Virtual screening for development of new effective compounds against Staphylococcus aureus.

PubMed

Diniz, Roseane Costa; Soares, Lucas Weba; da Silva, Luis Claudio Nascimento

2018-03-26

Staphylococcus aureus is a notorious pathogenic bacterium causing a wide range of diseases from soft-tissue contamination, to more serious and deep-seated infections. This species is highlighted by its ability to express several kinds of virulence factors and to acquire genes related to drug resistance. Target this number of factors to design any drug is not an easy task. In this review we discuss the importance of computational methods to impulse the development of new drugs against S. aureus. The application of docking methods to screen large library of natural or synthetic compounds and to provide insights into action mechanisms is demonstrated. Particularly, highlighted the studies that validated in silico results with biochemical and microbiological assays. We also comment the computer-aided design of new molecules using some known inhibitors. The confirmation of in silico results with biochemical and microbiological assays allowed the identification of lead molecules that could be used for drug design such as rhodomyrtone, quinuclidine, berberine (and their derivative compounds). The fast development in the computational methods is essential to improve our ability to discovery new drugs, as well as to expand understanding about drug-target interactions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The application of uniplex, duplex, and multiplex PCR for the absence of specified microorganism testing of pharmaceutical excipients and drug products.

PubMed

Ragheb, Suzan M; Yassin, Aymen S; Amin, Magdy A

2012-01-01

Notable progress has been made in methods that encourage the use of polymerase chain reaction (PCR) as a rapid and accurate tool in microbiological testing of pharmaceuticals. In this study, the detection of the four main specified microorganisms according to the pharmacopeial recommendations, Salmonella spp, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, was optimized in different pharmaceutical dosage forms and raw materials. Uniplex PCR was performed for the detection of each microorganism individually targeting the conserved region in each bacterial genome. Further optimizations were done to perform duplex and multiplex PCR assays considering relative concentrations of competitor primers used in the reaction. The uniplex PCR amplicons were successfully sequenced, confirming the conservation of used primers. Other validation parameters such as specificity, sensitivity, and robustness were examined closely. The method provides a high-throughput screening method to test different pharmaceutical preparations for specified microorganisms for the detection of microbiological contamination. Strict regulations govern the production of pharmaceutical products whether they are sterile or nonsterile. Certain official tests are carried out in microbiology testing laboratory in any pharmaceutical production facility to ensure the pharmaceuticals microbiological quality according to the standard pharmacopeial recommendations. Nonsterile products must be free of specified microorganisms that are used as a check for their quality. Topical preparations must be free of Pseudomonas aeruginosa and Staphylococcus aureus, and oral preparations must be free of Salmonella spp and Escherichia coli. Conventional microbiological methods are time-consuming, labor-intensive, and require long incubation times, resulting in delaying the release of the products. In this study, we tested and validated a polymerase chain reaction identification approach to detect indicator bacteria in pharmaceutical preparations. The method depends on amplification of certain conserved genes located in the four specified bacteria. The method is optimized to be carried out individually or collectively to detect all indicator bacteria in a single reaction in different forms of pharmaceutical products.

Strategies for preventing group B streptococcal infections in newborns: a nation-wide survey of Italian policies.

PubMed

Tzialla, Chryssoula; Berardi, Alberto; Farina, Claudio; Clerici, Pierangelo; Borghesi, Alessandro; Viora, Elsa; Scollo, Paolo; Stronati, Mauro

2017-11-02

There are no Italian data regarding the strategies for preventing neonatal group B streptococcal (GBS) infection. We conducted a national survey in order to explore obstetrical, neonatal and microbiological practices for the GBS prevention. Three distinct questionnaires were sent to obstetricians, neonatologists and microbiologists. Questionnaires included data on prenatal GBS screening, maternal risk factors, intrapartum antibiotic prophylaxis, microbiological information concerning specimen processing and GBS antimicrobial susceptibility. All respondent obstetrical units used the culture-based screening approach to identify women who should receive intrapartum antibiotic prophylaxis, and more than half of the microbiological laboratories (58%) reported using specimen processing consistent with CDC guidelines. Most neonatal units (89 out of 107, 82%) reported using protocols for preventing GBS early-onset sepsis consistent with CDC guidelines. The screening-based strategy is largely prevalent in Italy, and most protocols for preventing GBS early-onset sepsis are consistent with CDC guidelines. However, we found discrepancies in practices among centers that may reflect the lack of Italian guidelines issued by public health organizations.

A rapid, efficient and sensitive plate assay for detection and screening of l-asparaginase-producing microorganisms.

PubMed

Mahajan, Richi V; Saran, Saurabh; Saxena, Rajendra K; Srivastava, Ayush K

2013-04-01

l-Asparaginase-producing microbes are conventionally screened on phenol red l-asparagine-containing plates. However, sometimes the contrast of the zone obtained (between yellow and pink) is not very sharp and distinct. In the present investigation, an improved method for screening of the microorganisms producing extracellular l-asparaginase is reported wherein bromothymol blue (BTB) is incorporated as pH indicator in l-asparagine-containing medium instead of phenol red. Plates containing BTB at acidic pH are yellow and turn dark blue at alkaline pH. Thus, a dense dark blue zone is formed around microbial colonies producing l-asparaginase, differentiating between enzyme producers and non-producers. The present method is more sensitive and accurate than the conventional method for screening of both fungi and bacteria producing extracellular l-asparaginase. Furthermore, BTB gives a transient green colour at neutral pH (7.0) and dark blue colour at higher pH 8.0-9.0, indicating the potency of the microorganism for l-asparaginase production. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Advances in biosensor development for the screening of antibiotic residues in food products of animal origin - A comprehensive review.

PubMed

Gaudin, Valérie

2017-04-15

Antibiotic residues may be found in food of animal origin, since veterinary drugs are used for preventive and curative purposes to treat animals. The control of veterinary drug residues in food is necessary to ensure consumer safety. Screening methods are the first step in the control of antibiotic residues in food of animal origin. Conventional screening methods are based on different technologies, microbiological methods, immunological methods or physico-chemical methods (e.g. thin-layer chromatography, HPLC, LC-MS/MS). Screening methods should be simple, quick, inexpensive and specific, with low detection limits and high sample throughput. Biosensors can meet some of these requirements. Therefore, the development of biosensors for the screening of antibiotic residues has been increasing since the 1980s. The present review provides extensive and up-to-date findings on biosensors for the screening of antibiotic residues in food products of animal origin. Biosensors are constituted of a bioreceptor and a transducer. In the detection of antibiotic residues, even though antibodies were the first bioreceptors to be used, new kinds of bioreceptors are being developed more and more (enzymes, aptamers, MIPs); their advantages and drawbacks are discussed in this review. The different categories of transducers (electrochemical, mass-based biosensors, optical and thermal) and their potential applications for the screening of antibiotic residues in food are presented. Moreover, the advantages and drawbacks of the different types of transducers are discussed. Lastly, outlook and the future development of biosensors for the control of antibiotic residues in food are highlighted. Copyright © 2016. Published by Elsevier B.V.

Non-targeted workflow for identification of antimicrobial compounds in animal feed using bioassay-directed screening in combination with liquid chromatography-high resolution mass spectrometry.

PubMed

Wegh, Robin S; Berendsen, Bjorn J A; Driessen-Van Lankveld, Wilma D M; Pikkemaat, Mariël G; Zuidema, Tina; Van Ginkel, Leen A

2017-11-01

A non-targeted workflow is reported for the isolation and identification of antimicrobial active compounds using bioassay-directed screening and LC coupled to high-resolution MS. Suspect samples are extracted using a generic protocol and fractionated using two different LC conditions (A and B). The behaviour of the bioactive compound under these different conditions yields information about the physicochemical properties of the compound and introduces variations in co-eluting compounds in the fractions, which is essential for peak picking and identification. The fractions containing the active compound(s) obtained with conditions A and B are selected using a microbiological effect-based bioassay. The selected bioactive fractions from A and B are analysed using LC combined with high-resolution MS. Selection of relevant signals is automatically carried out by selecting all signals present in both bioactive fractions A and B, yielding tremendous data reduction. The method was assessed using two spiked feed samples and subsequently applied to two feed samples containing an unidentified compound showing microbial growth inhibition. In all cases, the identity of the compound causing microbiological inhibition was successfully confirmed.

Detection of Carbapenemase Production in a Collection of Enterobacteriaceae with Characterized Resistance Mechanisms from Clinical and Environmental Origins by Use of Both Carba NP and Blue-Carba Tests.

PubMed

García-Fernández, Sergio; Morosini, María-Isabel; Gijón, Desirèe; Beatobe, Lorena; Ruiz-Garbajosa, Patricia; Domínguez, Lucas; Cantón, Rafael; Valverde, Aránzazu

2016-02-01

Rapid-screening methods to confirm the presence of resistance mechanisms in multidrug-resistant bacteria are currently recommended. Carba NP and Blue-Carba tests were evaluated in carbapenemase-producing Enterobacteriaceae from hospital (n = 102) and environmental (n = 57) origins for detecting the different molecular classes among them. Both methods showed to be fast and cost-effective, with high sensitivity (98% to 100%) and specificity (100%), and may be easily introduced in the routine laboratory. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

PCR screening reveals considerable unexploited biosynthetic potential of ansamycins and a mysterious family of AHBA-containing natural products in actinomycetes.

PubMed

Wang, H-X; Chen, Y-Y; Ge, L; Fang, T-T; Meng, J; Liu, Z; Fang, X-Y; Ni, S; Lin, C; Wu, Y-Y; Wang, M-L; Shi, N-N; He, H-G; Hong, K; Shen, Y-M

2013-07-01

Ansamycins are a family of macrolactams that are synthesized by type I polyketide synthase (PKS) using 3-amino-5-hydroxybenzoic acid (AHBA) as the starter unit. Most members of the family have strong antimicrobial, antifungal, anticancer and/or antiviral activities. We aimed to discover new ansamycins and/or other AHBA-containing natural products from actinobacteria. Through PCR screening of AHBA synthase gene, we identified 26 AHBA synthase gene-positive strains from 206 plant-associated actinomycetes (five positives) and 688 marine-derived actinomycetes (21 positives), representing a positive ratio of 2·4-3·1%. Twenty-five ansamycins, including eight new compounds, were isolated from six AHBA synthase gene-positive strains through TLC-guided fractionations followed by repeated column chromatography. To gain information about those potential ansamycin gene clusters whose products were unknown, seven strains with phylogenetically divergent AHBA synthase genes were subjected to fosmid library construction. Of the seven gene clusters we obtained, three show characteristics for typical ansamycin gene clusters, and other four, from Micromonospora spp., appear to lack the amide synthase gene, which is unusual for ansamycin biosynthesis. The gene composition of these four gene clusters suggests that they are involved in the biosynthesis of a new family of hybrid PK-NRP compounds containing AHBA substructure. PCR screening of AHBA synthase is an efficient approach to discover novel ansamycins and other AHBA-containing natural products. This work demonstrates that the AHBA-based screening method is a useful approach for discovering novel ansamycins and other AHBA-containing natural products from new microbial resources. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

Comparative study of three screening tests, two microbiological tube tests, and a multi-sulphonamide ELISA kit for the detection of antimicrobial and sulphonamide residues in eggs.

PubMed

Gaudin, V; Hedou, C; Rault, A; Sanders, P; Verdon, E

2009-04-01

The screening of antimicrobial residues in eggs is an especially important subject. Three different commercial kits for the screening of sulphonamides and other antimicrobials in eggs were validated in accordance with Decision 2002/657/EC: one enzyme-linked immunoabsorbant assay (ELISA) kit multi-sulphonamides (from RAISIO Diagnostics) and two microbiological tests (a Premi test from DSM and an Explorer kit from Zeu-Inmunotec). The false-positive rates were lower than 2% for all kits. The detection capabilities (CCbeta) have to be as low as possible for banned substances and lower than the maximum residue limit (MRL) when MRLs have been set. The sensitivity of the Premi test was better than that of the Explorer test, probably because of the dilution of the eggs before the Explorer test was used. The CCbeta values towards most of the tested sulphonamides were satisfactory with the Premi test (< or = 100 microg kg(-1)). Performance in a proficiency test for the detection of sulphonamides in eggs with the Premi test confirmed these results. The detection capabilities of tetracycline and doxycycline were at the level of the MRL or twice the MRL maximum. The detection capabilities for chlortetracycline and oxytetracycline were higher (four to six times the MRL). The detection capabilities for amoxicillin, neomycin, tylosin and erythromycin were lower than their respective MRLs. Detection capabilities for sulphonamides were much lower for the ELISA kit than for microbiological tests. The ELISA kit could be recommended for the targeted screening of sulphonamides in eggs. On the other hand, the Explorer and Premi tests could be used as wide screening tests allowing the detection of most of the antimicrobial families.

Matrix approach to the simultaneous detection of multiple potato pathogens by real-time PCR.

PubMed

Nikitin, M M; Statsyuk, N V; Frantsuzov, P A; Dzhavakhiya, V G; Golikov, A G

2018-03-01

Create a method for highly sensitive, selective, rapid and easy-to-use detection and identification of economically significant potato pathogens, including viruses, bacteria and oomycetes, be it single pathogen, or a range of various pathogens occurring simultaneously. Test-systems for real-time PCR, operating in the unified amplification regime, have been developed for Phytophthora infestans, Pectobacterium atrosepticum, Dickeya dianthicola, Dickeya solani, Ralstonia solanacearum, Pectobacterium carotovorum, Clavibacter michiganensis subsp. sepedonicus, potato viruses Y (ordinary and necrotic forms as well as indiscriminative test system, detecting all forms), A, X, S, M, potato leaf roll virus, potato mop top virus and potato spindle tuber viroid. The test-systems (including polymerase and revertase) were immobilized and lyophilized in miniature microreactors (1·2 μl) on silicon DNA/RNA microarrays (micromatrices) to be used with a mobile AriaDNA ® amplifier. Preloaded 30-reaction micromatrices having shelf life of 3 and 6 months (for RNA- and DNA-based pathogens, respectively) at room temperature with no special conditions were successfully tested on both reference and field samples in comparison with traditional ELISA and microbiological methods, showing perfect performance and sensitivity (1 pg). The accurate, rapid and user-friendly diagnostic system in a micromatrix format may significantly contribute to pathogen screening and phytopathological studies. © 2018 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

The prevalence and bacteriology of asymptomatic bacteriuria among antenatal patients in Nnamdi Azikiwe University Teaching Hospital Nnewi; South Eastern Nigeria.

PubMed

Oli, A N; Okafor, C I; Ibezim, E C; Akujiobi, C N; Onwunzo, M C

2010-12-01

Urinary tract infection in pregnancy leads to poor pregnancy outcome. Diagnosis and treatment of asymptomatic bacteriuria markedly improves pregnancy outcome as well as reduce the incidence of acute pyelonephritis. To determine the prevalence and bacteriology of asymptomatic bacteriuria among Antenatal patients in our centre, and to know if routine screening will be justifiable. This was a prospective study carried out between April and August 2008. Sample size was statistically determined. Women who consented were interviewed and mid stream urine samples were collected and processed in the microbiology laboratory, using standard microbiological methods. Out of 357 women studied, 65(18.21%) had significant bacteriuria. Escherichia coli was the commonest isolate (25.6%), while proteus mirabilis was the least frequent isolate (3.66%). Women in third trimester had the highest prevalence (25.68%) while those in the first trimester had the least (15.79%). Women that had only primary education had the highest prevalence (27.50%) while those that had tertiary education had the least prevalence (21.10%). The prevalence of significant asymptomatic bacteriuria among the women studied was high. Screening of all the pregnant women and treatment will reduce the incidence and complications of overt urinary tract infection in pregnancy among these women.

Microbiological investigations

NASA Technical Reports Server (NTRS)

Ferguson, J. K.; Taylor, G. R.; Mieszkuc, B. J.

1975-01-01

The crew microbiology program was conducted to evaluate lunar contamination, to detect potentially pathogenic microoganisms, to identify medically important microorganisms recovered from ill crewmen, to aid in diagnosis and treatment, and to collect microbiological data that would aid in elucidating the response of the crew microbial autoflora to the space flight environment and in evaluating the resultant effect on the crewmember. Microbiological sampling of selected sites in the command module was initiated in support of the quarantine program. During lunar quarantine missions, microbial screening was accomplished for all support personnel to be isolated with the returning crewman. Virology support for the Apollo project consisted of characterization of the viral and mycoplasma flora of the crewmembers and performance of viral serology for crewmembers, crew contacts, and key mission personnel. Procedures and results are discussed in detail.

Evaluation of high-resolution melting curve analysis of ligation-mediated real-time PCR, a rapid method for epidemiological typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) pathogens.

PubMed

Woksepp, Hanna; Ryberg, Anna; Billström, Hanna; Hällgren, Anita; Nilsson, Lennart E; Marklund, Britt-Inger; Olsson-Liljequist, Barbro; Schön, Thomas

2014-12-01

A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Susceptibility Testing of Medically Important Parasites.

PubMed

Genetu Bayih, Abebe; Debnath, Anjan; Mitre, Edward; Huston, Christopher D; Laleu, Benoît; Leroy, Didier; Blasco, Benjamin; Campo, Brice; Wells, Timothy N C; Willis, Paul A; Sjö, Peter; Van Voorhis, Wesley C; Pillai, Dylan R

2017-07-01

In the last 2 decades, renewed attention to neglected tropical diseases (NTDs) has spurred the development of antiparasitic agents, especially in light of emerging drug resistance. The need for new drugs has required in vitro screening methods using parasite culture. Furthermore, clinical laboratories sought to correlate in vitro susceptibility methods with treatment outcomes, most notably with malaria. Parasites with their various life cycles present greater complexity than bacteria, for which standardized susceptibility methods exist. This review catalogs the state-of-the-art methodologies used to evaluate the effects of drugs on key human parasites from the point of view of drug discovery as well as the need for laboratory methods that correlate with clinical outcomes. Copyright © 2017 American Society for Microbiology.

Rapid bacteriological screening of cosmetic raw materials by using bioluminescence.

PubMed

Nielsen, P; Van Dellen, E

1989-01-01

Incoming cosmetic raw materials are routinely tested for microbial content. Standard plate count methods require up to 72 h. A rapid, sensitive, and inexpensive raw material screening method was developed that detects the presence of bacteria by means of ATP (bioluminescence). With a 24-h broth enrichment, the minimum bacterial ATP detection threshold of 1 cfu/g sample can be achieved using purified firefly luciferin-luciferase and an ATP releasing reagent. By using this rapid screen, microbiologically free material may be released for production within 24 h, while contaminated material undergoes further quantitative and identification testing. In order for a raw material to be validated for this method it must be evaluated for (1) a potential nonmicrobial light-contributing reaction resulting in a false positive or, (2) degradation of the ATP giving a false negative, and (3) confirmation that the raw material has not overwhelmed the buffering capacity of the enrichment broth. The key criteria for a rapid screen was the sensitivity to detect less than one colony forming unit per g product, the speed to do this within 24 h, and cost efficiency. Bioluminescence meets these criteria. With an enrichment step, it can detect less than one cfu/g sample. After the enrichment step, analysis time per sample is approximately 2 min and the cost for material and reagents is less than one dollar per sample.

Preemptive Isolation Precautions of Patients at High Risk for Methicillin-Resistant Staphylococcus aureus in Combination With Ultrarapid Polymerase Chain Reaction Screening as an Effective Tool for Infection Control.

PubMed

Hallak, Ghias; Neuner, Bruno; Schefold, Joerg C; Gorzelniak, Kerstin; Rapsch, Brigitte; Pfüller, Roland; Stengel, Dirk; Wellmann, Jürgen; Ekkernkamp, Axel; Walter, Michael

2016-12-01

This sequential nonrandomized intervention study investigated the role of preemptive isolation precautions plus ultrarapid polymerase chain reaction screening for methicillin-resistant Staphylococcus aureus (MRSA). Compared with no prophylactic isolation plus conventional microbiology MRSA screening, nosocomial MRSA colonization and total MRSA incidence per 10,000 patient days significantly decreased. Infect Control Hosp Epidemiol 2016;1489-1491.

Microfluidics in microbiology: putting a magnifying glass on microbes.

PubMed

Siddiqui, Sanya; Tufenkji, Nathalie; Moraes, Christopher

2016-09-12

Microfluidic technologies enable unique studies in the field of microbiology to facilitate our understanding of microorganisms. Using miniaturized and high-throughput experimental capabilities in microfluidics, devices with controlled microenvironments can be created for microbial studies in research fields such as healthcare and green energy. In this research highlight, we describe recently developed tools for diagnostic assays, high-throughput mutant screening, and the study of human disease development as well as a future outlook on microbes for renewable energy.

Water microbiology. Bacterial pathogens and water.

PubMed

Cabral, João P S

2010-10-01

Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water-cholera, typhoid fever and bacillary dysentery-is presented, focusing on the biology and ecology of the causal agents and on the diseases' characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters.

Water Microbiology. Bacterial Pathogens and Water

PubMed Central

Cabral, João P. S.

2010-01-01

Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water—cholera, typhoid fever and bacillary dysentery—is presented, focusing on the biology and ecology of the causal agents and on the diseases’ characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters. PMID:21139855

Recent actuality about Bacillus cereus and human milk bank: a new sensitive method for microbiological analysis of pasteurized milk.

PubMed

Rigourd, V; Barnier, J P; Ferroni, A; Nicloux, M; Hachem, T; Magny, J F; Lapillonne, A; Frange, P; Nassif, X; Bille, E

2018-05-03

Three cases of Bacillus cereus infection or colonization occurred in the same region in France, and milk from the milk bank was suspected as a possible common source of contamination. All Batches delivered to the three cases complied with the requirements of the bacteriological reference method recommended by good practices guidelines. Still, a retrospective analysis with a more sensitive method showed one batch to contain B. cereus, however straincomparison revealed no epidemiological link betweenisolates from patients and those from the milk. Consequently, in accordance with the precautionary principle, we developed a new sensitive method for the screening of pasteurized milk for pathogenic bacteria. From January 1 to August 31, 2017, 2526 samples of pasteurized milk were prospectively included in the study. We showed that a 20 mL sample of pasteurized milk incubated for 18 h at 37 °C under aerobic conditions was favoring the detection of B. Cereus. The nonconformity rate was 6.3% for the reference method and 12.6% for the improved method (p < 0.0001). Nonconformity was due to the presence of B. cereus in 88.5% of cases for the improved method and 53% of cases for the reference method (p < 0.0001). Thus our new method is improves the microbiological safety of the product distributed and only moderately increases the rate of bacteriological nonconformity .

Profile and microbiological isolates of asymptomatic bacteriuria among pregnant women in Abakaliki, Nigeria

PubMed Central

Onu, Fidelis Agwu; Ajah, Leonard Ogbonna; Ezeonu, Paul Olisaemeka; Umeora, Odidika Ugochukwu Joannes; Ibekwe, Perpetus Chudi; Ajah, Monique Iheoma

2015-01-01

Background Detecting and treating asymptomatic bacteriuria (ASB) prevents urinary tract infection and its consequences. The cost-effectiveness of routine screening for ASB in pregnancy is controversial. In populations with high prevalence, however, it is worthwhile and justifiable. Aim To determine the profile, prevalence, microbiological isolates, and risk factors of ASB among booking antenatal clinic attendees in Abakaliki, Nigeria. Materials and methods This was a cross-sectional study involving booking antenatal clinic attendees at the Federal Teaching Hospital, Abakaliki, who met the inclusion criteria. This study occurred between January and December, 2012. The midstream urine samples of these women were subjected to microscopy, culture, and sensitivity. Results A total of 300 randomly selected booking antenatal clinic attendees participated in the study; 74 of them had ASB, giving a prevalence of 24.7%. With the exception of rural residence, sociodemographic and obstetric characteristics did not influence the risk of ASB among the participants in this study. Staphylococcus aureus was the commonest organism isolated. The majority of the organisms were sensitive to ofloxacin and ceftriaxone. Conclusion There is a high prevalence of ASB among pregnant women in Abakaliki. With the exception of rural dwelling, sociodemographic and obstetric characteristics did not significantly influence the risk of ASB among these pregnant women. Therefore, routine ASB screening of pregnant women is recommended in our environment. PMID:26244027

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

PubMed Central

Zhu, Yan; Hassan, Yousef I.; Lepp, Dion; Shao, Suqin; Zhou, Ting

2017-01-01

Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification. PMID:28387743

Microbial Impact on Success of Human Exploration Missions

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Groves, T. O.; Paloski, W. H. (Technical Monitor)

2000-01-01

The purpose of this study is to identify microbiological risks associated with space exploration and identify potential countermeasures available. Identification of microbial risks associated with space habitation requires knowledge of the sources and expected types of microbial agents. Crew data along with environmental data from water, surfaces, air, and free condensate are utilized in risk examination. Data from terrestrial models are also used. Microbial risks to crew health include bacteria, fungi, protozoa, and viruses. Adverse effects of microbes include: infections, allergic reactions, toxin production, release of volatiles, food spoilage, plant disease, material degradation, and environmental contamination. Risk is difficult to assess because of unknown potential changes in microbes (e.g., mutation) and the human host (e.g., immune changes). Prevention of adverse microbial impacts is preferred over remediation. Preventative measures include engineering measures (e.g., air filtration), crew microbial screening, acceptability standards, and active verification by onboard monitoring. Microbiological agents are important risks to human health and performance during space flight and risks increase with mission duration. Acceptable risk level must be defined. Prevention must be given high priority. Careful screening of crewmembers and payloads is an important element of any risk mitigation plan. Improved quantitation of microbiological risks is a high priority.

Experience of microbiological screening of human hepatocytes for clinical transplantation.

PubMed

Lehec, Sharon C; Hughes, Robin D; Mitry, Ragai R; Graver, Michelle A; Verma, Anita; Wade, Jim J; Dhawan, Anil

2009-01-01

Hepatocyte transplantation is being used in patients with liver-based metabolic disorders and acute liver failure. Hepatocytes are isolated from unused donor liver tissue under GMP conditions. Cells must be free of microbiological contamination to be safe for human use. The experience of microbiological screening during 72 hepatocyte isolation procedures at one center is reported. Samples were taken at different stages of the process and tested using a blood culture bottle system and Gram stain. Bacterial contamination was detected in 37.5% of the UW organ preservative solutions used to transport the liver tissue to the Cell Isolation Unit. After tissue processing the contamination was reduced to 7% overall in the final hepatocyte product, irrespective of the presence of initial contamination of the transport solution. The most common organisms recovered were coagulase-negative staphylococci, a skin commensal. A total of 41 preparations of fresh or cryopreserved hepatocytes were used for cell transplantation in children with liver-based metabolic disorders without any evidence of sepsis due to infusion of hepatocytes. In conclusion, the incidence of bacterial contamination of the final product was low, confirming the suitability of the organs used, hepatocyte isolation procedure, and the environmental conditions of the clean room.

Protocol for a systematic review of quantitative burn wound microbiology in the management of burns patients.

PubMed

Kwei, Johnny; Halstead, Fenella D; Dretzke, Janine; Oppenheim, Beryl A; Moiemen, Naiem S

2015-11-06

Sepsis from burn injuries can result from colonisation of burn wounds, especially in large surface area burns. Reducing bacterial infection will reduce morbidity and mortality, and mortality for severe burns can be as high as 15 %. There are various quantitative and semi-quantitative techniques to monitor bacterial load on wounds. In the UK, burn wounds are typically monitored for the presence or absence of bacteria through the collection and culture of swabs, but no absolute count is obtained. Quantitative burn wound culture provides a measure of bacterial count and is gaining increased popularity in some countries. It is however more resource intensive, and evidence for its utility appears to be inconsistent. This systematic review therefore aims to assess the evidence on the utility and reliability of different quantitative microbiology techniques in terms of diagnosing or predicting clinical outcomes. Standard systematic review methods aimed at minimising bias will be employed for study identification, selection and data extraction. Bibliographic databases and ongoing trial registers will be searched and conference abstracts screened. Studies will be eligible if they are prospective studies or systematic reviews of burn patients (any age) for whom quantitative microbiology has been performed, whether it is compared to another method. Quality assessment will be based on quality assessment tools for diagnostic and prognostic studies and tailored to the review as necessary. Synthesis is likely to be primarily narrative, but meta-analysis may be considered where clinical and methodological homogeneity exists. Given the increasing use of quantitative methods, this is a timely systematic review, which will attempt to clarify the evidence base. As far as the authors are aware, it will be the first to address this topic. PROSPERO, CRD42015023903.

Microbiological diagnosis of human papilloma virus infection.

PubMed

Mateos-Lindemann, Maria Luisa; Pérez-Castro, Sonia; Rodríguez-Iglesias, Manuel; Pérez-Gracia, Maria Teresa

2017-11-01

Infection with human papillomavirus (HPV) is the leading cause of sexually transmitted infection worldwide. This virus generally causes benign lesions, such as genital warts, but persistent infection may lead to cervical cancer, anal cancer, vaginal cancer, and oropharyngeal cancer, although less frequently. Cervical cancer is a severe disease with a high mortality in some countries. Screening with cytology has been very successful in the last few years, but nowadays there are numerous studies that confirm that cytology should be replaced with the detection of HPV as a first line test in population based screening. There are several commercially available FDA approved tests for screening of cervical cancer. A new strategy, based on individual detection of the high risk genotypes HPV16 and HPV18, present in 70% of cervical cancer biopsies, has been proposed by some experts, and is going to be implemented in most countries in the future. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Analysis of microbiological screen test data for antimicrobial residues in food animals.

PubMed

Dey, B P; Thaler, Alice; Gwozdz, Frank

2003-05-01

This study analyzes the National Residue Program (NRP) of the Food Safety and Inspection Service (FSIS), United States Department of Agriculture (USDA), data for the years 1983-1998 to determine the effectiveness of all three microbiological screen tests that were developed and used by the FSIS to control antimicrobial residues in food animals. The Swab Test On Premises (STOP) was the first screen test introduced in slaughterhouses, followed by the Calf Antibiotic Sulfonamide Test (CAST) and the Fast Antimicrobial Screen Test (FAST). The data for STOP indicates that during 1983-1998, the rate of food animal carcasses with violative levels of antimicrobial residues reduced from 2.33% to 0.45% under the monitoring plan and under the surveillance plan, the rate reduced from 55.1% to 0.56%. Similarly, the data for CAST indicates that the rate of calf carcasses with violative levels of antimicrobial residue also declined significantly during those years. Because of its higher sensitivity and shorter analytical time, the use of FAST started in 1995. By 1999, it had practically replaced the use of STOP and CAST in bovine species. The use of only one test such as FAST instead of different tests has removed confusion for testing different species of food animals and thereby has enhanced the efficiency of the NRP.

Evaluation of PDA Technical Report No 33. Statistical Testing Recommendations for a Rapid Microbiological Method Case Study.

PubMed

Murphy, Thomas; Schwedock, Julie; Nguyen, Kham; Mills, Anna; Jones, David

2015-01-01

New recommendations for the validation of rapid microbiological methods have been included in the revised Technical Report 33 release from the PDA. The changes include a more comprehensive review of the statistical methods to be used to analyze data obtained during validation. This case study applies those statistical methods to accuracy, precision, ruggedness, and equivalence data obtained using a rapid microbiological methods system being evaluated for water bioburden testing. Results presented demonstrate that the statistical methods described in the PDA Technical Report 33 chapter can all be successfully applied to the rapid microbiological method data sets and gave the same interpretation for equivalence to the standard method. The rapid microbiological method was in general able to pass the requirements of PDA Technical Report 33, though the study shows that there can be occasional outlying results and that caution should be used when applying statistical methods to low average colony-forming unit values. Prior to use in a quality-controlled environment, any new method or technology has to be shown to work as designed by the manufacturer for the purpose required. For new rapid microbiological methods that detect and enumerate contaminating microorganisms, additional recommendations have been provided in the revised PDA Technical Report No. 33. The changes include a more comprehensive review of the statistical methods to be used to analyze data obtained during validation. This paper applies those statistical methods to analyze accuracy, precision, ruggedness, and equivalence data obtained using a rapid microbiological method system being validated for water bioburden testing. The case study demonstrates that the statistical methods described in the PDA Technical Report No. 33 chapter can be successfully applied to rapid microbiological method data sets and give the same comparability results for similarity or difference as the standard method. © PDA, Inc. 2015.

The Impact of Apollo-Era Microbiology on Human Space Flight

NASA Technical Reports Server (NTRS)

Elliott, T. F; Castro, V. A.; Bruce, R. J.; Pierson, D. L.

2014-01-01

The microbiota of crewmembers and the spacecraft environment contributes significant risk to crew health during space flight missions. NASA reduces microbial risk with various mitigation methods that originated during the Apollo Program and continued to evolve through subsequent programs: Skylab, Shuttle, and International Space Station (ISS). A quarantine of the crew and lunar surface samples, within the Lunar Receiving Laboratory following return from the Moon, was used to prevent contamination with unknown extraterrestrial organisms. The quarantine durations for the crew and lunar samples were 21 days and 50 days, respectively. A series of infections among Apollo crewmembers resulted in a quarantine before launch to limit exposure to infectious organisms. This Health Stabilization Program isolated the crew for 21 days before flight and was effective in reducing crew illness. After the program developed water recovery hardware for Apollo spacecraft, the 1967 National Academy of Science Space Science Board recommended the monitoring of potable water. NASA implemented acceptability limits of 10 colony forming units (CFU) per mL and the absence of viable E. coli, anaerobes, yeasts, and molds in three separate 150 mL aliquots. Microbiological investigations of the crew and spacecraft environment were conducted during the Apollo program, including the Apollo-Soyuz Test Project and Skylab. Subsequent space programs implemented microbial screening of the crew for pathogens and acceptability limits on spacecraft surfaces and air. Microbiology risk mitigation methods have evolved since the Apollo program. NASA cancelled the quarantine of the crew after return from the lunar surface, reduced the duration of the Health Stabilization Program; and implemented acceptability limits for spacecraft surfaces and air. While microbial risks were not a main focus of the early Mercury and Gemini programs, the extended duration of Apollo flights resulted in the increased scrutiny of impact of the space flight environment on crew health. The lessons learned during that era of space flight continue to impact microbiology risk mitigation in space programs today.

Microbiological Quality and Food Safety of Plants Grown on ISS Project

NASA Technical Reports Server (NTRS)

Wheeler, Raymond M. (Compiler)

2014-01-01

The goal of this project is to select and advance methods to enable real-time sampling, microbiological analysis, and sanitation of crops grown on the International Space Station (ISS). These methods would validate the microbiological quality of crops grown for consumption to ensure safe and palatable fresh foods. This would be achieved through the development / advancement of microbiological sample collection, rapid pathogen detection and effective sanitation methods that are compatible with a microgravity environment.

[Bacterial identification methods in the microbiology laboratory].

PubMed

Bou, Germán; Fernández-Olmos, Ana; García, Celia; Sáez-Nieto, Juan Antonio; Valdezate, Sylvia

2011-10-01

In order to identify the agent responsible of the infectious process and understanding the pathogenic/pathological implications, clinical course, and to implement an effective antimicrobial therapy, a mainstay in the practice of clinical microbiology is the allocation of species to a microbial isolation. In daily routine practice microbiology laboratory phenotypic techniques are applied to achieve this goal. However, they have some limitations that are seen more clearly for some kinds of microorganism. Molecular methods can circumvent some of these limitations, although its implementation is not universal. This is due to higher costs and the level of expertise required for thei implementation, so molecular methods are often centralized in reference laboratories and centers. Recently, proteomics-based methods made an important breakthrough in the field of diagnostic microbiology and will undoubtedly have a major impact on the future organization of the microbiology services. This paper is a short review of the most noteworthy aspects of the three bacterial identification methods described above used in microbiology laboratories. Copyright © 2011 Elsevier España, S.L. All rights reserved.

[Exploring New Drug Targets through the Identification of Target Molecules of Bioactive Natural Products].

PubMed

Arai, Masayoshi

2016-01-01

With the development of cell biology and microbiology, it has become easy to culture many types of animal cells and microbes, and they are frequently used for phenotypic screening to explore medicinal seeds. On the other hand, it is recognized that cells and pathogenic microbes present in pathologic sites and infected regions of the human body display unique properties different from those under general culture conditions. We isolated several bioactive compounds from marine medicinal resources using constructed bioassay-guided separation focusing on the unique changes in the characteristics of cells and pathogenic microbes (Mycobacterium spp.) in the human body under disease conditions. In addition, we also carried out identification studies of target molecules of the bioactive compounds by methods utilizing the gene expression profile, transformants of cells or microbes, synthetic probe molecules of the isolated compounds, etc., since bioactive compounds isolated from the phenotypic screening system often target new molecules. This review presents our phenotypic screening systems, isolation of bioactive compounds from marine medicinal resources, and target identification of bioactive compounds.

Development of Multiwell-Plate Methods Using Pure Cultures of Methanogens To Identify New Inhibitors for Suppressing Ruminant Methane Emissions.

PubMed

Weimar, M R; Cheung, J; Dey, D; McSweeney, C; Morrison, M; Kobayashi, Y; Whitman, W B; Carbone, V; Schofield, L R; Ronimus, R S; Cook, G M

2017-08-01

Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H 2 and CO 2 that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for medium preparation, assay duration, inhibitor solvents, and culture volume) were optimized to achieve robust and reproducible growth in a high-throughput microtiter plate format. The method was validated using published methanogen inhibitors and statistically assessed for sensitivity and reproducibility. The Sigma-Aldrich LOPAC library containing 1,280 pharmacologically active compounds and an in-house natural product library (120 compounds) were screened against M. maripaludis as a proof of utility. This screen identified a number of bioactive compounds, and MIC values were confirmed for some of them against M. maripaludis and M. AbM4. The developed method provides a significant increase in throughput for screening compound libraries and can now be used to screen larger compound libraries to discover novel methanogen-specific inhibitors for the mitigation of ruminant methane emissions. IMPORTANCE Methane emissions from ruminants are a significant contributor to global greenhouse gas emissions, and new technologies are required to control emissions in the agriculture technology (agritech) sector. The discovery of small-molecule inhibitors of methanogens using high-throughput phenotypic (growth) screening against compound libraries (synthetic and natural products) is an attractive avenue. However, phenotypic inhibitor screening is currently hindered by our inability to grow methanogens in a high-throughput format. We have developed, optimized, and validated a high-throughput 96-well microtiter plate assay for growing environmental and rumen methanogens. Using this platform, we identified several new inhibitors of methanogen growth, demonstrating the utility of this approach to fast track the development of methanogen-specific inhibitors for controlling ruminant methane emissions. Copyright © 2017 American Society for Microbiology.

Evaluating the utility of syndromic surveillance algorithms for screening to detect potentially clonal hospital infection outbreaks

PubMed Central

Talbot, Thomas R; Schaffner, William; Bloch, Karen C; Daniels, Titus L; Miller, Randolph A

2011-01-01

Objective The authors evaluated algorithms commonly used in syndromic surveillance for use as screening tools to detect potentially clonal outbreaks for review by infection control practitioners. Design Study phase 1 applied four aberrancy detection algorithms (CUSUM, EWMA, space-time scan statistic, and WSARE) to retrospective microbiologic culture data, producing a list of past candidate outbreak clusters. In phase 2, four infectious disease physicians categorized the phase 1 algorithm-identified clusters to ascertain algorithm performance. In phase 3, project members combined the algorithms to create a unified screening system and conducted a retrospective pilot evaluation. Measurements The study calculated recall and precision for each algorithm, and created precision-recall curves for various methods of combining the algorithms into a unified screening tool. Results Individual algorithm recall and precision ranged from 0.21 to 0.31 and from 0.053 to 0.29, respectively. Few candidate outbreak clusters were identified by more than one algorithm. The best method of combining the algorithms yielded an area under the precision-recall curve of 0.553. The phase 3 combined system detected all infection control-confirmed outbreaks during the retrospective evaluation period. Limitations Lack of phase 2 reviewers' agreement indicates that subjective expert review was an imperfect gold standard. Less conservative filtering of culture results and alternate parameter selection for each algorithm might have improved algorithm performance. Conclusion Hospital outbreak detection presents different challenges than traditional syndromic surveillance. Nevertheless, algorithms developed for syndromic surveillance have potential to form the basis of a combined system that might perform clinically useful hospital outbreak screening. PMID:21606134

Rapid containment of nosocomial transmission of a rare community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) clone, responsible for the Staphylococcal Scalded Skin Syndrome (SSSS).

PubMed

Lamanna, Onofrio; Bongiorno, Dafne; Bertoncello, Lisa; Grandesso, Stefano; Mazzucato, Sandra; Pozzan, Giovanni Battista; Cutrone, Mario; Chirico, Michela; Baesso, Flavia; Brugnaro, Pierluigi; Cafiso, Viviana; Stefani, Stefania; Campanile, Floriana

2017-01-06

The aims of this study were to identify the source and the transmission pathway for a Staphylococcal Scalded Skin Syndrome (SSSS) outbreak in a maternity setting in Italy over 2 months, during 2014; to implement appropriate control measures in order to prevent the epidemic spread within the maternity ward; and to identify the Methicillin-Resistant Staphylococcus aureus (MRSA) epidemic clone. Epidemiological and microbiological investigations, based on phenotyping and genotyping methods, were performed. All neonates involved in the outbreak underwent clinical and microbiological investigations to detect the cause of illness. Parents and healthcare workers were screened for Staphylococcus aureus to identify asymptomatic carriers. The SSSS outbreak was due to the cross-transmission of a rare clone of ST5-CA-MRSA-SCCmecV-spa type t311, exfoliative toxin A-producer, isolated from three neonates, one mother (from her nose and from dermatological lesions due to pre-existing hand eczema) and from a nurse (colonized in her nose by this microorganism). The epidemiological and microbiological investigation confirmed these as two potential carriers. A rapid containment of these infections was obtained only after implementation of robust swabbing of mothers and healthcare workers. The use of molecular methodologies for typing was able to identify all carriers and to trace the transmission.

Evaluation of the performance of the IQ-Check kits and the USDA Microbiology Laboratory Guidebook methods for detection of Shiga toxin-producing Escherichia coli (STEC) and STEC and Salmonella simultaneously in ground beef.

PubMed

Baranzoni, G M; Fratamico, P M; Boccia, F; Bagi, L K; Kim, G-H; Anastasio, A; Pepe, T

2017-03-01

To evaluate the performance of the IQ-Check kits and the USDA Microbiology Laboratory Guidebook (MLG) methods for detection of the top seven Shiga toxin-producing Escherichia coli (STEC) (O157:H7, O26, O45, O103, O111, O121 and O145) in ground beef and both STEC and Salmonella in co-inoculated samples. Ground beef samples inoculated with ~10 CFU of STEC or both STEC and Salmonella Typhimurium were stored at 4°C for 72 h, followed by screening with the IQ-Check and BAX System kit (MLG) methods that employ different enrichment media. STEC and S. Typhimurium were detected after 12 and 18 h and their presence was confirmed by colony isolation. Both methods were able to detect STEC in ground beef after 12 h of enrichment in samples inoculated with low levels of the pathogen. STEC and S. Typhimurium can be detected and isolated in co-inoculated ground beef samples. The IQ-Check methods are comparable to the MLG methods for detection of STEC and simultaneous detection of STEC and S. Typhimurium in seeded ground beef after a short enrichment time, thus the IQ-Check method can be useful for the food industry for rapid detection of these pathogens. Published 2016. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Donor-derived infection--the challenge for transplant safety.

PubMed

Fishman, Jay A; Grossi, Paolo A

2014-11-01

Organ transplantation, including of the heart, lung, kidney, liver, pancreas, and small bowel, is considered the therapy of choice for end-stage organ failure. Each year, over 70,000 organs are implanted worldwide. One donor may provide multiple organs, as well as corneas and other tissues, for multiple recipients. The degree of risk for transmission of infection carried with grafts, notably of viruses, is largely unknown and, for a specific organ, difficult to assess. The approach to microbiological screening of organ donors varies with national and regional regulations and with the availability and performance of microbiological assays used for potential donors. Transmission of both expected or common, and unexpected infections has been observed in organ transplants, generally recognized after development of clusters of infections among recipients of organs from a common donor. Other than for unusual or catastrophic events, few data exist that define the incidence and manifestations of donor-derived infections or the ideal assays to use in screening to prevent such transmissions. Absolute prevention of the transmission of donor-derived infections in organ transplantation is not possible. However, improvements in screening technologies will enhance the safety of transplantation in the future.

Production of the antimicrobial peptides Caseicin A and B by Bacillus isolates growing on sodium caseinate.

PubMed

Kent, R M; Guinane, C M; O'Connor, P M; Fitzgerald, G F; Hill, C; Stanton, C; Ross, R P

2012-08-01

The aim of this study was to identify Bacillus isolates capable of degrading sodium caseinate and subsequently to generate bioactive peptides with antimicrobial activity. Sodium caseinate (2.5% w/v) was inoculated separately with 16 Bacillus isolates and allowed to ferment overnight. Protein breakdown in the fermentates was analysed using gel permeation-HPLC (GP-HPLC) and screened for peptides (<3-kDa) with MALDI-TOF mass spectrometry. Caseicin A (IKHQGLPQE) and caseicin B (VLNENLLR), two previously characterized antimicrobial peptides, were identified in the fermentates of both Bacillus cereus and Bacillus thuringiensis isolates. The caseicin peptides were subsequently purified by RP-HPLC and antimicrobial assays indicated that the peptides maintained the previously identified inhibitory activity against the infant formula pathogen Cronobacter sakazakii. We report a new method using Bacillus sp. to generate two previously characterized antimicrobial peptides from casein. This study highlights the potential to exploit Bacillus sp. or the enzymes they produce for the generation of bioactive antimicrobial peptides from bovine casein. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

Determination of the Chronic Mammalian Toxicological Effects of TNT (twenty-Four Month Chronic Toxicity/Carcinogenicity Study of Trinitrotoluene (TNT) in the B6C3F1 Hybrid Mouse). Volume 1

DTIC Science & Technology

1984-12-01

chemistry parameters (see section l1.D.) Results of pretreatment health screen were within limits for the mice of this strain and age. Microbiological ...negative as measured by Microbiological Associates, Bethesda MD. Animals received 5002 rodent chow from arrival urtil their termina~lon, except during a...CARCINOGENICITY STUDY OF FRINITROTOLUENE IN THE B6C3FI MOUSE. ’EST DIET CONCENTRATION OF TNT TESI DOSE % % A x 100 - K!E!Th (mg,/kg/day) SEX INTENDED ANALYSED REL

Acetic acid as a decontamination method for sink drains in a nosocomial outbreak of metallo-β-lactamase-producing Pseudomonas aeruginosa.

PubMed

Stjärne Aspelund, A; Sjöström, K; Olsson Liljequist, B; Mörgelin, M; Melander, E; Påhlman, L I

2016-09-01

Pseudomonas aeruginosa may colonize water systems via biofilm formation. In hospital environments, contaminated sinks have been associated with nosocomial transmission. Here we describe a prolonged outbreak of a metallo-β-lactamase-producing P. aeruginosa (Pae-MBL) associated with sink drains, and propose a previously unreported decontamination method with acetic acid. To describe a nosocomial outbreak of Pae-MBL associated with hospital sink drains and to evaluate acetic acid as a decontamination method. The outbreak was investigated by searching the microbiology database, microbiological sampling and strain typing. Antibacterial and antibiofilm properties of acetic acid were evaluated in vitro. Pae-MBL-positive sinks were treated with 24% acetic acid once weekly and monitored with repeated cultures. Fourteen patients with positive cultures for Pae-MBL were identified from 2008 to 2014. The patients had been admitted to three wards, where screening discovered Pae-MBL in 12 sink drains located in the patient bathrooms. Typing of clinical and sink drain isolates revealed identical or closely related strains. Pae-MBL biofilm was highly sensitive to acetic acid with a minimum biofilm eradication concentration of 0.75% (range: 0.19-1.5). Weekly treatment of colonized sink drains with acetic acid resulted in negative cultures and terminated transmission. Acetic acid is highly effective against Pae-MBL biofilms, and may be used as a simple method to decontaminate sink drains and to prevent nosocomial transmission. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Verification of the new detection method for irradiated spices based on microbial survival by collaborative blind trial

NASA Astrophysics Data System (ADS)

Miyahara, M.; Furuta, M.; Takekawa, T.; Oda, S.; Koshikawa, T.; Akiba, T.; Mori, T.; Mimura, T.; Sawada, C.; Yamaguchi, T.; Nishioka, S.; Tada, M.

2009-07-01

An irradiation detection method using the difference of the radiation sensitivity of the heat-treated microorganisms was developed as one of the microbiological detection methods of the irradiated foods. This detection method is based on the difference of the viable cell count before and after heat treatment (70 °C and 10 min). The verification by collaborative blind trial of this method was done by nine inspecting agencies in Japan. The samples used for this trial were five kinds of spices consisting of non-irradiated, 5 kGy irradiated, and 7 kGy irradiated black pepper, allspice, oregano, sage, and paprika, respectively. As a result of this collaboration, a high percentage (80%) of the correct answers was obtained for irradiated black pepper and allspice. However, the method was less successful for irradiated oregano, sage, and paprika. It might be possible to use this detection method for preliminary screening of the irradiated foods but further work is necessary to confirm these findings.

Multiplex Polymerase Chain Reaction for Identification of Shigellae and Four Shigella Species Using Novel Genetic Markers Screened by Comparative Genomics.

PubMed

Kim, Hyun-Joong; Ryu, Ji-Oh; Song, Ji-Yeon; Kim, Hae-Yeong

2017-07-01

In the detection of Shigella species using molecular biological methods, previously known genetic markers for Shigella species were not sufficient to discriminate between Shigella species and diarrheagenic Escherichia coli. The purposes of this study were to screen for genetic markers of the Shigella genus and four Shigella species through comparative genomics and develop a multiplex polymerase chain reaction (PCR) for the detection of shigellae and Shigella species. A total of seven genomic DNA sequences from Shigella species were subjected to comparative genomics for the screening of genetic markers of shigellae and each Shigella species. The primer sets were designed from the screened genetic markers and evaluated using PCR with genomic DNAs from Shigella and other bacterial strains in Enterobacteriaceae. A novel Shigella quintuplex PCR, designed for the detection of Shigella genus, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, was developed from the evaluated primer sets, and its performance was demonstrated with specifically amplified results from each Shigella species. This Shigella multiplex PCR is the first to be reported with novel genetic markers developed through comparative genomics and may be a useful tool for the accurate detection of the Shigella genus and species from closely related bacteria in clinical microbiology and food safety.

Screening of filamentous fungi for antimicrobial silver nanoparticles synthesis.

PubMed

Ottoni, Cristiane Angélica; Simões, Marta Filipa; Fernandes, Sara; Dos Santos, Jonas Gomes; da Silva, Elda Sabino; de Souza, Rodrigo Fernando Brambilla; Maiorano, Alfredo Eduardo

2017-12-01

The present work had the goal of screening a batch of 20 fungal strains, isolated from sugar cane plantation soil, in order to identify those capable of biosynthesis of silver nanoparticles. These nanoparticles are known to have a large and effective application in clinical microbiology. Four strains were found to be capable of biosynthesis of silver nanoparticles. The biosynthesised nanoparticles were characterised by UV-vis spectroscopy, scanning electron microscopy, EDX, and XRD. They were found to have an average size of 30-100 nm, a regular round shape, and potential antimicrobial activity against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. The antimicrobial activity was found to be directly related to the nanoparticles concentration. Mycogenic synthesis of nanoparticles is a green biogenic process preferable to other alternatives. Because fungi are great producers of extracellular enzymes this process makes scaling-up an easier task with high importance for clinical microbiology on the fight against microbial resistance, as well as for other industrial applications.

A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill.

PubMed

Zhang, Shuangfei; Hu, Zhong; Wang, Hui

2018-01-01

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants.

A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

PubMed Central

Zhang, Shuangfei; Hu, Zhong; Wang, Hui

2018-01-01

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants. PMID:29628913

Evaluation of mericon E. coli O157 Screen Plus and mericon E. coli STEC O-Type Pathogen Detection Assays in Select Foods: Collaborative Study, First Action 2017.05.

PubMed

Bird, Patrick; Benzinger, M Joseph; Bastin, Benjamin; Crowley, Erin; Agin, James; Goins, David; Armstrong, Marcia

2018-05-01

QIAGEN mericon Escherichia coli O157 Screen Plus and mericon E. coli Shiga toxin-producing E. coli (STEC) O-Type Pathogen Detection Assays use Real-Time PCR technology for the rapid, accurate detection of E. coli O157 and the "big six" (O26, O45, O103, O111, O121, O145) (non-O157 STEC) in select food types. Using a paired study design, the assays were compared with the U.S. Department of Agriculture, Food Safety Inspection Service Microbiology Laboratory Guidebook Chapter 5.09 reference method for the detection of E. coli O157:H7 in raw ground beef. Both mericon assays were evaluated using the manual and an automated DNA extraction method. Thirteen technicians from five laboratories located within the continental United States participated in the collaborative study. Three levels of contamination were evaluated. Statistical analysis was conducted according to the probability of detection (POD) statistical model. Results obtained for the low-inoculum level test portions produced a difference between laboratories POD (dLPOD) value with a 95% confidence interval of 0.00 (-0.12, 0.12) for the mericon E. coli O157 Screen Plus with manual and automated extraction and mericon E. coli STEC O-Type with manual extraction and -0.01 (-0.13, 0.10) for the mericon E. coli STEC O-Type with automated extraction. The dLPOD results indicate equivalence between the candidate methods and the reference method.

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.

REMOVING ORGANIC CONTAMINANTS OF REGULATORY INTEREST WITH MEMBRANE PROCESSES: USEPA'S SCREENING STUDIES

EPA Science Inventory

The 1996 amendments to the Safe Drinking Water Act require the US Environmental Protection Agency (USEPA) to establish a list of unregulated microbiological and chemical contaminants to aid in priority-setting for the Agency's drinking water program. This list, known as the Cont...

Bacterial contamination of amniotic membrane in a tissue bank from Iran.

PubMed

Aghayan, Hamid Reza; Goodarzi, Parisa; Baradaran-Rafii, Alireza; Larijani, Bagher; Moradabadi, Leila; Rahim, Fakher; Arjmand, Babak

2013-09-01

Human Amniotic Membrane (AM) transplantation can promote tissue healing and reduce inflammation, tissue scarring and neovascularization. Homa Peyvand Tamin (HPT) tissue bank has focused on manufacturing human cell and tissue based products including AM. The purpose of this study is to evaluate and identify bacterial contamination of AMs that is produced by HPT for several ophthalmic applications. From July 2006 to April 2011, 122 placentas from cesarean sections were retrieved by HPT after obtaining informed consent from the donors. Besides testing donor's blood sample for viral markers, microbiological evaluation was performed pre and post processing. During tissue processing, decontamination was performed by an antibiotic cocktail including; Gentamicin, Ceftriaxone and Cloxacillin. Of 271 cesarean section AM donors who were screened as potential donors, 122 were accepted for processing and assessed for microbiological contamination. Donors' age were between 21 and 41 years (Mean = 27.61 ± 0.24). More than 92% of mothers were in their first or second gravidity with full term pregnancies. The most prevalent organisms were Staphylococci species (72.53%). After processing, contamination rates markedly decreased by 84.62% (p value = 0.013). According to our results, most of bacterial contaminations were related to donation process and the contamination pattern suggests procurement team as a source. Therefore we recommend that regular training programs should be implemented by tissue banks for procurement staff. These programs should focus on improved donor screening and proper aseptic technique for tissue retrieval. We also suggest that tissue banks should periodically check the rate and types of tissue contaminations. These data help them to find system faults and to update processing methods.

A flowchart for managing sexually transmitted infections among Nigerian adolescent females.

PubMed Central

Obunge, O. K.; Brabin, L.; Dollimore, N.; Kemp, J.; Ikokwu-Wonodi, C.; Babatunde, S.; White, S.; Briggs, N. D.; Hart, C. A.

2001-01-01

OBJECTIVE: To devise a flowchart suitable for assessing risk of trichomoniasis, chlamydia and gonorrhoea in an adolescent population, not all of whom will be sexually experienced or currently in a relationship. METHODS: The data used to derive the flowchart were generated from cross-sectional microbiological surveys of girls aged 14-19 years in Port Harcourt, Nigeria. The flowchart screened on the basis of: (i) sexual experience; (ii) recent sexual activity; (iii) a positive urine leukocyte esterase (LE) test; and (iv) among LE negatives, a history of malodorous/pruritic discharge. FINDINGS: Using this flowchart, we found that 26.2% of all adolescents screened would receive treatment for cervicitis and vaginitis. Chlamydial, gonococcal, and trichomonal infections were correctly diagnosed in 37.5%, 66.7%, and 50% of the cases, respectively. CONCLUSION: Although the flowchart is more suitable for an adolescent population than the vaginal discharge algorithm used in syndromic management protocols, it still lacks precision and needs adapting to local settings. PMID:11357208

Application of phenotypic microarrays to environmental microbiology

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

Borglin, sharon; Joyner, Dominique; DeAngelis, Kristen

2012-01-01

Environmental organisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. This review describes applications of phenotype arrays to anaerobic and thermophilic microorganisms, use of the plates in stress response studies, in development of culture media for newly discovered strains, and for assessment of phenotype of environmental communities. Also discussed are considerationsmore » and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting.« less

Screen of micro-organisms for inducing the production of dragon's blood by leaf of Dracaena cochinchinensis.

PubMed

Wang, X H; Zhang, C H; Wang, Y; Gomes-Laranjo, J

2010-11-01

To screen micro-organisms for inducing the production of dragon's blood, which is normally produced by stem xylem and by leaf of Dracaena cochinchinensis, and to evaluate the product by comparing with the standard. Thirty microbial strains were isolated from D. cochinchinensis leaves. Three of them were confirmed to elicit the leaf of D. cochinchinensis producing dragon's blood after inoculation. Upon elicitation, all of the 6-month-old leaves of the inducible trees produced dragon's blood; 60-70% of the 1-year-old leaves elicited produced the resin. All the three strains were identified as Colletotrichum gloeosporioide by morphological and molecular methods. The leaf resin had a similar TLC profile and antioxidant activities to the standard resin. In particular, it had a higher total flavonol content and antimicrobial activity than the standard. Upon the induction of the screened C. gloeosporioide mycelia, D. cochinchinensis leaf produced dragon's blood with higher total flavone content and antimicrobial activity than the standard dragon's blood. This work has provided a strategy for producing dragon's blood in a sustainable way using leaves of C. gloeosporioides by fungal elicitation. © 2010 The Authors. © 2010 The Society for Applied Microbiology.

Selection and evaluation of micro-organisms for biocontrol of Verticillium dahliae in olive.

PubMed

Varo, A; Raya-Ortega, M C; Trapero, A

2016-09-01

To identify potential biological control agents against Verticillium wilt in olive through a mass screening approach. A total of 47 strains and nine mixtures of micro-organisms were evaluated against Verticillium dahliae in a three stage screening: (i) in vitro, by the effect on the mycelial growth and spore germination of the pathogen; (ii) in natural infested soil, by the effect on the reduction of microsclerotia of the pathogen; (iii) in planta, by the effect on the infection of olive plants under controlled conditions. Various fungal and bacterial strains and mixtures inhibited the pathogen and showed consistent biocontrol activity against Verticillium wilt of olive. The screening has resulted in promising fungi and bacteria strains with antagonistic activity against Verticillium, such as two non-pathogenic Fusarium oxysporum, one Phoma sp., one Pseudomonas fluorescens and two mixtures of micro-organisms that may possess multiple modes of action. This study provides a practical basis for the potential use of selected strains as biocontrol agents for the protection of olive plants against V. dahliae infection. In addition, our study presented an effective method to evaluate antagonistic micro-organisms of V. dahliae in olive. © 2016 The Society for Applied Microbiology.

Costs and possible benefits of a two-tier infection control management strategy consisting of active screening for multidrug-resistant organisms and tailored control measures.

PubMed

Mutters, N T; Günther, F; Frank, U; Mischnik, A

2016-06-01

Multidrug-resistant organisms (MDROs) are an economic burden, and infection control (IC) measures are cost- and labour-intensive. A two-tier IC management strategy was developed, including active screening, in order to achieve effective use of limited resources. Briefly, high-risk patients were differentiated from other patients, distinguished according to type of MDRO, and IC measures were implemented accordingly. To evaluate costs and benefits of this IC management strategy. The study period comprised 2.5 years. All high-risk patients underwent microbiological screening. Gram-negative bacteria (GNB) were classified as multidrug-resistant (MDR) and extensively drug-resistant (XDR). Expenses consisted of costs for staff, materials, laboratory, increased workload and occupational costs. In total, 39,551 patients were screened, accounting for 24.5% of all admissions. Of all screened patients, 7.8% (N=3,104) were MDRO positive; these patients were mainly colonized with vancomycin-resistant enterococci (37.3%), followed by meticillin-resistant Staphylococcus aureus (30.3%) and MDR-GNB (28.3%). The median length of stay (LOS) for all patients was 10 days (interquartile range 3-20); LOS was twice as long in colonized patients (P<0.001). Screening costs totalled 255,093.82€, IC measures cost 97,701.36€, and opportunity costs were 599,225.52€. The savings of this IC management strategy totalled 500,941.84€. Possible transmissions by undetected carriers would have caused additional costs of 613,648.90-4,974,939.26€ (i.e. approximately 600,000-5 million €). Although the costs of a two-tier IC management strategy including active microbiological screening are not trivial, these data indicate that the approach is cost-effective when prevented transmissions are included in the cost estimate. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Evaluation of the HB&L System for the Microbiological Screening of Storage Medium for Organ-Cultured Corneas.

PubMed

Camposampiero, D; Grandesso, S; Zanetti, E; Mazzucato, S; Solinas, M; Parekh, M; Frigo, A C; Gion, M; Ponzin, D

2013-01-01

Aims. To compare HB&L and BACTEC systems for detecting the microorganisms contaminating the corneal storage liquid preserved at 31°C. Methods. Human donor corneas were stored at 4°C followed by preservation at 31°C. Samples of the storage medium were inoculated in BACTEC Peds Plus/F (aerobic microorganisms), BACTEC Plus Anaerobic/F (anaerobic microorganisms), and HB&L bottles. The tests were performed (a) after six days of storage, (b) end of storage, and (c) after 24 hours of preservation in deturgescent liquid sequentially. 10,655 storage and deturgescent media samples were subjected to microbiological control using BACTEC (6-day incubation) and HB&L (24-hour incubation) systems simultaneously. BACTEC positive/negative refers to both/either aerobic and anaerobic positives/negatives, whereas HB&L can only detect the aerobic microbes, and therefore the positives/negatives depend on the presence/absence of aerobic microorganisms. Results. 147 (1.38%) samples were identified positive with at least one of the two methods. 127 samples (134 identified microorganisms) were positive with both HB&L and BACTEC. 14 HB&L+/BACTEC- and 6 BACTEC+/HB&L- were identified. Sensitivity (95.5%), specificity (99.8%), and positive (90.1%) and negative predictive values (99.9%) were high with HB&L considering a 3.5% annual contamination rate. Conclusion. HB&L is a rapid system for detecting microorganisms in corneal storage medium in addition to the existing methods.

FT-IR spectroscopy as a tool for rapid identification and intra-species characterization of airborne filamentous fungi.

PubMed

Fischer, Guido; Braun, Silvia; Thissen, Ralf; Dott, Wolfgang

2006-01-01

Identification of microfungi is time-consuming due to cultivation and microscopic examination and can be influenced by the interpretation of the macro- and micro-morphological characters observed. Fungal conidia contain mycotoxins that may be present in bioaerosols and thus the capacity for production of mycotoxins (and allergens) needs to be investigated to create a basis for reliable risk assessment in environmental and occupational hygiene. The present investigation aimed to create a simple but sophisticated method for the preparation of samples and the identification of airborne fungi by FT-IR spectroscopy. The method was suited to reproducibly differentiate Aspergillus and Penicillium species on the generic, the species, and the strain level. There are strong indications that strains of one taxon differing in metabolite production can be reliably distinguished by FT-IR spectroscopy (e.g. Aspergillus parasiticus). On the other hand, species from different taxa being similar in secondary metabolite production showed comparably higher similarities. The results obtained here can serve as a basis for the development of a database for species identification and strain characterization of microfungi. The method presented here will improve and facilitate the risk assessment in case of bioaerosol exposure, as strains with different physiological properties (e.g. toxic, non-toxic) could be differentiated. Moreover, it has the potential to significantly improve the identification of microfungi in various fields of applied microbiological research, e.g. high throughput screening in view of specific physiological properties, biodiversity studies, inventories in environmental microbiology, and quality control measures.

Simple method for quantifying microbiologically assisted chloramine decay in drinking water.

PubMed

Sathasivan, Arumugam; Fisher, Ian; Kastl, George

2005-07-15

In a chloraminated drinking water distribution system, monochloramine decays due to chemical and microbiological reactions. For modeling and operational control purposes, it is necessary to know the relative contribution of each type of reaction, but there was no method to quantify these contributions separately. A simple method was developed to do so. It compares monochloramine decay rates of processed (0.2 microm filtered or microbiologically inhibited by adding 100 microg of silver/L as silver nitrate) and unprocessed samples under controlled temperature conditions. The term microbial decay factor (Fm) was defined and derived from this method, to characterize the relative contribution of microbiologically assisted monochloramine decay to the total monochloramine decay observed in bulk water. Fm is the ratio between microbiologically assisted monochloramine decay and chemical decay of a given water sample measured at 20 degrees C. One possible use of the method is illustrated, where a service reservoir's bulk and inlet waters were sampled twice and analyzed for both the traditional indicators and the microbial decay factor. The microbial decay factor values alone indicated that more microbiologically assisted monochloramine decay was occurring in one bulk water than the other. In contrast, traditional nitrification indicators failed to show any difference. Further analysis showed that the microbial decay factor is more sensitive and that it alone can provide an early warning.

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 3 2012-01-01 2012-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 3 2014-01-01 2014-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

Urogenital tract infections in pregnancy at King Edward VIII Hospital, Durban, South Africa.

PubMed

Dietrich, M; Hoosen, A A; Moodley, J; Moodley, S

1992-02-01

To evaluate the role of detecting asymptomatic bacteriuria and endocervical infections in the black prenatal patients attending King Edward VIII Hospital (KEH), Durban, with the view of justifying a screening programme. Screening for syphilis and human immunodeficiency virus (HIV) infection were also evaluated. 181 asymptomatic black prenatal patients attending the antenatal clinic for their first antenatal visit volunteered for the study and gave their written consent. Examination of each prenatal patient included obtaining of endocervical swabs to detect endocervical infections (C trachomatis, N gonorrhoeae), serum for syphilitic and HIV testing, and a midstream specimen of urine for microscopy and culture. Asymptomatic bacteriuria was found in 5.6% of patients in this study. Cervical infections were diagnosed microbiologically in 8.2% of women. These were N gonorrhoeae in 4.1% and C trachomatis in 4.7%. Serological tests for sexually transmitted diseases showed the presence of syphilis in 7.6% and antibody to the HIV in 1.9%. Overall, one or more sexually transmitted diseases were found in 16.5% of the women studied. This study suggests that all women presenting for routine antenatal care in a setting such as Durban should be screened for lower genital tract infections. Ideally this should include a midstream urine specimen for culture, serum for syphilitic and HIV antibody testing and endocervical swabs for sexually transmitted pathogens. In developing communities, however, more reliable and cheaper methods of endocervical screening need to be available before antenatal screening for cervico-vaginal infections can be justified.

[Effectiveness of human papillomavirus genotyping for detection of high-grade anal intraepithelial neoplasia compared to anal cytology].

