phenol-chloroform-isoamyl alcohol to permit downstream analysis. The total processing time to remove both fractions from the swab was less than 20 min. Short tandem repeat (STR) analysis of these fractions obtained from PCT treatment and alkaline lysis generated clean profiles of female epithelial DNA and male sperm DNA for 1:1 mixtures of female and male cells and predominant male profiles for mixtures up to 5:1 female to male cells. By reducing the time and increasing the recovery of DNA from cotton swabs, this new method presents a novel and potentially useful procedure for forensic differential extractions.

Comparison of rapid diagnostic tests to detect Mycobacterium avium subsp. paratuberculosis disseminated infection in bovine liver.

PubMed

Zarei, Mehdi; Ghorbanpour, Masoud; Tajbakhsh, Samaneh; Mosavari, Nader

2017-08-01

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, a chronic enteritis in cattle and other domestic and wild ruminants. The presence of MAP in tissues other than intestines and associated lymph nodes, such as meat and liver, is a potential public health concern. In the present study, the relationship between the results of rapid diagnostic tests of the Johne's disease, such as serum ELISA, rectal scraping PCR, and acid-fast staining, and the presence of MAP in liver was evaluated. Blood, liver, and rectal scraping samples were collected from 200 slaughtered cattle with unknown Johne's disease status. ELISA was performed to determine the MAP antibody activity in the serum. Acid-fast staining was performed on rectal scraping samples, and PCR was performed on rectal scraping and liver samples. PCR-positive liver samples were used for mycobacterial culture. Overall, the results of this study demonstrated that MAP can be detected and cultured from liver of slaughtered cattle and rapid diagnostic tests of Johne's disease have limited value in detecting cattle with MAP infection in liver. These findings show that the presence of MAP in liver tissue may occur in cows with negative results for rapid diagnostic tests and vice versa. Hence, liver might represent another possible risk of human exposure to MAP. Given concerns about a potential zoonotic role for MAP, these results show the necessity to find new methods for detecting cattle with MAP disseminated infection.

Demographic variation in community-based MRSA skin and soft tissue infection in Auckland, New Zealand.

PubMed

Ritchie, Stephen R; Fraser, John D; Libby, Eric; Morris, Arthur J; Rainey, Paul B; Thomas, Mark G

2011-04-15

To estimate the burden of skin and soft tissue infection caused by Staphylococcus aureus (S. aureus), and to determine the effects of ethnicity and age on the rate of skin and soft tissue due to MRSA in the Auckland community. We reviewed the culture and susceptibility results of all wound swabs processed by Auckland's only community microbiology laboratory in 2007. Demographic data for a random sample of 1000 people who had a wound swab collected and for all people from whom a methicillin-resistant S. aureus (MRSA) strain was isolated were obtained and compared to demographic data for the total population of Auckland. S. aureus was isolated from 23853/47047 (51%) wound swab cultures performed in 2007; the estimated annual incidence of S. aureus isolation from a wound swab was 1847/100,000 people; and the estimated annual incidence of MRSA isolation from a wound swab was 145/100,000 people. Maori and Pacific people had higher rates of non-multiresistant MRSA infection compared with New Zealand European and Asian people; elderly New Zealand European people had much higher rates of multiresistant MRSA infections compared with people from other ethnic groups. S. aureus is a very common cause of disease in the community and the incidence of infection with MRSA subtypes varies with ethnicity.

Feeding supplemental dried distiller's grains increases faecal shedding of Escherichia coli O157 in experimentally inoculated calves.

PubMed

Jacob, M E; Parsons, G L; Shelor, M K; Fox, J T; Drouillard, J S; Thomson, D U; Renter, D G; Nagaraja, T G

2008-04-01

Escherichia coli O157 is an important foodborne pathogen and asymptomatic cattle serve as major reservoirs for human infection. We have shown a positive association between feeding distiller's grains and E. coli O157 prevalence in feedlot cattle. The objective of this study was to determine the effect of feeding dried distiller's grain (DDG) on faecal shedding of E. coli O157 in calves experimentally inoculated with E. coli O157. Holstein calves (five per treatment group), fed steam-flaked corn-based high-grain diets supplemented with 0% (control) or 25% DDG, were orally inoculated with a five-strain mixture (6 x 10(9) CFU/calf) of nalidixic acid-resistant (NalR) E. coli O157. Faecal samples were taken three times per week for 6 weeks to determine the prevalence and concentration of Nal E. coli O157. At the end of the study (day 43), calves were euthanized and necropsied. Ruminal, caecum, colon, and rectal contents, and rectoanal mucosal swab (RAMS) samples were collected at necropsy to determine NalR E. coli O157 concentration. There was a trend for an interaction between treatment and faecal sampling day. The concentration of NalR E. coli O157 in the faeces was significantly higher in faecal samples from calves fed DDG compared with control calves on days 35, 37, 39 and 42. At necropsy, the concentration of NalR E. coli O157 was higher in the caecum (P = 0.01), colon (P = 0.03) and rectum (P = 0.01) from calves fed DDG compared with control animals. The number of sites at necropsy positive for NalR E. coli O157 was higher in calves fed DDG compared with calves in the control treatment (P < 0.001). Our results indicate that E. coli O157 gut persistence and faecal prevalence increased in calves fed DDG, which potentially have important implications for food safety.

Accuracy of dry vaginal self-sampling for detecting high-risk human papillomavirus infection in cervical cancer screening: a cross-sectional study.

PubMed

Haguenoer, K; Giraudeau, B; Gaudy-Graffin, C; de Pinieux, I; Dubois, F; Trignol-Viguier, N; Viguier, J; Marret, H; Goudeau, A

2014-08-01

Cervical cancer screening coverage remains insufficient in most countries. Testing self-collected samples for high-risk human papillomavirus (HR-HPV) could be an alternative to the Pap smear, but costs, sampling methods and transport issues hamper its wide use. Our objective was to compare diagnostic accuracy of 2 vaginal self-collection methods, a dry swab (vsc-DRY) or swab in liquid medium (vsc-LIQ), for detecting HR-HPV cervical infection assessed by a cervical clinician-collected sample in liquid medium (ccc-LIQ). Women 20 to 65 years attending a Pap smear were recruited between September, 2009 and March, 2011. Each sample (3 per woman) underwent HPV DNA testing. Samples were classified as HR-HPV+ with detection of at least one HR-HPV or probable HR-HPV type. Of 734 women included, 722 had complete HPV data. HR-HPV was detected in 20.9% of ccc-LIQ samples. Estimated sensitivity and specificity to detect HR-HPV in vsc-DRY samples were 88.7% and 92.5%, respectively, and in vsc-LIQ samples, 87.4% and 90.9%. Cytology findings were abnormal for 79 women (10.9%): among 27 samples of low-grade squamous intraepithelial lesions, 25 were HR-HPV+ in vsc-DRY, vsc-LIQ and ccc-LIQ samples. Among 6 samples of high-grade squamous intraepithelial lesions, all were HR-HPV+ in vsc-DRY samples, 1 was HR-HPV- in vsc-LIQ samples and 1 was HR-HPV- in ccc-LIQ samples. Vaginal self-sampling with a dry swab is accurate to detect HR-HPV infection as compared with cervical clinician-collection and accurate as compared with cytology results. This cheap and easy-to-ship sampling method could be widely used in a cervical cancer screening program. Copyright © 2014 Elsevier Inc. All rights reserved.

