Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches

PubMed Central

Rogers, Geraint B; Daniels, Thomas WV; Tuck, Andrew; Carroll, Mary P; Connett, Gary J; David, Gondi JP; Bruce, Kenneth D

2009-01-01

Background Drawing from previous studies, the traditional routine diagnostic microbiology evaluation of samples from chronic respiratory conditions may provide an incomplete picture of the bacteria present in airways disease. Here, the aim was to determine the extent to which routine diagnostic microbiology gave a different assessment of the species present in sputa when analysed by using culture-independent assessment. Methods Six different media used in routine diagnostic microbiology were inoculated with sputum from twelve patients. Bacterial growth on these plates was harvested and both RNA and DNA extracted. DNA and RNA were also extracted directly from the same sample of sputum. All nucleic acids served as templates for PCR and reverse transcriptase-PCR amplification of "broad range" bacterial 16S rRNA gene regions. The regions amplified were separated by Terminal Restriction Fragment Length Polymorphism (T-RFLP) profiling and compared to assess the degree of overlap between approaches. Results A mean of 16.3 (SD 10.0) separate T-RF band lengths in the profiles from each sputum sample by Direct Molecular Analysis, with a mean of 8.8 (SD 5.8) resolved by DNA profiling and 13.3 (SD 8.0) resolved by RNA profiling. In comparison, 8.8 (SD 4.4) T-RF bands were resolved in profiles generated by Culture-derived Molecular Analysis. There were a total of 184 instances of T-RF bands detected in the direct sputum profiles but not in the corresponding culture-derived profiles, representing 83 different T-RF band lengths. Amongst these were fifteen instances where the T-RF band represented more than 10% of the total band volume (with a mean value of 23.6%). Eight different T-RF band lengths were resolved as the dominant band in profiles generated directly from sputum. Of these, only three were detected in profiles generated from the corresponding set of cultures. Conclusion Due to their focus on isolation of a small group of recognised pathogens, the use of culture

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.

[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.

[Post-mortem microbiology analysis].

PubMed

Fernández-Rodríguez, Amparo; Alberola, Juan; Cohen, Marta Cecilia

2013-12-01

Post-mortem microbiology is useful in both clinical and forensic autopsies, and allows a suspected infection to be confirmed. Indeed, it is routinely applied to donor studies in the clinical setting, as well as in sudden and unexpected death in the forensic field. Implementation of specific sampling techniques in autopsy can minimize the possibility of contamination, making interpretation of the results easier. Specific interpretation criteria for post-mortem cultures, the use of molecular diagnosis, and its fusion with molecular biology and histopathology have led to post-mortem microbiology playing a major role in autopsy. Multidisciplinary work involving microbiologists, pathologists, and forensic physicians will help to improve the achievements of post-mortem microbiology, prevent infectious diseases, and contribute to a healthier population. Crown Copyright © 2012. Published by Elsevier Espana. All rights reserved.

Prospects for microbiological solutions to environmental pollution with plastics.

PubMed

Krueger, Martin C; Harms, Hauke; Schlosser, Dietmar

2015-11-01

Synthetic polymers, commonly named plastics, are among the most widespread anthropogenic pollutants of marine, limnic and terrestrial ecosystems. Disruptive effects of plastics are known to threaten wildlife and exert effects on natural food webs, but signs for and knowledge on plastic biodegradation are limited. Microorganisms are the most promising candidates for an eventual bioremediation of environmental plastics. Laboratory studies have reported various effects of microorganisms on many types of polymers, usually by enzymatic hydrolysis or oxidation. However, most common plastics have proved to be highly recalcitrant even under conditions known to favour microbial degradation. Knowledge on environmental degradation is yet scarcer. With this review, we provide a comprehensive overview of the current knowledge on microbiological degradation of several of the most common plastic types. Furthermore, we illustrate the analytical challenges concerning the evaluation of plastic biodegradation as well as constraints likely standing against the evolution of effective biodegradation pathways.

ENVIRONMENTAL MONITORING FOR PUBLIC ACCESS AND COMMUNITY TRACKING (EMPACT) PROGRAM MICROBIOLOGICAL MONITORING OF RECREATIONAL WATER

EPA Science Inventory

Current Environmental Protection Agency (EPA) recommended microbiological monitoring practices for bathing beach water quality were suggested in 1968, as a part of the fecal coliform guideline developed by the Federal Water Pollution Control Administration. The guideline stated ...

Molecular epidemiology and virulence characteristics of Staphylococcus aureus nasal colonization in medical laboratory staff: comparison between microbiological and non-microbiological laboratories.

PubMed

Xie, Xiaoying; Dai, Xinlu; Ni, Lijia; Chen, Baiji; Luo, Zhaofan; Yao, Yandan; Wu, Xiquan; Li, Hongyu; Huang, Songyin

2018-03-12

Medical laboratory staff are a high-risk population for colonization of Staphylococcus aureus (S. aureus) due to direct and dense contact with the pathogens; however, there is limited information about this colonization. This study sought to determine the prevalence and molecular characteristics of nasal colonization by S. aureus in medical laboratory staff in Guangzhou, southern China, and to compare the differences between microbiological laboratory (MLS) and non-microbiological laboratory (NMLS) staff. S. aureus colonization was assessed by nasal swab cultures from 434 subjects, including 130 MLSs and 304 NMLSs from 33 hospitals in Guangzhou. All S. aureus isolates underwent the antimicrobial susceptibility test, virulence gene detection and molecular typing. The overall prevalence of S. aureus carriage was 20.1% (87/434), which was higher in MLSs than in NMLSs (26.2% vs. 17.4%, P < 0.05), while the prevalence of Methicillin-resistant S. aureus (MRSA) was similar. Living with hospital staff was associated with S. aureus carriage. The majority of the isolates harboured various virulence genes, and those in MLSs appeared less resistant to antibiotics and more virulent than their counterparts. A total of 37 different spa types were detected; among these, t338, t437, t189 and t701 were the most frequently encountered types. T338 was the main spa type contributing to nasal colonization Methicillin-sensitive S. aureus (MSSA) (13.0%), and t437-SCCmec IV was predominant in MRSA isolates (40%). These findings provide insight into the risk factors, molecular epidemiology and virulence gene profiles of S. aureus nasal carriage among the medical laboratory staff in Guangzhou.

Molecular environmental geochemistry

NASA Astrophysics Data System (ADS)

O'Day, Peggy A.

1999-05-01

The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at

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.

Overview and challenges of molecular technologies in the veterinary microbiology laboratory.

PubMed

Cunha, Mónica V; Inácio, João

2015-01-01

Terrestrial, aquatic, and aerial animals, either domestic or wild, humans, and plants all face similar health threats caused by infectious agents. Multifaceted anthropic pressure caused by an increasingly growing and resource-demanding human population has affected biodiversity at all scales, from the DNA molecule to the pathogen, to the ecosystem level, leading to species declines and extinctions and, also, to host-pathogen coevolution processes. Technological developments over the last century have also led to quantic jumps in laboratorial testing that have highly impacted animal health and welfare, ameliorated animal management and animal trade, safeguarded public health, and ultimately helped to "secure" biodiversity. In particular, the field of molecular diagnostics experienced tremendous technical progresses over the last two decades that significantly have contributed to our ability to study microbial pathogens in the clinical and research laboratories. This chapter highlights the strengths, weaknesses, opportunities, and threats (or challenges) of molecular technologies in the framework of a veterinary microbiology laboratory, in view of the latest advances.

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

Microbiological and molecular characterization of Corynebacterium diphtheriae isolated in Algeria between 1992 and 2015.

PubMed

Benamrouche, N; Hasnaoui, S; Badell, E; Guettou, B; Lazri, M; Guiso, N; Rahal, K

2016-12-01

The objectives of this study were to undertake the microbiological and molecular characterization of Corynebacterium diphtheriae isolates collected in Algeria during epidemic and post-epidemic periods between 1992 and 2015. Microbiological characterization includes the determination of biotype and toxigenicity status using phenotypic and genotypic methods. Antimicrobial susceptibility was determined by the E-test method. Molecular characterization was performed by multi-locus sequence typing. In total, there were 157 cases of C. diphtheriae isolates, 127 in patients with respiratory diphtheria and 30 with ozena. Isolates with a mitis biotype were predominant (122 out of 157; 77.7%) followed by belfanti (28 out of 157; 17.8%) and gravis biotype (seven out of 157; 4.5%). Toxigenic isolates were predominant in the period 1992-2006 (74 out of 134) whereas in the period 2007-2015, only non-toxigenic isolates circulated (23 out of 23). All 157 isolates were susceptible to erythromycin, gentamicin, vancomycin and cotrimoxazole. Reduced susceptibility to penicillin G, cefotaxime, tetracycline and chloramphenicol was detected in 90 (57.3%), 88 (56.1%), 112 (71.3%) and 90 (57.3%) isolates, respectively. Multi-locus sequence typing analysis indicates that sequence type 116 (ST-116) was the most frequent, with 65 out of 100 isolates analysed, in particular during the epidemic period 1992-1999 (57 out of 65 isolates). In the post-epidemic period, 2000-2015, 13 different sequence types were isolated. All belfanti isolates (ten out of 100 isolates) belonged to closely related sequence types grouped in a phylogenetically distinct eBurst group and were collected exclusively in ozena cases. In conclusion, the epidemic period was associated with ST-116 while the post-epidemic period was characterized by more diversity. Belfanti isolates are grouped in a phylogenetically distinct clonal complex. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases

Environmental Microbiology Modules. Final Report.

ERIC Educational Resources Information Center

Walke, Raymond H.; Walke, Jayne G.

This publication is the result of a project to develop microbiology instructional materials for vocational college students. These materials are a series of self-paced modules. Each module includes a pre-test, an introduction and historical packet, an organizational packet to set the framework for in-depth study, one or more in-depth packets, a…

The Swiss Society of Microbiology: Small Bugs, Big Questions and Cool Answers.

PubMed

Greub, Gilbert; Holliger, Christof; Sanglard, Dominique; Schrenzel, Jacques; Thiel, Volker; Viollier, Patrick

2016-12-21

The Swiss Society for Microbiology (SSM) represents around 700 scientists working in the fields of medical (human and veterinary), microbial biotechnology as well as fundamental, environmental, and food microbiology. Five sections: Clinical Microbiology, Environmental Microbiology, Mycology, Prokaryotic Biology, and Virology reflects the main interests of the membership.

The case for biocentric microbiology.

PubMed

Aziz, Ramy Karam

2009-08-04

Microbiology is a relatively modern scientific discipline intended to objectively study microorganisms, including pathogens and nonpathogens. However, since its birth, this science has been negatively affected by anthropocentric convictions, including rational and irrational beliefs. Among these, for example, is the artificial separation between environmental and medical microbiology that weakens both disciplines. Anthropocentric microbiology also fails to properly answer questions concerning the evolution of microbial pathogenesis. Here, I argue that an exclusively biocentric microbiology is imperative for improving our understanding not only of the microbial world, but also of our own species, our guts, and the world around us.

Yeast Biofilm as a Bridge Between Medical and Environmental Microbiology Across Different Detection Techniques.

PubMed

Roscini, Luca; Vassiliou, Alice; Corte, Laura; Casagrande Pierantoni, Debora; Robert, Vincent; Tascini, Carlo; Mattana, Sara; Alunni Cardinali, Martina; Orfanos, Stylianos E; Fioretto, Daniele; Cardinali, Gianluigi

2018-03-01

Medical and environmental microbiology have two distinct, although very short, histories stemming, the first from the pioneering works of Sommelweiss, Pasteur, Lister and Koch, the second mainly from the studies of Bejerink and Winogradsky. These two branches of microbiology evolved and specialized separately producing distinct communities and evolving rather different approaches and techniques. The evidence accumulated in recent decades indicate that indeed most of the medically relevant microorganisms have a short circulation within the nosocomial environment and a larger one involving the external, i.e. non-nosocomial, and the hospital environments. This evidence suggests that the differences between approaches should yield to a convergent approach aimed at solving the increasing problem represented by infectious diseases for the increasingly less resistant human communities. Microbial biofilm is one of the major systems used by these microbes to resist the harsh conditions of the natural and anthropic environment, and the even worse ones related to medical settings. This paper presents a brief outline of the converging interest of both environmental and medical microbiology toward a better understanding of microbial biofilm and of the various innovative techniques that can be employed to characterize, in a timely and quantitative manner, these complex structures. Among these, micro-Raman along with micro-Brillouin offer high hopes of describing biofilms both at the subcellular and supercellular level, with the possibility of characterizing the various landscapes of the different biofilms. The possibility of adding a taxonomic identification of the cells comprising the biofilm is a complex aspect presenting several technical issues that will require further studies in the years to come.

Chemical and microbiological experimentation for development of environmental control and life support systems

NASA Technical Reports Server (NTRS)

Whitman, G. A.; Wilson, M. E.; Cole, H. E.; Traweek, M.

1992-01-01

Microbiological techniques are under study with a view to the identification of viable microorganisms in liquid cultures, improve the identification of stressed organisms, and determine the biocidal activity of iodine and other chemicals on isolates from recycled water. A quality-assurance program has been implemented to validate data employed in making decisions concerning engineering and human health and safety. Analytical laboratory refinements will strongly aid the development of environmental control and life-support systems.

[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.

The biochemistry and molecular biology of xenobiotic polymer degradation by microorganisms.

PubMed

Kawai, Fusako

2010-01-01

Research on microbial degradation of xenobiotic polymers has been underway for more than 40 years. It has exploited a new field not only in applied microbiology but also in environmental microbiology, and has greatly contributed to polymer science by initiating the design of biodegradable polymers. Owing to the development of analytical tools and technology, molecular biological and biochemical advances have made it possible to prospect for degrading microorganisms in the environment and to determine the mechanisms involved in biodegradation when xenobiotic polymers are introduced into the environment and are exposed to microbial attack. In this review, the molecular biological and biochemical aspects of the microbial degradation of xenobiotic polymers are summarized, and possible applications of potent microorganisms, enzymes, and genes in environmental biotechnology are suggested.