PubMed

Padilla-España, Laura; Repiso-Jiménez, Juan Bosco; Fernández-Sánchez, Fernando; Pereda, Teresa; Rivas-Ruiz, Francisco; Fernández-Morano, Teresa; de la Torre-Lima, Javier; Palma, Fermín; Redondo, Maximino; de Troya-Martín, Magdalena

2016-01-01

The incidence of high-grade anal intraepithelial neoplasia (HGAIN) -with an aetiological based on high-risk types of human papillomavirus- is increasing in some high-risk groups. Screening for HGAIN includes routine anal cytology and, more recently, HPV genotyping. The main objective of this study was to determine the sensitivity and specificity of anal cytology and HPV genotyping for the detection of HGAIN. This is a study to determine the correlation of cytological and microbiological findings with anal biopsy findings in a cohort of patients at high risk of developing AIN referred to the department of sexually transmitted infections of the Hospital Costa del Sol, Spain, between January 2008 and December 2014. Of the 151 patients subjected to screening, a total of 92 patients, all of them with the result of three screening test (anal cytology, genotyping and biopsy) were included in the study. Just under two-thirds (62%) of them were HIV-positive. The sensitivity and specificity of anal cytology to detect HGAIN were 52.8 and 85.7%, respectively (k: 0.328), and 78 and 62.8% to detect two or more HPV oncogenic genotypes (k: 0.417). The detection of oncogenic HPV genotypes allowed the identification of 23 new cases of HGAIN that had been underdiagnosed with anal cytology, with 14 cases containing at least three high-risk genotypes. Anal cytology did not show enough sensitivity in HGAIN screening. HPV genotyping has shown to be a useful tool to detect HGAIN cases, although it could lead to an over-diagnosis as a solitary screening procedure. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

The anti-biofilm activity of lemongrass (Cymbopogon flexuosus) and grapefruit (Citrus paradisi) essential oils against five strains of Staphylococcus aureus.

PubMed

Adukwu, E C; Allen, S C H; Phillips, C A

2012-11-01

To determine the sensitivity of five strains of Staphylococcus aureus to five essential oils (EOs) and to investigate the anti-biofilm activity of lemongrass and grapefruit EOs. Antimicrobial susceptibility screening was carried out using the disk diffusion method. All of the strains tested were susceptible to lemongrass, grapefruit, bergamot and lime EOs with zones of inhibition varying from 2·85 to 8·60 cm although they were resistant to lemon EO. Lemongrass EO inhibited biofilm formation at 0·125% (v/v) as measured by colorimetric assay and at 0·25% (v/v) no metabolic activity was observed as determined by 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) reduction. Grapefruit EO did not show any anti-biofilm activity. Following exposure to lemongrass EO extensive disruption to Staph. aureus biofilms was shown under scanning electron microscopy. In comparison to the other EOs tested, lemongrass exhibited the most effective antimicrobial and anti-biofilm activity. The effect of lemongrass EO highlights its potential against antibiotic resistant Staph. aureus in the healthcare environment. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

A comprehensive survey of Aeromonas sp. and Vibrio sp. in seabirds from southeastern Brazil: outcomes for public health.

PubMed

Cardoso, M D; Lemos, L S; Roges, E M; de Moura, J F; Tavares, D C; Matias, C A R; Rodrigues, D P; Siciliano, S

2018-05-01

To perform a microbiological survey regarding the presence, prevalence and characterization of Aeromonas sp. and Vibrio sp. in debilitated wrecked marine birds recovered from the centre-north coast of the state of Rio de Janeiro, Brazil. Swabs obtained from 116 alive and debilitated wrecked marine birds, comprising 19 species, from the study area were evaluated by biochemical methods. Antimicrobial susceptibility tests and pathogenicity gene screening were performed for bacterial strains of public health importance. Vibrio sp. and Aeromonas sp. were identified, as well as certain pathogenic genes and resistance to selected antimicrobials. This study demonstrates that the identified bacteria, mainly Vibrio sp., are fairly prevalent and widespread among several species of seabirds and highlights the importance of migratory birds in bacterial dispersion. In addition, it demonstrates the importance of the bacterial strains regarding their pathogenic potential. Therefore, seabirds can act as bacterial reservoirs, and their monitoring is of the utmost importance in a public health context. The study comprehensively evaluates the importance of seabirds as bacteria of public health importance reservoirs, since birds comprising several pathogenic bacterial species were evaluated. © 2018 The Society for Applied Microbiology.

Successful Application of Active Learning Techniques to Introductory Microbiology.

ERIC Educational Resources Information Center

Hoffman, Elizabeth A.

2001-01-01

Points out the low student achievement in microbiology courses and presents an active learning method applied in an introductory microbiology course which features daily quizzes, cooperative learning activities, and group projects. (Contains 30 references.) (YDS)

Sterilization validation for medical devices at IRASM microbiological laboratory—Practical approaches

NASA Astrophysics Data System (ADS)

Trandafir, Laura; Alexandru, Mioara; Constantin, Mihai; Ioniţă, Anca; Zorilă, Florina; Moise, Valentin

2012-09-01

EN ISO 11137 established regulations for setting or substantiating the dose for achieving the desired sterility assurance level. The validation studies can be designed in particular for different types of products. Each product needs distinct protocols for bioburden determination and sterility testing. The Microbiological Laboratory from Irradiation Processing Center (IRASM) deals with different types of products, mainly for the VDmax25 method. When it comes to microbiological evaluation the most challenging was cotton gauze. A special situation for establishing the sterilization validation method appears in cases of cotton packed in large quantities. The VDmax25 method cannot be applied for items with average bioburden more than 1000 CFU/pack, irrespective of the weight of the package. This is a method limitation and implies increased costs for the manufacturer when choosing other methods. For microbiological tests, culture condition should be selected in both cases of the bioburden and sterility testing. Details about choosing criteria are given.

Enterobacter cloacae complex isolated from shrimps from Vietnam encoding blaIMI-1, resistant to carbapenems but not cephalosporins.

PubMed

Brouwer, Michael S M; Rapallini, Michel; Geurts, Yvon; Harders, Frank; Bossers, Alex; Mevius, Dik J; Wit, Ben; Veldman, Kees T

2018-04-23

In August of 2017, a batch of Penaeus monodon (Asian tiger shrimp) and Penaues vannamei (White leg shrimp), originating from fish farms in Vietnam, were screened for the presence of carbapenamase producing Enterobacteriaceae (CPE).…. Copyright © 2018 American Society for Microbiology.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1988-01-01

Chapter A4, methods for collection and analyses of aquatic biological and microbiological samples, contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity and bioassay. Each method is summarized, and the applications, interferences, apparatus, reagents, analyses, calculations, reporting of results, precisions, and references are given. Part 2 consists of a glossary. Part 3 is a list of taxonomic references. (USGS)

Rapid method for direct identification of bacteria in urine and blood culture samples by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: intact cell vs. extraction method.

PubMed

Ferreira, L; Sánchez-Juanes, F; Muñoz-Bellido, J L; González-Buitrago, J M

2011-07-01

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a fast and reliable technology for the identification of microorganisms with proteomics approaches. Here, we compare an intact cell method and a protein extraction method before application on the MALDI plate for the direct identification of microorganisms in both urine and blood culture samples from clinical microbiology laboratories. The results show that the intact cell method provides excellent results for urine and is a good initial method for blood cultures. The extraction method complements the intact cell method, improving microorganism identification from blood culture. Thus, we consider that MALDI-TOF MS performed directly on urine and blood culture samples, with the protocols that we propose, is a suitable technique for microorganism identification, as compared with the routine methods used in the clinical microbiology laboratory. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Diagnostic microbiology in veterinary dermatology: present and future.

PubMed

Guardabassi, Luca; Damborg, Peter; Stamm, Ivonne; Kopp, Peter A; Broens, Els M; Toutain, Pierre-Louis

2017-02-01

The microbiology laboratory can be perceived as a service provider rather than an integral part of the healthcare team. The aim of this review is to discuss the current challenges of providing a state-of-the-art diagnostic veterinary microbiology service including the identification (ID) and antimicrobial susceptibility testing (AST) of key pathogens in veterinary dermatology. The Study Group for Veterinary Microbiology (ESGVM) of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) identified scientific, technological, educational and regulatory issues impacting the predictive value of AST and the quality of the service offered by microbiology laboratories. The advent of mass spectrometry has significantly reduced the time required for ID of key pathogens such as Staphylococcus pseudintermedius. However, the turnaround time for validated AST methods has remained unchanged for many years. Beyond scientific and technological constraints, AST methods are not harmonized and clinical breakpoints for some antimicrobial drugs are either missing or inadequate. Small laboratories, including in-clinic laboratories, are usually not adequately equipped to run up-to-date clinical microbiologic diagnostic tests. ESGVM recommends the use of laboratories employing mass spectrometry for ID and broth micro-dilution for AST, and offering assistance by expert microbiologists on pre- and post-analytical issues. Setting general standards for veterinary clinical microbiology, promoting antimicrobial stewardship, and the development of new, validated and rapid diagnostic methods, especially for AST, are among the missions of ESGVM. © 2017 The Authors. Veterinary Dermatology published by John Wiley & Sons Ltd on behalf of the ESVD and ACVD.

Microbiological Surveillance and State of the Art Technological Strategies for the Prevention of Dialysis Water Pollution

PubMed Central

Bolasco, Piergiorgio; Contu, Antonio; Meloni, Patrizia; Vacca, Dorio; Galfrè, Andrea

2012-01-01

Methods: The present report attempts to illustrate the positive impact on the microbiological quality of dialysis patients over a 15-year period through the progressive implementation of state-of-the-art technological strategies and the optimization of microbiological surveillance procedures in five dialysis units in Sardinia. Results: Following on better microbiological, quality controls of dialysis water and improvement of procedures and equipment, a drastic improvement of microbiological water quality was observed in a total of 945 samples. The main aim was to introduce the use of microbiological culture methods as recommended by the most important guidelines. The microbiological results obtained have led to a progressive refining of controls and introduction of new materials and equipment, including two-stage osmosis and piping distribution rings featuring a greater capacity to prevent biofilm adhesion. The actions undertaken have resulted in unexpected quality improvements. Conclusions: Dialysis water should be viewed by the nephrologist as a medicinal product exerting a demonstrable positive impact on microinflammation in dialysis patients. A synergic effort between nephrologists and microbiologists undoubtedly constitutes the most effective means of preventing dialysis infections. PMID:23066395

Cost-benefit and effectiveness analysis of rapid testing for MRSA carriage in a hospital setting.

PubMed

Henson, Gay; Ghonim, Elham; Swiatlo, Andrea; King, Shelia; Moore, Kimberly S; King, S Travis; Sullivan, Donna

2014-01-01

A cost-effectiveness analysis was conducted comparing the polymerase chain reaction assay and traditional microbiological culture as screening tools for the identification of methicillin-resistant Staphylococcus aureus (MRSA) in patients admitted to the pediatric and surgical intensive care units (PICU and SICU) at a 722 bed academic medical center. In addition, the cost benefits of identification of colonized MRSA patients were determined. The cost-effectiveness analysis employed actual hospital and laboratory costs, not patient costs. The actual cost of the PCR assay was higher than the microbiological culture identification of MRSA ($602.95 versus $364.30 per positive carrier identified). However, this did not include the decreased turn-around time of PCR assays compared to traditional culture techniques. Patient costs were determined indirectly in the cost-benefit analysis of clinical outcome. There was a reduction in MRSA hospital-acquired infection (3.5 MRSA HAI/month without screening versus 0.6/month with screening by PCR). A cost-benefit analysis based on differences in length of stay suggests an associated savings in hospitalization costs: MRSA HAI with 29.5 day median LOS at $63,810 versus MRSA identified on admission with 6 day median LOS at $14,561, a difference of $49,249 per hospitalization. Although this pilot study was small and it is not possible to directly relate the cost-effectiveness and cost-benefit analysis due to confounding factors such as patient underlying morbidity and mortality, a reduction of 2.9 MRSA HAI/month associated with PCR screening suggests potential savings in hospitalization costs of $142,822 per month.

Influence of dissolved oxygen convection on well sampling

USGS Publications Warehouse

Vroblesky, D.A.; Casey, C.C.; Lowery, M.A.

2007-01-01

Convective transport of dissolved oxygen (D.O.) from shallow to deeper parts of wells was observed as the shallow water in wells in South Carolina became cooler than the deeper water in the wells due to seasonal changes. Wells having a relatively small depth to water were more susceptible to thermally induced convection than wells where the depth to water was greater because the shallower water levels were more influenced by air temperature. The potential for convective transport of D.O. to maintain oxygenated conditions in a well screened in an anaerobic aquifer was diminished as ground water exchange through the well screen increased and as oxygen demand increased. Transport of D.O. to the screened interval can adversely affect the ability of passive samplers to produce accurate concentrations of oxygen-sensitive solutes such as iron, other redox indicators, and microbiological data. A comparison of passive sampling to low-flow sampling in a well undergoing convection, however, showed general agreement of volatile organic compound concentrations. During low-flow sampling, the pumped water may be a mixture of convecting water from within the well casing and aquifer water moving inward through the screen. This mixing of water during low-flow sampling can substantially increase equilibration times, can cause false stabilization of indicator parameters, can give false indications of the redox state, and can provide microbiological data that are not representative of the aquifer conditions. Data from this investigation show that simple in-well devices can effectively mitigate convective transport of oxygen. The devices can range from inflatable packers to simple, inexpensive baffle systems. ?? 2007 National Ground Water Association.

Antimicrobial potential of metabolites extracted from bacterial symbionts associated with marine sponges in coastal area of Gulf of Mannar Biosphere, India.

PubMed

Skariyachan, S; G Rao, A; Patil, M R; Saikia, B; Bharadwaj Kn, V; Rao Gs, J

2014-03-01

Marine coastal areas of India have vast diversity of sponges which harbours many endosymbiotic bacteria which are the source of many potential antimicrobial metabolites. This study focuses the screening and characterization of drug-producing bacteria symbiotically which are associated with marine sponges collected from Gulf of Mannar, South Coast India. Six different sponges were collected and they were identified on the basis of their morphology. The drug-producing isolates were screened by agar overlay method towards various clinical strains. The secondary metabolites were characterized and were found to be quinones, alkaloids, flavanoids and flavonyl glycosides. The metabolites showed significant inhibitory properties against clinical strains that were further identified as chromophoric and fluorophoric in nature. Ethyl acetate extracts of chromophore and floureophore substances showed significant inhibitory properties against Methicillin resistant Staphylococcus aureus (MRSA) and Salmonella typhi respectively. 16S rRNA gene sequencing of theses isolates revealed that chomophore-producing strain were closely related to Pseudomonas spp. RHLB12, isolated from Callyspongia spp. and floureophore-producing bacteria was related to Bacillus licheniformis T6-1 which was isolated from Haliclona spp. Hence, our study demonstrated that antimicrobial metabolites extracted from symbiotic bacteria associated with marine sponges have high therapeutic potential against many bacterial pathogens including multidrug-resistant strains. This is the first study demonstrating antimicrobial potential of flurophoric and chromophoric metabolites extracted from bacterial biosymbionts associated with marine sponges. Our study has significant scope as Indian coastal area especially harbours vast varieties of sponges with novel secondary metabolites-producing organisms. The natural metabolites extracted from sponge-derived bacteria pave novel therapeutic remedy against various pathogens when most of them are emerged as extreme drug resistant superbugs. Letters in Applied Microbiology © 2013 The Society for Applied Microbiology.

A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics.

PubMed

Perry, John D

2017-04-01

In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including Pseudomonas aeruginosa, group B streptococci, Clostridium difficile, Campylobacter spp., and Yersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant Acinetobacter spp., and Enterobacteriaceae with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics. © Crown copyright 2017.

A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics

PubMed Central

2017-01-01

SUMMARY In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including Pseudomonas aeruginosa, group B streptococci, Clostridium difficile, Campylobacter spp., and Yersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant Acinetobacter spp., and Enterobacteriaceae with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics. PMID:28122803

Diagnostic value and cost utility analysis for urine Gram stain and urine microscopic examination as screening tests for urinary tract infection.

PubMed

Wiwanitkit, Viroj; Udomsantisuk, Nibhond; Boonchalermvichian, Chaiyaporn

2005-06-01

The aim of this study was to evaluate the diagnostic properties of urine Gram stain and urine microscopic examination for screening for urinary tract infection (UTI), and to perform an additional cost utility analysis. This descriptive study was performed on 95 urine samples sent for urine culture to the Department of Microbiology, Faculty of Medicine, Chulalongkorn University. The first part of the study was to determine the diagnostic properties of two screening tests (urine Gram stain and urine microscopic examination). Urine culture was set as the gold standard and the results from both methods were compared to this. The second part of this study was to perform a cost utility analysis. The sensitivity of urine Gram stain was 96.2%, the specificity 93.0%, the positive predictive value 94.3% and the negative predictive value 95.2%. False positives occurred with a frequency of 7.0% and false negatives 3.8%. For the microscopic examination, the sensitivity was 65.4%, specificity 74.4%, positive predictive value 75.6% and negative predictive value 64.0%. False positives occurred with a frequency of 25.6% and false negatives 34.6%. Combining urine Gram stain and urine microscopic examination, the sensitivity was 98.1%, specificity 74.4%, positive predictive value 82.3% and negative predictive value 97.0%. False positives occurred with a frequency of 25.6% and false negatives 1.9%. However, the cost per utility of the combined method was higher than either urine microscopic examination or urine Gram stain alone. Urine Gram stain provided the lowest cost per utility. Economically, urine Gram stain is the proper screening tool for presumptive diagnosis of UTI.

Evaluation of the HISCL Anti-Treponema pallidum Assay as a Screening Test for Syphilis.

PubMed

An, Jingna; Chen, Qixia; Liu, Qianqian; Rao, Chenli; Li, Dongdong; Wang, Tingting; Tao, Chuanmin; Wang, Lanlan

2015-07-01

The resurgence of syphilis in recent years has become a serious threat to public health worldwide, and the serological detection of specific antibodies against Treponema pallidum remains the most reliable method for laboratory diagnosis of syphilis. This study examined the performance of the recently launched HISCL anti-Treponema pallidum (anti-TP) assay as a screening test for syphilis in a high-volume laboratory. The HISCL anti-TP assay was tested in 300 preselected syphilis-positive samples, 704 fresh syphilis-negative samples, 48 preselected potentially interfering samples, and 30 "borderline" samples and was compared head to head with the commercially available Lumipulse G TP-N. In this study, the HISCL anti-TP assay was in perfect agreement with the applied testing algorithms with an overall agreement of 100%, comparable to that of Lumipulse G TP-N (99.63%). The sensitivity and specificity of the HISCL anti-TP assay were 100% (95% confidence interval [CI], 98.42% to 100%) and 100% (95% CI, 99.37% to 100%), respectively. Considering the excellent ease of use and automation, high throughput, and its favorable sensitivity and specificity, the HISCL anti-TP assay may represent a new choice for syphilis screening in high-volume laboratories. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Development of an Intracellular Screen for New Compounds Able To Inhibit Mycobacterium tuberculosis Growth in Human Macrophages.

PubMed

Sorrentino, Flavia; Gonzalez del Rio, Ruben; Zheng, Xingji; Presa Matilla, Jesus; Torres Gomez, Pedro; Martinez Hoyos, Maria; Perez Herran, Maria Esther; Mendoza Losana, Alfonso; Av-Gay, Yossef

2016-01-01

Here we describe the development and validation of an intracellular high-throughput screening assay for finding new antituberculosis compounds active in human macrophages. The assay consists of a luciferase-based primary identification assay, followed by a green fluorescent protein-based secondary profiling assay. Standard tuberculosis drugs and 158 previously recognized active antimycobacterial compounds were used to evaluate assay robustness. Data show that the assay developed is a short and valuable tool for the discovery of new antimycobacterial compounds. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Evaluation of the boson chemiluminescence immunoassay as a first-line screening test in the ECDC algorithm for syphilis serodiagnosis in a population with a high prevalence of syphilis.

PubMed

Qiu, Xin-Hui; Zhang, Ya-Feng; Chen, Yu-Yan; Zhang, Qiao; Chen, Fu-Yi; Liu, Long; Fan, Jin-Yi; Gao, Kun; Zhu, Xiao-Zhen; Zheng, Wei-Hong; Zhang, Hui-Lin; Lin, Li-Rong; Liu, Li-Li; Tong, Man-Li; Zhang, Chang-Gong; Niu, Jian-Jun; Yang, Tian-Ci

2015-04-01

We developed a new Boson chemiluminescence immunoassay (CIA) and evaluated its application with cross-sectional analyses. Our results indicated that the Boson CIA demonstrated strong discriminatory power in diagnosing syphilis and that it can be used as a first-line screening test for syphilis serodiagnosis using the European Centre for Disease Prevention and Control algorithm or as a confirmatory test when combined with a patient's clinical history. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Microbiological survey of raw and ready-to-eat leafy green vegetables marketed in Italy.

PubMed

Losio, M N; Pavoni, E; Bilei, S; Bertasi, B; Bove, D; Capuano, F; Farneti, S; Blasi, G; Comin, D; Cardamone, C; Decastelli, L; Delibato, E; De Santis, P; Di Pasquale, S; Gattuso, A; Goffredo, E; Fadda, A; Pisanu, M; De Medici, D

2015-10-01

The presence of foodborne pathogens (Salmonella spp., Listeria monocytogenes, Escherichia coli O157:H7, thermotolerant Campylobacter, Yersinia enterocolitica and norovirus) in fresh leafy (FL) and ready-to-eat (RTE) vegetable products, sampled at random on the Italian market, was investigated to evaluate the level of risk to consumers. Nine regional laboratories, representing 18 of the 20 regions of Italy and in which 97.7% of the country's population resides, were involved in this study. All laboratories used the same sampling procedures and analytical methods. The vegetable samples were screened using validated real-time PCR (RT-PCR) methods and standardized reference ISO culturing methods. The results show that 3.7% of 1372 fresh leafy vegetable products and 1.8% of 1160 "fresh-cut" or "ready-to-eat" (RTE) vegetable retailed in supermarkets or farm markets, were contaminated with one or more foodborne pathogens harmful to human health. Copyright © 2015 Elsevier B.V. All rights reserved.

Occurrence of antimicrobial residues in Brazilian food animals in 2008 and 2009.

PubMed

Nonaka, C K V; Oliveira, A M G; Paiva, C R; Almeida, M P; Rezende, C P; Moraes, C G O; Botelho, B G; Souza, L F; Dias, P G

2012-01-01

Brazil is one of the most important countries as a producer and exporter of cattle and poultry. In 2009 cattle accounted for 30% of the export market and 41.4% for poultry meat. The Brazilian National Residues and Contaminants Control Plan (PNCRC) follows the guidelines set by the Codex Alimentarius Commission and checks compliance maximum residue limits (MRLs) to ensure the quality of these commodities. Kidney samples (n = 2978) were analysed between January 2008 and December 2009. Fifteen antibiotics of the macrolide and aminoglycoside groups (clindamycin, eritromycin, lincomycin, tylmicosin, tylosin, amikacin, apramycin, dihydrostreptomycin, gentamycin, higromycin, kanamycin, neomycin, spectinomycin, streptomycin, tobramycin) were determined by a microbiological screening method (FAST) and confirmed/quantified using liquid chromatography (LC-MS/MS and UPLC-MS/MS). In 2008, 1459 samples were analysed by a screening test and liquid chromatography with only one sample (0.07%) exceeded Brazilian legislation limits (>MRL). In 2009, 1519 samples were analysed and none exceeding Brazilian legislation limits (>MRL). The slaughterhouses of 16 states were monitored during the year of 2008, and 18 states were monitored in 2009, being the major producing states most sampled by the PNCRC.

Prevalence of Trichomonas vaginalis and Human papillomavirus in female sex workers in Central Veracruz, Mexico.

PubMed

Muñoz-Ramírez, Azucena; López-Monteon, Aracely; Ramos-Ligonio, Angel; Méndez-Bolaina, Enrique; Guapillo-Vargas, Mario R B

2018-03-13

Female sex workers (FSWs) have been considered a key population for sexually transmitted infections (STIs); therefore, they are periodically screened as a requirement to obtain a work card. However, there is insufficient epidemiological data on STIs among FSWs in Mexico. The detection of Trichomonas vaginalis is limited to microscopic studies and the molecular screening of Human papillomavirus (HPV) is only done to women 35 years of age and older. The objective of this study was to determine the prevalence of T. vaginalis and HPV infections in FSWs in the city of Orizaba, Veracruz, Mexico. Samples from 105 FSWs were obtained by cervical swab and analyzed. The identification of T. vaginalis and HPV was performed by molecular methods. HPV DNA was identified in 5.71% of the samples with the presence of HPV16, HPV18, and HPV58. A percentage of 25.7% samples were positive for T. vaginalis for optical microscopy and 23.8% for PCR. The results of the study indicate the need to incorporate more sensitive methods for the timely diagnosis of STIs as well as comprehensive health promotion programs directed to the most vulnerable groups among FSWs. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

In situ detection of microbial c-type cytochrome based on intrinsic peroxidase-like activity using screen-printed carbon electrode.

PubMed

Wen, Junlin; He, Daigui; Yu, Zhen; Zhou, Shungui

2018-08-15

C-type cytochromes (c-cyts) facilitate microbial extracellular electron transfer and play critical roles in biogeochemical cycling, bioelectricity generation and bioremediation. In this study, a simple and effective method has been developed to detect microbial c-cyts by means of peroxidase mimetic reaction on screen-printed carbon electrode (SPCE). To this end, bacteria cells were immobilized onto the working electrode surface of SPCE by a simple drop casting. After introducing 3,3',5,5'-tetramethylbenzidine (TMB) solution, microbial c-cyts with peroxidase-like activity catalyze the oxidation of TMB in the presence of hydrogen peroxide. The oxidized TMB was electrochemically determined and the current signal was employed to calculate the c-cyts content. This electrochemical method is highly sensitive for microbial c-cyts with a low detection limit of 40.78 fmol and a wide detection range between 51.70 fmol and 6.64 pmol. Moreover, the proposed technique can be universally expanded to detect c-cyts in other bacteria species such as Fontibacter ferrireducens, Pseudomonas aeruginosa, Comamonas guangdongensis and Escherichia coli. Furthermore, the proposed method confers an in situ facile and quantitative c-cyts detection without any destructive sample preparations, complex electrode modifications and expensive enzyme- or metal particle- based signal amplification. The suggested method advances an intelligent strategy for in situ quantification of microbial c-cyts and consequently holds promising application potential in microbiology and environmental science. Copyright © 2018 Elsevier B.V. All rights reserved.

[Authorized Qualifications of Staff Conducting Examinations in the Field of Clinical Microbiology].

PubMed

Nishiyama, Hiroyuki

2015-04-01

Because of the increase in healthcare-associated infections, appearance of highly resistant bacteria, and that of emerging/re-emerging infectious diseases, it is necessary for the skills of clinical microbiological technologists and the associated technology to be improved. Technologist in Microbiology (4,717 certified) and Specialist in Microbiology (58 certified) are authorized qualifications in the field of examination for clinical microbiology, with a history of 60 years, and Clinical Microbiological Technologist (670 certified) and Infection Control Microbiological Technologist (ICMT) (528 certified) are necessary qualifications to become a member of an infection control team. As problems to be resolved, clarifying the relationships among the authorized qualifications, reconsidering the fairness of evaluating written examinations, and further consideration of the administration method for an increasing number of examinees need to be tackled.

A microbiological method for determining serum levels of broad spectrum β-lactam antibiotics in critically ill patients.

PubMed

Fridlund, Jimmy; Woksepp, Hanna; Schön, Thomas

2016-10-01

Recent studies show that suboptimal blood levels of β-lactam antibiotics are present in intensive care unit (ICU) patients. A common reference method for assessing drug concentrations is liquid chromatography coupled with mass-spectrometry (LC-MS) which is highly accurate but rarely available outside reference centres. Thus, our aim was to develop a microbiological method for monitoring β-lactam antibiotic serum levels which could be used at any hospital with a microbiological laboratory. The method was developed as a 96-well broth microdilution format to assess the concentrations of cefotaxime (CTX), meropenem (MER), and piperacillin (PIP). Patient serum containing antibiotics were diluted in suspensions of bacteria with known minimal inhibitory concentrations (MICs). Serum antibiotic concentrations were calculated by dividing the MIC with the dilution factor at which the serum inhibited growth of the bacterial suspension. Serum (n=88) from ICU patients at four hospitals in south-east Sweden were analysed and compared to LC-MS analysis. The overall accuracy and precision for spiked samples and patient samples was within the pre-set target of ±20.0% for all drugs. There was a significant correlation between the microbiological assay and LC-MS for the patient samples (CTX: r=0.86, n=31; MER: r=0.96, n=11; PIP: r=0.88, n=39) and the agreement around the clinical cut-off for CTX (4.0mg/l), MER (2.0mg/l) and PIP (16.0mg/l) was 90%, 100% and 87%, respectively. The microbiological method has a performance for determination of serum levels of meropenem, piperacillin and cefotaxime suitable for clinical use. It is an inexpensive method applicable in any microbiology laboratory. Copyright © 2016 Elsevier B.V. All rights reserved.

What do physicians tell laboratories when requesting tests? A multi-method examination of information supplied to the microbiology laboratory before and after the introduction of electronic ordering.

PubMed

Georgiou, Andrew; Prgomet, Mirela; Toouli, George; Callen, Joanne; Westbrook, Johanna

2011-09-01

The provision of relevant clinical information on pathology requests is an important part of facilitating appropriate laboratory utilization and accurate results interpretation and reporting. (1) To determine the quantity and importance of handwritten clinical information provided by physicians to the Microbiology Department of a hospital pathology service; and (2) to examine the impact of a Computerized Provider Order Entry (CPOE) system on the nature of clinical information communication to the laboratory. A multi-method and multi-stage investigation which included: (a) a retrospective audit of all handwritten Microbiology requests received over a 1-month period in the Microbiology Department of a large metropolitan teaching hospital; (b) the administration of a survey to laboratory professionals to investigate the impact of different clinical information on the processing and/or interpretation of tests; (c) an expert panel consisting of medical staff and senior scientists to assess the survey findings and their impact on pathology practice and patient care; and (d) a comparison of the provision and value of clinical information before CPOE, and across 3 years after its implementation. The audit of handwritten requests found that 43% (n=4215) contained patient-related clinical information. The laboratory survey showed that 97% (84/86) of the different types of clinical information provided for wound specimens and 86% (43/50) for stool specimens were shown to have an effect on the processing or interpretation of the specimens by one or more laboratory professionals. The evaluation of the impact of CPOE revealed a significant improvement in the provision of useful clinical information from 2005 to 2008, rising from 90.1% (n=749) to 99.8% (n=915) (p<.0001) for wound specimens and 34% (n=129) to 86% (n=422) (p<.0001) for stool specimens. This study showed that the CPOE system provided an integrated platform to access and exchange valuable patient-related information between physicians and the laboratory. These findings have important implications for helping to inform decisions about the design and structure of CPOE screens and what data entry fields should be designated or made voluntary. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

[Validation and verfication of microbiology methods].

PubMed

Camaró-Sala, María Luisa; Martínez-García, Rosana; Olmos-Martínez, Piedad; Catalá-Cuenca, Vicente; Ocete-Mochón, María Dolores; Gimeno-Cardona, Concepción

2015-01-01

Clinical microbiologists should ensure, to the maximum level allowed by the scientific and technical development, the reliability of the results. This implies that, in addition to meeting the technical criteria to ensure their validity, they must be performed with a number of conditions that allows comparable results to be obtained, regardless of the laboratory that performs the test. In this sense, the use of recognized and accepted reference methodsis the most effective tool for these guarantees. The activities related to verification and validation of analytical methods has become very important, as there is continuous development, as well as updating techniques and increasingly complex analytical equipment, and an interest of professionals to ensure quality processes and results. The definitions of validation and verification are described, along with the different types of validation/verification, and the types of methods, and the level of validation necessary depending on the degree of standardization. The situations in which validation/verification is mandatory and/or recommended is discussed, including those particularly related to validation in Microbiology. It stresses the importance of promoting the use of reference strains as controls in Microbiology and the use of standard controls, as well as the importance of participation in External Quality Assessment programs to demonstrate technical competence. The emphasis is on how to calculate some of the parameters required for validation/verification, such as the accuracy and precision. The development of these concepts can be found in the microbiological process SEIMC number 48: «Validation and verification of microbiological methods» www.seimc.org/protocols/microbiology. Copyright © 2013 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Prevalence of methicillin-sensitive and methicillin-resistant Staphylococcus aureus in pregnant women.

PubMed

Chen, Katherine T; Huard, Richard C; Della-Latta, Phyllis; Saiman, Lisa

2006-09-01

To estimate the extent of Staphylococcus aureus vaginal-rectal colonization among pregnant women as severe S aureus infections have emerged in pregnant and postpartum women and infants. We conducted a prospective surveillance study for methicillin-sensitive S aureus and methicillin-resistant S aureus on all routine de-identified vaginal-rectal prenatal group B streptococcus (GBS) screening cultures submitted to the microbiology laboratory of a tertiary-care facility from January to July 2005. Standard microbiologic techniques and molecular analyses were used to detect community-associated methicillin-resistant S aureus strains. As opposed to health care-associated methicillin-resistant S aureus isolates, community-associated methicillin-resistant S aureus isolates were defined as those possessing the type IV or type V staphylococcal chromosomal cassette mec element and usually lacking a multidrug-resistant phenotype. A total of 2,963 GBS screening cultures were analyzed, from which 743 (25.1%, 95% confidence interval [CI] 23.5-26.7%) GBS isolates and 507 (17.1%, 95% CI 15.7-18.5%) S aureus isolates were identified. Group B streptococcus colonization was significantly associated with S aureus colonization (prevalence odds ratio 2.1, 95% CI 1.7-2.5, P < .001). Of the S aureus isolates, 14 (2.8%, 95% CI 1.4-4.2%) were methicillin-resistant, and 13 of these were determined to be community-associated methicillin-resistant S aureus. The prevalence of S aureus colonization identified in GBS screening cultures from pregnant women was substantial and associated with GBS co-colonization. Although we do not advocate routine screening of pregnant women for methicillin-sensitive S aureus and methicillin-resistant S aureus colonization, we recommend continued monitoring of both methicillin-sensitive S aureus and methicillin-resistant S aureus infections in this population and their infants.

Evaluation of a Microbiological Multi-Residue System on the detection of antibacterial substances in ewe milk.

PubMed

Althaus, Rafael; Berruga, Maria Isabel; Montero, Ana; Roca, Marta; Molina, Maria Pilar

2009-01-19

To protect both, public health and the dairy industry, from the presence of antibiotic residues in milk, control programmes have been established, which include the needed screening tests. This work focuses on the application of a Microbiological Multi-Residue System in ewe milk, a method based on the use of six different plates, each seeded with one of the following bacteria: Geobacillus stearothermophilus var. calidolactis (beta-lactams), Bacillus subtilis at pH 8.0 (aminoglycosides), Kocuria rhizophila (macrolides), Escherichia coli (quinolones), B. cereus (tetracyclines) and B. subtilis at pH 7.0 (sulphonamides), respectively. Twenty-three antimicrobial substances were analysed and a logistic regression was established for each substance assayed to relate the antibiotic concentration and the zone of microbial growth inhibition. Great linearity in the response was observed (regression coefficients of over 0.97). This fact suggests the possibility of establishing a decision level of antibiotic concentrations near to the Maximum Residue Limits (MRL). Zones of inhibition were suggested as proposed action levels for the different antimicrobial groups (diameters of inhibition of 18 mm for the aminoglycoside, beta-lactam and sulphonamide plates; 19 mm for the tetracycline plate, 21 mm for the macrolide plate, and 24 mm for the quinolone plate). Specificity and cross-reactivity were also assayed.

Screening and Scoring of Antimicrobial and Biological Activities of Italian Vulnerary Plants against Major Oral Pathogenic Bacteria

PubMed Central

Ferrazzano, Gianmaria F.; Roberto, Lia; Catania, Maria Rosaria; Chiaviello, Angela; De Natale, Antonino; Roscetto, Emanuela; Pinto, Gabriele; Pollio, Antonino; Ingenito, Aniello; Palumbo, Giuseppe

2013-01-01

This study aims to evaluate the activity of Italian vulnerary plants against the most important oral pathogenic bacteria. This estimate was accomplished through a fivefold process: (a) a review of ethnobotanical and microbiological data concerning the Italian vulnerary plants; (b) the development of a scoring system to rank the plants; (c) the comparative assessment of microbiological properties; (d) the assessment of potential cytotoxic effects on keratinocyte-like cells and gingival fibroblasts in culture by XTT cell viability assay; (e) clinical evaluation of the most suitable plant extract as antibacterial agent in a home-made mouthwash. The study assays hexane (H), ethanol (E), and water (W) extracts from 72 plants. The agar diffusion method was used to evaluate the activity against Streptococcus mutans, Streptococcus sobrinus, Lactobacillus casei, and Actinomyces viscosus. Twenty-two plants showed appreciable activity. The extracts showing the strongest antibacterial power were those from Cotinus coggygria Scop., Equisetum hyemale L., Helichrysum litoreum Guss, Juniperus communis L., and Phyllitis scolopendrium (L.) Newman subsp. scolopendrium. The potential cytotoxic effect of these extracts was assessed. On the basis of these observations, a mouth-rinse containing the ethanolic extract of H. litoreum has been tested in vivo, resulting in reduction of the salivary concentration of S. mutans. PMID:24302963

Aloe vera herbal dentifrices for plaque and gingivitis control: a systematic review.

PubMed

Dhingra, K

2014-04-01

To evaluate the effectiveness of aloe vera containing herbal dentifrices in improving plaque control and gingival health. A manual and electronic literature (MEDLINE and Cochrane Central Register of Controlled Trials) search was performed up to July 2012, for randomized controlled trials presenting clinical, microbiological, immunological, and patient-centered data for the efficacy of aloe vera herbal dentifrices for controlling plaque and gingival inflammation in patients with gingivitis. From 79 titles and abstracts, eight full-text articles were screened and finally two randomized controlled trials were selected. These randomized controlled trials reported that aloe vera dentifrices were similar in efficacy to control dentifrices in effectively reducing plaque and gingival inflammation in gingivitis patients based on the assessment of clinical, microbiological, and patient-centered treatment outcomes. However, many important details (composition and characteristics of aloe vera and control dentifrices along with appropriate randomization, blinding, and outcomes assessed) were lacking in these trials, and therefore, the quality of reporting and methods was generally flawed with high risk of bias. Even though there are some promising results, the clinical effectiveness of aloe vera herbal dentifrices is not sufficiently defined at present and warrants further investigations based on reporting guidelines of herbal CONSORT statement. © 2013 John Wiley & Sons A/S.

Preface: 5th International Symposium on the Interface between Analytical Chemistry and Microbiology - April 19th to 21st, 2004: Hosted at Pacific Northwest National Laboratory

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

Allmaier, Guenter; Wunschel, David S.; Wahl, Karen L.

2004-04-19

This is an introduction to a special issue of the Journal of microbiological Methods based on a recent meeting held at PNNL: the 5th International Symposium on the Interface between Analytical Chemistry and Microbiology.

Review of microfluidic microbioreactor technology for high-throughput submerged microbiological cultivation

PubMed Central

Hegab, Hanaa M.; ElMekawy, Ahmed; Stakenborg, Tim

2013-01-01

Microbial fermentation process development is pursuing a high production yield. This requires a high throughput screening and optimization of the microbial strains, which is nowadays commonly achieved by applying slow and labor-intensive submerged cultivation in shake flasks or microtiter plates. These methods are also limited towards end-point measurements, low analytical data output, and control over the fermentation process. These drawbacks could be overcome by means of scaled-down microfluidic microbioreactors (μBR) that allow for online control over cultivation data and automation, hence reducing cost and time. This review goes beyond previous work not only by providing a detailed update on the current μBR fabrication techniques but also the operation and control of μBRs is compared to large scale fermentation reactors. PMID:24404006

Infectious Disease Transmission during Organ and Tissue Transplantation

PubMed Central

Kuehnert, Matthew J.; Fishman, Jay A.

2012-01-01

Infectious disease transmission through organ and tissue transplantation has been associated with severe complications in recipients. Determination of donor-derived infectious risk associated with organ and tissue transplantation is challenging and limited by availability and performance characteristics of current donor epidemiologic screening (e.g., questionnaire) and laboratory testing tools. Common methods and standards for evaluating potential donors of organs and tissues are needed to facilitate effective data collection for assessing the risk for infectious disease transmission. Research programs can use advanced microbiological technologies to define infectious risks posed by pathogens that are known to be transplant transmissible and provide insights into transmission potential of emerging infectious diseases for which transmission characteristics are unknown. Key research needs are explored. Stakeholder collaboration for surveillance and research infrastructure is required to enhance transplant safety. PMID:22840823

[30 years since the first AIDS cases were reported: history and the present part III].

PubMed

Brůčková, Marie

2012-12-01

The end of the article features the development of HIV/AIDS diagnosis and its implementation in the Czech Republic. The establishment of the National Reference Laboratory for AIDS (NRL AIDS) at the National Institute of Public Health late in 1985 is mentioned and its responsibilities as the methodology centre in the areas of HIV/AIDS laboratory diagnosis and epidemiology are specified. In cooperation with the respective experts, a pilot HIV/AIDS prevalence study was conducted in the Czech Republic. The general criteria for HIV/AIDS laboratory diagnosis were set for both blood transfusion service and microbiology laboratories. Early in 1987, mass screening of blood donors was introduced in blood transfusion centres and in the second half of the same year, the HIV screening program was extended to selected microbiology laboratories. The NRL AIDS established a unified data reporting system, analyzed the results at the national level, and since 1989, has been reporting the outcomes to the international AIDS, and later HIV/AIDS, reporting system. The NRL AIDS also participated in a number of international projects in the areas of the research and development of laboratory techniques and epidemiological surveillance.

Mexican unpasteurised fresh cheeses are contaminated with Salmonella spp., non-O157 Shiga toxin producing Escherichia coli and potential uropathogenic E. coli strains: A public health risk.

PubMed

Guzman-Hernandez, Rosa; Contreras-Rodriguez, Araceli; Hernandez-Velez, Rosa; Perez-Martinez, Iza; Lopez-Merino, Ahide; Zaidi, Mussaret B; Estrada-Garcia, Teresa

2016-11-21

Fresh cheeses are a main garnish of Mexican food. Consumption of artisanal fresh cheeses is very common and most of them are made from unpasteurised cow milk. A total of 52 fresh unpasteurised cheeses of five different types were purchased from a variety of suppliers from Tabasco, Mexico. Using the most probable number method, 67% and 63% of samples were positive for faecal coliforms and E. coli, respectively; revealing their low microbiological quality. General hygienic conditions and practices of traditional cheese manufacturers were poor; most establishments had unclean cement floors, all lacked windows and doors screens, and none of the food-handlers wore aprons, surgical masks or bouffant caps. After analysing all E. coli isolates (121 strains) for the presence of 26 virulence genes, results showed that 9 (17%) samples were contaminated with diarrheagenic E. coli strains, 8 harboured non-O157 Shiga toxin producing E. coli (STEC), and one sample contained both STEC and diffusely adherent E. coli strains. All STEC strains carried the stx1 gene. Potential uropathogenic E. coli (UPEC) strains were isolated from 15 (29%) samples; the most frequent gene combination was fimA-agn43. Two samples were contaminated with Salmonella. The results demonstrated that unpasteurised fresh cheeses produced in Tabasco are of poor microbiological quality and may frequently harbour foodborne pathogens. Food safety authorities in Mexico need to conduct more rigorous surveillance of fresh cheeses. Furthermore, simple and inexpensive measures as establishing programs emphasizing good hand milking practices and hygienic manufacturing procedures may have a major effect on improving the microbiological quality of these food items. Copyright © 2016 Elsevier B.V. All rights reserved.

Simultaneous Identification of Potential Pathogenicity Factors of Mycoplasma agalactiae in the Natural Ovine Host by Negative Selection.

PubMed

Hegde, Shivanand; Hegde, Shrilakshmi; Zimmermann, Martina; Flöck, Martina; Spergser, Joachim; Rosengarten, Renate; Chopra-Dewasthaly, Rohini

2015-07-01

Mycoplasmas possess complex pathogenicity determinants that are largely unknown at the molecular level. Mycoplasma agalactiae serves as a useful model to study the molecular basis of mycoplasma pathogenicity. The generation and in vivo screening of a transposon mutant library of M. agalactiae were employed to unravel its host colonization factors. Tn4001mod mutants were sequenced using a novel sequencing method, and functionally heterogeneous pools containing 15 to 19 selected mutants were screened simultaneously through two successive cycles of sheep intramammary infections. A PCR-based negative selection method was employed to identify mutants that failed to colonize the udders and draining lymph nodes in the animals. A total of 14 different mutants found to be absent from ≥ 95% of samples were identified and subsequently verified via a second round of stringent confirmatory screening where 100% absence was considered attenuation. Using this criterion, seven mutants with insertions in genes MAG1050, MAG2540, MAG3390, uhpT, eutD, adhT, and MAG4460 were not recovered from any of the infected animals. Among the attenuated mutants, many contain disruptions in hypothetical genes, implying their previously unknown role in M. agalactiae pathogenicity. These data indicate the putative role of functionally different genes, including hypothetical ones, in the pathogenesis of M. agalactiae. Defining the precise functions of the identified genes is anticipated to increase our understanding of M. agalactiae infections and to develop successful intervention strategies against it. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Evaluation and implementation of a membrane filter method for Cronobacter detection in drinking water.

PubMed

Liu, Hui; Yang, Yuelian; Cui, Jinghua; Liu, Lanzheng; Liu, Huiyuan; Hu, Guangchun; Shi, Yuwen; Li, Jian

2013-07-01

A membrane filter (MF) method was evaluated for its suitability for qualitative and quantitative analyses of Cronobacter spp. in drinking water by pure strains of Cronobacter and non-Cronobacter, and samples spiked with chlorinated Cronobacter sakazakii ATCC 29544. The applicability was verified by the tests: for pure strains, the sensitivity and the specificity were both 100%; for spiked samples, the MF method recovered 82.8 ± 10.4% chlorinated ATCC 29544 cells. The MF method was also applied to screen Cronobacter spp. in drinking water samples from municipal water supplies on premises (MWSP) and small community water supplies on premises (SCWSP). The isolation rate of Cronobacter spp. from SCWSP samples was 31/114, which was significantly higher than that from MWSP samples which was 1/131. Besides, the study confirmed the possibility of using total coliform as an indicator of contamination level of Cronobacter spp. in drinking water, and the acquired correct positive rate was 96%. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Rapid Detection of Escherichia coli O157:H7 in Fresh Lettuce Based on Localized Surface Plasmon Resonance Combined with Immunomagnetic Separation.

PubMed

Lee, Nari; Choi, Sung-Wook; Chang, Hyun-Joo; Chun, Hyang Sook

2018-05-01

This study presents a method for rapid detection of Escherichia coli O157:H7 in fresh lettuce based on the properties of target separation and localized surface plasmon resonance of immunomagnetic nanoparticles. The multifunctional immunomagnetic nanoparticles enabling simultaneous separation and detection were prepared by synthesizing magnetic nanoparticles (ca. 10 nm in diameter) composed of an iron oxide (Fe 3 O 4 ) core and gold shell and then conjugating these nanoparticles with the anti- E. coli O157:H7 antibodies. The application of multifunctional immunomagnetic nanoparticles for detecting E. coli O157:H7 in a lettuce matrix allowed detection of the presence of <1 log CFU mL -1 without prior enrichment. In contrast, the detection limit of the conventional plating method was 2.74 log CFU mL -1 . The method, which requires no preenrichment, provides an alternative to conventional microbiological detection methods and can be used as a rapid screening tool for a large number of food samples.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1989-01-01

The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section.This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples.Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

High-performance liquid chromatographic method for potency determination of amoxicillin in commercial preparations and for stability studies.

PubMed Central

Hsu, M C; Hsu, P W

1992-01-01

A reversed-phase column liquid chromatographic method was developed for the assay of amoxicillin and its preparations. The linear calibration range was 0.2 to 2.0 mg/ml (r = 0.9998), and recoveries were generally greater than 99%. The high-performance liquid chromatographic assay results were compared with those obtained from a microbiological assay of bulk drug substance and capsule, injection, and granule formulations containing amoxicillin and degraded amoxicillin. At the 99% confidence level, no significant intermethod differences were noted for the paired results. Commercial formulations were also analyzed, and the results obtained by the proposed method closely agreed with those found by the microbiological method. The results indicated that the proposed method is a suitable substitute for the microbiological method for assays and stability studies of amoxicillin preparations. PMID:1416827

Vitamin B12 assays compared by use of patients sera with low vitamin B12 content

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

Sheridan, B.L.; Pearce, L.C.

1985-05-01

The authors compared four radioisotope dilution (RD) methods and a microbiological assay for measuring concentrations of vitamin B12 in a selected panel of serum samples from patients known to be deficient in the vitamin. Low (less than 100 ng/L) and borderline (100-180 ng/L) results were similar between methods, but use of the manufacturers recommended ranges for borderline results would have changed the diagnostic classifications for 22 of 38 samples. Results of all the RD methods inter-correlated well, but less so with the microbiological assay. Borderline, nondiagnostic results were common to all methods, and no apparent advantage was gained from usingmore » the microbiological assay.« less

[Complicated urinary tract infections--from the perspective of the medical technologist].

PubMed

Nagasawa, Zenzo

2002-07-01

We would like to propose re-establishment of the protocol for ordering a clinical microbiology laboratory test after a bedside screening test using urine reagent strip when urinary tract infection is suspected. Media for isolation shall be chosen by the clinical microbiology laboratory after checking turbidity and microscopic examination of the urine specimen. In cases of complicated urinary tract infections, quantitative culture should be performed to investigate changes in the number of microorganism to grasp condition of super infection. In such infections, there are many cases in which multiple microorganism growth including glucose non-fermenting gram-negative bacilli can be recognized. Therefore, it is necessary to inspect colonies on media as long as possible (24 hrs culture may be short in some cases). The protocol for microorganism identification and susceptibility test for such specimen varies in each laboratory, considering the Health Insurance Point System (reimbursement system by MHW). It is necessary to communicate with physicians and to refer to past results to proceed with the laboratory test properly. Therefore, a Certified Clinical Microbiology Medical Technologist is needed and the role played by such staff is important.

Experiments with Writing to Teach Microbiology.

ERIC Educational Resources Information Center

Cannon, Robert E.

1990-01-01

Described are the experiences of one teacher with the teaching of writing in college level microbiology, virology, and immunology courses. Assignments, methods, evaluation, and student responses are discussed. (CW)

Selection and screening of microbial consortia for efficient and ecofriendly degradation of plastic garbage collected from urban and rural areas of Bangalore, India.

PubMed

Skariyachan, Sinosh; Megha, M; Kini, Meghna Niranjan; Mukund, Kamath Manali; Rizvi, Alya; Vasist, Kiran

2015-01-01

Industrialization and urbanization have led to massive accumulation of plastic garbage all over India. The persistence of plastic in soil and aquatic environment has become ecological threat to the metropolitan city such as Bangalore, India. Present study investigates an ecofriendly, efficient and cost-effective approach for plastic waste management by the screening of novel microbial consortia which are capable of degrading plastic polymers. Plastic-contaminated soil and water samples were collected from six hot spots of urban and rural areas of Bangalore. The plastic-degrading bacteria were enriched, and degradation ability was determined by zone of clearance method. The percentage of polymer degradation was initially monitored by weight loss method, and the main isolates were characterized by standard microbiology protocols. These isolates were used to form microbial consortia, and the degradation efficiency of the consortia was compared with individual isolate and known strains obtained from the Microbial Type Culture Collection (MTCC) and Gene Bank, India. One of the main enzymes responsible for polymer degradation was identified, and the biodegradation mechanism was hypothesized by bioinformatics studies. From this study, it is evident that the bacteria utilized the plastic polymer as a sole source of carbon and showed 20-50% weight reduction over a period of 120 days. The two main bacteria responsible for the degradation were microbiologically characterized to be Pseudomonas spp. These bacteria could grow optimally at 37 °C in pH 9.0 and showed 35-40% of plastic weight reduction over 120 days. These isolates were showed better degradation ability than known strains from MTCC. The current study further revealed that the microbial consortia formulated by combining Psuedomonas spp. showed 40 plastic weight reduction over a period of 90 days. Further, extracellular lipase, one of the main enzymes responsible for polymer degradation, was identified. The computational docking studies suggested that polyethylene glycol and polystyrene present in the plastics might have good interaction towards the microbial lipase with stable binding and interacting forces which probably could be one of the reasons for the degradative mechanisms.

An audit of Cryptosporidium and Giardia detection in Scottish National Health Service Diagnostic Microbiology Laboratories.

PubMed

Alexander, C L; Currie, S; Pollock, K; Smith-Palmer, A; Jones, B L

2017-06-01

Giardia duodenalis and Cryptosporidium species are protozoan parasites capable of causing gastrointestinal disease in humans and animals through the ingestion of infective faeces. Whereas Cryptosporidium species can be acquired locally or through foreign travel, there is the mis-conception that giardiasis is considered to be largely travel-associated, which results in differences in laboratory testing algorithms. In order to determine the level of variation in testing criteria and detection methods between diagnostic laboratories for both pathogens across Scotland, an audit was performed. Twenty Scottish diagnostic microbiology laboratories were invited to participate with questions on sample acceptance criteria, testing methods, testing rates and future plans for pathogen detection. Reponses were received from 19 of the 20 laboratories representing each of the 14 territorial Health Boards. Detection methods varied between laboratories with the majority performing microscopy, one using a lateral flow immunochromatographic antigen assay, another using a manually washed plate-based enzyme immunoassay (EIA) and one laboratory trialling a plate-based EIA automated with an EIA plate washer. Whereas all laboratories except one screened every stool for Cryptosporidium species, an important finding was that significant variation in the testing algorithm for detecting Giardia was noted with only four laboratories testing all diagnostic stools. The most common criteria were 'travel history' (11 laboratories) and/or 'when requested' (14 laboratories). Despite only a small proportion of stools being examined in 15 laboratories for Giardia (2%-18% of the total number of stools submitted), of interest is the finding that a higher positivity rate was observed for Giardia than Cryptosporidium in 10 of these 15 laboratories. These findings highlight that the underreporting of Giardia in Scotland is likely based on current selection and testing algorithms.

Human Health Screening and Public Health Significance of ...

EPA Pesticide Factsheets

The source water and treated drinking water from twenty five drinking water treatment plants (DWTPs) across the United States were sampled in 2010 – 2012. Samples were analyzed for 247 contaminants using 15 chemical and microbiological methods. Most of these contaminants are not regulated currently either in drinking water or in discharges to ambient water by the United States Environmental Protection Agency (EPA) or other U.S. regulatory agencies. This analysis shows that there is little public health concern for most of the contaminants detected in treated water from the 25 DWTPs participating in this study. For vanadium, the calculated MOE was less than the screening MOE in two DWTPs. Additional study, for example a national survey may be needed to determine the number of people ingesting vanadium above a level of concern. In addition, the concentrations of lithium found in treated water from several DWTPs are within the range previous research has suggested to have a human health effect. Additional investigation of this issue may also be appropriate. Finally, new toxicological data suggests that exposure to manganese at levels in public water supplies may present a public health concern which may warrant a more robust assessment of this information. This paper provides a screening-level human health risk assessment using the margin of exposure of exposure approach, of contaminants of emerging concern detected in drinking water. As far as we are a

Human health screening and public health significance of contaminants of emerging concern detected in public water supplies

USGS Publications Warehouse

Benson, Robert; Conerly, Octavia D.; Sander, William; Batt, Angela L.; Boone, J. Scott; Furlong, Edward T.; Glassmeyer, Susan T.; Kolpin, Dana W.; Mash, Heath

2017-01-01

The source water and treated drinking water from twenty five drinking water treatment plants (DWTPs) across the United States were sampled in 2010–2012. Samples were analyzed for 247 contaminants using 15 chemical and microbiological methods. Most of these contaminants are not regulated currently either in drinking water or in discharges to ambient water by the U. S. Environmental Protection Agency (USEPA) or other U.S. regulatory agencies. This analysis shows that there is little public health concern for most of the contaminants detected in treated water from the 25 DWTPs participating in this study. For vanadium, the calculated Margin of Exposure (MOE) was less than the screening MOE in two DWTPs. For silicon, the calculated MOE was less than the screening MOE in one DWTP. Additional study, for example a national survey may be needed to determine the number of people ingesting vanadium and silicon above a level of concern. In addition, the concentrations of lithium found in treated water from several DWTPs are within the range previous research has suggested to have a human health effect. Additional investigation of this issue is necessary. Finally, new toxicological data suggest that exposure to manganese at levels in public water supplies may present a public health concern which will require a robust assessment of this information.

Human health screening and public health significance of contaminants of emerging concern detected in public water supplies.

PubMed

Benson, Robert; Conerly, Octavia D; Sander, William; Batt, Angela L; Boone, J Scott; Furlong, Edward T; Glassmeyer, Susan T; Kolpin, Dana W; Mash, Heath E; Schenck, Kathleen M; Simmons, Jane Ellen

2017-02-01

The source water and treated drinking water from twenty five drinking water treatment plants (DWTPs) across the United States were sampled in 2010-2012. Samples were analyzed for 247 contaminants using 15 chemical and microbiological methods. Most of these contaminants are not regulated currently either in drinking water or in discharges to ambient water by the U. S. Environmental Protection Agency (USEPA) or other U.S. regulatory agencies. This analysis shows that there is little public health concern for most of the contaminants detected in treated water from the 25 DWTPs participating in this study. For vanadium, the calculated Margin of Exposure (MOE) was less than the screening MOE in two DWTPs. For silicon, the calculated MOE was less than the screening MOE in one DWTP. Additional study, for example a national survey may be needed to determine the number of people ingesting vanadium and silicon above a level of concern. In addition, the concentrations of lithium found in treated water from several DWTPs are within the range previous research has suggested to have a human health effect. Additional investigation of this issue is necessary. Finally, new toxicological data suggest that exposure to manganese at levels in public water supplies may present a public health concern which will require a robust assessment of this information. Published by Elsevier B.V.

Treatment of genital mycoplasma in colonized pregnant women in late pregnancy is associated with a lower rate of premature labour and neonatal complications.

PubMed

Vouga, M; Greub, G; Prod'hom, G; Durussel, C; Roth-Kleiner, M; Vasilevsky, S; Baud, D

2014-10-01

Mycoplasma hominis and Ureaplasma spp. may colonize the human genital tract and have been associated with adverse pregnancy outcomes such as preterm labour and preterm premature rupture of membranes. However, as these bacteria can reside in the normal vaginal flora, there are controversies regarding their true role during pregnancy and so the need to treat these organisms. We therefore conducted a retrospective analysis to evaluate the treatment of genital mycoplasma in 5377 pregnant patients showing symptoms of potential obstetric complications at 25-37 weeks of gestation. Women presenting with symptoms were routinely screened by culture for the presence of these bacteria and treated with clindamycin when positive. Compared with uninfected untreated patients, women treated for genital mycoplasma demonstrated lower rates of premature labour. Indeed preterm birth rates were, respectively, 40.9% and 37.7% in women colonized with Ureaplasma spp. and M. hominis, compared with 44.1% in uncolonized women (Ureaplasma spp., p 0.024; M. hominis, p 0.001). Moreover, a reduction of neonatal complications rates was observed, with 10.9% of newborns developing respiratory diseases in case of Ureaplasma spp. colonization and 5.9% in the presence of M. hominis, compared with 12.8% in the absence of those bacteria (Ureaplasma spp., p 0.050; M. hominis, p <0.001). Microbiological screening of Ureaplasma spp. and/or M. hominis and pre-emptive antibiotic therapy of symptomatic pregnant women in late pregnancy might represent a beneficial strategy to reduce premature labour and neonatal complications. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

[Travels and spreading of multi-resistant bacteria].

PubMed

Nitsch-Osuch, Aneta

2017-05-23

The increasing number of international travel for tourism, business and for medical reasons rises the risk of spreading of multi-resistant bacteria. It has been shown that an intercontinental travel, mainly to Asia (Indian Subcontinent), promotes a colonization of the digestive tract, mainly by multi-resistant Enterobacteriaceae (MRE) and increases the risk of symptomatic infections caused by these agents. The colonization of the digestive tract by MRE is reported in 29-88% of travelers. It sustains 3 to 12 months, respectively in 10% and 2% of travelers. Risk factors for the acquisition of colonization with MRE include: travel duration and destination, treatment with betalactam antibiotics during the travel, the use of local medical services, including hospitalization, presence of gastrointestinal symptoms during the travel (mainly diarrhea), age >65 years. The need of the hospitalization during the travel increases the risk of colonization, but is not a prerequisite factor for the acquisition of the colonization, as cases of the MRE carriage are reported in patients who had never used medical services outside the country. It indicates other possible transmission routes, including food. In order to reduce the risk of MRE spreading, it is recommended to ask patients about a history of travel and treatment within the last 12 months. All patient who report such events and require hospitalization in their home countries should be microbiologically screened. Hospitalized patients colonized with multiple resistant bacteria require an isolation or cohortation. Educational activities related to the hand hygiene compliance should be performed. The risk of the home transmission of MRE is not high, it lasts for a short period (up to 3 months). Routine microbiological testing for all persons returning from an international or intercontinental travel is not recommended, neither microbiological screening among their households.

Field Application of the Micro Biological Survey Method for a Simple and Effective Assessment of the Microbiological Quality of Water Sources in Developing Countries

PubMed Central

Arienzo, Alyexandra; Sobze, Martin Sanou; Wadoum, Raoul Emeric Guetiya; Losito, Francesca; Colizzi, Vittorio; Antonini, Giovanni

2015-01-01

According to the World Health Organization (WHO) guidelines, “safe drinking-water must not represent any significant risk to health over a lifetime of consumption, including different sensitivities that may occur between life stages”. Traditional methods of water analysis are usually complex, time consuming and require an appropriately equipped laboratory, specialized personnel and expensive instrumentation. The aim of this work was to apply an alternative method, the Micro Biological Survey (MBS), to analyse for contaminants in drinking water. Preliminary experiments were carried out to demonstrate the linearity and accuracy of the MBS method and to verify the possibility of using the evaluation of total coliforms in 1 mL of water as a sufficient parameter to roughly though accurately determine water microbiological quality. The MBS method was then tested “on field” to assess the microbiological quality of water sources in the city of Douala (Cameroon, Central Africa). Analyses were performed on both dug and drilled wells in different periods of the year. Results confirm that the MBS method appears to be a valid and accurate method to evaluate the microbiological quality of many water sources and it can be of valuable aid in developing countries. PMID:26308038

Microbiological water methods: quality control measures for Federal Clean Water Act and Safe Drinking Water Act regulatory compliance.

PubMed

Root, Patsy; Hunt, Margo; Fjeld, Karla; Kundrat, Laurie

2014-01-01

Quality assurance (QA) and quality control (QC) data are required in order to have confidence in the results from analytical tests and the equipment used to produce those results. Some AOAC water methods include specific QA/QC procedures, frequencies, and acceptance criteria, but these are considered to be the minimum controls needed to perform a microbiological method successfully. Some regulatory programs, such as those at Code of Federal Regulations (CFR), Title 40, Part 136.7 for chemistry methods, require additional QA/QC measures beyond those listed in the method, which can also apply to microbiological methods. Essential QA/QC measures include sterility checks, reagent specificity and sensitivity checks, assessment of each analyst's capabilities, analysis of blind check samples, and evaluation of the presence of laboratory contamination and instrument calibration and checks. The details of these procedures, their performance frequency, and expected results are set out in this report as they apply to microbiological methods. The specific regulatory requirements of CFR Title 40 Part 136.7 for the Clean Water Act, the laboratory certification requirements of CFR Title 40 Part 141 for the Safe Drinking Water Act, and the International Organization for Standardization 17025 accreditation requirements under The NELAC Institute are also discussed.

Field Application of the Micro Biological Survey Method for a Simple and Effective Assessment of the Microbiological Quality of Water Sources in Developing Countries.

PubMed

Arienzo, Alyexandra; Sobze, Martin Sanou; Wadoum, Raoul Emeric Guetiya; Losito, Francesca; Colizzi, Vittorio; Antonini, Giovanni

2015-08-25

According to the World Health Organization (WHO) guidelines, "safe drinking-water must not represent any significant risk to health over a lifetime of consumption, including different sensitivities that may occur between life stages". Traditional methods of water analysis are usually complex, time consuming and require an appropriately equipped laboratory, specialized personnel and expensive instrumentation. The aim of this work was to apply an alternative method, the Micro Biological Survey (MBS), to analyse for contaminants in drinking water. Preliminary experiments were carried out to demonstrate the linearity and accuracy of the MBS method and to verify the possibility of using the evaluation of total coliforms in 1 mL of water as a sufficient parameter to roughly though accurately determine water microbiological quality. The MBS method was then tested "on field" to assess the microbiological quality of water sources in the city of Douala (Cameroon, Central Africa). Analyses were performed on both dug and drilled wells in different periods of the year. Results confirm that the MBS method appears to be a valid and accurate method to evaluate the microbiological quality of many water sources and it can be of valuable aid in developing countries.

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples.

PubMed

Meir-Gruber, Lital; Manor, Yossi; Gefen-Halevi, Shiraz; Hindiyeh, Musa Y; Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

2016-01-01

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage.

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples

PubMed Central

Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

2016-01-01

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage. PMID:27780222

Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

PubMed

Gunar, O V; Sakhno, N G

2015-12-30

The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Simple fluorescence-based high throughput cell viability assay for filamentous fungi.

PubMed

Chadha, S; Kale, S P

2015-09-01

Filamentous fungi are important model organisms to understand the eukaryotic process and have been frequently exploited in research and industry. These fungi are also causative agents of serious diseases in plants and humans. Disease management strategies include in vitro susceptibility testing of the fungal pathogens to environmental conditions and antifungal agents. Conventional methods used for antifungal susceptibilities are cumbersome, time-consuming and are not suitable for a large-scale analysis. Here, we report a rapid, high throughput microplate-based fluorescence method for investigating the toxicity of antifungal and stress (osmotic, salt and oxidative) agents on Magnaporthe oryzae and compared it with agar dilution method. This bioassay is optimized for the resazurin reduction to fluorescent resorufin by the fungal hyphae. Resazurin bioassay showed inhibitory rates and IC50 values comparable to the agar dilution method and to previously reported IC50 or MICs for M. oryzae and other fungi. The present method can screen range of test agents from different chemical classes with different modes of action for antifungal activities in a simple, sensitive, time and cost effective manner. A simple fluorescence-based high throughput method is developed to test the effects of stress and antifungal agents on viability of filamentous fungus Magnaporthe oryzae. This resazurin fluorescence assay can detect inhibitory effects comparable to those obtained using the growth inhibition assay with added advantages of simplicity, time and cost effectiveness. This high throughput viability assay has a great potential in large-scale screening of the chemical libraries of antifungal agents, for evaluating the effects of environmental conditions and hyphal kinetic studies in mutant and natural populations of filamentous fungi. © 2015 The Society for Applied Microbiology.

Effect of Oregano Essential Oil and Aqueous Oregano Infusion Application on Microbiological Properties of Samarella (Tsamarella), a Traditional Meat Product of Cyprus.

PubMed

Ulusoy, Beyza; Hecer, Canan; Kaynarca, Doruk; Berkan, Şifa

2018-03-21

Different types of dried meat products manufactured by different drying and curing methods are very common and well-known with a long history all over the world. Samarella (tsamarella) is one of these products and is famous among traditionally produced meat products in Cypriot gastronomy. The aim of this study was to investigate the effect of oregano essential oil (OEO) and aqueous oregano infusion (AOI) applications on the microbiological properties of samarella. In order to carry out this study, traditional methods were followed for experimental production of samarella. As a result of this study, five percent OEO application was found to be more effective to reduce microbiological counts but this ratio of OEO application was not accepted by panelists. According to all microbiological results correlated with the sensorial scores, it is concluded that one percent OEO application can be used for samarella production as an alternative preservative method.

Effect of Oregano Essential Oil and Aqueous Oregano Infusion Application on Microbiological Properties of Samarella (Tsamarella), a Traditional Meat Product of Cyprus

PubMed Central

Hecer, Canan; Kaynarca, Doruk; Berkan, Şifa

2018-01-01

Different types of dried meat products manufactured by different drying and curing methods are very common and well-known with a long history all over the world. Samarella (tsamarella) is one of these products and is famous among traditionally produced meat products in Cypriot gastronomy. The aim of this study was to investigate the effect of oregano essential oil (OEO) and aqueous oregano infusion (AOI) applications on the microbiological properties of samarella. In order to carry out this study, traditional methods were followed for experimental production of samarella. As a result of this study, five percent OEO application was found to be more effective to reduce microbiological counts but this ratio of OEO application was not accepted by panelists. According to all microbiological results correlated with the sensorial scores, it is concluded that one percent OEO application can be used for samarella production as an alternative preservative method. PMID:29561804

Experimental methods for studying microbial survival in extraterrestrial environments.