High Prevalence of Multidrug-Resistant Mycoplasma genitalium in Human Immunodeficiency Virus-Infected Men Who Have Sex With Men in Alabama.

PubMed

Dionne-Odom, Jodie; Geisler, William M; Aaron, Kristal J; Waites, Ken B; Westfall, Andrew O; Van Der Pol, Barbara; Xiao, Li

2018-02-10

We tested for Mycoplasma genitalium in 157 HIV-infected men. Urogenital and rectal prevalence were 10.8% and 6.4%. Macrolide resistance mutations were detected in 70.6% and 80% of urogenital and rectal samples, and fluoroquinolone resistance mutations in 26.7% and 40%, respectively.

Leprosy Associated with Atypical Cutaneous Leishmaniasis in Nicaragua and Honduras.

PubMed

Soto, Lucrecia Acosta; Caballero, Nelson; Fuentes, Lesny Ruth; Muñoz, Pedro Torres; Gómez Echevarría, Jose Ramón; López, Montserrat Pérez; Bornay Llinares, Fernando Jorge; Stanford, John L; Stanford, Cynthia A; Donoghue, Helen D

2017-10-01

In Central America, few cases of leprosy have been reported, but the disease may be unrecognized. Diagnosis is based on clinical criteria and histology. Preliminary field work in Nicaragua and Honduras found patients, including many children, with skin lesions clinically suggestive of atypical cutaneous leishmaniasis or indeterminate leprosy. Histology could not distinguish these diseases although acid-fast organisms were visible in a few biopsies. Lesions healed after standard antimicrobial therapy for leprosy. In the present study, patients, family members, and other community members were skin-tested and provided nasal swabs and blood samples. Biopsies were taken from a subgroup of patients with clinical signs of infection. Two laboratories analyzed samples, using local in-house techniques. Mycobacterium leprae , Leishmania spp. and Leishmania infantum were detected using polymerase chain reactions. Mycobacterium leprae DNA was detected in blood samples and nasal swabs, including some cases where leprosy was not clinically suspected. Leishmania spp. were also detected in blood and nasal swabs. Most biopsies contained Leishmania DNA and coinfection of Leishmania spp. with M. leprae occurred in 33% of cases. Mycobacterium leprae DNA was also detected and sequenced from Nicaraguan and Honduran environmental samples. In conclusion, leprosy and leishmaniasis are present in both regions, and leprosy appears to be widespread. The nature of any relationship between these two pathogens and the epidemiology of these infections need to be elucidated.

Assessing DNA recovery from chewing gum.

PubMed

Eychner, Alison M; Schott, Kelly M; Elkins, Kelly M

2017-01-01

The purpose of this study was to evaluate which DNA extraction method yields the highest quantity of DNA from chewing gum. In this study, several popular extraction methods were tested, including Chelex-100, phenol-chloroform-isoamyl alcohol (PCIA), DNA IQ, PrepFiler, and QIAamp Investigator, and the quantity of DNA recovered from chewing gum was determined using real-time polymerase chain reaction with Quantifiler. Chewed gum control samples were submitted by anonymous healthy adult donors, and discarded environmental chewing gum samples simulating forensic evidence were collected from outside public areas (e.g., campus bus stops, streets, and sidewalks). As expected, results indicate that all methods tested yielded sufficient amplifiable human DNA from chewing gum using the wet-swab method. The QIAamp performed best when DNA was extracted from whole pieces of control gum (142.7 ng on average), and the DNA IQ method performed best on the environmental whole gum samples (29.0 ng on average). On average, the QIAamp kit also recovered the most DNA from saliva swabs. The PCIA method demonstrated the highest yield with wet swabs of the environmental gum (26.4 ng of DNA on average). However, this method should be avoided with whole gum samples (no DNA yield) due to the action of the organic reagents in dissolving and softening the gum and inhibiting DNA recovery during the extraction.

First serological and molecular evidence of PPRV occurrence in Ghardaïa district, center of Algeria.

PubMed

Kardjadj, Moustafa; Ben-Mahdi, Meriem-Hind; Luka, Pam Dachung

2015-10-01

In February 2012, an outbreak of peste des petits ruminants (PPR) was suspected in Ghardaïa district at the center of Algeria. Clinical, serological, and molecular investigations were performed to confirm the occurrence of PPRV. The overall morbidity, mortality, and case fatality rates of the ten flocks investigated were 12.2, 2.5, and 20.3 %, respectively. At the flock level, positivity to PPR was 100, 90, and 100 % by competitive ELISA (c-ELISA), RT-PCR of blood samples, and oculo-nasal swabs, respectively. At the individual levels, the present study showed that out of 186 samples collected from the same animals 17/62 (27.41 %), 14/62 (22.85 %), and 36/62 (58.06 %) were positive by c-ELISA, RT-PCR of blood samples, and RT PCR of oculo-nasal swabs, respectively. The positivity of PPR was significantly higher using RT-PCR of oculo-nasal swabs than c-ELISA and RT-PCR of blood samples. The N gene partial sequence of five PPRV-positive amplicons revealed 100 % homology among them and phylogenetically belonged to lineage IV. The sequences also showed similarity range of 97-99 % with the strains implicated in the Moroccan and Tunisian outbreaks, however, suggesting that a similar strain is circulating across this area of the Maghreb and highlighting the need for a regional control approach.

Comparison of false-negative rates and limits of detection following macrofoam-swab sampling of Bacillus anthracis surrogates via Rapid Viability PCR and plate culture.