The study on molecular structure and microbiological activity of alkali metal 3-hydroxyphenylycetates

NASA Astrophysics Data System (ADS)

Samsonowicz, M.; Regulska, E.; Kowczyk-Sadowy, M.; Butarewicz, A.; Lewandowski, W.

2017-10-01

The biological activity of chemical compounds depends on their molecular structure. In this paper molecular structure of 3-hydroxyphenylacetates in comparison to 3-hydroxyphenylacetic acid was studied. FT-IR, FT-Raman and NMR spectroscopy and density functional theory (DFT) calculations was used. The B3LYP/6-311++G(d,p) hybrid functional method was used to calculate optimized geometrical structures of studied compounds. The Mulliken, APT, MK, ChelpG and NBO atomic charges as well as dipole moment and energy values were calculated. Theoretical chemical shifts in NMR spectra and the wavenumbers and intensities of the bands in vibrational spectra were analyzed. Calculated parameters were compared to experimental characteristic of studied compounds. Microbiological analysis of studied compounds was performed relative to: Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli and Klebsiella oxytoca. The relationship between spectroscopic and structure parameters of studied compounds in regard to their activity was analyzed.

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®

Replication, lies and lesser-known truths regarding experimental design in environmental microbiology.

PubMed

Lennon, Jay T

2011-06-01

A recent analysis revealed that most environmental microbiologists neglect replication in their science (Prosser, 2010). Of all peer-reviewed papers published during 2009 in the field's leading journals, slightly more than 70% lacked replication when it came to analyzing microbial community data. The paucity of replication is viewed as an 'endemic' and 'embarrassing' problem that amounts to 'bad science', or worse yet, as the title suggests, lying (Prosser, 2010). Although replication is an important component of experimental design, it is possible to do good science without replication. There are various quantitative techniques - some old, some new - that, when used properly, will allow environmental microbiologists to make strong statistical conclusions from experimental and comparative data. Here, I provide examples where unreplicated data can be used to test hypotheses and yield novel information in a statistically robust manner. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

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 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

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.

The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

PubMed

Moreno, Inmaculada; Cicinelli, Ettore; Garcia-Grau, Iolanda; Gonzalez-Monfort, Marta; Bau, Davide; Vilella, Felipe; De Ziegler, Dominique; Resta, Leonardo; Valbuena, Diana; Simon, Carlos

2018-06-01

, concordance was present in 37 samples (22 double positive and 15 double negative), a matching rate of 56.92%. When cases of potential contamination and/or noncultivable bacteria were considered, the accuracy increased to 66.15%. Of these 65 patients, only 27 patients had consistent histological + hysteroscopic diagnosis, revealing 58.64% of nonconcordant results. Only 13 of 65 patients (20%) had consistent histology + hysteroscopy + microbial culture results. In these cases, the molecular microbiology matched in 10 cases showing a diagnostic accuracy of 76.92%. Interestingly, the molecular microbiology confirmed over half of the isolated pathogens and provided additional detection of nonculturable microorganisms. These results were confirmed by the microbiome assessed by next-generation sequencing. In the endometrial samples with concordant histology + hysteroscopy + microbial culture results, the molecular microbiology diagnosis demonstrates 75% sensitivity, 100% specificity, 100% positive and 25% negative predictive values, and 0% false-positive and 25% false-negative rates. The molecular microbiology method describe herein is a fast and inexpensive diagnostic tool that allows for the identification of culturable and nonculturable endometrial pathogens associated with chronic endometritis. The results obtained were similar to all 3 classic diagnostic methods together with a degree of concordance of 76.92% providing an opportunity to improve the clinical management of infertile patients with a risk of experiencing this ghost endometrial pathology. Copyright © 2018 Elsevier Inc. All rights reserved.

MOLECULAR DIAGNOSTICS - ANOTHER PIECE IN THE ENVIRONMENTAL PUZZLE

EPA Science Inventory

Molecular biology offers sensitive and expedient tools for the detection of exposure to environmental stressors. Molecular approaches provide the means for detection of the "first cellular event(s)" in response to environmental changes-specifically, immediate changes in gene expr...

Microbiology Made Relevant

ERIC Educational Resources Information Center

Cronholm, Lois S.; Metz, Mildred C.

1976-01-01

Described are two hospital-based laboratory exercises which helped students perceive the relationship between the principles of microbiology and the practice of nursing. The exercises involved an environmental study focusing on problems of nosocomial infection and a study of patients hospitalized with infectious diseases. (Author/MS)

Microbiology operations and facilities aboard restructured Space Station Freedom

NASA Technical Reports Server (NTRS)

Cioletti, Louis A.; Mishra, S. K.; Pierson, Duane L.

1992-01-01

With the restructure and funding changes for Space Station Freedom, the Environmental Health System (EHS)/Microbiology Subsystem revised its scheduling and operational requirements for component hardware. The function of the Microbiology Subsystem is to monitor the environmental quality of air, water, and internal surfaces and, in part, crew health on board Space Station. Its critical role shall be the identification of microbial contaminants in the environment that may cause system degradation, produce unsanitary or pathogenic conditions, or reduce crew and mission effectiveness. EHS/Microbiology operations and equipment shall be introduced in concert with a phased assembly sequence, from Man Tended Capability (MTC) through Permanently Manned Capability (PMC). Effective Microbiology operations and subsystem components will assure a safe, habitable, and useful spacecraft environment for life sciences research and long-term manned exploration.

Kinetic Modeling of Microbiological Processes

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

Liu, Chongxuan; Fang, Yilin

Kinetic description of microbiological processes is vital for the design and control of microbe-based biotechnologies such as waste water treatment, petroleum oil recovery, and contaminant attenuation and remediation. Various models have been proposed to describe microbiological processes. This editorial article discusses the advantages and limiation of these modeling approaches in cluding tranditional, Monod-type models and derivatives, and recently developed constraint-based approaches. The article also offers the future direction of modeling researches that best suit for petroleum and environmental biotechnologies.

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

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.

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

MALDI-TOF-mass spectrometry applications in clinical microbiology.

PubMed

Seng, Piseth; Rolain, Jean-Marc; Fournier, Pierre Edouard; La Scola, Bernard; Drancourt, Michel; Raoult, Didier

2010-11-01

MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost-effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.

Control of metallic corrosion through microbiological route.

PubMed

Maruthamuthu, S; Ponmariappan, S; Mohanan, S; Palaniswamy, N; Palaniappan, R; Rengaswamy, N S

2003-09-01

Involvement of biofilm or microorganisms in corrosion processes is widely acknowledged. Although majority of the studies on microbiologically induced corrosion (MIC) have concentrated on aerobic/anaerobic bacteria. There are numerous aerobic bacteria, which could hinder the corrosion process. The microbiologically produced exopolymers provide the structural frame work for the biofilm. These polymers combine with dissolved metal ions and form organometallic complexes. Generally heterotrophic bacteria contribute to three major processes: (i) synthesis of polymers (ii) accumulation of reserve materials like poly-beta-hydroxy butrate (iii) production of high molecular weight extracellular polysaccharides. Poly-beta-hydroxy butyrate is a polymer of D(-)beta-hydroxy butrate and has a molecular weight between 60,000 and 2,50,000. Some extracellular polymers also have higher molecular weights. It seems that higher molecular weight polymer acts as biocoating. In the present review, role of biochemistry on corrosion inhibition and possibilities of corrosion inhibition by various microbes are discussed. The role of bacteria on current demand during cathodic protection is also debated. In addition, some of the significant contributions made by CECRI in this promising area are highlighted.

Microbiological Detection Systems for Molecular Analysis of Environmental Water and Soil Samples

EPA Science Inventory

Multiple detection systems are being targeted to track various species and genotypes of pathogens found in environmental samples with the overreaching goal of developing analytical separation and detection techniques for Salmonella enterica Serovars Typhi, Cryptosporidium parvum,...

Teaching microbiology to undergraduate students in the humanities and the social sciences.

PubMed

Oren, Aharon

2015-10-01

This paper summarizes my experiences teaching a 28-hour course on the bacterial world for undergraduate students in the humanities and the social sciences at the Hebrew University of Jerusalem. This course was offered in the framework of a program in which students must obtain credit points for courses offered by other faculties to broaden their education. Most students had little biology in high school and had never been exposed to the basics of chemistry. Using a historical approach, highlighting the work of pioneers such as van Leeuwenhoek, Koch, Fleming, Pasteur, Winogradsky and Woese, I covered a broad area of general, medical, environmental and evolutionary microbiology. The lectures included basic concepts of organic and inorganic chemistry necessary to understand the principles of fermentations and chemoautotrophy, and basic molecular biology to explain biotechnology using transgenic microorganisms and molecular phylogeny. Teaching the basics of microbiology to intelligent students lacking any background in the natural sciences was a rewarding experience. Some students complained that, in spite of my efforts, basic concepts of chemistry remained beyond their understanding. But overall the students' evaluation showed that the course had achieved its goal. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Syndromic Panel-Based Testing in Clinical Microbiology.

PubMed

Ramanan, Poornima; Bryson, Alexandra L; Binnicker, Matthew J; Pritt, Bobbi S; Patel, Robin

2018-01-01

The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections. While these panel-based assays have the clear advantages of a rapid turnaround time and the detection of a large number of microorganisms and promise to improve health care, they present certain challenges, including cost and the definition of ideal test utilization strategies (i.e., optimal ordering) and test interpretation. Copyright © 2017 American Society for Microbiology.

A review of current and future molecular diagnostic tests for use in the microbiology laboratory.

PubMed

Jannes, Geert; De Vos, Daniel

2006-01-01

Nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratories. Similar to conventional tests, the first-generation deoxyribonucleic acid assays determined only a single analyte. Recent improvements in detection technologies have paved the way for the development of multiparameter assays using macroarrays or micro-arrays, while the introduction of closed-tube real-time polymerase chain reaction systems has resulted in the development of rapid microbial diagnostics with a reduced contamination risk. The use of these new molecular technologies is not restricted to detection and identification of microbial pathogens but also can be used for genotyping, allowing one to determine antibiotic resistance or to perform microbial fingerprinting.

Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

PubMed Central

Cazanave, Charles; Greenwood-Quaintance, Kerryl E.; Hanssen, Arlen D.; Karau, Melissa J.; Schmidt, Suzannah M.; Gomez Urena, Eric O.; Mandrekar, Jayawant N.; Osmon, Douglas R.; Lough, Lindsay E.; Pritt, Bobbi S.; Steckelberg, James M.

2013-01-01

We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround time. We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, and we compared the results to those with sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty. We studied 434 subjects with knee (n = 272) or hip (n = 162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, of sonicate fluid culture, and of PCR were 70.1, 72.9, and 77.1%, respectively. Specificities were 97.9, 98.3, and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (P = 0.04). PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection and provides same-day PJI diagnosis with definition of microbiology. The high assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure. PMID:23658273

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…

Assessment of chloroethene biodegradation in the subsurface by microbiological, molecular and isotopic tools

NASA Astrophysics Data System (ADS)

Schmidt, K. R.; Kranzioch, I.; Heidinger, M.; Ertl, S.; Tiehm, A.

2012-04-01

A multiple lines of evidence approach to assess the biodegradation potential of contaminated sites includes - site investigation analysing pollutant distribution (compounds, concentrations, isotopic composition) and hydrochemical conditions (redox conditions) - determination of the presence of pollutant degrading bacteria in the field by microbiological (most probable number, MPN) and molecular (polymerase chain reaction, PCR) methods - analysis of degradation processes in the laboratory by microcosms with determination of site specific isotopic enrichment factors enabling the quantification of biodegradation processes in the field. Results will be shown of the application of such a multiple lines of evidence approach at a chloroethene-contaminated site in Frankenthal, Germany. In anaerobic groundwater microcosms, reductive transformation of perchloroethene (PCE) and trichloroethene (TCE) was observed to mainly proceed to cis-1,2-dichloroethene (cDCE). 16S-PCR analysis showed a wide distribution of halorespiring bacteria capable of PCE degradation to cDCE, whereas Dehalococcoides - the only organisms described so far being able of complete reductive dechlorination down to ethene - was only found in one groundwater sample. Aerobic microcosms showed metabolic degradation of the lower chlorinated compounds cDCE and vinyl chloride (VC). Co-metabolic degradation of cDCE with VC as auxiliary substrate occurred, too. Significant stable carbon isotope fractionation was observed during anaerobic degradation of PCE and TCE as well as during aerobic degradation of cDCE and VC. Compiling the results of the different assessment methods, sequential dechlorination - PCE/TCE to cDCE anaerobically and cDCE to CO2 aerobically - was demonstrated to occur at the Frankenthal site. The extent of biodegradation in the field was calculated based on the enrichment factors determined in microcosms and the 13C-isotopic composition of the contaminants on site. The application of molecular

Trends in wine microbiology.

PubMed

Ramón, D

1997-12-01

During the last few years many winemakers have started to use pure Saccharomyces cerevisiae strains, frequently isolated from their own geographical regions, to produce wines of more reproductable quality. This microbiological simplification has opened the way for the genetic modification of wine yeast strains. This review concerns the application of molecular techniques in oenology, not only from the point of view of the construction of recombinant strains but also for the study of the population dynamics of wine fermentations.

Microbiologic Testing for 503A Sterile-Compounding Pharmacies.