PubMed

Olsson-Francis, Karen; Cockell, Charles S

2010-01-01

Microorganisms can be used as model systems for studying biological responses to extraterrestrial conditions; however, the methods for studying their response are extremely challenging. Since the first high altitude microbiological experiment in 1935 a large number of facilities have been developed for short- and long-term microbial exposure experiments. Examples are the BIOPAN facility, used for short-term exposure, and the EXPOSE facility aboard the International Space Station, used for long-term exposure. Furthermore, simulation facilities have been developed to conduct microbiological experiments in the laboratory environment. A large number of microorganisms have been used for exposure experiments; these include pure cultures and microbial communities. Analyses of these experiments have involved both culture-dependent and independent methods. This review highlights and discusses the facilities available for microbiology experiments, both in space and in simulation environments. A description of the microorganisms and the techniques used to analyse survival is included. Finally we discuss the implications of microbiological studies for future missions and for space applications. Copyright 2009 Elsevier B.V. All rights reserved.

Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection.

PubMed

Slavchev, Aleksandar; Kovacs, Zoltan; Koshiba, Haruki; Nagai, Airi; Bázár, György; Krastanov, Albert; Kubota, Yousuke; Tsenkova, Roumiana

2015-01-01

Development of efficient screening method coupled with cell functionality evaluation is highly needed in contemporary microbiology. The presented novel concept and fast non-destructive method brings in to play the water spectral pattern of the solution as a molecular fingerprint of the cell culture system. To elucidate the concept, NIR spectroscopy with Aquaphotomics were applied to monitor the growth of sixteen Lactobacillus bulgaricus one Lactobacillus pentosus and one Lactobacillus gasseri bacteria strains. Their growth rate, maximal optical density, low pH and bile tolerances were measured and further used as a reference data for analysis of the simultaneously acquired spectral data. The acquired spectral data in the region of 1100-1850nm was subjected to various multivariate data analyses - PCA, OPLS-DA, PLSR. The results showed high accuracy of bacteria strains classification according to their probiotic strength. Most informative spectral fingerprints covered the first overtone of water, emphasizing the relation of water molecular system to cell functionality.

Response to the Questions Posed by the Food Safety and Inspection Service Regarding Determination of the Most Appropriate Technologies to Adopt for FSIS Routine and Baseline Microbiological Analysis

USDA-ARS?s Scientific Manuscript database

The National Advisory Committee on Microbiological Criteria for Foods (NACMCF) should provide guidance to assist with the United States Department of Agriculture, Food Safety and Inspection Service (USDA/FSIS) Agency’s goal of moving into the next generation of microbiological testing methods. To do...

Screening and treating asymptomatic bacteriuria in pregnancy.

PubMed

Lumbiganon, Pisake; Laopaiboon, Malinee; Thinkhamrop, Jadsada

2010-04-01

Asymptomatic bacteriuria (ASB) in pregnancy, if left undiagnosed and appropriately treated can lead to acute pyelonephritis in mothers and low birth weight in infants. Urine culture is the gold standard for diagnosing ASB. Unfortunately, urine culture is limitedly available. The present review aims at evaluating performance of various screening tests and effectiveness of antibiotic regimens for ASB. Positive dipslide test is very likely to have a definitive diagnosis of ASB, whereas a negative result effectively rules out ASB. Available evidences regarding the performance of urine dipstick are still conflicting, it is currently not appropriate to recommend urine dipstick for screening ASB in pregnancy. Choice of antibiotics should be guided by antimicrobial susceptibility testing whenever possible. Nitrofurantoin seems to be antibiotic of choice for ASB in pregnancy. Seven-day regimen of antibiotics gives a better microbiological cure rate but no difference in important clinical outcomes compared with 1-day regimen. Dipslide culture is a promising screening test for ASB. Pregnant women with ASB should be treated with 7-day regimen of antibiotics, although 1-day regimen might be appropriate in some settings. More research is needed for identifying appropriate screening tests for ASB.

Rectal swab screening assays of public health importance in molecular diagnostics: Sample adequacy control.

PubMed

Glisovic, Sanja; Eintracht, Shaun; Longtin, Yves; Oughton, Matthew; Brukner, Ivan

Rectal swabs are routinely used by public health authorities to screen for multi-drug resistant enteric bacteria including vancomycin-resistant enterococci (VRE) and carbapenem-resistant enterobacteriaceae (CRE). Screening sensitivity can be influenced by the quality of the swabbing, whether performed by the patient (self-swabbing) or a healthcare practitioner. One common exclusion criterion for rectal swabs is absence of "visible soiling" from fecal matter. In our institution, this criterion excludes almost 10% of rectal swabs received in the microbiology laboratory. Furthermore, over 30% of patients in whom rectal swabs are cancelled will not be re-screened within the next 48h, resulting in delays in removing infection prevention measures. We describe two quantitative polymerase chain reaction (qPCR)-based assays, human RNAse P and eubacterial 16S rDNA, which might serve as suitable controls for sampling adequacy. However, lower amounts of amplifiable human DNA make the 16s rDNA assay a better candidate for sample adequacy control. Copyright © 2017. Published by Elsevier Ltd.

[Methods of identification and assessment of safety of genetically modified microorganisms in manufacture food production].

PubMed

Khovaev, A A; Nesterenko, L N; Naroditskiĭ, B S

2011-01-01

Methods of identification of genetically modified microorganisms (GMM), used in manufacture food on control probes are presented. Results of microbiological and molecular and genetic analyses of food products and their components important in microbiological and genetic expert examination of GMM in foods are considered. Examination of biosafety of GMM are indicated.

Microbiological safety of commercial prime rib preparation methods: thermal inactivation of Salmonella spp. in mechanically tenderized beef roasts

USDA-ARS?s Scientific Manuscript database

A survey of food service operations in a medium-size Midwestern city was conducted to evaluate the microbiological safety of prime rib preparation methods relative to survival of Salmonella spp. in both intact and tenderized (non-intact) product. All six restaurants visited seared rib eye roasts (ai...

Mathematical models of cell factories: moving towards the core of industrial biotechnology.

PubMed

Cvijovic, Marija; Bordel, Sergio; Nielsen, Jens

2011-09-01

Industrial biotechnology involves the utilization of cell factories for the production of fuels and chemicals. Traditionally, the development of highly productive microbial strains has relied on random mutagenesis and screening. The development of predictive mathematical models provides a new paradigm for the rational design of cell factories. Instead of selecting among a set of strains resulting from random mutagenesis, mathematical models allow the researchers to predict in silico the outcomes of different genetic manipulations and engineer new strains by performing gene deletions or additions leading to a higher productivity of the desired chemicals. In this review we aim to summarize the main modelling approaches of biological processes and illustrate the particular applications that they have found in the field of industrial microbiology. © 2010 The Authors. Journal compilation © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Recognition of Streptococcus pseudoporcinus Colonization in Women as a Consequence of Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Group B Streptococcus Identification.

PubMed

Suwantarat, Nuntra; Grundy, Maureen; Rubin, Mayer; Harris, Renee; Miller, Jo-Anne; Romagnoli, Mark; Hanlon, Ann; Tekle, Tsigereda; Ellis, Brandon C; Witter, Frank R; Carroll, Karen C

2015-12-01

During a 14-month period of using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for group B streptococcus (GBS) identification, we recovered 32 (1%) Streptococcus pseudoporcinus isolates from 3,276 GBS screening cultures from female genital sources (25 isolates from pregnant women and 7 from nonpregnant women). An additional two S. pseudoporcinus isolates were identified from a urine culture and a posthysterectomy wound culture. These isolates were found to cross-react with three different GBS antigen agglutination kits, PathoDx (Remel) (93%), Prolex (Pro-Lab Diagnostics) (38%), and Streptex (Remel) (53%). New approaches to bacterial identification in routine clinical microbiology laboratories may affect the prevalence of S. pseudoporcinus. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Comparative phytochemical analysis and antibacterial efficacy of in vitro and in vivo extracts from East Indian sandalwood tree (Santalum album L.).

PubMed

Misra, B B; Dey, S

2012-12-01

Sandalwood oil has been found in numerous therapeutic applications in traditional medicines such as Chinese traditional medicine and Ayurveda. However, there are no comparative accounts available in the literature that focused on in vitro and in vivo tree sample-derived extracts. Combined dichloromethane and methanol extracts were obtained from in vitro samples, that is, callus, somatic embryo and seedlings, and in vivo from leaves of non-oil-yielding young and oil-yielding matured trees. Phytochemical evaluation of the extracts reveals that the tree is rich in terpenoids, saponin, phenolics and tannins. The antibacterial properties of the five extracts were compared with sandalwood oil by screening against nine Gram-negative and five Gram-positive bacterial strains by disc diffusion, agar spot and TLC bioautography methods. Minimum inhibitory concentration (MIC) for sandalwood oil was determined to be in the range of 0·078-5 μg ml(-1) for most of the test micro-organisms screened. Bioautography results indicated the presence of potential antimicrobial constituents in somatic embryo extracts and sandalwood oil. Among the extracts screened, the somatic embryo extracts showed the strongest antibacterial activity comparable only with sandalwood oil and matured tree leaves' extract. The findings presented here also suggest that apart from sandalwood oil, other parts of this tree across developmental stages are also enriched with antibacterial principles. This study constitutes the first systematic investigation on phytochemical composition and antimicrobial efficacy of sandalwood tree across in vitro and in vivo developmental stages screened against thirteen bacterial strains by four methods. Using a battery of antimicrobial assay techniques, it is possible to follow the differential bioactive metabolic richness of plant parts, to decipher, for example comparable efficacy of somatic embryo extracts and sandalwood oil. © 2012 The Society for Applied Microbiology.

Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data--The Influence of Different Parameters in a Routine Clinical Microbiology Laboratory.

PubMed

Kohlmann, Rebekka; Gatermann, Sören G

2016-01-01

Many clinical microbiology laboratories report on cumulative antimicrobial susceptibility testing (cAST) data on a regular basis. Criteria for generation of cAST reports, however, are often obscure and inconsistent. Whereas the CLSI has published a guideline for analysis and presentation of cAST data, national guidelines directed at clinical microbiology laboratories are not available in Europe. Thus, we sought to describe the influence of different parameters in the process of cAST data analysis in the setting of a German routine clinical microbiology laboratory during 2 consecutive years. We developed various program scripts to assess the consequences ensuing from different algorithms for calculation of cumulative antibiograms from the data collected in our clinical microbiology laboratory in 2013 and 2014. One of the most pronounced effects was caused by exclusion of screening cultures for multi-drug resistant organisms which decreased the MRSA rate in some cases to one third. Dependent on the handling of duplicate isolates, i.e. isolates of the same species recovered from successive cultures on the same patient during the time period analyzed, we recorded differences in resistance rates of up to 5 percentage points for S. aureus, E. coli and K. pneumoniae and up to 10 percentage points for P. aeruginosa. Stratification by site of care and specimen type, testing of antimicrobials selectively on resistant isolates, change of interpretation rules and analysis at genus level instead of species level resulted in further changes of calculated antimicrobial resistance rates. The choice of parameters for cAST data analysis may have a substantial influence on calculated antimicrobial resistance rates. Consequently, comparability of cAST reports from different clinical microbiology laboratories may be limited. We suggest that laboratories communicate the strategy used for cAST data analysis as long as national guidelines for standardized cAST data analysis and reporting do not exist in Europe.

Asymptomatic bacteriuria in pregnancy: epidemiological, clinical and microbiological approach.

PubMed

Gebre-Selassie, S

1998-07-01

Asymptomatic urinary tract infection is a risk factor for fetal and maternal morbidity including development of pyelonephritis, premature labor and impaired intra-uterine development. In this study, 326 pregnant and 100 non-pregnant control women were screened for significant asymptomatic bacteriuria from April 8 to July 25, 1997 to gain insight into the prevalence rate, clinical characteristics of the disease and microbiological assessments of the causative agents. All the subjects were clinically identified to have no signs and symptoms of urinary tract infection (UTI). The age ranges of the study and control groups were between 15-40 years for both groups with mean of 25.1 and 25.3 years, respectively. Bacteriological screening of mid-stream urine (MSU) revealed that 24/326 (7%) and 3/100 (3%) were positive for asymptomatic bacteriuria in the study group and controls, respectively (P < 0.05). Further biochemical species identification showed that Escherichia coli was found in 11/24 (46%) followed by coagulase-negative staphylococci (CNS) in 8/24 (33%) and Citrobacter freundii in 2/24 (8%). Others found in smaller number included Staphylococcus aureus, Enterobacter cloacae and Proteus rettgeri in 1/24 (4%) each. Antimicrobial susceptibility test revealed that 10/11 (91%) of the E. coli isolates were resistant to ampicillin and amoxicillin and 10/11 (91%) of them sensitive to nitrofurantoin.

Viral pathogen discovery

PubMed Central

Chiu, Charles Y

2015-01-01

Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples. Although numerous challenges remain to be addressed, including the bioinformatics analysis and interpretation of large datasets, these technologies have been successful in rapidly identifying emerging outbreak threats, screening vaccines and other biological products for microbial contamination, and discovering novel viruses associated with both acute and chronic illnesses. Downstream studies such as genome assembly, epidemiologic screening, and a culture system or animal model of infection are necessary to establish an association of a candidate pathogen with disease. PMID:23725672

Performance of the OraQuick HCV rapid antibody test for screening exposed patients in a hepatitis C outbreak investigation.

PubMed

Gao, Fengxiang; Talbot, Elizabeth A; Loring, Carol H; Power, Jill J; Dionne-Odom, Jodie; Alroy-Preis, Sharon; Jackson, Patricia; Bean, Christine L

2014-07-01

During a nosocomial hepatitis C outbreak, emergency public clinics employed the OraQuick HCV rapid antibody test on site, and all results were verified by a standard enzyme immunoassay (EIA). Of 1,157 persons, 1,149 (99.3%) exhibited concordant results between the two tests (16 positive, 1,133 negative). The sensitivity, specificity, positive predictive value, and negative predictive value were 94.1%, 99.5%, 72.7%, and 99.9%, respectively. OraQuick performed well as a screening test during an outbreak investigation and could be integrated into future hepatitis C virus (HCV) outbreak testing algorithms. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Comparison of Two Phenotypic Algorithms To Detect Carbapenemase-Producing Enterobacteriaceae

PubMed Central

Dortet, Laurent; Bernabeu, Sandrine; Gonzalez, Camille

2017-01-01

ABSTRACT A novel algorithm designed for the screening of carbapenemase-producing Enterobacteriaceae (CPE), based on faropenem and temocillin disks, was compared to that of the Committee of the Antibiogram of the French Society of Microbiology (CA-SFM), which is based on ticarcillin-clavulanate, imipenem, and temocillin disks. The two algorithms presented comparable negative predictive values (98.6% versus 97.5%) for CPE screening among carbapenem-nonsusceptible Enterobacteriaceae. However, since 46.2% (n = 49) of the CPE were correctly identified as OXA-48-like producers by the faropenem/temocillin-based algorithm, it significantly decreased the number of complementary tests needed (42.2% versus 62.6% with the CA-SFM algorithm). PMID:28607010

Ethnopharmacological surveys and pharmacological studies of plants used in traditional medicine in the treatment of HIV/AIDS opportunistic diseases in Gabon.

PubMed

Tchouya, Guy Raymond Feuya; Souza, Alain; Tchouankeu, Jean Claude; Yala, Jean-Fabrice; Boukandou, Marlaine; Foundikou, Hibrahim; Obiang, Giresse Delphang Nguema; Boyom, Fabrice Fekam; Mabika, Rolande Mabika; Menkem, Elisabeth Zeuko'o; Ndinteh, Derek Tantoh; Lebibi, Jacques

2015-03-13

Ethnopharmacological surveys were conducted in two regions of Gabon. This led to highlighting some of the medicinal plants used by local populations in the management of HIV/AIDS opportunistic diseases. Two regions with the highest occurrence of HIV/AIDS cases were visited and ethnopharmarcological data was gathered. These regions were the Estuaire Province (Libreville and its neighborhood) and the Haut-Ogooué Province (Franceville and its neighborhood). The opportunistic diseases and symptomatic conditions considered during this study were: diarrhea, respiratory tract infections, cough, tuberculosis, abscesses, stomach ache, skin rashes, venereal diseases, typhoid fever, anemia, general tiredness, hepatitis and vomiting. The reported species were evaluated through three parameters: specificity, reliability and frequency. Plant parts of relevant species were harvested and extracted with an aqueous alcohol solution (ethanol/water: 1/1). The extracts obtained were submitted to phytochemical screening and in vitro microbiological assays on some clinical isolates and ATCC strains, involved in HIV/AIDS opportunistic diseases through the Agar well diffusion and Microbroth dilution methods. Among the 52 species identified during this survey, Coelocaryon klainei Pierre ex Heckel (Myristicaceae), Dacryodes klaineana (Pierre) H.J. Lam (Bursecaceae), Phyllanthus diandrus Pax (Euphorbiaceae), Saccoglotys gabonensis (Baill.) Urb. (Humiriaceae) and Tetrorchidium didymostemon (Baill.) Pax & K. Hoffm. (Euphorbiaceae) were submitted to in vitro microbiological assays. Phyllanthus diandrus bark and leaves show best antibacterial activities against Pseudomonas aeruginosa and Klebsiella pneumoniae with MIC value of 0.25 respectively. Phytochemical screening revealed the presence in all the plant parts extracts of potentially bioactive molecules, including polyphenols, especially flavonoids and tannins. It is concluded that some of these plants might be submitted to further scientific studies, including the identification and isolation of bioactive principles, that could be developed to drugs for the treatment of HIV/AIDS opportunistic diseases. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Detection of non-O157 Shiga toxin-producing Escherichia coli in 375 grams of beef trim enrichments across multiple commercial PCR detection platforms.

PubMed

Wheeler, Sarita Raengpradub; Heard, Preciaus; Dufour, Christophe; Thevenot-Sergentet, Delphine; Loukiadis, Estelle; Flowers, Russell S; McMahon, Wendy

2015-01-01

Although serotype O157:H7 remains the pathogenic Shiga toxin-producing Escherichia coli (STEC) of primary concern worldwide, some focus in the United States has shifted to six particular non-O157 STEC serogroups (O26, O45, O103, O111, O121, and O145). Some of these serogroups have also emerged as concerns elsewhere around the world, including Europe. The objective of this work was to compare commercial detection methods with the U.S. Department of Agriculture (USDA) reference method for detection of non-O157 STEC in 375 g of beef trim using a limit of detection study design. Overall, the commercial platforms performed well, showing similar levels of sensitivity for detection of presumptive positives for O45, O26, O103, and O121 (PCR screen results only). For O111, one method that utilizes an integrated immunomagnetic separation and PCR approach was more sensitive than a PCR-only screen approach. Additionally, one commercial method showed more presumptive and confirmed positives overall. Use of an immunomagnetic separation tool, such as antibody-coated beads, aided considerably with the confirmation procedures and is an important step when confirming suspect samples. A secondary goal of this study was to evaluate isolation and International Organization for Standardization confirmation protocols used in Europe compared with strategies provided by the USDA Microbiology Laboratory Guidebook (MLG). Generally, results from the USDA confirmation plates (modified Rainbow agar) were better than the European Union confirmation plates (MacConkey agar with or without rhamnose). In summary, detection of non-O157 STEC in 375 g of beef trim can be performed by any of the three methods on the market evaluated in the study.

Association between positive corneal rim cultures and microbiology screening protocols in Ontario.

PubMed

Sharma, Rahul A; Park, John S Y; Wang, Yao; Zhang, Tinghua; Sharpen, Linda; Dixon, William; Mather, Rookaya

2018-06-01

(i) To assess the rate of positive microbiological cultures of corneas prepared by the Eye Bank of Canada (Ontario Division) between January 1, 2012, and December 31, 2013; (ii) to review the microbiology protocols at the 5 major transplant centres in Ontario; and (iii) to assess the incidence of endophthalmitis during the study period. Retrospective chart review. A total of 4186 consecutive cultured corneal tissues prepared by the Eye Bank from January 1, 2012, to December 31, 2013. Rates of culture-positive cornea rims and incidence of postkeratoplasty endophthalmitis at 5 surgical centres in Ontario were determined, and the protocols used to culture rims at each site were concurrently reviewed. Culture results were analyzed via logistic regression for positive cultures. The rate of positive cultures at each sites were as follows: centre A, 3.74%; centre B, 3.26%; centre C, 0.51%; centre D, 0.48%; and centre E, 0.04%. Centres A, B, and D were noted to have significantly higher positive rates than centre E. In comparing microbiology protocols, longer incubation period (11 days) was 12 times more likely to be associated with higher positive culture rates than shorter period (4-5 days). Six-month follow-up of all keratoplasties revealed zero reported cases of endophthalmitis. A literature review regarding the predictive value of routine culturing reveals conflicting data. Our findings suggest that differences in the microbiology protocols directly influence the rates of positive rim cultures. Without a standardized protocol, it is not possible to evaluate the predictive value of routine corneal rim culturing in predicting postkeratoplasty endophthalmitis. Copyright © 2018. Published by Elsevier Inc.

Surface Microbiology of Smartphone Screen Protectors Among Healthcare Professionals.

PubMed

Raza, Ibrahim; Raza, Awais; Razaa, Syed Ahmad; Sadar, Ahmad Bani; Qureshi, Ahmad Uzair; Talib, Usama; Chi, Gerald

2017-12-26

The use of smartphones with touch screens has become a norm for healthcare professionals (HCP). The risk of smart screen contamination has been proven, and guidelines are available to deal with possible contamination. A large number of smartphone users apply plastic or glass screen protectors onto their mobile phone screens to prevent scratches. However, these materials are not scratch proof, and their antipathogenic properties have not been studied. We have conducted a study to determine the frequency of smartphone screen protector contamination and compared the data with contamination on the bare area on the same mobile screens. The sample size included only HCPs working in acute care settings and having at least eight hours of exposure time every day. A total of 64 samples were collected, which reported 62.5% (n = 40/64) positive culture swabs from the protected areas of the screen and 45.3% (n = 29/64) from the unprotected area of the screen. Micrococcus and Gram-negative rods grew only on samples taken from the protected area whereas the bare area showed no such growth. There was no statistically significant difference in the frequency based on smart screen size, duration of use during duty hours, or the setting where it was used. Smartphone screen protectors from healthcare providers may harbor pathogenic bacteria, especially in acute care settings. Coagulase-negative Staphylococci followed by Bacillus species were the most commonly yielded bacteria among house officers and postgraduate trainees in the present study.

High-pressure liquid chromatography analysis of antibiotic susceptibility disks.

PubMed Central

Hagel, R B; Waysek, E H; Cort, W M

1979-01-01

The analysis of antibiotic susceptibility disks by high-pressure liquid chromatography (HPLC) was investigated. Methods are presented for the potency determination of mecillinam, ampicillin, carbenicillin, and cephalothin alone and in various combinations. Good agreement between HPLC and microbiological data is observed for potency determinations with recoveries of greater than 95%. Relative standard deviations of lower than 2% are recorded for each HPLC method. HPLC methods offer improved accuracy and greater precision when compared to the standard microbiological methods of analysis for susceptibility disks. PMID:507793

AmpC β-lactamases in nosocomial isolates of Klebsiella pneumoniae from India

PubMed Central

Gupta, Varsha; Kumarasamy, Karthikeyan; Gulati, Neelam; Garg, Ritu; Krishnan, Padma; Chander, Jagdish

2012-01-01

Background & objectives: AmpC β-lactamases are clinically significant since these confer resistance to cephalosporins in the oxyimino group, 7-α methoxycephalosporins and are not affected by available β-lactamase inhibitors. In this study we looked for both extended spectrum β-lactamases (ESBL) and AmpC β-lactamases in Klebsiella pneumoniae clinical isolates. Methods: One hundred consecutive, non-duplicate clinical isolates of K. pneumoniae collected over a period of one year (June 2008 - June 2009) were included in the study. An antibiotic susceptibility method was used with 10 antibiotics for Gram-negative infections which helped in screening for ESBL and AmpC β-lactamases and also in confirmation of ESBL production. The detection of AmpC β-lactamases was done based on screening and confirmatory tests. For screening, disc diffusion zones of cefoxitin <18 mm was taken as cefoxitin resistant. All cefoxitin resistant isolates were tested further by AmpC disk test and modified three dimensional test. Multiplex-PCR was performed for screening the presence of plasmid-mediated AmpC genes. Results: Of the 100 isolates of K. pneumoniae studied, 48 were resistant to cefoxitin on screening. AmpC disk test was positive in 32 (32%) isolates. This was also confirmed with modified three dimensional test. Indentation indicating strong AmpC producer was observed in 25 isolates whereas little distortion (weak AmpC) was observed in 7 isolates. ESBL detection was confirmed by a modification of double disk synergy test in 56 isolates. Cefepime was the best cephalosporin in synergy with tazobactam for detecting ESBL production in isolates co-producing AmpC β-lactamases. The subsets of isolates phenotypically AmpC β-lactamase positive were subjected to amplification of six different families of AmpC gene using multiplex PCR. The sequence analysis revealed 12 CMY-2 and eight DHA-1 types. Interpretation & conclusions: Tazobactam was the best β-lactamase inhibitor for detecting ESBL in presence of AmpC β-lactamase as this is a very poor inducer of AmpC gene. Amongst cephalosporins, cefepime was the best cephalosporin in detecting ESBL in presence of AmpC β-lactamase as it is least hydrolyzed by AmpC enzymes. Cefepime-tazobactam combination disk test would be a simple and best method in detection of ESBLs in Enterobacteriaceae co-producing AmpC β-lactamase in the routine diagnostic microbiology laboratories. PMID:22960890

Microbiology Education in Nursing Practice.

PubMed

Durrant, Robert J; Doig, Alexa K; Buxton, Rebecca L; Fenn, JoAnn P

2017-01-01

Nurses must have sufficient education and training in microbiology to perform many roles within clinical nursing practice (e.g., administering antibiotics, collecting specimens, preparing specimens for transport and delivery, educating patients and families, communicating results to the healthcare team, and developing care plans based on results of microbiology studies and patient immunological status). It is unclear whether the current microbiology courses required of nursing students in the United States focus on the topics that are most relevant to nursing practice. To gauge the relevance of current microbiology education to nursing practice, we created a confidential, web-based survey that asked nurses about their past microbiology education, the types of microbiology specimens they collect, their duties that require knowledge of microbiology, and how frequently they encounter infectious diseases in practice. We used the survey responses to develop data-driven recommendations for educators who teach microbiology to pre-nursing and nursing students. Two hundred ninety-six Registered Nurses (RNs) completed the survey. The topics they deemed most relevant to current practice were infection control, hospital-acquired infections, disease transmission, and collection and handling of patient specimens. Topics deemed least relevant were the Gram stain procedure and microscope use. In addition, RNs expressed little interest in molecular testing methods. This may reflect a gap in their understanding of the uses of these tests, which could be bridged in a microbiology course. We now have data in support of anecdotal evidence that nurses are most engaged when learning about microbiology topics that have the greatest impact on patient care. Information from this survey will be used to shift the focus of microbiology courses at our university to topics more relevant to nursing practice. Further, these findings may also support an effort to evolve national recommendations for microbiology education in pre-nursing and nursing curricula.

Microbiology Education in Nursing Practice†

PubMed Central

Durrant, Robert J.; Doig, Alexa K.; Buxton, Rebecca L.; Fenn, JoAnn P.

2017-01-01

Nurses must have sufficient education and training in microbiology to perform many roles within clinical nursing practice (e.g., administering antibiotics, collecting specimens, preparing specimens for transport and delivery, educating patients and families, communicating results to the healthcare team, and developing care plans based on results of microbiology studies and patient immunological status). It is unclear whether the current microbiology courses required of nursing students in the United States focus on the topics that are most relevant to nursing practice. To gauge the relevance of current microbiology education to nursing practice, we created a confidential, web-based survey that asked nurses about their past microbiology education, the types of microbiology specimens they collect, their duties that require knowledge of microbiology, and how frequently they encounter infectious diseases in practice. We used the survey responses to develop data-driven recommendations for educators who teach microbiology to pre-nursing and nursing students. Two hundred ninety-six Registered Nurses (RNs) completed the survey. The topics they deemed most relevant to current practice were infection control, hospital-acquired infections, disease transmission, and collection and handling of patient specimens. Topics deemed least relevant were the Gram stain procedure and microscope use. In addition, RNs expressed little interest in molecular testing methods. This may reflect a gap in their understanding of the uses of these tests, which could be bridged in a microbiology course. We now have data in support of anecdotal evidence that nurses are most engaged when learning about microbiology topics that have the greatest impact on patient care. Information from this survey will be used to shift the focus of microbiology courses at our university to topics more relevant to nursing practice. Further, these findings may also support an effort to evolve national recommendations for microbiology education in pre-nursing and nursing curricula. PMID:28861140

Proceedings of the U.S. Geological Survey Interdisciplinary Microbiology Workshop, Estes Park, Colorado, October 15-17, 2008

USGS Publications Warehouse

Briggs, Kay Marano

2010-01-01

Preface A U.S. Geological Survey Interdisciplinary Microbiology Workshop was held in Estes Park, Colorado, on October 15-17, 2008. Participants came from all USGS regions and disciplines. This report contains abstracts from 36 presentations and 35 poster sessions and notes from 5 breakout sessions. The seven presentation topics follow: Ecology of wildlife and fish disease Mechanisms of fish and wildlife disease Microbial ecology Geographic patterns/visualization Public health and water quality Geomicrobiology Ecosystem function The six poster session topics follow: Wildlife disease Disease detection methods Water quality Microbial ecology Metabolic processes Tools and techniques Five working groups met in breakout sessions on October 16, 2008. The highlights for each working group are summarized in this report, and their goals are listed below: Working Group I: to plan a Fact Sheet on interdisciplinary microbiology in the USGS Working Group II: to plan a USGS interdisciplinary microbiology Web site Working Group III: to suggest ways to broadcast and publicize the types of microbiology conducted at the USGS Working Group IV: to identify emerging issues in USGS interdisciplinary microbiology research Working Group V: to identify potential opportunities for interdisciplinary microbiology work at the USGS After the workshop, the USGS interdisciplinary microbiology Web site was activated in June 2009 at http://microbiology.usgs.gov/.

[Mass spectrometry in the clinical microbiology laboratory].

PubMed

Jordana-Lluch, Elena; Martró Català, Elisa; Ausina Ruiz, Vicente

2012-12-01

Infectious diseases are still a cause of high mortality and morbidity rates. Current microbiological diagnostic methods are based on culture and phenotypic identification of isolated microorganisms, which can be obtained in about 24-48 h. Given that the microbiological identification is of major importance for patient management, new diagnostic methods are needed in order to detect and identify microorganisms in a timely and accurate manner. Over the last few years, several molecular techniques based on the amplification of microbial nucleic acids have been developed with the aim of reducing the time needed for the identification of the microorganisms involved in different infectious processes. On the other hand, mass spectrometry has emerged as a rapid and consistent alternative to conventional methods for microorganism identification. This review describes the most widely used mass spectrometry technologies -matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization time-of-flight (ESI-TOF)-, both for protein and nucleic acid analysis, as well as the commercial platforms available. Related publications of most interest in clinical microbiology are also reviewed. Copyright © 2011 Elsevier España, S.L. All rights reserved.

Recent advances in diagnostic microbiology.

PubMed

Bravo, Lulette Tricia C; Procop, Gary W

2009-07-01

The past decade has seen a surge in the development of a variety of molecular diagnostics designed to rapidly identify or characterize medically important microorganisms. We briefly review important advances in molecular microbiology, and then discuss specific assays that have been implemented in clinical microbiology laboratories throughout the country. We also discuss emerging methods and technologies that will soon be more widely used for the prompt and accurate detection of the agents of infectious diseases.

Sampling methods and data generation

USDA-ARS?s Scientific Manuscript database

The study of forensic microbiology is an inherent blend of forensic science and microbiology, and both disciplines have recently been undergoing rapid advancements in technology that are allowing for exciting new research avenues. The integration of two different disciplines poses challenges becaus...

Antimicrobial Testing Methods & Procedures: MB-10-06

EPA Pesticide Factsheets

Describes the procedures used to log-in, prepare, and evaluate the quality of media and reagents used in microbiological assays by the Microbiology Laboratory Branch (MLB), for use in the quality evaluation of media and reagents used by MLB.

Methods for microbiological and immunological studies of space flight crews

NASA Technical Reports Server (NTRS)

Taylor, G. R. (Editor); Zaloguev, S. N. (Editor)

1978-01-01

Systematic laboratory procedures compiled as an outgrowth of a joint U.S./U.S.S.R. microbiological-immunological experiment performed during the Apollo-Soyuz Test Project space flight are presented. Included are mutually compatible methods for the identification of aerobic and microaerophilic bacteria, yeast and yeastlike microorganisms, and filamentous fungi; methods for the bacteriophage typing of Staphylococcus aureus; and methods for determining the sensitivity of S. aureus to antibiotics. Immunological methods using blood and immunological and biochemical methods using salivary parotid fluid are also described. Formulas for media and laboratory reagents used are listed.

Emerging Technologies for the Clinical Microbiology Laboratory

PubMed Central

Buchan, Blake W.

2014-01-01

SUMMARY In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory. PMID:25278575

Resident training in microbiology.

PubMed

Haller, Barbara L

2007-06-01

To meet the challenges of diagnosis and management of infectious diseases, clinical pathology residents must receive comprehensive training in microbiology, learn to think critically, develop problem-solving skills, and take active roles as laboratory consultants. Residents well trained in clinical microbiology become capable laboratory professionals, developing cost-effective testing strategies, decreasing risk for medical errors, and improving patient care. Newer methods for diagnosing infectious disease, such as real-time polymerase chain reaction, microarrays for pathogen detection, and rapid assays for antigen or antibody detection, have become standard. Knowledge of infectious disease principles, drug therapeutic options, and drug resistance is also important. Suggestions for training and for assessing resident competency in clinical microbiology are presented.

Microbiological surveillance and state of the art technological strategies for the prevention of dialysis water pollution.

PubMed

Bolasco, Piergiorgio; Contu, Antonio; Meloni, Patrizia; Vacca, Dorio; Galfrè, Andrea

2012-08-01

The present report attempts to illustrate the positive impact on the microbiological quality of dialysis patients over a 15-year period through the progressive implementation of state-of-the-art technological strategies and the optimization of microbiological surveillance procedures in five dialysis units in Sardinia. Following on better microbiological, quality controls of dialysis water and improvement of procedures and equipment, a drastic improvement of microbiological water quality was observed in a total of 945 samples. The main aim was to introduce the use of microbiological culture methods as recommended by the most important guidelines. The microbiological results obtained have led to a progressive refining of controls and introduction of new materials and equipment, including two-stage osmosis and piping distribution rings featuring a greater capacity to prevent biofilm adhesion. The actions undertaken have resulted in unexpected quality improvements. Dialysis water should be viewed by the nephrologist as a medicinal product exerting a demonstrable positive impact on microinflammation in dialysis patients. A synergic effort between nephrologists and microbiologists undoubtedly constitutes the most effective means of preventing dialysis infections.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology.

PubMed

Clark, Andrew E; Kaleta, Erin J; Arora, Amit; Wolk, Donna M

2013-07-01

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology

PubMed Central

Clark, Andrew E.; Kaleta, Erin J.; Arora, Amit

2013-01-01

SUMMARY Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the “nuts and bolts” of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care. PMID:23824373

Target-Specific Assay for Rapid and Quantitative Detection of Mycobacterium chimaera DNA.

PubMed

Zozaya-Valdés, Enrique; Porter, Jessica L; Coventry, John; Fyfe, Janet A M; Carter, Glen P; Gonçalves da Silva, Anders; Schultz, Mark B; Seemann, Torsten; Johnson, Paul D R; Stewardson, Andrew J; Bastian, Ivan; Roberts, Sally A; Howden, Benjamin P; Williamson, Deborah A; Stinear, Timothy P

2017-06-01

Mycobacterium chimaera is an opportunistic environmental mycobacterium belonging to the Mycobacterium avium - M. intracellulare complex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasive M. chimaera infections following cardiac surgery. Investigations suggest worldwide spread of a specific M. chimaera clone, associated with contaminated hospital heater-cooler units used during the surgery. Given the global dissemination of this clone, its potential to cause invasive disease, and the laboriousness of current culture-based diagnostic methods, there is a pressing need to develop rapid and accurate diagnostic assays specific for M. chimaera Here, we assessed 354 mycobacterial genome sequences and confirmed that M. chimaera is a phylogenetically coherent group. In silico comparisons indicated six DNA regions present only in M. chimaera We targeted one of these regions and developed a TaqMan quantitative PCR (qPCR) assay for M. chimaera with a detection limit of 100 CFU/ml in whole blood spiked with bacteria. In vitro screening against DNA extracted from 40 other mycobacterial species and 22 bacterial species from 21 diverse genera confirmed the in silico -predicted specificity for M. chimaera Screening 33 water samples from heater-cooler units with this assay highlighted the increased sensitivity of PCR compared to culture, with 15 of 23 culture-negative samples positive by M. chimaera qPCR. We have thus developed a robust molecular assay that can be readily and rapidly deployed to screen clinical and environmental specimens for M. chimaera . Copyright © 2017 American Society for Microbiology.

Horizontal transmission of group B streptococcus in a neonatal intensive care unit

PubMed Central

Morinis, Julia; Shah, Jay; Murthy, Prashanth; Fulford, Martha

2011-01-01

The incidence of early-onset group B streptococcal (GBS) sepsis in the neonatal population has decreased substantially since the introduction of maternal intrapartum antibiotic prophylaxis and routine prenatal screening. However, these strategies have not reduced the incidence of late-onset GBS infections. Additional research pertaining to the transmission of late-onset GBS infections is required to develop effective preventive methods. The present report describes probable horizontal transmission of late-onset GBS infection among three infants in a neonatal intensive care unit. GBS strain confirmation was based on the microbiological picture, antibiogram and pulsed-field gel electrophoresis. These cases highlight the morbidity associated with late-onset GBS disease and the importance of considering horizontal transmission as an etiological factor in GBS infection in the newborn period. Further studies assessing horizontal transmission in late-onset GBS disease may improve prevention and early intervention. PMID:22654550

Horizontal transmission of group B streptococcus in a neonatal intensive care unit.

PubMed

Morinis, Julia; Shah, Jay; Murthy, Prashanth; Fulford, Martha

2011-06-01

The incidence of early-onset group B streptococcal (GBS) sepsis in the neonatal population has decreased substantially since the introduction of maternal intrapartum antibiotic prophylaxis and routine prenatal screening. However, these strategies have not reduced the incidence of late-onset GBS infections. Additional research pertaining to the transmission of late-onset GBS infections is required to develop effective preventive methods. The present report describes probable horizontal transmission of late-onset GBS infection among three infants in a neonatal intensive care unit. GBS strain confirmation was based on the microbiological picture, antibiogram and pulsed-field gel electrophoresis. These cases highlight the morbidity associated with late-onset GBS disease and the importance of considering horizontal transmission as an etiological factor in GBS infection in the newborn period. Further studies assessing horizontal transmission in late-onset GBS disease may improve prevention and early intervention.

An indigenously developed nitrite kit to aid in the diagnosis of urinary tract infection.

PubMed

Sood, S; Upadhyaya, P; Kapil, A; Lodha, R; Jain, Y; Bagga, A

1999-09-01

To evaluate the utility of an indigenously developed nitrite kit for the rapid diagnosis of urinary tract infection (UTI) METHODS: 1018 urine specimens were collected from all cases where there was clinical suspicion of UTI. Samples were cultured as per standard microbiological protocol. Presence of nitrites was indicated by the development of purple color on addition of color developing solution and compared with the set of graded positive and negative controls also provided in the Kit. The results of the nitrite kit were compared with the semi-quantitative urine culture as the gold standard. The sensitivity, specificity, positive predictive and negative predictive values were 47%, 87%, 31% and 93%, respectively. Nitrite kit as a screening test can decrease the work load in the clinical bacteriology laboratory. More importantly in a field set up that is devoid of culture facilities, it can be used to correctly predict the absence of UTI.

[Practical considerations for high resolution anoscopy in patients infected with human immunodeficiency virus].

PubMed

Iribarren-Díaz, Mauricio; Ocampo Hermida, Antonio; González-Carreró Fojón, Joaquín; Alonso-Parada, María; Rodríguez-Girondo, Mar

2014-12-01

Anal cancer is uncommon in the general population, however its incidence is increasing significantly in certain risk groups, mainly in men who have sex with men, and particularly those infected with human immunodeficiency virus. High resolution anoscopy technique is currently considered the standard in the diagnosis of anal intraepithelial neoplasia, but at present there is no agreed standard method between health areas. High resolution anoscopy is an affordable technique that can be critical in the screening of anal carcinoma and its precursor lesions, but is not without difficulties. We are currently studying the most effective strategy for managing premalignant anal lesions, and with this article we attempt to encourage other groups interested in reducing the incidence of an increasing neoplasia. Copyright © 2013 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS.

PubMed

Bechy-Loizeau, Anne-Laure; Flandrois, Jean-Pierre; Abaibou, Hafid

2015-07-01

On the ISS, as on Earth, water is an essential element for life and its quality control on a regular basis allows to ensure the health of the crew and the integrity of equipment. Currently, microbial water analysis onboard ISS still relies on the traditional culture-based microbiology methods. Molecular methods based on the amplification of nucleic acids for microbiological analysis of water quality show enormous potential and are considered as the best alternative to culture-based methods. For this reason, the Midass, a fully integrated and automated prototype was designed conjointly by ESA and bioMérieux for a rapid monitoring of the microbiological quality of air. The prototype allows air sampling, sample processing and the amplification/detection of nucleic acids. We describe herein the proof of principle of an analytical approach based on molecular biology that could fulfill the ESA's need for a rapid monitoring of the microbiological quality of recycled water onboard ISS. Both concentration and recovery of microorganisms are the main critical steps when the microfiltration technology is used for water analysis. Among filters recommended standards for monitoring the microbiological quality of the water, the polycarbonate filter was fully in line with the requirements of the ISO 7704-1985 standard in terms of efficacy of capture and recovery of bacteria. Moreover, this filter does not retain nucleic acids on the surface and has no inhibitory effect on their downstream processing steps such as purification and amplification/detection. Although the Midass system was designed for the treatment of air samples, the first results on the integration of PC filters were encouraging. Nevertheless, system modifications are needed to better adapt the Midass system for the monitoring of the microbiological water quality. Copyright © 2015 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Comparison of the Microbiological Quality and Safety between Conventional and Organic Vegetables Sold in Malaysia

PubMed Central

Kuan, Chee-Hao; Rukayadi, Yaya; Ahmad, Siti H.; Wan Mohamed Radzi, Che W. J.; Thung, Tze-Young; Premarathne, Jayasekara M. K. J. K.; Chang, Wei-San; Loo, Yuet-Ying; Tan, Chia-Wanq; Ramzi, Othman B.; Mohd Fadzil, Siti N.; Kuan, Chee-Sian; Yeo, Siok-Koon; Nishibuchi, Mitsuaki; Radu, Son

2017-01-01

Given the remarkable increase of public interest in organic food products, it is indeed critical to evaluate the microbiological risk associated with consumption of fresh organic produce. Organic farming practices including the use of animal manures may increase the risk of microbiological contamination as manure can act as a vehicle for transmission of foodborne pathogens. This study aimed to determine and compare the microbiological status between organic and conventional fresh produce at the retail level in Malaysia. A total of 152 organic and conventional vegetables were purchased at retail markets in Malaysia. Samples were analyzed for mesophilic aerobic bacteria, yeasts and molds, and total coliforms using conventional microbiological methods. Combination methods of most probable number-multiplex polymerase chain reaction (MPN-mPCR) were used to detect and quantify foodborne pathogens, including Escherichia coli O157:H7, Shiga toxin-producing E. coli (STEC), Listeria monocytogenes, Salmonella Typhimurium, and Salmonella Enteritidis. Results indicated that most types of organic and conventional vegetables possessed similar microbial count (P > 0.05) of mesophilic aerobic bacteria, yeasts and molds, and total coliforms. E. coli O157:H7 and S. Typhimurium were not detected in any sample analyzed in this study. Among the 152 samples tested, only the conventional lettuce and organic carrot were tested positive for STEC and S. Enteritidis, respectively. L. monocytogenes were more frequently detected in both organic (9.1%) and conventional vegetables (2.7%) as compared to E. coli O157:H7, S. Typhimurium, and S. Enteritidis. Overall, no trend was shown that either organically or conventionally grown vegetables have posed greater microbiological risks. These findings indicated that one particular type of farming practices would not affect the microbiological profiles of fresh produce. Therefore, regardless of farming methods, all vegetables should be subjected to appropriate post-harvest handling practices from farm to fork to ensure the quality and safety of the fresh produce. PMID:28824567

Comparison of the Microbiological Quality and Safety between Conventional and Organic Vegetables Sold in Malaysia.

PubMed

Kuan, Chee-Hao; Rukayadi, Yaya; Ahmad, Siti H; Wan Mohamed Radzi, Che W J; Thung, Tze-Young; Premarathne, Jayasekara M K J K; Chang, Wei-San; Loo, Yuet-Ying; Tan, Chia-Wanq; Ramzi, Othman B; Mohd Fadzil, Siti N; Kuan, Chee-Sian; Yeo, Siok-Koon; Nishibuchi, Mitsuaki; Radu, Son

2017-01-01

Given the remarkable increase of public interest in organic food products, it is indeed critical to evaluate the microbiological risk associated with consumption of fresh organic produce. Organic farming practices including the use of animal manures may increase the risk of microbiological contamination as manure can act as a vehicle for transmission of foodborne pathogens. This study aimed to determine and compare the microbiological status between organic and conventional fresh produce at the retail level in Malaysia. A total of 152 organic and conventional vegetables were purchased at retail markets in Malaysia. Samples were analyzed for mesophilic aerobic bacteria, yeasts and molds, and total coliforms using conventional microbiological methods. Combination methods of most probable number-multiplex polymerase chain reaction (MPN-mPCR) were used to detect and quantify foodborne pathogens, including Escherichia coli O157:H7, Shiga toxin-producing E. coli (STEC), Listeria monocytogenes, Salmonella Typhimurium, and Salmonella Enteritidis. Results indicated that most types of organic and conventional vegetables possessed similar microbial count ( P > 0.05) of mesophilic aerobic bacteria, yeasts and molds, and total coliforms. E. coli O157:H7 and S . Typhimurium were not detected in any sample analyzed in this study. Among the 152 samples tested, only the conventional lettuce and organic carrot were tested positive for STEC and S . Enteritidis, respectively. L. monocytogenes were more frequently detected in both organic (9.1%) and conventional vegetables (2.7%) as compared to E. coli O157:H7, S . Typhimurium, and S . Enteritidis. Overall, no trend was shown that either organically or conventionally grown vegetables have posed greater microbiological risks. These findings indicated that one particular type of farming practices would not affect the microbiological profiles of fresh produce. Therefore, regardless of farming methods, all vegetables should be subjected to appropriate post-harvest handling practices from farm to fork to ensure the quality and safety of the fresh produce.

Interpretation of Blood Microbiology Results - Function of the Clinical Microbiologist.

PubMed

Kristóf, Katalin; Pongrácz, Júlia

2016-04-01

The proper use and interpretation of blood microbiology results may be one of the most challenging and one of the most important functions of clinical microbiology laboratories. Effective implementation of this function requires careful consideration of specimen collection and processing, pathogen detection techniques, and prompt and precise reporting of identification and susceptibility results. The responsibility of the treating physician is proper formulation of the analytical request and to provide the laboratory with complete and precise patient information, which are inevitable prerequisites of a proper testing and interpretation. The clinical microbiologist can offer advice concerning the differential diagnosis, sampling techniques and detection methods to facilitate diagnosis. Rapid detection methods are essential, since the sooner a pathogen is detected, the better chance the patient has of getting cured. Besides the gold-standard blood culture technique, microbiologic methods that decrease the time in obtaining a relevant result are more and more utilized today. In the case of certain pathogens, the pathogen can be identified directly from the blood culture bottle after propagation with serological or automated/semi-automated systems or molecular methods or with MALDI-TOF MS (matrix-assisted laser desorption-ionization time of flight mass spectrometry). Molecular biology methods are also suitable for the rapid detection and identification of pathogens from aseptically collected blood samples. Another important duty of the microbiology laboratory is to notify the treating physician immediately about all relevant information if a positive sample is detected. The clinical microbiologist may provide important guidance regarding the clinical significance of blood isolates, since one-third to one-half of blood culture isolates are contaminants or isolates of unknown clinical significance. To fully exploit the benefits of blood culture and other (non- culture based) diagnoses, the microbiologist and the clinician should interact directly.

Screening for Cryptococcal Antigenaemia in Patients Accessing an Antiretroviral Treatment Program in South Africa

PubMed Central

Jarvis, Joseph N; Lawn, Stephen D; Vogt, Monica; Bangani, Nonzwakazi; Wood, Robin; Harrison, Thomas S

2009-01-01

Background Cryptococcal meningitis is a leading cause of death in AIDS patients and contributes substantially to the high early mortality in antiretroviral treatment (ART) programs in low-resource settings. Screening for cryptococcal antigen (CRAG) in patients enrolling in ART programs may identify those at risk of cryptococcal meningitis and permit targeted use of pre-emptive therapy. Methods In this retrospective study, CRAG was measured in stored plasma samples obtained from patients as they enrolled in a well characterised ART cohort in South Africa. The predictive value of screening for CRAG prior to ART for development of microbiologically confirmed cryptococcal meningitis or death during the first year of follow-up was determined. Results Of 707 participants with a baseline median CD4 count of 97 (IQR 46-157) cells/μL, 46 (7%) had a positive CRAG. Antigenaemia was 100% sensitive for predicting development of cryptococcal meningitis during the first year of ART and in multivariate analysis was an independent predictor of mortality (AHR 3.2, 95%CI 1.5-6.6). Most (92%) cases of cryptococcal meningitis developed in patients with a CD4 count ≤100 cells/μL. In this sub-set of patients, a CRAG titre ≥1 in 8 was 100% sensitive and 96% specific for predicting incident cryptococcal meningitis during the first year of ART in those with no previous history of the disease. Conclusions CRAG screening prior to commencing ART in patients with a CD4 count ≤100 cells/μL is highly effective at identifying those at risk of cryptococcal meningitis and death and might permit implementation of a targeted pre-emptive treatment strategy. PMID:19222372

Anti-Rhodotorula activity of mycophenolic acid enhanced in the presence of polyene antibiotic nystatin.

PubMed

Kinoshita, H; Wongsuntornpoj, S; Ihara, F; Nihira, T

2017-02-01

Rhodotorula species are opportunistic pathogens, which cause not only systemic fungaemia but also other localized infections. Despite serious side effects such as nephrotoxicity and hypokalemia, amphotericin B (a polyene antifungal) has been commonly prescribed for Rhodotorula infection because Rhodotorula species are resistant against a candin family of antifungal agents. In this study, novel active compounds against Rhodotorula species were screened from the extracts of entomopathogenic fungi based on the synergistic effect of polyene nystatin (NYS), which causes efficient targeting of compounds due to increased permeability through the fungal cell membrane. Around 37% of culture extracts from 31 entomopathogenic fungal strains showed anti-Rhodotorula activity in the synergistic bioassay system, suggesting that the coexistence assay with NYS enhanced the discovery of anti-Rhodotorula compounds. Judging from various physicochemical data, the active component from strain HF763 was identified as an immunosuppressant drug, mycophenolic acid (MPA). The minimum inhibitory concentration of MPA against three pathogenic Rhodotorula strains was determined, focusing on the synergistic effect with NYS. The results revealed that the values decreased by at least 87% in the presence of NYS, indicating that MPA showed a synergistic effect with NYS. This study aimed to screen active compounds against Rhodotorula species that are resistant to a candin family of antifungal agents, from entomopathogenic fungi. Assuming that most of the latent antifungal compounds do not exert their activity due to their inability to penetrate the membrane, we took advantage of polyene nystatin in the screening to increase permeability through the fungal cell membrane. The result of the screening revealed hidden antifungal activity of mycophenolic acid, demonstrating that the method applied in this study unlocks the potentials of bioresources, and proposes a new remedy for mycosis. © 2016 The Society for Applied Microbiology.

Effect of a triclosan/PVM/MA copolymer/fluoride dentifrice on volatile sulfur compounds in vitro.

PubMed

Pilch, S; Williams, M I; Cummins, D

2005-01-01

The objective of the investigation was to document the in vitro efficacy of a triclosan/PVM/MA copolymer/fluoride (TCF) dentifrice against the formation of volatile sulfur compounds (VSC) as well as the growth of H2S-producing bacteria. Clinical studies using organoleptic judges, gas chromatography, or a portable sulfide monitor have generally been employed in the assessment of treatments for the control of oral malodor. However, these studies are not appropriate for screening purposes because of the expense and time required. An in vitro method was developed for the purpose of screening new compounds, agents or formulations for their ability to control VSC formation and for determining bio-equivalence of efficacy when implementing changes in existing formulations. The method combines basic microbiological methods, dynamic flow cell techniques and head space analysis. The in vitro VSC method was validated by comparing the efficacy of two dentifrices containing TCF with a control fluoride dentifrice as the TCF products have been clinically proven to control oral malodor. In the validation studies, the TCF-containing dentifrices were significantly better (P < 0.05) than the control dentifrice in inhibiting VSC formation and reducing H(2)S-producing bacteria. For example, when compared with baseline, the TCF dentifrices reduced VSC formation between 42 and 49% compared with the control dentifrice which reduced VSC formation 3%. There was no significant difference (P > 0.05) between the two TCF dentifrice formulations. Using an in vitro breath VSC model, it has been demonstrated that two variants of a dentifrice containing triclosan, PVM/MA copolymer and fluoride have efficacy that is significantly better than a control fluoridated dentifrice and that there is no significant difference between the triclosan/PVM/MA copolymer/fluoride dentifrice variants.

[Current panorama of the teaching of microbiology and parasitology in Spain].

PubMed

Cantón, Rafael; Sánchez-Romero, María Isabel; Gómez-Mampaso, Enrique

2010-10-01

The training program of residents in microbiology and parasitology in Spain includes clinical skills, ranging from the diagnostic approach to the patient and adequate sample collection for diagnosis of infectious diseases to antimicrobial therapy and infection control measures. Training also includes new challenges in clinical microbiology that ensure residents' participation in infection control programs of health-care associated infections, training in the resolution of public health problems, and application of new molecular microbiology methods. Specialization in clinical microbiology may be undertaken by graduates in Medicine, Biology, Biochemistry and Chemistry. The training is performed in accredited microbiology laboratories at different hospitals (n = 61) across the country through 4-year residency programs. In the last few years, there has been a major imbalance between the number of intended residents (0.17 per 100,000 inhabitants) and those graduating as specialists in clinical microbiology (0.13 per 100,000 inhabitants), with wide variations across the country. The current tendency in Europe is to strengthen the role of clinical microbiologists as key figures in the diagnosis of infectious diseases and in public health microbiology. Training programs have been hampered by the practice of sending samples for microbiological tests to external, centralized multipurpose laboratories with few clinical microbiologists and without a core curriculum. Essential elements in the training of specialists in clinical microbiology are a close relationship between the laboratory and the clinical center and collaboration with other specialists. Copyright © 2010 Elsevier España S.L. All rights reserved.

Candida bloodstream infection: a clinical microbiology laboratory perspective.

PubMed

Pongrácz, Júlia; Kristóf, Katalin

2014-09-01

The incidence of Candida bloodstream infection (BSI) has been on the rise in several countries worldwide. Species distribution is changing; an increase in the percentage of non-albicans species, mainly fluconazole non-susceptible C. glabrata was reported. Existing microbiology diagnostic methods lack sensitivity, and new methods need to be developed or further evaluation for routine application is necessary. Although reliable, standardized methods for antifungal susceptibility testing are available, the determination of clinical breakpoints remains challenging. Correct species identification is important and provides information on the intrinsic susceptibility profile of the isolate. Currently, acquired resistance in clinical Candida isolates is rare, but reports indicate that it could be an issue in the future. The role of the clinical microbiology laboratory is to isolate and correctly identify the infective agent and provide relevant and reliable susceptibility data as soon as possible to guide antifungal therapy.

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.

Biomarkers of Tuberculosis Severity and Treatment Effect: A Directed Screen of 70 Host Markers in a Randomized Clinical Trial

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

Sigal, G. B.; Segal, M. R.; Mathew, A.

More efficacious treatment regimens are needed for tuberculosis, however, drug development is impeded by a lack of reliable biomarkers of disease severity and of treatment effect. We conducted a directed screen of host biomarkers in participants enrolled in a tuberculosis clinical trial to address this need. Serum samples from 319 protocol-correct, culture-confirmed pulmonary tuberculosis patients treated under direct observation as part of an international, phase 2 trial were screened for 70 markers of infection, inflammation, and metabolism. Biomarker assays were specifically developed for this study and quantified using a novel, multiplexed electrochemiluminescence assay. We evaluated the association of biomarkers withmore » baseline characteristics, as well as with detailed microbiologic data, using Bonferroni-adjusted, linear regression models. Across numerous analyses, seven proteins, SAA1, PCT, IL-1, IL-6, CRP, PTX-3 and MMP-8, showed recurring strong associations with markers of baseline disease severity, smear grade and cavitation; were strongly modulated by tuberculosis treatment; and had responses that were greater for patients who culture-converted at 8 weeks. With treatment, all proteins decreased, except for osteocalcin, MCP-1 and MCP-4, which significantly increased. Several previously reported putative tuberculosis-associated biomarkers (HOMX1, neopterin, and cathelicidin) were not significantly associated with treatment response. In conclusion, across a geographically diverse and large population of tuberculosis patients enrolled in a clinical trial, several previously reported putative biomarkers were not significantly associated with treatment response, however, seven proteins had recurring strong associations with baseline radiographic and microbiologic measures of disease severity, as well as with early treatment response, deserving additional study. Keywords: host immune response; tuberculosis; biomarkers; clinical trials« less

Identification of Haemophilus influenzae Type b Isolates by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Månsson, Viktor; Resman, Fredrik; Kostrzewa, Markus; Nilson, Bo; Riesbeck, Kristian

2015-07-01

Haemophilus influenzae type b (Hib) is, in contrast to non-type b H. influenzae, associated with severe invasive disease, such as meningitis and epiglottitis, in small children. To date, accurate H. influenzae capsule typing requires PCR, a time-consuming and cumbersome method. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) provides rapid bacterial diagnostics and is increasingly used in clinical microbiology laboratories. Here, MALDI-TOF MS was evaluated as a novel approach to separate Hib from other H. influenzae. PCR-verified Hib and non-Hib reference isolates were selected based on genetic and spectral characteristics. Mass spectra of reference isolates were acquired and used to generate different classification algorithms for Hib/non-Hib differentiation using both ClinProTools and the MALDI Biotyper software. A test series of mass spectra from 33 Hib and 77 non-Hib isolates, all characterized by PCR, was used to evaluate the algorithms. Several algorithms yielded good results, but the two best were a ClinProTools model based on 22 separating peaks and subtyping main spectra (MSPs) using MALDI Biotyper. The ClinProTools model had a sensitivity of 100% and a specificity of 99%, and the results were 98% reproducible using a different MALDI-TOF MS instrument. The Biotyper subtyping MSPs had a sensitivity of 97%, a specificity of 100%, and 93% reproducibility. Our results suggest that it is possible to use MALDI-TOF MS to differentiate Hib from other H. influenzae. This is a promising method for rapidly identifying Hib in unvaccinated populations and for the screening and surveillance of Hib carriage in vaccinated populations. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Development of a new CARD-FISH protocol for quantification of Legionella pneumophila and its application in two hospital cooling towers.

PubMed

Kirschner, A K T; Rameder, A; Schrammel, B; Indra, A; Farnleitner, A H; Sommer, R

2012-06-01

Open cooling towers are frequent sources of infections with Legionella pneumophila. The gold standard for the detection of Leg. pneumophila is based on cultivation lasting up to 10 days and detecting only culturable cells. Alternative fluorescence in situ hybridization (FISH) protocols have been proposed, but they result in faint fluorescence signals and lack specificity because of cross-hybridization with other Legionella species. Our aim was thus to develop a new FISH protocol for rapid and specific detection of Leg. pneumophila in water samples. A novel catalysed reporter deposition FISH (CARD-FISH) protocol for the detection of Leg. pneumophila was developed, which significantly enhanced signal intensity as well as specificity of the probe through the use of a novel competitor probe. The developed protocol was compared with the culture method for monitoring the seasonal development of culturable and nonculturable Leg. pneumophila in two hospital cooling tower systems. Seasonal fluctuations of Leg. pneumophila concentrations detected via CARD-FISH were related to the development of the total bacterial community in both cooling towers, with temperature and biocide as the main factors controlling this development. Our results clearly showed that the majority of the Leg. pneumophila cells were in a nonculturable state. Thus, detection of Leg. pneumophila with culture methods may underestimate the total numbers of Leg. pneumophila present. Rapid, sensitive and specific detection and quantification of Leg. pneumophila in water systems is prerequisite for reliable risk estimation. The new protocol significantly improves current methodology and can be used to monitor and screen for Leg. pneumophila concentrations in cooling towers or other water systems. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Evaluation of the Sysmex UF1000i flow cytometer for ruling out bacterial urinary tract infection.

PubMed

De Rosa, Rita; Grosso, Shamanta; Bruschetta, Graziano; Avolio, Manuela; Stano, Paola; Modolo, Maria Luisa; Camporese, Alessandro

2010-08-05

Urine culture is one of the most frequently requested tests in microbiology, and it represents the gold standard for the diagnosis of UTIs. Considering the high prevalence of negative results and the long TAT of the culture test, the use of a rapid and reliable screening method is becoming more and more important, as it reduces the workload, the TAT of negative results, and above all, unnecessary antibiotic prescription. The Sysmex UF1000i is a new urine flow cytometry analyzer capable of quantifying urinary particles, including BACT, WBCs, and YLCs. To evaluate the analytical performance of the UF1000i as a method for ruling out UTIs, we examined 1349 urine samples and compared the UF1000i results with standard urine culture results. With instrument cut-off values of 170BACTx10(6)/L and 150WBCsx10(6)/L, we obtained a sensitivity of 98.8%, a specificity of 76.5%, a NPV of 99.5%, and four false negative results (1.2%), avoiding the culture of 57.1% of samples. The Sysmex UF1000i was capable of improving the efficiency of a routine microbiology laboratory by processing 100samples/h and providing negative results in a few minutes, thus reducing unnecessary testing with an acceptable number of false negative results. In addition, the preliminary evaluation of B_FSC and B_FLH parameters from bacteria histograms seems to be useful for the distinction of bacterial strains detected (Gram-negatives versus Gram-positives). In fact when B_FSC was less than 30 ch, it allowed the distinction of Gram-negative bacteria in 97% of the samples. Copyright 2010 Elsevier B.V. All rights reserved.

Commutability of food microbiology proficiency testing samples.

PubMed

Abdelmassih, M; Polet, M; Goffaux, M-J; Planchon, V; Dierick, K; Mahillon, J

2014-03-01

Food microbiology proficiency testing (PT) is a useful tool to assess the analytical performances among laboratories. PT items should be close to routine samples to accurately evaluate the acceptability of the methods. However, most PT providers distribute exclusively artificial samples such as reference materials or irradiated foods. This raises the issue of the suitability of these samples because the equivalence-or 'commutability'-between results obtained on artificial vs. authentic food samples has not been demonstrated. In the clinical field, the use of noncommutable PT samples has led to erroneous evaluation of the performances when different analytical methods were used. This study aimed to provide a first assessment of the commutability of samples distributed in food microbiology PT. REQUASUD and IPH organized 13 food microbiology PTs including 10-28 participants. Three types of PT items were used: genuine food samples, sterile food samples and reference materials. The commutability of the artificial samples (reference material or sterile samples) was assessed by plotting the distribution of the results on natural and artificial PT samples. This comparison highlighted matrix-correlated issues when nonfood matrices, such as reference materials, were used. Artificially inoculated food samples, on the other hand, raised only isolated commutability issues. In the organization of a PT-scheme, authentic or artificially inoculated food samples are necessary to accurately evaluate the analytical performances. Reference materials, used as PT items because of their convenience, may present commutability issues leading to inaccurate penalizing conclusions for methods that would have provided accurate results on food samples. For the first time, the commutability of food microbiology PT samples was investigated. The nature of the samples provided by the organizer turned out to be an important factor because matrix effects can impact on the analytical results. © 2013 The Society for Applied Microbiology.

School outbreak of Escherichia coli O157 with high levels of transmission, Staffordshire, England, February 2012.

PubMed

Bayliss, Laura; Carr, Robert; Edeghere, Obaghe; Knapper, Elizabeth; Nye, Kathy; Harvey, Gareth; Adak, Goutam; Duggal, Harsh

2016-09-01

Verocytotoxin-producing Escherichia coli (VTEC) are bacteria that cause infectious gastroenteritis and in certain settings can cause widespread infection due to secondary transmission. We describe the findings of an investigation of a school-based outbreak of VTEC in Staffordshire, England. Outbreak investigation at a school in February 2012 after two children were diagnosed with VTEC infection. Cases were defined as pupils and staff (or their household contacts) with gastrointestinal symptoms or asymptomatic screened persons, with laboratory confirmed VTEC O157 infection (phage type 32, verocytotoxin 2) occurring on or after 1 February 2012. Microbiological tests of food and faecal samples plus screening of asymptomatic contacts were undertaken. Epidemiological and clinical data were descriptively analysed. Thirty-eight cases were detected. Nineteen were asymptomatic and identified via screening of 191 pupils. Infection was introduced into the school from an earlier household cluster, followed by extensive person-to-person transmission within the nursery/infant group with limited spread to the wider school population. Control measures included several interventions, in particular, universal screening of pupils and staff. Screening during school outbreaks is not underpinned by guidance but proved to be a key control measure. Screening of asymptomatic contacts should be considered in similar outbreaks. © Crown copyright 2015.

AN OVERVIEW OF PATHOGEN RESEARCH IN THE MICROBIOLOGICAL AND CHEMICAL EXPOSURE ASSESSMENT RESEARCH DIVISION

EPA Science Inventory

The Microbiological and Chemical Exposure Assessment Research Division of the EPA Office of Research and Development's National Exposure Research Laboratory has a robust in-house research program aimed at developing better occurrence and exposure methods for waterborne pathogens....

Mass Spectrometry and Multiplex Antigen Assays to Assess Microbial Quality and Toxin Production of Staphylococcus aureus Strains Isolated from Clinical and Food Samples

PubMed Central

Attien, Paul; Sina, Haziz; Moussaoui, Wardi; Zimmermann-Meisse, Gaëlle; Dadié, Thomas; Keller, Daniel; Riegel, Philippe; Edoh, Vincent; Kotchoni, Simeon O.; Djè, Marcellin; Prévost, Gilles

2014-01-01

The aim of our study was to investigate the microbial quality of meat products and on some clinical samples in Abidjan focused on Staphylococcus genus and the toxin production profile of Staphylococcus aureus (S. aureus) isolated. Bacteria were collected from 240 samples of three meat products sold in Abidjan and 180 samples issued from clinical infections. The strains were identified by both microbiological and MALDI-TOF-MS methods. The susceptibility to antibiotics was determined by the disc diffusion method. The production of Panton-Valentine Leukocidin, LukE/D, and epidermolysins was screened using radial gel immunodiffusion. The production of staphylococcal enterotoxins and TSST-1 was screened by a Bio-Plex Assay. We observed that 96/240 of meat samples and 32/180 of clinical samples were contaminated by Staphylococcus. Eleven species were isolated from meats and 4 from clinical samples. Forty-two S. aureus strains were isolated from ours samples. Variability of resistance was observed for most of the tested antibiotics but none of the strains displays a resistance to imipenem and quinolones. We observed that 89% of clinical S. aureus were resistant to methicillin against 58% for those issued from meat products. All S. aureus isolates issued from meat products produce epidermolysins whereas none of the clinical strains produced these toxins. The enterotoxins were variably produced by both clinical and meat product samples. PMID:24987686

Evaluation of colorimetric loop-mediated isothermal amplification assay for visual detection of Streptococcus agalactiae and Streptococcus iniae in tilapia.