PubMed

Hutchison, J R; Piepel, G F; Amidan, B G; Hess, B M; Sydor, M A; Deatherage Kaiser, B L

2018-05-01

We evaluated the effects of Bacillus anthracis surrogates, low surface concentrations, surface materials and assay methods on false-negative rate (FNR) and limit of detection (LOD 95 ) for recovering Bacillus spores using a macrofoam-swab sampling procedure. Bacillus anthracis Sterne or Bacillus atrophaeus Nakamura spores were deposited over a range of low target concentrations (2-500 per coupon) onto glass, stainless steel, vinyl tile and plastic. Samples were assayed using a modified Rapid Viability-PCR (mRV-PCR) method and the traditional plate culture method to obtain FNR and LOD 95 results. Mean FNRs tended to be lower for mRV-PCR compared to culturing, and increased as spore concentration decreased for all surface materials. Surface material, but not B. anthracis surrogate, influenced FNRs with the mRV-PCR method. The mRV-PCR LOD 95 was lowest for glass and highest for vinyl tile. LOD 95 values overall were lower for mRV-PCR than for the culture method. This study adds to the limited data on FNR and LOD 95 for mRV-PCR and culturing methods with low concentrations of B. anthracis sampled from various surface materials by the CDC macrofoam-swab method. These are key inputs for planning characterization and clearance studies for low contamination levels of B. anthracis. © 2018 The Society for Applied Microbiology.

Role of human milk oligosaccharides in Group B Streptococcus colonisation

PubMed Central

Andreas, Nicholas J; Al-Khalidi, Asmaa; Jaiteh, Mustapha; Clarke, Edward; Hyde, Matthew J; Modi, Neena; Holmes, Elaine; Kampmann, Beate; Mehring Le Doare, Kirsty

2016-01-01

Group B Streptococcus (GBS) infection is a major cause of morbidity and mortality in infants. The major risk factor for GBS disease is maternal and subsequent infant colonisation. It is unknown whether human milk oligosaccharides (HMOs) protect against GBS colonisation. HMO production is genetically determined and linked to the Lewis antigen system. We aimed to investigate the association between HMOs and infant GBS colonisation between birth and postnatal day 90. Rectovaginal swabs were collected at delivery, as well as colostrum/breast milk, infant nasopharyngeal and rectal swabs at birth, 6 days and days 60–89 postpartum from 183 Gambian mother/infant pairs. GBS colonisation and serotypes were determined using culture and PCR. 1H nuclear magnetic resonance spectroscopy was used to characterise the mother's Lewis status and HMO profile in breast milk. Mothers who were Lewis-positive were significantly less likely to be colonised by GBS (X2=12.50, P<0.001). Infants of Lewis-positive mothers were less likely GBS colonised at birth (X2=4.88 P=0.03) and more likely to clear colonisation between birth and days 60–89 than infants born to Lewis-negative women (P=0.05). There was no association between Secretor status and GBS colonisation. In vitro work revealed that lacto-N-difucohexaose I (LNDFHI) correlated with a reduction in the growth of GBS. Our results suggest that HMO such as LNDFHI may be a useful adjunct in reducing maternal and infant colonisation and hence invasive GBS disease. Secretor status offers utility as a stratification variable in GBS clinical trials. PMID:27588204

Isolation of Escherichia coli and Salmonella spp. from free-ranging wild animals.

PubMed

Iovine, Renata de Oliveira; Dejuste, Catia; Miranda, Flávia; Filoni, Claudia; Bueno, Marina Galvão; de Carvalho, Vania Maria

2015-01-01

Increasing interactions between humans, domestic animals and wildlife may result in inter-species transmission of infectious agents. To evaluate the presence of pathogenic E. coli and Salmonella spp. and to test the antimicrobial susceptibility of isolates, rectal swabs from 36 different free-ranging wild mammals were taken from two distinct natural sites in Brazil: Cantareira State Park (CSP, state of São Paulo) and Santa Isabel do Rio Negro Region (SIRNR, state of Amazonas). The swabs were randomly collected and processed for bacterial isolation, identification, characterization and antimicrobial resistance. Eighteen E. coli strains from CSP and 20 from SIRNR were recovered from 14 and 22 individuals, respectively. Strains from animals captured in CSP, the site with the greatest anthropization, exhibited a higher range and percentage of virulence genes, including an eae+/bfpA+ strain. Antimicrobial resistance was verified in strains originating from both sites; however, in strains from SIRNR, aminopenicillins were almost the exclusive antimicrobial class to which strains exhibited resistance, whereas in CSP there were strains resistant to cephalosporins, sulfonamide, aminoglycoside, tetracycline and fluoroquinolone, in addition to strains exhibiting multidrug resistance. Two strains of Salmonella enterica that are known to be associated with reptiles, serotypes Belem and 60:r:e,n,z15, were recovered only from Amazonian animals and showed susceptibility to all classes of antimicrobials that were tested. Although the potential impact of these pathogens on wildlife remains unknown, bacteria isolated from free-ranging wild animals may provide relevant information about environmental health and should therefore be more deeply studied.

Enterovirus spectrum from the active surveillance of hand foot and mouth disease patients under the clinical trial of inactivated Enterovirus A71 vaccine in Jiangsu, China, 2012-2013.

PubMed

Yao, Xin; Bian, Lian-Lian; Lu, Wei-Wei; Li, Jing-Xin; Mao, Qun-Ying; Wang, Yi-Ping; Gao, Fan; Wu, Xing; Ye, Qiang; Xu, Miao; Li, Xiu-Ling; Zhu, Feng-Cai; Liang, Zheng-Lun

2015-12-01

Epidemiological data from active surveillance on human enterovirus, which could cause hand, foot, and mouth disease, were limited. An active surveillance system was used to investigate the enterovirus spectrum and the incidence of different enteroviruses in infants aged 6-35 months in Jiangsu Province from 2012 to 2013. Fifty-nine infants were randomly selected from 522 non-EV-A71/CV-A16 HFMD patients. We collected 173 throat swabs and 174 rectal swabs from these infants. RT-PCR was used to amplify 5'-UTR and VP1 regions of enteroviruses and the serotypes were determined by the sequence comparison using BLAST. Twenty-one non-EV-A71/CA16 enterovirus serotypes were detected in those infants. E16, E18 were firstly reported in HFMD patients. The four top common non-EV-A71/CV-A enteroviruses among infants were CV-B3, CV-A10, CV-A6, and E9 with the HFMD incidence rates at 1.4%, 0.84%, 0.56%, and 0.47%, respectively. Over 20.8% patients were co-infected with multiple enteroviruses. Neither the course of sickness nor clinical symptoms of the co-infected patients was more severe than those infected with single enterovirus. Two patients were infected different enterovirus successively within 2 months. Several new enterovirus serotypes and multiple models of infection associated with HFMD were discovered through the active surveillance system. These data provide a better understanding of the viral etiology of HFMD. © 2015 Wiley Periodicals, Inc.