PubMed

Mixon, William; Roth, Abby

2017-01-01

Compounding pharmacists must ensure that the sterile preparations they dispense are free of microbiologic contamination. Working in a cleanroom under controlled conditions (proper differential air pressure, temperature, and humidity; acceptable levels of viable and nonviable airborne particles and surface counts, etc.) and testing the efficacy of cleaning and disinfecting practices via environmental monitoring (viable-air and surface testing, glove-fingertip-thumb testing, etc.) are essential to preparing contamination-free medications. Sterile-compounding pharmacists must understand how to monitor their cleanroom environment and, if they perform testing in house, to interpret the results of simple microbiologic tests (a skill helpful even when tests are outsourced to a contract laboratory). In this article, which pertains to 503A sterile compounding, and is based on the current version of United States Pharmacopeia (USP) Chapter <797>, basic concepts in microbiology and the microbial tests that can be performed and interpreted in house and those that must be outsourced are discussed. Streamlining communication with contract laboratory personnel is reviewed. Requirements for an inhouse microbiology laboratory are presented, and the advantages and disadvantages of inhouse and outsourced testing are examined. A list of suggested reading is provided for easy reference. In a subsequent article, environmental monitoring and analysis will be addressed in detail. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

Changing needs, opportunities and constraints for the 21st century microbiology laboratory.

PubMed

Van Eldere, J

2005-04-01

Clinical microbiologists and microbiology laboratories are experiencing changes due to evolving views on 'healthcare delivery' as an economic activity, due to changes in the medical environment and the demographics of the workforce, and technical evolution. Cost-effectiveness of laboratory procedures has been achieved through consolidation and integration of laboratories. Consolidation offers economy of scale and reduction in numbers of on-site staff, but also leads to separation of microbiologists from their clinical colleagues. Integration puts different laboratory disciplines under a single management, and leads to reorganisation of laboratories along common work-lines. Cost-savings combined with on-site availability of laboratories are achieved at the expense of a reduction in the influence of microbiologists in the daily running of the laboratory. Medically, there is growing emphasis on evidence-based diagnostics. Because of time-delays inherent in culturing, microbiology through rapid testing is mandatory. There is an increasing shortage in Europe and the USA of trained microbiology laboratory technicians and microbiologists. This reinforces the trend towards more automation and integration. Technological advances, particularly in molecular diagnostics, offer the possibility of rapid reporting and improvement of the impact of clinical microbiology on patient management. Molecular tests, however, fit perfectly the concept of an integrated laboratory and may further loosen the link between microbiologist and microbiology tests. The challenge for clinical microbiology will be to use new techniques to improve its cost-effectiveness and impact on infectious disease management. The future organisation of microbiology laboratories must support this but is itself of secondary importance. The training of future microbiologist must prepare them for this changing environment.

[Laboratory unification: advantages and disadvantages for clinical microbiology].

PubMed

Andreu, Antonia; Matas, Lurdes

2010-10-01

This article aims to reflect on which areas or tasks of microbiology laboratories could be unified with those of clinical biochemistry, hematology, immunology or pathology laboratories to benefit patients and the health system, as well as the areas that should remain independent since their amalgamation would not only fail to provide a benefit but could even jeopardize the quality of microbiological diagnosis, and consequently patient care. To do this, the distinct analytic phases of diagnosis are analyzed, and the advantages and disadvantages of amalgamation are evaluated in each phase. The pros and cons of the unification of certain areas such as the computer system, occupational risk units, customer service, purchasing logistics, and materials storage, etc, are also discussed. Lastly, the effect of unification on urgent microbiology diagnosis is analyzed. Microbiological diagnosis should be unique. The microbiologist should perform an overall evaluation of the distinct techniques used for a particular patient, both those that involve direct diagnosis (staining, culture, antigen detection techniques or molecular techniques) and indirect diagnosis (antibody detection). Moreover, the microbiology laboratory should be independent, with highly trained technicians and specialists in microbiology that provide added value as experts in infection and as key figures in the process of establishing a correct etiological diagnosis. Copyright © 2010 Elsevier España S.L. All rights reserved.

Molecular analysis of point-of-use municipal drinking water microbiology.

PubMed

Holinger, Eric P; Ross, Kimberly A; Robertson, Charles E; Stevens, Mark J; Harris, J Kirk; Pace, Norman R

2014-02-01

Little is known about the nature of the microbiology in tap waters delivered to consumers via public drinking water distribution systems (DWDSs). In order to establish a broader understanding of the microbial complexity of public drinking waters we sampled tap water from seventeen different cities between the headwaters of the Arkansas River and the mouth of the Mississippi River and determined the bacterial compositions by pyrosequencing small subunit rRNA genes. Nearly 98% of sequences observed among all systems fell into only 5 phyla: Proteobacteria (35%), Cyanobacteria (29%, including chloroplasts), Actinobacteria (24%, of which 85% were Mycobacterium spp.), Firmicutes (6%), and Bacteroidetes (3.4%). The genus Mycobacterium was the most abundant taxon in the dataset, detected in 56 of 63 samples (16 of 17 cities). Among the more rare phylotypes, considerable variation was observed between systems, and was sometimes associated with the type of source water, the type of disinfectant, or the concentration of the environmental pollutant nitrate. Abundant taxa (excepting Cyanobacteria and chloroplasts) were generally similar from system to system, however, regardless of source water type or local land use. The observed similarity among the abundant taxa between systems may be a consequence of the selective influence of chlorine-based disinfection and the common local environments of DWDS and premise plumbing pipes. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

2001 Gordon Research Conference on Applied and Environmental Microbiology. Final progress report [agenda and attendee list

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

Drake, Harold

2001-07-26

The Gordon Research Conference on Applied and Environmental Microbiology was held at Connecticut College, New London, Connecticut, July 22-27, 2001. The conference was attended by 121 participants. The attendees represented the spectrum of endeavor in this field, coming from academia, industry, and government laboratories, and included US and foreign scientists, senior researchers, young investigators, and students. Emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate discussion about the key issues in the field today. Session topics included the following: Environmental and applied genomics, Cell-to-cell signalingmore » and multicellular behavior, Emerging technologies and methods, Novel metabolisms and ecosystems, Directed evolution of enzymes and pathways, Symbiotic and trophic relationships, Synthesis and application of novel biopolymers, and Microbes at the oxic-anoxic interface. There was also a special lecture titled ''Under the umbrella of the big tree: microbial biology into the 21st century.''« less

Planned Environmental Microbiology Aspects of Future Lunar and Mars Missions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Castro, Victoria A.; Pierson, Duane L.

2006-01-01

With the establishment of the Constellation Program, NASA has initiated efforts designed similar to the Apollo Program to return to the moon and subsequently travel to Mars. Early lunar sorties will take 4 crewmembers to the moon for 4 to 7 days. Later missions will increase in duration up to 6 months as a lunar habitat is constructed. These missions and vehicle designs are the forerunners of further missions destined for human exploration of Mars. Throughout the planning and design process, lessons learned from the International Space Station (ISS) and past programs will be implemented toward future exploration goals. The standards and requirements for these missions will vary depending on life support systems, mission duration, crew activities, and payloads. From a microbiological perspective, preventative measures will remain the primary techniques to mitigate microbial risk. Thus, most of the effort will focus on stringent preflight monitoring requirements and engineering controls designed into the vehicle, such as HEPA air filters. Due to volume constraints in the CEV, in-flight monitoring will be limited for short-duration missions to the measurement of biocide concentration for water potability. Once long-duration habitation begins on the lunar surface, a more extensive environmental monitoring plan will be initiated. However, limited in-flight volume constraints and the inability to return samples to Earth will increase the need for crew capabilities in determining the nature of contamination problems and method of remediation. In addition, limited shelf life of current monitoring hardware consumables and limited capabilities to dispose of biohazardous trash will drive flight hardware toward non-culture based methodologies, such as hardware that rapidly distinguishes biotic versus abiotic surface contamination. As missions progress to Mars, environmental systems will depend heavily on regeneration of air and water and biological waste remediation and

Critical Readiness Review EHS Water Quality and Microbiology

NASA Technical Reports Server (NTRS)

Woo, Cindy

2010-01-01

Presentation reviews the status in reference to the Environmental, Health and Safety (EHS) of the water quality and microbiology for the International Space Station. It includes information about crew training, hardware delivery, and those items that will be returned for study.

The evolution of teaching and learning medical microbiology and infectious diseases at NUS.

PubMed

Taylor, M B; Chow, V T K

2005-07-01

Infectious diseases were rife during the early years of the Singapore Medical College, which was established in 1905. The current Department of Microbiology in the National University of Singapore (NUS) has its historical roots in the Departments of Bacteriology and Parasitology, which were established in 1925 and 1950 respectively. With the achievements since its inception, and with its present research focus on Infectious Diseases, Immunology, Applied and Environmental Microbiology, it is poised to face the microbiological challenges of the 21st century. Over the decades, the structure of the medical microbiology course in NUS has modernised, culminating in the current emphasis on its practical utility in clinical practice. Coordinated by the Department of Microbiology, the Microbiology and Infectious Diseases module and the Immunology module both adopt integrated multidisciplinary approaches that aim to introduce students to the language and fundamental concepts in microbiology, infectious diseases and immunology.

[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.

Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh, Saudi Arabia.

PubMed

AlWakeel, Suaad S

2017-09-01

This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis , alpha-hemolytic streptococci, Staphylococcus hominis , coagulase-negative staphylococci, Leuconostoc mesenteroides , Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (<60% sensitivity) to the antibiotics ampicillin, erythromycin, clarithromycin and norfloxacin were observed. Ninety-seven percent similarity to the microbial bank species was noted when the isolates were compared to it. Most hematological indices recorded were within the normal range. In conclusion, exposure to toxic fumes and compounds within fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

[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.

Microbiology and Moisture Uptake of Desert Soils

NASA Astrophysics Data System (ADS)

Kress, M. E.; Bryant, E. P.; Morgan, S. W.; Rech, S.; McKay, C. P.

2005-12-01

We have initiated an interdisciplinary study of the microbiology and water content of desert soils to better understand microbial activity in extreme arid environments. Water is the one constituent that no organism can live without; nevertheless, there are places on Earth with an annual rainfall near zero that do support microbial ecosystems. These hyperarid deserts (e.g. Atacama and the Antarctic Dry Valleys) are the closest terrestrial analogs to Mars, which is the subject of future exploration motivated by the search for life beyond Earth. We are modeling the moisture uptake by soils in hyperarid environments to quantify the environmental constraints that regulate the survival and growth of micro-organisms. Together with the studies of moisture uptake, we are also characterizing the microbial population in these soils using molecular and culturing methods. We are in the process of extracting DNA from these soils using MoBio extraction kits. This DNA will be used as a template to amplify bacterial and eukaryotic ribosomal DNA to determine the diversity of the microbial population. We also have been attempting to determine the density of organisms by culturing on one-half strength R2A agar. The long-range goal of this research is to identify special adaptations of terrestrial life that allow them to inhabit extreme arid environments, while simultaneously quantifying the environmental parameters that enforce limits on these organisms' growth and survival.

The future of predictive microbiology: strategic research, innovative applications and great expectations.

PubMed

McMeekin, Tom; Bowman, John; McQuestin, Olivia; Mellefont, Lyndal; Ross, Tom; Tamplin, Mark

2008-11-30

This paper considers the future of predictive microbiology by exploring the balance that exists between science, applications and expectations. Attention is drawn to the development of predictive microbiology as a sub-discipline of food microbiology and of technologies that are required for its applications, including a recently developed biological indicator. As we move into the era of systems biology, in which physiological and molecular information will be increasingly available for incorporation into models, predictive microbiologists will be faced with new experimental and data handling challenges. Overcoming these hurdles may be assisted by interacting with microbiologists and mathematicians developing models to describe the microbial role in ecosystems other than food. Coupled with a commitment to maintain strategic research, as well as to develop innovative technologies, the future of predictive microbiology looks set to fulfil "great expectations".

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.

A Critical Assessment of Microbiological Biogas to Biomethane Upgrading Systems.

PubMed

Rittmann, Simon K-M R

2015-01-01

Microbiological biogas upgrading could become a promising technology for production of methane (CH(4)). This is, storage of irregular generated electricity results in a need to store electricity generated at peak times for use at non-peak times, which could be achieved in an intermediate step by electrolysis of water to molecular hydrogen (H(2)). Microbiological biogas upgrading can be performed by contacting carbon dioxide (CO(2)), H(2) and hydrogenotrophic methanogenic Archaea either in situ in an anaerobic digester, or ex situ in a separate bioreactor. In situ microbiological biogas upgrading is indicated to require thorough bioprocess development, because only low volumetric CH(4) production rates and low CH(4) fermentation offgas content have been achieved. Higher volumetric production rates are shown for the ex situ microbiological biogas upgrading compared to in situ microbiological biogas upgrading. However, the ex situ microbiological biogas upgrading currently suffers from H(2) gas liquid mass transfer limitation, which results in low volumetric CH(4) productivity compared to pure H(2)/CO(2) conversion to CH(4). If waste gas utilization from biological and industrial sources can be shown without reduction in volumetric CH(4) productivity, as well as if the aim of a single stage conversion to a CH(4) fermentation offgas content exceeding 95 vol% can be demonstrated, ex situ microbiological biogas upgrading with pure or enrichment cultures of methanogens could become a promising future technology for almost CO(2)-neutral biomethane production.

Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives.

PubMed

Jung, Jaejoon; Park, Woojun

2015-03-01

Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.

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

Design of a Tablet Computer App for Facilitation of a Molecular Blood Culture Test in Clinical Microbiology and Preliminary Usability Evaluation.