PubMed

Suebsing, R; Kampeera, J; Tookdee, B; Withyachumnarnkul, B; Turner, W; Kiatpathomchai, W

2013-10-01

Streptococcus agalactiae and Strep. iniae are bacterial pathogens that cause streptococcosis in many fish species. An accelerated colorimetric loop-mediated isothermal amplification (LAMP) assay with pre-addition of calcein was established, and the transmission and detection of Strep. agalactiae and Strep. iniae in tilapia under natural aquatic environment were investigated. A positive reaction was observed by a colour change from orange to green through the naked eyes after completion at 63°C for 30 min with 10 times higher sensitivity than that of nested PCR assays and without cross-amplification with other fish bacterial pathogens. All sample types of Nile and red tilapia (broodstock, fertilized egg, fry) were Strep. agalactiae- and Strep. iniae positive by this new method, implying that they could be vertically transmitted. With its application for screening broodstock and fry before stocking and for monitoring fish health in grow-out ponds, the method would become very useful in fish farming industry. The application of colorimetric LAMP with pre-addition of calcein offers simple, rapid and sensitive technique with applicability for small field laboratories. This technique explored the possible vertical transmission mode of Strep. agalactiae and Strep. iniae under natural aquatic environment. It could be such preliminary data provided for the screening broodstock before breeding and/or the specific-pathogen-free production. © 2013 The Society for Applied Microbiology.

[Infection control team (ICT) in cooperation with microbiology laboratories].

PubMed

Okazaki, Mitsuhiro

2012-10-01

Infection control as a medical safety measure is an important issue in all medical facilities. In order to tackle this measure, cooperation between the infection control team (ICT) and microbiological laboratory is indispensable. Multiple drug-resistant bacteria have shifted from Gram-positive bacteria to Gram-negative bacilli within the last ten years. There are also a variety of bacilli, complicating the examination method and test results further. Therefore, cooperation between the ICT and microbiological laboratory has become important to understand examination results and to use them. In order to maintain functional cooperation, explanatory and communicative ability between the microbiological laboratory and ICT is required every day. Such positive information exchange will develop into efficient and functional ICT activity.

Water bags as a potential vehicle for transmitting disease in a West African capital, Bissau.

PubMed

Bordalo, Adriano A; Machado, Ana

2015-01-01

Street vendors of chilled packaged water have an increasing role in meeting the drinking water demand of people on the move in developing nations. Hygienic conditions can be questionable, and water quality screening scarce or non-existent. In order to ascertain the quality of the packaged water sold by street vendors in Bissau, the capital of the Western African country Guinea-Bissau, water bags were screened in 2011 and during the 2012 cholera outbreak for key physical, chemical and microbiological parameters. Water used to fill the hand-filled hand-tied bags originated from communal tap water and melted ice. All samples (n=36) were microbiologically contaminated, although levels showed a pronounced variability (e.g. 7-493 372 cfu 250 ml(-1) for Escherichia coli). In 2012, the fecal contamination levels increased (p<0.05), and Vibrio cholerae was detected in all water bags obtained from the neighborhood where the outbreak started. Findings showed that all packaged water samples were unfit for human consumption and during the 2012 cholera outbreak represented a potential vehicle for the spread of the disease. The design of measures to decrease the risk associated to the consumption of highly contaminated chilled water is clearly required. © The Author 2014. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The role of lager beer yeast in oxidative stability of model beer.

PubMed

Berner, T S; Arneborg, N

2012-03-01

In this study, we investigated the relationship between the ability of lager brewing yeast strains to tolerate oxidative stress and their ability to produce oxidative stable model beer. Screening of 21 lager brewing yeast strains against diamide and paraquat showed that the oxidative stress resistance was strain dependent. Fermentation of model wort in European Brewing Convention tubes using three yeast strains with varying oxidative stress resistances resulted in three model beers with different rates of radical formation as measured by electron spin resonance in forced ageing experiments. Interestingly, the strain with the lowest oxidative stress resistance and lowest secretion of thioredoxin, as measured by Western blotting, resulted in the highest uptake of iron, as measured by inductively coupled plasma-mass spectrometry, and the slowest formation of radicals in the model beers. A more oxidative stable beer is not obtained by a more-oxidative-stress-tolerant lager brewing yeast strain, exhibiting a higher secretion of thioredoxin, but rather by a less-oxidative-stress-tolerant strain, exhibiting a higher iron uptake. To obtain lager beers with enhanced oxidative stability, yeast strains should be screened for their low oxidative stress tolerance and/or high ability to take up iron rather than for their high oxidative stress tolerance and/or high ability to secrete thioredoxin. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Validation Study of Rapid Assays of Bioburden, Endotoxins and Other Contamination.

PubMed

Shintani, Hideharu

2016-01-01

Microbial testing performed in support of pharmaceutical and biopharmaceutical production falls into three main categories: detection (qualitative), enumeration (quantitative), and characterization/identification. Traditional microbiological methods are listed in the compendia and discussed by using the conventional growth-based techniques, which are labor intensive and time consuming. In general, such tests require several days of incubation for microbial contamination (bioburden) to be detected, and therefore management seldom is able to take proactive corrective measures. In addition, microbial growth is limited by the growth medium used and incubation conditions, thus impacting testing sensitivity, accuracy, and reproducibility. 　For more than 20 years various technology platforms for rapid microbiological methods (RMM) have been developed, and many have been readily adopted by the food industry and clinical microbiology laboratories. Their use would certainly offer drug companies faster test turnaround times to accommodate the aggressive deadlines for manufacturing processes and product release. Some rapid methods also offer the possibility for real-time microbial analyses, enabling management to respond to microbial contamination events in a more timely fashion, and can provide cost savings and higher efficiencies in quality control testing laboratories. Despite the many proven business and quality benefits and the fact that the FDA's initiative to promote the use of process analytical technology (PAT) includes rapid microbial methods, pharmaceutical and biopharmaceutical industries have been somewhat slow to embrace alternative microbial methodologies for several reasons. The major reason is that the bioburden counts detected by the incubation method and rapid assay are greatly divergent. 　The use of rapid methods is a dynamic field in applied microbiology and one that has gained increased attention nationally and internationally over time. This topic has been extensively addressed at conferences and in published documents around the world. More recently, the use of alternative methods for control of the microbiological quality of pharmaceutical products and materials used in pharmaceutical production has been addressed by the compendia in an attempt to facilitate implementation of these technologies by pharmaceutical companies. The author presents some of the rapid method technologies under evaluation or in use by pharmaceutical microbiologists and the current status of the implementation of alternative microbial methods.

Rapid detection, characterization, and enumeration of foodborne pathogens.

PubMed

Hoorfar, J

2011-11-01

As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based on the author's scientific work that has contributed with the following new developments to this field: (i) serologic tests for large-scale screening, surveillance, or eradication programs, (ii) same-day detection of Salmonella that otherwise was considered as difficult to achieve, (iii) pathogen enumeration following a short log-phase enrichment, (iv) detection of foodborne pathogens in air samples, and finally (v) biotracing of pathogens based on mathematical modeling, even in the absence of isolate. Rapid methods are discussed in a broad global health perspective, international food supply, and for improvement of quantitative microbial risk assessments. The need for quantitative sample preparation techniques, culture-independent, metagenomic-based detection, online monitoring, a global validation infrastructure has been emphasized. The cost and ease of use of rapid assays remain challenging obstacles to surmount. © 2011 The Author. APMIS © 2011 APMIS.

Association of plasmid-mediated quinolone resistance and virulence markers in Escherichia coli isolated from water.

PubMed

Mendonça, Nuno; Ramalho, Joana; Vieira, Pedro; Da Silva, Gabriela Jorge

2012-06-01

This work aimed to investigate the association of the carriage of plasmid-mediated quinolone resistance (PMQR) genes, the virulence potential encoded in pathogenicity islands (PAIs) and the phylogenetic background in Escherichia coli strains isolated from waters of diverse origin. Antimicrobial susceptibilities were determined by the disc diffusion method. Screening for PMQR (qnr, aac(6')-Ib-variant and qepA) genes, PAIs and the determination of phylogroup was performed by PCR. Nineteen percent of strains were resistant to nalidixic acid, 11% to ciprofloxacin and 5% to gentamicin. qnrA was the only PMQR detected in 16% of strains, susceptible to quinolones and grouped in phylogenetic lineage B1. Sixty-seven percent of the isolates were assigned to the less-virulent groups A and B1. PAIs IV(536) and II(CFT073) were detected in 16 and 3% of the isolates, respectively. All PAIs were detected in the phylogroups D and B1. The presence of PAIs in isolates from waters may represent an increased risk for public health, as they were isolated from samples collected from surface and drinking waters. As E. coli is an important indicator of microbiological water quality, and also a potential pathogen, routine analysis for its detection could be complemented by screening for virulence factors and antimicrobial genes.

Cholinesterase inhibitor (Altenuene) from an endophytic fungus Alternaria alternata: optimization, purification and characterization.

PubMed

Bhagat, J; Kaur, A; Kaur, R; Yadav, A K; Sharma, V; Chadha, B S

2016-10-01

The aim of this study was to screen endophytic fungi isolated from Vinca rosea for their potential to produce acetylcholinesterase (AChE) inhibitors. Endophytic fungi isolated from V. rosea (Catharanthus roseus), were screened for AChE inhibitor production using Ellman's method. Maximum inhibition against AChE (78%) was observed in an isolate VS-10, identified to be Alternaria alternata on morphological and molecular basis. The isolate also inhibited butyrylcholinesterase (73%). Significant increase (1·3 fold) was achieved after optimization of process parameters using one variable at time approach. The inhibitor was purified using chromatographic techniques. The structure elucidation of the inhibitor was carried out using spectroscopic techniques and was identified to be 'altenuene'. The purified inhibitor possessed antioxidant potential as revealed by dot blot assay. The insecticidal potential of purified inhibitor was evaluated by feeding Spodoptora litura on diet amended with inhibitor. It evinced significant larval mortality. Endophytic A. alternata can serve as a source of dual cholinesterase inhibitor 'altenuene' with significant antioxidant and insecticidal activity. This is the first report on acetylcholinestearse inhibitory activity of altenuene. Alternaria alternata has the potential to produce a dual ChE inhibitor with antioxidant activity useful in the treatment of neurodegenerative disorders and in agriculture as biocontrol agent. © 2016 The Society for Applied Microbiology.

Microbiological methods for surveillance of carrier status of multiresistant bacteria.

PubMed

Oteo, Jesús; Bou, Germán; Chaves, Fernando; Oliver, Antonio

2017-12-01

The presence of colonised patients is one of the main routes for the spread of multiresistant bacteria, and its containment is a clinical and public health priority. Surveillance studies are essential for early detection of colonisation by these bacteria. This article discusses the different microbiological methods, both based on culturing and molecular methods, for detection of carriers of multiresistant bacteria. Those species with a high clinical/epidemiological impact or generating therapeutic difficulties are included: Methicillin-resistant Staphylococcus aureus, Enterococcus spp. resistant to glycopeptides, enterobacteriaceae producing extended spectrum β-lactamases and plasmid-mediated AmpC, carbapenemases producing enterobacteriaceae, Acinetobacter baumannii and multiresistant Pseudomonas aeruginosa. The information in this document should be considered as a structure matrix to be tailored to the specific needs of each centre. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Real-Time PCR in Clinical Microbiology: Applications for Routine Laboratory Testing

PubMed Central

Espy, M. J.; Uhl, J. R.; Sloan, L. M.; Buckwalter, S. P.; Jones, M. F.; Vetter, E. A.; Yao, J. D. C.; Wengenack, N. L.; Rosenblatt, J. E.; Cockerill, F. R.; Smith, T. F.

2006-01-01

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory. PMID:16418529

Providing a sound habitat for man in space

NASA Astrophysics Data System (ADS)

Stranger-Johannessen, Maria

Microbiological growth on materials in an indoor environment contributes to the well known "sick building syndrome". The inhabitants' health and well-being is affected by injurious vapours and odours given off to the air. This is particularly pronounced in new and better tightened houses with unconventional building materials and wider employment of air conditioning. The European Space Agency has recognized the problems to be expected in a totally closed and self-supported long-term habitat and has induced work on the selection of materials, resistant to microbiological growth, and on other microbial contamination control measures. Requirements and procedures are being established as a basis for the microbiological cleanliness of the manned space environment and for the avoidance of microbiological growth on materials and equipment. Methods are being developed, suitable for testing and predicting the resistivity to microbiological growth of materials to be used in long-term space habitats.

Evaluation of two recommended disinfection methods for cleaning cloths used in food services of southern Brazil

PubMed Central

Bartz, Sabrina; Tondo, Eduardo Cesar

2013-01-01

In the State of Rio Grande do Sul (RS), Southern Brazil, a good manufacturing practices regulation was published recommending two disinfection methods for cleaning cloths used in food services. The aim of the present study was to evaluate the efficacy of those methods. Cleaning cloths were sampled without prior notice at food services, on common working days. For the analyses, the cloths were divided in two sub-samples, being one of them microbiologically analyzed. The second sub-sample was further divided in two pieces and submitted to hand washing for two minutes. After that, one piece was boiled in water for 15 min and the other one was soaked in a 200 ppm sodium hypochlorite solution for 15 min. Both pieces of cloth were submitted to microbiological analyses. Cleaning cloths presented total aerobic mean counts of 6.9 ± 6.7 log/cm2. All cleaning cloths presented coliform contamination, and 40% demonstrated mean counts of 6.2 ± 5.6 log/cm2. Presumptive S. aureus mean counts of 5.5 ± 4.9 log/cm2 were found. No statistic correlation was observed among the number of meals served daily in the food services and the microbiological contamination levels. After washing and disinfection, microbiological counts were significantly (p < 0.05) reduced by both methods, achieving an approximately 5 log reduction. The reductions achieved by the sodium hypochlorite soaking method and the boiling method were not significantly different. Thus, it was possible to conclude that both recommended methods were suitable to disinfect cleaning cloths used in food services. PMID:24516443

Evaluation of two recommended disinfection methods for cleaning cloths used in food services of southern Brazil.

PubMed

Bartz, Sabrina; Tondo, Eduardo Cesar

2013-01-01

In the State of Rio Grande do Sul (RS), Southern Brazil, a good manufacturing practices regulation was published recommending two disinfection methods for cleaning cloths used in food services. The aim of the present study was to evaluate the efficacy of those methods. Cleaning cloths were sampled without prior notice at food services, on common working days. For the analyses, the cloths were divided in two sub-samples, being one of them microbiologically analyzed. The second sub-sample was further divided in two pieces and submitted to hand washing for two minutes. After that, one piece was boiled in water for 15 min and the other one was soaked in a 200 ppm sodium hypochlorite solution for 15 min. Both pieces of cloth were submitted to microbiological analyses. Cleaning cloths presented total aerobic mean counts of 6.9 ± 6.7 log/cm(2). All cleaning cloths presented coliform contamination, and 40% demonstrated mean counts of 6.2 ± 5.6 log/cm(2). Presumptive S. aureus mean counts of 5.5 ± 4.9 log/cm(2) were found. No statistic correlation was observed among the number of meals served daily in the food services and the microbiological contamination levels. After washing and disinfection, microbiological counts were significantly (p < 0.05) reduced by both methods, achieving an approximately 5 log reduction. The reductions achieved by the sodium hypochlorite soaking method and the boiling method were not significantly different. Thus, it was possible to conclude that both recommended methods were suitable to disinfect cleaning cloths used in food services.

[Frequency of Candida in root canals of teeth with primary and persistent endodontic infections].

PubMed

Bernal-Treviño, Angel; González-Amaro, Ana María; Méndez González, Verónica; Pozos-Guillen, Amaury

Microbiological identification in endodontic infections has focused mainly on bacteria without giving much attention to yeasts, which, due to their virulence factors, can affect the outcomes of root canal treatment. To determine the frequency of Candida in anaerobic conditions in root canals with primary and persistent endodontic infection, as well as to evaluate a microbiological sampling method using aspiration compared to the traditional absorption method with paper points. Fifty microbiological samples were obtained from teeth of 47 patients requiring endodontic treatments, due to either primary or persistent infections. Two microbiological sampling methods were used: an aspiration method, and the traditional paper point absorption method. In each of these methods, two types of medium were used (M 1 -M 4 ). Samples were cultured under anaerobic conditions until reaching 0.5 McFarland turbidity, and then inoculated on Sabouraud dextrose, as well as on anaerobic enriched blood agar plates. Macroscopic and microscopic observations of the colonies were performed. The germ-tube test, growth on CHROMagar, and biochemical identification were performed on the isolated yeasts. Fungal infection was found in 18 (36%) samples out of the 50 teeth evaluated. In the 18 samples positive for fungal infection, 15 out of 36 (41.6%) teeth were taken from a primary infection, and 3 out of 14 (21.4%) from a persistent infection. The aspiration method using Sabouraud dextrose medium recovered a greater diversity of species. Yeasts frequency was higher in teeth with primary infections compared to teeth with persistent infections. The predominant yeast species was Candida albicans. The aspirating sampling method was more efficient in the recovery of Candida isolates than the traditional absorption method. Copyright © 2018 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure.

PubMed

Pinot, C; Deredjian, A; Nazaret, S; Brothier, E; Cournoyer, B; Segonds, C; Favre-Bonté, S

2011-11-01

Aim of the study is to identify accurately Stenotrophomonas maltophilia isolates recovered from environmental and clinical samples. Recovery of Sten. maltophilia-like isolates from soil samples using the vancomycin, imipenem, amphotericin B (VIA) selective agar medium enabled distinction of various morphotype colonies. A set of soil and clinical isolates was tested for species identification using different methods. 16S rDNA analyses showed the dark green with a blue halo morphotype to be typical Sten. maltophilia strains. The API-20NE, Vitek-2 and Biolog phenotypic analyses typically used for the identification of clinical isolates did not perform well on these soil isolates. The species-specific PCR screening targeting Sten. maltophilia 23S rDNA and the multiplex smeD/ggpS PCR, differentiating Sten. maltophilia from Stenotrophomonas rhizophila, were tested for improvement of these identification schemes. The latter multiplex PCR identified all isolates tested in this study, whatever be their origin. Isolation on VIA medium and confirmation of Sten. maltophilia species membership by smeD PCR is proposed to identify environmental and clinical isolates of Sten. maltophilia. The proposed approach enables isolation and identification of Sten. maltophilia from different environments in an easy and rapid way. This approach will be useful to accurately manage studies on the abundance and distribution of Sten. maltophilia in hospital and nonhospital environments. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Antimicrobial activity of wild mushroom extracts against clinical isolates resistant to different antibiotics.

PubMed

Alves, M J; Ferreira, I C F R; Martins, A; Pintado, M

2012-08-01

This work aimed to screen the antimicrobial activity of aqueous methanolic extracts of 13 mushroom species, collected in Bragança, against several clinical isolates obtained in Hospital Center of Trás-os-Montes and Alto Douro, Portugal. Microdilution method was used to determine the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC). MIC results showed that Russula delica and Fistulina hepatica extracts inhibited the growth of gram-negative (Escherichia coli, Morganella morganni and Pasteurella multocida) and gram-positive (Staphylococcus aureus, MRSA, Enterococcus faecalis, Listeria monocytogenes, Streptococcus agalactiae and Streptococcus pyogenes) bacteria. A bactericide effect of both extracts was observed in Past. multocida, Strep. agalactiae and Strep. pyogenes with MBC of 20, 10 and 5 mg ml⁻¹, respectively. Lepista nuda extract exhibited a bactericide effect upon Past. multocida at 5 mg ml⁻¹ and inhibited Proteus mirabilis at 20 mg ml⁻¹. Ramaria botrytis extract showed activity against Enterococcus faecalis and L. monocytogenes, being bactericide for Past. multocida, Strep. agalactiae (MBCs 20 mg ml⁻¹) and Strep. pyogenes (MBC 10 mg ml⁻¹). Leucopaxillus giganteus extract inhibited the growth of E. coli and Pr. mirabilis, being bactericide for Past. multocida, Strep. pyogenes and Strep. agalactiae. Fistulina hepatica, R. botrytis and R. delica are the most promising species as antimicrobial agents. Mushroom extracts could be an alternative as antimicrobials against pathogenic micro-organisms resistant to conventional treatments. © 2012The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Characterisation of STEC and other diarrheic E. coli isolated on CHROMagar™STEC at a tertiary referral hospital, Cape Town.

PubMed

Kalule, John Bosco; Keddy, Karen H; Nicol, Mark P

2018-06-08

Shiga toxin producing E. coli (STEC) is an emerging zoonotic pathogen that can cause acute renal failure, especially in children. Clinical microbiology laboratories may fail to detect STEC and other diarrhoeic E. coli unless purposive rigorous screening procedures are followed using appropriate diagnostic technology; CHROMagar™STEC has rarely been used for isolation of African diarrhoeic E. coli hence characteristics of isolates on this medium are not yet fully understood. This study aimed to determine the prevalence and characteristics of STEC and other diarrhoeic E. coli isolated on CHROMagar™STEC from stool samples submitted to the microbiology laboratory of a South African public sector tertiary care hospital. In total, 733 stool samples were tested. Of these, 4.5% (33/733) possessed diarrhoeic E. coli. Of the diarrheic E. coli, 5/33 (15.2%) were STEC, 15/33 (45.5%) EAggEC, 6/33 (18.2%) atypical EPEC, 5/33 (15.2%) typical EPEC, and 1/33 (3%) DAEC. None of the STEC isolates had been identified by routine testing (based on using sorbitol media to test for E. coli O157: H7 strains and not the other STEC) in the laboratory. Of the 33 strains, 55% (95% CI = 40.8-72.7) showed resistance to ampicillin. CHROMagar™STEC enabled detection of tellurite - resistant diarrhoeic E. coli that would be missed using routine methods. Further studies are needed to determine the proportion and characteristics of those which might have been missed using this approach.

Microbiological Characterization of the International Space Station Water Processor Assembly External Filter Assembly S/N 01

NASA Technical Reports Server (NTRS)

Weir, Natalee; Wilson, Mark; Yoets, Airan; Yoets, Airan; Molina, Thomas; Bruce, Rebekah; Sitler, Glenn; Carter, Layne

2012-01-01

The External Filter Assembly (EFA) S/N 01 is a mesh screen filter with a pore size of approximately 300 micron that was installed in the International Space Station (ISS) Water Processor Assembly (WPA) between the Waste Tank and the Mostly Liquid Separator (MLS) on February 11, 2010 to protect clearances in the MLS solenoid valve SV_1121_3. A removal & replacement of the EFA Filter was performed on March 22, 2011 in response to increasing pressure across the Waste Tank solenoid valve SV_1121_1 and the EFA Filter. The EFA Filter was returned on ULF6 and received in the Boeing Huntsville Laboratory on June 13, 2011. The filter was aseptically removed from the housing, and the residual water was collected for enumeration and identification of bacteria and fungi. Swab samples of the filter surface were also collected for microbiological enumeration and identification. Sample analyses were performed by Boeing Huntsville Laboratory and NASA Johnson Space Center Microbiology for comparison. Photographic documentation of the EFA filter was performed using a stereo microscope and environmental scanning electron microscope. This paper characterizes the amount and types of microorganisms on the filter surface and in the residual water from the filter housing following 1 year of utilization in the ISS WPA.

Microbiological quality of spinach irrigated with reclaimed wastewater and roof-harvest water

USDA-ARS?s Scientific Manuscript database

Aims: The effect of reclaimed wastewater (RCW) and roof-harvest rainwater (RHW) on microbiological quality of irrigated spinach was investigated. Methods and Results: Spinach grown in controlled environment chamber was irrigated by RCW, RHW, or creek water (CW; control water) for four weeks, and th...

Introduction of Molecular Methods into a Food Microbiology Curriculum

ERIC Educational Resources Information Center

Pleitner, Aaron M.; Hammons, Susan R.; McKenzie, Emily; Cho, Young-Hee; Oliver, Haley F.

2014-01-01

Maintaining current, relevant curriculum in undergraduate Food Microbiology courses is essential for training future experts in food quality and safety. Having an understanding of the fundamental techniques (for example, polymerase chain reaction [PCR]) that are used in the food industry and regulatory agencies is critical for students entering…

Agreement between gastrointestinal panel testing and standard microbiology methods for detecting pathogens in suspected infectious gastroenteritis: Test evaluation and meta-analysis in the absence of a reference standard.

PubMed

Freeman, Karoline; Tsertsvadze, Alexander; Taylor-Phillips, Sian; McCarthy, Noel; Mistry, Hema; Manuel, Rohini; Mason, James

2017-01-01

Multiplex gastrointestinal pathogen panel (GPP) tests simultaneously identify bacterial, viral and parasitic pathogens from the stool samples of patients with suspected infectious gastroenteritis presenting in hospital or the community. We undertook a systematic review to compare the accuracy of GPP tests with standard microbiology techniques. Searches in Medline, Embase, Web of Science and the Cochrane library were undertaken from inception to January 2016. Eligible studies compared GPP tests with standard microbiology techniques in patients with suspected gastroenteritis. Quality assessment of included studies used tailored QUADAS-2. In the absence of a reference standard we analysed test performance taking GPP tests and standard microbiology techniques in turn as the benchmark test, using random effects meta-analysis of proportions. No study provided an adequate reference standard with which to compare the test accuracy of GPP and conventional tests. Ten studies informed a meta-analysis of positive and negative agreement. Positive agreement across all pathogens was 0.93 (95% CI 0.90 to 0.96) when conventional methods were the benchmark and 0.68 (95% CI: 0.58 to 0.77) when GPP provided the benchmark. Negative agreement was high in both instances due to the high proportion of negative cases. GPP testing produced a greater number of pathogen-positive findings than conventional testing. It is unclear whether these additional 'positives' are clinically important. GPP testing has the potential to simplify testing and accelerate reporting when compared to conventional microbiology methods. However the impact of GPP testing upon the management, treatment and outcome of patients is poorly understood and further studies are needed to evaluate the health economic impact of GPP testing compared with standard methods. The review protocol is registered with PROSPERO as CRD42016033320.

A review of microbiology service learning.

PubMed

Webb, Ginny

2017-02-01

Service learning is a teaching method that incorporates community engagement into the curriculum of a course. Service learning is becoming increasingly popular on college campuses and across disciplines. Studies have shown many benefits to service learning for the students and the community they serve. Service learning has been incorporated into science courses, including microbiology. This review will address the benefits to service learning and provide an overview of the various types of service-learning projects that have been completed in microbiology courses. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ebselen, a Small-Molecule Capsid Inhibitor of HIV-1 Replication.

PubMed

Thenin-Houssier, Suzie; de Vera, Ian Mitchelle S; Pedro-Rosa, Laura; Brady, Angela; Richard, Audrey; Konnick, Briana; Opp, Silvana; Buffone, Cindy; Fuhrmann, Jakob; Kota, Smitha; Billack, Blase; Pietka-Ottlik, Magdalena; Tellinghuisen, Timothy; Choe, Hyeryun; Spicer, Timothy; Scampavia, Louis; Diaz-Griffero, Felipe; Kojetin, Douglas J; Valente, Susana T

2016-04-01

The human immunodeficiency virus type 1 (HIV-1) capsid plays crucial roles in HIV-1 replication and thus represents an excellent drug target. We developed a high-throughput screening method based on a time-resolved fluorescence resonance energy transfer (HTS-TR-FRET) assay, using the C-terminal domain (CTD) of HIV-1 capsid to identify inhibitors of capsid dimerization. This assay was used to screen a library of pharmacologically active compounds, composed of 1,280in vivo-active drugs, and identified ebselen [2-phenyl-1,2-benzisoselenazol-3(2H)-one], an organoselenium compound, as an inhibitor of HIV-1 capsid CTD dimerization. Nuclear magnetic resonance (NMR) spectroscopic analysis confirmed the direct interaction of ebselen with the HIV-1 capsid CTD and dimer dissociation when ebselen is in 2-fold molar excess. Electrospray ionization mass spectrometry revealed that ebselen covalently binds the HIV-1 capsid CTD, likely via a selenylsulfide linkage with Cys198 and Cys218. This compound presents anti-HIV activity in single and multiple rounds of infection in permissive cell lines as well as in primary peripheral blood mononuclear cells. Ebselen inhibits early viral postentry events of the HIV-1 life cycle by impairing the incoming capsid uncoating process. This compound also blocks infection of other retroviruses, such as Moloney murine leukemia virus and simian immunodeficiency virus, but displays no inhibitory activity against hepatitis C and influenza viruses. This study reports the use of TR-FRET screening to successfully identify a novel capsid inhibitor, ebselen, validating HIV-1 capsid as a promising target for drug development. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

A simple phenotypic method for screening of MCR-1-mediated colistin resistance.

PubMed

Coppi, M; Cannatelli, A; Antonelli, A; Baccani, I; Di Pilato, V; Sennati, S; Giani, T; Rossolini, G M

2018-02-01

To evaluate a novel method, the colistin-MAC test, for phenotypic screening of acquired colistin resistance mediated by transferable mcr-1 resistance determinants, based on colistin MIC reduction in the presence of dipicolinic acid (DPA). The colistin-MAC test consists in a broth microdilution method, in which colistin MIC is tested in the absence or presence of DPA (900 μg/mL). Overall, 74 colistin-resistant strains of Enterobacteriaceae (65 Escherichia coli and nine other species), including 61 strains carrying mcr-1-like genes and 13 strains negative for mcr genes, were evaluated with the colistin-MAC test. The presence of mcr-1-like and mcr-2-like genes was assessed by real-time PCR and end-point PCR. For 20 strains, whole-genome sequencing data were also available. A ≥8-fold reduction of colistin MIC in the presence of DPA was observed with 59 mcr-1-positive strains, including 53 E. coli of clinical origin, three E. coli transconjugants carrying MCR-1-encoding plasmids, one Enterobacter cloacae complex and two Citrobacter spp. Colistin MICs were unchanged, increased or at most reduced by twofold with the 13 mcr-negative colistin-resistant strains (nine E. coli and four Klebsiella pneumoniae), but also with two mcr-1-like-positive K. pneumoniae strains. The colistin-MAC test could be a simple phenotypic test for presumptive identification of mcr-1-positive strains among isolates of colistin-resistant E. coli, based on a ≥8-fold reduction of colistin MIC in the presence of DPA. Evaluation of the test with a larger number of strains, species and mcr-type resistance determinants would be of interest. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring

PubMed Central

Vierheilig, J.; Savio, D.; Ley, R. E.; Mach, R. L.; Farnleitner, A. H.

2016-01-01

The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multicompartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems. PMID:26606090

Quantification of the level of fat-soluble vitamins in feed based on the novel microemulsion electrokinetic chromatography (MEEKC) method.

PubMed

Olędzka, Ilona; Kowalski, Piotr; Bałuch, Alicja; Bączek, Tomasz; Paradziej-Łukowicz, Jolanta; Taciak, Marcin; Pastuszewska, Barbara

2014-02-01

Simultaneous quantification of liposoluble vitamins is not a new area of interest, since these compounds co-determine the nutritional quality of food and feed, a field widely explored in the human and animal diet. However, the development of appropriate methods is still a matter of concern, especially when the vitamin composition is highly complex, as is the case with feed designated for laboratory animals, representing a higher health and microbiological status. A method combining microemulsion electrokinetic chromatography (MEEKC) with liquid-liquid extraction was developed for the determination of four fat-soluble vitamins in animal feed. A separation medium consisting of 25 mmol L⁻¹ phosphate buffer (pH 2.5), 2-propanol, 1-butanol, sodium dodecyl sulfate and octane allowed the simultaneous determination of vitamins A, D, E and K within a reasonable time of 25 min. The polarity of the separation voltage was reversed in view of the strongly suppressed electro-osmotic flow, and the applied voltage was set at 12 kV. The fat-soluble vitamins were separated in the order of decreasing hydrophobicity. It was proved that the proposed MEEKC method was sufficiently specific and sensitive for screening fat-soluble vitamins in animal feed samples after their sterilization. © 2013 Society of Chemical Industry.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

PubMed

Alcaide, F; Amlerová, J; Bou, G; Ceyssens, P J; Coll, P; Corcoran, D; Fangous, M-S; González-Álvarez, I; Gorton, R; Greub, G; Hery-Arnaud, G; Hrábak, J; Ingebretsen, A; Lucey, B; Marekoviċ, I; Mediavilla-Gradolph, C; Monté, M R; O'Connor, J; O'Mahony, J; Opota, O; O'Reilly, B; Orth-Höller, D; Oviaño, M; Palacios, J J; Palop, B; Pranada, A B; Quiroga, L; Rodríguez-Temporal, D; Ruiz-Serrano, M J; Tudó, G; Van den Bossche, A; van Ingen, J; Rodriguez-Sanchez, B

2018-06-01

The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Greeson, Phillip E.; Ehlke, T.A.; Irwin, G.A.; Lium, B.W.; Slack, K.V.

1977-01-01

Chapter A4 contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 discusses biological sampling and sampling statistics. The statistical procedures are accompanied by examples. Part 2 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity, and bioassays. Each method is summarized, and the application, interferences, apparatus, reagents, collection, analysis, calculations, reporting of results, precision and references are given. Part 3 consists of a glossary. Part 4 is a list of taxonomic references.

Competency assessment of microbiology medical laboratory technologists in Ontario, Canada.

PubMed

Desjardins, Marc; Fleming, Christine Ann

2014-08-01

Accreditation in Ontario, Canada, requires that licensed clinical laboratories participate in external quality assessment (also known as proficiency testing) and perform competency evaluation of their staff. To assess the extent of ongoing competency assessment practices, the Quality Management Program--Laboratory Services (QMP-LS) Microbiology Committee surveyed all 112 licensed Ontario microbiology laboratories. The questionnaire consisted of a total of 21 questions that included yes/no, multiple-choice, and short-answer formats. Participants were asked to provide information about existing programs, the frequency of testing, what areas are evaluated, and how results are communicated to the staff. Of the 111 responding laboratories, 6 indicated they did not have a formal evaluation program since they perform only limited bacteriology testing. Of the remaining 105 respondents, 87% perform evaluations at least annually or every 2 years, and 61% include any test or task performed, whereas 16% and 10% focus only on problem areas and high-volume complex tasks, respectively. The most common methods of evaluation were review of external quality assessment (EQA) challenges, direct observation, and worksheet review. With the exception of one participant, all communicate results to staff, and most take remedial action to correct the deficiencies. Although most accredited laboratories have a program to assess the ongoing competency of their staff, the methods used are not standardized or consistently applied, indicating that there is room for improvement. The survey successfully highlighted potential areas for improvement and allowed the QMP-LS Microbiology Committee to provide guidance to Ontario laboratories for establishing or improving existing microbiology-specific competency assessment programs. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Microbiological methods for the water recovery systems test, revision 1.1

NASA Technical Reports Server (NTRS)

Rhoads, Tim; Kilgore, M. V., Jr.; Mikell, A. T., Jr.

1990-01-01

Current microbiological parameters specified to verify microbiological quality of Space Station Freedom water quality include the enumeration of total bacteria, anaerobes, aerobes, yeasts and molds, enteric bacteria, gram positives, gram negatives, and E. coli. In addition, other parameters have been identified as necessary to support the Water Recovery Test activities to be conducted at the NASA/MSFC later this year. These other parameters include aerotolerant eutrophic mesophiles, legionellae, and an additional method for heterotrophic bacteria. If inter-laboratory data are to be compared to evaluate quality, analytical methods must be eliminated as a variable. Therefore, each participating laboratory must utilize the same analytical methods and procedures. Without this standardization, data can be neither compared nor validated between laboratories. Multiple laboratory participation represents a conservative approach to insure quality and completeness of data. Invariably, sample loss will occur in transport and analyses. Natural variance is a reality on any test of this magnitude and is further enhanced because biological entities, capable of growth and death, are specific parameters of interest. The large variation due to the participation of human test subjects has been noted with previous testing. The resultant data might be dismissed as 'out of control' unless intra-laboratory control is included as part of the method or if participating laboratories are not available for verification. The purpose of this document is to provide standardized laboratory procedures for the enumeration of certain microorganisms in water and wastewater specific to the water recovery systems test. The document consists of ten separate cultural methods and one direct count procedure. It is not intended nor is it implied to be a complete microbiological methods manual.

Estimation of the POD function and the LOD of a qualitative microbiological measurement method.

PubMed

Wilrich, Cordula; Wilrich, Peter-Theodor

2009-01-01

Qualitative microbiological measurement methods in which the measurement results are either 0 (microorganism not detected) or 1 (microorganism detected) are discussed. The performance of such a measurement method is described by its probability of detection as a function of the contamination (CFU/g or CFU/mL) of the test material, or by the LOD(p), i.e., the contamination that is detected (measurement result 1) with a specified probability p. A complementary log-log model was used to statistically estimate these performance characteristics. An intralaboratory experiment for the detection of Listeria monocytogenes in various food matrixes illustrates the method. The estimate of LOD50% is compared with the Spearman-Kaerber method.

Evaluation of the performance of the IQ-check kits and the USDA microbiology laboratory guidebook methods for detection of Shiga Toxin-Producing E. coli (STEC) and STEC and Salmonella simultaneously in ground beef

USDA-ARS?s Scientific Manuscript database

Aims: To evaluate the performance of the IQ-Check kits and the USDA Microbiology Laboratory Guidebook (MLG) methods for detection of the top 7 Shiga toxin-producing E. coli (STEC) (O157:H7, O26, O45, O103, O111, O121, and O145) in ground beef and both STEC and Salmonella in co-inoculated samples. M...

Are the defined substrate-based methods adequate to determine the microbiological quality of natural recreational waters?

PubMed

Valente, Marta Sofia; Pedro, Paulo; Alonso, M Carmen; Borrego, Juan J; Dionísio, Lídia

2010-03-01

Monitoring the microbiological quality of water used for recreational activities is very important to human public health. Although the sanitary quality of recreational marine waters could be evaluated by standard methods, they are time-consuming and need confirmation. For these reasons, faster and more sensitive methods, such as the defined substrate-based technology, have been developed. In the present work, we have compared the standard method of membrane filtration using Tergitol-TTC agar for total coliforms and Escherichia coli, and Slanetz and Bartley agar for enterococci, and the IDEXX defined substrate technology for these faecal pollution indicators to determine the microbiological quality of natural recreational waters. ISO 17994:2004 standard was used to compare these methods. The IDEXX for total coliforms and E. coli, Colilert, showed higher values than those obtained by the standard method. Enterolert test, for the enumeration of enterococci, showed lower values when compared with the standard method. It may be concluded that more studies to evaluate the precision and accuracy of the rapid tests are required in order to apply them for routine monitoring of marine and freshwater recreational bathing areas. The main advantages of these methods are that they are more specific, feasible and simpler than the standard methodology.

Colloquium and Report on Systems Microbiology: Beyond Microbial Genomics

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

Merry R. Buckley

The American Academy of Microbiology convened a colloquium June 4-6, 2004 to confer about the scientific promise of systems microbiology. Participants discussed the power of applying a systems approach to the study of biology and to microbiology in particular, specifics about current research efforts, technical bottlenecks, requirements for data acquisition and maintenance, educational needs, and communication issues surrounding the field. A number of recommendations were made for removing barriers to progress in systems microbiology and for improving opportunities in education and collaboration. Systems biology, as a concept, is not new, but the recent explosion of genomic sequences and related datamore » has revived interest in the field. Systems microbiology, a subset of systems biology, represents a different approach to investigating biological systems. It attempts to examine the emergent properties of microorganisms that arise from the interplay of genes, proteins, other macromolecules, small molecules, organelles, and the environment. It is these interactions, often nonlinear, that lead to the emergent properties of biological systems that are generally not tractable by traditional approaches. As a complement to the long-standing trend toward reductionism, systems microbiology seeks to treat the organism or community as a whole, integrating fundamental biological knowledge with genomics, metabolomics, and other data to create an integrated picture of how a microbial cell or community operates. Systems microbiology promises not only to shed light on the activities of microbes, but will also provide biology the tools and approaches necessary for achieving a better understanding of life and ecosystems. Microorganisms are ideal candidates for systems biology research because they are relatively easy to manipulate and because they play critical roles in health, environment, agriculture, and energy production. Potential applications of systems microbiology research range from improvements in the management of bacterial infections to the development of commercial-scale microbial hydrogen generation. A number of technical challenges must be met to realize the potential of systems microbiology. Development of a new, comprehensive systems microbiology database that would be available to the entire research community was identified as the single most critical need. Other challenges include difficulties in measuring single-cell parameters, limitations in identifying and measuring metabolites and other products, the inability to cultivate diverse microbes, limits on data accessibility, computational limitations associated with data integration, the lack of sufficient functional gene annotations, needs for quantitative proteomics, and the inapplicability of current high throughput methods to all areas of systems microbiology. Difficulties have also been encountered in acquiring the necessary data, assuring the quality of that data, and in making data available to the community in a useful format. Problems with data quality assurance and data availability could be partially offset by launching a dedicated systems microbiology database. To be of greatest value to the field, a database should include systems data from all levels of analysis, including sequences, microarray data, proteomics data, metabolite measurements, data on protein-protein or protein-nucleic interactions, carbohydrate and small RNA profiles, information on cell surface markers, and appropriate supporting data. Regular updates of these databases and adherence to agreed upon data format standards are critical to the success of these resources. It was recommended that educational requirements for undergraduate and graduate students in microbiology be amended to better prepare the next generation of researchers for the quantitative requirements of applying systems microbiology methods in their work. Systems microbiology research is too complex to be the sole property of any single academic discipline. The contributions of microbiologists, computer scientists, control theorists, biostatisticians, and others are all required to move the field forward. Since research in systems microbiology demands the contributions of a diverse array of professionals, collaboration across disciplines and national borders should be strongly encouraged by research bodies and funding agencies. Although the details of systems microbiology research are probably not of interest to the average individual, the potential applications and benefits of these types of investigations should be conveyed to the lay public.« less

Lysinibacillus fusiformis M5 Induces Increased Complexity in Bacillus subtilis 168 Colony Biofilms via Hypoxanthine.

PubMed

Gallegos-Monterrosa, Ramses; Kankel, Stefanie; Götze, Sebastian; Barnett, Robert; Stallforth, Pierre; Kovács, Ákos T

2017-11-15

In recent years, biofilms have become a central subject of research in the fields of microbiology, medicine, agriculture, and systems biology, among others. The sociomicrobiology of multispecies biofilms, however, is still poorly understood. Here, we report a screening system that allowed us to identify soil bacteria which induce architectural changes in biofilm colonies when cocultured with Bacillus subtilis We identified the soil bacterium Lysinibacillus fusiformis M5 as an inducer of wrinkle formation in B. subtilis colonies mediated by a diffusible signaling molecule. This compound was isolated by bioassay-guided chromatographic fractionation. The elicitor was identified to be the purine hypoxanthine using mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. We show that the induction of wrinkle formation by hypoxanthine is not dependent on signal recognition by the histidine kinases KinA, KinB, KinC, and KinD, which are generally involved in phosphorylation of the master regulator Spo0A. Likewise, we show that hypoxanthine signaling does not induce the expression of biofilm matrix-related operons epsABCDEFGHIJKLMNO and tasA-sipW-tapA Finally, we demonstrate that the purine permease PbuO, but not PbuG, is necessary for hypoxanthine to induce an increase in wrinkle formation of B. subtilis biofilm colonies. Our results suggest that hypoxanthine-stimulated wrinkle development is not due to a direct induction of biofilm-related gene expression but rather is caused by the excess of hypoxanthine within B. subtilis cells, which may lead to cell stress and death. IMPORTANCE Biofilms are a bacterial lifestyle with high relevance regarding diverse human activities. Biofilms can be beneficial, for instance, in crop protection. In nature, biofilms are commonly found as multispecies communities displaying complex social behaviors and characteristics. The study of interspecies interactions will thus lead to a better understanding and use of biofilms as they occur outside laboratory conditions. Here, we present a screening method suitable for the identification of multispecies interactions and showcase L. fusiformis as a soil bacterium that is able to live alongside B. subtilis and modify the architecture of its biofilms. Copyright © 2017 American Society for Microbiology.

Public Health Response to US Cases of Candida auris, a Globally Emerging, Multidrug-Resistant Yeast, 2013–2017

PubMed Central

Tsay, Sharon; Welsh, Rory M; Adams, Eleanor H; Chow, Nancy A; Gade, Lalitha; Berkow, Elizabeth L; Lutterloh, Emily; Quinn, Monica; Chaturvedi, Sudha; Fernandez, Rafael; Giardina, Rosalie; Greenko, Jane; Southwick, Karen; Kerins, Janna L; Black, Stephanie; Kemble, Sarah K; Barrett, Patricia M; Greeley, Rebecca; Barton, Kerri; Shannon, Dj; Kallen, Alexander; Shugart, Alicia; Litvintseva, Anastasia P; Lockhart, Shawn; Chiller, Tom; Jackson, Brendan R; Vallabhaneni, Snigdha

2017-01-01

Abstract Background Candida auris is an often multidrug-resistant yeast that causes invasive infections and, unlike most Candida species, spreads in healthcare facilities. CDC released a clinical alert in June 2016 requesting reporting of C. auris cases. We investigated cases to contain transmission and inform prevention measures for this novel organism. Methods Clinical cases were defined as C. auris from any clinical specimen from a patient in the United States. Response to cases included implementation of infection control measures, enhanced cleaning and disinfection, and testing of close contacts for C. auris colonisation (isolation from a person’s axilla or groin was defined as a screening case). Microbiology records were reviewed at reporting facilities for missed cases. All isolates were forwarded to CDC for confirmation, antifungal susceptibility testing, and whole-genome sequencing (WGS). Results As of April 13, 2017, 61 clinical cases of C. auris were reported from six states: New York (39), New Jersey (15), Illinois (4), Indiana (1), Maryland (1), and Massachusetts (1). All but two occurred since 2016 (Figure). An additional 32 screening cases were identified among contacts. Median age of clinical case-patients was 70 years (range 21–96); 56% were male. Nearly, all had underlying medical conditions and extensive exposure to healthcare facilities before infection. Most clinical isolates were from blood (38, 62%), followed by urine (8, 13%) and respiratory tract (5, 8%). Among the first 35 isolates, 30 (86%) were resistant to fluconazole, 15 (43%) to amphotericin B, and one (3%) to caspofungin. No isolate was resistant to all three. WGS revealed isolates from each state were highly related and different from other states, suggestive of transmission. Microbiology record reviews did not identify additional cases before 2016. Conclusion C. auris is an emerging pathogen, with similarities to multidrug-resistant bacteria, that has been transmitted in US healthcare settings. CDC and public health partners are committed to prompt and aggressive action through investigation of cases and heightened infection control practices to halt its spread. Disclosures All authors: No reported disclosures.

Milk and blood biomarkers associated to the clinical efficacy of a probiotic for the treatment of infectious mastitis.

PubMed

Espinosa-Martos, I; Jiménez, E; de Andrés, J; Rodríguez-Alcalá, L M; Tavárez, S; Manzano, S; Fernández, L; Alonso, E; Fontecha, J; Rodríguez, J M

2016-06-01

Previous studies have shown the efficacy of oral administration of selected lactobacilli strains to treat mastitis. The objective of this study was to find microbiological, biochemical and/or immunological biomarkers of the probiotic effect. Women with (n=23) and without (n=8) symptoms of mastitis received three daily doses (10(9) cfu) of Lactobacillus salivarius PS2 for 21 days. Samples of milk, blood and urine were collected before and after the probiotic intervention, and screened for a wide spectrum of microbiological, biochemical and immunological parameters. In the mastitis group, L. salivarius PS2 intake led to a reduction in milk bacterial counts, milk and blood leukocyte counts and interleukin (IL)-8 level in milk, an increase in those of immunoglobulin (Ig)E, IgG3, epidermal growth factor and IL-7, a modification of the milk electrolyte profile, and a reduction of some oxidative stress biomarkers. Such biomarkers will be useful in future clinical studies involving a larger cohort.

Microbiological assay for the determination of meropenem in pharmaceutical dosage form.

PubMed

Mendez, Andreas S L; Weisheimer, Vanessa; Oppe, Tércio P; Steppe, Martin; Schapoval, Elfrides E S

2005-04-01

Meropenem is a highly active carbapenem antibiotic used in the treatment of a wide range of serious infections. The present work reports a microbiological assay, applying the cylinder-plate method, for the determination of meropenem in powder for injection. The validation method yielded good results and included linearity, precision, accuracy and specificity. The assay is based on the inhibitory effect of meropenem upon the strain of Micrococcus luteus ATCC 9341 used as the test microorganism. The results of assay were treated statistically by analysis of variance (ANOVA) and were found to be linear (r=0.9999) in the range of 1.5-6.0 microg ml(-1), precise (intra-assay: R.S.D.=0.29; inter-assay: R.S.D.=0.94) and accurate. A preliminary stability study of meropenem was performed to show that the microbiological assay is specific for the determination of meropenem in the presence of its degradation products. The degraded samples were also analysed by the HPLC method. The proposed method allows the quantitation of meropenem in pharmaceutical dosage form and can be used for the drug analysis in routine quality control.

Phytase-active yeasts from grain-based food and beer.

PubMed

Nuobariene, L; Hansen, A S; Jespersen, L; Arneborg, N

2011-06-01

To screen yeast strains isolated from grain-based food and beer for phytase activity to identify high phytase-active strains. The screening of phytase-positive strains was carried out at conditions optimal for leavening of bread dough (pH 5·5 and 30°C), in order to identify strains that could be used for the baking industry. Two growth-based tests were used for the initial testing of phytase-active strains. Tested strains belonged to six species: Saccharomyces cerevisiae, Saccharomyces pastorianus, Saccharomyces bayanus, Kazachstania exigua (former name Saccharomyces exiguus), Candida krusei (teleomorph Issachenkia orientalis) and Arxula adeninivorans. On the basis of initial testing results, 14 strains were selected for the further determination of extracellular and intracellular (cytoplasmic and/or cell-wall bound) phytase activities. The most prominent strains for extracellular phytase production were found to be S. pastorianus KVL008 (a lager beer strain), followed by S. cerevisiae KVL015 (an ale beer strain) and C. krusei P2 (isolated from sorghum beer). Intracellular phytase activities were relatively low in all tested strains. Herein, for the first time, beer-related strains of S. pastorianus and S. cerevisiae are reported as phytase-positive strains. The high level of extracellular phytase activity by the strains mentioned previously suggests them to be strains for the production of wholemeal bread with high content of bioavailable minerals. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Atypical microbial infections of digestive tract may contribute to diarrhea in mucopolysaccharidosis patients: a MPS I case study

PubMed Central

Węgrzyn, Grzegorz; Kurlenda, Julianna; Liberek, Anna; Tylki-Szymańska, Anna; Czartoryska, Barbara; Piotrowska, Ewa; Jakóbkiewicz-Banecka, Joanna; Węgrzyn, Alicja

2005-01-01

Background Mucopolysaccharidoses are heritable, metabolic diseases caused by deficiency in an activity of one of specific lysosomal enzymes involved in degradation of mucoplysaccharides (glycosaminoglycans). Among many medical problems of patients with mucopolysaccharidoses, there are frequent episodes of diarrhea of unknown etiology. Case presentation A girl, diagnosed enzymatically for mucopolysaccharidosis type I (deficiency of α-L-iduronidase) at the age of 3 years and 9 months, was investigated until the age of 5 years and 4 months. Frequent loose stools and episodes of diarrhea, often accompanied by vomiting, were encountered. Detailed microbiological analyses were performed and atypical microbial infections (most often enetropathogenic Escherichia coli, but also other species, like Pseudomonas aeruginosa or Staphylococcus aureus, as well as adenoviruses) of the digestive tract were found in most severe diarrhea episodes. Often, isolations of pathogenic bacterial strains from stools of the investigated patient suffering from diarrhea were not obvious during the first screening, and only detailed microbiological studies, including re-isolation of colonies, gave the results of isolation of particular pathogenic strains (especially in the case of enetropathogenic E. coli). Conclusion We conclude that atypical microbial infections of digestive tract may contribute significantly to diarrhea in mucopolysaccaridosis patients. Since isolated strains were not typical and their isolation was often possible only after detailed investigation (not during a standard screening), such atypical microbial infections of digestive tract of mucopolysaccharidosis patients could be usually overlooked to date. Importantly, these atypical infections could be effectively treated with antimicrobial agents. PMID:15882450

Asymptomatic group B streptococcal bacteriuria among pregnant women in Saudi Arabia.

PubMed

Ahmad, S

2015-01-01

This study aims to determine the asymptomatic bacteriuria in pregnancy due to GBS and its antimicrobial sensitivity pattern for planning strategy for the management of these cases and also to determine the relationship between asymptomatic bacteriuria and pyuria. A total of 3863 consecutive urine specimens were collected from 3863 pregnant women with asymptomatic bacteriuria attending the obstetrics and gynaecology department of our hospital over a period of two years. Specimens were processed using standard microbiological procedures. All the subjects were evaluated for bacteriuria. The prevalence of asymptomatic bacteriuria due to group B streptococci (GBS) was 82/3863 (2.1%) among pregnant women in Saudi Arabia. Among these, 69/82 patients (84.2%) had clinical and microbiological features consistent with cystitis, versus 13/82 (15.8%) for pyelonephritis. About 51.2% (42/82) of the patients who had urine analysis performed had positive results based on positive urinary leucocyte esterase and pyuria. Disc-diffusion analysis of all 82 GBS isolates showed that they were highly susceptible to Augmentin and linezolid. Screening for bacteriuria in pregnancy and proper treatment must be considered as an essential part of antenatal care in this community. To prevent asymptomatic bacteriuria complications, all pregnant women should be screened at the first antenatal visit. A negative test for pyuria is not a reliable indicator of the absence of asymptomatic bacteriuria in pregnant women. Further, ongoing surveillance and evaluation of outcomes in pregnancies complicated by GBS bacteriuria is required to optimise maternal and newborn care.

Purification, characterization and application of a novel antimicrobial peptide from Andrias davidianus blood.

PubMed

Pei, J; Feng, Z; Ren, T; Sun, H; Han, H; Jin, W; Dang, J; Tao, Y

2018-01-01

The Andrias davidianus has been known as a traditional Chinese medicine for a long time. Its blood is considered as a waste or by-product of the meat production industry. Although there are reports on isolation of the antimicrobial peptides from different resources, there are no reports of their isolation from A. davidianus blood. In this work, an antimicrobial peptide, andricin B, was isolated from the blood of A. davidianus by an innovative method in which the magnetic liposome adsorption was combined with reversed-phase high-performance liquid chromatography. The structure, antimicrobial activity and safety of andricin B were further investigated. Amino acid sequence was determined by N-terminal sequencing and found to be Gly-Leu-Thr-Arg-Leu-Phe-Ser-Val-Ile-Lys. Circular dichroism (CD) spectra and prediction of three-dimensional structure by bioinformatics software suggested the presence of a well-defined random coil conformation. Andricin B was found to be active against all bacteria tested in this study as well as some fungi. The minimum inhibitory concentrations (MICs) were in the range 8-64 μg ml -1 . Moreover, the haemolytic testing also suggested that andricin B could be considered safe at the MICs. Finally, andricin B was shown to inhibit the growth of Staphylococcus aureus in the cooked meat of A. davidianus. This study shows that andricin B is a promising novel antimicrobial peptide that may provide further insights towards the development of new drugs. This is the pioneer study on screening and isolation of antimicrobial peptide from the blood of Andrias davidianus. Here, we have developed a novel method by combining magnetic liposomes adsorption with reversed-phase high-performance liquid chromatography to purify and screen the antimicrobial peptides. From this screen, we identified a novel antimicrobial peptide which we name as andricin B. Andricin B is unique as it checks the growth of both Gram-positive and Gram-negative bacteria as well as few fungal species. © 2017 The Society for Applied Microbiology.

Performance assessment of urine flow cytometry (UFC) to screen urines to reflex to culture in immunocompetent and immunosuppressed hosts.

PubMed

Stefanovic, Aleksandra; Roscoe, Diane; Ranasinghe, Romali; Wong, Titus; Bryce, Elizabeth; Porter, Charlene; Lim, Adelina; Grant, Jennifer; Ng, Karen; Pudek, Morris

2017-09-01

Urine flow cytometry (UFC) is an automated method to quantify bacterial and white blood cell (WBC) counts. We aimed to determine whether a threshold for these parameters can be set to use UFC as a sensitive screen to predict which urine samples will subsequently grow in culture. Urines submitted to our microbiology laboratory at a tertiary care centre from 22 July 2015-17 February 2016 underwent UFC (Sysmex UF-1000i) analysis, regular urinalysis and urine culture. Positive urine cultures were defined as growth ≥104 c.f.u. ml-1 of organisms associated with urinary tract infections. The correlation of UFC bacterial and WBC counts with urine culture was assessed using receiver operating characteristics curves. The sensitivity (SN), specificity (SP), negative predictive values (NPVs), positive predictive values (PPVs) and false negative rate (FNR) were calculated at various thresholds in immunocompetent and immunosuppressed patients. A total of 15 046 urine specimens were submitted, of which 14 908 were analysable in the study. The average time to UFC result from receipt in the laboratory was 0.76 h (+/-1.04). The test performance at a set threshold of UFC bacteria ≥20 or WBC >5 was: SN=96.0 %, SP=39.2 %, PPV=47.0 %, NPV=94.5 % and FNR=4.0 %. This threshold eliminates 26 % of urine cultures. Immunosuppressed hosts had a lower sensitivity of 90.6 % and a higher FNR of 9.4 %. UFC is a rapid and sensitive method to screen out urine samples that will subsequently be negative and to reflex urines to culture that will subsequently grow. UFC results are available within 1 h from receipt and enable the elimination of culture when the set threshold is not met.

[Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics].

PubMed

Nagy, Erzsébet; Abrók, Marianna; Bartha, Noémi; Bereczki, László; Juhász, Emese; Kardos, Gábor; Kristóf, Katalin; Miszti, Cecilia; Urbán, Edit

2014-09-21

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures.

Group Projects as a Method of Promoting Student Scientific Communication and Collaboration in a Public Health Microbiology Course

ERIC Educational Resources Information Center

Walton, Kristen L. W.; Baker, Jason C.

2009-01-01

Communication of scientific and medical information and collaborative work are important skills for students pursuing careers in health professions and other biomedical sciences. In addition, group work and active learning can increase student engagement and analytical skills. Students in our public health microbiology class were required to work…

Reliability and Validity of a Questionnaire to Measure Consumer Knowledge regarding Safe Practices to Prevent Microbiological Contamination in Restaurants

ERIC Educational Resources Information Center

Uggioni, Paula Lazzarin; Salay, Elisabette

2013-01-01

Objective: The objective of this study was to develop a validated and reliable questionnaire to measure consumer knowledge regarding safe practices to prevent microbiological contamination in restaurants and commercial kitchens. Methods: Non-probabilistic samples of individuals were interviewed in the city of Campinas, Brazil. Questionnaire items…

[Clinical usefulness of urine-formed elements' information obtained from bacteria detection by flow cytometry method that uses nucleic acid staining].

PubMed

Nakagawa, Hiroko; Yuno, Tomoji; Itho, Kiichi

2009-03-01

Recently, specific detection method for Bacteria, by flow cytometry method using nucleic acid staining, was developed as a function of automated urine formed elements analyzer for routine urine testing. Here, we performed a basic study on this bacteria analysis method. In addition, we also have a comparison among urine sediment analysis, urine Gram staining and urine quantitative cultivation, the conventional methods performed up to now. As a result, the bacteria analysis with flow cytometry method that uses nucleic acid staining was excellent in reproducibility, and higher sensitivity compared with microscopic urinary sediment analysis. Based on the ROC curve analysis, which settled urine culture method as standard, cut-off level of 120/microL was defined and its sensitivity = 85.7%, specificity = 88.2%. In the analysis of scattergram, accompanied with urine culture method, among 90% of rod positive samples, 80% of dots were appeared in the area of 30 degrees from axis X. In addition, one case even indicated that analysis of bacteria by flow cytometry and scattergram of time series analysis might be helpful to trace the progress of causative bacteria therefore the information supposed to be clinically significant. Reporting bacteria information with nucleic acid staining flow cytometry method is expected to contribute to a rapid diagnostics and treatment of urinary tract infections. Besides, the contribution to screening examination of microbiology and clinical chemistry, will deliver a more efficient solution to urine analysis.

Future of diagnostic microbiology.

PubMed

Khardori, N

2014-01-01

Diagnostic Microbiology is the tool that makes it possible to identify the exact etiology of infectious diseases and the most optimal therapy at the level of individual patients as well as communities. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes are easily cultivable. This is followed by biochemical methods for identification which also require hours and sometimes days. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time to reporting. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible. This review gives a historical perspective on diagnostic microbiology, discusses the pitfalls of current methodology and provides an overview of newer and future methods.

Application of chemometric methods for assessment and modelling of microbiological quality data concerning coastal bathing water in Greece.

PubMed

Papaioannou, Agelos; Rigas, George; Papastergiou, Panagiotis; Hadjichristodoulou, Christos

2014-12-02

Worldwide, the aim of managing water is to safeguard human health whilst maintaining sustainable aquatic and associated terrestrial, ecosystems. Because human enteric viruses are the most likely pathogens responsible for waterborne diseases from recreational water use, but detection methods are complex and costly for routine monitoring, it is of great interest to determine the quality of coastal bathing water with a minimum cost and maximum safety. This study handles the assessment and modelling of the microbiological quality data of 2149 seawater bathing areas in Greece over 10-year period (1997-2006) by chemometric methods. Cluster analysis results indicated that the studied bathing beaches are classified in accordance with the seasonality in three groups. Factor analysis was applied to investigate possible determining factors in the groups resulted from the cluster analysis, and also two new parameters were created in each group; VF1 includes E. coli, faecal coliforms and total coliforms and VF2 includes faecal streptococci/enterococci. By applying the cluster analysis in each seasonal group, three new groups of coasts were generated, group A (ultraclean), group B (clean) and group C (contaminated). The above analysis is confirmed by the application of discriminant analysis, and proves that chemometric methods are useful tools for assessment and modeling microbiological quality data of coastal bathing water on a large scale, and thus could attribute to effective and economical monitoring of the quality of coastal bathing water in a country with a big number of bathing coasts, like Greece. Significance for public healthThe microbiological protection of coastal bathing water quality is of great interest for the public health authorities as well as for the economy. The present study proves that this protection can be achieved by monitoring only two microbiological parameters, E. coli and faecal streptococci/enterococci instead four microbiological parameters (the two mentioned above plus Total coliforms and Faecal coliforms) that are usually monitored today. As a consequence, countries, especially those with large quantities of coastal bathing sites, can perform microbiological monitoring of their bathing waters by checking only the mentioned two parameters, thus ensuring economies of scale. Thus, funds can be used in other actions to preserve the quality of coastal water and human health. This in turn, would aid in the assessment of the quality of coastal bathing waters and provide a more timely indication of bathing water quality, hence contributing to the immediate health protection of bathers.

Application of next generation sequencing in clinical microbiology and infection prevention.

PubMed

Deurenberg, Ruud H; Bathoorn, Erik; Chlebowicz, Monika A; Couto, Natacha; Ferdous, Mithila; García-Cobos, Silvia; Kooistra-Smid, Anna M D; Raangs, Erwin C; Rosema, Sigrid; Veloo, Alida C M; Zhou, Kai; Friedrich, Alexander W; Rossen, John W A

2017-02-10

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

Reprint of "Application of next generation sequencing in clinical microbiology and infection prevention".

PubMed

Deurenberg, Ruud H; Bathoorn, Erik; Chlebowicz, Monika A; Couto, Natacha; Ferdous, Mithila; García-Cobos, Silvia; Kooistra-Smid, Anna M D; Raangs, Erwin C; Rosema, Sigrid; Veloo, Alida C M; Zhou, Kai; Friedrich, Alexander W; Rossen, John W A

2017-05-20

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements. Copyright © 2017. Published by Elsevier B.V.

Identification and ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry characterization of biosurfactants, including a new surfactin, isolated from oil-contaminated environments.

PubMed

Moro, Glaci V; Almeida, Rafaela T R; Napp, Amanda P; Porto, Carla; Pilau, Eduardo J; Lüdtke, Diogo S; Moro, Angélica V; Vainstein, Marilene H

2018-05-14

Biosurfactant-producing bacteria were isolated from samples collected in areas contaminated with crude oil. The isolates were screened for biosurfactant production using qualitative drop-collapse test, oil-spreading and emulsification assays, and measurement of their tensoactive properties. Five isolates tested positive for in the screening experiments and displayed decrease in the surface tension below 30 mN m -1 . The biosurfactants produced by these isolates were further investigated and their molecular identification revealed that they are bacteria related to the Bacillus genus. Additionally, the biosurfactants produced were chemically characterized via UHPLC-HRMS experiments, indicating the production of surfactin homologues, including a new class of these molecules. © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

C-reactive protein as a screening test for HIV-associated pulmonary tuberculosis prior to antiretroviral therapy in South Africa.

PubMed

Shapiro, Adrienne E; Hong, Ting; Govere, Sabina; Thulare, Hilary; Moosa, Mahomed-Yunus; Dorasamy, Afton; Wallis, Carole L; Celum, Connie L; Grosset, Jacques; Drain, Paul K

2018-05-28

There is an urgent need for more accurate screening tests for tuberculosis(TB). We assessed the diagnostic accuracy of C-reactive protein (CRP) as a screening test for active TB in HIV-infected ambulatory adults. CRP levels were measured in blood collected at the time of HIV testing.Diagnostic accuracy of CRP for pulmonary TB was calculated (reference standard: TB culture), compared to the WHO 4-symptom screen, consisting of cough, fever, night sweats, and weight loss. Diagnostic accuracy was also calculated for CRP in a larger cohort of HIV-infected adults with a positive symptom screen (reference standard: clinical or microbiological TB). Among 425 HIV-infected outpatients systematically tested for pulmonary TB, TB culture was positive in 42 (10%), 279 (66%) had at least one TB-related symptom and 197 (46%) had a CRP >5 mg/L. The sensitivity of CRP and the TB symptom screen to detect TB was the same (90.5%; 95%CI 77.4-97.3) but specificity of CRP was higher than for the TB symptom screen (58.5% vs. 37.1%, p<0.001). Of persons with no symptoms and normal CRP, 99 (98%) had no TB. In another cohort of 749 patients presenting with at least one TB-related symptom and clinically evaluated, CRP had a sensitivity of 98.7% and specificity of 48.3%. In HIV-infected outpatients, CRP was as sensitive but substantially more specific than TB symptom screening. Use of CRP as a screening tool to exclude active TB could identify the same number of HIV-associated TB cases, but reduce the use of diagnostic sputum testing in TB-endemic regions.

Cost-effectiveness study of the microbiological diagnosis of tuberculosis using geneXpert MTB/RIF®.

PubMed

Herráez, Óscar; Asencio-Egea, María Ángeles; Huertas-Vaquero, María; Carranza-González, Rafael; Castellanos-Monedero, Jesús; Franco-Huerta, María; Barberá-Farré, José Ramón; Tenías-Burillo, José María

To perform a cost-effectiveness analysis of a molecular biology technique for the diagnosis of tuberculosis compared to the classical diagnostic alternative. A cost-effectiveness analysis was performed to evaluate the theoretical implementation of a molecular biology method including two alternative techniques for early detection of Mycobacterium tuberculosis Complex, and resistance to rifampicin (alternative1: one determination in selected patients; alternative2: two determinations in all the patients). Both alternatives were compared with the usual procedure for microbiological diagnosis of tuberculosis (staining and microbiological culture), and was accomplished on 1,972 patients in the period in 2008-2012. The effectiveness was measured in QALYs, and the uncertainty was assessed by univariate, multivariate and probabilistic analysis of sensitivity. A value of €8,588/QALYs was obtained by the usual method. Total expenditure with the alternative1 was €8,487/QALYs, whereas with alternative2, the cost-effectiveness ratio amounted to €2,960/QALYs. Greater diagnostic efficiency was observed by applying the alternative2, reaching a 75% reduction in the number of days that a patient with tuberculosis remains without an adequate treatment, and a 70% reduction in the number of days that a patient without tuberculosis remains in hospital. The implementation of a molecular microbiological technique in the diagnosis of tuberculosis is extremely cost-effective compared to the usual method. Its introduction into the routine diagnostic procedure could lead to an improvement in quality care for patients, given that it would avoid both unnecessary hospitalisations and treatments, and reflected in economic savings to the hospital. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Environmental bacteria produce abundant and diverse antibiofilm compounds.