Monitoring genotoxic exposure in uranium miners

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

Sram, R.J.; Binkova, B.; Dobias, L.

1993-03-01

Recent data from deep uranium mines in Czechoslovakia indicated that in addition to radon daughter products, miners are also exposed to chemical mutagens. Mycotoxins were identified as a possible source of mutagenicity present in the mines. Various methods of biomonitoring were used to examine three groups of miners from different uranium mines. Cytogenetic analysis of peripheral lymphocytes, unscheduled DNA synthesis (UDS) in lymphocytes, and lipid peroxidation (LPO) in both plasma and lymphocytes were studied on 66 exposed miners and 56 controls. Throat swabs were taken from 116 miners and 78 controls. Significantly increased numbers of aberrant cells were found inmore » all groups of miners, as well as decreased UDS values in lymphocytes and increased LPO plasma levels in comparison to controls. Molds were detected in throat swabs from 27% of miners, and 58% of these molds were embryotoxic. Only 5% of the control samples contained molds and none of them was embryotoxic. The following mycotoxins were isolated from miners' throat swab samples: rugulosin, sterigmatocystin, mycophenolic acid, brevianamid A, citreoviridin, citrinin, penicilic acid, and secalonic acid. These data suggest that mycotoxins are a genotoxic factor affecting uranium miners.« less

Monitoring genotoxic exposure in uranium miners.

PubMed Central

Srám, R J; Binková, B; Dobiás, L; Rössner, P; Topinka, J; Veselá, D; Veselý, D; Stejskalová, J; Bavorová, H; Rericha, V

1993-01-01

Recent data from deep uranium mines in Czechoslovakia indicated that in addition to radon daughter products, miners are also exposed to chemical mutagens. Mycotoxins were identified as a possible source of mutagenicity present in the mines. Various methods of biomonitoring were used to examine three groups of miners from different uranium mines. Cytogenetic analysis of peripheral lymphocytes, unscheduled DNA synthesis (UDS) in lymphocytes, and lipid peroxidation (LPO) in both plasma and lymphocytes were studied on 66 exposed miners and 56 controls. Throat swabs were taken from 116 miners and 78 controls. Significantly increased numbers of aberrant cells were found in all groups of miners, as well as decreased UDS values in lymphocytes and increased LPO plasma levels in comparison to controls. Molds were detected in throat swabs from 27% of miners, and 58% of these molds were embryotoxic. Only 5% of the control samples contained molds and none of them was embryotoxic. The following mycotoxins were isolated from miners' throat swab samples: rugulosin, sterigmatocystin, mycophenolic acid, brevianamid A, citreoviridin, citrinin, penicilic acid, and secalonic acid. These data suggest that mycotoxins are a genotoxic factor affecting uranium miners. PMID:8319649

Isolation and identification of bovine Brucella isolates from Pakistan by biochemical tests and PCR.

PubMed

Ali, Shahzad; Ali, Qurban; Melzer, Falk; Khan, Iahtasham; Akhter, Shamim; Neubauer, Heinrich; Jamal, Syed M

2014-01-01

Brucellosis is endemic in bovines in Pakistan. The Brucella species and biovars involved, however, are unknown. The objectives of the present study were to isolate and characterize brucellae from seropositive milk samples, aborted fetuses, and vaginal swabs of cattle and buffaloes which had recently aborted. The seropositive milk samples, aborted fetuses, and vaginal swabs of cattle and buffaloes were collected from the Potohar Plateau, Pakistan. Isolation of brucellae was done on modified Farrell's serum dextrose agar. Isolates were characterized by conventional biotyping methods, while molecular typing was done by genus (B4/B5) and species-specific (Brucella abortus, Brucella melitensis, Brucella ovis, and Brucella suis) polymerase chain reaction (PCR). A total of 30 isolates were recovered from milk (n = 5), aborted fetuses (n = 13), and vaginal swabs (n = 12). Most isolates were from cattle (56.7 %). All of them were identified as B. abortus biovar 1 based on conventional biotyping methods and genus and species-specific PCR. This preliminary study provides the first report on the prevalence of B. abortus biovar 1 in cattle and buffaloes in Pakistan.

Looking for Microbes in a Spacecraft Assembly Clean Room

NASA Image and Video Library

2013-11-06

A microbiologist collects a swab sample from the floor of a spacecraft assembly clean room at NASA Jet Propulsion Laboratory where samples such as this are taken frequently during the assembly of a spacecraft and analyzed.

Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples

PubMed Central

Leach, L.; Zhu, Y.

2017-01-01

ABSTRACT Candida auris is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 (ITS2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1 C. auris CFU/PCR. The performance of the C. auris real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected C. auris DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired C. auris. The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of C. auris and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities. PMID:29187562

Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples.

PubMed

Leach, L; Zhu, Y; Chaturvedi, S

2018-02-01

Candida auris is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 ( ITS 2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1 C. auris CFU/PCR. The performance of the C. auris real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected C. auris DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired C. auris The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of C. auris and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities. Copyright © 2018 Leach et al.

PERSONAL CHARACTERISTICS OF OLDER PRIMARY CARE PATIENTS WHO PROVIDE A BUCCAL SWAB FOR APOE TESTING AND BANKING OF GENETIC MATERIAL: THE SPECTRUM STUDY

PubMed Central

Bogner, Hillary R.; Wittink, Marsha N.; Merz, Jon F.; Straton, Joseph B.; Cronholm, Peter F.; Rabins, Peter V.; Gallo, Joseph J.

2009-01-01

OBJECTIVE To determine the personal characteristics and reasons associated with providing a buccal swab for APOE genetic testing in a primary care study. METHODS The study sample consisted of 342 adults aged 65 years and older recruited from primary care settings. RESULTS In all, 88% of patients agreed to provide a DNA sample for APOE genotyping and 78% of persons providing a sample agreed to banking of the DNA. Persons aged 80 years and older and African-Americans were less likely to participate in APOE genotyping. Concern about confidentiality was the most common reason for not wanting to provide a DNA sample or to have DNA banked. CONCLUSION We found stronger relationships between sociodemographic variables of age and ethnicity with participation in genetic testing than we did between level of educational attainment, gender, function, cognition, and affect. PMID:15692195

Next-Generation Sequencing of Matched Primary and Metastatic Rectal Adenocarcinomas Demonstrates Minimal Mutation Gain and Concordance to Colonic Adenocarcinomas.