PubMed

Samson, Lasse L; Pape-Haugaard, Louise; Meltzer, Michelle C; Fuchs, Martin; Schønheyder, Henrik C; Hejlesen, Ole

2016-03-18

User mobility is an important aspect of the development of clinical information systems for health care professionals. Mobile phones and tablet computers have obtained widespread use by health care professionals, offering an opportunity for supporting the access to patient information through specialized applications (apps) while supporting the mobility of the users. The use of apps for mobile phones and tablet computers may support workflow of complex tasks, for example, molecular-based diagnostic tests in clinical microbiology. Multiplex Blood Culture Test (MuxBCT) is a molecular-based diagnostic test used for rapid identification of pathogens in positive blood cultures. To facilitate the workflow of the MuxBCT, a specialized tablet computer app was developed as an accessory to the diagnostic test. The app aims to reduce the complexity of the test by step-by-step guidance of microscopy and to assist users in reaching an exact bacterial or fungal diagnosis based on blood specimen observations and controls. Additionally, the app allows for entry of test results, and communication thereof to the laboratory information system (LIS). The objective of the study was to describe the design considerations of the MuxBCT app and the results of a preliminary usability evaluation. The MuxBCT tablet app was developed and set up for use in a clinical microbiology laboratory. A near-live simulation study was conducted in the clinical microbiology laboratory to evaluate the usability of the MuxBCT app. The study was designed to achieve a high degree of realism as participants carried out a scenario representing the context of use for the MuxBCT app. As the MuxBCT was under development, the scenario involved the use of molecular blood culture tests similar to the MuxBCT for identification of microorganisms from positive blood culture samples. The study participants were observed, and their interactions with the app were recorded. After the study, the participants were debriefed to

Design of a Tablet Computer App for Facilitation of a Molecular Blood Culture Test in Clinical Microbiology and Preliminary Usability Evaluation

PubMed Central

Pape-Haugaard, Louise; Meltzer, Michelle C; Fuchs, Martin; Schønheyder, Henrik C; Hejlesen, Ole

2016-01-01

Background User mobility is an important aspect of the development of clinical information systems for health care professionals. Mobile phones and tablet computers have obtained widespread use by health care professionals, offering an opportunity for supporting the access to patient information through specialized applications (apps) while supporting the mobility of the users. The use of apps for mobile phones and tablet computers may support workflow of complex tasks, for example, molecular-based diagnostic tests in clinical microbiology. Multiplex Blood Culture Test (MuxBCT) is a molecular-based diagnostic test used for rapid identification of pathogens in positive blood cultures. To facilitate the workflow of the MuxBCT, a specialized tablet computer app was developed as an accessory to the diagnostic test. The app aims to reduce the complexity of the test by step-by-step guidance of microscopy and to assist users in reaching an exact bacterial or fungal diagnosis based on blood specimen observations and controls. Additionally, the app allows for entry of test results, and communication thereof to the laboratory information system (LIS). Objective The objective of the study was to describe the design considerations of the MuxBCT app and the results of a preliminary usability evaluation. Methods The MuxBCT tablet app was developed and set up for use in a clinical microbiology laboratory. A near-live simulation study was conducted in the clinical microbiology laboratory to evaluate the usability of the MuxBCT app. The study was designed to achieve a high degree of realism as participants carried out a scenario representing the context of use for the MuxBCT app. As the MuxBCT was under development, the scenario involved the use of molecular blood culture tests similar to the MuxBCT for identification of microorganisms from positive blood culture samples. The study participants were observed, and their interactions with the app were recorded. After the study, the

[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.

Clinical microbiology informatics.

PubMed

Rhoads, Daniel D; Sintchenko, Vitali; Rauch, Carol A; Pantanowitz, Liron

2014-10-01

The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

One Small Step for the Gram Stain, One Giant Leap for Clinical Microbiology.

PubMed

Thomson, Richard B

2016-06-01

The Gram stain is one of the most commonly performed tests in the clinical microbiology laboratory, yet it is poorly controlled and lacks standardization. It was once the best rapid test in microbiology, but it is no longer trusted by many clinicians. The publication by Samuel et al. (J. Clin. Microbiol. 54:1442-1447, 2016, http://dx.doi.org/10.1128/JCM.03066-15) is a start for those who want to evaluate and improve Gram stain performance. In an age of emerging rapid molecular results, is the Gram stain still relevant? How should clinical microbiologists respond to the call to reduce Gram stain error rates? Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Communicating Microbiology Concepts from Multiple Contexts through Poster Presentations.

PubMed

Gruss, Amy Borello

2018-01-01

Accredited environmental engineering degrees require graduates to be able to apply their scholarship to concepts of professional practice and design. This transferable skill of relating what you learn in one setting to another situation is vital for all professions, not just engineering. A course project involving designing and presenting a professional poster was implemented to enhance student mastery in Environmental Engineering Microbiology while also developing communication and transferable skills vital for all majors. Students were asked to read a contemporary non-fiction book relating to microbiology and expand upon the book's thesis by integrating course content, news articles, and peer-reviewed journal articles. They then were required to present this information in class using a professional poster. Students felt the project allowed them to synthesize and organize information, analyze ideas, and integrate ideas from various sources. These transferable skills are vital for students and professionals alike to be able to communicate advanced information and master a topic.

IPMP 2013 - A comprehensive data analysis tool for predictive microbiology

USDA-ARS?s Scientific Manuscript database

Predictive microbiology is an area of applied research in food science that uses mathematical models to predict the changes in the population of pathogenic or spoilage microorganisms in foods undergoing complex environmental changes during processing, transportation, distribution, and storage. It f...

Molecular ecological network analyses.

PubMed

Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng; He, Zhili; Luo, Feng; Zhou, Jizhong

2012-05-30

-accessible now (http://ieg2.ou.edu/MENA). The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

Microbiological aspects of clean room technology as applied to surgery, with special reference to unidirectional airflow systems

NASA Technical Reports Server (NTRS)

Wardle, M. D.

1974-01-01

The microbiological aspects of clean room technology as applied to surgery were reviewed. The following pertinent subject areas were examined: (1) clean room technology per se and its utilization for surgery, (2) microbiological monitoring of the clean room surgical environment, (3) clean rooms and their impact on operating room environmental microbiology, and (4) the effect of the technology on surgical wound infection rates. Conclusions were drawn for each topic investigated.

The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata).

PubMed

Raftos, D A; Melwani, A R; Haynes, P A; Muralidharan, S; Birch, G F; Amaral, V; Thompson, E L; Taylor, D A

2016-09-14

This review describes our recent work on environmental stress in Sydney rock oysters, focusing on the identification of molecular biomarkers for ecotoxicological analysis. We begin by describing the environmental pressures facing coastal estuaries in Australia, with particular reference to Sydney Harbour. After providing that context, we summarise our transcriptional and proteomic analyses of Sydney rock oysters responding to chemical contamination and other forms of environmental stress. This work has shown that the intracellular processes of oysters are highly responsive to environmental threats. Our data agree with the broader literature, which suggests that there is a highly conserved intracellular stress response in oysters involving a limited number of biological processes. We conclude that many effective molecular markers for environmental biomonitoring are likely to lie within these biological pathways.

Look@NanoSIMS--a tool for the analysis of nanoSIMS data in environmental microbiology.

PubMed

Polerecky, Lubos; Adam, Birgit; Milucka, Jana; Musat, Niculina; Vagner, Tomas; Kuypers, Marcel M M

2012-04-01

We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Clinical Microbiology Informatics

PubMed Central

Sintchenko, Vitali; Rauch, Carol A.; Pantanowitz, Liron

2014-01-01

SUMMARY The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future. PMID:25278581

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

Predictive microbiology: Quantitative science delivering quantifiable benefits to the meat industry and other food industries.

PubMed

McMeekin, T A

2007-09-01

Predictive microbiology is considered in the context of the conference theme "chance, innovation and challenge", together with the impact of quantitative approaches on food microbiology, generally. The contents of four prominent texts on predictive microbiology are analysed and the major contributions of two meat microbiologists, Drs. T.A. Roberts and C.O. Gill, to the early development of predictive microbiology are highlighted. These provide a segue into R&D trends in predictive microbiology, including the Refrigeration Index, an example of science-based, outcome-focussed food safety regulation. Rapid advances in technologies and systems for application of predictive models are indicated and measures to judge the impact of predictive microbiology are suggested in terms of research outputs and outcomes. The penultimate section considers the future of predictive microbiology and advances that will become possible when data on population responses are combined with data derived from physiological and molecular studies in a systems biology approach. Whilst the emphasis is on science and technology for food safety management, it is suggested that decreases in foodborne illness will also arise from minimising human error by changing the food safety culture.

Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology.

PubMed

Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K P; Woo, Patrick C Y

2015-10-22

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10-49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n=2), Pichia (Candida) norvegensis (n=2), Candida tropicalis (n=1) and Saccharomyces cerevisiae (n=1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study.

Salty Microbiology

ERIC Educational Resources Information Center

Schneegurt, Mark A.; Wedel, Adrianne N.; Pokorski, Edward W.

2004-01-01

Using microbiology activities in the classroom is an effective way for teachers to address National Standards in the life sciences. However, common microbiology activities that involve swabbing doorknobs and hands are too risky due to the likelihood of culturing human pathogens. In addition, making sterile media and maintaining sterile conditions…

Communicating Microbiology Concepts from Multiple Contexts through Poster Presentations †

PubMed Central

2018-01-01

Accredited environmental engineering degrees require graduates to be able to apply their scholarship to concepts of professional practice and design. This transferable skill of relating what you learn in one setting to another situation is vital for all professions, not just engineering. A course project involving designing and presenting a professional poster was implemented to enhance student mastery in Environmental Engineering Microbiology while also developing communication and transferable skills vital for all majors. Students were asked to read a contemporary non-fiction book relating to microbiology and expand upon the book’s thesis by integrating course content, news articles, and peer-reviewed journal articles. They then were required to present this information in class using a professional poster. Students felt the project allowed them to synthesize and organize information, analyze ideas, and integrate ideas from various sources. These transferable skills are vital for students and professionals alike to be able to communicate advanced information and master a topic. PMID:29904521

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.

Project environmental microbiology as related to planetary quarantine

NASA Technical Reports Server (NTRS)

Pflug, I. J.

1974-01-01

Microbiological analyses of soil particles allow for the following conclusions: (1) there is a considerable range in the values of aerobic, mesophilic microbial counts associated with different size soil fractions; (2) as soil particle size increases, there is an increase in the mean microbial concentration per particle; (3) plate counts of aerobic, mesophilic organisms in unheated soils yielded a mean concentration of about six organisms per particle for the smallest soil fraction; (4) aerobic, mesophilic counts for sonicated particles heated at 80 C for 20 minutes yielded mean values of about two organisms per particle for the smallest particles; (5) some actinomycetes associated with the soil fractions could survive dry heat treatment at 110 C for one hour; and (6) soil particles stored under ambient laboratory conditions for 2.5 years aerobic, mesophilic plate counts which were comparable or slightly greater than the counts for more recently collected soil.

Etiology of parapneumonic effusion and pleural empyema in children. The role of conventional and molecular microbiological tests.

PubMed

Krenke, Katarzyna; Sadowy, Ewa; Podsiadły, Edyta; Hryniewicz, Waleria; Demkow, Urszula; Kulus, Marek

2016-07-01

An increasing incidence of parapneumonic effusion and pleural empyema (PPE/PE) has been reported in recent studies. As only few data on etiology of PPE/PE in Central Europe have been reported, we undertook a study on the etiology of PPE/PE in children, using both standard culture and molecular techniques. This prospective study was conducted between June 2011 and December 2013. Consecutive children with PPE/PE complicating community acquired pneumonia, who required diagnostic/therapeutic thoracentesis were included. Blood and pleural fluid samples for microbiological cultures were collected. Molecular methods were applied to identify Streptococcus pneumonia, Haemophilus influenzae, Staphylococcus aureus, Streptococcus pyogenes, Mycoplasma pneumoniae, Chlamydophila pneumoniae, and respiratory viruses in pleural fluid. The study group included 64 children, median age 4 (1-15). Seven of 64 (10.9%) blood cultures and 11 of 64 (17.2%) pleural fluid cultures revealed bacterial growth. The most common bacteria detected was S. pneumoniae (13 blood and pleural fluid samples from 11/64 (17.2%) children). DNA sequences of typical bacteria were found in 29/64 (45.3%) pleural fluid samples. S. pneumoniae was identified in 90% of these samples. The most common serotypes were: serotype 6B in 9/26 (36.6%), 19A in 6/26 (23%), serotype 3 in 3/26 (11.5%), 6A and 23F (both in 2/26 i.e. 7.7%) patients. Molecular methods identified atypical bacteria in 8/58 (13.8%) and respiratory viruses in 12/58 (20.7%) pleural fluid samples. S. pneumoniae, in particular serotype 6B and 19A, is the most common etiologic agent of PPE/PE in Polish children. The use of PCR significantly improves pathogen identification in pleural fluid. Copyright © 2016 Elsevier Ltd. All rights reserved.

Technological Microbiology: Development and Applications

PubMed Central

Vitorino, Luciana C.; Bessa, Layara A.

2017-01-01

Over thousands of years, modernization could be predicted for the use of microorganisms in the production of foods and beverages. However, the current accelerated pace of new food production is due to the rapid incorporation of biotechnological techniques that allow the rapid identification of new molecules and microorganisms or even the genetic improvement of known species. At no other time in history have microorganisms been so present in areas such as agriculture and medicine, except as recognized villains. Currently, however, beneficial microorganisms such as plant growth promoters and phytopathogen controllers are required by various agricultural crops, and many species are being used as biofactories of important pharmacological molecules. The use of biofactories does not end there: microorganisms have been explored for the synthesis of diverse chemicals, fuel molecules, and industrial polymers, and strains environmentally important due to their biodecomposing or biosorption capacity have gained interest in research laboratories and in industrial activities. We call this new microbiology Technological Microbiology, and we believe that complex techniques, such as heterologous expression and metabolic engineering, can be increasingly incorporated into this applied science, allowing the generation of new and improved products and services. PMID:28539920

Automation in Clinical Microbiology

PubMed Central

Ledeboer, Nathan A.

2013-01-01

Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories. PMID:23515547

Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology

PubMed Central

Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K. P.; Woo, Patrick C. Y.

2015-01-01

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study. PMID:26506340

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.

Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

PubMed Central

Narihiro, Takashi; Sekiguchi, Yuji

2011-01-01

Summary For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers. PMID:21375721

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

Diagnostic Molecular Microbiology: A 2018 Snapshot.

PubMed

Fairfax, Marilynn Ransom; Bluth, Martin H; Salimnia, Hossein

2018-06-01

Molecular biological techniques have evolved expeditiously and in turn have been applied to the detection of infectious disease. Maturation of these technologies and their coupling with related technological advancement in fluorescence, electronics, digitization, nanodynamics, and sensors among others have afforded clinical medicine additional tools toward expedient identification of infectious organisms at concentrations and sensitivities previously unattainable. These advancements have been adapted in select settings toward addressing clinical demands for more timely and effective patient management. Copyright © 2018 Elsevier Inc. All rights reserved.