PubMed

Farmer, J T; Shimkevitch, A V; Reilly, P S; Mlynek, K D; Jensen, K S; Callahan, M T; Bushaw-Newton, K L; Kaplan, J B

2014-12-01

The aim of this study was to isolate novel antibiofilm compounds produced by environmental bacteria. Cell-free extracts were prepared from lawns of bacteria cultured on agar. A total of 126 bacteria isolated from soil, cave and river habitats were employed. Extracts were tested for their ability to inhibit Staphylococcus aureus biofilm in a 96-well microtitre plate assay. A total of 55/126 extracts (44%) significantly inhibited Staph. aureus biofilm. Seven extracts were selected for further analysis. The antibiofilm activities in all seven extracts exhibited unique patterns of molecular mass, chemical polarity, heat stability and spectrum of activity against Staph. aureus, Staphylococcus epidermidis and Pseudomonas fluorescens, suggesting that these seven antibiofilm activities were mediated by unique chemical compounds with different mechanisms of action. Environmental bacteria produce abundant and diverse antibiofilm compounds. Screening cell-free extracts is a useful method for identifying secreted compounds that regulate biofilm formation. Such compounds may represent a novel source of antibiofilm agents for technological development. © 2014 The Society for Applied Microbiology.

Level of impact on the public health of universal human immunodeficiency virus screening in an Emergency Department.

PubMed

Reyes-Urueña, Juliana; Fernàndez-López, Laura; Force, Luis; Daza, Manel; Agustí, Cristina; Casabona, Jordi

The aim of this study was to determine the prevalence of HIV and the acceptability of rapid testing in an emergency department (ED), Barcelona (6/07/2011 to 8/03/2013). A convenience sample was used, depending on nurse availability in the ED. Participants signed an informed consent. Results were confirmed by conventional methods. A total of 2,140 individuals were offered testing, and 5% rejected taking part (107/2,140). Three subjects (3/2,033 [0.15%]) had confirmed reactive test. Individuals with a higher education were more likely to perform a rapid HIV test in ED (P<.005). A low prevalence of new HIV diagnoses was found among participants, although there was a high acceptability rate to perform rapid testing in the ED. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Streptococcus pneumoniae-associated pneumonia complicated by purulent pericarditis: case series *

PubMed Central

Cillóniz, Catia; Rangel, Ernesto; Barlascini, Cornelius; Piroddi, Ines Maria Grazia; Torres, Antoni; Nicolini, Antonello

2015-01-01

Abstract Objective: In the antibiotic era, purulent pericarditis is a rare entity. However, there are still reports of cases of the disease, which is associated with high mortality, and most such cases are attributed to delayed diagnosis. Approximately 40-50% of all cases of purulent pericarditis are caused by Gram-positive bacteria, Streptococcus pneumoniae in particular. Methods: We report four cases of pneumococcal pneumonia complicated by pericarditis, with different clinical features and levels of severity. Results: In three of the four cases, the main complication was cardiac tamponade. Microbiological screening (urinary antigen testing and pleural fluid culture) confirmed the diagnosis of severe pneumococcal pneumonia complicated by purulent pericarditis. Conclusions: In cases of pneumococcal pneumonia complicated by pericarditis, early diagnosis is of paramount importance to avoid severe hemodynamic compromise. The complications of acute pericarditis appear early in the clinical course of the infection. The most serious complications are cardiac tamponade and its consequences. Antibiotic therapy combined with pericardiocentesis drastically reduces the mortality associated with purulent pericarditis. PMID:26398760

Clinical outcomes in cystic fibrosis patients with Trichosporon respiratory infection.

PubMed

Esther, Charles R; Plongla, Rongpong; Kerr, Alan; Lin, Feng-Chang; Gilligan, Peter

2016-09-01

Relationships between clinical outcomes and novel respiratory pathogens such as Trichosporon are not well understood. Respiratory cultures from CF patients were screened for novel pathogens Trichosporon and Chryseobacterium as well as other pathogens over 28months. Relationships between microbiologic and clinical data were assessed using univariate and multivariate methods. Of 4934 respiratory cultures from 474 CF patients, 37 cultures from 10 patients were Trichosporon positive. Patients with positive Trichosproron cultures had a greater decline in FEV1 over time (-3.9%/year vs. -1.3%/year, p<0.05), whereas Chryseobacterium did not influence lung function. These findings were confirmed in multivariate analyses that included age, gender, and other common pathogens as confounders. Treatment of Trichosporon infected patients was associated with improved lung function. Trichosporon can be recovered from a small but clinically meaningful fraction of CF patients. The presence of Trichosporon, but not Chryseobacterium, is associated with greater declines in lung function. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Method for stitching microbial images using a neural network

NASA Astrophysics Data System (ADS)

Semenishchev, E. A.; Voronin, V. V.; Marchuk, V. I.; Tolstova, I. V.

2017-05-01

Currently an analog microscope has a wide distribution in the following fields: medicine, animal husbandry, monitoring technological objects, oceanography, agriculture and others. Automatic method is preferred because it will greatly reduce the work involved. Stepper motors are used to move the microscope slide and allow to adjust the focus in semi-automatic or automatic mode view with transfer images of microbiological objects from the eyepiece of the microscope to the computer screen. Scene analysis allows to locate regions with pronounced abnormalities for focusing specialist attention. This paper considers the method for stitching microbial images, obtained of semi-automatic microscope. The method allows to keep the boundaries of objects located in the area of capturing optical systems. Objects searching are based on the analysis of the data located in the area of the camera view. We propose to use a neural network for the boundaries searching. The stitching image boundary is held of the analysis borders of the objects. To auto focus, we use the criterion of the minimum thickness of the line boundaries of object. Analysis produced the object located in the focal axis of the camera. We use method of recovery of objects borders and projective transform for the boundary of objects which are based on shifted relative to the focal axis. Several examples considered in this paper show the effectiveness of the proposed approach on several test images.

Sampling and Data Analysis for Environmental Microbiology

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

Murray, Christopher J.

2001-06-01

A brief review of the literature indicates the importance of statistical analysis in applied and environmental microbiology. Sampling designs are particularly important for successful studies, and it is highly recommended that researchers review their sampling design before heading to the laboratory or the field. Most statisticians have numerous stories of scientists who approached them after their study was complete only to have to tell them that the data they gathered could not be used to test the hypothesis they wanted to address. Once the data are gathered, a large and complex body of statistical techniques are available for analysis ofmore » the data. Those methods include both numerical and graphical techniques for exploratory characterization of the data. Hypothesis testing and analysis of variance (ANOVA) are techniques that can be used to compare the mean and variance of two or more groups of samples. Regression can be used to examine the relationships between sets of variables and is often used to examine the dependence of microbiological populations on microbiological parameters. Multivariate statistics provides several methods that can be used for interpretation of datasets with a large number of variables and to partition samples into similar groups, a task that is very common in taxonomy, but also has applications in other fields of microbiology. Geostatistics and other techniques have been used to examine the spatial distribution of microorganisms. The objectives of this chapter are to provide a brief survey of some of the statistical techniques that can be used for sample design and data analysis of microbiological data in environmental studies, and to provide some examples of their use from the literature.« less

Whole genome sequencing in clinical and public health microbiology

PubMed Central

Kwong, J. C.; McCallum, N.; Sintchenko, V.; Howden, B. P.

2015-01-01

SummaryGenomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology. The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology. Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories. As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future. Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure. PMID:25730631

Whole genome sequencing in clinical and public health microbiology.

PubMed

Kwong, J C; McCallum, N; Sintchenko, V; Howden, B P

2015-04-01

Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology.Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future.Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.

Rapid and easy detection of low-level resistance to vancomycin in methicillin-resistant Staphylococcus aureus by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Asakura, Kota; Azechi, Takuya; Sasano, Hiroshi; Matsui, Hidehito; Hanaki, Hideaki; Miyazaki, Motoyasu; Takata, Tohru; Sekine, Miwa; Takaku, Tomoiku; Ochiai, Tomonori; Komatsu, Norio; Shibayama, Keigo; Katayama, Yuki; Yahara, Koji

2018-01-01

Vancomycin-intermediately resistant Staphylococcus aureus (VISA) and heterogeneous VISA (hVISA) are associated with treatment failure. hVISA contains only a subpopulation of cells with increased minimal inhibitory concentrations, and its detection is problematic because it is classified as vancomycin-susceptible by standard susceptibility testing and the gold-standard method for its detection is impractical in clinical microbiology laboratories. Recently, a research group developed a machine-learning classifier to distinguish VISA and hVISA from vancomycin-susceptible S. aureus (VSSA) according to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) data. Nonetheless, the sensitivity of hVISA classification was found to be 76%, and the program was not completely automated with a graphical user interface. Here, we developed a more accurate machine-learning classifier for discrimination of hVISA from VSSA and VISA among MRSA isolates in Japanese hospitals by means of MALDI-TOF MS data. The classifier showed 99% sensitivity of hVISA classification. Furthermore, we clarified the procedures for preparing samples and obtaining MALDI-TOF MS data and developed all-in-one software, hVISA Classifier, with a graphical user interface that automates the classification and is easy for medical workers to use; it is publicly available at https://github.com/bioprojects/hVISAclassifier. This system is useful and practical for screening MRSA isolates for the hVISA phenotype in clinical microbiology laboratories and thus should improve treatment of MRSA infections.

Rapid and easy detection of low-level resistance to vancomycin in methicillin-resistant Staphylococcus aureus by matrix-assisted laser desorption ionization time-of-flight mass spectrometry

PubMed Central

Asakura, Kota; Azechi, Takuya; Sasano, Hiroshi; Matsui, Hidehito; Hanaki, Hideaki; Miyazaki, Motoyasu; Takata, Tohru; Sekine, Miwa; Takaku, Tomoiku; Ochiai, Tomonori; Komatsu, Norio; Shibayama, Keigo

2018-01-01

Vancomycin-intermediately resistant Staphylococcus aureus (VISA) and heterogeneous VISA (hVISA) are associated with treatment failure. hVISA contains only a subpopulation of cells with increased minimal inhibitory concentrations, and its detection is problematic because it is classified as vancomycin-susceptible by standard susceptibility testing and the gold-standard method for its detection is impractical in clinical microbiology laboratories. Recently, a research group developed a machine-learning classifier to distinguish VISA and hVISA from vancomycin-susceptible S. aureus (VSSA) according to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) data. Nonetheless, the sensitivity of hVISA classification was found to be 76%, and the program was not completely automated with a graphical user interface. Here, we developed a more accurate machine-learning classifier for discrimination of hVISA from VSSA and VISA among MRSA isolates in Japanese hospitals by means of MALDI-TOF MS data. The classifier showed 99% sensitivity of hVISA classification. Furthermore, we clarified the procedures for preparing samples and obtaining MALDI-TOF MS data and developed all-in-one software, hVISA Classifier, with a graphical user interface that automates the classification and is easy for medical workers to use; it is publicly available at https://github.com/bioprojects/hVISAclassifier. This system is useful and practical for screening MRSA isolates for the hVISA phenotype in clinical microbiology laboratories and thus should improve treatment of MRSA infections. PMID:29522576

Bioprofiling of Salicaceae bud extracts through high-performance thin-layer chromatography hyphenated to biochemical, microbiological and chemical detections.

PubMed

Hage, Salim; Morlock, Gertrud E

2017-03-24

The buds of poplars (Populus L.) and willows (Salix L.), both from the same family (Salicaceae Mirbel), are increasingly used in gemmotherapy and importantly contribute to the production of the physiologically active propolis by European bee Apis mellifera L. In order to study their phenolic profiles, polar extracts of buds from P. nigra L. were compared to those of P. alba L. and S. alba L. through high-performance thin-layer chromatography (HPTLC). Five chemotypical patterns were distinguished after derivatisation with the Natural Product reagent and confirmed by principal component analysis. The HPTLC analysis was directly hyphenated to various microbiological and biochemical assays as well as spectrometric techniques, directly linking to active molecules in the chromatograms. At a glance, polyvalent compounds were evident when all derivatisation and activity assays, to which HPTLC was hyphenated at ease, were combined together. In Populus buds, at least three antimicrobial compound zones were detected using Aliivibrio fischeri and Bacillus subtilis bioassays, and one phyto-œstrogen with the planar yeast œstrogen screen. In all samples, several inhibitors of acetyl- and butyrylcholinesterase and rabbit liver esterase were detected. Hyphenation to high resolution mass spectrometry supported the assignment of bioactive compounds, as shown for chrysin as selective cholinesterase inhibitor as well as caffeic acid and galangin as antimicrobials in P. nigra and P. alba. This fast and cost-efficient method can be appropriately extended and applied to the botanical origin determination and quality control of bud extracts and propolis samples. Copyright © 2017 Elsevier B.V. All rights reserved.

International External Quality Assurance for Laboratory Diagnosis of Diphtheria ▿

PubMed Central

Neal, S. E.; Efstratiou, A.

2009-01-01

The diphtheria surveillance network (DIPNET) encompassing National Diphtheria Reference Centers from 25 European countries is a Dedicated Surveillance Network recognized by the European Commission. A key DIPNET objective is the quality assessment of microbiological procedures for diphtheria across the European Union and beyond. A detailed questionnaire on the level of reference laboratory services and an external quality assessment (EQA) panel comprising six simulated throat specimens were sent to 34 centers. Twenty-three centers are designated National Diphtheria Reference Centers, with the laboratory in the United Kingdom being the only WHO Collaborating Centre. A variety of screening and identification tests were used, including the cysteinase test (20/34 centers), pyrazinamidase test (17/34 centers), and commercial kits (25/34 centers). The classic Elek test for toxigenicity testing is mostly used (28/34 centers), with variations in serum sources and antitoxin concentrations. Many laboratories reported problems obtaining Elek reagents or media. Only six centers produced acceptable results for all six specimens. Overall, 21% of identification and 13% of toxigenicity reports were unacceptable. Many centers could not isolate the target organism, and most found difficulties with the specimens that contained Corynebacterium striatum as a commensal contaminant. Nineteen centers generated either false-positive or negative toxigenic results, which may have caused inappropriate medical management. The discrepancies in this diphtheria diagnostics EQA alarmingly reflect the urgent need to improve laboratory performance in diphtheria diagnostics in Europe, standardize feasible and robust microbiological methods, and build awareness among public health authorities. Therefore, DIPNET recommends that regular workshops and EQA distributions for diphtheria diagnostics should be supported and maintained. PMID:19828749

ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications.

PubMed

Verhoeven, Joost Theo Petra; Canuti, Marta; Munro, Hannah J; Dufour, Suzanne C; Lang, Andrew S

2018-04-19

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (<5 US dollars per sample) and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing and microbiome profiling. ViDiT-CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal-cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT-CACTUS demonstrated its validity in a wide range of microbiology applications and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.

Antimicrobial activity of plant extracts against the honeybee pathogens, Paenibacillus larvae and Ascosphaera apis and their topical toxicity to Apis mellifera adults.

PubMed

Chaimanee, V; Thongtue, U; Sornmai, N; Songsri, S; Pettis, J S

2017-11-01

To explore alternative nonchemical control measures against two honeybee pathogens, Paenibacillus larvae and Ascosphaera apis, 37 plant species were screened for antimicrobial activity. The activity of selected plant extracts was screened using an in vitro disc diffusion assay and the minimal inhibitory concentration (MIC) was determined by the broth microdilution method. The results showed that 36 plant extracts had some antibacterial activity on P. larvae by disc diffusion assay. Chromolaena odorata showed the greatest antibacterial activity against P. larvae (MIC 16-64 μg ml -1 ). Of the 37 tested plants, only seven species, Amomum krervanh, Allium sativum, Cinnamomum sp., Piper betle, Piper ribesioides, Piper sarmentosum and Syzygium aromaticum had inhibitory effects on A. apis (MICs of 32-64 μg ml -1 ). The results demonstrated that promising plant extracts were not toxic to adult bees at the concentrations used in this study. The results demonstrate the potential antimicrobial activity of natural products against honeybee diseases caused by P. larvae and A. apis. Chromolaena odorata in particular showed high bioactivity against P. larvae. Further study is recommended to develop these nonchemical treatments against American foulbrood and chalkbrood in honeybees. This work proposes new natural products for the control of American foulbrood and chalkbrood in honeybees. © 2017 The Society for Applied Microbiology.

Guidelines for the public health management of typhoid and paratyphoid in England: practice guidelines from the National Typhoid and Paratyphoid Reference Group.

PubMed

Balasegaram, S; Potter, A L; Grynszpan, D; Barlow, S; Behrens, R H; Lighton, L; Booth, L; Inamdar, L; Neal, K; Nye, K; Lawrence, J; Jones, J; Gray, I; Tolley, D; Lane, C; Adak, B; Cummins, A; Addiman, S

2012-09-01

The Typhoid and Paratyphoid Reference Group (TPRG) was convened by the Health Protection Agency (HPA) and the Chartered Institute of Environmental Health (CIEH) to revise guidelines for public health management of enteric fever. This paper presents the new guidelines for England and their rationale. Methods include literature reviews including grey literature such as audit data and case studies; analysis of enhanced surveillance data from England, Wales and Northern Ireland; review of clearance and screening schedules in use in other non-endemic areas; and expert consensus. The evidence and principles underpinning the new guidance are summarised. Significant changes from previous guidance include: • Algorithms to guide risk assessment and management, based on risk group and travel history; • Outline of investigation of non-travel cases; • Simplified microbiological clearance schedules for cases and contacts; • Targeted co-traveller screening and a "warn and inform" approach for contacts; • Management of convalescent and chronic carriers. The guidelines were launched in February 2012. Feedback has been positive: the guidelines are reported to be clear, systematic, practical and risk-based. An evaluation of the guidelines is outlined and will add to the evidence base. There is potential for simplification and consistency between international guidelines. Copyright © 2012 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Efficiency tests of samplers for microbiological aerosols, a review

NASA Technical Reports Server (NTRS)

Henningson, E.; Faengmark, I.

1984-01-01

To obtain comparable results from studies using a variety of samplers of microbiological aerosols with different collection performances for various particle sizes, methods reported in the literature were surveyed, evaluated, and tabulated for testing the efficiency of the samplers. It is concluded that these samplers were not thoroughly tested, using reliable methods. Tests were conducted in static air chambers and in various outdoor and work environments. Results are not reliable as it is difficult to achieve stable and reproducible conditions in these test systems. Testing in a wind tunnel is recommended.

The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives.

PubMed

Endimiani, Andrea; Jacobs, Michael R

2016-06-01

The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbiological assay of the Marshall Space Flight Center neutral buoyancy simulator

NASA Technical Reports Server (NTRS)

Beyerle, F. J.

1973-01-01

A neutral buoyancy simulator tank system is described in terms of microbiological and medical safety for astronauts. The system was designed to simulate a gravity-free state for evaluation of orbital operations in a microorganism-free environment. Methods for the identification and elimination of specific microorganisms are dealt with as measures for a pure system of space environment simulation.

Use of Long-Term E. Coli Cultures: To Study Generation of Genetic Diversity & Teach General Microbiology Laboratory Skills

ERIC Educational Resources Information Center

Petrie, Angela; Finkel, Steven E.; Erbe, Jarrod

2005-01-01

A novel method of studying the generation of genetic diversity in an undergraduate microbiology laboratory is described. The basis of this approach is the accumulation of mutations that confer a competitive advantage, or growth advantage in stationary phase (GASP) phenotype, to E. coli grown in stationary phase for extended periods of time.

Mycoplasma genitalium and Trichomonas vaginalis in France: a point prevalence study in people screened for sexually transmitted diseases.

PubMed

Pereyre, S; Laurier Nadalié, C; Bébéar, C

2017-02-01

Mycoplasma genitalium and Trichomonas vaginalis are common causes of sexually transmitted infections, but limited prevalence data are available in France. We aimed to evaluate the prevalence of M. genitalium and T. vaginalis infections and to assess prevalence by gender, age, sample collection sites and clinical symptoms. A multicentre collection of specimens was intended to obtain a nationwide overview of the epidemiology. Between September 2014 and January 2015, a total of 2652 consecutive urogenital specimens submitted to the microbiology diagnostic departments of 16 French university hospitals for Chlamydia trachomatis and Neisseria gonorrhoeae detection were collected. M. genitalium and T. vaginalis prevalence were evaluated using a commercial real-time PCR kit. Clinical data from patients were anonymously collected. T. vaginalis and M. genitalium prevalence were 1.7% (95% confidence interval 1.3-2.4) and 3.4% (95% confidence interval 2.8-4.2), respectively, and did not differ between gender or age groups, except M. genitalium prevalence between men and women in the 35- to 44-year age group (5.9 vs. 1.5%; p 0.03). M. genitalium prevalence was significantly higher in patients receiving care in sexually transmitted infection clinics, abortion centres, family planning clinics and prisons than in gynaecologic, obstetric and reproduction centres (4.0 vs. 1.7%, p 0.009). Among M. genitalium- and T. vaginalis-positive patients, 70.9 and 61.5% were asymptomatic, respectively. The low T. vaginalis prevalence does not justify systematic screening for this organism in France. Conversely, selective screening for M. genitalium may be warranted in care settings that receive presumably high-risk sexual behaviour patients, regardless of symptoms. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Microbiological effectiveness of household water treatment technologies under field use conditions in rural Tanzania.

PubMed

Mohamed, Hussein; Clasen, Thomas; Njee, Robert Mussa; Malebo, Hamisi M; Mbuligwe, Stephen; Brown, Joe

2016-01-01

To assess the microbiological effectiveness of several household water treatment and safe storage (HWTS) options in situ in Tanzania, before consideration for national scale-up of HWTS. Participating households received supplies and instructions for practicing six HWTS methods on a rotating 5-week basis. We analysed 1202 paired samples (source and treated) of drinking water from 390 households, across all technologies. Samples were analysed for thermotolerant (TTC) coliforms, an indicator of faecal contamination, to measure effectiveness of treatment in situ. All HWTS methods improved microbial water quality, with reductions in TTC of 99.3% for boiling, 99.4% for Waterguard ™ brand sodium hypochlorite solution, 99.5% for a ceramic pot filter, 99.5% for Aquatab ® sodium dichloroisocyanurate (NaDCC) tablets, 99.6% for P&G Purifier of Water ™ flocculent/disinfectant sachets, and 99.7% for a ceramic siphon filter. Microbiological performance was relatively high compared with other field studies and differences in microbial reductions between technologies were not statistically significant. Given that microbiological performance across technologies was comparable, decisions regarding scale-up should be based on other factors, including uptake in the target population and correct, consistent, and sustained use over time. © 2015 John Wiley & Sons Ltd.

Reasons for testing women for genital Chlamydia trachomatis infection in the Calgary region

PubMed Central

Church, Deirdre L; Zentner, Ali; Semeniuk, Heather; Henderson, Elizabeth; Read, Ron

2003-01-01

OBJECTIVE: To determine the clinical reason(s) for screening women with varying degrees of risk for genital Chlamydia trachomatis (CT) in the Calgary region. DESIGN: Women aged 15 to 75 years were enrolled at various patient care locations. Pertinent risk factors for genital CT infection were recorded and a gynecological examination was performed. Two endocervical swabs and a first-void urine sample were collected for CT detection using two different nucleic acid amplification test methods. SETTING: Calgary is an urban region that provides healthcare services to a population of almost one million people. Microbiology services are provided by Calgary Laboratory Services through a centralized regional laboratory service. MAIN RESULTS: 504 women with a mean age of 28.1 ±SD 8.22 years were enrolled. Two hundred ninety-one women (57.8%) were at high risk for acquiring genital CT infection. Twenty-eight (5.6%) tested positive for CT infection and almost all of these women (26 of 28, 93%) had risk factors for acquiring infection. Of the high-risk women, 9.8% were CT positive versus only 1.3% of women at low risk (P=0.0001). Only two of 152 (1.3%) women older than 30 years had genital CT infections. Although most women were asymptomatic, those with laboratory-confirmed CT infection were more likely to have genitourinary symptoms. Three hundred forty-three of 476 (72%) women who did not have genital CT infection had no risk factors, and screening was done as part of a routine gynecological examination for other purposes (prenatal visit, Pap smear). CONCLUSION: Women without risk factors are being screened routinely for genital CT infection as part of a routine gynecological examination done for other reasons. Elimination of the routine screening of low-risk women older than 30 years of age would decrease the current regional utilization of CT tests by as much as one-third. PMID:18159423

Utility of Gram stain for the microbiological analysis of burn wound surfaces.

PubMed

Elsayed, Sameer; Gregson, Daniel B; Lloyd, Tracie; Crichton, Marilyn; Church, Deirdre L

2003-11-01

Surface swab cultures have attracted attention as a potential alternative to biopsy histology or quantitative culture methods for microbiological burn wound monitoring. To our knowledge, the utility of adding a Gram-stained slide in this context has not been evaluated previously. To determine the degree of correlation of Gram stain with culture for the microbiological analysis of burn wound surfaces. Prospective laboratory analysis. Urban health region/centralized diagnostic microbiology laboratory. Burn patients hospitalized in any Calgary Health Region burn center from November 2000 to September 2001. Gram stain plus culture of burn wound surface swab specimens obtained during routine dressing changes or based on clinical signs of infection. Degree of correlation (complete, high, partial, none), including weighted kappa statistic (kappa(w)), of Gram stain with culture based on quantitative microscopy and degree of culture growth. A total of 375 specimens from 50 burn patients were evaluated. Of these, 239 were negative by culture and Gram stain, 7 were positive by Gram stain only, 89 were positive by culture only, and 40 were positive by both methods. The degree of complete, high, partial, and no correlation of Gram stain with culture was 70.9% (266/375), 1.1% (4/375), 2.4% (9/375), and 25.6% (96/375), respectively. The degree of correlation for all 375 specimens, as expressed by the weighted kappa statistic, was found to be fair (kappa(w) = 0.32).Conclusion.-The Gram stain is not suitable for the microbiological analysis of burn wound surfaces.

Antimicrobial Testing Methods & Procedures Developed by EPA's Microbiology Laboratory

EPA Pesticide Factsheets

We develop antimicrobial testing methods and standard operating procedures to measure the effectiveness of hard surface disinfectants against a variety of microorganisms. Find methods and procedures for antimicrobial testing.

Production Methods in Industrial Microbiology.

ERIC Educational Resources Information Center

Gaden, Elmer L., Jr.

1981-01-01

Compares two methods (batch and continuous) in which microorganisms are used to produce industrial chemicals. Describes batch and continuous stirred-tank reactors and offers reasons why the batch method may be preferred. (JN)

Corridor consultations and the medical microbiological record: is patient safety at risk?

PubMed Central

Heard, S R; Roberts, C; Furrows, S J; Kelsey, M; Southgate, L

2003-01-01

The performance procedures of the General Medical Council are aimed at identifying seriously deficient performance in a doctor. The performance procedures require the medical record to be of a standard that enables the next doctor seeing the patient to give adequate care based on the available information. Setting standards for microbiological record keeping has proved difficult. Over one fifth of practising medical microbiologists (including virologists) in the UK (139 of 676) responded to a survey undertaken by the working group developing the performance procedures for microbiology, to identify current practice and to develop recommendations for agreement within the profession about the standards of the microbiological record. The cumulative frequency for the surveyed recording methods used indicated that at various times 65% (90 of 139) of respondents used a daybook, 62% (86 of 139) used the back of the clinical request card, 57% (79 of 139) used a computer record, and 22% (30 of 139) used an index card system to record microbiological advice, suggesting wide variability in relation to how medical microbiologists maintain clinical records. PMID:12499432

Basic research for the future: Opportunities in microbiology for the coming decade

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

Payne, W.J.

1996-12-31

Not since Leeuwenhoek reported finding {open_quotes}animalcules{close_quotes} in a variety of natural materials have research opportunities in microbiology looked so promising. Researchers have developed methods to analyze the historic and evolutionary progression of bacteria, fungi, and viruses. The significance of the remarkable diversity found in the microbial realm is just beginning to emerge. Biotechnology companies are exploiting microorganisms in remarkable ways. Seemingly new, devastating pathogens have appeared and {open_quotes}old{close_quotes} pathogens have become resistant to antiobiotics. All these factors serve to invigorate interest in microbiology. Seldom have the challenges seemed more intense or more exciting. Recognizing the significance of these issues, themore » American Academy of Microbiology convened a colloquium of experts in the microbiological sciences May 4-7, 1996, in Washington, D.C. The colloquim sought primarily to identify those research areas most clearly deserving future attention, those most likely to provide optimal return on scientific and monetary investment, and those offering the greatest promise for solving critical problems over the coming decade.« less

Microbiological monitoring for the US Geological Survey National Water-Quality Assessment Program

USGS Publications Warehouse

Francy, Donna S.; Myers, Donna N.; Helsel, Dennis R.

2000-01-01

Data to characterize the microbiological quality of the Nation?s fresh, marine, and estuarine waters are usually collected for local purposes, most often to judge compliance with standards for protection of public health in swimmable or drinkable waters. Methods and procedures vary with the objectives and practices of the parties collecting data and are continuously being developed or modified. Therefore, it is difficult to provide a nationally consistent picture of the microbial quality of the Nation?s waters. Study objectives and guidelines for a national microbiological monitoring program are outlined in this report, using the framework of the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) program. A national program is designed to provide long-term data on the presence of microbiological pathogens and indicators in ground water and surface water to support effective water policy and management. Three major groups of waterborne pathogens affect the public health acceptability of waters in the United States?bacteria, protozoa, and viruses. Microbiological monitoring in NAWQA would be designed to assess the occurrence, distribution, and trends of pathogenic organisms and indicators in surface waters and ground waters; relate the patterns discerned to factors that help explain them; and improve our understanding of the processes that control microbiological water quality.

Comparison of phenotypic tests for the detection of metallo-beta-lactamases in clinical isolates of Pseudomonas aeruginosa.

PubMed

Lucena, Andréa; Dalla Costa, Libera M; Nogueira, Keite da Silva; Matos, Adriana P; Gales, Ana C; Raboni, Sonia M

2014-12-01

Metallo-β-lactamase (MBL)-producing gram-negative bacteria are an increasing public health concern worldwide. Screening tests for the rapid and specific identification of these pathogens are essential, and should be included among routine diagnostics in laboratories. This study aimed to determine the MBL frequency among carbapenem-resistant Pseudomonas aeruginosa isolates, and to evaluate the accuracy of different tests in screening for MBL production. From January 2001 to December 2008, a total of 142 imipenem-non-susceptible P. aeruginosa strains were isolated from distinct clinical samples from hospitalized patients. These isolates were examined by PCR, MBL E-test, double-disk synergy test (DDST), and combined disk (CD) test. The minimal inhibitory concentration (MIC; μg/mL) was determined by agar dilution, and pulsed field gel electrophoresis (PFGE) was performed on all samples. Sequencing was performed to confirm and define the MBL variant and subtype. Using PCR and DNA sequence analysis, 93 strains were confirmed positive for MBLs, 91 strains for the blaSPM-1 gene, 1 strain for the blaIMP-1 gene, and 1 strain for the blaIMP-16 gene. PFGE displayed a clonal pattern. The sensitivities, specificities, positive and negative predictive values were evaluated for all tests. The DDST assay (CAZ-MPA) was the optimal method for screening MBL production in P. aeruginosa strains. However, the results of the CD assay (IMP/EDTA) showed close agreement with those of the DDST. In addition, the CD assay allowed a more objective interpretation and did not require the use of a toxic substance. Copyright © 2013 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

[Screening with angiographic images prior to (99m)Tc-HMPAO labelled leukocyte scintigraphy in the diagnosis of periprosthetic infection].

PubMed

Granados, U; Fuster, D; Soriano, A; García, S; Bori, G; Martínez, J C; Mayoral, M; Perlaza, P; Tomás, X; Pons, F

2015-01-01

To evaluate the impact of the angioscintigrapy of the three phase bone scan as screening method to rule out infection of the hip and knee prosthesis prior to performing the (99m)Tc-HMPAO leukocyte scintigraphy. A total of 120 (70 women, 50 men; mean age 71±11years) with clinical suspicion of hip (n=63) or knee (n=57) infection of the prosthesis and clinical suspicion of infection were evaluated prospectively. All patients underwent three-phase bone scan (angioscintigraphy, vascular and bone phase) and (99m)Tc-HMPAO-labelled white blood cell scintigraphy. Final diagnosis of infection was made by microbiological documentation or clinical follow-up for at least 12months. Eighteen out of 120 patients were diagnosed of infection of hip prosthesis (n=10) or knee prosthesis (n=8). The angioscintigraphy was positive in 15/18 infected cases and in 21/102 of the non-infected cases with a sensitivity of 83%, specificity of 79% and negative predictive value of 97%. Sensitivity and specificity of (99m)Tc-HMPAO leukocyte scintigraphy were 72% and 95%, respectively. If the leukocyte labeled scintigraphies had been used exclusively for patients with positive angioscintigraphy, this would have saved up to 70% of the (99m)Tc-HMPAO leukocyte scintigraphies performed. There were no cases of infection with positive labeled leukocyte scintigraphy and negative angioscintigraphy. Angioscintigraphy (blood flow phase of bone scan) is a useful technique for screening for hip and knee joint prosthesis infection, significantly reducing the need for (99m)Tc-HMPAO leukocyte scintigraphy without affecting the sensitivity of the technique. Copyright © 2014 Elsevier España, S.L.U. and SEMNIM. All rights reserved.

Comparison of Three Biochemical Tests for Rapid Detection of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae.

PubMed

Poirel, Laurent; Fernández, Javier; Nordmann, Patrice

2016-02-01

Enterobacterial isolates producing clavulanic-inhibited extended-spectrum β-lactamases (ESBLs) are increasingly spreading in the community and are often responsible for nosocomial infections. Rapid biochemical tests have been developed recently for their detection. Three tests, namely, the Rapid ESBL NDP test, the β-Lacta test, and the Rapid ESBL Screen, have been evaluated with a collection of 108 well-characterized strains, including wild-type strains, strains producing ESBLs, overexpressed cephalosporinases, and carbapenemases. The ESBL NDP test and the Rapid ESBL Screen (a copy of the ESBL NDP test) are aimed at detecting ESBL producers, while the β-Lacta test is aimed at detecting not only ESBL producers but also cephalosporinase and carbapenemase producers. The sensitivity and specificity for detecting ESBL producers (n = 60) were 95% and 100% for the Rapid ESBL NDP test, 80% and 87% (after 30 min) and 92% and 83% (after 2 h) for the Rapid ESBL Screen, and 88% and 71% for the β-Lacta test, respectively. Varied and time-consuming detection (up to 2 h) of ESBLs by the Rapid ESBL Screen and concomitant and varied detection of producers of AmpC and several types of carbapenemases correspond to significant shortcomings of using the Rapid Screen ESBL and β-Lacta tests, respectively. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The microbiology of Bandji, palm wine of Borassus akeassii from Burkina Faso: identification and genotypic diversity of yeasts, lactic acid and acetic acid bacteria.

PubMed

Ouoba, L I I; Kando, C; Parkouda, C; Sawadogo-Lingani, H; Diawara, B; Sutherland, J P

2012-12-01

To investigate physicochemical characteristics and especially genotypic diversity of the main culturable micro-organisms involved in fermentation of sap from Borassus akeassii, a newly identified palm tree from West Africa. Physicochemical characterization was performed using conventional methods. Identification of micro-organisms included phenotyping and sequencing of: 26S rRNA gene for yeasts, 16S rRNA and gyrB genes for lactic acid bacteria (LAB) and acetic acid bacteria (AAB). Interspecies and intraspecies genotypic diversities of the micro-organisms were screened respectively by amplification of the ITS1-5.8S rDNA-ITS2/16S-23S rDNA ITS regions and repetitive sequence-based PCR (rep-PCR). The physicochemical characteristics of samples were: pH: 3.48-4.12, titratable acidity: 1.67-3.50 mg KOH g(-1), acetic acid: 0.16-0.37%, alcohol content: 0.30-2.73%, sugars (degrees Brix): 2.70-8.50. Yeast included mainly Saccharomyces cerevisiae and species of the genera Arthroascus, Issatchenkia, Candida, Trichosporon, Hanseniaspora, Kodamaea, Schizosaccharomyces, Trigonopsis and Galactomyces. Lactobacillus plantarum was the predominant LAB species. Three other species of Lactobacillus were also identified as well as isolates of Leuconostoc mesenteroides, Fructobacillus durionis and Streptococcus mitis. Acetic acid bacteria included nine species of the genus Acetobacter with Acetobacter indonesiensis as predominant species. In addition, isolates of Gluconobacter oxydans and Gluconacetobacter saccharivorans were also identified. Intraspecies diversity was observed for some species of micro-organisms including four genotypes for Acet. indonesiensis, three for Candida tropicalis and Lactobacillus fermentum and two each for S. cerevisiae, Trichosporon asahii, Candida pararugosa and Acetobacter tropicalis. fermentation of palm sap from B. akeassii involved multi-yeast-LAB-AAB cultures at genus, species and intraspecies level. First study describing microbiological and physicochemical characteristics of palm wine from B. akeassii. Genotypic diversity of palm wine LAB and AAB not reported before is demonstrated and this constitutes valuable information for better understanding of the fermentation which can be used to improve the product quality and develop added value by-products. © 2012 The Society for Applied Microbiology.

Diagnostic trends in Clostridium difficile detection in Finnish microbiology laboratories.

PubMed

Könönen, Eija; Rasinperä, Marja; Virolainen, Anni; Mentula, Silja; Lyytikäinen, Outi

2009-12-01

Due to increased interest directed to Clostridium difficile-associated infections, a questionnaire survey of laboratory diagnostics of toxin-producing C. difficile was conducted in Finland in June 2006. Different aspects pertaining to C. difficile diagnosis, such as requests and criteria used for testing, methods used for its detection, yearly changes in diagnostics since 1996, and the total number of investigations positive for C. difficile in 2005, were asked in the questionnaire, which was sent to 32 clinical microbiology laboratories, including all hospital-affiliated and the relevant private clinical microbiology laboratories in Finland. The situation was updated by phone and email correspondence in September 2008. In June 2006, 28 (88%) laboratories responded to the questionnaire survey; 24 of them reported routinely testing requested stool specimens for C. difficile. Main laboratory methods included toxin detection (21/24; 88%) and/or anaerobic culture (19/24; 79%). In June 2006, 18 (86%) of the 21 laboratories detecting toxins directly from feces, from the isolate, or both used methods for both toxin A (TcdA) and B (TcdB), whereas only one laboratory did so in 1996. By September 2008, all of the 23 laboratories performing diagnostics for C. difficile used methods for both TcdA and TcdB. In 2006, the number of specimens processed per 100,000 population varied remarkably between different hospital districts. In conclusion, culturing C. difficile is common and there has been a favorable shift in toxin detection practice in Finnish clinical microbiology laboratories. However, the variability in diagnostic activity reported in 2006 creates a challenge for national monitoring of the epidemiology of C. difficile and related diseases.

Black Stains: a microbiological analysis and a view on familiarity and susceptibility to tooth decay of patients in childhood.

PubMed

Tripodi, D; Martinelli, D; Pasini, M; Giuca, M R; D'Ercole, S

2016-12-01

Assess prevalence, familial predisposition and susceptibility to caries of Black Stains (BS). Evaluate the microbiological composition of BS, saliva and subgingival plaque. Sixty nine subjects with BS (test group) and 120 subjects without BS (control group) were analysed for oral status. For each BS-patient, a BS-deposit, 1 ml of saliva and subgingival plaque were collected and microbiologically analysed. Five deciduous teeth with BS were observed under SEM. This study showed a BS prevalence similar to that of the Mediterranean area and a familiality. The microbiological origin of BS was confirmed by SEM and culture method and the BS flora differ from that of supragingival plaque. Predominance in BS and saliva of Actinomycetes and the low salivary prevalence of S. mutans and L. acidophilus may be related with low caries incidence in BS patients. The high presence of Actinomyces spp can be a causative factor for BS.

Microbiological and biochemical spoilage of smoke-dried fishes sold in West African open markets.

PubMed

Ikutegbe, Victoria; Sikoki, Francis

2014-10-15

Proximate composition and microbiological characteristics of pre-dried Chrysichthys nigrodigitatus and Pseudotolithus typus were studied over a period of 4weeks to determine the health risks associated with delayed consumption. All analyses were conducted using standard microbiological and chemical methods. Results showed a general decline in microbiological safety and nutritive characteristics of both fish species over time, with an observed increase in microbial loads over time. Aspergillus flavus was also present on both species which makes consumption of the fishes hazardous to the health of consumers due to its ability to produce carcinogenic aflatoxins. In order to minimise the health risks to consumers, it is recommended that smoke-dried fishes be consumed with minimal delay and cooked properly before consumption. The findings of this study will prove important in the development of more stringent regulations regarding food safety in Nigeria. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Indicators of water microbial pollution: problems and perspectives].

PubMed

Nusca, A; D'Alessandro, D; Funari, E

2008-01-01

Conventional indicators of fecal contamination provide a precious contribution in evaluating water microbiological quality. In recent years some important issues have sprung up which have risen doubts about their reliability and have suggested a revision of their function. In developed countries, where the law regarding water quality is very strict, there have been several outbreaks, even though conventional indicators of fecal pollution pointed an appropriate microbiological quality. These outbreaks have been imputed to new pathogenic microorganisms which are often characterized by a great resistance to disinfection treatments than conventional indicators. In order to obtain an appropriate microbiological quality of waters, various approaches have been started such as the Water Safety Plans by World Health Organization the revision of the functions of suitable indicators (of the water quality), the setting up of specific methods either for pathogen microorganisms and for a quick surveying of an inadequate microbiological water quality.

Candida spp. in oral cancer and oral precancerous lesions.

PubMed

Gall, Francesca; Colella, Giuseppe; Di Onofrio, Valeria; Rossiello, Raffaele; Angelillo, Italo Francesco; Liguori, Giorgio

2013-07-01

To assess the presence of Candida spp. in lesions of the oral cavity in a sample of patients with precancer or cancer of the mouth and evaluate the limitations and advantages of microbiological and histological methods, 103 subjects with precancerous or cancerous lesions and not treated were observed between 2007 and 2009. The presence of Candida in the lesions was analyzed by microbiological and histological methods. Cohen's k statistic was used to assess the agreement between culture method and staining techniques. Forty-eight (47%) patients had cancer and 55 (53%) patients had precancerous lesions. Candida spp. were isolated from 31 (30%) patients with cancerous lesions and 33 (32%) with precancerous lesions. C. albicans was the most frequent species isolated in the lesions. The k value showed a fair overall agreement for comparisons between culture method and PAS (0.2825) or GMS (0.3112). This study supports the frequent presence of Candida spp. in cancer and precancerous lesions of the oral cavity. Both microbiological investigations and histological techniques were reliable for detection of Candida spp. It would be desirable for the two techniques to be considered complementary in the detection of yeast infections in these types of lesions.

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.

Efficacy of the FilmArray blood culture identification panel for direct molecular diagnosis of infectious diseases from samples other than blood.

PubMed

Micó, Miquel; Navarro, Ferran; de Miniac, Daniela; González, Yésica; Brell, Albert; López, Cristina; Sánchez-Reus, Ferran; Mirelis, Beatriz; Coll, Pere

2015-12-01

Molecular-based techniques reduce the delay in diagnosing infectious diseases and therefore contribute to better patient outcomes. We assessed the FilmArray blood culture identification (BCID) panel (Biofire Diagnostics/bioMérieux) directly on clinical specimens other than blood: cerebrospinal, joint, pleural and ascitic fluids, bronchoscopy samples and abscesses. We compared the results from 88 samples obtained by culture-based techniques. The percentage of agreement between the two methods was 75 % with a Cohen κ value of 0.51. Global sensitivity and specificity using the FilmArray BCID panel were 71 and 97 %, respectively. Sensitivity was poorer in samples with a low bacterial load, such as ascitic and pleural fluids (25 %), whereas the sensitivity for abscess samples was high (89 %). These findings suggest that the FilmArray BCID panel could be useful to perform microbiological diagnosis directly from samples other than positive blood cultures, as it offers acceptable sensitivity and moderate agreement with conventional microbiological methods. Nevertheless, cost-benefit studies should be performed before introducing this method into algorithms for microbiological diagnostics.

Diagnostic methods to determine microbiology of postpartum endometritis in South Asia: laboratory methods protocol used in the Postpartum Sepsis Study: a prospective cohort study.

PubMed

Shakoor, Sadia; Reller, Megan E; LeFevre, Amnesty; Hotwani, Aneeta; Qureshi, Shahida M; Yousuf, Farheen; Islam, Mohammad Shahidul; Connor, Nicholas; Rafiqullah, Iftekhar; Mir, Fatima; Arif, Shabina; Soofi, Sajid; Bartlett, Linda A; Saha, Samir

2016-02-25

The South Asian region has the second highest risk of maternal death in the world. To prevent maternal deaths due to sepsis and to decrease the maternal mortality ratio as per the World Health Organization Millenium Development Goals, a better understanding of the etiology of endometritis and related sepsis is required. We describe microbiological laboratory methods used in the maternal Postpartum Sepsis Study, which was conducted in Bangladesh and Pakistan, two populous countries in South Asia. Postpartum maternal fever in the community was evaluated by a physician and blood and urine were collected for routine analysis and culture. If endometritis was suspected, an endometrial brush sample was collected in the hospital for aerobic and anaerobic culture and molecular detection of bacterial etiologic agents (previously identified and/or plausible). The results emanating from this study will provide microbiologic evidence of the etiology and susceptibility pattern of agents recovered from patients with postpartum fever in South Asia, data critical for the development of evidence-based algorithms for management of postpartum fever in the region.

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues?

PubMed Central

Welker, Martin; Pincus, David; Charrier, Jean-Philippe; Girard, Victoria

2017-01-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement. PMID:28840984

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues?

PubMed

van Belkum, Alex; Welker, Martin; Pincus, David; Charrier, Jean Philippe; Girard, Victoria

2017-11-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement. © The Korean Society for Laboratory Medicine.

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology.

PubMed

Rossen, J W A; Friedrich, A W; Moran-Gilad, J

2018-04-01

Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. To review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. Review of the literature and expert opinion. In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories. Further development is required to improve the workflow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic field. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Atmospheric microbiology in the northern Caribbean during African dust events

USGS Publications Warehouse

Griffin, Dale W.; Kellogg, C.A.; Garrison, V.H.; Lisle, J.T.; Borden, T.C.; Shinn, E.A.

2003-01-01

Between July 2000 and August 2001 forty-three air samples were collected in the northern Caribbean: Twenty-six in the US Virgin Islands, and 17 samples aboard ship during two 1-week cruises. Samples were collected during African dust events and non-dust conditions and screened for the presence of culturable bacteria and fungi. A total of 3,652 liters of air were collected during non-dust conditions, with 19 bacteria and 28 fungi being recovered. During dust conditions a total of 2,369 liters of air were screened resulting in the recovery of 171 bacteria and 76 fungi. A statistically significant difference was found between the two data sets. These results support previous African dust research and further demonstrate that dust particles can serve as a vessel for the global dispersion of bacteria and fungi. Dustborne microorganisms may play a significant role in the ecology and health of downwind ecosystems.

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

AFNOR validation of Premi Test, a microbiological-based screening tube-test for the detection of antimicrobial residues in animal muscle tissue.

PubMed

Gaudin, Valerie; Juhel-Gaugain, Murielle; Morétain, Jean-Pierre; Sanders, Pascal

2008-12-01

Premi Test contains viable spores of a strain of Bacillus stearothermophilus which is sensitive to antimicrobial residues, such as beta-lactams, tetracyclines, macrolides and sulphonamides. The growth of the strain is inhibited by the presence of antimicrobial residues in muscle tissue samples. Premi Test was validated according to AFNOR rules (French Association for Normalisation). The AFNOR validation was based on the comparison of reference methods (French Official method, i.e. four plate test (FPT) and the STAR protocol (five plate test)) with the alternative method (Premi Test). A preliminary study was conducted in an expert laboratory (Community Reference Laboratory, CRL) on both spiked and incurred samples (field samples). Several method performance criteria (sensitivity, specificity, relative accuracy) were estimated and are discussed, in addition to detection capabilities. Adequate agreement was found between the alternative method and the reference methods. However, Premi Test was more sensitive to beta-lactams and sulphonamides than the FPT. Subsequently, a collaborative study with 11 laboratories was organised by the CRL. Blank and spiked meat juice samples were sent to participants. The expert laboratory (CRL) statistically analysed the results. It was concluded that Premi Test could be used for the routine determination of antimicrobial residues in muscle of different animal origin with acceptable analytical performance. The detection capabilities of Premi Test for beta-lactams (amoxicillin, ceftiofur), one macrolide (tylosin) and tetracycline were at the level of the respective maximum residue limits (MRL) in muscle samples or even lower.

Is This the Carbapenemase Test We've Been Waiting for? A Multicenter Evaluation of the Modified Carbapenem Inactivation Method.

PubMed

Butler-Wu, Susan M; Abbott, April N

2017-08-01

A plethora of phenotypic methods exist for the detection of carbapenemases; however, clinical laboratories have struggled for years with accurate, objective phenotypic detection of carbapenemase activity in Enterobacteriaceae In this issue of the Journal of Clinical Microbiology , V. M. Pierce et al. (J Clin Microbiol 55:2321-2333, 2017, https://doi.org/10.1128/JCM.00193-17) report on a multicenter evaluation of the modified carbapenem inactivation method (mCIM). The high sensitivity, specificity, reproducibility, and ease of interpretation associated with the mCIM for Enterobacteriaceae will likely lead to its adoption by clinical laboratories. Copyright © 2017 American Society for Microbiology.

Rapid microbiological screening for tuberculosis in HIV-positive patients on the first day of acute hospital admission by systematic testing of urine samples using Xpert MTB/RIF: a prospective cohort in South Africa.

PubMed

Lawn, Stephen D; Kerkhoff, Andrew D; Burton, Rosie; Schutz, Charlotte; van Wyk, Gavin; Vogt, Monica; Pahlana, Pearl; Nicol, Mark P; Meintjes, Graeme

2015-08-14

Autopsy studies of HIV/AIDS-related hospital deaths in sub-Saharan Africa reveal frequent failure of pre-mortem diagnosis of tuberculosis (TB), which is found in 34-64 % of adult cadavers. We determined the overall prevalence and predictors of TB among consecutive unselected HIV-positive adults requiring acute hospital admission and the comparative diagnostic yield obtained by screening urine and sputum samples obtained on day 1 of admission with Xpert MTB/RIF (Xpert). To determine overall TB prevalence accurately, comprehensive clinical sampling (sputum, urine, blood plus other relevant samples) was done and TB was defined by detection of Mycobacterium tuberculosis in any sample using Xpert and/or mycobacterial liquid culture. To evaluate a rapid screening strategy, we compared the diagnostic yield of Xpert testing sputum samples and urine samples obtained with assistance from a respiratory study nurse in the first 24 h of admission. Unselected HIV-positive acute adult new medical admissions (n = 427) who were not receiving TB treatment were enrolled irrespective of clinical presentation or symptom profile. From 2,391 cultures and Xpert tests done (mean, 5.6 tests/patient) on 1,745 samples (mean, 4.1 samples/patient), TB was diagnosed in 139 patients (median CD4 cell count, 80 cells/μL). TB prevalence was very high (32.6 %; 95 % CI, 28.1-37.2 %; 139/427). However, patient symptoms and risk factors were poorly predictive for TB. Overall, ≥1 non-respiratory sample(s) tested positive in 115/139 (83 %) of all TB cases, including positive blood cultures in 41/139 (29.5 %) of TB cases. In the first 24 h of admission, sputum (spot and/or induced samples) and urine were obtainable from 37.0 % and 99.5 % of patients, respectively (P <0.001). From these, the proportions of total TB cases (n = 139) that were diagnosed by Xpert testing sputum, urine or both sputum and urine combined within the first 24 h were 39/139 (28.1 %), 89/139 (64.0 %) and 108/139 (77.7 %) cases, respectively (P <0.001). The very high prevalence of active TB and its non-specific presentation strongly suggest the need for routine microbiological screening for TB in all HIV-positive medical admissions in high-burden settings. The incremental diagnostic yield from Xpert testing urine was very high and this strategy might be used to rapidly screen new admissions, especially if sputum is difficult to obtain.

Residual antibiotics in decontaminated human cardiovascular tissues intended for transplantation and risk of falsely negative microbiological analyses.

PubMed

Buzzi, Marina; Guarino, Anna; Gatto, Claudio; Manara, Sabrina; Dainese, Luca; Polvani, Gianluca; Tóthová, Jana D'Amato

2014-01-01

We investigated the presence of antibiotics in cryopreserved cardiovascular tissues and cryopreservation media, after tissue decontamination with antibiotic cocktails, and the impact of antibiotic residues on standard tissue bank microbiological analyses. Sixteen cardiovascular tissues were decontaminated with bank-prepared cocktails and cryopreserved by two different tissue banks according to their standard operating procedures. Before and after decontamination, samples underwent microbiological analysis by standard tissue bank methods. Cryopreserved samples were tested again with and without the removal of antibiotic residues using a RESEP tube, after thawing. Presence of antibiotics in tissue homogenates and processing liquids was determined by a modified agar diffusion test. All cryopreserved tissue homogenates and cryopreservation media induced important inhibition zones on both Staphylococcus aureus- and Pseudomonas aeruginosa-seeded plates, immediately after thawing and at the end of the sterility test. The RESEP tube treatment markedly reduced or totally eliminated the antimicrobial activity of tested tissues and media. Based on standard tissue bank analysis, 50% of tissues were found positive for bacteria and/or fungi, before decontamination and 2 out of 16 tested samples (13%) still contained microorganisms after decontamination. After thawing, none of the 16 cryopreserved samples resulted positive with direct inoculum method. When the same samples were tested after removal of antibiotic residues, 8 out of 16 (50%) were contaminated. Antibiotic residues present in tissue allografts and processing liquids after decontamination may mask microbial contamination during microbiological analysis performed with standard tissue bank methods, thus resulting in false negatives.

Residual Antibiotics in Decontaminated Human Cardiovascular Tissues Intended for Transplantation and Risk of Falsely Negative Microbiological Analyses

PubMed Central

Gatto, Claudio; Manara, Sabrina; Dainese, Luca; Polvani, Gianluca; Tóthová, Jana D'Amato

2014-01-01

We investigated the presence of antibiotics in cryopreserved cardiovascular tissues and cryopreservation media, after tissue decontamination with antibiotic cocktails, and the impact of antibiotic residues on standard tissue bank microbiological analyses. Sixteen cardiovascular tissues were decontaminated with bank-prepared cocktails and cryopreserved by two different tissue banks according to their standard operating procedures. Before and after decontamination, samples underwent microbiological analysis by standard tissue bank methods. Cryopreserved samples were tested again with and without the removal of antibiotic residues using a RESEP tube, after thawing. Presence of antibiotics in tissue homogenates and processing liquids was determined by a modified agar diffusion test. All cryopreserved tissue homogenates and cryopreservation media induced important inhibition zones on both Staphylococcus aureus- and Pseudomonas aeruginosa-seeded plates, immediately after thawing and at the end of the sterility test. The RESEP tube treatment markedly reduced or totally eliminated the antimicrobial activity of tested tissues and media. Based on standard tissue bank analysis, 50% of tissues were found positive for bacteria and/or fungi, before decontamination and 2 out of 16 tested samples (13%) still contained microorganisms after decontamination. After thawing, none of the 16 cryopreserved samples resulted positive with direct inoculum method. When the same samples were tested after removal of antibiotic residues, 8 out of 16 (50%) were contaminated. Antibiotic residues present in tissue allografts and processing liquids after decontamination may mask microbial contamination during microbiological analysis performed with standard tissue bank methods, thus resulting in false negatives. PMID:25397402

Internal audit in a microbiology laboratory.

PubMed Central

Mifsud, A J; Shafi, M S

1995-01-01

AIM--To set up a programme of internal laboratory audit in a medical microbiology laboratory. METHODS--A model of laboratory based process audit is described. Laboratory activities were examined in turn by specimen type. Standards were set using laboratory standard operating procedures; practice was observed using a purpose designed questionnaire and the data were analysed by computer; performance was assessed at laboratory audit meetings; and the audit circle was closed by re-auditing topics after an interval. RESULTS--Improvements in performance scores (objective measures) and in staff morale (subjective impression) were observed. CONCLUSIONS--This model of process audit could be applied, with amendments to take local practice into account, in any microbiology laboratory. PMID:7665701

[Microbiological validation of the composition of "decaceol", an antiseptic prolonged-release drug].

PubMed

Dykyĭ, I L; Zaĭtsev, O I; Filimonova, N I

2002-01-01

With the aid of different microbiological methods, antimicrobal properties of decametoxine, a home-produced antiseptic, were studied together with those of the synthetic zoelite NaA-base drug preparation. The antimicrobial activity of the above drug has been shown to be of a synergistic character that makes it a very promising medical agent which will, we believe, come to be widely used in medical practice.

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards.

PubMed

Lech, Tomasz

2016-05-01

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum,Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereuss train was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Two efficient nitrite-reducing Lactobacillus strains isolated from traditional fermented pork (Nanx Wudl) as competitive starter cultures for Chinese fermented dry sausage.

PubMed

Chen, Xi; Li, Jiapeng; Zhou, Tong; Li, Jinchun; Yang, Junna; Chen, Wenhua; Xiong, Youling L

2016-11-01

Lactic acid bacteria isolated from traditional Dong pork product (Nanx Wudl) were investigated for their potential as starter cultures for Chinese fermented dry sausages. Based on preliminary screening, Lactobacillus plantarum CMRC6 and Lactobacillus sakei CMRC15, both showing excellent nitrite-reducing capacity, were used as single-strain starter cultures. For comparison, a commercial composite starter was also tested. In CMRC6 and CMRC15-inoculated sausages, lactic acid bacteria dominated the microflora and improved the microbiological safety by suppression of Enterobacteriaceae growth. Nitrite content of all inoculated sausages declined rapidly during ripening compared to non-inoculated. Texture profiles analysis showed inoculated sausages had more pronounced textural development during ripening. Sensory evaluation indicated CMRC6 and CMRC15-fermented sausages had comparable or more desirable organoleptic characteristics than sausage made with commercial starters. Therefore, CMRC6 and CMRC15 are promising candidates as multi-functional starter cultures for microbiological safety and residual nitrite control in gourmet Chinese dry sausage production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Competency Assessment of Microbiology Medical Laboratory Technologists in Ontario, Canada

PubMed Central

Fleming, Christine Ann

2014-01-01

Accreditation in Ontario, Canada, requires that licensed clinical laboratories participate in external quality assessment (also known as proficiency testing) and perform competency evaluation of their staff. To assess the extent of ongoing competency assessment practices, the Quality Management Program—Laboratory Services (QMP-LS) Microbiology Committee surveyed all 112 licensed Ontario microbiology laboratories. The questionnaire consisted of a total of 21 questions that included yes/no, multiple-choice, and short-answer formats. Participants were asked to provide information about existing programs, the frequency of testing, what areas are evaluated, and how results are communicated to the staff. Of the 111 responding laboratories, 6 indicated they did not have a formal evaluation program since they perform only limited bacteriology testing. Of the remaining 105 respondents, 87% perform evaluations at least annually or every 2 years, and 61% include any test or task performed, whereas 16% and 10% focus only on problem areas and high-volume complex tasks, respectively. The most common methods of evaluation were review of external quality assessment (EQA) challenges, direct observation, and worksheet review. With the exception of one participant, all communicate results to staff, and most take remedial action to correct the deficiencies. Although most accredited laboratories have a program to assess the ongoing competency of their staff, the methods used are not standardized or consistently applied, indicating that there is room for improvement. The survey successfully highlighted potential areas for improvement and allowed the QMP-LS Microbiology Committee to provide guidance to Ontario laboratories for establishing or improving existing microbiology-specific competency assessment programs. PMID:24899030

Microbiological purity assessment of cosmetics used by one and several persons and cosmetics after their expiry date

PubMed

Skowron, Krzysztof; Jakubicz, Agnieszka; Budzyńska, Anna; Kaczmarek, Agnieszka; Grudlewska, Katarzyna; Reśliński, Adrian; Gospodarek-Komkowska, Eugenia

Microbiological purity of cosmetics provides safety of users during their use, prevents physicochemical changes of a preparation, infections and diseases of the skin. The aim of this study was to assess the level of microbiological contamination of cosmetics used by one person and by several people and cosmetics after their expiry date in relations to standards for marketed cosmetics, ensuring safety of their use. This study was conducted using 55 samples representing 19 types of cosmetics, divided into three groups: used by one person, used by several people and after the expiry date. In cosmetic samples the general numbers of aerobic mesophilic bacteria were determined with the spread plate method on tryptic-soy agar. The presence of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans were also checked. The number of aerobic mesophylic bacteria in the tested cosmetics ranged from the level below the method detectability to 1.3×107 cfu/g or ml. The presence of Staphylococcus spp. was found in 11 (20.0%) tested cosmetic samples and of P. aeruginosa in one tested preparation. Yeasts C. albicans were not detected, whereas contamination with fungi Aspergillus spp. and Penicillium spp. ranging from 0.5×101 to 1.5×101 cfu/g or ml was recorded in four cosmetics. The level of microbiological contamination of cosmetics used by several people was higher than that of cosmetics used by one person. Cosmetics after the expiry date showed the highest microbiological contamination. The number of users of cosmetic and it expiry date exceeding influenced the level of microbial contamination of preparations.

Diagnostic performance of blood culture bottles for vitreous culture compared to conventional microbiological cultures in patients with suspected endophthalmitis.

PubMed

Kehrmann, Jan; Chapot, Valerie; Buer, Jan; Rating, Philipp; Bornfeld, Norbert; Steinmann, Joerg

2018-05-01

The purpose of this investigation was to evaluate the performance of blood culture bottles in comparison to conventional microbiological culture techniques in detecting causative microorganisms of endophthalmitis and to determine their anti-infective susceptibility profiles. All consecutive cases with clinically suspected endophthalmitis in a university-based ophthalmology department between January 2009 and December 2016 were analysed in this retrospective comparative case series. Samples from 247 patients with suspected endophthalmitis underwent microbiological diagnostic work-up. All three culture methods were performed from 140 vitreous specimens. Vitreous fluid specimens were inoculated in blood culture bottles, aerobic and anaerobic broth solutions, and on solid media. Anti-infective susceptibility profiles were evaluated by semi-automated methods and/or gradient diffusion methods. Microorganisms were grown in 82 of 140 specimens for which all methods were performed (59%). Microorganisms were more frequently grown from blood culture bottles (55%) compared to broth solution (45%, p = 0.007) and solid media (33%, p < 0.0001). Considerable differences in the performance among culture media were detected for fungal pathogens. All grown fungi were detected by blood culture bottles (11 of 11, 100%). Broth solution recovered 64% and solid media 46% of grown fungi. No Gram-positive bacterium was resistant to vancomycin and all Gram-negative pathogens except for one isolate were susceptible to third-generation cephalosporins. In suspected endophthalmitis patients, blood culture bottles have a higher overall pathogen detection rate from vitreous fluid compared to conventional microbiological media, especially for fungi. The initial intravitreal antibiotic therapy with vancomycin plus third-generation cephalosporins appears to be an appropriate treatment approach for bacterial endophthalmitis.

Brewing for Students: An Inquiry-Based Microbiology Lab †

PubMed Central

Sato, Brian K.; Alam, Usman; Dacanay, Samantha J.; Lee, Amanda K.; Shaffer, Justin F.

2015-01-01

In an effort to improve and assess student learning, there has been a push to increase the incorporation of discovery-driven modules and those that contain real-world relevance into laboratory curricula. To further this effort, we have developed, implemented, and assessed an undergraduate microbiology laboratory experiment that requires students to use the scientific method while brewing beer. The experiment allows students to brew their own beer and characterize it based on taste, alcohol content, calorie content, pH, and standard reference method. In addition, we assessed whether students were capable of achieving the module learning objectives through a pre-/posttest, student self-evaluation, exam-embedded questions, and an associated worksheet. These objectives included describing the role of the brewing ingredients and predicting how altering the ingredients would affect the characteristics of the beer, amongst others. By completing this experimental module, students accomplished the module objectives, had greater interest in brewing, and were more likely to view beer in scientific terms. Journal of Microbiology & Biology Education PMID:26753030

Effect of different packaging methods and storage temperature on microbiological and physicochemical quality characteristics of meatball.

PubMed

Yilmaz, I; Demirci, M

2010-06-01

The objective of this research was to determine physicochemical changes and microbiological quality of the different packaged meatball samples. Meatball samples in polystyrene tray were closed with polyethylene film (PS packs), vacuumed and modified atmosphere packaged, (MAP) (65% N(2), 35% CO(2)), and held under refrigerated display (4 °C) for 8, 16 and 16 days for PS packs, vacuum and MAP, respectively. Microbial load, free fatty acids and thiobarbituric acid values of the samples tended to increase with storage time. Bacteria counts of the raw meatball samples increased 2 log cycles at the end of storage compared with initial values. Meatball samples can be stored without any microbiological problem for 7 days at 4 °C. Results from this study suggested that shelf-life assigned to modified-MAP and vacuum-packed meatballs may be appropriate. Meatball samples underwent physical deformation when they were packed before vacuum process. With these negative factors considered, MAP is superior to other two packs methods.

Brewing for Students: An Inquiry-Based Microbiology Lab.

PubMed

Sato, Brian K; Alam, Usman; Dacanay, Samantha J; Lee, Amanda K; Shaffer, Justin F

2015-12-01

In an effort to improve and assess student learning, there has been a push to increase the incorporation of discovery-driven modules and those that contain real-world relevance into laboratory curricula. To further this effort, we have developed, implemented, and assessed an undergraduate microbiology laboratory experiment that requires students to use the scientific method while brewing beer. The experiment allows students to brew their own beer and characterize it based on taste, alcohol content, calorie content, pH, and standard reference method. In addition, we assessed whether students were capable of achieving the module learning objectives through a pre-/posttest, student self-evaluation, exam-embedded questions, and an associated worksheet. These objectives included describing the role of the brewing ingredients and predicting how altering the ingredients would affect the characteristics of the beer, amongst others. By completing this experimental module, students accomplished the module objectives, had greater interest in brewing, and were more likely to view beer in scientific terms. Journal of Microbiology & Biology Education.

A study of the impact of collaborative learning on student learning of major concepts in a microbiology laboratory exercise

NASA Astrophysics Data System (ADS)

Baumgarten, Kristyne A.

This study investigated the possible relationship between collaborative learning strategies and the learning of core concepts. This study examined the differences between two groups of nursing students enrolled in an introductory microbiology laboratory course. The control group consisted of students enrolled in sections taught in the traditional method. The experimental group consisted of those students enrolled in the sections using collaborative learning strategies. The groups were assessed on their degrees of learning core concepts using a pre-test/post-test method. Scores from the groups' laboratory reports were also analyzed. There was no difference in the two group's pre-test scores. The post-test scores of the experimental group averaged 11 points higher than the scores of the control group. The lab report scores of the experimental group averaged 15 points higher than those scores of the control group. The data generated from this study demonstrated that collaborative learning strategies can be used to increase students learning of core concepts in microbiology labs.

The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms.