PubMed

Crumley, Suzanne M; Pepper, Kristi L; Phan, Alexandria T; Olsen, Randall J; Schwartz, Mary R; Portier, Bryce P

2016-06-01

-Colorectal carcinoma is the third most common cause of cancer death in males and females in the United States. Rectal adenocarcinoma can have distinct therapeutic and surgical management from colonic adenocarcinoma owing to its location and anatomic considerations. -To determine the oncologic driver mutations and better understand the molecular pathogenesis of rectal adenocarcinoma in relation to colon adenocarcinoma. -Next-generation sequencing was performed on 20 cases of primary rectal adenocarcinoma with a paired lymph node or solid organ metastasis by using an amplicon-based assay of more than 2800 Catalogue of Somatic Mutations in Cancer (COSMIC)-identified somatic mutations. -Next-generation sequencing data were obtained on both the primary tumor and metastasis from 16 patients. Most rectal adenocarcinoma cases demonstrated identical mutations in the primary tumor and metastasis (13 of 16, 81%). The mutations identified, listed in order of frequency, included TP53, KRAS, APC, FBXW7, GNAS, FGFR3, BRAF, NRAS, PIK3CA, and SMAD4. -The somatic mutations identified in our rectal adenocarcinoma cohort showed a strong correlation to those previously characterized in colonic adenocarcinoma. In addition, most rectal adenocarcinomas harbored identical somatic mutations in both the primary tumor and metastasis. These findings demonstrate evidence that rectal adenocarcinoma follows a similar molecular pathogenesis as colonic adenocarcinoma and that sampling either the primary or metastatic lesion is valid for initial evaluation of somatic mutations and selection of possible targeted therapy.

MicroRNA Expression Profiling to Identify and Validate Reference Genes for the Relative Quantification of microRNA in Rectal Cancer.

PubMed

Eriksen, Anne Haahr Mellergaard; Andersen, Rikke Fredslund; Pallisgaard, Niels; Sørensen, Flemming Brandt; Jakobsen, Anders; Hansen, Torben Frøstrup

2016-01-01

MicroRNAs (miRNAs) play important roles in regulating biological processes at the post-transcriptional level. Deregulation of miRNAs has been observed in cancer, and miRNAs are being investigated as potential biomarkers regarding diagnosis, prognosis and prediction in cancer management. Real-time quantitative polymerase chain reaction (RT-qPCR) is commonly used, when measuring miRNA expression. Appropriate normalisation of RT-qPCR data is important to ensure reliable results. The aim of the present study was to identify stably expressed miRNAs applicable as normaliser candidates in future studies of miRNA expression in rectal cancer. We performed high-throughput miRNA profiling (OpenArray®) on ten pairs of laser micro-dissected rectal cancer tissue and adjacent stroma. A global mean expression normalisation strategy was applied to identify the most stably expressed miRNAs for subsequent validation. In the first validation experiment, a panel of miRNAs were analysed on 25 pairs of micro dissected rectal cancer tissue and adjacent stroma. Subsequently, the same miRNAs were analysed in 28 pairs of rectal cancer tissue and normal rectal mucosa. From the miRNA profiling experiment, miR-645, miR-193a-5p, miR-27a and let-7g were identified as stably expressed, both in malignant and stromal tissue. In addition, NormFinder confirmed high expression stability for the four miRNAs. In the RT-qPCR based validation experiments, no significant difference between tumour and stroma/normal rectal mucosa was detected for the mean of the normaliser candidates miR-27a, miR-193a-5p and let-7g (first validation P = 0.801, second validation P = 0.321). MiR-645 was excluded from the data analysis, because it was undetected in 35 of 50 samples (first validation) and in 24 of 56 samples (second validation), respectively. Significant difference in expression level of RNU6B was observed between tumour and adjacent stromal (first validation), and between tumour and normal rectal mucosa (second validation). We recommend the mean expression of miR-27a, miR-193a-5p and let-7g as normalisation factor, when performing miRNA expression analyses by RT-qPCR on rectal cancer tissue.

Use of prostate-specific antigen (PSA) to measure semen exposure resulting from male condom failures: implications for contraceptive efficacy and the prevention of sexually transmitted disease.

PubMed

Walsh, Terri L; Frezieres, Ron G; Peacock, Karen; Nelson, Anita L; Clark, Virginia A; Bernstein, Leslie; Wraxall, Brian G D

2003-02-01

Accurate measurement of semen exposure resulting from condom failures can refine public health messages and improve predictions of condom efficacy in preventing pregnancy and HIV transmission. Eight hundred and thirty couples enrolled in a condom efficacy study were asked to collect a baseline sample of ejaculate from the inside of the first study condom they used and to collect a postcoital vaginal sample whenever a study condom broke or slipped off during intercourse. All samples were quantitatively tested for prostate-specific antigen (PSA), a substance found only in human semen, using rocket immunoelectrophoresis, and inspected microscopically for presence of sperm. Sixty-eight baseline ejaculate samples collected from the inside of the first study condom by couples who subsequently experienced a condom failure averaged 13.4 microg PSA per swab and 79% of the samples averaged one or more sperm per high power field (hpf). Seventy-nine postcoital vaginal samples obtained after a condom break averaged 5.7 microg PSA per swab and only 38% averaged one or more sperm per hpf. The PSA results indicated a 50% reduction in semen exposure compared to baseline levels (p = 0.0001). Seventeen samples obtained after a condom slip-off averaged 2.5 microg PSA per swab and none of the samples averaged one or more sperm per hpf. The PSA results indicated an 80% reduction in semen exposure compared to baseline levels (p = 0.0001). Our results suggest that even condoms that fail reduce the risk of pregnancy and the transmission of sexually transmitted disease compared to unprotected intercourse. We also used PSA results to adjust a model designed to predict consistent-use pregnancy rates from condom breakage and slippage data.

Detection of equine herpesvirus in horses with idiopathic keratoconjunctivitis and comparison of three sampling techniques.