The Molecular Recognition Paradigm of Environmental Chemicals with Biomacromolecules.

PubMed

Zhang, Wenjing; Pan, Liumeng; Wang, Haifei; Lv, Xuan; Ding, Keke

2017-01-01

The interactions of ligands with biomacromolecules play a fundamental role in almost all bioprocesses occuring in living organisms. The binding of ligands can cause the conformational changes of biomacromolecules, possibly affecting their physiological functions. The interactions of ligands with biomacromolecules are thus becoming a research hotspot. However, till now, there still lacks a systematic compilation of review with the focus on the interactions between environmental chemicals and biomacromolecules. In this review, we focus on the molecular recognition paradigm of environmental chemicals with biomacromolecules and chemical basis for driving the complex formation. The state-of-the-art review on in vitro and in silico studies on interaction of organic chemicals with transport proteins, nuclear receptors and CYP450 enzymes was provided, and the enantioselective interactions of chiral environmental chemicals was also mentioned.

The Mediterranean non-indigenous ascidian Polyandrocarpa zorritensis: Microbiological accumulation capability and environmental implications.

PubMed

Stabili, Loredana; Licciano, Margherita; Longo, Caterina; Lezzi, Marco; Giangrande, Adriana

2015-12-15

We investigated the bacterial accumulation and digestion capability of Polyandrocarpa zorritensis, a non-indigenous colonial ascidian originally described in Peru and later found in the Mediterranean. Microbiological analyses were carried out on homogenates from "unstarved" and "starved" ascidians and seawater from the same sampling site (Adriatic Sea, Italy). Culturable heterotrophic bacteria (22 °C), total culturable bacteria (37 °C) and vibrios abundances were determined on Marine Agar 2216, Plate Count Agar and TCBS Agar, respectively. Microbial pollution indicators were measured by the most probable number method. All the examined microbiological groups were accumulated by ascidians but differently digested. An interesting outcome is the capability of P. zorritensis to digest allochthonous microorganisms such as coliforms as well as culturable bacteria at 37 °C, counteracting the effects of microbial pollution. Thus, the potential exploitation of these filter feeders to restore polluted seawater should be taken into consideration in the management of this alien species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbiological and biochemical origins of human axillary odour.

PubMed

James, A Gordon; Austin, Corrine J; Cox, Diana S; Taylor, David; Calvert, Ralph

2013-03-01

The generation of malodour on various sites of the human body is caused by the microbial biotransformation of odourless natural secretions into volatile odorous molecules. On the skin surface, distinctive odours emanate, in particular, from the underarm (axilla), where a large and permanent population of microorganisms thrives on secretions from the eccrine, apocrine and sebaceous glands. Traditional culture-based microbiological studies inform us that this resident microbiota consists mainly of Gram-positive bacteria of the genera Staphylococcus, Micrococcus, Corynebacterium and Propionibacterium. Among the molecular classes that have been implicated in axillary malodour are short- and medium-chain volatile fatty acids, 16-androstene steroids and, most recently, thioalcohols. Most of the available evidence suggests that members of the Corynebacterium genus are the primary causal agents of axillary odour, with the key malodour substrates believed to originate from the apocrine gland. In this article, we examine, in detail, the microbiology and biochemistry of malodour formation on axillary skin, focussing on precursor-product relationships, odour-forming enzymes and metabolic pathways and causal organisms. As well as reviewing the literature, some relevant new data are presented and considered alongside that already available in the public domain to reach an informed view on the current state-of-the-art, as well as future perspectives. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. 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...

21 CFR 866.2540 - Microbiological incubator.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 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, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 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...

[Onsite microbiology services and outsourcing microbiology and offsite laboratories--advantage and disadvantage, thinking of effective utilization].

PubMed

Hosokawa, Naoto

2011-10-01

In recent years, budget restrictions have prompted hospital managers to consider outsourcing microbiology service. But there are many advantages onsite microbiology services. Onsite microbiology services have some advantages. 1) High recovery rate of microorganism. 2) Shorter turn around time. 3) Easy to communicate between physician and laboratory technician. 4) Effective utilization of blood culture. 5) Getting early information about microorganism. 6) Making antibiogram (microbiological local factor). 7) Getting information for infection control. The disadvantages are operating costs and labor cost. The important point of maximal utilization of onsite microbiology service is close communication between physicians to microbiology laboratory. It will be able to provide prompt and efficient report to physicians through discussion about Gram stain findings, agar plate media findings and epidemiological information. The rapid and accurate identification of pathogen affords directed therapy, thereby decreasing the use of broad-spectrum antibiotics and shortening the length of hospital stay and unnecessary ancillary procedures. When the physician use outsourcing microbiology services, should discuss with offsite laboratories about provided services. Infection control person has to arrange data of susceptibility about every isolate and monitoring multi-drug resistant organism. Not only onsite microbiology services but also outsourcing microbiology services, to communicate bedside and laboratory is most important point of effective utilization.

Internal quality assurance in diagnostic microbiology: A simple approach for insightful data.

PubMed

Scherz, Valentin; Durussel, Christian; Greub, Gilbert

2017-01-01

Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91.8%) molecular analyses were concordant. Among the discordances in molecular biology analyses, 6 results were low positive samples that turned out negative, likely due to stochastic repartition of nucleic acids. Moreover, one identified retranscription error led us to implement automated results transmission from the Applied Biosystems instruments to the laboratory information system (LIS). Regarding Gram stain microscopy, 560 out of 745 (75.2%) of compared parameters were concordant. As many as 67 out of 84 (79.8%) pairs of culture results were similar, including 16 sterile pairs, 27 having identical identification or description and semi-quantification and 24 only showing variations in semi-quantification with identical description or identification of colonies. Seventeen pairs had diverging identification or description of colonies. Culture was twice only done for one member of the pairs. Regarding antibiotic susceptibility testing, a major discrepancy was observed in 5 out of 48 results (10.4%). In conclusion, serological tests were highly reproducible. Molecular diagnosis also revealed to be robust except when the amounts of nucleic acids present in the sample were close to the limits of detection. Conventional microbiology was less robust with major discrepancies reaching 39.5% of the samples for microscopy. Similarly, culture and antibiotic susceptibility testing were prone to discrepancies. This work was ground for

One Small Step for the Gram Stain, One Giant Leap for Clinical Microbiology

PubMed Central

2016-01-01

The Gram stain is one of the most commonly performed tests in the clinical microbiology laboratory, yet it is poorly controlled and lacks standardization. It was once the best rapid test in microbiology, but it is no longer trusted by many clinicians. The publication by Samuel et al. (J. Clin. Microbiol. 54:1442–1447, 2016, http://dx.doi.org/10.1128/JCM.03066-15) is a start for those who want to evaluate and improve Gram stain performance. In an age of emerging rapid molecular results, is the Gram stain still relevant? How should clinical microbiologists respond to the call to reduce Gram stain error rates? PMID:27008876

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 5 2014-10-01 2014-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 5 2013-10-01 2013-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 5 2012-10-01 2012-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 5 2011-10-01 2011-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

Opportunities and challenges for the use of molecular proxies in environmental reconstructions

NASA Astrophysics Data System (ADS)

Jansen, Boris

2017-04-01

The last decades have seen a dramatic increase in the use of organic matter from soils and sediments as molecular proxy for reconstructing past dynamics of vegetation and climate. Applications range from the use of changes in preserved leaf wax lipid patterns or d13C signatures of organic matter to reconstruct shifts in vegetation composition, to the use of changes in d2H patterns as a past humidity / precipitation proxy. Particularly exciting in this respect are recent developments with respect to combining various molecular proxies. For instance by compound specific d13C and d2H analysis of selected lipids that themselves are used as vegetation proxy. However, as with all scientific development, all that glitters is not gold. Together with great promise, successful application of molecular proxies to reconstruct past environmental change also comes with several important challenges. For instance, to what extent are plant lipid patterns used for vegetation reconstruction affected by genotypic plasticity of the producing plant species? How might the heterogeneity of environmental and biochemical processes on/in different plant species interfere with the successful use of d2H and d13C patterns? What is the influence of differences in input routes into a soil or sedimentary archive, e.g. aboveground vs. belowground, on the desired reconstruction? In this presentation I will discuss both the opportunities and the challenges of the use of organic matter as molecular proxy in environmental reconstructions, using several recent examples of research from our group.

Consolidated clinical microbiology laboratories.

PubMed

Sautter, Robert L; Thomson, Richard B

2015-05-01

The manner in which medical care is reimbursed in the United States has resulted in significant consolidation in the U.S. health care system. One of the consequences of this has been the development of centralized clinical microbiology laboratories that provide services to patients receiving care in multiple off-site, often remote, locations. Microbiology specimens are unique among clinical specimens in that optimal analysis may require the maintenance of viable organisms. Centralized laboratories may be located hours from patient care settings, and transport conditions need to be such that organism viability can be maintained under a variety of transport conditions. Further, since the provision of rapid results has been shown to enhance patient care, effective and timely means for generating and then reporting the results of clinical microbiology analyses must be in place. In addition, today, increasing numbers of patients are found to have infection caused by pathogens that were either very uncommon in the past or even completely unrecognized. As a result, infectious disease specialists, in particular, are more dependent than ever on access to high-quality diagnostic information from clinical microbiology laboratories. In this point-counterpoint discussion, Robert Sautter, who directs a Charlotte, NC, clinical microbiology laboratory that provides services for a 40-hospital system spread over 3 states in the southeastern United States explains how an integrated clinical microbiology laboratory service has been established in a multihospital system. Richard (Tom) Thomson of the NorthShore University HealthSystem in Evanston, IL, discusses some of the problems and pitfalls associated with large-scale laboratory consolidation. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Circadian clocks in the cnidaria: environmental entrainment, molecular regulation, and organismal outputs.

PubMed

Reitzel, Adam M; Tarrant, Ann M; Levy, Oren

2013-07-01

The circadian clock is a molecular network that translates predictable environmental signals, such as light levels, into organismal responses, including behavior and physiology. Regular oscillations of the molecular components of the clock enable individuals to anticipate regularly fluctuating environmental conditions. Cnidarians play important roles in benthic and pelagic marine environments and also occupy a key evolutionary position as the likely sister group to the bilaterians. Together, these attributes make members of this phylum attractive as models for testing hypotheses on roles for circadian clocks in regulating behavior, physiology, and reproduction as well as those regarding the deep evolutionary conservation of circadian regulatory pathways in animal evolution. Here, we review and synthesize the field of cnidarian circadian biology by discussing the diverse effects of daily light cycles on cnidarians, summarizing the molecular evidence for the conservation of a bilaterian-like circadian clock in anthozoan cnidarians, and presenting new empirical data supporting the presence of a conserved feed-forward loop in the starlet sea anemone, Nematostella vectensis. Furthermore, we discuss critical gaps in our current knowledge about the cnidarian clock, including the functions directly regulated by the clock and the precise molecular interactions that drive the oscillating gene-expression patterns. We conclude that the field of cnidarian circadian biology is moving rapidly toward linking molecular mechanisms with physiology and behavior.

Circadian Clocks in the Cnidaria: Environmental Entrainment, Molecular Regulation, and Organismal Outputs

PubMed Central

Reitzel, Adam M.; Tarrant, Ann M.; Levy, Oren

2013-01-01

The circadian clock is a molecular network that translates predictable environmental signals, such as light levels, into organismal responses, including behavior and physiology. Regular oscillations of the molecular components of the clock enable individuals to anticipate regularly fluctuating environmental conditions. Cnidarians play important roles in benthic and pelagic marine environments and also occupy a key evolutionary position as the likely sister group to the bilaterians. Together, these attributes make members of this phylum attractive as models for testing hypotheses on roles for circadian clocks in regulating behavior, physiology, and reproduction as well as those regarding the deep evolutionary conservation of circadian regulatory pathways in animal evolution. Here, we review and synthesize the field of cnidarian circadian biology by discussing the diverse effects of daily light cycles on cnidarians, summarizing the molecular evidence for the conservation of a bilaterian-like circadian clock in anthozoan cnidarians, and presenting new empirical data supporting the presence of a conserved feed-forward loop in the starlet sea anemone, Nematostella vectensis. Furthermore, we discuss critical gaps in our current knowledge about the cnidarian clock, including the functions directly regulated by the clock and the precise molecular interactions that drive the oscillating gene-expression patterns. We conclude that the field of cnidarian circadian biology is moving rapidly toward linking molecular mechanisms with physiology and behavior. PMID:23620252

The theory and application of space microbiology: China's experiences in space experiments and beyond.

PubMed

Liu, Changting

2017-02-01

Microorganisms exhibit high adaptability to extreme environments of outer space via phenotypic and genetic changes. These changes may affect astronauts in the space environment as well as on Earth because mutant microbes will inevitably return with the spacecraft. However, the role and significance of these phenotypic changes and the underlying mechanisms are important unresolved questions in the field of space biology. By reviewing, especially the Chinese studies, we propose a space microbial molecular effect theory, that is, the space environment affects the nature of genes and the molecular structure of microorganisms to produce phenotypic changes. In this review, we discussed three basic theories for the research of space microbiology, including (1) space microbial pathogenicity and virulence mutations and the human mutualism theory; (2) space microbial drug-resistance mutations and metabolism associated with space pharmaceuticals theory; (3) space corrosion, microbial decontamination, and new materials technology theory. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Outbreak of Salmonella enteritidis PT14b gastroenteritis at a restaurant in England: the use of molecular typing to achieve a successful prosecution.