PubMed

Ingham, Colin J; Sprenkels, Ad; Bomer, Johan; Molenaar, Douwe; van den Berg, Albert; van Hylckama Vlieg, Johan E T; de Vos, Willem M

2007-11-13

A miniaturized, disposable microbial culture chip has been fabricated by microengineering a highly porous ceramic sheet with up to one million growth compartments. This versatile culture format, with discrete compartments as small as 7 x 7 mum, allowed the growth of segregated microbial samples at an unprecedented density. The chip has been used for four complementary applications in microbiology. (i) As a fast viable counting system that showed a dynamic range of over 10,000, a low degree of bias, and a high culturing efficiency. (ii) In high-throughput screening, with the recovery of 1 fluorescent microcolony in 10,000. (iii) In screening for an enzyme-based, nondominant phenotype by the targeted recovery of Escherichia coli transformed with the plasmid pUC18, based on expression of the lacZ reporter gene without antibiotic-resistance selection. The ease of rapid, successive changes in the environment of the organisms on the chip, needed for detection of beta-galactosidase activity, highlights an advantageous feature that was also used to screen a metagenomic library for the same activity. (iv) In high-throughput screening of >200,000 isolates from Rhine water based on metabolism of a fluorogenic organophosphate compound, resulting in the recovery of 22 microcolonies with the desired phenotype. These isolates were predicted, on the basis of rRNA sequence, to include six new species. These four applications suggest that the potential for such simple, readily manufactured chips to impact microbial culture is extensive and may facilitate the full automation and multiplexing of microbial culturing, screening, counting, and selection.

Challenges encountered in the diagnosis of tuberculous otitis media: case report and literature review.

PubMed

Dale, O T; Clarke, A R; Drysdale, A J

2011-07-01

To report a rare case of tuberculous otitis media, and to highlight barriers to clinical and microbiological diagnosis. Case report and literature review. Tuberculous otitis media is a rare cause of chronic ear infection in the UK. Its symptoms may mimic a range of other otological conditions, including otitis media, chronic suppurative otitis media, cholesteatoma and necrotising otitis media. This case report highlights the challenges of obtaining a clinical diagnosis of tuberculous otitis media, and emphasises the fact that screening for acid-fast bacilli is not sufficient, in isolation, to rule out mycobacterial infection.

The clinical and microbiological correlates of premature rupture of membranes.

PubMed

Karat, C; Madhivanan, P; Krupp, K; Poornima, S; Jayanthi, N V; Suguna, J S; Mathai, E

2006-10-01

Prematurity is the cause of 85% of neonatal morbidity and mortality. Premature rupture of the membranes (PROM) is associated with 30-40% of preterm deliveries. A case-control study conducted between July 2002 and 2003 examined the correlates and risk factors for PROM in Mysore, India. WBCs in vaginal fluid, leucocytes in urine, UTI and infection with E. coli, S. aureus, C. albicans and BV were significantly associated with PROM. BV, E. coli and WBCs in vaginal fluid were independent risk factors. Screening and treatment of BV and E. coli infection in pregnancy may reduce the risk of PROM.

Development of freeze dried vegetables

NASA Technical Reports Server (NTRS)

Larson, R. W.

1970-01-01

The development of freeze dried vegetables to be used in the Apollo food system is discussed. After the initial selection and screening of vegetables, several types of freeze dried vegetables were prepared in small batches. From these small batches, two vegetables were judged satisfactory for further testing and evaluation. These vegetables, mashed potatoes and asparagus, were subjected to storage at 100 deg plus or minus 5 F. for two weeks and then taste tested. The vegetables were also tested to determine if they complied with the microbiological requirements for Apollo food. The space food prototype production guide for the vegetables is submitted.

An integrated approach to control a prolonged outbreak of multidrug-resistant Pseudomonas aeruginosa in an intensive care unit.

PubMed

Knoester, M; de Boer, M G J; Maarleveld, J J; Claas, E C J; Bernards, A T; de Jonge, E; van Dissel, J T; Veldkamp, K E

2014-04-01

In this paper we aim to provide insight into the complexity of outbreak management in an intensive care unit (ICU) setting. In October 2010 four patients on the ICU of our tertiary care centre were colonized or infected with a multidrug-resistant strain of Pseudomonas aeruginosa (MDR-PA). An outbreak investigation was carried out and infection control measures were taken in an attempt to identify a potential source and stop transmission. The outbreak investigation included descriptive epidemiology, comprising retrospective case finding by reviewing the laboratory information system back to 2004 and prospective case finding by patient screening for MDR-PA. Furthermore, microbiological analysis, environmental screening and a case-control study were carried out. Infection control measures consisted of re-education of healthcare personnel on basic hygiene measures, auditing of hygiene procedures used in daily practice by infection control practitioners, and stepwise up-regulation of isolation measures. From February 2009 to January 2012, 44 patients on our ICU were found to be MDR-PA positive. MDR-PA isolates of the 44 patients showed two distinct AFLP patterns, with homology within each of the AFLP clusters of more than 93%. The VIM metallo-β-lactamase gene was detected in 20 of 21 tested isolates. A descriptive epidemiology investigation identified the rooms with the highest numbers of MDR-PA positive patients. The case-control study showed three factors to be independently associated with MDR-PA positivity: admission to ICU subunit 1 (OR, 6.1; 95% CI, 1.7, 22), surgery prior to or during admission (OR, 5.7; 95% CI, 1.6, 20) and being warmed-up with the warm-air blanket (OR, 3.6; 95% CI, 1.2, 11). After three environmental screening rounds, with sampling of sinks, furniture and devices in the ICU, without revealing a clear common source, a fourth environmental investigation included culturing of faucet aerators. Two faucets were found to be positive for MDR-PA and were replaced. The occurrence of new cases decreased with the strengthening of infection control measures and declined further with the removal of the common source. With this integrated approach a prolonged outbreak of P. aeruginosa was controlled. Contaminated faucet aerators on the ICU probably served as a persisting source, while interpatient transmission by medical staff was a likely way of spread. Seven months after the last case (January 2012) and 3 months after cessation of extended isolation measures (May 2012), single cases started to occur on the ICU, with a total of seven patients in the past year. No common source has yet been found. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Transformation From a Conventional Clinical Microbiology Laboratory to Full Automation.

PubMed

Moreno-Camacho, José L; Calva-Espinosa, Diana Y; Leal-Leyva, Yoseli Y; Elizalde-Olivas, Dolores C; Campos-Romero, Abraham; Alcántar-Fernández, Jonathan

2017-12-22

To validate the performance, reproducibility, and reliability of BD automated instruments in order to establish a fully automated clinical microbiology laboratory. We used control strains and clinical samples to assess the accuracy, reproducibility, and reliability of the BD Kiestra WCA, the BD Phoenix, and BD Bruker MALDI-Biotyper instruments and compared them to previously established conventional methods. The following processes were evaluated: sample inoculation and spreading, colony counts, sorting of cultures, antibiotic susceptibility test, and microbial identification. The BD Kiestra recovered single colonies in less time than conventional methods (e.g. E. coli, 7h vs 10h, respectively) and agreement between both methodologies was excellent for colony counts (κ=0.824) and sorting cultures (κ=0.821). Antibiotic susceptibility tests performed with BD Phoenix and disk diffusion demonstrated 96.3% agreement with both methods. Finally, we compared microbial identification in BD Phoenix and Bruker MALDI-Biotyper and observed perfect agreement (κ=1) and identification at a species level for control strains. Together these instruments allow us to process clinical urine samples in 36h (effective time). The BD automated technologies have improved performance compared with conventional methods, and are suitable for its implementation in very busy microbiology laboratories. © American Society for Clinical Pathology 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

[Microbiological analysis of red octopus in fishing ports of Campeche, Mexico].

PubMed

Estrella-Gómez, Neyi; Escalante-Réndiz, Diana; González-Burgos, Araceli; Sosa-Cordero, Delta; Rojas-Herrera, Rafael

2016-08-01

In this work we studied the microbiological quality of the red octopus given its important economic and social impact on the region South-Southeast of Mexico. Samples were taken in different areas of capture of the species and analyzed with biochemical tests described in the Mexican official standards, identifying strains belonging to the genus Vibrio, Salmonella and faecal coliforms, and E. coli O157: H7. We used the BAx System for the identification of microorganisms through their bacterial DNA. The results obtained in biochemical and molecular methods were confirmed. Bland-Altman statistical method pointed out that both techniques can be used interchangeably. McNemar test showed that both methods have the same efficacy for the identification of pathogens (value X2=0.5 ρ=0.4795). The microbiological quality of the octopus in the South-Southeast region of Mexico is deficient due to the presence of pathogenic intestinal flora that might represent an epidemiological risk. The indexes established by the regulations suggest the need to apply effective and rapid identification technologies, such as the BAx System.This alternative method of analysis can contribute to the implementation of effective strategies that allow compliance with the minimal sanitary specifications during the processing of fishing products, thus strengthening the control systems to decrease the risks of epidemiological outbreaks in the region.

[Microbiological point of care tests].

PubMed

Book, Malte; Lehmann, Lutz Eric; Zhang, Xianghong; Stüber, Frank

2010-11-01

It is well known that the early initiation of a specific antiinfective therapy is crucial to reduce the mortality in severe infection. Procedures culturing pathogens are the diagnostic gold standard in such diseases. However, these methods yield results earliest between 24 to 48 hours. Therefore, severe infections such as sepsis need to be treated with an empirical antimicrobial therapy, which is ineffective in an unknown fraction of these patients. Today's microbiological point of care tests are pathogen specific and therefore not appropriate for an infection with a variety of possible pathogens. Molecular nucleic acid diagnostics such as polymerase chain reaction (PCR) allow the identification of pathogens and resistances. These methods are used routinely to speed up the analysis of positive blood cultures. The newest PCR based system allows the identification of the 25 most frequent sepsis pathogens by PCR in parallel without previous culture in less than 6 hours. Thereby, these systems might shorten the time of possibly insufficient antiinfective therapy. However, these extensive tools are not suitable as point of care diagnostics. Miniaturization and automating of the nucleic acid based method is pending, as well as an increase of detectable pathogens and resistance genes by these methods. It is assumed that molecular PCR techniques will have an increasing impact on microbiological diagnostics in the future. © Georg Thieme Verlag Stuttgart · New York.

Evaluation of the Biomic V3 Microbiology System for Identification of Selected Species on BBL CHROMagar Orientation Agar and CHROMagar MRSA Medium ▿

PubMed Central

Baron, Ellen Jo; D'Souza, Holly; Qi Wang, Andrew; Gibbs, David L.

2008-01-01

The Biomic V3 microbiology system identifies bacteria by reading the color of colonies selected by the user. For CHROMagar orientation, Biomic results agreed with conventional methods for 94% of the strains assayed. For CHROMagar MRSA, Biomic correctly identified 100% of the strains tested and did not misidentify two methicillin-susceptible Staphylococcus aureus strains growing on the plates. PMID:18701661

Microbiological sampling of returned Surveyor 3 electrical cabling

NASA Technical Reports Server (NTRS)

Knittel, M. D.; Favero, M. S.; Green, R. H.

1972-01-01

A piece of electrical wiring bundle running from the television camera to another part of the spacecraft was selected for microbiological examination. Sampling methods are discussed. The results presented show that no viable microorganisms were recovered from the part of the Surveyor 3 cable which was tested. Factors that could have contributed to the sterility of the cable are thermal vacuum testing, natural dieoff, change in pressure during launch, and lunar vacuum and temperature.

A Review of Green Strategies to Prevent or Mitigate Microbiologically Influenced Corrosion

DTIC Science & Technology

2007-01-01

microbiologically influenced corrosion (MIC) has may provide nutrients for regrowth. been to use oxidising (e.g. chlorine, bromine, ozone ) Videla et al...MPN method: 6cells/cm2 Total bacteria Figure 6. Number of bacteria in biofilm using two detection techniques : fluorescent antibody (FA) and most...nitrite, lation of nitrate- utilising bacteria in the system. nitrous oxide or nitrogen and oxidising sulfide to Hubert et al. (2006) suggested that

A cylinder-plate method for microbiological assay of clavulanic acid.

PubMed

Hamedi, J; Shahverdi, A R; Samadi, N; Mohammadi, A; Shiran, M; Akhondi, S

2006-12-01

Clavulanic acid is a natural occurring beta-lactam product of Streptomyces clavuligerus and is a potent inhibitor of bacterial beta-lactamases. The present work reports a microbiological assay based on the cylinder-plate method for determination of clavulanic acid. The assay is based on the inhibitory effect of clavulanic acid in combination with penicillin G upon Escherichia coli ATCC 35218, which is used as the test organism. The correlation between clavulanic acid concentration and the inhibitory effect on E. coli was linear (r > 0.99) and in the range of 8-20 microg/ml. These results indicate that the proposed method is appropriate for the determination of clavulanic acid in commercial samples and can be used in routine quality control.

Evaluation of a multiplex real-time PCR method for detecting shiga toxin-producing Escherichia coli in beef and comparison to the U.S. Department of Agriculture Food Safety and Inspection Service Microbiology laboratory guidebook method.

PubMed

Fratamico, Pina M; Wasilenko, Jamie L; Garman, Bradley; Demarco, Daniel R; Varkey, Stephen; Jensen, Mark; Rhoden, Kyle; Tice, George

2014-02-01

The "top-six" non-O157 Shiga toxin-producing Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) most frequently associated with outbreaks and cases of foodborne illnesses have been declared as adulterants in beef by the U.S. Department of Agriculture Food Safety and Inspection Service (FSIS). Regulatory testing in beef began in June 2012. The purpose of this study was to evaluate the DuPont BAX System method for detecting these top six STEC strains and strains of E. coli O157:H7. For STEC, the BAX System real-time STEC suite was evaluated, including a screening assay for the stx and eae virulence genes and two panel assays to identify the target serogroups: panel 1 detects O26, O111, and O121, and panel 2 detects O45, O103, O145. For E. coli O157:H7, the BAX System real-time PCR assay for this specific serotype was used. Sensitivity of each assay for the PCR targets was ≥1.23 × 10(3) CFU/ml in pure culture. Each assay was 100% inclusive for the strains tested (20 to 50 per assay), and no cross-reactivity with closely related strains was observed in any of the assays. The performance of the BAX System methods was compared with that of the FSIS Microbiology Laboratory Guidebook (MLG) methods for detection of the top six STEC and E. coli O157:H7 strains in ground beef and beef trim. Generally, results of the BAX System method were similar to those of the MLG methods for detecting non-O157 STEC and E. coli O157:H7. Reducing or eliminating novobiocin in modified tryptic soy broth (mTSB) may improve the detection of STEC O111 strains; one beef trim sample inoculated with STEC O111 produced a negative result when enriched in mTSB with 8 mg/liter novobiocin but was positive when enriched in mTSB without novobiocin. The results of this study indicate the feasibility of deploying a panel of real-time PCR assay configurations for the detection and monitoring of the top six STEC and E. coli O157:H7 strains in beef. The approach could easily be adapted for additional multiplex assays should regulations expand to include other O serogroups or virulence genes.

Microbiological concerns and methodological approaches related to bacterial water quality in spaceflight

NASA Technical Reports Server (NTRS)

Pyle, Barry H.; Mcfeters, Gordon A.

1992-01-01

A number of microbiological issues are of critical importance to crew health and system performance in spacecraft water systems. This presentation reviews an army of these concerns which include factors that influence water treatment and disinfection in spaceflight such as biofilm formation and the physiological responses of bacteria in clean water systems. Factors associated with spaceflight like aerosol formation under conditions of microgravity are also discussed within the context of airborne infections such as Legionellosis. Finally, a spectrum of analytical approaches is reviewed to provide an evaluation of methodological alternatives that have been suggested or used to detect microorganisms of interest in water systems. These range from classical approaches employing colony formation on specific microbiological growth media to direct (i.e. microscopic) and indirect (e.g. electrochemical) methods as well as the use of molecular approaches and gene probes. These techniques are critically evaluated for their potential utility in determining microbiological water quality through the detection of microorganisms under the influence of ambient environmental stress inherent in spaceflight water systems.

[Dr Guillermo Contreras Da Silva, a relevant figure in the development of Chilean microbiology].

PubMed

Cabello, Felipe C

2008-02-01

The influence of the work of Dr. Guillermo Contreras Da Silva and his colaborators on the evolution of microbiology in Chile is briefly analyzed. Dr. Contreras was trained in modern virology at Yale University with Dr. J. Melnick under the sponsorhip of the Rockefeller Foundation. During this training, he used serological methods to classify Cocksakie viruses. After his return to Chile, he studied the epidemiology of enteroviruses, including poliovirus. His laboratory, the country's first in modern virology, took an active role in Chile's first Sabin polio vaccination in 1961. Dr. Contreras and his group transformed the teaching and the character of microbiology in Chile from a descriptive medically oriented discipline into an autonomous, quantitative and experimental science. They modernized microbiology with the introduction of molecular biology and microbial genetics and fostered collaborations with allied biological sciences. Dr. Contreras was a Guggenheim Fellow, and until his retirement, was the Chief of the Viral Products Division, Bureau of Biologies, Ottawa, Canada.

Trichomycosis (Trichobacteriosis): Clinical and Microbiological Experience with 56 Cases

PubMed Central

Bonifaz, Alexandro; Váquez-González, Denisse; Fierro, Leonel; Araiza, Javier; Ponce, Rosa María

2013-01-01

Background: Trichomycosis is asymptomatic bacterial infection of the axillary hairs caused by Corynebacterium sp. Objective: to bring a series of cases of trichomycosis, its clinical and microbiological experience. Materials and Methods: This report consists in a linear and observational retrospective study of 15 years of cases of trichomycosis confirmed clinically and microbiologically. Results: Fifty six confirmed cases of trichomycosis were included in this report. The majority were men 53/56 (94.6%), mean age was 32.5 years. The most commonly affected area was the axilla (92%), trichomycosis flava was the principal variant 55/56 (98.2%) and signs and symptoms associated were hyperhidrosis (87.5%), hairs’ texture change (57.1%) and odor (35.7%). Bacterial concretions were observed in all cases, and the predominant causative agent in 89.3% of all cases was Corynebacterium sp. Thirty patients were included in therapeutic portion of the study, and 28 (93.3%) of them experienced a clinical and microbiological cure. Conclusion: Trichomycosis is asymptomatic, superficial infection, which primarily affects axillary hairs. PMID:23960390

Health surveillance of specific pathogen-free and conventionally-housed mice and rats in Korea.

PubMed

Seok, Seunghyeok; Park, Jonghwan; Cho, Suna; Baek, Minwon; Lee, Huiyoung; Kim, Dongjae; Yang, Kihwa; Jang, Dongdeuk; Han, Beomseok; Nam, Kitaek; Park, Jaehak

2005-01-01

The present study contains information about proper microbiological monitoring of laboratory animals' health and the standardization of microbiological monitoring methods in Korea. Microbiological quality control for laboratory animals, composed of biosecurity and health surveillance, is essential to guard against research complications and public health dangers that have been associated with adventitious infections. In this study, one hundred and twenty-two mice and ninety rats from laboratory animal breeding companies and one animal facility of the national universities in Korea were monitored in 2000-2003. Histopathologically, thickening of the alveolar walls and lymphocytic infiltration around the bronchioles were observed in mice and rats from microbiologically contaminated facilities. Cryptosporidial oocysts were observed in the gastric pits of only conventionally-housed mice and rats. Helicobacter spp. infection was also detected in 1 of 24 feces DNA samples in mice and 9 of 40 feces DNA samples in rats by PCR in 2003, but they were not Helicobacter hepaticus. This paper describes bacteriological, parasitological, and virological examinations of the animals.

Large two-centre study into the prevalence of Mycoplasma genitalium and Trichomonas vaginalis in the Netherlands.

PubMed

de Jong, A S; Rahamat-Langendoen, J C; van Alphen, Ptw; Hilt, N; van Herk, Cmc; Pont, Sbeh; Melchers, Wjg; van de Bovenkamp, Jhb

2016-09-01

Mycoplasma genitalium and Trichomonas vaginalis are common sexually transmitted infections (STIs). In the Netherlands, testing for M. genitalium and T. vaginalis is not recommended for first-line STI screening. Recent reports about the increasing antimicrobial resistance in M. genitalium raise concern about the adequacy of current empirical treatment regimens. It is necessary to have insight in the prevalence of M. genitalium and T. vaginalis in order to evaluate current first-line STI screening and treatment protocols. During a five-month period, samples sent to two large medical microbiology diagnostic centres in the Netherlands for STI screening (Chlamydia trachomatis and Neisseria gonorrhoeae) were retrospectively tested for the prevalence of M. genitalium and T. vaginalis using the Diagenode S-DiaMGTV kit. A total of 1569 samples from 1188 unique patients (55.4% female) were tested. M. genitalium was the second most prevalent STI detected (4.5% of the patients), after C. trachomatis (8.3%). T. vaginalis was detected in 1.4% of the patients, comparable to the prevalence of N. gonorrhoeae (1.3%). Dual infections were only detected in a small number of patients (1.0%). Incorporation of M. genitalium into routine STI screening should be considered, because of its relatively high prevalence, the consequences of its detection for antibiotic treatment and because of the availability of easy-to-use molecular diagnostic tests. For T. vaginalis, routine screening may be considered, depending on local prevalence and (sub)population. © The Author(s) 2015.

[Microbiological surveillance in patients treated by bone marrow transplantation (author's transl)].

PubMed

Haralambie, E; Linzenmeier, G; Nowrousian, M; Schäfer, R; Schmidt, C G

1980-01-01

Patients suffering from acute leukemia were treated by bone marrow transplantation under strict gnotobiotic conditions. The microbiological surveillance was performed during three phases: the admission phase, the phase of decontamination and reverse isolation and the reconventionalisation phase. During the second phase no infections of exogenous origine occurred. All clinically manifest infections in this phase were induced by unsuppressed endogenous bacteria. In our study the bacteria of oropharynx was the main source of infections therefore this biotop deserves special attention during the microbiological surveillance of the immune compromised host. In leukemia patients selective decontamination will be the method of choice, but considering the possibility of GvHR in patients with bone marrow transplantation a complete decontamination should be achieved.

Stethoscope disinfection campaign in a Nigerian teaching hospital:results of a before-and-after study.

PubMed

Uneke, Chigozie J; Ndukwe, Chinwendu D; Nwakpu, Kingsley O; Nnabu, Richard C; Ugwuoru, Cletus D; Prasopa-Plaizier, Nittita

2014-01-15

This study aimed to assess the impact of a stethoscope disinfection sensitization campaign among doctors and nurses in a Nigerian teaching hospital. The design was a before-and-after study. Pre-program measurements were used to provide a baseline against which the post-program results were compared. Interventions that promoted compliance with stethoscope disinfection practice that were implemented included training and education on stethoscope disinfection and introduction of 70% isopropyl alcohol disinfectant at points-of-care places. Microbiological assessment of stethoscopes used by health workers was conducted after the intervention and the outcome was compared with the pilot study results. After the intervention, of the 89 stethoscopes screened, 18 (20.2%) were contaminated with bacterial agents. A higher prevalence of stethoscope contamination was observed among stethoscopes from the intensive care unit (66.7%), the VIP unit (50%), and the antenatal unit (37.5%). The main isolates were Staphylococcus aureus (44.4%) and Escherichia coli (50%). The antibiotic sensitivity assessment indicated that the bacterial isolates were resistant to nearly all the antibiotics tested. All the 89 health workers whose stethoscopes were screened after the intervention admitted to cleaning their stethoscopes after seeing each patient, representing a compliance rate of 100%, unlike the 15% compliance at the pilot phase. The baseline stethoscope contamination rate was 78.5% versus 20.2% post-intervention. Training and education and introduction of alcohol-based disinfectants inexpensive but very effective methods to improve stethoscope disinfection compliance among health workers in low-income settings.

Development of a loop-mediated isothermal amplification assay for the detection of Streptococcus agalactiae in bovine milk.

PubMed

Bosward, Katrina L; House, John K; Deveridge, Amber; Mathews, Karen; Sheehy, Paul A

2016-03-01

Streptococcus agalactiae is a well-characterized bovine mastitis pathogen that is known to be highly contagious and capable of spreading rapidly in affected dairy herds. Loop-mediated isothermal amplification (LAMP) is a novel molecular diagnostic method that has the capability to provide rapid, cost-effective screening for pathogens to support on-farm disease control and eradication programs. In the current study, a LAMP test was developed to detect S. agalactiae in milk. The assay was validated on a bank of existing clinical mastitis milk samples that had previously been identified as S. agalactiae positive via traditional microbiological culture techniques and PCR. The LAMP assay was conducted on bacterial colonies and DNA extracted from milk in tube- and plate-based formats using multiple detection platforms. The 1-h assay conducted at 64 °C exhibited repeatability (coefficient of variation) of 2.07% (tube) and 8.3% (plate), sensitivity to ~20 pg of extracted DNA/reaction, and specificity against a panel of known bacterial mastitis pathogens. Of the 109 known S. agalactiae isolates assessed by LAMP directly from bacterial cells in culture, 108 were identified as positive, in accordance with PCR analysis. The LAMP analysis from the corresponding milk samples indicated that 104 of these milks exhibited a positive amplification curve. Although exhibiting some limitations, this assay provides an opportunity for rapid screening of milk samples to facilitate on-farm management of this pathogen. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

(GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts?

PubMed

Ramírez-Castrillón, Mauricio; Mendes, Sandra Denise Camargo; Inostroza-Ponta, Mario; Valente, Patricia

2014-01-01

In microbiology, identification of all isolates by sequencing is still unfeasible in small research laboratories. Therefore, many yeast diversity studies follow a screening procedure consisting of clustering the yeast isolates using MSP-PCR fingerprinting, followed by identification of one or a few selected representatives of each cluster by sequencing. Although this procedure has been widely applied in the literature, it has not been properly validated. We evaluated a standardized protocol using MSP-PCR fingerprinting with the primers (GTG)5 and M13 for the discrimination of wine associated yeasts in South Brazil. Two datasets were used: yeasts isolated from bottled wines and vineyard environments. We compared the discriminatory power of both primers in a subset of 16 strains, choosing the primer (GTG)5 for further evaluation. Afterwards, we applied this technique to 245 strains, and compared the results with the identification obtained by partial sequencing of the LSU rRNA gene, considered as the gold standard. An array matrix was constructed for each dataset and used as input for clustering with two methods (hierarchical dendrograms and QAPGrid layout). For both yeast datasets, unrelated species were clustered in the same group. The sensitivity score of (GTG)5 MSP-PCR fingerprinting was high, but specificity was low. As a conclusion, the yeast diversity inferred in several previous studies may have been underestimated and some isolates were probably misidentified due to the compliance to this screening procedure.

(GTG)5 MSP-PCR Fingerprinting as a Technique for Discrimination of Wine Associated Yeasts?

PubMed Central

Inostroza-Ponta, Mario; Valente, Patricia

2014-01-01

In microbiology, identification of all isolates by sequencing is still unfeasible in small research laboratories. Therefore, many yeast diversity studies follow a screening procedure consisting of clustering the yeast isolates using MSP-PCR fingerprinting, followed by identification of one or a few selected representatives of each cluster by sequencing. Although this procedure has been widely applied in the literature, it has not been properly validated. We evaluated a standardized protocol using MSP-PCR fingerprinting with the primers (GTG)5 and M13 for the discrimination of wine associated yeasts in South Brazil. Two datasets were used: yeasts isolated from bottled wines and vineyard environments. We compared the discriminatory power of both primers in a subset of 16 strains, choosing the primer (GTG)5 for further evaluation. Afterwards, we applied this technique to 245 strains, and compared the results with the identification obtained by partial sequencing of the LSU rRNA gene, considered as the gold standard. An array matrix was constructed for each dataset and used as input for clustering with two methods (hierarchical dendrograms and QAPGrid layout). For both yeast datasets, unrelated species were clustered in the same group. The sensitivity score of (GTG)5 MSP-PCR fingerprinting was high, but specificity was low. As a conclusion, the yeast diversity inferred in several previous studies may have been underestimated and some isolates were probably misidentified due to the compliance to this screening procedure. PMID:25171185

Validation of a Five Plate Test, the STAR protocol, for the screening of antibiotic residues in muscle from different animal species according to European Decision 2002/657/EC.

PubMed

Gaudin, V; Hedou, C; Rault, A; Verdon, E

2010-07-01

The STAR protocol is a Five Plate Test (FPT) developed several years ago at the Community Reference Laboratory (CRL) for the screening of antimicrobial residues in milk and muscle. This paper presents the validation of this method according to European Decision 2002/657/EC and to an internal guideline for validation. A validation protocol based on 'simulated tissues' and on a list of 16 representative antimicrobials to be validated was implemented in our laboratory during several months for the STAR protocol. The performance characteristics of the method were determined (specificity, detection capabilities CCbeta, applicability, ruggedness). In conclusion, the STAR protocol is applicable to the broad-spectrum detection of antibiotic residues in muscles of different animal species (pig, cattle, sheep, poultry). The method has good specificity (false-positive rate = 4%). The detection capabilities were determined for 16 antibiotics from different families in relation to their respective maximum residue limit (MRL): beta-lactams (penicillins and cephalosporins < or = MRL), tetracyclines (< or = MRL and < or = 2.5 MRL), macrolides (2 MRL), quinolones (< or = 2 MRL), some sulphonamides (< or = 3 MRL), and trimethoprim (2 MRL). However, the sensitivity of the STAR protocol towards aminoglycosides (> 8 MRL) and florfenicol (< or = 10 MRL) was unsatisfactory (>MRL). The two objectives of this study were met: firstly, to validate the STAR protocol according to European Decision 2002/657/EC, then to demonstrate that the validation guideline developed to implement this decision is applicable to microbiological plate tests even for muscle. The use of simulated tissue appeared a good compromise between spiked discs with antibiotic solutions and incurred tissues. In addition, the choice of a list of representative antibiotics allowed the reduction of the scope of the validation, which was already costly in time and effort.

Stability of extemporaneously prepared preservative-free prochlorperazine nasal spray.

PubMed

Yellepeddi, Venkata K

2018-01-01

The stability of an extemporaneously prepared preservative-free prochlorperazine 5-mg/mL nasal spray was evaluated. The preservative-free prochlorperazine nasal spray was prepared by adding 250 mg of prochlorperazine edisylate to 50 mL of citrate buffer in a low-density polyethylene nasal spray bottle. A stability-indicating high-performance liquid chromatography (HPLC) method was developed and validated using the major degradant prochlorperazine sulfoxide and by performing forced-degradation studies. For chemical stability studies, 3 100-μL samples of the preservative-free prochlorperazine from 5 nasal spray bottles stored at room temperature were collected at days 0, 20, 30, 45, and 60 and were assayed in triplicate using the stability-indicating HPLC method. Microbiological testing involved antimicrobial effectiveness testing based on United States Pharmacopeia ( USP ) chapter 51 and quantitative microbiological enumeration of aerobic bacteria, yeasts, and mold based on USP chapter 61. Samples for microbiological testing were collected at days 0, 30, and 60. The stability-indicating HPLC method clearly identified the degradation product prochlorperazine sulfoxide without interference from prochlorperazine. All tested solutions retained over 90% of the initial prochlorperazine concentration for the 60-day study period. There were no detectable changes in color, pH, and viscosity in any sample. There was no growth of bacteria, yeast, and mold for 60 days in all samples tested. An extemporaneously prepared preservative-free nasal spray solution of prochlorperazine edisylate 5 mg/mL was physically, chemically, and microbiologically stable for 60 days when stored at room temperature in low-density polyethylene bottles. Copyright © 2018 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures

PubMed Central

McMahon, Tanis C.; Blais, Burton W.; Wong, Alex; Carrillo, Catherine D.

2017-01-01

Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of current methods for EHEC detection in foods. PMID:28303131

Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures.

PubMed

McMahon, Tanis C; Blais, Burton W; Wong, Alex; Carrillo, Catherine D

2017-01-01

Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin ( stx ) and intimin ( eae )]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae -negative STEC and eae -positive E. coli , but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets ( stx and eae ) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli . By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae -negative STEC and eae -positive E. coli (0-2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of current methods for EHEC detection in foods.

Evolution of microbiological analytical methods for dairy industry needs

PubMed Central

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry’s needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards. PMID:24570675

Evolution of microbiological analytical methods for dairy industry needs.

PubMed

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry's needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards.

A two-hour antibiotic susceptibility test by ATP-bioluminescence.

PubMed

March Rosselló, Gabriel Alberto; García-Loygorri Jordán de Urries, María Cristina; Gutiérrez Rodríguez, María Purificación; Simarro Grande, María; Orduña Domingo, Antonio; Bratos Pérez, Miguel Ángel

2016-01-01

The antibiotic susceptibility test (AST) in Clinical Microbiology laboratories is still time-consuming, and most procedures take 24h to yield results. In this study, a rapid antimicrobial susceptibility test using ATP-bioluminescence has been developed. The design of method was performed using five ATCC collection strains of known susceptibility. This procedure was then validated against standard commercial methods on 10 strains of enterococci, 10 staphylococci, 10 non-fermenting gram negative bacilli, and 13 Enterobacteriaceae from patients. The agreement obtained in the sensitivity between the ATP-bioluminescence method and commercial methods (E-test, MicroScan and VITEK2) was 100%. In summary, the preliminary results obtained in this work show that the ATP-bioluminescence method could provide a fast and reliable AST in two hours. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Rapid Diagnosis of Bloodstream Infections with PCR Followed by Mass Spectrometry

PubMed Central

Jordana-Lluch, Elena; Carolan, Heather E.; Giménez, Montserrat; Sampath, Rangarajan; Ecker, David J.; Quesada, M. Dolores; Mòdol, Josep M.; Arméstar, Fernando; Blyn, Lawrence B.; Cummins, Lendell L.; Ausina, Vicente; Martró, Elisa

2013-01-01

Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood. A total of 247 whole blood samples and paired blood cultures were prospectively obtained from 175 patients with a suspicion of sepsis. Both sample types were analyzed using the PCR/ESI-MS technology, and the results were compared with those obtained by conventional identification methods. The overall agreement between conventional methods and PCR/ESI-MS performed in blood culture aliquots was 94.2% with 96.8% sensitivity and 98.5% specificity for the molecular method. When comparing conventional methods with PCR/ESI-MS performed in whole blood specimens, the overall agreement was 77.1% with 50% sensitivity and 93.8% specificity for the molecular method. Interestingly, the PCR/ESI-MS technology led to the additional identification of 13 pathogens that were not found by conventional methods. Using the PCR/ESI-MS technology the microbiological diagnosis of bloodstream infections could be anticipated in about half of the patients in our setting, including a small but significant proportion of patients newly diagnosed. Thus, this promising technology could be very useful for the rapid diagnosis of sepsis in combination with traditional methods. PMID:23626775

Analytical procedures for water-soluble vitamins in foods and dietary supplements: a review.

PubMed

Blake, Christopher J

2007-09-01

Water-soluble vitamins include the B-group vitamins and vitamin C. In order to correctly monitor water-soluble vitamin content in fortified foods for compliance monitoring as well as to establish accurate data banks, an accurate and precise analytical method is a prerequisite. For many years microbiological assays have been used for analysis of B vitamins. However they are no longer considered to be the gold standard in vitamins analysis as many studies have shown up their deficiencies. This review describes the current status of analytical methods, including microbiological assays and spectrophotometric, biosensor and chromatographic techniques. In particular it describes the current status of the official methods and highlights some new developments in chromatographic procedures and detection methods. An overview is made of multivitamin extractions and analyses for foods and supplements.

Flow cytometry as a method for the evaluation of raw material, product and process in the dairy industry.

PubMed

Ruszczyńska, A; Szteyn, J; Wiszniewska-Laszczych, A

2007-01-01

Producing dairy products which are safe for consumers requires the constant monitoring of the microbiological quality of raw material, the production process itself and the end product. Traditional methods, still a "gold standard", require a specialized laboratory working on recognized and validated methods. Obtaining results is time- and labor-consuming and do not allow rapid evaluation. Hence, there is a need for a rapid, precise method enabling the real-time monitoring of microbiological quality, and flow cytometry serves this function well. It is based on labeling cells suspended in a solution with fluorescent dyes and pumping them into a measurement zone where they are exposed to a precisely focused laser beam. This paper is aimed at presenting the possibilities of applying flow cytometry in the dairy industry.

Quality in the molecular microbiology laboratory.

PubMed

Wallace, Paul S; MacKay, William G

2013-01-01

In the clinical microbiology laboratory advances in nucleic acid detection, quantification, and sequence analysis have led to considerable improvements in the diagnosis, management, and monitoring of infectious diseases. Molecular diagnostic methods are routinely used to make clinical decisions based on when and how to treat a patient as well as monitor the effectiveness of a therapeutic regime and identify any potential drug resistant strains that may impact on the long term patient treatment program. Therefore, confidence in the reliability of the result provided by the laboratory service to the clinician is essential for patient treatment. Hence, suitable quality assurance and quality control measures are important to ensure that the laboratory methods and service meet the necessary regulatory requirements both at the national and international level. In essence, the modern clinical microbiology laboratory ensures the appropriateness of its services through a quality management system that monitors all aspects of the laboratory service pre- and post-analytical-from patient sample receipt to reporting of results, from checking and upholding staff competency within the laboratory to identifying areas for quality improvements within the service offered. For most European based clinical microbiology laboratories this means following the common International Standard Organization (ISO9001) framework and ISO15189 which sets out the quality management requirements for the medical laboratory (BS EN ISO 15189 (2003) Medical laboratories-particular requirements for quality and competence. British Standards Institute, Bristol, UK). In the United States clinical laboratories performing human diagnostic tests are regulated by the Centers for Medicare and Medicaid Services (CMS) following the requirements within the Clinical Laboratory Improvement Amendments document 1988 (CLIA-88). This chapter focuses on the key quality assurance and quality control requirements within the modern microbiology laboratory providing molecular diagnostics.

Intersecting Virtual Patients and Microbiology: Fostering a culture of learning.

PubMed

McCarthy, David; O'Gorman, Ciaran; Gormley, Gerard

2015-10-01

The use and integration of Technology Enhanced Learning (TEL) resources in medical education has attracted considerable commentary and support. "Virtual Patients" are one such resource. Whilst evidence exists supporting the benefits of these resources, there has not been specific consideration of their implications for teaching microbiology; nor attention paid to both the internal and external factors that influence learner engagement with virtual patients. The principle aims of this study are to identify factors that explicitly and implicitly influence the student's interaction with a microbiology virtual patient resource and how these interactions reflect upon the use of the resource. A mixed method quantitative (online questionnaire; n=161) and qualitative (student focus groups; N=11) study was undertaken amongst third year medical students enrolled at Queen's University Belfast in the academic year 2012-2013. The results supported prior evidence that virtual patients are a useful learning tool (mean score of 5.09 out of 7) that helped them to integrate microbiology principles with clinical experiences. How students used the virtual patients and the depth of the subsequent benefits was dependent upon their perception of the importance of the resource. This was influenced by a number of factors including how the resources were presented and positioned within the curriculum, whether they were formally examined or timetabled and the importance attributed by peers who had already completed the examinations. Integration of virtual patients into the microbiology curriculum is widely endorsed and may even be considered superior to other methods of teaching. How students use these resources is dependent upon a positive perception of their importance. Educators should be aware of the factors that shape this perception when integrating TEL resources into curricula.

Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

PubMed Central

Kell, Douglas; Potgieter, Marnie; Pretorius, Etheresia

2015-01-01

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically ‘nonculturable’ on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as ‘persisters’. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one’s bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit. PMID:26629334

Validated measurements of microbial loads on environmental surfaces in intensive care units before and after disinfecting cleaning.

PubMed

Frickmann, H; Bachert, S; Warnke, P; Podbielski, A

2018-03-01

Preanalytic aspects can make results of hygiene studies difficult to compare. Efficacy of surface disinfection was assessed with an evaluated swabbing procedure. A validated microbial screening of surfaces was performed in the patients' environment and from hands of healthcare workers on two intensive care units (ICUs) prior to and after a standardized disinfection procedure. From a pure culture, the recovery rate of the swabs for Staphylococcus aureus was 35%-64% and dropped to 0%-22% from a mixed culture with 10-times more Staphylococcus epidermidis than S. aureus. Microbial surface loads 30 min before and after the cleaning procedures were indistinguishable. The quality-ensured screening procedure proved that adequate hygiene procedures are associated with a low overall colonization of surfaces and skin of healthcare workers. Unchanged microbial loads before and after surface disinfection demonstrated the low additional impact of this procedure in the endemic situation when the pathogen load prior to surface disinfection is already low. Based on a validated screening system ensuring the interpretability and reliability of the results, the study confirms the efficiency of combined hand and surface hygiene procedures to guarantee low rates of bacterial colonization. © 2017 The Society for Applied Microbiology.

The current screening programme for congenital transmission of Chagas disease in Catalonia, Spain.

PubMed

Basile, L; Oliveira, I; Ciruela, P; Plasencia, A

2011-09-22

Due to considerable numbers of migrants from Chagas disease-endemic countries living in Catalonia, the Catalonian Health Department has recently implemented a screening programme for preventing congenital transmission, targeting Latin American pregnant women who attend antenatal consultations. Diagnosis of Trypanosoma cruzi infection in women is based on two positive serological tests. Screening of newborns from mothers with positive serology is based on a parasitological test during the first 48 hours of life and/or conventional serological analysis at the age of nine months. If either of these tests is positive, treatment with benznidazole is started following the World Health Organization's recommendations. The epidemiological surveillance of the programme is based on the Microbiological Reporting System of Catalonia, a well established network of laboratories. Once a positive case is reported, the responsible physician is asked to complete a structured epidemiological questionnaire. Clinical and demographic data are registered in the Voluntary Case Registry of Chagas Disease, a database administered by the Catalonian Health Department. It is expected that this programme will improve the understanding of the real burden of Chagas disease in the region. Furthermore, this initiative could encourage the implementation of similar programmes in other regions of Spain and even in other European countries.

Microbiological quality of take-away cooked rice and chicken sandwiches: effectiveness of food hygiene training of the management.

PubMed

Little, C L; Barnes, J; Mitchell, R T

2002-12-01

During August 2001 a microbiological study of ready-to-eat cooked rice from take-aways and of chicken sandwiches made on the premises from sandwich bars was undertaken. The intention was to identify risk factors in the production, storage and handling of cooked rice and sandwiches, and to establish their effect on microbiological quality. Examination of cooked rice revealed that the majority of samples (87%; 442 of 508) were of satisfactory/acceptable microbiological quality; 50 (10%) were unsatisfactory, and 16 (3%) were of unacceptable quality due to Bacillus cereus and/or other Bacillus spp in excess of 10(5) cfu/g. The microbiological quality of cooked rice was associated with cuisine type (p < 0.00001), rice type (p < 0.01), cooking (p < 0.01), serving methods (p < 0.00001), and management food hygiene training (p < 0.01). Examination of chicken sandwiches found that most (75%; 335 of 449) were of satisfactory/acceptable microbiological quality and 114 (25%) were unsatisfactory. Acceptable microbiological quality of sandwiches was associated with sandwich bars that had hazard analysis in place (p < 0.05). Smaller businesses, as indicated by Local Authority Inspectors' Consumer at Risk scores, were more likely to have samples classified as unsatisfactory or unacceptable compared to larger businesses (p < 0.001). The majority (90%) of premises had hand-washing facilities accessible and available for use, although only over half (55%) were correctly used as judged by the sampling officer. Where the manager of the premises had received some form of food hygiene training, food safety procedures such as the hazard analysis system were more likely to be in place (p < 0.0001).

Super-long Anabiosis of Ancient Microorganisms in Ice and Terrestrial Models for Development of Methods to Search for Life on Mars, Europa and other Planetary Bodies

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Duxbury, N. S.; Bobin, N. E.; Fukuchi, M.; Hoover, R. B.; Kanda, H.; Mitskevich, I. N.; Mulyukin, A. L.; Naganuma, T.; Poglazova, M. N.;

Role of microbiological culture and polymerase chain reaction (PCR) of actinomyces in medication-related osteonecrosis of the jaw (MRONJ).

PubMed

Panya, Sappasith; Fliefel, Riham; Probst, Florian; Tröltzsch, Matthias; Ehrenfeld, Michael; Schubert, Sören; Otto, Sven

2017-03-01

We hypothesized that local infection plays a critical role in the pathogenesis of medication-related osteonecrosis of the jaw (MRONJ). Recent developments in molecular methods have revolutionized new approaches for the rapid detection of microorganisms including those difficult to culture. The aim of our study is to identify the bacterial profiles in MRONJ by microbiological culture and polymerase chain reactions (PCR). A retrospective analysis was performed on MRONJ patients from 2008 to 2014. The bacterial profile from MRONJ bone samples was determined using microbiological culture and PCR. Ninety five patients fulfilled the inclusion criteria with mean age of 69.85 ± 8.71 years. A female predilection was detected. The mandible was more commonly affected than maxilla. Tooth extraction was the frequent triggering factor. Breast cancer was the primary cause for administration and intravenous bisphosphonates were the most commonly administrated antiresorptive drugs. The majority of patients were classified as stage 2. Posterior teeth were most commonly affected. Based on bone culture results, the most common microorganism were both actinomyces and mixed flora. PCR confirmed the presence of actinomyces in 55 patients. Our data suggest that PCR might be an innovative method for detection of microorganisms difficult to culture using traditional microbiological techniques. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Development and validation of qualitative SYBR®Green real-time PCR for detection and discrimination of Listeria spp. and Listeria monocytogenes.

PubMed

Barbau-Piednoir, Elodie; Botteldoorn, Nadine; Yde, Marc; Mahillon, Jacques; Roosens, Nancy H

2013-05-01

A combination of four qualitative SYBR®Green qPCR screening assays targeting two levels of discrimination: Listeria genus (except Listeria grayi) and Listeria monocytogenes, is presented. These assays have been developed to be run simultaneously using the same polymerase chain reaction (PCR) programme. The paper also proposes a new validation procedure to specifically validate qPCR assays applied to food microbiology according to two guidelines: the ISO 22118 norm and the "Definition of minimum performance requirements for analytical methods of GMO testing". The developed assays target the iap, prs and hlyA genes that belong to or neighbour the virulence cluster of Listeria spp. The selected primers were designed to amplify short fragments (60 to 103 bp) in order to obtain optimal PCR efficiency (between 97 and 107 % efficiency). The limit of detection of the SYBR®Green qPCR assays is two to five copies of target genes per qPCR reaction. These assays are highly accurate (98.08 and 100 % accuracy for the Listeria spp. and L. monocytogenes assays, respectively).

Healthcare Personnel Attire and Devices as Fomites: A Systematic Review.

PubMed

Haun, Nicholas; Hooper-Lane, Christopher; Safdar, Nasia

2016-11-01

BACKGROUND Transmission of pathogens within the hospital environment remains a hazard for hospitalized patients. Healthcare personnel clothing and devices carried by them may harbor pathogens and contribute to the risk of pathogen transmission. OBJECTIVE To examine bacterial contamination of healthcare personnel attire and commonly used devices. METHODS Systematic review. RESULTS Of 1,175 studies screened, 72 individual studies assessed contamination of a variety of items, including white coats, neckties, stethoscopes, and mobile electronic devices, with varied pathogens including Staphylococcus aureus, including methicillin-resistant S. aureus, gram-negative rods, and enterococci. Contamination rates varied significantly across studies and by device but in general ranged from 0 to 32% for methicillin-resistant S. aureus and gram-negative rods. Enterococcus was a less common contaminant. Few studies explicitly evaluated for the presence of Clostridium difficile. Sampling and microbiologic techniques varied significantly across studies. Four studies evaluated for possible connection between healthcare personnel contaminants and clinical isolates with no unequivocally direct link identified. CONCLUSIONS Further studies to explore the relationship between healthcare personnel attire and devices and clinical infection are needed. Infect Control Hosp Epidemiol 2016;1-7.

Influence of bulking agents on physical, chemical, and microbiological properties during the two-stage composting of green waste.

PubMed

Zhang, Lu; Sun, Xiangyang

2016-02-01

A recyclable organic bulking agent (BA) that can be screened and was developed to optimize green waste (GW) composting. This study investigated the use of wood chips (WC) (at 0%, 15%, and 25%) and/or composted green waste (CGW) (at 0%, 25%, and 35%) as the BAs in the two-stage composting of GW. The combined addition of WC and CGW improved the conditions of composting process and the quality of compost product in terms of composting temperature, porosity, water retention, particle-size distribution, pH, electrical conductivity (EC), cation exchange capacity (CEC), nitrogen losses, humification indices, microbial numbers, enzyme activities, macro- and micro-nutrient contents, and toxicity to germinating seeds. The compost matured in only 22days with the optimized two-stage composting method rather than in the 90-270days typically required for traditional composting. The optimal two-stage composting process and the best quality of compost product were obtained with the combined addition of 15% WC and 35% CGW. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Review of PAT Strategies in Secondary Solid Oral Dosage Manufacturing of Small Molecules.

PubMed

Laske, Stephan; Paudel, Amrit; Scheibelhofer, Otto

2017-03-01

Pharmaceutical solid oral dosage product manufacturing is a well-established, yet revolutionizing area. To this end, process analytical technology (PAT) involves interdisciplinary and multivariate (chemical, physical, microbiological, and mathematical) methods for material (e.g., materials, intermediates, products) and process (e.g., temperature, pressure, throughput, etc.) analysis. This supports rational process modeling and enhanced control strategies for improved product quality and process efficiency. Therefore, it is often difficult to orient and find the relevant, integrated aspects of the current state-of-the-art. Especially, the link between fundamental research, in terms of sensor and control system development, to the application both in laboratory and manufacturing scale, is difficult to comprehend. This review compiles a nonexhaustive overview on current approaches from the recognized academia and industrial practices of PAT, including screening, selection, and final implementations in solid oral dosage manufacturing, through a wide diversity of use cases. Finally, the authors attempt to extract a common consensus toward developing PAT application guidance for different unit operations of drug product manufacturing. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Approach to the Investigation and Management of Patients With Candida auris, an Emerging Multidrug-Resistant Yeast.

PubMed

Tsay, Sharon; Kallen, Alexander; Jackson, Brendan R; Chiller, Tom M; Vallabhaneni, Snigdha

2018-01-06

Candida auris is an emerging, multidrug-resistant yeast that can spread in healthcare settings. It can cause invasive infections with high mortality and is difficult to identify using traditional yeast identification methods. Candida auris has been reported in more than a dozen countries, and as of August 2017, 112 clinical cases have been reported in the United States. Candida auris can colonize skin and persist in the healthcare environment, allowing for transmission between patients. Prompt investigation and aggressive interventions, including notification to public health agencies, implementation of contact precautions, thorough environmental cleaning and disinfection, infection control assessments, contact tracing and screening of contacts to assess for colonization, and retrospective review of microbiology records and prospective surveillance for cases at laboratories are all needed to limit the spread of C. auris. This review summarizes the current recommended approach to manage cases and control transmission of C. auris in healthcare facilities. Published by Oxford University Press for the Infectious Diseases Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Emerging Strategies and Integrated Systems Microbiology Technologies for Biodiscovery of Marine Bioactive Compounds

PubMed Central

Rocha-Martin, Javier; Harrington, Catriona; Dobson, Alan D.W.; O’Gara, Fergal

2014-01-01

Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds. PMID:24918453

Cost analysis in a clinical microbiology laboratory.

PubMed

Brezmes, M F; Ochoa, C; Eiros, J M

2002-08-01

The use of models for business management and cost control in public hospitals has led to a need for microbiology laboratories to know the real cost of the different products they offer. For this reason, a catalogue of microbiological products was prepared, and the costs (direct and indirect) for each product were analysed, along with estimated profitability. All tests performed in the microbiology laboratory of the "Virgen de la Concha" Hospital in Zamora over a 2-year period (73192 tests) were studied. The microbiological product catalogue was designed using homogeneity criteria with respect to procedures used, workloads and costs. For each product, the direct personnel costs (estimated from workloads following the method of the College of American Pathologists, 1992 version), the indirect personnel costs, the direct and indirect material costs and the portion of costs corresponding to the remaining laboratory costs (capital and structural costs) were calculated. The average product cost was 16.05 euros. The average cost of a urine culture (considered, for purposes of this study, as a relative value unit) reached 13.59 euros, with a significant difference observed between positive and negative cultures (negative urine culture, 10.72 euros; positive culture, 29.65 euros). Significant heterogeneity exists, both in the costs of different products and especially in the cost per positive test. The application of a detailed methodology of cost analysis facilitates the calculation of the real cost of microbiological products. This information provides a basic tool for establishing clinical management strategies.

Microbiological Challenge Testing for Listeria Monocytogenes in Ready-to-Eat Food: A Practical Approach.

PubMed

Spanu, Carlo; Scarano, Christian; Ibba, Michela; Pala, Carlo; Spanu, Vincenzo; De Santis, Enrico Pietro Luigi

2014-12-09

Food business operators (FBOs) are the primary responsible for the safety of food they place on the market. The definition and validation of the product's shelf-life is an essential part for ensuring microbiological safety of food and health of consumers. In the frame of the Regulation (EC) No 2073/2005 on microbiological criteria for foodstuffs, FBOs shall conduct shelf-life studies in order to assure that their food does not exceed the food safety criteria throughout the defined shelf-life. In particular this is required for ready-to-eat (RTE) food that supports the growth of Listeria monocytogenes . Among other studies, FBOs can rely on the conclusion drawn by microbiological challenge tests. A microbiological challenge test consists in the artificial contamination of a food with a pathogen microorganism and aims at simulating its behaviour during processing and distribution under the foreseen storage and handling conditions. A number of documents published by international health authorities and research institutions describes how to conduct challenge studies. The authors reviewed the existing literature and described the methodology for implementing such laboratory studies. All the main aspects for the conduction of L. monocytogenes microbiological challenge tests were considered, from the selection of the strains, preparation and choice of the inoculum level and method of contamination, to the experimental design and data interpretation. The objective of the present document is to provide an exhaustive and practical guideline for laboratories that want to implement L. monocytogenes challenge testing on RTE food.

Microbiological Challenge Testing for Listeria Monocytogenes in Ready-to-Eat Food: A Practical Approach

PubMed Central

Scarano, Christian; Ibba, Michela; Pala, Carlo; Spanu, Vincenzo; De Santis, Enrico Pietro Luigi

2014-01-01

Food business operators (FBOs) are the primary responsible for the safety of food they place on the market. The definition and validation of the product’s shelf-life is an essential part for ensuring microbiological safety of food and health of consumers. In the frame of the Regulation (EC) No 2073/2005 on microbiological criteria for foodstuffs, FBOs shall conduct shelf-life studies in order to assure that their food does not exceed the food safety criteria throughout the defined shelf-life. In particular this is required for ready-to-eat (RTE) food that supports the growth of Listeria monocytogenes. Among other studies, FBOs can rely on the conclusion drawn by microbiological challenge tests. A microbiological challenge test consists in the artificial contamination of a food with a pathogen microorganism and aims at simulating its behaviour during processing and distribution under the foreseen storage and handling conditions. A number of documents published by international health authorities and research institutions describes how to conduct challenge studies. The authors reviewed the existing literature and described the methodology for implementing such laboratory studies. All the main aspects for the conduction of L. monocytogenes microbiological challenge tests were considered, from the selection of the strains, preparation and choice of the inoculum level and method of contamination, to the experimental design and data interpretation. The objective of the present document is to provide an exhaustive and practical guideline for laboratories that want to implement L. monocytogenes challenge testing on RTE food. PMID:27800369

Clinical and epidemiological characterization of a lymphogranuloma venereum outbreak in Madrid, Spain: co-circulation of two variants.

PubMed

Rodríguez-Domínguez, M; Puerta, T; Menéndez, B; González-Alba, J M; Rodríguez, C; Hellín, T; Vera, M; González-Sainz, F J; Clavo, P; Villa, M; Cantón, R; Del Romero, J; Galán, J C

2014-03-01

The lymphogranuloma venereum (LGV) outbreak described in the Netherlands in 2003, increased the interest in the genotyping of Chlamydia trachomatis. Although international surveillance programmes were implemented, these studies slowly decreased in the following years. Now data have revealed a new accumulation of LGV cases in those European countries with extended surveillance programmes. Between March 2009 and November 2011, a study was carried out to detect LGV cases in Madrid. The study was based on screening of C. trachomatis using commercial kits, followed by real-time pmpH-PCR discriminating LGV strains, and finally ompA gene was sequenced for phylogenetic reconstruction. Ninety-four LGV infections were identified. The number of cases increased from 10 to 30 and then to 54 during 2009-2011. Incidence of LGV was strongly associated with men who have sex with men; but in 2011, LGV cases were described in women and heterosexual men. Sixty-nine patients were also human immunodeficiency virus (HIV) positive, with detectable viral loads at the moment of LGV diagnosis, suggesting a high-risk of co-transmission. In fact, in four patients the diagnosis of HIV was simultaneous with LGV infection. The conventional treatment with doxycycline was prescribed in 75 patients, although in three patients the treatment failed. The sequencing of the ompA gene permitted identification of two independent transmission nodes. One constituted by 25 sequences identical to the L2b variant, and a second node including 37 sequences identical to L2. This epidemiological situation characterized by the co-circulation of two LGV variants has not been previously described, reinforcing the need for screening and genotyping of LGV strains. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Routine screening of harmful microorganisms in beach sands: implications to public health

USGS Publications Warehouse

Sabino, Raquel; Rodrigues, R.; Costa, I.; Carneiro, Carlos; Cunha, M.; Duarte, A.; Faria, N.; Ferriera, F.C.; Gargate, M.J.; Julio, C.; Martins, M.L.; Nevers, Meredith; Oleastro, M.; Solo-Gabriele, H.; Verissimo, C.; Viegas, C.; Whitman, Richard L.; Brandao, J.

2014-01-01

Beaches worldwide provide recreational opportunities to hundreds of millions of people and serve as important components of coastal economies. Beach water is often monitored for microbiological quality to detect the presence of indicators of human sewage contamination so as to prevent public health outbreaks associated with water contact. However, growing evidence suggests that beach sand can harbor microbes harmful to human health, often in concentrations greater than the beach water. Currently, there are no standards for monitoring, sampling, analyzing, or managing beach sand quality. In addition to indicator microbes, growing evidence has identified pathogenic bacteria, viruses, and fungi in a variety of beach sands worldwide. The public health threat associated with these populations through direct and indirect contact is unknown because so little research has been conducted relating to health outcomes associated with sand quality. In this manuscript, we present the consensus findings of a workshop of experts convened in Lisbon, Portugal to discuss the current state of knowledge on beach sand microbiological quality and to develop suggestions for standardizing the evaluation of sand at coastal beaches. The expert group at the “Microareias 2012” workshop recommends that 1) beach sand should be screened for a variety of pathogens harmful to human health, and sand monitoring should then be initiated alongside regular water monitoring; 2) sampling and analysis protocols should be standardized to allow proper comparisons among beach locations; and 3) further studies are needed to estimate human health risk with exposure to contaminated beach sand. Much of the manuscript is focused on research specific to Portugal, but similar results have been found elsewhere, and the findings have worldwide implications.

[A rarely isolated bacterium in microbiology laboratories: Streptococcus uberis].

PubMed

Eryıldız, Canan; Bukavaz, Şebnem; Gürcan, Şaban; Hatipoğlu, Osman

2017-04-01

Streptococcus uberis is a gram-positive bacterium that is mostly responsible for mastitis in cattle. The bacterium rarely has been associated with human infections. Conventional phenotyphic methods can be inadequate for the identification of S.uberis; and in microbiology laboratories S.uberis is confused with the other streptococci and enterococci isolates. Recently, molecular methods are recommended for the accurate identification of S.uberis isolates. The aim of this report is to present a lower respiratory tract infection case caused by S.uberis and the microbiological methods for identification of this bacterium. A 66-year-old male patient with squamous cell lung cancer who received radiotherapy was admitted in our hospital for the control. According to the chest X-Ray, patient was hospitalized with the prediagnosis of ''cavitary tumor, pulmonary abscess''. In the first day of the hospitalization, blood and sputum cultures were drawn. Blood culture was negative, however, Candida albicans was isolated in the sputum culture and it was estimated to be due to oral lesions. After two weeks from the hospitalization, sputum sample was taken from the patient since he had abnormal respiratory sounds and cough complaint. In the Gram stained smear of the sputum there were abundant leucocytes and gram-positive cocci, and S.uberis was isolated in both 5% sheep blood and chocolate agar media. Bacterial identification and antibiotic susceptibility tests were performed by VITEK 2 (Biomerieux, France) and also, the bacterium was identified by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) based VITEK MS system as S.uberis. The isolate was determined susceptible to ampicillin, erythromycin, clindamycin, levofloxacin, linezolid, penicillin, cefotaxime, ceftriaxone, tetracycline and vancomycin. 16S, 23S ribosomal RNA and 16S-23S intergenic spacer gene regions were amplified with specific primers and partial DNA sequence analysis of 16S rRNA polymerase chain reaction (PCR) products were performed by 3500xL Genetic Analyzer (Applied Biosystems, USA). According to the partial 16S rRNA gene sequencing results, bacterium was confirmed as S.uberis. This report makes a significant contribution to the number of case reports of human infections caused by S.uberis as the identification was performed by current microbiological methods in our case. In conclusion, S.uberis should be evaluated as an opportunistic pathogen among the immunosuppressed patients and in addition to phenotypic bacteriological methods, the other recent microbiological methods should also be utilized for the identification.

Comparison of high-pressure liquid chromatography and microbiological assay for determination of ciprofloxacin tablets in human plasma employed in bioequivalence and pharmacokinetics study.

PubMed

Khan, Muhammad Khalid; Khan, Muhammad Farid; Mustafa, Ghulam; Sualah, Mohammed

2012-01-01

Ciprofloxacin was given orally to 28 healthy male volunteers for single oral dose of 500mg; Plasma samples were collected at different time's interval between 0 and 12h and analyzed both by high pressure liquid chromatography and by a microbiological assay. The detection limits (LOD) were 0.02μg/ml and 0.1μg/ml, for both methods respectively. For each method, coefficients of variation (R(2)) were 0.9995 and 0.9918 in plasma and limit of quantitation (LOQ).02 and 0.5μg/ml. The Comparison of means maximum concentration 2.68 μg/ml at 1.5 hr for test and 2.43 μg/ml are attain in HPLC method of Reference at 2hrs respectively. The plasma concentrations measured by microbiological assay of reference tablet are 3.95μg/ml (mean ± SE) at 1 hour and 3.80μg/ml (mean ± SE) at 1 hour. The concentrations in plasma measured by microbiological method were markedly higher than the high-pressure liquid chromatography values which indicates the presence of antimicrobially active metabolites. The mean ± SE values of pharmacokinetic parameters calculated by HPLC method, for total area under the curve (AUC 0-oo) were 13.11, and 11.91 h.mg/l for both test and reference tablets respectively. The mean ± SE values of clearance measured in l/h were 44.91 and 48.42 respectively. The elimination rate constant Kel [l/h] showed 0.17 l/h for test and 0.15 l/h reference tablets and likewise, absorption half-life expressed in hours shown 0.67 h for test and 1.04 h for reference respectively. The Mean Residence Time for test is 5.48 h and 5.49 h for reference. The mean ± SE values of pharmacokinetic parameters (Microbiological assay) for total area under the curve (AUC 0-oo) were 22.11 and 19.33 h.mg/l for both test and reference tablets respectively. The mean ± SE values of clearance measured in l/h were 29.02 and 31.63 respectively. The elimination rate constant Kel [l/h] showed 0.21 l/h for test and 0.20 l/h reference tablets and likewise, absorption half-life expressed in hours shown 0.86h for test and 0.56 h for reference respectively. The Mean Residence Time for test is 5.27 h and 4.67 h for reference. Significant difference observed between two methods.

A Novel Fluorescence Resonance Energy Transfer-Based Screen in High-Throughput Format To Identify Inhibitors of Malarial and Human Glucose Transporters.

PubMed

Kraft, Thomas E; Heitmeier, Monique R; Putanko, Marina; Edwards, Rachel L; Ilagan, Ma Xenia G; Payne, Maria A; Autry, Joseph M; Thomas, David D; Odom, Audrey R; Hruz, Paul W

2016-12-01

The glucose transporter PfHT is essential to the survival of the malaria parasite Plasmodium falciparum and has been shown to be a druggable target with high potential for pharmacological intervention. Identification of compounds against novel drug targets is crucial to combating resistance against current therapeutics. Here, we describe the development of a cell-based assay system readily adaptable to high-throughput screening that directly measures compound effects on PfHT-mediated glucose transport. Intracellular glucose concentrations are detected using a genetically encoded fluorescence resonance energy transfer (FRET)-based glucose sensor. This allows assessment of the ability of small molecules to inhibit glucose uptake with high accuracy (Z' factor of >0.8), thereby eliminating the need for radiolabeled substrates. Furthermore, we have adapted this assay to counterscreen PfHT hits against the human orthologues GLUT1, -2, -3, and -4. We report the identification of several hits after screening the Medicines for Malaria Venture (MMV) Malaria Box, a library of 400 compounds known to inhibit erythrocytic development of P. falciparum Hit compounds were characterized by determining the half-maximal inhibitory concentration (IC 50 ) for the uptake of radiolabeled glucose into isolated P. falciparum parasites. One of our hits, compound MMV009085, shows high potency and orthologue selectivity, thereby successfully validating our assay for antimalarial screening. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

[Microbiological diagnosis of imported malaria].

PubMed

Torrús, Diego; Carranza, Cristina; Manuel Ramos, José; Carlos Rodríguez, Juan; Rubio, José Miguel; Subirats, Mercedes; Ta-Tang, Thuy-Huong

2015-07-01

Current diagnosis of malaria is based on the combined and sequential use of rapid antigen detection tests (RDT) of Plasmodium and subsequent visualization of the parasite stained with Giemsa solution in a thin and thick blood smears. If an expert microscopist is not available, should always be a sensitive RDT to rule out infection by Plasmodium falciparum, output the result immediately and prepare thick smears (air dried) and thin extensions (fixed with methanol) for subsequent staining and review by an expert microscopist. The RDT should be used as an initial screening test, but should not replace microscopy techniques, which should be done in parallel. The diagnosis of malaria should be performed immediately after clinical suspicion. The delay in laboratory diagnosis (greater than 3 hours) should not prevent the initiation of empirical antimalarial treatment if the probability of malaria is high. If the first microscopic examination and RDT are negative, they must be repeated daily in patients with high suspicion. If suspicion remains after three negative results must be sought the opinion of an tropical diseases expert. Genomic amplification methods (PCR) are useful as confirmation of microscopic diagnosis, to characterize mixed infections undetectable by other methods, and to diagnose asymptomatic infections with submicroscopic parasitaemia. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

Monitoring of microbial cell viability using nanostructured electrodes modified with Graphene/Alumina nanocomposite.

PubMed

Hassan, Rabeay Y A; Mekawy, Moataz M; Ramnani, Pankaj; Mulchandani, Ashok

2017-05-15

Microbial infections are rapidly increasing; however most of the existing microbiological and molecular detection methods are time consuming and/or cannot differentiate between the viable and dead cells which may overestimate the risk of infections. Therefore, a bioelectrochemical sensing platform with a high potential to the microbial-electrode interactions was designed based on decorated graphene oxide (GO) sheet with alumina (Al 2 O 3 ) nanocrystals. GO-Al 2 O 3 nanocomposite was synthesized using self-assembly of GO and Al 2 O 3 and characterized using the scanning electron microscopy (SEM), transmission electron microscopy (TEM), x-ray diffraction (XRD), Raman-spectroscopy, electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). Enhancement of electrocatalytic activity of the composite-modified electrode was demonstrated. Thus, using the GO-Al 2 O 3 nanocomposite modified electrode, the cell viability was determined by monitoring the bioelectrochemical response of the living microbial cells (bacteria and yeast) upon stimulation with carbon source. The bioelectrochemical assay was optimized to obtain high sensitivity and the method was applied to monitor cell viability and screen susceptibility of metabolically active cells (E. coli, B. subtilis, Enterococcus, P. aeruginosa and Salmonella typhi) to antibiotics such as ampicillin and kanamycin. Therefore, the developed assay is suitable for cell proliferation and cytotoxicity testing. Copyright © 2017 Elsevier B.V. All rights reserved.

Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks!