PubMed

Hollingsworth, Steven R; Pusterla, Nicola; Kass, Philip H; Good, Kathryn L; Brault, Stephanie A; Maggs, David J

2015-09-01

To determine the role of equine herpesvirus (EHV) in idiopathic keratoconjunctivitis in horses and to determine whether sample collection method affects detection of EHV DNA by quantitative polymerase chain reaction (qPCR). Twelve horses with idiopathic keratoconjunctivitis and six horses without signs of ophthalmic disease. Conjunctival swabs, corneal scrapings, and conjunctival biopsies were collected from 18 horses: 12 clinical cases with idiopathic keratoconjunctivitis and six euthanized controls. In horses with both eyes involved, the samples were taken from the eye judged to be more severely affected. Samples were tested with qPCR for EHV-1, EHV-2, EHV-4, and EHV-5 DNA. Quantity of EHV DNA and viral replicative activity were compared between the two populations and among the different sampling techniques; relative sensitivities of the sampling techniques were determined. Prevalence of EHV DNA as assessed by qPCR did not differ significantly between control horses and those with idiopathic keratoconjunctivitis. Sampling by conjunctival swab was more likely to yield viral DNA as assessed by qPCR than was conjunctival biopsy. EHV-1 and EHV-4 DNA were not detected in either normal or IKC-affected horses; EHV-2 DNA was detected in two of 12 affected horses but not in normal horses. EHV-5 DNA was commonly found in ophthalmically normal horses and horses with idiopathic keratoconjunctivitis. Because EHV-5 DNA was commonly found in control horses and in horses with idiopathic keratoconjunctivitis, qPCR was not useful for the etiological diagnosis of equine keratoconjunctivitis. Conjunctival swabs were significantly better at obtaining viral DNA samples than conjunctival biopsy in horses in which EHV-5 DNA was found. © 2015 American College of Veterinary Ophthalmologists.

Bacterial assemblages differ between compartments within the coral holobiont

NASA Astrophysics Data System (ADS)

Sweet, M. J.; Croquer, A.; Bythell, J. C.

2011-03-01

It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the `snot sucker') was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the `snot sucker' and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.

Dual quantification of dapivirine and maraviroc in cervicovaginal secretions from ophthalmic tear strips and polyester-based swabs via liquid chromatographic-tandem mass spectrometric (LC-MS/MS) analysis.

PubMed

Parsons, Teresa L; Emory, Joshua F; Seserko, Lauren A; Aung, Wutyi S; Marzinke, Mark A

2014-09-01

Topical microbicidal agents are being actively pursued as a modality to prevent HIV viral transmission during sexual intercourse. Quantification of antiretroviral agents in specimen sources where antiviral activity is elicited is critical, and drug measurements in cervicovaginal fluid can provide key information on local drug concentrations. Two antiretroviral drugs, dapivirine and maraviroc, have gained interest as vaginal microbicidal agents, and rugged methods are required for their quantification in cervicovaginal secretions. Cervicovaginal fluid spiked with dapivirine and maraviroc were applied to ophthalmic tear strips or polyester-based swabs to mimic collection procedures used in clinical studies. Following sample extraction and the addition of isotopically labeled internal standards, samples were subjected to liquid chromatographic-tandem mass spectrometric (LC-MS/MS) analysis using a Waters BEH C8, 50mm×2.1mm, 1.7μm particle size column, on an API 4000 mass analyzer operated in selective reaction monitoring mode. The method was validated according to FDA Bioanalytical Method Validation guidelines. Due to the disparate saturation capacity of the tested collection devices, the analytical measuring ranges for dapivirine and maravirocin cervicovaginal fluid on the ophthalmic tear strip were 0.05-25ng/tear strip, and 0.025-25ng/tear strip, respectively. As for the polyester-based swab, the analytical measuring ranges were 0.25-125ng/swab for dapivirine and 0.125-125ng/swab for maraviroc. Dilutional studies were performed for both analytes to extended ranges of 25,000ng/tear strip and 11,250ng/swab. Standard curves were generated via weighted (1/x(2)) linear or quadratic regression of calibrators. Precision, accuracy, stability and matrix effects studies were all performed and deemed acceptable according to the recommendations of the FDA Bioanalytical Method Validation guidelines. A rugged LC-MS/MS method for the dual quantification of dapivirine and maraviroc in cervicovaginal fluid using two unique collection devices has been developed and validated. The described method meets the criteria to support large research trials. Copyright © 2014 Elsevier B.V. All rights reserved.

Dual Quantification of Dapivirine and Maraviroc in Cervicovaginal Secretions from Ophthalmic Tear Strips and Polyester-Based Swabs via Liquid Chromatographic-Tandem Mass Spectrometric (LC-MS/MS) Analysis

PubMed Central

Parsons, Teresa L.; Emory, Joshua F.; Seserko, Lauren A.; Aung, Wutyi S.; Marzinke, Mark A.

2014-01-01

Background Topical microbicidal agents are being actively pursued as a modality to prevent HIV viral transmission during sexual intercourse. Quantification of antiretroviral agents in specimen sources where antiviral activity is elicited is critical, and drug measurements in cervicovaginal fluid can provide key information on local drug concentrations. Two antiretroviral drugs, dapivirine and maraviroc, have gained interest as vaginal microbicidal agents, and rugged methods are required for their quantification in cervicovaginal secretions. Methods Cervicovaginal fluid spiked with dapivirine and maraviroc were applied to ophthalmic tear strips or polyester-based swabs to mimic collection procedures used in clinical studies. Following sample extraction and the addition of isotopically-labeled internal standards, samples were subjected to liquid chromatographic-tandem mass spectrometric (LC-MS/MS) analysis using a Waters BEH C8, 50 × 2.1 mm, 1.7 µm particle size column, on an API 4000 mass analyzer operated in selective reaction monitoring mode. The method was validated according to FDA Bioanalytical Method Validation guidelines. Results Due to the disparate saturation capacity of the tested collection devices, the analytical measuring ranges for dapivirine and maravirocin cervicovaginal fluid on the ophthalmic tear strip were 0.05 to 25 ng/tear strip, and 0.025 to 25 ng/tear strip, respectively. As for the polyester-based swab, the analytical measuring ranges were 0.25 to 125 ng/swab for dapivirine and 0.125 to 125 ng/swab for maraviroc. Dilutional studies were performed for both analytes to extended ranges of 25,000 ng/tear strip and 11,250 ng/swab. Standard curves were generated via weighted (1/x2) linear or quadratic regression of calibrators. Precision, accuracy, stability and matrix effects studies were all performed and deemed acceptable according to the recommendations of the FDA Bioanalytical Method Validation guidelines. Conclusions A rugged LC-MS/MS method for the dual quantification of dapivirine and maraviroc in cervicovaginal fluid using two unique collection devices has been developed and validated. The described method meets the criteria to support large research trials. PMID:25005891

Availability of safe drinking-water: the answer to cholera outbreak? Nabua, Camarines Sur, Philippines, 2012.