PubMed

Chatt, C; Nicholds-Trainor, D; Scrivener, A; Suleman, S; Harvey, M; Dallman, T; Hawker, J; Sibal, B

2017-10-01

To describe an outbreak of Salmonella enteritidis phage type (PT) 14b in people who had eaten at a restaurant, and the investigation and subsequent prosecution of the food business operator (FBO). The local health protection team and environmental health department formed an outbreak control team to investigate the outbreak. Epidemiological, microbiological, and environmental investigations were undertaken. Epidemiological investigations involved case finding and interviews. Microbiological investigation: stool samples from the suspected cases and environmental samples from the implicated food business were investigated. Salmonella isolates obtained were subjected to multiple locus variable-number tandem repeat analysis (MLVA) profiling and whole genome sequencing. In addition, adenosine triphosphate (ATP) hygiene swab tests were used to verify the quality of cleaning procedures and data loggers were used to determine the water temperature of the mechanical dishwasher. Fifteen cases of illness where the causative agent was shown to be S. enteritidis PT14b were identified, all of whom had eaten at the same restaurant. S. enteritidis PT14b was also identified from three of the 11 food and environmental samples taken at the restaurant and found to have the same MLVA profile as the cases. A case for prosecution was built and the FBO was successfully prosecuted in July 2015. This investigation highlighted that the use of molecular typing as part of thorough epidemiological, microbiological, and environmental investigations can present a robust case for prosecution against restaurants which pose a risk to public health. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Evolution across the Curriculum: Microbiology

PubMed Central

Burmeister, Alita R.; Smith, James J.

2016-01-01

An integrated understanding of microbiology and evolutionary biology is essential for students pursuing careers in microbiology and healthcare fields. In this Perspective, we discuss the usefulness of evolutionary concepts and an overall evolutionary framework for students enrolled in microbiology courses. Further, we propose a set of learning goals for students studying microbial evolution concepts. We then describe some barriers to microbial evolution teaching and learning and encourage the continued incorporation of evidence-based teaching practices into microbiology courses at all levels. Next, we review the current status of microbial evolution assessment tools and describe some education resources available for teaching microbial evolution. Successful microbial evolution education will require that evolution be taught across the undergraduate biology curriculum, with a continued focus on applications and applied careers, while aligning with national biology education reform initiatives. Journal of Microbiology & Biology Education PMID:27158306

Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

ERIC Educational Resources Information Center

Oerther, Daniel B.

2002-01-01

Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

Child toy safety: An interdisciplinary approach to unravel the microbiological hazard posed by soap bubbles.

PubMed

Amoruso, Irene; Bertoncello, Chiara; Caravello, Gianumberto; Giaccone, Valerio; Baldovin, Tatjana

2015-11-01

In 2012 some children developed sepsis after playing together with a soap bubble toy. Microbiological testing revealed heavy contamination of the soap solution, which reasonably represented the vehicle of infection. We investigated the issue with a multidisciplinary approach: review of toy safety legislation; microbiological testing of additional samples; query of the RAPEX database for non-compliant soap bubbles; identification of major manufacturing districts. Microbiological contamination of industrial soap bubbles was widespread. Sixty-three notifications of batches contaminated by environmental microorganisms and opportunistic pathogens had been reported. The Chinese had a virtual monopoly of the soap bubble market. We identified two main manufacturing districts in Guangdong Province, both notable for degradation of their water resources. The use of untreated water for the industrial production of soap bubbles may explain the bacterial contamination. Existing legislation provides an unsatisfactory approach for managing microbiological hazards in sensitive toy categories and for identifying responsible parties in import and export of the products.

Molecular building blocks and their architecture in biologically/environmentally compatible soft matter chemical machinery.

PubMed

Toyota, Taro; Banno, Taisuke; Nitta, Sachiko; Takinoue, Masahiro; Nomoto, Tomonori; Natsume, Yuno; Matsumura, Shuichi; Fujinami, Masanori

2014-01-01

This review briefly summarizes recent developments in the construction of biologically/environmentally compatible chemical machinery composed of soft matter. Since environmental and living systems are open systems, chemical machinery must continuously fulfill its functions not only through the influx and generation of molecules but also via the degradation and dissipation of molecules. If the degradation or dissipation of soft matter molecular building blocks and biomaterial molecules/polymers can be achieved, soft matter particles composed of them can be used to realize chemical machinery such as selfpropelled droplets, drug delivery carriers, tissue regeneration scaffolds, protocell models, cell-/tissuemarkers, and molecular computing systems.

Microbiology of Waste Treatment.

ERIC Educational Resources Information Center

Unz, Richard F.

1978-01-01

Presents a literature review of the microbiology of waste treatment, covering publications of 1976-77. This review includes topics such as: (1) sanitary microbiology; (2) wastewater disinfectant; (3) viruses in wastewater; and (4) wastewater microbial populations. A list of 142 references is also presented. (HM)

[The modern microbiology in the clinical managing].

PubMed

Casal Román, Manuel

2012-01-01

The tuberculosis is one of the most important and mortal diseases of the world. The microbiological confirmatory diagnosis and the microbiological therapeutic orientation are fundamental nowadays in the tuberculosis in AIDS and in the Resistant tuberculosis. They are described throughout the time by the classic Microbiology: From 1882 to final 20th century (130 years). With the modern current Microbiology: In the beginning of the 21st century (20-30 years). And as will be done with the future Microbiology: From the years 2020-30. The important advances are outlined in the modern and future clinical microbiology, for the control of the Tuberculosis.

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

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.

Detection and Molecular Characterization of Gemycircularvirus from Environmental Samples in Brazil.

PubMed

da Silva Assis, Matheus Ribeiro; Vieira, Carmen Baur; Fioretti, Julia Monassa; Rocha, Mônica Simões; de Almeida, Pedro Ivo Neves; Miagostovich, Marize Pereira; Fumian, Tulio Machado

2016-12-01

Gemycircularvirus (GemyCV) is a group of viruses which has been recently proposed as a new viral genus detected in fecal and environmental samples around the world. GemyCVs have been detected in human blood, brain tissue, cerebrospinal fluid, and stool sample. In the present study, we demonstrate for the first time, through molecular detection and characterization, the presence of GemyCVs in environmental samples from Brazil. Our results show a percentage of positivity ranging from 69 (25/36) to 97 % (35/36) in river water samples collected in Manaus, Amazon region, and wastewater from a wastewater treatment plant located in Rio de Janeiro, respectively, revealing GemyCVs as an important environmental contaminant.

[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.

Microbiological Food Safety Surveillance in China

PubMed Central

Pei, Xiaoyan; Li, Ning; Guo, Yunchang; Liu, Xiumei; Yan, Lin; Li, Ying; Yang, Shuran; Hu, Jing; Zhu, Jianghui; Yang, Dajin

2015-01-01

Microbiological food safety surveillance is a system that collects data regarding food contamination by foodborne pathogens, parasites, viruses, and other harmful microbiological factors. It helps to understand the spectrum of food safety, timely detect food safety hazards, and provide relevant data for food safety supervision, risk assessment, and standards-setting. The study discusses the microbiological surveillance of food safety in China, and introduces the policies and history of the national microbiological surveillance system. In addition, the function and duties of different organizations and institutions are provided in this work, as well as the generation and content of the surveillance plan, quality control, database, and achievement of the microbiological surveillance of food safety in China. PMID:26343705

Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution.

PubMed

Skinner, Michael K

2015-04-26

Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Internal quality assurance in diagnostic microbiology: A simple approach for insightful data

PubMed Central

Scherz, Valentin; Durussel, Christian

2017-01-01

Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91.8%) molecular analyses were concordant. Among the discordances in molecular biology analyses, 6 results were low positive samples that turned out negative, likely due to stochastic repartition of nucleic acids. Moreover, one identified retranscription error led us to implement automated results transmission from the Applied Biosystems instruments to the laboratory information system (LIS). Regarding Gram stain microscopy, 560 out of 745 (75.2%) of compared parameters were concordant. As many as 67 out of 84 (79.8%) pairs of culture results were similar, including 16 sterile pairs, 27 having identical identification or description and semi-quantification and 24 only showing variations in semi-quantification with identical description or identification of colonies. Seventeen pairs had diverging identification or description of colonies. Culture was twice only done for one member of the pairs. Regarding antibiotic susceptibility testing, a major discrepancy was observed in 5 out of 48 results (10.4%). In conclusion, serological tests were highly reproducible. Molecular diagnosis also revealed to be robust except when the amounts of nucleic acids present in the sample were close to the limits of detection. Conventional microbiology was less robust with major discrepancies reaching 39.5% of the samples for microscopy. Similarly, culture and antibiotic susceptibility testing were prone to discrepancies. This work was ground for

42 CFR 493.821 - Condition: Microbiology.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes of...

42 CFR 493.821 - Condition: Microbiology.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 5 2014-10-01 2014-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes of...

42 CFR 493.821 - Condition: Microbiology.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 5 2011-10-01 2011-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes of...

42 CFR 493.821 - Condition: Microbiology.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 5 2013-10-01 2013-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes of...

42 CFR 493.821 - Condition: Microbiology.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 5 2012-10-01 2012-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes of...

Microbiology

ERIC Educational Resources Information Center

Spooner, D.

1973-01-01

Describes various types of training programs carried out in the study of microbiology. Indicates that the need for new energy sources and the expansion of medical schools and food industry may lead to an increasing demand for qualified microbiologists. (CC)

Rapid diagnostic testing for community-acquired pneumonia: can innovative technology for clinical microbiology be exploited?

PubMed

Yu, Victor L; Stout, Janet E

2009-12-01

Two nonsynchronous events have affected the management of community-acquired pneumonia (CAP): spiraling empiricism for CAP and the "golden era" of clinical microbiology. The development of broad-spectrum antibiotics has led to widespread empiric use without ascertaining the etiology of the infecting microbe. Unfortunately, this approach clashes with the second event, which is the advent of molecular-based microbiology that can identify the causative pathogen rapidly at the point of care. The urinary antigen is a most effective rapid test that has allowed targeted therapy for Legionnaire disease at the point of care. The high specificity (> 90%) allows the clinician to administer appropriate anti-Legionella therapy based on a single rapid test; however, its low sensitivity (76%) means that a notable number of cases of Legionnaire disease will go undiagnosed if other tests, especially culture, are not performed. Further, culture for Legionella is not readily available. If a culture is not performed, epidemiologic identification of the source of the bacterium cannot be ascertained by molecular fingerprinting of the patient and the putative source strain. We recommend resurrection of the basic principles of infectious disease, which are to identify the microbial etiology of the infection and to use narrow, targeted antimicrobial therapy. To reduce antimicrobial overuse with subsequent antimicrobial resistance, these basic principles must be applied in concert with traditional and newer tests in the clinical microbiology laboratory.

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.

Microbiologic factors affecting Clostridium difficile recurrence.

PubMed

Chilton, C H; Pickering, D S; Freeman, J

2018-05-01

Recurrent Clostridium difficile infection (rCDI) places a huge economic and practical burden on healthcare facilities. Furthermore, rCDI may affect quality of life, leaving patients in an rCDI cycle and dependant on antibiotic therapy. To discuss the importance of microbiologic factors in the development of rCDI. Literature was drawn from a search of PubMed from 2000 onwards with the search term 'recurrent Clostridium difficile infection' and further references cited within these articles. Meta-analyses and systematic reviews have shown that CDI and rCDI risk factors are similar. Development of rCDI is attendant on many factors, including immune status or function, comorbidities and concomitant treatments. Studies suggest that poor bacterial diversity is correlated with clinical rCDI. Narrow-spectrum gut microflora-sparing antimicrobials (e.g. surotomycin, cadazolid, ridinilazole) are in development for CDI treatment, while microbiota therapeutics (faecal microbiota transplantation, nontoxigenic C. difficile, stool substitutes) are increasingly being explored. rCDI can only occur when viable C. difficile spores are present, either within the gut lumen after infection or when reacquired from the environment. C. difficile spore germination can be influenced by gut environmental factors resulting from dysbiosis, and spore outgrowth may be affected stage by some antimicrobials (e.g. fidaxomicin, ramoplanin, oritavancin). rCDI is a significant challenge for healthcare professionals, requiring a multifaceted approach; optimized infection control to minimize reinfection; C. difficile-targeted antibiotics to minimize dysbiosis; and gut microflora restoration to promote colonization resistance. These elements should be informed by our understanding of the microbiologic factors involved in both C. difficile itself and the gut microbiome. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

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.

Culture-independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil-bioremediation.

PubMed

Dashti, Narjes; Ali, Nedaa; Salamah, Samar; Khanafer, Majida; Al-Shamy, Ghada; Al-Awadhi, Husain; Radwan, Samir S

2018-04-15

To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples. The study described the dynamics of bacterial communities during bioremediation. The main limitation associated with this molecular approach, namely of not distinguishing hydrocarbonoclastic taxa from others, was overcome by consulting the literature for the hydrocarbonoclastic potential of taxa related to those identified in this study. By doing so, it was concluded that the hydrocarbonoclastic bacterial taxa were much more diverse than those captured by the culture-dependent approach. The molecular analysis also revealed the frequent occurrence of nifH-genes in the total genomic DNA extracts of all the studied environmental samples, which reflects a nitrogen-fixation potential. Nitrogen fertilization is long known to enhance microbial oil-bioremediation. The study revealed that bioaugmentation using plant rhizospheres or soil with long history of oil-pollution was more effective in oil-removal in the desert soil than in seawater microcosms. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Computational Molecular Modeling for Evaluating the Toxicity of Environmental Chemicals: Prioritizing Bioassay Requirements

EPA Science Inventory

This commentary provides an overview of the challenges that arise from applying molecular modeling tools developed and commonly used for pharmaceutical discovery to the problem of predicting the potential toxicities of environmental chemicals.

[Microbiological diagnosis of HIV infection].

PubMed

López-Bernaldo de Quirós, Juan Carlos; Delgado, Rafael; García, Federico; Eiros, José M; Ortiz de Lejarazu, Raúl

2007-12-01

Currently, there are around 150,000 HIV-infected patients in Spain. This number, together with the fact that this disease is now a chronic condition since the introduction of antiretroviral therapy, has generated an increasing demand on the clinical microbiology laboratories in our hospitals. This increase has occurred not only in the diagnosis and treatment of opportunistic diseases, but also in tests related to the diagnosis and therapeutic management of HIV infection. To meet this demand, the Sociedad de Enfermedades Infecciosas y Microbiología Clinica (Spanish Society of Infectious Diseases and Clinical Microbiology) has updated its standard Procedure for the microbiological diagnosis of HIV infection. The main advances related to serological diagnosis, plasma viral load, and detection of resistance to antiretroviral drugs are reviewed in this version of the Procedure.