PubMed

Simões, Alexandra S; Couto, Isabel; Toscano, Cristina; Gonçalves, Elsa; Póvoa, Pedro; Viveiros, Miguel; Lapão, Luís V

2016-01-01

In Europe, each year, more than four milion patients acquire a healthcare-associated infection (HAI) and almost 40 thousand die as a direct consequence of it. Regardless of many stategies to prevent and control HAIs, they remain an important cause of morbidity and mortality worldwide with a significant economic impact: a recent estimate places it at the ten billion dollars/year. The control of HAIs requires a prompt and efficient identification of the etiological agent and a rapid communication with the clinician. The Microbiology Laboratory has a significant role in the prevention and control of these infections and is a key element of any Infection Control Program. The work of the Microbiology Laboratory covers microbial isolation and identification, determination of antimicrobial susceptibility patterns, epidemiological surveillance and outbreak detection, education, and report of quality assured results. In this paper we address the role and importance of the Microbiology Laboratory in the prevention and control of HAI and in Antibiotic Stewardship Programs and how it can be leveraged when combined with the use of information systems. Additionally, we critically review some challenges that the Microbiology Laboratory has to deal with, including the selection of analytic methods and the proper use of communication channels with other healthcare services.

Comparison of high-pressure liquid chromatography and microbiological assay for the determination of biliary elimination of ciprofloxacin in humans.

PubMed Central

Brogard, J M; Jehl, F; Monteil, H; Adloff, M; Blickle, J F; Levy, P

1985-01-01

Serum kinetics and biliary, urinary, and fecal elimination of ciprofloxacin, a new quinolone derivative, were studied in 12 recently cholecystectomized patients provided with T-tube drainage during 24 h after oral administration of a single 500-mg dose of this substance. Drug concentrations were measured by both high-pressure liquid chromatography (HPLC) and microbiological assay. The results were comparable for the concentrations in serum (average of peaks, 2.0 +/- 0.2 micrograms/ml by HPLC and 2.3 +/- 0.3 micrograms/ml by the microbiological method) and urine (0 to 6 h, 267 +/- 74 and 241 +/- 58 micrograms/ml, respectively). This was not the case for biliary values, for which the microbiological assay yielded significantly higher concentrations than did HPLC (average of peak concentrations, 21.2 +/- 2.6 and 16.0 +/- 2.5 micrograms/ml, respectively [P less than 0.02]), nor for total 24-h biliary output (2,167 +/- 288 and 1,587 +/- 222 micrograms, respectively [P less than 0.01]). This suggests hepatic biotransformation of ciprofloxacin into microbiologically active metabolites. The apparent broad antibacterial spectrum of ciprofloxacin and its higher biliary levels than simultaneously determined serum concentrations suggest that this derivative is suitable for the treatment of biliary tract infections. PMID:2939796

Microbiological parameters of aggregates in typical chernozems of long-term field experiments

NASA Astrophysics Data System (ADS)

Zhelezova, A. D.; Tkhakakhova, A. K.; Yaroslavtseva, N. V.; Garbuz, S. A.; Lazarev, V. I.; Kogut, B. M.; Kutovaya, O. V.; Kholodov, V. A.

2017-06-01

The changes in microbiological parameters of aggregates (1-2 mm) in typical chernozems under different land uses as dependent on the intensity and character of anthropogenic loads were studied with the help of the real-time polymerase chain reaction (PCR). The samples from the following long-term field experiments were examined: permanent black fallow, continuous cultivation of potato, 17-year-old unmanaged fallow after permanent black fallow, and annually mown reserved steppe. The soil samples were treated in two ways. In the first case, the samples were air-dried, sieved through the screens to separate aggregate fraction of 1-2 mm, and microbiological parameters were determined in this fraction. In the second case, the samples were frozen immediately after the sampling, and the aggregates of 1-2 mm were manually separated from the samples before the PCR analysis. It was shown that air-dry aggregates of chernozems could be used for the quantitative analysis of DNA of microbial community in comparative studies. According to the quantitative estimate of the content of DNA fragments from different phylogenetic groups, the bacterial community was most sensitive to the type of the soil use, and its restoration after the removal of extreme anthropogenic loads proceeded faster than that of other microorganisms. The content of archaeal DNA in the chernozem under the 17-year-old unmanaged fallow did not differ significantly from its content in the annually plowed chernozems. The changes in the content of micromycetal DNA related to anthropogenic load decrease were intermediate between changes in the contents of archaeal and bacterial DNA.

Multiclass method for the determination of 62 antibiotics in milk.

PubMed

Moretti, Simone; Cruciani, Gabriele; Romanelli, Sara; Rossi, Rosanna; Saluti, Giorgio; Galarini, Roberta

2016-09-01

A multiclass method for screening and confirmatory analysis of antimicrobial residues in milk has been developed and validated. Sixty-two antibiotics belonging to ten different drug families (amphenicols, cephalosporins, lincosamides, macrolides, penicillin, pleuromutilins, quinolones, rifamycins, sulfonamides and tetracyclines) have been included. After the addition of an aqueous solution of EDTA, the milk samples were extracted twice with acetonitrile, evaporated and dissolved in ammonium acetate. After centrifugation, 10 µl were analysed using LC-Q-Orbitrap operating in positive electrospray ionization mode. The method was validated in bovine milk in the range 2-150 µg kg(-1) for all antibiotics; for four compounds with maximum residue limits higher than 100 µg kg(-1) , the validation interval has been extended until 333 µg kg(-1) . The estimated performance characteristics were satisfactory complying with the requirements of Commission Decision 2002/657/EC. Good accuracies were obtained also taking advantage from the versatility of the hybrid mass analyser. Identification criteria were achieved verifying the mass accuracy and ion ratio of two ions, including the pseudomolecular one, where possible. Finally, the developed procedure was applied to 13 real cases of suspect milk samples (microbiological assay) confirming the presence of one or more antibiotics, although frequently, the maximum residue limits were not exceeded. The availability of rapid multiclass confirmatory methods can avoid wastes of suspect, but compliant, raw milk samples. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Towards objective hand hygiene technique assessment: validation of the ultraviolet-dye-based hand-rubbing quality assessment procedure.

PubMed

Lehotsky, Á; Szilágyi, L; Bánsághi, S; Szerémy, P; Wéber, G; Haidegger, T

2017-09-01

Ultraviolet spectrum markers are widely used for hand hygiene quality assessment, although their microbiological validation has not been established. A microbiology-based assessment of the procedure was conducted. Twenty-five artificial hand models underwent initial full contamination, then disinfection with UV-dyed hand-rub solution, digital imaging under UV-light, microbiological sampling and cultivation, and digital imaging of the cultivated flora were performed. Paired images of each hand model were registered by a software tool, then the UV-marked regions were compared with the pathogen-free sites pixel by pixel. Statistical evaluation revealed that the method indicates correctly disinfected areas with 95.05% sensitivity and 98.01% specificity. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

MALDI-TOF MS in the Microbiology Laboratory: Current Trends.

PubMed

Schubert, Sören; Kostrzewa, Markus

2017-01-01

Within less than a decade matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a gold standard for microbial identification in clinical microbiology laboratories. Besides identification of microorganisms the typing of single strains as well as the antibiotic and antimycotic resistance testing has come into focus in order to speed up the microbiological diagnostic. However, the full potential of MALDI-TOF MS has not been tapped yet and future technological advancements will certainly expedite this method towards novel applications and enhancement of current practice. So, the following chapter shall be rather a brainstorming and forecast of how MALDI-TOF MS will develop to influence clinical diagnostics and microbial research in the future. It shall open up the stage for further discussions and does not claim for overall validity.

Genomics and metagenomics in medical microbiology.

PubMed

Padmanabhan, Roshan; Mishra, Ajay Kumar; Raoult, Didier; Fournier, Pierre-Edouard

2013-12-01

Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology. Copyright © 2013 Elsevier B.V. All rights reserved.

Compilation of Annual Reports of the Navy ELF (Extremely Low Frequency) Communications System Ecological Monitoring Program. Volume 1. Tabs A-E.

DTIC Science & Technology

1984-07-01

mhhhhmhhmmm EEmhohEEmhmhEE EohhEohEEEEohI 1111 11111_L25 1.18 6 MICROCOPY RESOLUTION TESI CHART 95. Pedon Classification: Typic Dystrochrept, sandy, mixed...prepared by team researchers in the MTU Forestry Department and delivered to the Environmental Microbiology lab in the Department of Biological Sciences...unsuccessful. Using methods given in a presentation at the 1982 American Society for Microbiology Annual Meetings, virtually no bacteria of any type were

Comparative Analysis of Subtyping Methods against a Whole- Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

DTIC Science & Technology

2015-01-01

enterica serovar En- teritidis. Food Microbiology 34:164 –173. http://dx.doi.org/10.1016/j.fm .2012.11.012. 11. Dewaele I, Rasschaert G, Bertrand S...MVLST showed the potential to trace major lineages and ecological origins of S. enterica serotype Enteritidis. Our results suggested that whole-genome...in Journal of Clinical Microbiology , Vol. 53 (1) (2015), (3 (1). DoD Components reserve a royalty-free, nonexclusive and irrevocable right to

Researching Seeds: Films, Sanitation Methods, Microbiological Growth, Viability, and Selection for New Crops

NASA Technical Reports Server (NTRS)

Padgett, Niki; Smith, Trent

2018-01-01

A major factor in long-term human exploration of the solar system is crop growth in microgravity. Space crops can provide fresh, nutritious food to supplement diets for astronauts. Important factors impacting space plant growth and consumption are water delivery to root zone in microgravity, sanitation methods for microbiological safety, plant responses to light quality/spectrum, and identifying optimal edible plants suitable for growth on the International Space Station (ISS). Astronauts growing their own food on the ISS provides necessary data for crop production for long duration deep space missions. The seed film project can be used in Advanced Plant Habitat and Veggies that are currently being utilized on the ISS.

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

PubMed

Garrity, George M

2016-08-01

Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Surface microbial contamination in hospitals: A pilot study on methods of sampling and the use of proposed microbiologic standards.

PubMed

Claro, Tânia; O'Reilly, Marese; Daniels, Stephen; Humphreys, Hilary

2015-09-01

Contamination of hospital surfaces by bacteria is increasingly recognized. We assessed commonly touched surfaces using contact plates and Petrifilms (3M, St. Paul, MN) and compared the results against proposed microbiology standards. Toilet door handles were the most heavily contaminated (7.97 ± 0.68 colony forming units [CFU]/cm(2)) and exceeded proposed standards on 74% of occasions. Petrifilms detected statistically higher CFU from bedside lockers. Further research is required on the use of standards and methods of sampling. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Screening for urinary tract infection in women with hyperemesis gravidarum.

PubMed

Tan, Peng Chiong; King, Anthonia Siaw Jia; Omar, Siti Zawiah

2012-01-01

The aim of this study was to evaluate urine microscopy, dipstick analysis and urinary symptoms in screening for urinary tract infection (UTI) in hyperemesis gravidarum (HG).   A prospective cross-sectional study was performed on women at first hospitalization for HG. A clean-catch mid-stream urine sample from each recruit was sent for microscopy (for bacteria, leucocytes and erythrocytes), dipstick analysis (for leukocyte esterase, nitrites, protein and hemoglobin) and microbiological culture. The presence of current urinary symptoms was elicited by questionnaire. UTI is defined as at least 10(5) colony-forming units/mL of a single uropathogen on culture. Screening test parameters were analyzed against UTI. UTI was diagnosed in 15/292 subjects (5.1%). Receiver-operator characteristic curve analysis of microscopic urine leucocytes revealed area under the curve=0.64, 95% confidence interval (CI) 0.5-0.79, P=0.063 and erythrocytes area under the curve=0.53, 95%CI 0.39-0.67, P=0.67 for UTI indicating the limited screening utility of these parameters. Microscopic bacteriuria (likelihood ratio [LR] 1.1, 95%CI 0.7-1.5) and urine dipstick leukocyte esterase (LR 1.4, 95%CI 1.1-1.8), nitrites (LR 2.3, 95%CI 0.3-17.2), protein (LR 1.0, 95%CI 0.7-1.6) and hemoglobin (LR 0.8, 95%CI 0.4-1.5) were not useful screening tests for UTI in HG. Elicited symptoms were also not predictive of UTI. Urine microscopy, dipstick analysis and urinary symptoms were not useful in screening for UTI in HG. UTI should be established by urine culture in HG before starting antibiotic treatment. © 2011 The Authors. Journal of Obstetrics and Gynaecology Research © 2011 Japan Society of Obstetrics and Gynecology.

Evaluation of the UVB-screening capacity and restorative effects exerted by farnesol gel on UVB-caused sunburn.

PubMed

Wu, Guan Xuan; Huang, Han Hsiang; Chang, Huoy Rou; Kuo, Shyh Ming

2018-04-01

Farnesol, a natural 15-carbon organic compound, has various microbiological and cellular activities. It has been found to exert apoptosis-inducing effects against carcinoma cells as well as antiallergic and anti-inflammatory effects in vivo. In the current study, a series of formulations composed of various concentrations of hydroxypropyl methylcellulose (HPMC) with the addition of hyaluronan (HA) and xanthan gum (XG) was designed to evaluate the UVB-screening and H 2 O 2 -eliminating effects of farnesol in normal fibroblasts. Farnesol at 0.005, 0.0075, and 0.01% exhibited significant capacity for H 2 O 2 scavenging; at 0.0025%, it showed insignificant effects. Under 120-min UVB exposure, screening with plural gel composed of 0.0025% farnesol, 0.5% HA, and 0.5% XG containing 1.5% or 2% HPMC retained normal fibroblast viability. After 60-min exposure to UVB, screening with plural gel composed of farnesol, HA, XG, and 0.5%, 1.0%, 1.5%, or 2% HPMC decreased the ratio of the G1 phase and increased ratio of the S phase in comparison with the accumulated cell cycle of the normal fibroblasts without screening. The gel with 2% HPMC displayed the strongest cell cycle-reversal ability. In vivo histopathological results showed that the prepared plural gels with 0.5% or 2% HPMC and farnesol, HA, and XG had greater antiphotoaging and reparative effects against UVB-induced changes and damage in the skin. In conclusion, the current in vitro and in vivo results demonstrated that the prepared plural composed of 0.0025% farnesol, 0.5% HA, 0.5% XG, and 2% HPMC possessed the greatest UVB-screening capacity and the strongest restorative effects on UVB-induced sunburned skin. © 2018 Wiley Periodicals, Inc.

The prevalence and determinants of active tuberculosis among diabetes patients in Cape Town, South Africa, a high HIV/TB burden setting.

PubMed

Berkowitz, Natacha; Okorie, Adaeze; Goliath, Rene; Levitt, Naomi; Wilkinson, Robert J; Oni, Tolu

2018-04-01

Studies addressing the association between diabetes mellitus (DM) and tuberculosis (TB) in sub-Saharan Africa are limited. We assessed the prevalence of active TB among DM patients at a primary care clinic, and identified risk factors for prevalent TB. A cross-sectional study was conducted in adult DM patients attending a clinic in Khayelitsha, Cape Town. Participants were screened for active TB (symptom screening and microbiological diagnosis) and HIV. Among 440 DM patients screened, the active TB prevalence was 3.0% (95% CI 1.72-5.03). Of the 13 prevalent TB cases, 53.9% (n = 7; 95% CI 27.20-78.50) had no TB symptoms, and 61.5% (n = 8; 95% CI 33.30-83.70) were HIV-1 co-infected. There were no significant differences in either fasting plasma glucose or HbA 1c levels between TB and non-TB participants. On multivariate analysis, HIV-1 infection (OR 11.3, 95% CI 3.26-39.42) and hemoptysis (OR 31.4, 95% CI 3.62-273.35) were strongly associated with prevalent active TB, with no differences in this association by age or gender. The prevalence of active TB among DM patients was 4-fold higher than the national prevalence; suggesting the need for active TB screening, particularly if hemoptysis is reported. Our results highlight the importance of HIV screening in this older population group. The high prevalence of sub-clinical TB among those diagnosed with TB highlights the need for further research to determine how best to screen for active TB in high-risk TB/HIV population groups and settings. Copyright © 2018. Published by Elsevier B.V.

Agricultural reuse of municipal wastewater through an integral water reclamation management.

PubMed

Intriago, Juan Carlo; López-Gálvez, Francisco; Allende, Ana; Vivaldi, Gaetano Alessandro; Camposeo, Salvatore; Nicolás Nicolás, Emilio; Alarcón, Juan José; Pedrero Salcedo, Francisco

2018-05-01

The DESERT-prototype, a state-of-the-art compact combination of water treatment technologies based on filtration and solar-based renewable energy, was employed to reclaim water for agricultural irrigation. Water reclaimed through the DESERT-prototype (PW) from a secondary effluent of a wastewater treatment plant, as well as conventional irrigation water (CW) and the secondary effluent (SW) itself, were employed to cultivate baby romaine lettuces in a greenhouse in Murcia (Spain), by means of drip and sprinkler irrigation methods, thus establishing six treatments. Assessments of physicochemical and microbiological quality of irrigation water, as well as agronomic and microbiological quality of crops from all treatments, showed that results associated to PW complied in all cases with relevant standards and guidelines. In contrast, results linked to SW and CW presented certain non-compliance cases of water and crop microbiological quality. These assessments lead to conclude that the DESERT-prototype is an appropriate technology for safe water reclamation oriented to agricultural production, that can be complemented by a proper irrigation method in reaching safety targets. Copyright © 2018 Elsevier Ltd. All rights reserved.

Rapid test for the detection of hazardous microbiological material

NASA Astrophysics Data System (ADS)

Mordmueller, Mario; Bohling, Christian; John, Andreas; Schade, Wolfgang

2009-09-01

After attacks with anthrax pathogens have been committed since 2001 all over the world the fast detection and determination of biological samples has attracted interest. A very promising method for a rapid test is Laser Induced Breakdown Spectroscopy (LIBS). LIBS is an optical method which uses time-resolved or time-integrated spectral analysis of optical plasma emission after pulsed laser excitation. Even though LIBS is well established for the determination of metals and other inorganic materials the analysis of microbiological organisms is difficult due to their very similar stoichiometric composition. To analyze similar LIBS-spectra computer assisted chemometrics is a very useful approach. In this paper we report on first results of developing a compact and fully automated rapid test for the detection of hazardous microbiological material. Experiments have been carried out with two setups: A bulky one which is composed of standard laboratory components and a compact one consisting of miniaturized industrial components. Both setups work at an excitation wavelength of λ=1064nm (Nd:YAG). Data analysis is done by Principal Component Analysis (PCA) with an adjacent neural network for fully automated sample identification.

EPA METHOD STUDY 8, TOTAL MERCURY IN WATER

EPA Science Inventory

The Environmental Monitoring and Support Laboratory-Cincinnati of EPA conducts EPA's quality assurance program for the water laboratories and assists EPA laboratories in the choice of methods for physical, chemical, biological and microbiological analyses. The responsibility for ...

Biotechnology Laboratory Methods.

ERIC Educational Resources Information Center

Davis, Robert H.; Kompala, Dhinakar S.

1989-01-01

Describes a course entitled "Biotechnology Laboratory" which introduces a variety of laboratory methods associated with biotechnology. Describes the history, content, and seven experiments of the course. The seven experiments are selected from microbiology and molecular biology, kinetics and fermentation, and downstream…

Prevalence of pulmonary tuberculosis among prison inmates: A cross-sectional survey at the Correctional and Detention Facility of Abidjan, Côte d'Ivoire

PubMed Central

Koffi, Ange; Danel, Christine; Ouassa, Timothée; Blehoué, Marcel-Angora; Ouattara, Eric; Assemien, Jeanne-d’Arc; Masumbuko, Jean-Marie; Coffie, Patrick; Cartier, Nathalie; Laurent, Arnaud; Raguin, Gilles; Malvy, Denis; N’Dri-Yoman, Thérèse; Eholié, Serge P.; Domoua, Serge K.

2017-01-01

Background In Côte d’Ivoire, a TB prison program has been developed since 1999. This program includes offering TB screening to prisoners who show up with TB symptoms at the infirmary. Our objective was to estimate the prevalence of pulmonary TB among inmates at the Correctional and Detention Facility of Abidjan, the largest prison of Côte d’Ivoire, 16 years after this TB program was implemented. Methods Between March and September 2015, inmates, were screened for pulmonary TB using systematic direct smear microscopy, culture and chest X-ray. All participants were also proposed HIV testing. TB was defined as either confirmed (positive culture), probable (positive microscopy and/or chest X-ray findings suggestive of TB) or possible (signs or symptoms suggestive of TB, no X-Ray or microbiological evidence). Factors associated with confirmed tuberculosis were analysed using multivariable logistic regression. Results Among the 943 inmates screened, 88 (9.3%) met the TB case definition, including 19 (2.0%) with confirmed TB, 40 (4.2%) with probable TB and 29 (3.1%) with possible TB. Of the 19 isolated TB strains, 10 (53%) were TB drug resistant, including 7 (37%) with multi-resistance. Of the 10 patients with TB resistant strain, only one had a past history of TB treatment. HIV prevalence was 3.1% overall, and 9.6%among TB cases. Factors associated with confirmed TB were age ≥30 years (Odds Ratio 3.8; 95% CI 1.1–13.3), prolonged cough (Odds Ratio 3.6; 95% CI 1.3–9.5) and fever (Odds Ratio 2.7; 95% CI 1.0–7.5). Conclusion In the country largest prison, pulmonary TB is still 10 (confirmed) to 44 times (confirmed, probable or possible) as frequent as in the Côte d’Ivoire general population, despite a long-time running symptom-based program of TB detection. Decreasing TB prevalence and limiting the risk of MDR may require the implementation of annual in-cell TB screening campaigns that systematically target all prison inmates. PMID:28759620

Characterization of multidrug-resistant diabetic foot ulcer enterococci.

PubMed

Semedo-Lemsaddek, Teresa; Mottola, Carla; Alves-Barroco, Cynthia; Cavaco-Silva, Patrícia; Tavares, Luís; Oliveira, Manuela

2016-02-01

Diabetes mellitus is a highly prevalent chronic progressive disease with complications that include diabetic-foot ulcers. Enterococci isolated from diabetic-foot infections were identified, evaluated by macro-restriction analysis, and screened for virulence traits and antimicrobial resistance. All isolates were considered multidrug-resistant, cytolysin and gelatinase producers, and the majority also demonstrated the ability to produce biofilms. These results indicate the importance of enterococci in diabetic-foot infection development and persistence, especially regarding their biofilm-forming ability and resistance to clinically relevant antibiotics. Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Microbiological evaluation of female patients in STD clinics.

PubMed

Iyer, S V; Deodhar, L; Gogate, A

1991-03-01

A total of 215 women patients attending the STD clinic were evaluated in an attempt to isolate the different microorganisms in sexually transmitted diseases (STD). Mycoplasmas (30.22%), Candida species (20.00%), Trichomonas vaginalis (wet mount study; 15.81%), beta haemolytic streptococci (13.48%), Neisseria gonorrhoeae (9.30%), Staphylococcus aureus (13.95%), inclusion bodies of Chlamydia trachomatis (11.60%) and Gram negative organisms (9.30%) were isolated from these patients. Sera of all patients screened for HBsAg by ELISA showed a carrier rate of 12.5 per cent; 29.8 per cent sera were reactive in the VDRL test at the dilutions varying from 1:4 to 1:64.

Current and Future Technologies for Microbiological Decontamination of Cereal Grains.

PubMed

Los, Agata; Ziuzina, Dana; Bourke, Paula

2018-06-01

Cereal grains are the most important staple foods for mankind worldwide. The constantly increasing annual production and yield is matched by demand for cereals, which is expected to increase drastically along with the global population growth. A critical food safety and quality issue is to minimize the microbiological contamination of grains as it affects cereals both quantitatively and qualitatively. Microorganisms present in cereals can affect the safety, quality, and functional properties of grains. Some molds have the potential to produce harmful mycotoxins and pose a serious health risk for consumers. Therefore, it is essential to reduce cereal grain contamination to the minimum to ensure safety both for human and animal consumption. Current production of cereals relies heavily on pesticides input, however, numerous harmful effects on human health and on the environment highlight the need for more sustainable pest management and agricultural methods. This review evaluates microbiological risks, as well as currently used and potential technologies for microbiological decontamination of cereal grains. © 2018 Institute of Food Technologists®.

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

Controlling organic chemical hazards in food manufacturing: a hazard analysis critical control points (HACCP) approach.

PubMed

Ropkins, K; Beck, A J

2002-08-01

Hazard analysis by critical control points (HACCP) is a systematic approach to the identification, assessment and control of hazards. Effective HACCP requires the consideration of all hazards, i.e., chemical, microbiological and physical. However, to-date most 'in-place' HACCP procedures have tended to focus on the control of microbiological and physical food hazards. In general, the chemical component of HACCP procedures is either ignored or limited to applied chemicals, e.g., food additives and pesticides. In this paper we discuss the application of HACCP to a broader range of chemical hazards, using organic chemical contaminants as examples, and the problems that are likely to arise in the food manufacturing sector. Chemical HACCP procedures are likely to result in many of the advantages previously identified for microbiological HACCP procedures: more effective, efficient and economical than conventional end-point-testing methods. However, the high costs of analytical monitoring of chemical contaminants and a limited understanding of formulation and process optimisation as means of controlling chemical contamination of foods are likely to prevent chemical HACCP becoming as effective as microbiological HACCP.

[Consensus for antimicrobial susceptibility testing for Enterobacteriaceae. Subcommittee on Antimicrobials, SADEBAC (Argentinian Society of Clinical Bacteriology), Argentinian Association of Microbiology].

PubMed

Famiglietti, A; Quinteros, M; Vázquez, M; Marín, M; Nicola, F; Radice, M; Galas, M; Pasterán, F; Bantar, C; Casellas, J M; Kovensky Pupko, J; Couto, E; Goldberg, M; Lopardo, H; Gutkind, G; Soloaga, R

2005-01-01

Taking into account previous recommendations from the National Committee for Clinical Laboratory Standards (NCCLS), the Antimicrobial Committee, Sociedad Argentina de Bacteriología Clínica (SADEBAC), Asociación Argentina de Microbiología (AAM), and the experience from its members and some invited microbiologists, a consensus was obtained for antimicrobial susceptibility testing and interpretation in most frequent enterobacterial species isolated from clinical samples in our region. This document describes the natural antimicrobial resistance of some Enterobacteriaceae family members, including the resistance profiles due to their own chromosomal encoded beta-lactamases. A list of the antimicrobial agents that should be tested, their position on the agar plates, in order to detect the most frequent antimicrobial resistance mechanisms, and considerations on which antimicrobial agents should be reported regarding to the infection site and patient characteristics are included. Also, a description on appropriate phenotypic screening and confirmatory test for detection of prevalent extended spectrum beta-lactamases in our region are presented. Finally, a summary on frequent antimicrobial susceptibility profiles and their probably associated resistance mechanisms, and some infrequent antimicrobial resistance profiles that deserve confirmation are outlined.

Microbiological assay for the analysis of certain macrolides in pharmaceutical dosage forms.

PubMed

Mahmoudi, A; Fourar, R E-A; Boukhechem, M S; Zarkout, S

2015-08-01

Clarithromycin (CLA) and roxithromycin (ROX) are macrolide antibiotics with an expanded spectrum of activity that are commercially available as tablets. A microbiological assay, applying the cylinder-plate method and using a strain of Micrococcus luteus ATCC 9341 as test organism, has been used and validated for the quantification of two macrolide drugs; CLA and ROX in pure and pharmaceutical formulations. The validation of the proposed method was carried out for linearity, precision, accuracy and specificity. The linear dynamic ranges were from 0.1 to 0.5μg/mL for both compounds. Logarithmic calibration curve was obtained for each macrolide (r>0.989) with statistically equal slopes varying from 3.275 to 4.038, and a percentage relative standard deviation in the range of 0.24-0.92%. Moreover, the method was applied successfully for the assay of the studied drugs in pharmaceutical tablet dosage forms. Recovery from standard addition experiments in commercial products was 94.71-96.91% regarding clarithromycin and 93.94-98.12% regarding roxithromycin, with a precision (%RSD) 1.32-2.11%. Accordingly, this microbiological assay can be used for routine quality control analysis of titled drugs in tablet formulations. Copyright © 2015 Elsevier B.V. All rights reserved.

Gnotobiotic pigs-derivation and rearing.

PubMed

Miniats, O P; Jol, D

1978-10-01

The procurement, rearing, nutrition and microbiological monitoring of gnotobiotic pigs and a method for conditioning of primary, colostrum-deprived, specific pathogen free pigs is described. As compared to the established hysterectomy and closed hysterotomy methods for the derivation of gnotobiotic piglets an alternative approach, open caesarian section with the sow maintained under general halothane-nitrous oxide anaesthesia and the introduction of each fetus into the sterile isolator via a liquid germicidal trap, was found to be more efficient and equally successful in providing viable and microbiologically sterile piglets. Two sterile commercially available milk diets, a special formula for orphan animals and condensed cow's milk, when the latter was supplemented with injectable vitamin E, selenium and iron, proved adequate for satisfactory health of the animals. Two types of pelleted starter rations, sterilized by 4.5 megarads of gamma irradiation, provided adequately for the nutritional needs of older gnotobiotic pigs. Results of microbiological monitoring indicated that the surgical and rearing methods employed were capable of preventing contamination of the animals with bacteria, mycoplasma, yeasts, molds, protozoa and helminths but probably could not exclude occasional vertically transmitted viral infections. Exposure of the animals for four weeks to selected strains of lactobacilli, fecal streptococci and Escherichia coli did not result in visible disease while they were maintained in isolators and conditioned them for transfer into a conventional microbial environment.

Development, Validation, and Application of the Microbiology Concept Inventory †

PubMed Central

Paustian, Timothy D.; Briggs, Amy G.; Brennan, Robert E.; Boury, Nancy; Buchner, John; Harris, Shannon; Horak, Rachel E. A.; Hughes, Lee E.; Katz-Amburn, D. Sue; Massimelli, Maria J.; McDonald, Ann H.; Primm, Todd P.; Smith, Ann C.; Stevens, Ann M.; Yung, Sunny B.

2017-01-01

If we are to teach effectively, tools are needed to measure student learning. A widely used method for quickly measuring student understanding of core concepts in a discipline is the concept inventory (CI). Using the American Society for Microbiology Curriculum Guidelines (ASMCG) for microbiology, faculty from 11 academic institutions created and validated a new microbiology concept inventory (MCI). The MCI was developed in three phases. In phase one, learning outcomes and fundamental statements from the ASMCG were used to create T/F questions coupled with open responses. In phase two, the 743 responses to MCI 1.0 were examined to find the most common misconceptions, which were used to create distractors for multiple-choice questions. MCI 2.0 was then administered to 1,043 students. The responses of these students were used to create MCI 3.0, a 23-question CI that measures students’ understanding of all 27 fundamental statements. MCI 3.0 was found to be reliable, with a Cronbach’s alpha score of 0.705 and Ferguson’s delta of 0.97. Test item analysis demonstrated good validity and discriminatory power as judged by item difficulty, item discrimination, and point-biserial correlation coefficient. Comparison of pre- and posttest scores showed that microbiology students at 10 institutions showed an increase in understanding of concepts after instruction, except for questions probing metabolism (average normalized learning gain was 0.15). The MCI will enable quantitative analysis of student learning gains in understanding microbiology, help to identify misconceptions, and point toward areas where efforts should be made to develop teaching approaches to overcome them. PMID:29854042

Impact of rearing conditions on the microbiological quality of raw retail poultry meat.

PubMed

Hardy, Bridgshe; Crilly, Nate; Pendleton, Sean; Andino, Ana; Wallis, Audra; Zhang, Nan; Hanning, Irene

2013-08-01

There is a gap in knowledge of microbiological quality in raw chicken products produced by nonconventional methods and no studies have reported the microbiological quality of turkeys produced under different rearing environments. Thus, the aim of this study was to compare the microbiological quality of conventionally and organically reared whole chicken and turkey carcasses purchased from 3 retail outlets in Knoxville, Tenn., U.S.A. A total of 100 raw broiler chickens organically (n = 50) and 50 raw turkey carcasses consisting of 3 brands reared either conventionally (n = 25) or organically (n = 25) were evaluated. The FDA BAM protocol for rinsing poultry carcasses was used to enumerate of aerobic bacteria, Campylobacter, and Staphylococcus spp., and for qualitative analysis of Salmonella. Organic chickens from one brand had the highest average counts of aerobic bacteria, Staphylococcus spp. and Campylobacter (4.8, 4.8, and 4.7 Log10 CFU/mL rinsate, respectively) while the other organic brand had the lowest average counts (3.4, 3.3, and 3.1, respectively) of all 4 brands evaluated. The organic turkeys had the highest average counts of these same bacteria (4, 3.9, and 3.8, respectively) compared to the 2 brands of conventional turkeys evaluated. Salmonella (5% prevalence) was isolated only from organic chickens and turkeys. From these data, it appears that the microbiological quality of the raw product was not dependent on rearing conditions and, thus, it cannot be assumed that organic raw poultry is safer than conventionally raised poultry in terms of microbiological quality. © 2013 Institute of Food Technologists®

Vancomycin heteroresistance in coagulase negative Staphylococcus blood stream infections from patients of intensive care units in Mansoura University Hospitals, Egypt.

PubMed

Mashaly, Ghada El-Saeed; El-Mahdy, Rasha Hassan

2017-09-19

Vancomycin heteroresistance in coagulase negative Staphylococci (CoNS) is a recent health concern especially in serious infections like bloodstream infections as it may lead to failure of therapy. Little information is available about the prevalence vancomycin heteroresistance in CoNS causing bloodstream infections in intensive care units (ICUs) patients of Mansoura University Hospitals (MUHs). This prospective study enrolled 743 blood samples collected from ICUs patients presented with clinical manifestations of bloodstream infections over the period extending from January 2014 to March 2016. Samples were processed, coagulase negative Staphylococci were identified by routine microbiological methods and the absence of coagulase activity. Species were identified by API Staph 32. Oxacillin resistant CoNS were identified by cefoxitin disc diffusion method. Susceptibility testing of isolated CoNS to vancomycin was carried out using vancomycin agar dilution method. Mec A gene detection by PCR was done for oxacillin resistant isolates. Screening for vancomycin heteroresistance was done on brain heart infusion (BHI) agar containing 4 μg/mL vancomycin. Confirmation of vancomycin heteroresistance was carried out by population analysis profile (PAP). A total of 58 isolates were identified as CoNS from patients of clinically suspected bloodstream infections. The identified species were 33 (56.9%) Staphylococcus epidermidis, 12 (20.7%) Staphylococcus capitis, 7 (12.1%) Staphylococcus haemolyticus, and 3 isolates (5.2%) Staphylococcus lugdunesis. Three isolates were unidentified by API Staph 32. Forty-four (75.9%) isolates were oxacillin resistant. Mec A gene was detected in all oxacillin resistant isolates. All isolates had susceptible vancomycin MICs by agar dilution. Nine isolates (15.5%) could grow on BHI agar containing 4 μg/mL vancomycin. These isolates showed heterogeneous profile of resistance to vancomycin by population analysis profile. Vancomycin heteroresistant CoNS causing bloodstream infections is growing unrecognized health hazard in ICUs patients. These isolates have susceptible vancomycin MICs. Screening methods are recommended and should be considered to improve clinical outcome in these high risk patients.

76 FR 63615 - Environmental Science Center Microbiology Laboratory; Notice of Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-13

...-dilution method (UDM) and the status and implementation of a new test method, the Organization for Economic... using the method for registration purposes, the method is currently in use as part of the post market... associated with the S. aureus and P. aeruginosa methodologies, which are designed to further optimize and...

CRENAME, A Molecular Microbiology Method Enabling Multiparametric Assessment of Potable/Drinking Water.

PubMed

Bissonnette, Luc; Maheux, Andrée F; Bergeron, Michel G

2017-01-01

The microbial assessment of potable/drinking water is done to ensure that the resource is free of fecal contamination indicators or waterborne pathogens. Culture-based methods for verifying the microbial safety are limited in the sense that a standard volume of water is generally tested for only one indicator (family) or pathogen.In this work, we describe a membrane filtration-based molecular microbiology method, CRENAME (Concentration Recovery Extraction of Nucleic Acids and Molecular Enrichment), exploiting molecular enrichment by whole genome amplification (WGA) to yield, in less than 4 h, a nucleic acid preparation which can be repetitively tested by real-time PCR for example, to provide multiparametric presence/absence tests (1 colony forming unit or microbial particle per standard volume of 100-1000 mL) for bacterial or protozoan parasite cells or particles susceptible to contaminate potable/drinking water.

Display screen and method of manufacture therefor

NASA Technical Reports Server (NTRS)

Dubin, Matthew B. (Inventor); Larson, Brent D. (Inventor)

2002-01-01

A screen assembly that combines an angle re-distributing prescreen with a conventional diffusion screen. The prescreen minimizes or eliminates the sensitivity of the screen assembly to projector location. The diffusion screen provides other desirable screen characteristics. Compatible screen structures, along with methods for fabricating high resolution prescreens and methods and devices for maintaining the desired relationship between the prescreen and the diffusion screen are contemplated.

Actinomyces and related organisms in human infections.

PubMed

Könönen, Eija; Wade, William G

2015-04-01

Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Proteome-based bacterial identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS): A revolutionary shift in clinical diagnostic microbiology.

PubMed

Nomura, Fumio

2015-06-01

Rapid and accurate identification of microorganisms, a prerequisite for appropriate patient care and infection control, is a critical function of any clinical microbiology laboratory. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a quick and reliable method for identification of microorganisms, including bacteria, yeast, molds, and mycobacteria. Indeed, there has been a revolutionary shift in clinical diagnostic microbiology. In the present review, the state of the art and advantages of MALDI-TOF MS-based bacterial identification are described. The potential of this innovative technology for use in strain typing and detection of antibiotic resistance is also discussed. This article is part of a Special Issue entitled: Medical Proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

[External quality control system in medical microbiology and parasitology in the Czech Republic].

PubMed

Slosárek, M; Petrás, P; Kríz, B

2004-11-01

The External Quality Control System (EQAS) of laboratory activities in medical microbiology and parasitology was implemented in the Czech Republic in 1993 with coded sera samples for diagnosis of viral hepatitis and bacterial strains for identification distributed to first participating laboratories. The number of sample types reached 31 in 2003 and the number of participating laboratories rised from 79 in 1993 to 421 in 2003. As many as 15.130 samples were distributed to the participating laboratories in 2003. Currently, almost all microbiology and parasitology laboratories in the Czech Republic involved in examination of clinical material participate in the EQAS. Based on the 11-year experience gained with the EQAS in the Czech Republic, the following benefits were observed: higher accuracy of results in different tests, standardisation of methods and the use of most suitable test kits.

Measurement uncertainty of the EU methods for microbiological examination of red meat.

PubMed

Corry, Janet E L; Hedges, Alan J; Jarvis, Basil

2007-09-01

Three parallel trials were made of EU methods proposed for the microbiological examination of red meat using two analysts in each of seven laboratories within the UK. The methods involved determination of aerobic colony count (ACC) and Enterobacteriaceae colony count (ECC) using simulated methods and a freeze-dried standardised culture preparation. Trial A was based on a simulated swab test, Trial B a simulated meat excision test and Trial C was a reference test on reconstituted inoculum. Statistical analysis (ANOVA) was carried out before and after rejection of outlying data. Expanded uncertainty values (relative standard deviation x2) for repeatability and reproducibility, based on the log10 cfu/ml, on the ACC ranged from +/-2.1% to +/-2.7% and from +/-5.5% to +/-10.5%, respectively, depending upon the test procedure. Similarly for the ECC, expanded uncertainty estimates for repeatability and reproducibility ranged from +/-4.6% to +/-16.9% and from +/-21.6% to +/-23.5%, respectively. The results are discussed in relation to the potential application of the methods.

Promoting microbiology education through the iGEM synthetic biology competition.

PubMed

Kelwick, Richard; Bowater, Laura; Yeoman, Kay H; Bowater, Richard P

2015-08-01

Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research. Synthetic biology projects have developed into wide-ranging training and educational experiences through iGEM, the International Genetically Engineered Machines competition. Elements of the competition are judged against specific criteria and teams can win medals and prizes across several categories. Collaboration is an important element of iGEM, and all DNA constructs synthesized by iGEM teams are made available to all researchers through the Registry for Standard Biological Parts. An overview of microbiological developments in the iGEM competition is provided. This review is targeted at educators that focus on microbiology and synthetic biology, but will also be of value to undergraduate and postgraduate students with an interest in this exciting subject area. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Addressing the key communication barriers between microbiology laboratories and clinical units: a qualitative study

PubMed Central

Skodvin, Brita; Aase, Karina; Brekken, Anita Løvås; Charani, Esmita; Lindemann, Paul Christoffer; Smith, Ingrid

2017-01-01

Abstract Background Many countries are on the brink of establishing antibiotic stewardship programmes in hospitals nationwide. In a previous study we found that communication between microbiology laboratories and clinical units is a barrier to implementing efficient antibiotic stewardship programmes in Norway. We have now addressed the key communication barriers between microbiology laboratories and clinical units from a laboratory point of view. Methods Qualitative semi-structured interviews were conducted with 18 employees (managers, doctors and technicians) from six diverse Norwegian microbiological laboratories, representing all four regional health authorities. Interviews were recorded and transcribed verbatim. Thematic analysis was applied, identifying emergent themes, subthemes and corresponding descriptions. Results The main barrier to communication is disruption involving specimen logistics, information on request forms, verbal reporting of test results and information transfer between poorly integrated IT systems. Furthermore, communication is challenged by lack of insight into each other’s area of expertise and limited provision of laboratory services, leading to prolonged turnaround time, limited advisory services and restricted opening hours. Conclusions Communication between microbiology laboratories and clinical units can be improved by a review of testing processes, educational programmes to increase insights into the other’s area of expertise, an evaluation of work tasks and expansion of rapid and point-of-care test services. Antibiotic stewardship programmes may serve as a valuable framework to establish these measures. PMID:28633405

Evaluation of Pharmacist Impact on Culture Review Process for Patients Discharged From the Emergency Department.

PubMed

Santiago, Ruben D; Bazan, Jose A; Brown, Nicole V; Adkins, Eric J; Shirk, Mary Beth

2016-10-01

Background: Accurate and timely review of microbiological test results is a core component of antimicrobial stewardship. There is documented success of these programs in the inpatient setting; however, emergency department (ED) patients are typically not included in these initiatives. Objectives: To assess the impact of an emergency medicine pharmacist (EMP)-facilitated review process of positive microbiological test results from patients discharged from the ED as measured by time to positive result review and number of indicated interventions completed. Methods: This was a retrospective study that compared EMP-facilitated to ED charge nurse (CN)-facilitated physician review of randomly selected positive microbiological test results. Groups were compared concurrently within the time frame of July 1, 2012 through December 31, 2012. Results: One hundred seventy-eight positive microbiological test results were included (EMP, n = 91; CN, n = 87). The median (IQR) time to initial review was 3 (1.0-6.3) hours for the EMP and 2 (0.3-5.5) hours for the CN group ( p = .35). Four percent (1/25) of indicated interventions were not completed in the EMP group versus 47% (14/30) in the CN group ( p = .0004). Conclusion: An EMP was significantly less likely to miss an intervention when indicated with no difference in time to review of positive microbiological results. These findings support the role of the EMP in antimicrobial stewardship in the ED.

Sodium Chloride Does Not Ensure Microbiological Safety of Foods: Cases and Solutions.

PubMed

Kim, Nam Hee; Cho, Tae Jin; Rhee, Min Suk

2017-01-01

Addition of salt or salt-containing water to food is one of the oldest and most effective preservation methods in history; indeed, salt-cured foods are generally recognized as microbiologically safe due to their high salinity. However, a number of microbiological risks remain. The microbiological hazards and risks associated with salt-cured foods must be addressed more in-depth as they are likely to be underestimated by previous studies. This review examined a number of scientific reports and articles about the microbiological safety of salt-cured foods, which included salted, brined, pickled, and/or marinated vegetables, meat, and seafood. The following subjects are covered in order: (1) clinical cases and outbreaks attributed to salt-cured foods; (2) the prevalence of foodborne pathogens in such foods; (3) the molecular, physiological, and virulent responses of the pathogens to the presence of NaCl in both laboratory media and food matrices; (4) the survival and fate of microorganisms in salt-cured foods (in the presence/absence of additional processes); and (5) the interaction between NaCl and other stressors in food processes (e.g., acidification, antimicrobials, drying, and heating). The review provides a comprehensive overview of potentially hazardous pathogens associated with salt-cured foods and suggests further research into effective intervention techniques that will reduce their levels in the food chain. Copyright © 2017 Elsevier Inc. All rights reserved.

Accurate Detection of Methicillin-Resistant Staphylococcus aureus in Mixtures by Use of Single-Bacterium Duplex Droplet Digital PCR.

PubMed

Luo, Jun; Li, Junhua; Yang, Hang; Yu, Junping; Wei, Hongping

2017-10-01

Accurate and rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is needed to screen MRSA carriers and improve treatment. The current widely used duplex PCR methods are not able to differentiate MRSA from coexisting methicillin-susceptible S. aureus (MSSA) or other methicillin-resistant staphylococci. In this study, we aimed to develop a direct method for accurate and rapid detection of MRSA in clinical samples from open environments, such as nasal swabs. The new molecular assay is based on detecting the cooccurrence of nuc and mecA markers in a single bacterial cell by utilizing droplet digital PCR (ddPCR) with the chimeric lysin ClyH for cell lysis. The method consists of (i) dispersion of an intact single bacterium into nanoliter droplets, (ii) temperature-controlled release of genomic DNA (gDNA) by ClyH at 37°C, and (iii) amplification and detection of the markers ( nuc and mecA ) using standard TaqMan chemistries with ddPCR. Results were analyzed based on MRSA index ratios used for indicating the presence of the duplex-positive markers in droplets. The method was able to achieve an absolute limit of detection (LOD) of 2,900 CFU/ml for MRSA in nasal swabs spiked with excess amounts of Escherichia coli , MSSA, and other mecA -positive bacteria within 4 h. Initial testing of 104 nasal swabs showed that the method had 100% agreement with the standard culture method, while the normal duplex qPCR method had only about 87.5% agreement. The single-bacterium duplex ddPCR assay is rapid and powerful for more accurate detection of MRSA directly from clinical specimens. Copyright © 2017 American Society for Microbiology.

EVALUATION AND IMPORTANCE OF SELECTED MICROBIOLOGICAL METHODS IN THE DIAGNOSIS OF HUMAN BRUCELLOSIS

PubMed Central

Šiširak, Maida; Hukić, Mirsada

2009-01-01

Brucellosis is an important public health problem in Bosnia and Herzegovina. The diagnosis of bru-cellosis in the country without any experiences with this kind of infection may be very difficult. The aim of this study was to evaluate diagnostic methods: Rose Bengal test, blood cultures and ELISA IgM and IgG in the patients with brucellosis. The study included 91 brucellosis patients in the period 2004 to 2007. All the patients were treated at the Clinic for Infectious Diseases, University of Sarajevo Clinics Centre. Blood cultures were positive in 28/91 (30, 8%) patients. This method often needs a long period of incubation and specimens need to be obtained early. These limitations make serology the most useful tool for the laboratory diagnosis of Brucella infection. Rose Bengal is a rapid plate agglutination test, very sensitive irrespective of the stage of the disease. In our study, Rose Bengal test was positive in all patients 91/91 (100, 0%). Brucella IgM antibodies with ELISA were positive in 59/91 (64, 8%). Brucella IgG antibodies with ELISA were positive in 51/91 (56%). In order to determine the diagnostic value of the different tests, we compared the sensitivity among test-methods: Rose Bengal test-100.0%, blood culture-30.8%, ELISA IgM-64.8% and ELISA IgG-56.1%. Sensitivity of test methods was different in the different stages of illness. It is necessary to use combination of different tests such are blood culture, Rose Bengal test and ELISA in order to ensure the diagnosis. Rose Bengal test is excellent for the screening. Blood culture is a method of choice for the diagnosis acute infection. ELISA is a very good method for the diagnostic chronic disease and relapse. PMID:19754473

ANALYTICAL METHOD READINESS FOR THE CONTAMINANT CANDIDATE LIST

EPA Science Inventory

The Contaminant Candidate List (CCL), which was promulgated in March 1998, includes 50 chemical and 10 microbiological contaminants/contaminant groups. At the time of promulgation, analytical methods were available for 6 inorganic and 28 organic contaminants. Since then, 4 anal...

Textbook of respiratory medicine

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

Murray, J.F.; Nadel, J.

1987-01-01

This book presents a clinical reference of respiratory medicine. It also details basic science aspects of pulmonary physiology and describes recently developed, sophisticated diagnostic tools and therapeutic methods. It also covers anatomy, physiology, pharmacology, and pathology; microbiologic, radiologic, nuclear medicine, and biopsy methods for diagnosis.

MOLECULAR DIVERSITY OF DRINKING WATER MICROBIAL COMMUNITIES: A PHYLOGENETIC APPROACH

EPA Science Inventory

Culture-based methods are traditionally used to determine microbiological quality of drinking water even though these methods are highly selective and tend to underestimate the densities and diversity bacterial populations inhabiting distribution systems. In order to better under...

Evaluation of membrane filter field monitors for microbiological air sampling

NASA Technical Reports Server (NTRS)

Fields, N. D.; Oxborrow, G. S.; Puleo, J. R.; Herring, C. M.

1974-01-01

Due to area constraints encountered in assembly and testing areas of spacecraft, the membrane filter field monitor (MF) and the National Aeronautics and Space Administration-accepted Reyniers slit air sampler were compared for recovery of airborne microbial contamination. The intramural air in a microbiological laboratory area and a clean room environment used for the assembly and testing of the Apollo spacecraft was studied. A significantly higher number of microorganisms was recovered by the Reyniers sampler. A high degree of consistency between the two sampling methods was shown by a regression analysis, with a correlation coefficient of 0.93. The MF samplers detected 79% of the concentration measured by the Reyniers slit samplers. The types of microorganisms identified from both sampling methods were similar.

Emerging applications of fluorescence spectroscopy in medical microbiology field.

PubMed

Shahzad, Aamir; Köhler, Gottfried; Knapp, Martin; Gaubitzer, Erwin; Puchinger, Martin; Edetsberger, Michael

2009-11-26

There are many diagnostic techniques and methods available for diagnosis of medically important microorganisms like bacteria, viruses, fungi and parasites. But, almost all these techniques and methods have some limitations or inconvenience. Most of these techniques are laborious, time consuming and with chances of false positive or false negative results. It warrants the need of a diagnostic technique which can overcome these limitations and problems. At present, there is emerging trend to use Fluorescence spectroscopy as a diagnostic as well as research tool in many fields of medical sciences. Here, we will critically discuss research studies which propose that Fluorescence spectroscopy may be an excellent diagnostic as well as excellent research tool in medical microbiology field with high sensitivity and specificity.

Application of MALDI-TOF mass spectrometry in clinical diagnostic microbiology.

PubMed

De Carolis, Elena; Vella, Antonietta; Vaccaro, Luisa; Torelli, Riccardo; Spanu, Teresa; Fiori, Barbara; Posteraro, Brunella; Sanguinetti, Maurizio

2014-09-12

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful technique for identification of microorganisms, changing the workflow of well-established laboratories so that its impact on microbiological diagnostics has been unparalleled. In comparison with conventional identification methods that rely on biochemical tests and require long incubation procedures, MALDI-TOF MS has the advantage of identifying bacteria and fungi directly from colonies grown on culture plates in a few minutes and with simple procedures. Numerous studies on different systems available demonstrate the reliability and accuracy of the method, and new frontiers have been explored besides microbial species level identification, such as direct identification of pathogens from positive blood cultures, subtyping, and drug susceptibility detection.

Laboratory Diagnosis of Parasites from the Gastrointestinal Tract.

PubMed

Garcia, Lynne S; Arrowood, Michael; Kokoskin, Evelyne; Paltridge, Graeme P; Pillai, Dylan R; Procop, Gary W; Ryan, Norbert; Shimizu, Robyn Y; Visvesvara, Govinda

2018-01-01

This Practical Guidance for Clinical Microbiology document on the laboratory diagnosis of parasites from the gastrointestinal tract provides practical information for the recovery and identification of relevant human parasites. The document is based on a comprehensive literature review and expert consensus on relevant diagnostic methods. However, it does not include didactic information on human parasite life cycles, organism morphology, clinical disease, pathogenesis, treatment, or epidemiology and prevention. As greater emphasis is placed on neglected tropical diseases, it becomes highly probable that patients with gastrointestinal parasitic infections will become more widely recognized in areas where parasites are endemic and not endemic. Generally, these methods are nonautomated and require extensive bench experience for accurate performance and interpretation. Copyright © 2017 American Society for Microbiology.

HIV association with conventional STDS (sexual transmitted diseases) in Lagos State, Nigeria.

PubMed

Otuonye, N M; Olukoya, D K; Odunukwe, N N; Idigbe, E O; Udeaja, M N; Bamidele, M; Onyewuchie, J I; Oparaugu, C T; Ayelari, O S; Oyekunle, B

2002-01-01

The study examined a possible association between HIV infection and conventional sexually transmitted diseases (STDS) in a population of 700 patients seen in some hospitals and clinics in Lagos State between November 1997 and December 1999. The patients were drawn mainly from LUTH and Jolad hospitals in Lagos State. In these hospitals, patients who presented with symptoms of STDS were screened clinically and microbiologically for agents of STDS and HIV antibodies. Screening was carried out using conventional methods. A total of 150 (21.5%) were found positive for various STDS while 550 (78.5%) were negative Also, 109 (15.8%) were sero-positive for HIV while 591 (84.4%) were sero-negative. The frequency of STDS diagnosed were, Treponema pallidum, 38(25.3%), Neisseria gonorrhoea 3(2.0%), Chlamydia trachomatis 26(17.3), Hepatitis B virus 60(40.0%) Staphylococcus aureaus, 20 (13.3%) and Candida albicans 3(2.0%). Data showed that Syphillis was the most prevalent STDS diagnosed while Calbicans and N. gonorrhoea are the least. Amongst the 150 (21.5%) patients positive with STDS, 82(54.65%) were found to be positive for HIV antibodies. The remaining 68(45.3%) patients were negative for HIV. The difference in sero-prevalence on the true group of patients rates was significant. The higher rate in the STDS patients strongly suggest some association between HIV infections andSTDS amongst the patients studied p = 0.05. It was also recorded that HIV-1 infection is four times more prevalent than HIV-2 in these patients.

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes.

PubMed

Azevedo, Analice C; Bento, Cláudia B P; Ruiz, Jeronimo C; Queiroz, Marisa V; Mantovani, Hilário C

2015-10-01

Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Careers in Microbiology...Horizons Unlimited

ERIC Educational Resources Information Center

Goldschmidt Millicent C.; Whitt, Dixie

1978-01-01

A broad range of present microbiological work is discussed in order to indicate the many possible careers now open in microbiology. Some areas are immunology, environmental microbiology, agricultural, industrial, and food microbiology, and space microbiology. An employment outlook is also given. (MDR)

Role of re-screening of cervical smears in internal quality control.

PubMed Central

Baker, A; Melcher, D; Smith, R

1995-01-01

AIMS--To investigate the use of rapid re-screening as a quality control method for previously screened cervical slides; to compare this method with 10% random re-screening and clinically indicated double screening. METHODS--Between June 1990 and December 1994, 117,890 negative smears were subjected to rapid re-screening. RESULTS--This study shows that rapid re-screening detects far greater numbers of false negative cases when compared with both 10% random re-screening and clinically indicated double screening, with no additional demand on human resources. The technique also identifies variation in the performance of screening personnel as an additional benefit. CONCLUSION--Rapid re-screening is an effective method of quality control. Although less sensitive, rapid re-screening should replace 10% random re-screening and selected re-screening as greater numbers of false negative results are detected while consuming less resources. PMID:8543619

Advances Afoot in Microbiology.

PubMed

Patel, Robin; Karon, Brad S

2017-07-01

In 2016, the American Academy of Microbiology convened a colloquium to examine point-of-care (POC) microbiology testing and to evaluate its effects on clinical microbiology. Colloquium participants included representatives from clinical microbiology laboratories, industry, and the government, who together made recommendations regarding the implementation, oversight, and evaluation of POC microbiology testing. The colloquium report is timely and well written (V. Dolen et al., Changing Diagnostic Paradigms for Microbiology , 2017, https://www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology?utm_source=Commentary&utm_medium=referral&utm_campaign=diagnostics). Emerging POC microbiology tests, especially nucleic acid amplification tests, have the potential to advance medical care. Copyright © 2017 American Society for Microbiology.

Current status of matrix-assisted laser desorption ionisation-time of flight mass spectrometry in the clinical microbiology laboratory.

PubMed

Kok, Jen; Chen, Sharon C A; Dwyer, Dominic E; Iredell, Jonathan R

2013-01-01

The integration of matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) into many clinical microbiology laboratories has revolutionised routine pathogen identification. MALDI-TOF MS complements and has good potential to replace existing phenotypic identification methods. Results are available in a more clinically relevant timeframe, particularly in bacteraemic septic shock. Novel applications include strain typing and the detection of antimicrobial resistance, but these are not widely used. This review discusses the technical aspects, current applications, and limitations of MALDI-TOF MS.

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Use with Positive Blood Cultures: Methodology, Performance, and Optimization.

PubMed

Faron, Matthew L; Buchan, Blake W; Ledeboer, Nathan A

2017-12-01

Early initiation of effective antibiotics for septic patients is essential for patient survival. Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized clinical microbiology for isolate identification and has the possibility to impact how blood culture testing is performed. This review discusses the various uses of MALDI-TOF MS for the identification and susceptibility testing of positive blood cultures, the performance of these methods, and the outcomes involved with its implementation. Copyright © 2017 American Society for Microbiology.

[Development of molecular detection of food-borne pathogenic bacteria using miniaturized microfluidic devices].

PubMed

Iván, Kristóf; Maráz, Anna

2015-12-20

Detection and identification of food-borne pathogenic bacteria are key points for the assurance of microbiological food safety. Traditional culture-based methods are more and more replaced by or supplemented with nucleic acid based molecular techniques, targeting specific (preferably virulence) genes in the genomes. Internationally validated DNA amplification - most frequently real-time polymerase chain reaction - methods are applied by the food microbiological testing laboratories for routine analysis, which will result not only in shortening the time for results but they also improve the performance characteristics (e.g. sensitivity, specificity) of the methods. Beside numerous advantages of the polymerase chain reaction based techniques for routine microbiological analysis certain drawbacks have to be mentioned, such as the high cost of the equipment and reagents, as well as the risk of contamination of the laboratory environment by the polymerase chain reaction amplicons, which require construction of an isolated laboratory system. Lab-on-a-chip systems can integrate most of these laboratory processes within a miniaturized device that delivers the same specificity and reliability as the standard protocols. The benefits of miniaturized devices are: simple - often automated - use, small overall size, portability, sterility due to single use possibility. These miniaturized rapid diagnostic tests are being researched and developed at the best research centers around the globe implementing various sample preparation and molecular DNA amplification methods on-chip. In parallel, the aim of the authors' research is to develop microfluidic Lab-on-a-chip devices for the detection and identification of food-borne pathogenic bacteria.

Bacterial safety of cell-based therapeutic preparations, focusing on haematopoietic progenitor cells.

PubMed

Störmer, M; Wood, E M; Schurig, U; Karo, O; Spreitzer, I; McDonald, C P; Montag, T

2014-05-01

Bacterial safety of cellular preparations, especially haematopoietic progenitor cells (HPCs), as well as advanced therapy medicinal products (ATMPs) derived from stem cells of various origins, present a challenge for physicians, manufacturers and regulators. The article describes the background and practical issues in this area and illustrates why sterility of these products cannot currently be guaranteed. Advantages and limitations of approaches both for classical sterility testing and for microbiological control using automated culture systems are discussed. The review considers novel approaches for growth-based rapid microbiological control with high sensitivity and faster availability of results, as well as new methods for rapid bacterial detection in cellular preparations enabling meaningful information about product contamination within one to two hours. Generally, however, these direct rapid methods are less sensitive and have greater sampling error compared with the growth-based methods. Opportunities for pyrogen testing of cell therapeutics are also discussed. There is an urgent need for development of novel principles and methods applicable to bacterial safety of cellular therapeutics. We also need a major shift in approach from the traditional view of sterility evaluation (identify anything and everything) to a new thinking about how to find what is clinically relevant within the time frame available for the special clinical circumstances in which these products are used. The review concludes with recommendations for optimization of microbiological control of cellular preparations, focusing on HPCs. © 2013 International Society of Blood Transfusion.

validated microbiological and HPLC methods for the determination of moxifloxacin in pharmaceutical preparations and human plasma.

PubMed

Abdelaziz, Ahmed A; Elbanna, Tarek E; Gamaleldeen, Noha M

2012-10-01

The article presents a comparison between microbiological and high performance liquid chromatographic (HPLC) assays for quantification of moxifloxacin in tablets, ophthalmic solutions and human plasma. The microbiological method employed a cylinder-plate agar diffusion assay using a strain of Esherichia coli ATCC 25922 as the test organism and phosphate buffer (pH8) as the diluent. The calibration curves were linear (R(2) > 0.98) over a concentration range of 0.125 to 16 µgml(-1). The within day and between days precisions were ≤ 4.47% and ≤ 6.39% respectively. Recovery values were between 89.4 and 110.2%. The HPLC assay used Hypersil(®) BDS C18 reversed phase column (250×4.6 mm, 5µm) with a mobile phase comprising 20 mM ammonium dihydrogen orthophosphate (pH3) and acetonitrile (75:25) and flowing at 1.5 ml/min. The detection was at 295nm. The calibration curves were linear (R(2) > 0.999) over the range of 0.125 to 16 µg ml(-1). The within day and between days precisions were ≤ 4.07% and ≤ 5.09% respectively. Recovery values were between 97.7 and 107.6%. Similar potencies were obtained after the analysis of moxifloxacin tablets and ophthalmic solutions by both methods. Also pharmacokinetic parameters were calculated after the analysis of plasma samples of six male healthhy volunteers by both validated methods.

A Streptococcus uberis transposon mutant screen reveals a negative role for LiaR homologue in biofilm formation.

PubMed

Salomäki, T; Karonen, T; Siljamäki, P; Savijoki, K; Nyman, T A; Varmanen, P; Iivanainen, A

2015-01-01

The environmental pathogen Streptococcus uberis causes intramammary infections in dairy cows. Because biofilm growth might contribute to Strep. uberis mastitis, we conducted a biological screen to identify genes potentially involved in the regulation of biofilm growth. By screening a transposon mutant library of Strep. uberis, we determined that the disruption of 13 genes (including hasA, coaC, clpP, miaA, nox and uidA) led to increased biofilm formation. One of the genes (SUB1382) encoded a homologue of the LiaR response regulator (RR) of the Bacillus subtilis two-component signalling system (TCS). Electrophoretic mobility shift assays revealed that DNA binding by LiaR was greatly enhanced by phosphorylation. Two-dimensional differential in-gel electrophoresis analyses of the liaR mutant and the parental Strep. uberis strain revealed five differentially produced proteins with at least a 1·5-fold change in relative abundance (P < 0·05). The DNA-binding protein LiaR is a potential regulator of biofilm formation by Strep. uberis. Several molecular primary and downstream targets involved in biofilm formation by Strep. uberis were identified. This provides a solid foundation for further studies on the regulation of biofilm formation in this important pathogen. © 2014 The Society for Applied Microbiology.

Nosocomial outbreak of staphyloccocal scalded skin syndrome in neonates in England, December 2012 to March 2013.

PubMed

Paranthaman, K; Bentley, A; Milne, L M; Kearns, A; Loader, S; Thomas, A; Thompson, F; Logan, M; Newitt, S; Puleston, R

2014-08-21

Staphylococcal scalded skin syndrome (SSSS) is a blistering skin condition caused by exfoliative toxin-producing strains of Staphylococcus aureus. Outbreaks of SSSS in maternity settings are rarely reported. We describe an outbreak of SSSS that occurred among neonates born at a maternity unit in England during December 2012 to March 2013. Detailed epidemiological and microbiological investigations were undertaken. Eight neonates were found to be infected with the outbreak strain of S. aureus, of spa type t346, representing a single pulsotype. All eight isolates contained genes encoding exfoliative toxin A (eta) and six of them contained genes encoding toxin B (etb). Nasal swabs taken during targeted staff screening yielded a staphylococcal carriage rate of 21% (17/80), but none contained the outbreak strain. Mass screening involving multi-site swabbing and pooled, enrichment culture identified a healthcare worker (HCW) with the outbreak strain. This HCW was known to have a chronic skin condition and their initial nasal screen was negative. The outbreak ended when they were excluded from work. This outbreak highlights the need for implementing robust swabbing and culture methodswhen conventional techniques are unsuccessful in identifying staff carrier(s). This study adds to the growing body of evidence on the role of HCWs in nosocomial transmission of S. aureus.

Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments.

PubMed

Jaeger, Philipp A; McElfresh, Cameron; Wong, Lily R; Ideker, Trey

2015-08-15

Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Screening, identification and characterization of bacteriocins produced by wine-isolated LAB strains.

PubMed

Ndlovu, B; Schoeman, H; Franz, C M A P; du Toit, M

2015-04-01

To screen and identify wine-isolated LAB strains for bacteriocin production, and to identify and characterize bacteriocins. One hundred and fifty-five LAB strains isolated from South African red wines undergoing spontaneous malolactic fermentation were screened for bacteriocin production. Eight isolates were identified to be bacteriocin producers and were identified as Enterococcus faecium. All eight isolates had the same phenotypic and genotypic profiles. The peptides were preliminarily identified as enterocin P using mass spectrometry and further confirmed by PCR-amplifying enterocin P gene. The enterocin activity was inhibited by α-Chymotrypsin, papain and proteinase K treatments. It was heat stable at 37, 60, 80 and 100°C and showed activity over a broad pH range of 2-10. The production of the enterocin followed that of primary metabolite kinetics and, it showed bactericidal effect to some wine spoilage LAB strains. Our study identified the presence of the enterocin-producing Enterococcus in wine. The enterocin was heat stable; with broad pH range and bactericidal effects to sensitive strains. This is one of very few studies that isolated Enterococcus species from wine. It is, however, the first to report presence of bacteriocin-producing Enterococcus in wine fermentation. © 2015 The Society for Applied Microbiology.

Accelerating early anti-tuberculosis drug discovery by creating mycobacterial indicator strains that predict mode of action.

PubMed

Boot, Maikel; Commandeur, Susanna; Subudhi, Amit K; Bahira, Meriem; Smith, Trever C; Abdallah, Abdallah M; van Gemert, Mae; Lelièvre, Joël; Ballell, Lluís; Aldridge, Bree B; Pain, Arnab; Speer, Alexander; Bitter, Wilbert

2018-04-16

Due to the rise of drug resistant forms of tuberculosis there is an urgent need for novel antibiotics to effectively combat these cases and shorten treatment regimens. Recently, drug screens using whole cell analyses have been shown to be successful. However, current high-throughput screens focus mostly on stricto sensu life-death screening that give little qualitative information. In doing so, promising compound scaffolds or non-optimized compounds that fail to reach inhibitory concentrations are missed. To accelerate early TB drug discovery, we performed RNA sequencing on Mycobacterium tuberculosis and Mycobacterium marinum to map the stress responses that follow upon exposure to sub-inhibitory concentrations of antibiotics with known targets: ciprofloxacin, ethambutol, isoniazid, streptomycin and rifampicin. The resulting dataset comprises the first overview of transcriptional stress responses of mycobacteria to different antibiotics. We show that antibiotics can be distinguished based on their specific transcriptional stress fingerprint. Notably, this fingerprint was more distinctive in M. marinum. We decided to use this to our advantage and continue with this model organism. A selection of diverse antibiotic stress genes was used to construct stress reporters. In total, three functional reporters were constructed to respond to DNA damage, cell wall damage and ribosomal inhibition. Subsequently, these reporter strains were used to screen a small anti-TB compound library to predict the mode of action. In doing so, we could identify the putative mode of action for three novel compounds, which confirms our approach. Copyright © 2018 American Society for Microbiology.

40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...

40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...

Human pathogens in marine mammal meat – a northern perspective.