PubMed

De Guzman, Alethea; de los Reyes, Vikki Carr; Sucaldito, Ma Nemia; Tayag, Enrique

2015-01-01

In May 2012, there were increasing diarrhoea cases and deaths reported from Nabua, Camarines Sur to the Philippines event-based surveillance system. An investigation was conducted to identify risk factors and determine transmission dynamics. A suspected case was defined as a resident of Nabua with at least three episodes of watery diarrhoea per day from 16 March to 22 June 2012. A confirmed case was defined as a suspected case positive for Vibrio cholerae. An environmental investigation was conducted and rectal swabs and water samples sent to the national reference laboratory for bacterial isolation. A 1:2 case-control study matching for age and sex was conducted. Data were analysed using Epi Info. There were 309 suspected cases with two deaths, and the most affected age group was children under five years (45%). Eight cases were positive for Vibrio cholerae Ogawa El Tor and one for Non-01. Water samples were positive for faecal coliforms and Aeromonas caviae. The case-control study showed that cases had a higher odds than controls of using unchlorinated water sources (odds ratio [OR] = 3.6; 95% confidence interval [CI]:1.6-8.5) and having toilets located within 20 m of a septic tank (OR = 2.7; 95% CI: 1.4-5.3). In multivariate analysis, the only significant factor was drinking from piped water (OR = 0.21; 95% CI: 0.09-0.49). In this cholera outbreak, drinking-water from unchlorinated wells was a significant risk factor. Future cholera control efforts should include not just improving water and sanitation systems but also intensified behaviour change campaigns.

Antimicrobial resistance and virulence profile of enterococci isolated from poultry and cattle sources in Nigeria.

PubMed

Ngbede, Emmanuel Ochefije; Raji, Mashood Abiola; Kwanashie, Clara Nna; Kwaga, Jacob Kwada Paghi

2017-03-01

This study investigated the occurrence, antimicrobial resistance and virulence of Enterococcus from poultry and cattle farms. Three hundred and ninety samples: cloacal/rectal swabs (n = 260) and manure (n = 130] were processed for recovery of Enterococcus species. Standard bacteriological methods were used to isolate, identify and characterize Enterococcus species for antimicrobial susceptibility and expression of virulence traits. Detection of antibiotic resistance and virulence genes was carried out by polymerase chain reaction. Enterococcus was recovered from 167 (42.8%) of the 390 samples tested with a predominance of Enterococcus faecium (27.7%). Other species detected were Enterococcus gallinarum, Enterococcus faecalis, Enterococcus hirae, Enterococcus raffinosus, Enterococcus avium, Enterococcus casseliflavus, Enterococcus mundtii and Enterococcus durans. All the isolates tested were susceptible to vancomycin, but resistance to tetracycline, erythromycin, ampicillin and gentamicin was also observed among 61.0, 61.0, 45.1 and 32.7% of the isolates, respectively. Sixty (53.1%) of the isolates were multidrug resistant presenting as 24 different resistance patterns with resistance to gentamicin-erythromycin-streptomycin-tetracycline (CN-ERY-STR-TET) being the most common (n = 11) pattern. In addition to expression of virulence traits (haemolysin, gelatinase, biofilm production), antibiotic resistance (tetK, tetL, tetM, tetO and ermB) and virulence (asa1, gelE, cylA) genes were detected among the isolates. Also, in vitro transfer of resistance determinants was observed among 75% of the isolates tested. Our data revealed poultry, cattle and manure in this area are hosts to varying Enterococcus species harbouring virulence and resistance determinants that can be transferred to other organisms and also are important for causing nosocomial infection.

Host Defense Proteins in Breast Milk and Neonatal Yeast Colonization.

PubMed

Chow, Brian D W; Reardon, Juliann L; Perry, Emily O; Laforce-Nesbitt, Sonia S; Tucker, Richard; Bliss, Joseph M

2016-02-01

Colonization increases risk for invasive candidiasis in neonates. Breast milk host defense proteins may affect yeast colonization of infants. This study aimed to evaluate breast milk host defense proteins relative to yeast colonization in infants. Infants admitted for longer than 72 hours to the neonatal intensive care unit at Women & Infants Hospital in Providence, Rhode Island, were eligible. After consent, expressed breast milk and swabs from oral, rectal, and inguinal sites from infants were cultured weekly for 12 weeks, or until discharge, transfer, or death. Breast milk was tested for levels of human lactoferrin, lysozyme, apolipoprotein J, mucin-1, dermcidin, and soluble CD14 using commercial ELISA. Concentrations of these components were compared in breast milk received by infants who were colonized or not colonized with yeast. From an original cohort of 130, 61 infants had samples available for this subanalysis. A convenience sample of stored breast milk was analyzed. Median lactoferrin, apolipoprotein J, and mucin-1 did not differ between colonized and uncolonized groups. Soluble CD14 was higher in the surface-colonized group (1.8 μg/mL, n = 12) compared with the surface-uncolonized group (1.6 μg/mL, n = 12, P = .02). Median lysozyme levels were higher in the surface-uncolonized group (483.0 ng/mL, n = 12) versus the surface-colonized group (298.3 ng/mL, n = 12, P = .04). Median dermcidin levels were higher in the surface-uncolonized group (19.4 ng/mL, n = 12) versus the surface-colonized group (8.7 ng/mL, n = 12, P = .04). This study shows an association between colonization with Candida in neonates and lower levels of lysozyme and dermcidin in received breast milk. Further study is needed to confirm these findings. © The Author(s) 2015.

Screening tests for Chlamydia trachomatis or Neisseria gonorrhoeae using the cobas 4800 PCR system do not require a second test to confirm: an audit of patients issued with equivocal results at a sexual health clinic in the Northwest of England, U.K.

PubMed

Hopkins, Mark J; Smith, Godfrey; Hart, Ian J; Alloba, Fath

2012-11-01

To assess the clinical utility of supplementary PCRs following a positive cobas 4800 CT/NG PCR screening test result. Laboratory reports, for Chlamydia trachomatis or Neisseria gonorrhoeae, issued to genitourinary medicine patients between April 2010 and April 2011 were reviewed retrospectively. Positive reports were routinely confirmed by supplementary PCRs and N gonorrhoeae culture. Clinical records of patients with unconfirmed positive (equivocal) reports were retrieved to determine if the infection was confirmed by a second sample obtained at patient recall and the impact of this process on antibiotic management. Over 15 000 patients were tested during the study period. The prevalence of chlamydia and gonorrhoea was 972 (5.75%) and 76 (0.50%), respectively. A further 78 chlamydia and 2 gonorrhoea equivocal reports were issued. Only 56 (72%) patients with an equivocal chlamydia report returned to the clinic, and of these, only 41 (73%) gave a second sample to retest. Positive predictive value (PPV) of the PCR screening test was calculated at 98.0% and 97.5% for detection of chlamydia infection from urine and rectal swabs, respectively. Most patients accepted antibiotic treatment before their infection status had been confirmed. Prevalence of gonorrhoea infection was low but the PPV of the screening PCR in urine specimens remained high (98.75%). Equivocal reports introduce delays to patient management, while the risk of unnecessary antibiotic therapy appears acceptable to most patients. The cobas 4800 CT/NG PCR screening assay can achieve UK testing standards (PPV >90%) for chlamydia, and low prevalence gonorrhoea in urine without supplementary tests. A patient-led confirmation algorithm is proposed.