Environmental controls on denitrifying communities and denitrification rates--Insights from molecular methods

USGS Publications Warehouse

Wallenstein, Matthew D.; Myrold, David D.; Firestone, Mary; Voytek, Mary

2006-01-01

The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3− pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.

[Analysis of the results of the 2010 External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology].

PubMed

Ruiz de Gopegui Bordes, Enrique; Serrano, M del Remedio Guna; Orta Mira, Nieves; Ovies, María Rosario; Poveda, Marta; Cardona, Concepción Gimeno

2011-12-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology includes controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology and molecular microbiology. This article presents the most important conclusions and lessons of the 2010 controls. As a whole, the results obtained in 2010 confirm the excellent skill and good technical standards found in previous years. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. The results of this program highlight the need to implement both internal and external controls to ensure maximal quality of microbiological tests(1). Copyright © 2011 Elsevier España S.L. All rights reserved.

A cost-effective interdisciplinary approach to microbiologic send-out test use.

PubMed

Aesif, Scott W; Parenti, David M; Lesky, Linda; Keiser, John F

2015-02-01

Use of reference laboratories for selected laboratory testing (send-out tests) represents a significant source of laboratory costs. As the use of more complex molecular analyses becomes common in the United States, strategies to reduce costs in the clinical laboratory must evolve in order to provide high-value, cost-effective medicine. To report a strategy that employs clinical pathology house staff and key hospital clinicians in the effective use of microbiologic send-out testing. The George Washington University Hospital is a 370-bed academic hospital in Washington, DC. In 2012 all requisitions for microbiologic send-out tests were screened by the clinical pathology house staff prior to final dispensation. Tests with questionable utility were brought to the attention of ordering clinicians through the use of interdisciplinary rounds and direct face-to-face consultation. Screening resulted in a cancellation rate of 38% of send-out tests, with proportional cost savings. Nucleic acid tests represented most of the tests screened and the largest percentage of cost saved through screening. Following consultation, requested send-out tests were most often canceled because of a lack of clinical indication. Direct face-to-face consultation with ordering physicians is an effective, interdisciplinary approach to managing the use of send-out testing in the microbiology laboratory.

Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

DOE PAGES

Nourbakhsh-Rey, Mehrnoush; Libault, Marc

2016-01-01

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hairmore » cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. Lastly, in this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.« less

Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

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

Nourbakhsh-Rey, Mehrnoush; Libault, Marc

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hairmore » cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. Lastly, in this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.« less

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.

[Microbiology laboratory as a base of information sending].

PubMed

Komori, Toshiaki; Fujita, Naohisa; Hirose, Yuri; Kimura, Takeshi; Kyotani, Noriko; Kurahashi, Satoko; Yamada, Yukiji; Ushiyama, Masaji; Yasumoto, Towa; Yuasa, Soh-ichi

2007-10-01

The goal of our microbiology laboratory is to provide an accurate microbiological result and a useful information for every healthcare workers (HCWs). For this purpose, we were trying to do several activities, such as improving the work-flow of microbiology testings, starting 365-day-open microbiology tests, providing some training courses of microbiology and sending many useful informations about infectious diseases and infection control. Before these activities, we needed another 5 microbiology technicians beside 3 technicians and had started the program to educate them. We have successfully finished it and enabled all plans begin in April, 2005. Since then we are open for 365 days and also sending HCWs many newsletters for performing effective microbiological testings via the intra-network system and having lectures for both doctors and nurses, especially for new resident doctors at the orientation. We had also the training course for certified infection control nurses and accepted two technicians from Africa, who came to study a basic microbiology via JICA. These activities have enabled every technician not only to report and analyze microbiological test result effectively but also to improve writing and presentation skills. Through these activities all technicians have realized that accurate and rapid information from a microbiology laboratory is a key to treat patients with infectious diseases and improve their prognosis. It is suggested that skill-up of technicians lead to report an accurate result in microbiology and at the same time improve the attitude for their job.

Molecular diagnostics: the changing culture of medical microbiology.

PubMed

Bullman, Susan; Lucey, Brigid; Sleator, Roy D

2012-01-01

Diagnostic molecular biology is arguably the fastest growing area in current laboratory-based medicine. Growth of the so called 'omics' technologies has, over the last decade, led to a gradual migration away from the 'one test, one pathogen' paradigm, toward multiplex approaches to infectious disease diagnosis, which have led to significant improvements in clinical diagnostics and ultimately improved patient care.

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.

Molecular Environmental Science: An Assessment of Research Accomplishments, Available Synchrotron Radiation Facilities, and Needs

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

Brown, G

2004-02-05

Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutantsmore » at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and their reactions

Marine molecular biology: an emerging field of biological sciences.

PubMed

Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G

2008-01-01

An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

Using Domestic and Free-Ranging Arctic Canid Models for Environmental Molecular Toxicology Research.

PubMed

Harley, John R; Bammler, Theo K; Farin, Federico M; Beyer, Richard P; Kavanagh, Terrance J; Dunlap, Kriya L; Knott, Katrina K; Ylitalo, Gina M; O'Hara, Todd M

2016-02-16

The use of sentinel species for population and ecosystem health assessments has been advocated as part of a One Health perspective. The Arctic is experiencing rapid change, including climate and environmental shifts, as well as increased resource development, which will alter exposure of biota to environmental agents of disease. Arctic canid species have wide geographic ranges and feeding ecologies and are often exposed to high concentrations of both terrestrial and marine-based contaminants. The domestic dog (Canis lupus familiaris) has been used in biomedical research for a number of years and has been advocated as a sentinel for human health due to its proximity to humans and, in some instances, similar diet. Exploiting the potential of molecular tools for describing the toxicogenomics of Arctic canids is critical for their development as biomedical models as well as environmental sentinels. Here, we present three approaches analyzing toxicogenomics of Arctic contaminants in both domestic and free-ranging canids (Arctic fox, Vulpes lagopus). We describe a number of confounding variables that must be addressed when conducting toxicogenomics studies in canid and other mammalian models. The ability for canids to act as models for Arctic molecular toxicology research is unique and significant for advancing our understanding and expanding the tool box for assessing the changing landscape of environmental agents of disease in the Arctic.

Molecular methods for septicemia diagnosis.

PubMed

Marco, Francesc

2017-11-01

Septicemia remains a major cause of hospital mortality. Blood culture remains the best approach to identify the etiological microorganisms when a bloodstream infection is suspected but it takes long time because it relies on bacterial or fungal growth. The introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology, DNA hybridization, microarrays or rapid PCR-based test significantly reduce the time to results. Tests for direct detection in whole blood samples are highly desirable because of their potential to identify bloodstream pathogens without waiting for blood cultures to become positive. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews these new molecular approaches (LightCycler SeptiFast, Magicplex sepsis real time, Septitest, VYOO, PCR/ESI-MS analysis, T2Candida). Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations

EPA Science Inventory

Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental wat...

Microbiology, philosophy and education.

PubMed

O'Malley, Maureen A

2016-09-01

There are not only many links between microbiological and philosophical topics, but good educational reasons for microbiologists to explore the philosophical issues in their fields. I examine three broad issues of classification, causality and model systems, showing how these philosophical dimensions have practical implications. I conclude with a discussion of the educational benefits for recognising the philosophy in microbiology. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular and genetic ecotoxicologic approaches to aquatic environmental bioreporting.

PubMed Central

Beaty, B J; Black, W C; Carlson, J O; Clements, W H; DuTeau, N; Harrahy, E; Nuckols, J; Kenneth, E; Olson, K E; Rayms-Keller, A

1998-01-01

Molecular and population genetic ecotoxicologic approaches are being developed for the utilization of arthropods as bioreporters of heavy metal mixtures in the environment. The explosion of knowledge in molecular biology, molecular genetics, and biotechnology provides an unparalleled opportunity to use arthropods as bioreporter organisms. Interspecific differences in aquatic arthropod populations have been previously demonstrated in response to heavy metal insult in the Arkansas River (AR) California Gulch Superfund site (CGSS). Population genetic analyses were conducted on the mayfly Baetis tricaudatus. Genetic polymorphisms were detected in polymerase chain reaction amplified 16S mitochondrial rDNA (a selectively neutral gene) of B tricaudatus using single-strand conformation polymorphism analysis. Genetic differences may have resulted from impediments to gene flow in the population caused by mortality arising from exposure to heavy metal mixture pollution. In laboratory studies a candidate metal-responsive mucinlike gene, which is metal and dose specific, has been identified in Chironomus tentans and other potential AR-CGSS bioreporter species. Population genetic analyses using the mucinlike gene may provide insight into the role of this selectable gene in determining the breeding structure of B. tricaudatus in the AR-CGSS and may provide mechanistic insight into determinants of aquatic arthropod response to heavy metal insult. Metal-responsive (MR) genes and regulatory sequences are being isolated, characterized, and assayed for differential gene expression in response to heavy metal mixture pollution in the AR-CGSS. Identified promoter sequences can then be engineered into previously developed MR constructs to provide sensitive in vitro assays for environmental bioreporting of heavy metal mixtures. The results of the population genetic studies are being entered into an AR geographic information system that contains substantial biological, chemical, and

Molecular approaches for the detection and monitoring of microbial communities in bioaerosols: A review.

PubMed

Yoo, Keunje; Lee, Tae Kwon; Choi, Eun Joo; Yang, Jihoon; Shukla, Sudheer Kumar; Hwang, Sang-Il; Park, Joonhong

2017-01-01

Bioaerosols significantly affect atmospheric processes while they undergo long-range vertical and horizontal transport and influence atmospheric chemistry and physics and climate change. Accumulating evidence suggests that exposure to bioaerosols may cause adverse health effects, including severe disease. Studies of bioaerosols have primarily focused on their chemical composition and largely neglected their biological composition and the negative effects of biological composition on ecosystems and human health. Here, current molecular methods for the identification, quantification, and distribution of bioaerosol agents are reviewed. Modern developments in environmental microbiology technology would be favorable in elucidation of microbial temporal and spatial distribution in the atmosphere at high resolution. In addition, these provide additional supports for growing evidence that microbial diversity or composition in the bioaerosol is an indispensable environmental aspect linking with public health. Copyright © 2016. Published by Elsevier B.V.

Establishment of microbiological safety criteria for foods in international trade. International Commission on Microbiological Specifications for Foods.

PubMed

1997-01-01

Microbiological safety is achieved by applying good hygienic practices throughout the food chain, "from farm to fork". Governmental food control is traditionally based on inspection of the facilities where foods are handled, and on testing food samples. Testing is usually applied to imported foods, when no information concerning the safety of a consignment is available. The microbiological safety is judged by means of microbiological criteria. Such criteria should, in the context of the WTO/SPS measures, be scientifically justified, and established according to the principles described by the Codex Alimentarius. However, microbiological testing is not a very reliable tool for consumer protection; the emphasis is currently shifting to the application of food safety management tools such as the Hazard Analysis Critical Control Point system (HACCP).

Environmentally Responsible Microbiological Production of Energetic Ingredients

DTIC Science & Technology

2007-11-01

effort was to develop an environmentally benign and economical microbial process for nitro-energetics production . The specific targets of this method...microbial production of nitro-based EM. As the processes and compounds of choice, RDX/HMX (nitramine) generation was selected. Microorganisms capable of...Current synthetic methods for the production of RDX and HMX utilize hexamine as the precursor. Hexamine is an industrial chemical available on a large

Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches.

PubMed

Logares, Ramiro; Haverkamp, Thomas H A; Kumar, Surendra; Lanzén, Anders; Nederbragt, Alexander J; Quince, Christopher; Kauserud, Håvard

2012-10-01

The incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges. HTS now allows a high-resolution exploration of the vast taxonomic and metabolic diversity present in the microbial world, which can provide an exceptional insight on global ecosystem functioning, ecological processes and evolution. This exploration has also economic potential, as we will have access to the evolutionary innovation present in microbial metabolisms, which could be used for biotechnological development. HTS is also challenging the research community, and the current bottleneck is present in the data analysis side. At the moment, researchers are in a sequence data deluge, with sequencing throughput advancing faster than the computer power needed for data analysis. However, new tools and approaches are being developed constantly and the whole process could be depicted as a fast co-evolution between sequencing technology, informatics and microbiologists. In this work, we examine the most popular and recently commercialized HTS platforms as well as bioinformatics methods for data handling and analysis used in microbial metagenomics. This non-exhaustive review is intended to serve as a broad state-of-the-art guide to researchers expanding into this rapidly evolving field. Copyright © 2012 Elsevier B.V. All rights reserved.

Microbiological and ecological responses to global environmental changes in polar regions (MERGE): An IPY core coordinating project

NASA Astrophysics Data System (ADS)

Naganuma, Takeshi; Wilmotte, Annick

2009-11-01

An integrated program, “Microbiological and ecological responses to global environmental changes in polar regions” (MERGE), was proposed in the International Polar Year (IPY) 2007-2008 and endorsed by the IPY committee as a coordinating proposal. MERGE hosts original proposals to the IPY and facilitates their funding. MERGE selected three key questions to produce scientific achievements. Prokaryotic and eukaryotic organisms in terrestrial, lacustrine, and supraglacial habitats were targeted according to diversity and biogeography; food webs and ecosystem evolution; and linkages between biological, chemical, and physical processes in the supraglacial biome. MERGE hosted 13 original and seven additional proposals, with two full proposals. It respected the priorities and achievements of the individual proposals and aimed to unify their significant results. Ideas and projects followed a bottom-up rather than a top-down approach. We intend to inform the MERGE community of the initial results and encourage ongoing collaboration. Scientists from non-polar regions have also participated and are encouraged to remain involved in MERGE. MERGE is formed by scientists from Argentina, Australia, Austria, Belgium, Brazil, Bulgaria, Canada, Egypt, Finland, France, Germany, Italy, Japan, Korea, Malaysia, New Zealand, Philippines, Poland, Russia, Spain, UK, Uruguay, USA, and Vietnam, and associates from Chile, Denmark, Netherlands, and Norway.