PubMed

Tryland, M; Nesbakken, T; Robertson, L; Grahek-Ogden, D; Lunestad, B T

2014-09-01

Only a few countries worldwide hunt seals and whales commercially. In Norway, hooded and harp seals and minke whales are commercially harvested, and coastal seals (harbour and grey seals) are hunted as game. Marine mammal meat is sold to the public and thus included in general microbiological meat control regulations. Slaughtering and dressing of marine mammals are performed in the open air on deck, and many factors on board sealing or whaling vessels may affect meat quality, such as the ice used for cooling whale meat and the seawater used for cleaning, storage of whale meat in the open air until ambient temperature is reached, and the hygienic conditions of equipment, decks, and other surfaces. Based on existing reports, it appears that meat of seal and whale does not usually represent a microbiological hazard to consumers in Norway, because human disease has not been associated with consumption of such foods. However, as hygienic control on marine mammal meat is ad hoc, mainly based on spot-testing, and addresses very few human pathogens, this conclusion may be premature. Additionally, few data from surveys or systematic quality control screenings have been published. This review examines the occurrence of potential human pathogens in marine mammals, as well as critical points for contamination of meat during the slaughter, dressing, cooling, storage and processing of meat. Some zoonotic agents are of particular relevance as foodborne pathogens, such as Trichinella spp., Toxoplasma gondii, Salmonella and Leptospira spp. In addition, Mycoplasma spp. parapoxvirus and Mycobacterium spp. constitute occupational risks during handling of marine mammals and marine mammal products. Adequate training in hygienic procedures is necessary to minimize the risk of contamination on board, and acquiring further data is essential for obtaining a realistic assessment of the microbiological risk to humans from consuming marine mammal meat.

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

PubMed Central

Bull, Alan T.; Ward, Alan C.; Goodfellow, Michael

2000-01-01

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology. PMID:10974127

NERL MICROBIAL PROGRAM WITH EMPHASIS ON PROTOZOAN METHODS

EPA Science Inventory

The National Exposure Research Laboratory's facility in Cincinnati is engated in a variety of microbiological research projects that include studies on bacteria, viruses, fungi and protozoa. One of these was a protzoology project to determine the best way to evaluate methods rep...

A literature review and update on the incidence and microbiology spectrum of postcataract surgery endophthalmitis over past two decades in India

PubMed Central

Lalitha, Prajna; Sengupta, Sabyasachi; Ravindran, Ravilla D; Sharma, Savitri; Joseph, Joveeta; Ambiya, Vikas; Das, Taraprasad

2017-01-01

Purpose: The purpose of this study was to review the incidence and microbiology of acute postcataract surgery endophthalmitis in India. Methods: Systematic review of English-language PubMed referenced articles on endophthalmitis in India published in the past 21 years (January 1992–December 2012), and retrospective chart review of 2 major eye care facilities in India in the past 5 years (January 2010–December 2014) were done. The incidence data were collected from articles that described “in-house” endophthalmitis and the microbiology data were collected from all articles. Both incidence and microbiological data of endophthalmitis were collected from two large eye care facilities. Case reports were excluded, except for the articles on cluster infection. Results: Six of 99 published articles reported the incidence of “in-house” acute postcataract surgery endophthalmitis, 8 articles reported the microbiology spectrum, and 11 articles described cluster infection. The clinical endophthalmitis incidence was between 0.04% and 0.15%. In two large eye care facilities, the clinical endophthalmitis incidence was 0.08% and 0.16%; the culture proven endophthalmitis was 0.02% and 0.08%. Gram-positive cocci (44%-64.8%; commonly, Staphylococcus species), and Gram-negative bacilli (26.2%–43%; commonly Pseudomonas species) were common bacteria in south India. Fungi (16.7%-70%; commonly Aspergillus flavus) were the common organisms in north India. Pseudomonas aeruginosa (73.3%) was the major organism in cluster infections. Conclusions: The incidence of postcataract surgery clinical endophthalmitis in India is nearly similar to the world literature. There is a regional difference in microbiological spectrum. A registry with regular and uniform national reporting will help formulate region specific management guidelines. PMID:28820151

Utilization of a clinical microbiology service at a Cambodian paediatric hospital and its impact on appropriate antimicrobial prescribing.

PubMed

Fox-Lewis, Shivani; Pol, Sreymom; Miliya, Thyl; Day, Nicholas P J; Turner, Paul; Turner, Claudia

2018-02-01

Antimicrobial resistance threatens human health worldwide. Antimicrobial misuse is a major driver of resistance. Promoting appropriate antimicrobial use requires an understanding of how clinical microbiology services are utilized, particularly in resource-limited settings. To assess the appropriateness of antimicrobial prescribing and the factors affecting utilization of the established clinical microbiology service (CMS). The CMS comprises the microbiology laboratory, clinical microbiologists (infection doctors) and antimicrobial treatment guidelines. This mixed-methods study was conducted at a non-governmental Cambodian paediatric hospital. Empirical and post-culture antimicrobial prescriptions were reviewed from medical records. The random sample included 10 outpatients per week in 2016 (retrospective) and 20 inpatients per week for 4 weeks in the medical, neonatal and intensive care wards (prospective). Post-culture prescriptions were assessed in patients with positive blood and cerebrospinal fluid cultures from 1 January 2014 to 31 December 2016. Focus group discussions and semi-structured interviews with clinicians explored barriers and facilitators to use of the CMS. Only 31% of outpatients were prescribed empirical antimicrobials. Post-culture prescriptions (394/443, 89%) were more likely to be appropriate than empirical prescriptions (447/535, 84%), based on treatment guidelines, microbiology advice and antimicrobial susceptibility test results (P = 0.015). Being comprehensive, accessible and trusted enabled CMS utilization. Clinical microbiologists provided a crucial human interface between the CMS and physicians. The main barriers were a strong clinical hierarchy and occasional communication difficulties. Antimicrobial prescribing in this hospital was largely appropriate. A culturally appropriate human interface linking the laboratory and physicians is essential in providing effective microbiology services and ensuring appropriate antimicrobial prescribing in resource-limited settings. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

Effectiveness of WHO's pragmatic screening algorithm for child contacts of tuberculosis cases in resource-constrained settings: a prospective cohort study in Uganda.

PubMed

Martinez, Leonardo; Shen, Ye; Handel, Andreas; Chakraburty, Srijita; Stein, Catherine M; Malone, LaShaunda L; Boom, W Henry; Quinn, Frederick D; Joloba, Moses L; Whalen, Christopher C; Zalwango, Sarah

2018-04-01

Tuberculosis is a leading cause of global childhood mortality; however, interventions to detect undiagnosed tuberculosis in children are underused. Child contact tracing has been widely recommended but poorly implemented in resource-constrained settings. WHO has proposed a pragmatic screening approach for managing child contacts. We assessed the effectiveness of this screening approach and alternative symptom-based algorithms in identifying secondary tuberculosis in a prospectively followed cohort of Ugandan child contacts. We identified index patients aged at least 18 years with microbiologically confirmed pulmonary tuberculosis at Old Mulago Hospital (Kampala, Uganda) between Oct 1, 1995, and Dec 31, 2008. Households of index patients were visited by fieldworkers within 2 weeks of diagnosis. Coprevalent and incident tuberculosis were assessed in household contacts through clinical, radiographical, and microbiological examinations for 2 years. Disease rates were compared among children younger than 16 years with and without symptoms included in the WHO pragmatic guideline (presence of haemoptysis, fever, chronic cough, weight loss, night sweats, and poor appetite). Symptoms could be of any duration, except cough (>21 days) and fever (>14 days). A modified WHO decision-tree designed to detect high-risk asymptomatic child contacts was also assessed, in which all asymptomatic contacts were classified as high risk (children younger than 3 years or immunocompromised [HIV-infected]) or low risk (aged 3 years or older and immunocompetent [HIV-negative]). We also assessed a more restrictive algorithm (ie, assessing only children with presence of chronic cough and one other tuberculosis-related symptom). Of 1718 household child contacts, 126 (7%) had coprevalent tuberculosis and 24 (1%) developed incident tuberculosis, diagnosed over the 2-year study period. Of these 150 cases of tuberculosis, 95 (63%) were microbiologically confirmed with a positive sputum culture. Using the WHO approach, 364 (21%) of 1718 child contacts had at least one tuberculosis-related symptom and 85 (23%) were identified as having coprevalent tuberculosis, 67% of all coprevalent cases detected (diagnostic odds ratio 9·8, 95% CI 6·8-14·5; p<0·0001). 1354 (79%) of 1718 child contacts had no symptoms, of whom 41 (3%) had coprevalent tuberculosis. The WHO approach was effective in contacts younger than 5 years: 70 (33%) of 211 symptomatic contacts had coprevalent disease compared with 23 (6%) of 367 asymptomatic contacts (p<0·0001). This approach was also effective in contacts aged 5 years and older: 15 (10%) of 153 symptomatic contacts had coprevalent disease compared with 18 (2%) of 987 asymptomatic contacts (p<0·0001). More coprevalent disease was detected in child contacts recommended for screening when the study population was restricted by HIV-serostatus (11 [48%] of 23 symptomatic HIV-seropositive child contacts vs two [7%] of 31 asymptomatic HIV-seropositive child contacts) or to only culture-confirmed cases (47 [13%] culture confirmed cases of 364 symptomatic child contacts vs 29 [2%] culture confirmed cases of 1354 asymptomatic child contacts). In the modified algorithm, high-risk asymptomatic child contacts were at increased risk for coprevalent disease versus low-risk asymptomatic contacts (14 [6%] of 224 vs 27 [2%] of 1130; p=0·0021). The presence of tuberculosis infection did not predict incident disease in either symptomatic or asymptomatic child contacts: in symptomatic contacts, eight (5%) of 169 infected contacts and six (5%) of 111 uninfected contacts developed incident tuberculosis (p=0·80). Among asymptomatic contacts, incident tuberculosis occurred in six (<1%) of 795 contacts infected at baseline versus four (<1%) of 518 contacts uninfected at baseline, respectively (p=1·00). WHO's pragmatic, symptom-based algorithm was an effective case-finding tool, especially in children younger than 5 years. A modified decision-tree identified 6% of asymptomatic child contacts at high risk for subclinical disease. Increasing the feasibility of child-contact tracing using these approaches should be encouraged to decrease tuberculosis-related paediatric mortality in high-burden settings, but this should be partnered with increasing access to microbiological point-of-care testing. National Institutes of Health, Tuberculosis Research Unit, AIDS International Training and Research Program of the Fogarty International Center, and the Center for AIDS Research. Copyright © 2018 Elsevier Ltd. All rights reserved.

Advances Afoot in Microbiology

PubMed Central

Karon, Brad S.

2017-01-01

ABSTRACT In 2016, the American Academy of Microbiology convened a colloquium to examine point-of-care (POC) microbiology testing and to evaluate its effects on clinical microbiology. Colloquium participants included representatives from clinical microbiology laboratories, industry, and the government, who together made recommendations regarding the implementation, oversight, and evaluation of POC microbiology testing. The colloquium report is timely and well written (V. Dolen et al., Changing Diagnostic Paradigms for Microbiology, 2017, https://www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology?utm_source=Commentary&utm_medium=referral&utm_campaign=diagnostics). Emerging POC microbiology tests, especially nucleic acid amplification tests, have the potential to advance medical care. PMID:28539341

Quantification of HTLV-1 Clonality and TCR Diversity

PubMed Central

Laydon, Daniel J.; Melamed, Anat; Sim, Aaron; Gillet, Nicolas A.; Sim, Kathleen; Darko, Sam; Kroll, J. Simon; Douek, Daniel C.; Price, David A.; Bangham, Charles R. M.; Asquith, Becca

2014-01-01

Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological “species” in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations. PMID:24945836

Stability of buprenorphine, haloperidol and glycopyrrolate mixture in a 0.9% sodium chloride solution.

PubMed

Jäppinen, A; Kokki, H; Naaranlahti, T J; Rasi, A S

1999-12-01

Combinations of opioids and adjuvant drug solutions are often used in clinical practice while little information is available on their microbiological or chemical stability. Currently there are no commercially available, prepacked, ready-to-use epidural or subcutaneous mixtures. Thus, epidural and subcutaneous analgesic mixtures must be prepared in the pharmacy on an as-needed basis. Such mixtures are typically used for the treatment of severe pain in cancer patients. The aim of this study was to investigate the microbiological and chemical stability of a buprenorphine, haloperidol and glycopyrrolate mixture in a 0.9% sodium chloride solution. A high performance liquid chromatographic (HPLC) method and pH-meter were used to conduct the analyses. Antimicrobial activity of each component was studied by an agar dilution method. According to the results from the chemical and microbiological stability studies, this mixture can be stored in polypropylene (PP) syringes and polyvinyl chloride (PVC) medication cassettes for at least 30 days at either 21 degrees C or 4 degrees C, and for 16 days in PP syringes at 36 degrees C, and for 9 days in PVC medication cassettes at 36 degrees C.

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards

PubMed Central

2016-01-01

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum, Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereus strain was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days. PMID:26896133

Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.

PubMed

Sibley, Christopher D; Peirano, Gisele; Church, Deirdre L

2012-04-01

Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections. Copyright © 2012 Elsevier B.V. All rights reserved.

Harmonisation of microbial sampling and testing methods for distillate fuels

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

Hill, G.C.; Hill, E.C.

1995-05-01

Increased incidence of microbial infection in distillate fuels has led to a demand for organisations such as the Institute of Petroleum to propose standards for microbiological quality, based on numbers of viable microbial colony forming units. Variations in quality requirements, and in the spoilage significance of contaminating microbes plus a tendency for temporal and spatial changes in the distribution of microbes, makes such standards difficult to implement. The problem is compounded by a diversity in the procedures employed for sampling and testing for microbial contamination and in the interpretation of the data obtained. The following paper reviews these problems andmore » describes the efforts of The Institute of Petroleum Microbiology Fuels Group to address these issues and in particular to bring about harmonisation of sampling and testing methods. The benefits and drawbacks of available test methods, both laboratory based and on-site, are discussed.« less

[Microbiological diagnosis of viral respiratory infections].

PubMed

Eiros, José M; Ortiz de Lejarazu, Raúl; Tenorio, Alberto; Casas, Inmaculada; Pozo, Francisco; Ruiz, Guillermo; Pérez-Breña, Pilar

2009-03-01

Acute respiratory infection is the most common disease occurring over a person's lifetime, with etiological variations determined mainly by age, environmental circumstances, the healthcare setting, and the underlying pathology. More than 200 different viruses distributed in six viral families have been implicated in the pathogenesis of respiratory tract infection. These facts are generating an increasing diagnostic demand that should be incorporated into the healthcare setting without delay. To meet this demand, the Spanish Society of Infectious Diseases and Clinical Microbiology has updated its Standard Procedure for the microbiological diagnosis of viral respiratory infection. This document contains an update primarily of infections caused by influenza viruses, and secondarily, infections due to other conventional and emerging respiratory viruses. In all cases, the methods for direct virological diagnosis (cell culture, and detection of antigens and nucleic acid) are reviewed, with special reference to techniques for molecular detection and genetic characterization.

The Czech External Quality Control system in medical microbiology and parasitology.

PubMed

Slosárek, M; Kríz, B

2000-11-01

The External Quality Control (EQC) system in activities of laboratories engaged in medical microbiology and parasitology was established in the Czech Republic in 1993 when to the first laboratories which applied coded serum samples were sent for diagnosis of viral hepatitis and bacterial strains for identification. In the course of years the number of control areas increased and in 2000 there were 31 and the number of those interested in participation in EQC increased from 79 in 1993 to 434 in 2000. This year a total of 13,239 samples will be sent to laboratories. Gradually thus almost all microbiological and parasitological laboratories concerned with examination of clinical material became involved. Seven-year experience with EQC in the Czech Republic revealed that gradually the results of various examinations became more accurate, that methods became standardized and the most suitable examination sets are used.

Effect of production variables on microbiological removal in locally-produced ceramic filters for household water treatment.

PubMed

Lantagne, Daniele; Klarman, Molly; Mayer, Ally; Preston, Kelsey; Napotnik, Julie; Jellison, Kristen

2010-06-01

Diarrhoeal diseases cause an estimated 1.87 million child deaths per year. Point-of-use filtration using locally made ceramic filters improves microbiological quality of stored drinking water and prevents diarrhoeal disease. Scaling-up ceramic filtration is inhibited by lack of universal quality control standards. We investigated filter production variables to determine their affect on microbiological removal during 5-6 weeks of simulated normal use. Decreases in the clay:sawdust ratio and changes in the burnable decreased effectiveness of the filter. Method of silver application and shape of filter did not impact filter effectiveness. A maximum flow rate of 1.7 l(-hr) was established as a potential quality control measure for one particular filter to ensure 99% (2- log(10)) removal of total coliforms. Further research is indicated to determine additional production variables associated with filter effectiveness and develop standardized filter production procedures prior to scaling-up.

Rifaximin Stability: A Look at UV, IR, HPLC, and Turbidimetry Methods.

PubMed

Kogawa, Ana Carolina; Salgado, Hérida Regina Nunes

2018-03-01

The study of the stability of medicines is mandated by the International Conference on Harmonization and the World Health Organization. Rifaximin, an antimicrobial marketed in the form of tablets, has no record of stability studies. Thus, the objective of the present work was to investigate the behavior and stability of rifaximin tablets for 6 months under simultaneous conditions of temperature and humidity by UV, IR, HPLC, and turbidimetry techniques. After 6 months of stability study, rifaximin tablets were shown to obey zero-order kinetics when analyzed by physicochemical methods and second-order kinetics when analyzed by a microbiological method. However, the UV method was not suitable for the evaluation of rifaximin. IR, HPLC, and turbidimetry methods can already be used to evaluate the stability of rifaximin tablets. It is important to analyze products with more than one type of method before releasing results mainly in the case of antimicrobial products in which the association of physicochemical and microbiological techniques must be a rule. Rifaximin tablets can be considered stable after 6 months under conditions of 40 ± 2°C and 75 ± 5% relative humidity.

Economic impact of rapid diagnostic methods in Clinical Microbiology: Price of the test or overall clinical impact.

PubMed

Cantón, Rafael; Gómez G de la Pedrosa, Elia

2017-12-01

The need to reduce the time it takes to establish a microbiological diagnosis and the emergence of new molecular microbiology and proteomic technologies has fuelled the development of rapid and point-of-care techniques, as well as the so-called point-of-care laboratories. These laboratories are responsible for conducting both techniques partially to response to the outsourcing of the conventional hospital laboratories. Their introduction has not always been accompanied with economic studies that address their cost-effectiveness, cost-benefit and cost-utility, but rather tend to be limited to the unit price of the test. The latter, influenced by the purchase procedure, does not usually have a regulated reference value in the same way that medicines do. The cost-effectiveness studies that have recently been conducted on mass spectrometry in the diagnosis of bacteraemia and the use of antimicrobials have had the greatest clinical impact and may act as a model for future economic studies on rapid and point-of-care tests. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Professional challenges and opportunities in clinical microbiology and infectious diseases in Europe.

PubMed

Read, Robert C; Cornaglia, Giuseppe; Kahlmeter, Gunnar

2011-05-01

The two closely linked specialties of clinical microbiology and infectious diseases face important challenges. We report the consensus of clinical microbiologists and infectious disease physicians assembled by the European Society for Clinical Microbiology and Infectious Diseases. Both specialties have different training requirements in different European countries and are not universally recognised as professions. The specialties are rapidly evolving as they adapt to the changing demands within hospital practice, including the need to deal with emerging infections, rapidly increasing internationalisation, and immigration. Clinical microbiology needs to develop and master technological advances such as laboratory automation and an avalanche of new methods for rapid diagnostics. Simultaneously, the pressure for concentration, amalgamation, and out-sourcing of laboratory services is ever-increasing. Infectious disease physicians have to meet the professional challenge of subspecialisation and the continual need to find new niches for their skills. Despite these challenges, each of these specialties continues to thrive in Europe and will enjoy important opportunities over the next few years. The recently formed European Centre for Disease Prevention and Control in Stockholm, Sweden, will increase demands in areas of surveillance of infectious diseases and antimicrobial resistance on both specialties. Copyright © 2011 Elsevier Ltd. All rights reserved.

Combination of microbiological culture and multiplex PCR increases the range of vaginal microorganisms identified in cervical cancer patients at high risk for bacterial vaginosis and vaginitis.

PubMed

Schmidt, Katarzyna; Cybulski, Zefiryn; Roszak, Andrzej; Grabiec, Alicja; Talaga, Zofia; Urbański, Bartosz; Odważna, Joanna; Wojciechowicz, Jacek

2015-05-01

Bacterial vaginosis (BV) and vaginitis in cervical cancer patients might becaused by mixed aerobic, anaerobic, and atypical bacteria. Since genital tract infections can be complicated, early and accurate identification of causal pathogens is vital. The purpose of this study was i) to determinate if currently used aerobic culture methods are sufficiently sensitive to identify pathogens that can appear in the cervix of women after cancer treatment; ii) to investigate if molecular methods can improve the diagnostic process of BV and vaginitis, as well as broaden the range of detectable pathogens that would otherwise be difficult to cultivate. A one-year hospital-based study was conducted in 2011/2012. Cervical swabs from 130 patients were examined by microbiological culture and multiplex PCR. Swab samples were positive for 107 and 93 women by microbiological culture and multiplex PCR, respectively The most common bacteria isolated from culture were: Escherichia coli, Enterococcus faecalis, Streptococcus agalactiae, and Staphylococcus aureus, and using the molecular technique were: Gardnerella vaginalis, Bacteroides fragilis, Ureoplasma ureoliticum/parvum, Mobiluncus curtisii and Atopobium vaginae. Multiplex PCR might contribute to the diagnosis of genital tract infections and it broadens the number of detectable microorganisms responsible for BV. Combination of these two methods may become the basis for standardized diagnosis of BV and vaginitis.

Comparison of the microbiological quality of environmentally friendly and conventionally grown vegetables sold at retail markets in Korea.

PubMed

Ryu, Jee-Hoon; Kim, Minju; Kim, Eun-Gyeong; Beuchat, Larry R; Kim, Hoikyung

2014-09-01

Fresh produce is usually eaten raw without cooking or heating, which may increase the probability of foodborne infection. The microbiological quality of 11 types of fresh, raw vegetables (romaine lettuce, sesame leaves, crown daisy, garlic chives, iceberg lettuce, cabbage, broccoli, leek, chili pepper, capsicum, and zucchini) purchased at retail markets in Iksan, Korea as affected by cultivation method (environmentally friendly vegetables [organic, pesticide-free, and low-pesticide vegetables] and conventionally grown vegetables) and harvest season was determined. Escherichia coli O157:H7 and Salmonella were not detected in all samples of vegetables tested. Aerobic mesophiles (>6 log cfu/g) were detected in environmentally friendly romaine lettuce and crown daisy and environmentally friendly and conventionally grown garlic chives, which also contained coliforms (>3 log cfu/g). Sesame leaf and crown daisy (regardless of cultivation method), as well as conventionally grown romaine lettuce and leek, contained >1 log cfu/g of E. coli. The overall microbiological quality of environmentally friendly and conventionally grown vegetables was not significantly different (P > 0.05). However, there were seasonal effects on populations of coliforms and generic E. coli on vegetables. The greatest numbers of microorganisms were isolated from environmentally friendly or conventionally grown vegetables purchased in winter. The vegetables, regardless of cultivation method or season, should be subjected to appropriate antimicrobial treatment to enhance their microbial safety. © 2014 Institute of Food Technologists®

A comparison of indexing methods to evaluate quality of soils subjected to different erosion: the role of soil microbiological properties.

NASA Astrophysics Data System (ADS)

Romaniuk, Romina; Lidia, Giuffre; Alejandro, Costantini; Norberto, Bartoloni; Paolo, Nannipieri

2010-05-01

Soil quality assessment is needed to evaluate the soil conditions and sustainability of soil and crop management properties, and thus requires a systematic approach to select and interpret soil properties to be used as indicators. The aim of this work was to evaluate and compare different indexing methods to assess quality of an undisturbed grassland soil (UN), a degraded pasture soil (GL) and a no tilled soil (NT) with four different A horizon depths (25, 23, 19 and 14 cm) reflecting a diverse erosion. Twenty four soil properties were measured from 0 to10 (1) and 10 to 20 cm. (2) and a minimum data set was chosen by multivariate principal component analysis (PCA) considering all measured soil properties together (A), or according to their classification in physical, chemical or microbiological (B) properties. The measured soil properties involved either inexpensive or not laborious standard protocols, to be used in routine laboratory analysis (simple soil quality index - SSQI), or a more laborious, time consuming and expensive protocols to determine microbial diversity and microbial functionality by methyl ester fatty acids (PLFA) and catabolic response profiles (CRP), respectively (complex soil quality index - CSQI). The selected properties were linearly normalized and integrated by the weight additive method to calculate SSQI A, SSQI B, CSQI A and CSQI B indices. Two microbiological soil quality indices (MSQI) were also calculated: the MSQI 1 only considered microbiological properties according to the procedure used for calculating SQI; the MSQI 2 was calculated by considering microbial carbon biomass (MCB), microbial activity (Resp) and functional diversity determined by CPR (E). The soil quality indices were SSQI A = MCB 1 + Particulate Organic Carbon (POC)1 + Mean Weight Diameter (MWD)1; SSQI B = Saturated hydraulic conductivity (K) 1 + Total Organic Carbon (TOC) 1 + MCB 1; CSQI A = MCB 1 + POC 1 + MWD 1; CSQI B = K 1+ TOC 1+ 0.3 * (MCB 1+ i/a +POC 1) + 0,05 * (E + cy/pre), where i/a and cy/pre are the iso/anteiso and cyclopropyl/precursors ratios determined by PLFA; MSQI 1 (0,3 * (MCB 1+ i/a 1 +POC 1) + 0,05 * (E 1+ cy/pre 1) ) and MSQI 2 (MCB 1+Resp 1+ E 1). All the calculated indices differentiated references plots (UN and GL), from those under no tillage (NT) system. Values were similar in NT plots with low erosion levels (NT 25 and 23) but higher than values of plots with high erosion (NT 19 and 14). Soil quality indices constructed by procedure B, (SSQI B and CSQI B) differentiated among the studied plots with the same or higher sensitivity than the other indices and allowed evaluating the impact of soil management practices and erosion on soil physical, chemical and microbiological properties. The lack of indicators representing all soil properties (physical, chemical and biological) in SQI constructed by procedure A could decrease the index sensitivity to changes in management; and the same may happen when physical, chemical and biological properties present different weights into the calculated SQI. The inclusion of CRP and PLFA data in the indices slightly increased or did not increase the index sensitivity (CSQI A and CSQI B). Generally microbiological indices (MSQI 1 and MSQI 2) were highly sensitive to soil erosion. However, we suggest that indices integrating physical, chemical and microbiological properties may give a more complete view of the soil quality than indices only based on measurement of a few microbiological properties.

Review Over a 3-Year Period of European Union Proficiency Tests for Detection of Staphylococcal Enterotoxins in Food Matrices.

PubMed

Nia, Yacine; Mutel, Isabelle; Assere, Adrien; Lombard, Bertrand; Auvray, Frederic; Hennekinne, Jacques-Antoine

2016-04-13

Staphylococcal food poisoning outbreaks are a major cause of foodborne illnesses in Europe and their notifications have been mandatory since 2005. Even though the European regulation on microbiological criteria for food defines a criterion on staphylococcal enterotoxin (SE) only in cheese and dairy products, European Food Safety Authority (EFSA) data reported that various types of food matrices are involved in staphylococcal food poisoning outbreaks. The European Screening Method (ESM) of European Union Reference Laboratory for Coagulase Positive Staphylococci (EURL CPS) was validated in 2011 for SE detection in food matrices and is currently the official method used for screening purposes in Europe. In this context, EURLCPS is annually organizing Inter-Laboratory Proficiency Testing Trials (ILPT) to evaluate the competency of the European countries' National Reference Laboratories (NRLs) to analyse SE content in food matrices. A total of 31 NRLs representing 93% of European countries participated in these ILPTs. Eight food matrices were used for ILPT over the period 2013-2015, including cheese, freeze-dried cheese, tuna, mackerel, roasted chicken, ready-to-eat food, milk, and pastry. Food samples were spiked with four SE types (i.e., SEA, SEC, SED, and SEE) at various concentrations. Homogeneity and stability studies showed that ILPT samples were both homogeneous and stable. The analysis of results obtained by participants for a total of 155 blank and 620 contaminated samples allowed for evaluation of trueness (>98%) and specificity (100%) of ESM. Further to the validation study of ESM carried out in 2011, these three ILPTs allowed for the assessment of the proficiency of the NRL network and the performance of ESM on a large variety of food matrices and samples. The ILPT design presented here will be helpful for the organization of ILPT on SE detection by NRLs or other expert laboratories.

Antibiotic Susceptibilities of Enterococcus Species Isolated from Hospital and Domestic Wastewater Effluents in Alice, Eastern Cape Province of South Africa

PubMed Central

Iweriebor, Benson Chuks; Gaqavu, Sisipho; Obi, Larry Chikwelu; Nwodo, Uchechukwu U.; Okoh, Anthony I.

2015-01-01

Background: Antimicrobial resistance in microorganisms are on the increase worldwide and are responsible for substantial cases of therapeutic failures. Resistance of species of Enterococcus to antibiotics is linked to their ability to acquire and disseminate antimicrobial resistance determinants in nature, and wastewater treatment plants (WWTPs) are considered to be one of the main reservoirs of such antibiotic resistant bacteria. We therefore determined the antimicrobial resistance and virulence profiles of some common Enterococcus spp that are known to be associated with human infections that were recovered from hospital wastewater and final effluent of the receiving wastewater treatment plant in Alice, Eastern Cape. Methods: Wastewater samples were simultaneously collected from two sites (Victoria hospital and final effluents of a municipal WWTP) in Alice at about one to two weeks interval during the months of July and August 2014. Samples were screened for the isolation of enterococci using standard microbiological methods. The isolates were profiled molecularly after targeted generic identification and speciation for the presence of virulence and antibiotic resistance genes. Results: Out of 66 presumptive isolates, 62 were confirmed to belong to the Enterococcus genusof which 30 were identified to be E. faecalis and 15 E. durans. The remaining isolates were not identified by the primers used in the screening procedure. Out of the six virulence genes that were targeted only three of them; ace, efaA, and gelE were detected. There was a very high phenotypic multiple resistance among the isolates and these were confirmed by genetic analyses. Conclusions: Analyses of the results obtained indicated that hospital wastewater may be one of the sources of antibiotic resistant bacteria to the receiving WWTP. Also, findings revealed that the final effluent discharged into the environment was contaminated with multi-resistant enterococci species thus posing a health hazard to the receiving aquatic environment as these could eventually be transmitted to humans and animals that are exposed to it. PMID:25893999

Fungal CYP51 Inhibitors VT-1161 and VT-1129 Exhibit Strong In Vitro Activity against Candida glabrata and C. krusei Isolates Clinically Resistant to Azole and Echinocandin Antifungal Compounds.

PubMed

Schell, W A; Jones, A M; Garvey, E P; Hoekstra, W J; Schotzinger, R J; Alexander, B D

2017-03-01

The in vitro activities of fungal CYP51 inhibitors VT-1161 and VT-1129 were determined for Candida glabrata ( n = 34) and C. krusei ( n = 50). C. glabrata isolates were screened for FKS gene mutations. All isolates were resistant clinically and/or in vitro to at least one standard antifungal compound. VT-1161 and VT-1129 MICs for all isolates were at least 5-fold below achievable human plasma levels for VT-1161. VT-1161 and VT-1129 are promising for the treatment of resistant C. glabrata and C. krusei infections. Copyright © 2017 American Society for Microbiology.

Assessment of internal contamination problems associated with bioregenerative air/water purification systems

NASA Technical Reports Server (NTRS)

Johnson, Anne H.; Bounds, B. Keith; Gardner, Warren

1990-01-01

The emphasis is to characterize the mechanisms of bioregenerative revitalization of air and water as well as to assess the possible risks associated with such a system in a closed environment. Marsh and aquatic plants are utilized for purposes of wastewater treatment as well as possible desalinization and demineralization. Foliage plants are also being screened for their ability to remove toxic organics from ambient air. Preliminary test results indicate that treated wastewater is typically of potable quality with numbers of pathogens such as Salmonella and Shigella significantly reduced by the artificial marsh system. Microbiological analyses of ambient air indicate the presence of bacilli as well as thermophilic actinomycetes.

Surveillance for Toxoplasma gondii in California mussels (Mytilus californianus) reveals transmission of atypical genotypes from land to sea.

PubMed

Shapiro, Karen; VanWormer, Elizabeth; Aguilar, Beatriz; Conrad, Patricia A

2015-11-01

Coastal habitat contamination with Toxoplasma gondii is a health risk to humans and marine wildlife, with infections documented in both nearshore and pelagic marine mammals. Due to lack of sensitive methods for detection of T. gondii in water, this study utilized an alternative surveillance approach for evaluating marine habitat contamination using wild mussels. The objectives of this study were to (i) validate sensitive molecular tools for T. gondii detection in mussels and (ii) apply optimized methods in a surveillance study to determine the prevalence and genotype(s) of T. gondii in mussels. Simplex polymerase chain reaction screening and multiplex genotyping assays were validated and then applied on 959 wild-caught mussels collected from central California. Thirteen mussels (1.4%) had detectable T. gondii DNA and the presence of T. gondii in mussels was significantly associated with proximity to freshwater run-off and collection during the wet season. Molecular characterization revealed alleles from T. gondii types I, II/III, X at the B1 locus, and a novel atypical B1 allele that was recently documented in T. gondii-infected carnivores from California. Findings demonstrate higher than previously reported T. gondii contamination of California coastlines, and describe novel strains of the parasite that further link terrestrial sources with marine contamination. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Synergism between hydrogen peroxide and seventeen acids against five agri-food-borne fungi and one yeast strain.

PubMed

Martin, H; Maris, P

2012-12-01

The objective of this study was to evaluate fungicidal efficacy of hydrogen peroxide administered in combination with 17 mineral and organic acids authorized for use in the food industry. The assays were performed on a 96-well microplate using a microdilution technique based on the checkerboard titration method. The six selected strains (one yeast and five fungi) were reference strains and strains representative of contaminating fungi found in the food industry. Each synergistic hydrogen peroxide/acid combination found after fifteen minutes contact time at 20 °C in distilled water was then tested in conditions simulating four different use conditions. Twelve combinations were synergistic in distilled water, eleven of these remained synergistic with one or more of the four mineral and organic interfering substances selected. Hydrogen peroxide/formic acid combination remained effective against four strains and was never antagonistic against the other two fungi. Combinations with propionic acid and acetic acid stayed synergistic against two strains. Those with oxalic acid and lactic acid kept their synergism only against Candida albicans. No synergism was detected against Penicillium cyclopium. Synergistic combinations of disinfectants were revealed, among them the promising hydrogen peroxide/formic acid combination. A rapid screening method developed in our laboratory for bacteria was adapted to fungi and used to reveal the synergistic potential of disinfectants and/or sanitizers combinations. © 2012 The Society for Applied Microbiology.

Direct Microscopy: A Useful Tool to Diagnose Oral Candidiasis in Children and Adolescents.

PubMed

Marty, Mathieu; Bourrat, Emmanuelle; Vaysse, Frédéric; Bonner, Mark; Bailleul-Forestier, Isabelle

2015-12-01

Oral candidiasis is one of the most common opportunistic fungal infections of the oral cavity in human. Among children, this condition represents one of the most frequent affecting the mucosa. Although most diagnoses are made based on clinical signs and features, a microbiological analysis is sometimes necessary. We performed a literature review on the diagnosis of oral candidiasis to identify the techniques most commonly employed in routine clinical practice. A Medline-PubMed search covering the last 10 years was performed. Microbiological techniques were used in cases requiring confirmation of the clinical diagnosis. In such cases, direct microscopy was the method most commonly used for diagnosing candidiasis. Direct microscopy appears as the method of choice for confirming clinical diagnosis and could become a routine chair-side technique.

Use of electron beam irradiation to improve the microbiological safety of Hippophae rhamnoides

NASA Astrophysics Data System (ADS)

Minea, R.; Nemţanu, M. R.; Manea, S.; Mazilu, E.

2007-09-01

Sea buckthorn ( Hippophae rhamnoides) is increasingly used in food supplements due to its dietary and medicinal compounds with a beneficial role in human diet and health. As many other medicinal plants, sea buckthorn can be contaminated with microorganisms which exerts an important impact on the overall quality of the products. Irradiation is an effective method for food preservation because it is able to destroy pathogenic microorganisms keeping the organoleptic and nutritional characteristics of the foods. The objective of the present study was to investigate the application of electron beam irradiation in order to improve the microbiological safety of sea buckthorn. The experimental results indicated that the electron beam treatment might be a good method to remove undesirable microorganisms from sea buckthorn without significant changes in its active principles.

Integration of electro-optical mechanical systems and medicine: where are we and where can we go?

NASA Astrophysics Data System (ADS)

Gourley, Mark F.; Gourley, Paul L.

1997-03-01

The marriage of microfabricated materials with microbiological systems will allow advances in medicine to proceed at an unprecedented pace. Biomedical research is placing new demands on speed and limits of detection to assay body tissues and fluids. Emerging microfabricated chip technologies from the engineering community offer researchers novel types of analysis of human samples. In guiding these developments, the ability to swiftly and accurately gain useful information for identification and establish a diagnosis, is of utmost importance. Current examples of such technology include DNA amplification and analysis, and fluorescent cell analysis by flow cytometry. Potential applications include the development of rapid techniques for examining large number of cells in tissue or in blood. These could serve as screening tools for the detection and quantification of abnormal cell types; for example malignant or HIV infected cells. Micro/nanofabrication methods will make these devices compact, providing access of this technology to point of care providers; in a clinic, ambulance, or on a battlefield. Currently, these tools are in the construction phase. Upon delivery to researchers, validation of these instruments leads to clinical demand that requires approval from the Food and Drug Administration. This paper outlines criteria that successful devices must satisfy.

In Vivo Caprine Model for Osteomyelitis and Evaluation of Biofilm-Resistant Intramedullary Nails

PubMed Central

Tran, Nhiem; Tran, Phong A.; Jarrell, John D.; Engiles, Julie B.; Thomas, Nathan P.; Young, Matthew D.; Hayda, Roman A.; Born, Christopher T.

2013-01-01

Bone infection remains a formidable challenge to the medical field. The goal of the current study is to evaluate antibacterial coatings in vitro and to develop a large animal model to assess coated bone implants. A novel coating consisting of titanium oxide and siloxane polymer doped with silver was created by metal-organic methods. The coating was tested in vitro using rapid screening techniques to determine compositions which inhibited Staphylococcus aureus growth, while not affecting osteoblast viability. The coating was then applied to intramedullary nails and evaluated in vivo in a caprine model. In this pilot study, a fracture was created in the tibia of the goat, and Staphylococcus aureus was inoculated directly into the bone canal. The fractures were fixed by either coated (treated) or non-coated intramedullary nails (control) for 5 weeks. Clinical observations as well as microbiology, mechanical, radiology, and histology testing were used to compare the animals. The treated goat was able to walk using all four limbs after 5 weeks, while the control was unwilling to bear weight on the fixed leg. These results suggest the antimicrobial potential of the hybrid coating and the feasibility of the goat model for antimicrobial coated intramedullary implant evaluation. PMID:23841085

A ten-year follow-up of human leptospirosis in Uruguay: an unresolved health problem.

PubMed

Schelotto, Felipe; Hernández, Elba; González, Sabina; Del Monte, Alicia; Ifran, Silvana; Flores, Karina; Pardo, Lorena; Parada, Daniel; Filippini, Mercedes; Balseiro, Victoria; Geymonat, Juan Pablo; Varela, Gustavo

2012-01-01

Leptospira spp. are delicate bacteria that cannot be studied by usual microbiological methods. They cause leptospirosis, a zoonotic disease transmitted to humans through infected urine of wild or domestic animals. We studied the incidence of this disease in the Uruguayan population, its epidemiologic and clinical features, and compared diagnostic techniques. After examining 6,778 suspect cases, we estimated that about 15 infections/100,000 inhabitants occurred yearly, affecting mainly young male rural workers. Awareness about leptospirosis has grown among health professionals, and its lethality has consequently decreased. Bovine infections were probably the principal source of human disease. Rainfall volumes and floods were major factors of varying incidence. Most patients had fever, asthenia, myalgias or cephalalgia, with at least one additional abnormal clinical feature. 30-40% of confirmed cases presented abdominal signs and symptoms, conjunctival suffusion and altered renal or urinary function. Jaundice was more frequent in patients aged > 40 years. Clinical infections followed an acute pattern and their usual outcome was complete recovery. Laboratory diagnosis was based on indirect micro-agglutination standard technique (MAT). Second serum samples were difficult to obtain, often impairing completion of diagnosis. Immunofluorescence was useful as a screening test and for early detection of probable infections.

High-Throughput Intracellular Antimicrobial Susceptibility Testing of Legionella pneumophila.

PubMed

Chiaraviglio, Lucius; Kirby, James E

2015-12-01

Legionella pneumophila is a Gram-negative opportunistic human pathogen that causes a severe pneumonia known as Legionnaires' disease. Notably, in the human host, the organism is believed to replicate solely within an intracellular compartment, predominantly within pulmonary macrophages. Consequently, successful therapy is predicated on antimicrobials penetrating into this intracellular growth niche. However, standard antimicrobial susceptibility testing methods test solely for extracellular growth inhibition. Here, we make use of a high-throughput assay to characterize intracellular growth inhibition activity of known antimicrobials. For select antimicrobials, high-resolution dose-response analysis was then performed to characterize and compare activity levels in both macrophage infection and axenic growth assays. Results support the superiority of several classes of nonpolar antimicrobials in abrogating intracellular growth. Importantly, our assay results show excellent correlations with prior clinical observations of antimicrobial efficacy. Furthermore, we also show the applicability of high-throughput automation to two- and three-dimensional synergy testing. High-resolution isocontour isobolograms provide in vitro support for specific combination antimicrobial therapy. Taken together, findings suggest that high-throughput screening technology may be successfully applied to identify and characterize antimicrobials that target bacterial pathogens that make use of an intracellular growth niche. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Directed evolution improves the fibrinolytic activity of nattokinase from Bacillus natto.

PubMed

Yongjun, Cai; Wei, Bao; Shujun, Jiang; Meizhi, Weng; Yan, Jia; Yan, Yin; Zhongliang, Zheng; Goulin, Zou

2011-12-01

Nattokinase (subtilisin NAT, NK) is a relatively effective microbial fibrinolytic enzyme that has been identified and characterized from Bacillus natto. In the current report, DNA family shuffling was used to improve the fibrinolytic activity of nattokinase. Three homologous genes from B. natto AS 1.107, Bacillus amyloliquefaciens CICC 20164 and Bacillus licheniformis CICC 10092 were shuffled to generate a mutant library. A plate-based method was used to screen the mutant libraries for improved activity. After three rounds of DNA shuffling, one desirable mutant with 16 amino acid substitutions was obtained. The mutant enzyme was purified and characterized. The kinetic measurements showed that the catalytic efficiency of the mutant NK was approximately 2.3 times higher than that of the wild-type nattokinase. In addition, the molecular modeling analysis suggested that the mutations affect the enzymatic function by changing the surface conformation of the substrate-binding pocket. The current study shows that the evolution of nattokinase with improved fibrinolytic activity by DNA family shuffling is feasible and provides useful references to facilitate the application of nattokinase in thrombolytic therapy. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

[The opportunities, challenges and trends in the rejuvenation of microbiology].

PubMed

Shen, Ping; Chen, Xiangdong

2010-01-01

In history, the development of microbiology had undergone two golden ages and some depression time as well. In the last two decades, the application of many physiochemical technologies including genomics, structural biology, bioinformatics, PCR, and high-resolution microscopy has led to a series of breakthroughs in microbiology. Microbiology has now awakened and entered its third golden age for development. This review discusses our view of the opportunities, challenges, and trends in the current advancement of microbiology. The topics include: (1) The two golden ages for microbiology in history. (2) The opportunities and challenges in the rejuvenation of microbiology. (3) The characteristics and trends of the current development of microbiology. (4) Integral microbiology--the hallmark of the third golden age.

42 CFR 455.452 - Other State screening methods.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 4 2013-10-01 2013-10-01 false Other State screening methods. 455.452 Section 455....452 Other State screening methods. Nothing in this subpart must restrict the State Medicaid agency from establishing provider screening methods in addition to or more stringent than those required by...

42 CFR 455.452 - Other State screening methods.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 4 2011-10-01 2011-10-01 false Other State screening methods. 455.452 Section 455....452 Other State screening methods. Nothing in this subpart must restrict the State Medicaid agency from establishing provider screening methods in addition to or more stringent than those required by...

Evaluation of a standard test method for screening fuels in soils

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

Sorini, S.S.; Schabron, J.F.

1996-12-31

A new screening method for fuel contamination in soils was recently developed as American Society for Testing and Materials (ASTM) Method D-5831-95, Standard Test Method for Screening Fuels in Soils. This method uses low-toxicity chemicals and can be sued to screen organic- rich soils, as well as being fast, easy, and inexpensive to perform. Fuels containing aromatic compounds, such as diesel fuel and gasoline, as well as other aromatic-containing hydrocarbon materials, such as motor oil, crude oil, and cola oil, can be determined. The screening method for fuels in soils was evaluated by conducting a Collaborative study on the method.more » In the Collaborative study, a sand and an organic soil spiked with various concentrations of diesel fuel were tested. Data from the Collaborative study were used to determine the reproducibility (between participants) and repeatability (within participants) precision of the method for screening the test materials. The Collaborative study data also provide information on the performance of portable field equipment (patent pending) versus laboratory equipment for performing the screening method and a comparison of diesel concentration values determined using the screening method versus a laboratory method.« less

Importance of closely spaced vertical sampling in delineating chemical and microbiological gradients in groundwater studies

USGS Publications Warehouse

Smith, R.L.; Harvey, R.W.; LeBlanc, D.R.

1991-01-01

Vertical gradients of selected chemical constituents, bacterial populations, bacterial activity and electron acceptors were investigated for an unconfined aquifer contaminated with nitrate and organic compounds on Cape Cod, Massachusetts, U.S.A. Fifteen-port multilevel sampling devices (MLS's) were installed within the contaminant plume at the source of the contamination, and at 250 and 2100 m downgradient from the source. Depth profiles of specific conductance and dissolved oxygen at the downgradient sites exhibited vertical gradients that were both steep and inversely related. Narrow zones (2-4 m thick) of high N2O and NH4+ concentrations were also detected within the contaminant plume. A 27-fold change in bacterial abundance; a 35-fold change in frequency of dividing cells (FDC), an indicator of bacterial growth; a 23-fold change in 3H-glucose uptake, a measure of heterotrophic activity; and substantial changes in overall cell morphology were evident within a 9-m vertical interval at 250 m downgradient. The existence of these gradients argues for the need for closely spaced vertical sampling in groundwater studies because small differences in the vertical placement of a well screen can lead to incorrect conclusions about the chemical and microbiological processes within an aquifer.Vertical gradients of selected chemical constituents, bacterial populations, bacterial activity and electron acceptors were investigated for an unconfined aquifer contaminated with nitrate and organic compounds on Cape Cod, Massachusetts, USA. Fifteen-port multilevel sampling devices (MLS's) were installed within the contaminant plume at the source of the contamination, and at 250 and 2100 m downgradient from the source. Depth profiles of specific conductance and dissolved oxygen at the downgradient sites exhibited vertical gradients that were both steep and inversely related. Narrow zones (2-4 m thick) of high N2O and NH4+ concentrations were also detected within the contaminant plume. A 27-fold change in bacterial abundance; a 35-fold change in frequency of dividing cells (FDC), an indicator of bacterial growth; a 23-fold change in 3H-glucose uptake, a measure of heterotrophic activity; and substantial changes in overall cell morphology were evident within a 9-m vertical interval at 250 m downgradient. The existence of these gradients argues for the need for closely spaced vertical sampling in ground-water studies because small differences in the vertical placement of a well screen can lead to incorrect conclusions about the chemical and microbiological processes within an aquifer.

A Systematic Evaluation of Field-Based Screening Methods for the Assessment of Anterior Cruciate Ligament (ACL) Injury Risk.

PubMed

Fox, Aaron S; Bonacci, Jason; McLean, Scott G; Spittle, Michael; Saunders, Natalie

2016-05-01

Laboratory-based measures provide an accurate method to identify risk factors for anterior cruciate ligament (ACL) injury; however, these methods are generally prohibitive to the wider community. Screening methods that can be completed in a field or clinical setting may be more applicable for wider community use. Examination of field-based screening methods for ACL injury risk can aid in identifying the most applicable method(s) for use in these settings. The objective of this systematic review was to evaluate and compare field-based screening methods for ACL injury risk to determine their efficacy of use in wider community settings. An electronic database search was conducted on the SPORTDiscus™, MEDLINE, AMED and CINAHL databases (January 1990-July 2015) using a combination of relevant keywords. A secondary search of the same databases, using relevant keywords from identified screening methods, was also undertaken. Studies identified as potentially relevant were independently examined by two reviewers for inclusion. Where consensus could not be reached, a third reviewer was consulted. Original research articles that examined screening methods for ACL injury risk that could be undertaken outside of a laboratory setting were included for review. Two reviewers independently assessed the quality of included studies. Included studies were categorized according to the screening method they examined. A description of each screening method, and data pertaining to the ability to prospectively identify ACL injuries, validity and reliability, recommendations for identifying 'at-risk' athletes, equipment and training required to complete screening, time taken to screen athletes, and applicability of the screening method across sports and athletes were extracted from relevant studies. Of 1077 citations from the initial search, a total of 25 articles were identified as potentially relevant, with 12 meeting all inclusion/exclusion criteria. From the secondary search, eight further studies met all criteria, resulting in 20 studies being included for review. Five ACL-screening methods-the Landing Error Scoring System (LESS), Clinic-Based Algorithm, Observational Screening of Dynamic Knee Valgus (OSDKV), 2D-Cam Method, and Tuck Jump Assessment-were identified. There was limited evidence supporting the use of field-based screening methods in predicting ACL injuries across a range of populations. Differences relating to the equipment and time required to complete screening methods were identified. Only screening methods for ACL injury risk were included for review. Field-based screening methods developed for lower-limb injury risk in general may also incorporate, and be useful in, screening for ACL injury risk. Limited studies were available relating to the OSDKV and 2D-Cam Method. The LESS showed predictive validity in identifying ACL injuries, however only in a youth athlete population. The LESS also appears practical for community-wide use due to the minimal equipment and set-up/analysis time required. The Clinic-Based Algorithm may have predictive value for ACL injury risk as it identifies athletes who exhibit high frontal plane knee loads during a landing task, but requires extensive additional equipment and time, which may limit its application to wider community settings.

Can volatile organic metabolites be used to simultaneously assess microbial and mite contamination level in cereal grains and coffee beans?

PubMed

Salvador, Angelo C; Baptista, Inês; Barros, António S; Gomes, Newton C M; Cunha, Angela; Almeida, Adelaide; Rocha, Silvia M

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC-ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC-ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans.

Can Volatile Organic Metabolites Be Used to Simultaneously Assess Microbial and Mite Contamination Level in Cereal Grains and Coffee Beans?

PubMed Central

Salvador, Ângelo C.; Baptista, Inês; Barros, António S.; Gomes, Newton C. M.; Cunha, Ângela; Almeida, Adelaide; Rocha, Silvia M.

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC×GC–ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC–ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC–ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans. PMID:23613710

Comparison of sensory, microbiological, and biochemical parameters of microwave versus indirect UHT fluid skim milk during storage.

PubMed

Clare, D A; Bang, W S; Cartwright, G; Drake, M A; Coronel, P; Simunovic, J

2005-12-01

Shelf-stable milk could benefit from sensory quality improvement. Current methods of heating cause flavor and nutrient degradation through exposure to overheated thermal exchange surfaces. Rapid heating with microwaves followed by sudden cooling could reduce or eliminate this problem. The objectives for this study were focused on designing and implementing continuous microwave thermal processing of skim fluid milks (white and chocolate) to compare sensory, microbiological, and biochemical parameters with conventionally prepared, indirect UHT milks. All test products were aseptically packaged and stored at ambient temperature for 12 mo. Every 3 mo, samples were taken for microbiological testing, reactive sulfhydryl determinations, active enzyme analysis, instrumental viscosity readings, color measurements, and descriptive sensory evaluation. Microbiological plate counts were negative on all milks at each time point. Enzymatic assays showed that plasmin was inactivated by both heat treatments. 5,5'-dithio-bis(2-nitrobenzoic acid) analysis, a measure of reactive sulfhydryl (-SH-) groups, showed that the initial thiol content was not significantly different between the microwave-processed and UHT-treated milks. However, both heating methods resulted in an increased thiol level compared with conventionally pasteurized milk samples due to the higher temperatures attained. Sulfhydryl oxidase, a milk enzyme that catalyzes disulfide bond formation using a variety of protein substrates, retained activity following microwave processing, and decreased during storage. Viscosity values were essentially equivalent in microwave- and UHT-heated white skim milks. Sensory analyses established that UHT-treated milks were visibly darker, and exhibited higher caramelized and stale/fatty flavors with increased astringency compared with the microwave samples. Sweet aromatic flavor and sweet taste decreased during storage in both UHT and microwave milk products, whereas stale/fatty flavors increased over time. Sensory effects were more apparent in white milks than in chocolate varieties. These studies suggest that microwave technology may provide a useful alternative processing method for delivery of aseptic milk products that retain a long shelf life.

Rapid Diagnosis of Smear-Negative Tuberculosis Using Immunology and Microbiology with Induced Sputum in HIV-Infected and Uninfected Individuals

PubMed Central

Breen, Ronan A. M.; Hardy, Gareth A. D.; Perrin, Felicity M. R.; Lear, Sara; Kinloch, Sabine; Smith, Colette J.; Cropley, Ian; Janossy, George; Lipman, Marc C. I.

2007-01-01

Rationale and Objectives Blood-based studies have demonstrated the potential of immunological assays to detect tuberculosis. However lung fluid sampling may prove superior as it enables simultaneous microbiological detection of mycobacteria to be performed. Until now this has only been possible using the expensive and invasive technique of broncho-alveolar lavage. We sought to evaluate an immunoassay using non-invasive induced-sputum to diagnose active tuberculosis. Methods and Results Prospective cohort study of forty-two spontaneous sputum smear-negative or sputum non-producing adults under investigation for tuberculosis. CD4 lymphocytes specific to purified-protein-derivative of Mycobacterium tuberculosis actively synthesising interferon-gamma were measured by flow cytometry and final diagnosis compared to immunoassay using a cut-off of 0.5%. Sixteen subjects (38%) were HIV-infected (median CD4 count [range] = 332 cells/µl [103–748]). Thirty-eight (90%) were BCG-vaccinated. In 27 subjects diagnosed with active tuberculosis, the median [range] percentage of interferon-gamma synthetic CD4+ lymphocytes was 2.77% [0–23.93%] versus 0% [0–2.10%] in 15 negative for active infection (p<0.0001). Sensitivity and specificity of the immunoassay versus final diagnosis of active tuberculosis were 89% (24 of 27) and 80% (12 of 15) respectively. The 3 positive assays in the latter group occurred in subjects diagnosed with quiescent/latent tuberculosis. Assay performance was unaffected by HIV-status, BCG-vaccination or disease site. Combining this approach with traditional microbiological methods increased the diagnostic yield to 93% (25 of 27) alongside acid-fast bacilli smear and 96% (26 of 27) alongside tuberculosis culture. Conclusions These data demonstrate for the first time that a rapid immunological assay to diagnose active tuberculosis can be performed successfully in combination with microbiological methods on a single induced-sputum sample. PMID:18092001

Autochthonous starter cultures and indigenous grape variety for regional wine production.

PubMed

Garofalo, C; El Khoury, M; Lucas, P; Bely, M; Russo, P; Spano, G; Capozzi, V

2015-06-01

To characterize Oenococcus oeni strains isolated from North-Apulian wines where malic acid degradation is usually achieved by spontaneous fermentations, and to determine the influence of bacterial inoculation time on the malolactic performances in 'Nero di Troia' wine using a complete autochthonous microbial regime. Oenococcus oeni strains from wines produced with the autochthonous (Apulia Region, southern Italy) grape variety 'Uva di Troia' were isolated, selected and characterized. Multilocus sequence typing and variable number tandem repeat analysis were used to investigate intraspecific diversity. Oenococcus oeni strains were tested in co-inoculation and in sequential inoculation, with two autochthonous yeast strains previously isolated from 'Nero di Troia' wine. After a preliminary screening using co-inoculation regime, the O. oeni strains were grouped in reason of the different behaviour in malic acid performances. Results suggested that the efficient degradation of malic acid in co-inoculation is a strain-dependent characteristic. Autochthonous yeast/bacterium combinations were identified as starter culture, and used in a co-inoculation approach, for vinification of regional wines. The 'microbial terroir' of typical fermented food and beverage production represents a dynamic sector of applied research in food microbiology. In this work, we propose the use of autochthonous bacteria and yeast for wine production from an indigenous grape variety. © 2015 The Society for Applied Microbiology.

The Bactec FX Blood Culture System Detects Brucella melitensis Bacteremia in Adult Patients within the Routine 1-Week Incubation Period.

PubMed

Sagi, Moshe; Nesher, Lior; Yagupsky, Pablo

2017-03-01

The performance of the Bactec FX blood culture system for detecting Brucella bacteremia within the routine 1-week incubation period was assessed in a prospective study conducted in an area in southern Israel in which Brucella melitensis is endemic. Aerobic vials (BD Bactec Plus Aerobic/F medium) inoculated with blood specimens obtained from adult patients with positive Rose-Bengal screening test results were monitored for 4 consecutive weeks, and blind subcultures of negative vials were performed on solid media on days 7 and 28. During a 16-month period, a total of 31 (35.2%) of 88 cultures, obtained from 19 (38.0%) of 50 patients, were positive for Brucella melitensis The blood culture instrument identified 30 (96.8%) of 31 positive vials within 7 days of incubation; the single positive vial that was missed by the automated readings was detected only by the blind subculture performed on day 28. It is concluded that the Bactec FX system is able to detect the vast majority of episodes of Brucella bacteremia within the 1-week incubation protocol instituted in most clinical microbiology laboratories and without the need to perform blind subcultures of negative vials, enabling early diagnosis and saving labor and incubation time and space. Copyright © 2017 American Society for Microbiology.

Interdisciplinary orthodontic treatment for a patient with generalized aggressive periodontitis: Assessment of IgG antibodies to identify type of periodontitis and correct timing of treatment.

PubMed

Ishihara, Yoshihito; Tomikawa, Kazuya; Deguchi, Toru; Honjo, Tadashi; Suzuki, Koji; Kono, Takayuki; Kuboki, Takuo; Kamioka, Hiroshi; Takashiba, Shogo; Yamashiro, Takashi

2015-06-01

Aggressive periodontitis is a great challenge to clinicians when providing orthodontic treatment because of the potential for progression of periodontal disease. In this article, we report the successful comprehensive orthodontic treatment of bimaxillary protrusion and severe crowding in an adult with generalized aggressive periodontitis. A woman, aged 22 years 7 months, with a chief complaint of incisal crowding was diagnosed with a skeletal Class I malocclusion associated with severe anterior crowding, possibly worsened by generalized aggressive periodontitis. In addition to a periodontal examination, a blood IgG antibody titer analysis and microbiologic examination for periodontal pathogens were used to diagnose the type of periodontal disease and determine the proper timing to initiate orthodontic treatment. The total active treatment period was 28 months, followed by periodontal prostheses and regeneration therapy. Consequently, satisfactory facial profile, occlusion, and periodontal health were maintained for at least 36 months. These results indicate that efficient screening is important for providing successful orthodontic treatment in patients with advanced periodontal disease. This report also demonstrates the diagnostic importance of blood IgG antibody titer assays and microbiologic examinations to detect periodontal pathogens. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Chryseobacterium meningosepticum infections in a dialysis unit.

PubMed

Perera, Shalinie; Palasuntheram, C

2004-06-01

Chryseobacterium species are Gram-negative bacteria with an unusual antibiotic profile. Chryseobacterium meningosepticum is the species most commonly encountered as a human pathogen. To study the microbiological, clinical and therapeutic features of C. meningosepticum infections in patients on dialysis, at Sri Jayewardenepura General Hospital (Teaching) (SJGH), and to trace the source of infections. A retrospective descriptive study. Dialysis unit of SJGH. population Patients who underwent long term haemodialysis (HD) and manual intermittent peritoneal dialysis (IPD) in the dialysis unit. Clinical and microbiological records of patients with C. meningosepticum infections over a period of 2 years were reviewed retrospectively. Environmental screening was carried out to detect a possible source of infection. Thirty five episodes of infection due to C. meningosepticum in 33 patients on HD and IPD were detected. There were 30 episodes of peritonitis, four of bacteraemia and one of asymptomatic colonization of a PD catheter. Isolates were resistant to aminoglycosides, chephalosporins and aztreonam, and sensitive to cotrimoxazole, vancomycin and rifampicin. They showed variable sensitivity to imipenem and ciprofloxacin. All except one patient had a favourable outcome. C. meningosepticum was cultured from a sink in the dialysis unit, but the original source of the organism was not known. C. meningosepticum could be an important pathogen in a dialysis unit, and fluoroquinolones and vancomycin are effective as empiric therapy.

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

PubMed Central

Smith, Andy; Southgate, Joel; Poplawski, Radoslaw; Bull, Matthew J.; Richardson, Emily; Ismail, Matthew; Thompson, Simon Elwood-; Kitchen, Christine; Guest, Martyn; Bakke, Marius

2016-01-01

The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data. PMID:28785418

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

PubMed

Connor, Thomas R; Loman, Nicholas J; Thompson, Simon; Smith, Andy; Southgate, Joel; Poplawski, Radoslaw; Bull, Matthew J; Richardson, Emily; Ismail, Matthew; Thompson, Simon Elwood-; Kitchen, Christine; Guest, Martyn; Bakke, Marius; Sheppard, Samuel K; Pallen, Mark J

2016-09-01

The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

The interdependence between screening methods and screening libraries.

PubMed

Shelat, Anang A; Guy, R Kiplin

2007-06-01

The most common methods for discovery of chemical compounds capable of manipulating biological function involves some form of screening. The success of such screens is highly dependent on the chemical materials - commonly referred to as libraries - that are assayed. Classic methods for the design of screening libraries have depended on knowledge of target structure and relevant pharmacophores for target focus, and on simple count-based measures to assess other properties. The recent proliferation of two novel screening paradigms, structure-based screening and high-content screening, prompts a profound rethink about the ideal composition of small-molecule screening libraries. We suggest that currently utilized libraries are not optimal for addressing new targets by high-throughput screening, or complex phenotypes by high-content screening.

Direct quantification and distribution of tetracycline-resistant genes in meat samples by real-time polymerase chain reaction.

PubMed

Guarddon, Mónica; Miranda, Jose M; Vázquez, Beatriz I; Cepeda, Alberto; Franco, Carlos M

2012-07-01

The evolution of antimicrobial-resistant bacteria has become a threat to food safety and methods to control them are necessary. Counts of tetracycline-resistant (TR) bacteria by microbiological methods were compared with those obtained by quantitative PCR (qPCR) in 80 meat samples. TR Enterobacteriaceae counts were similar between the count plate method and qPCR (P= 0.24), whereas TR aerobic mesophilic bacteria counts were significantly higher by the microbiological method (P < 0.001). The distribution of tetA and tetB genes was investigated in different types of meat. tetA was detected in chicken meat (40%), turkey meat (100%), pork (20%), and beef (40%) samples, whereas tetB was detected in chicken meat (45%), turkey meat (70%), pork (30%), and beef (35%) samples. The presence of tetracycline residues was also investigated by a receptor assay. This study offers an alternative and rapid method for monitoring the presence of TR bacteria in meat and furthers the understanding of the distribution of tetA and tetB genes. © 2012 Institute of Food Technologists®

[Progresses in screening active compounds from herbal medicine by affinity chromatography].

PubMed

Feng, Ying-shu; Tong, Shan-shan; Xu, Xi-ming; Yu, Jiang-nan

2015-03-01

Affinity chromatography is a chromatographic method for separating molecules using the binding characteristics of the stationary phase with potential drug molecules. This method can be performed as a high throughput screening method and a chromatographic separation method to screen a variety of active drugs. This paper summarizes the history of affinity chromatography, screening technology of affinity chromatography, and application of affinity chromatography in screening bio-active compounds in herbal medicines, and then discusses its application prospects, in order to broaden applications of the affinity chromatography in drug screening.

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells.

PubMed

Tamminen, Manu V; Virta, Marko P J

2015-01-01

Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some nonpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a rigid support for genetic material and therefore allow complete degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labeled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1), or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to highly complex environmental microbial communities as a target gene-based screen for individual microbes. The method provides a novel tool for enumerating functional cell populations in complex microbial communities. We envision that the method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples.

Genomewide screening for genes involved in biofilm formation and miconazole susceptibility in Saccharomyces cerevisiae.

PubMed

Vandenbosch, Davy; De Canck, Evelien; Dhondt, Inne; Rigole, Petra; Nelis, Hans J; Coenye, Tom

2013-12-01

Infections related to fungal biofilms are difficult to treat due to the reduced susceptibility of sessile cells to most antifungal agents. Previous research has shown that 1-10% of sessile Candida cells survive treatment with high doses of miconazole (a fungicidal imidazole). The aim of this study was to identify genes involved in fungal biofilm formation and to unravel the mechanisms of resistance of these biofilms to miconazole. To this end, a screening of a Saccharomyces cerevisiae deletion mutant bank was carried out. Our results revealed that genes involved in peroxisomal transport and the biogenesis of the respiratory chain complex IV play an essential role in biofilm formation. On the other hand, genes involved in transcription and peroxisomal and mitochondrial organization seem to highly influence the susceptibility to miconazole of yeast biofilms. Additionally, our data confirm previous findings on genes involved in biofilm formation and in general stress responses. Our data suggest the involvement of peroxisomes in biofilm formation and miconazole resistance in fungal biofilms. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Comparison of the BD MAX MRSA XT to the Cepheid™ Xpert® MRSA assay for the molecular detection of methicillin-resistant Staphylococcus aureus from nasal swabs.

PubMed

Mehta, Sanjay R; Estrada, Jasmine; Ybarra, Juan; Fierer, Joshua

2017-04-01

Variation in MRSA genotypes may affect the sensitivity of molecular assays to detect this organism. We compared 2 commonly used screening assays, the Cepheid™ Xpert® MRSA and the BD MAX™ MRSA XT on consecutively obtained nasal swabs from 479 subjects. Specimens giving discordant results were subjected to additional microbiologic and molecular testing. Six hundred forty-two (97.6%) of the 658 test results were concordant. Of the 16 discordant results from 12 subjects, additional results suggested that 9 (60%) of the 15 MRSA XT assays were likely correct, and 6 (40%) of the 15 Xpert® assays were likely correct. One discordant result could not be resolved. A mecA dropout and novel mec right-extremity junction (MREJ) sites led to false-positive and negative results by Xpert®. While both assays performed well, continued vigilance is needed to monitor for Staphylococcus aureus with novel MREJ sites, mecA dropouts, and mecC, leading to inaccurate results in screening assays. Published by Elsevier Inc.

Serological study of brucellosis in Argentine Creole sheep.

PubMed

López, Gustavo E; Peña, Sabrina; Escobar, Gabriela I; Hasan, Déborah B; Lucero, Nidia E

2018-01-05

Ovine cattle was introduced into America during the Spanish conquest with the second journey of Columbus to the Antilles and was disseminated throughout the region. In 1587, sheep were introduced into Argentina, later developing into the "Creole" breed. We selected 486 animals from different Argentine provinces with the aim of determining the serological status of brucellosis caused by Brucella melitensis and Brucella ovis. For the detection of antibodies against smooth Brucella spp., the Rose Bengal test (RBT) was performed as screening test while the serum agglutination test (SAT) and 2 mercapto-ethanol (2ME) were run as a confirmatory technique. Moreover, for the detection of antibodies against rough Brucella spp., we used the rapid slide agglutination test (RSAT) for screening and an indirect ELISA (IELISA) as confirmatory assay. This study showed that the total positive percentage of brucellosis due to B. ovis was 2.9%. Excluding the animals mixed with the Suffolk breed; seropositivity would be 0.6%. All animals tested negative for brucellosis caused by B. melitensis. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

21 CFR 866.2540 - Microbiological incubator.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540 Microbiological...

21 CFR 866.2540 - Microbiological incubator.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540 Microbiological...

21 CFR 866.2540 - Microbiological incubator.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540 Microbiological...