Estimates of the pharmacokinetics of famciclovir and its active metabolite penciclovir in young Asian elephants (Elephas maximus).

PubMed

Brock, A Paige; Isaza, Ramiro; Hunter, Robert P; Richman, Laura K; Montali, Richard J; Schmitt, Dennis L; Koch, David E; Lindsay, William A

2012-12-01

To determine plasma pharmacokinetics of penciclovir following oral and rectal administration of famciclovir to young Asian elephants (Elephas maximus). 6 healthy Asian elephants (5 females and 1 male), 4.5 to 9 years old and weighing 1,646 to 2,438 kg. Famciclovir was administered orally or rectally in accordance with an incomplete crossover design. Three treatment groups, each comprising 4 elephants, received single doses of famciclovir (5 mg/kg, PO, or 5 or 15 mg/kg, rectally); there was a minimum 12-week washout period between subsequent famciclovir administrations. Serial blood samples were collected after each administration. Samples were analyzed for famciclovir and penciclovir with a validated liquid chromatography-mass spectroscopy assay. Famciclovir was tolerated well for both routes of administration and underwent complete biotransformation to the active metabolite, penciclovir. Mean maximum plasma concentration of penciclovir was 1.3 μg/mL at 1.1 hours after oral administration of 5 mg/kg. Similar results were detected after rectal administration of 5 mg/kg. Mean maximum plasma concentration was 3.6 μg/mL at 0.66 hours after rectal administration of 15 mg/kg; this concentration was similar to results reported for humans receiving 7 mg/kg orally. Juvenile Asian elephants are susceptible to elephant endotheliotropic herpesvirus. Although most infections are fatal, case reports indicate administration of famciclovir has been associated with survival of 3 elephants. In Asian elephants, a dose of 8 to 15 mg of famciclovir/kg given orally or rectally at least every 8 hours may result in penciclovir concentrations that are considered therapeutic in humans.

Developmental validation of the DNAscan™ Rapid DNA Analysis™ instrument and expert system for reference sample processing.

PubMed

Della Manna, Angelo; Nye, Jeffrey V; Carney, Christopher; Hammons, Jennifer S; Mann, Michael; Al Shamali, Farida; Vallone, Peter M; Romsos, Erica L; Marne, Beth Ann; Tan, Eugene; Turingan, Rosemary S; Hogan, Catherine; Selden, Richard F; French, Julie L

2016-11-01

Since the implementation of forensic DNA typing in labs more than 20 years ago, the analysis procedures and data interpretation have always been conducted in a laboratory by highly trained and qualified scientific personnel. Rapid DNA technology has the potential to expand testing capabilities within forensic laboratories and to allow forensic STR analysis to be performed outside the physical boundaries of the traditional laboratory. The developmental validation of the DNAscan/ANDE Rapid DNA Analysis System was completed using a BioChipSet™ Cassette consumable designed for high DNA content samples, such as single source buccal swabs. A total of eight laboratories participated in the testing which totaled over 2300 swabs, and included nearly 1400 unique individuals. The goal of this extensive study was to obtain, document, analyze, and assess DNAscan and its internal Expert System to reliably genotype reference samples in a manner compliant with the FBI's Quality Assurance Standards (QAS) and the NDIS Operational Procedures. The DNAscan System provided high quality, concordant results for reference buccal swabs, including automated data analysis with an integrated Expert System. Seven external laboratories and NetBio, the developer of the technology, participated in the validation testing demonstrating the reproducibility and reliability of the system and its successful use in a variety of settings by numerous operators. The DNAscan System demonstrated limited cross reactivity with other species, was resilient in the presence of numerous inhibitors, and provided reproducible results for both buccal and purified DNA samples with sensitivity at a level appropriate for buccal swabs. The precision and resolution of the system met industry standards for detection of micro-variants and displayed single base resolution. PCR-based studies provided confidence that the system was robust and that the amplification reaction had been optimized to provide high quality results. The DNAscan integrated Expert System was examined as part of the Developmental Validation and successfully interpreted the over 2000 samples tested with over 99.998% concordant alleles. The system appropriately flagged samples for human review and failed both mixed samples and samples with insufficient genetic information. These results demonstrated the integrated Expert System makes correct allele calls without human intervention. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Internal validation of the RapidHIT® ID system.

PubMed

Wiley, Rachel; Sage, Kelly; LaRue, Bobby; Budowle, Bruce

2017-11-01

Traditionally, forensic DNA analysis has required highly skilled forensic geneticists in a dedicated laboratory to generate short tandem repeat (STR) profiles. STR profiles are routinely used either to associate or exclude potential donors of forensic biological evidence. The typing of forensic reference samples has become more demanding, especially with the requirement in some jurisdictions to DNA profile arrestees. The Rapid DNA (RDNA) platform, the RapidHIT ® ID (IntegenX ® , Pleasanton, CA), is a fully automated system capable of processing reference samples in approximately 90min with minimal human intervention. Thus, the RapidHIT ID instrument can be deployed to non-laboratory environments (e.g., booking stations) and run by trained atypical personnel such as law enforcement. In order to implement the RapidHIT ID platform, validation studies are needed to define the performance and limitations of the system. Internal validation studies were undertaken with four early-production RapidHIT ID units. Reliable and concordant STR profiles were obtained from reference buccal swabs. Throughout the study, no contamination was observed. The overall first-pass success rate with an "expert-like system" was 72%, which is comparable to another current RDNA platform commercially available. The system's second-pass success rate (involving manual interpretation on first-pass inconclusive results) increased to 90%. Inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect typing by the instrument system; however, substrate (i.e., swab type) did impact typing success. Additionally, one desirable feature not available with other Rapid systems is that in the event of a system failed run, a swab can be recovered and subsequently re-analyzed in a new sample cartridge. Therefore, rarely should additional sampling or swab consumption be necessary. The RapidHIT ID system is a robust and reliable tool capable of generating complete STR profiles within the forensic DNA typing laboratory or with proper training in decentralized environments by non-laboratory personnel. Copyright © 2017 Elsevier B.V. All rights reserved.