Environmental microbiology as related to planetary quarantine

NASA Technical Reports Server (NTRS)

Pflug, I. J.

1971-01-01

The experiments carried out to determine the effects of temperature and relative humidity on the survival rate of Bacillus subtillis var. niger spores are reported. The experiments were conducted in environmental chambers at temperatures of 75 and 90 C. Data are also included on the survival characteristics of the spores suspended in sucrose solutions at 90 C with water activities of 0.99, 0.9, and 0.85

Symbiosis in the Soil: Citizen Microbiology in Middle and High School Classrooms †

PubMed Central

McKenney, Erin; Flythe, Taylar; Millis, Courtney; Stalls, Jennifer; Urban, Julie M.; Dunn, Robert R.; Stevens, Julia L.

2016-01-01

Microorganisms are vital to environmental health, yet their association with disease often overshadows these benefits. Building citizen-science activities around the positive role of microorganisms and an understanding of their ubiquity can begin to dispel misconceptions while simultaneously engaging the public in research. Here, we describe a citizen-science microbiology project geared toward implementation in middle and high school classrooms. Students culture environmental microorganisms and document microbial diversity of plant root systems compared with adjacent bulk soil. Results contribute data toward research on microbiome recruitment of weeds and other successful plants while addressing core topics in science education. PMID:27047592

Molecularly imprinted fluorescent hollow nanoparticles as sensors for rapid and efficient detection λ-cyhalothrin in environmental water.

PubMed

Wang, Jixiang; Qiu, Hao; Shen, Hongqiang; Pan, Jianming; Dai, Xiaohui; Yan, Yongsheng; Pan, Guoqing; Sellergren, Börje

2016-11-15

Molecularly imprinted fluorescent polymers have shown great promise in biological or chemical separations and detections, due to their high stability, selectivity and sensitivity. In this work, molecularly imprinted fluorescent hollow nanoparticles, which could rapidly and efficiently detect λ-cyhalothrin (a toxic insecticide) in water samples, was reported. The molecularly imprinted fluorescent sensor showed excellent sensitivity (the limit of detection low to 10.26nM), rapid detection rate (quantitative detection of λ-cyhalothrin within 8min), regeneration ability (maintaining good fluorescence properties after 8 cycling operation) and appreciable selectivity over several structural analogs. Moreover, the fluorescent sensor was further used to detect λ-cyhalothrin in real samples form the Beijing-Hangzhou Grand Canal Water. Despite the relatively complex components of the environmental water, the molecularly imprinted fluorescent hollow nanosensor still showed good recovery, clearly demonstrating the potential value of this smart sensor nanomaterial in environmental monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

Industrial Microbiology.

ERIC Educational Resources Information Center

Demain, Arnold L.; Solomon, Nadine A.

1981-01-01

Presents an overview of the field of industrial microbiology, providing historical backgrounds of scientific discoveries in the field and descriptions of industrially important microorganisms. Applied research in industry is also detailed, with mention of gene amplification, DNA recombination, pharmaceutical approaches, and detoxification and…

[Molecular techniques in mycology].

PubMed

Rodríguez-Tudela, Juan Luis; Cuesta, Isabel; Gómez-López, Alicia; Alastruey-Izquierdo, Ana; Bernal-Martínez, Leticia; Cuenca-Estrella, Manuel

2008-11-01

An increasing number of molecular techniques for the diagnosis of fungal infections have been developed in the last few years, due to the growing prevalence of mycoses and the length of time required for diagnosis when classical microbiological methods are used. These methods are designed to resolve the following aspects of mycological diagnosis: a) Identification of fungi to species level by means of sequencing relevant taxonomic targets; b) early clinical diagnosis of invasive fungal infections; c) detection of molecular mechanisms of resistance to antifungal agents; and d) molecular typing of fungi. Currently, these methods are restricted to highly developed laboratories. However, some of these techniques will probably be available in daily clinical practice in the near future.

[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.

Imaging mass spectrometry in microbiology

PubMed Central

Watrous, Jeramie D.; Dorrestein, Pieter C.

2013-01-01

Mass spectrometry tools which allow for the 2-D visualization of the distribution of trace metals, metabolites, surface lipids, peptides and proteins directly from biological samples without the need for chemical tagging or antibodies are becoming increasingly useful for microbiology applications. These tools, comprised of different imaging mass spectrometry techniques, are ushering in an exciting new era of discovery by allowing for the generation of chemical hypotheses based on of the spatial mapping of atoms and molecules that can correlate to or transcend observed phenotypes. In this review, we explore the wide range of imaging mass spectrometry techniques available to microbiologists and describe their unique applications to microbiology with respect to the types of microbiology samples to be investigated. PMID:21822293

[METHOD OF INCREASING MICROBIOLOGICAL PURITY OF POWDER FROM COCOA-VELLA].

PubMed

Magomedov, G O; Cheremushkina, L V; Plotnikova, I V

2015-01-01

In the article there is described in detail the characteristic of the product of processing cocoa beans--cocoa-vella, there is presented a comparative analysis of the chemical composition, quality indices, the dispersive pattern, microbiological indices of the powder from the cocoa-vella in comparison to cocoa powder, obtained by traditional technology from the core of the cocoa beans. To improve the microbiological purity of the powder from the cocoa-vella there was suggested to be the modern and environmentally safe manner for the preparation of the powder The use of cocoa-vella disinfecting power by means of the electromagnetic field of ultrahigh frequency (RF EMF) was established to allow to obtain a product that meets the requirements of Technical Regulations of the Customs Union (TRCU 021/2011) on Food Safety. This work is of practical interest, since it helps to improve the safety of the powder from the cocoa-vella, and thus the quality of confectionery and food products based on it, which is relevant in terms of the management of a healthy diet.

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.

21 CFR 866.2350 - Microbiological assay culture medium.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2350...

21 CFR 866.2350 - Microbiological assay culture medium.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2350...

21 CFR 866.2350 - Microbiological assay culture medium.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2350...

21 CFR 866.2350 - Microbiological assay culture medium.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2350...

21 CFR 866.2350 - Microbiological assay culture medium.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2350...

Workshop on Molecular Evolution

NASA Technical Reports Server (NTRS)

Cummings, Michael P.

2004-01-01

Molecular evolution has become the nexus of many areas of biological research. It both brings together and enriches such areas as biochemistry, molecular biology, microbiology, population genetics, systematics, developmental biology, genomics, bioinformatics, in vitro evolution, and molecular ecology. The Workshop provides an important contribution to these fields in that it promotes interdisciplinary research and interaction, and thus provides a glue that sticks together disparate fields. Due to the wide range of fields addressed by the study of molecular evolution, it is difficult to offer a comprehensive course in a university setting. It is rare for a single institution to maintain expertise in all necessary areas. In contrast, the Workshop is uniquely able to provide necessary breadth and depth by utilizing a large number of faculty with appropriate expertise. Furthermore, the flexible nature of the Workshop allows for rapid adaptation to changes in the dynamic field of molecular evolution. For example, the 2003 Workshop included recently emergent research areas of molecular evolution of development and genomics.

Undergraduate Laboratory Exercises Specific to Food Spoilage Microbiology

ERIC Educational Resources Information Center

Snyder, Abigail B.; Worobo, Randy W.; Orta-Ramirez, Alicia

2016-01-01

Food spoilage has an enormous economic impact, and microbial food spoilage plays a significant role in food waste and loss; subsequently, an equally significant portion of undergraduate food microbiology instruction should be dedicated to spoilage microbiology. Here, we describe a set of undergraduate microbiology laboratory exercises that focus…

Isolation, Identification and Molecular Typing of Cryptococcus neoformans from Pigeon Droppings and Other Environmental Sources in Tripoli, Libya.

PubMed

Ellabib, Mohamed S; Aboshkiwa, Mohamed A; Husien, Walid M; D'Amicis, Roberta; Cogliati, Massimo

2016-08-01

Cryptococcus neoformans and C. gattii are the major cause of fungal meningitis, a potentially lethal mycosis. Since pigeon excreta and other environmental sources can be considered a significant environmental reservoir of this species in urban areas, 100 samples of pigeon excreta and 420 samples from Eucalyptus camaldulensis and Olea europaea (olive tree) around the city of Tripoli, Libya, were collected. C. neoformans was isolated and identified using standard biochemical assays from 46 samples: 34 from pigeon droppings, 3 from Eucalyptus trees and 9 from olive trees. Molecular typing revealed that all isolates from pigeon droppings belonged to molecular type VNI (C. neoformans var. grubii) and mating type αA, whereas those from trees included also the molecular type VNII and VNIII (AD hybrids). The present study reports, for the first time, information about the distribution of species, mating types and molecular types of C. neoformans/C. gattii species complex in Libya.

A molecular epidemiological study of methicillin-resistant Staphylococci environmental contamination in railway stations and coach stations in Guangzhou of China.

PubMed

Lin, J L; Peng, Y; Ou, Q T; Lin, D X; Li, Y; Ye, X H; Zhou, J L; Yao, Z J

2017-02-01

Methicillin-resistant Staphylococcus aureus (MRSA) has caused a series of public health problems since it was first found in 1961. However, there are few research studies on the MRSA environmental contamination in railway stations and coach stations. Therefore, the aim of this study was to determine MRSA environmental contamination in public transport stations. Between December 2013 and January 2014, 380 surface samples from three railway stations (180) and four coach stations (200) in Guangzhou were collected to isolate and determine the prevalence and characteristics of Staphylococci strains. 39·21% of all samples were Staphylococci isolates, 1·58% of Staphylococci isolates were MRSA isolates, and 6·05% were methicillin-susceptible S. aureus. The proportion of multidrug resistant among 149 Staphylococci isolates was 75·84%. None of MRSA isolates was identified with the Panton-Valentine Leukocidin (PVL) genes, and one of them was identified with the qac gene. Four MRSA isolates were Staphylococcal Cassette Chromosome mec IVa, and the other two were nontypeable. Staphylococcus aureus isolates were classified into several sequence types (STs), and STs showed possible cross-transmissions of isolates from various sources. Methicillin-resistant Staphylococci contamination prevalence was high, and the environment of stations may be the vectors transmitting the Staphylococci to passengers. This is the first study to comprehensively report the prevalence, antibiotic resistance, and molecular characteristics of contamination of Staphylococci isolates in railway stations and coach stations of China. It will have great public health implications on infection control in community settings because of the serious hazard of Staphylococci, especially methicillin-resistant Staphylococci. Our findings have provided evidence for relevant departments to reduce the contamination of Staphylococci in environment of public transport stations. © 2016 The Society for Applied

Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae, Prorocentrales).

PubMed

Boopathi, Thangavelu; Faria, Daphne Georgina; Cheon, Ju-Yong; Youn, Seok Hyun; Ki, Jang-Seu

2015-01-01

The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one-factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t-test, p < 0.05), than those for interspecies variations (> 2.9% and > 26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

PubMed

Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

2017-10-01

Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

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.

Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

PubMed Central

Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur

2015-01-01

We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC) and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs), bisphenols (BPs), and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA) and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK) signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors. PMID:26512648

Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans.

PubMed

Veldhoen, Nik; Ikonomou, Michael G; Helbing, Caren C

2012-02-01

Many species that contribute to the commercial and ecological richness of our marine ecosystems are harbingers of environmental change. The ability of organisms to rapidly detect and respond to changes in the surrounding environment represents the foundation for application of molecular profiling technologies towards marine sentinel species in an attempt to identify signature profiles that may reside within the transcriptome, proteome, or metabolome and that are indicative of a particular environmental exposure event. The current review highlights recent examples of the biological information obtained for marine sentinel teleosts, mammals, and invertebrates. While in its infancy, such basal information can provide a systems biology framework in the detection and evaluation of environmental chemical contaminant effects on marine fauna. Repeated evaluation across different seasons and local marine environs will lead to discrimination between signature profiles representing normal variation within the complex milieu of environmental factors that trigger biological response in a given sentinel species and permit a greater understanding of normal versus anthropogenic-associated modulation of biological pathways, which prove detrimental to marine fauna. It is anticipated that incorporation of contaminant-specific molecular signatures into current risk assessment paradigms will lead to enhanced wildlife management strategies that minimize the impacts of our industrialized society on marine ecosystems. Copyright © 2011 Elsevier Inc. All rights reserved.

Automation in the clinical microbiology laboratory.

PubMed

Novak, Susan M; Marlowe, Elizabeth M

2013-09-01

Imagine a clinical microbiology laboratory where a patient's specimens are placed on a conveyor belt and sent on an automation line for processing and plating. Technologists need only log onto a computer to visualize the images of a culture and send to a mass spectrometer for identification. Once a pathogen is identified, the system knows to send the colony for susceptibility testing. This is the future of the clinical microbiology laboratory. This article outlines the operational and staffing challenges facing clinical microbiology laboratories and the evolution of automation that is shaping the way laboratory medicine will be practiced in the future. Copyright © 2013 Elsevier Inc. All rights reserved.

Synthetic biology: Novel approaches for microbiology.

PubMed

Padilla-Vaca, Felipe; Anaya-Velázquez, Fernando; Franco, Bernardo

2015-06-01

In the past twenty years, molecular genetics has created powerful tools for genetic manipulation of living organisms. Whole genome sequencing has provided necessary information to assess knowledge on gene function and protein networks. In addition, new tools permit to modify organisms to perform desired tasks. Gene function analysis is speed up by novel approaches that couple both high throughput data generation and mining. Synthetic biology is an emerging field that uses tools for generating novel gene networks, whole genome synthesis and engineering. New applications in biotechnological, pharmaceutical and biomedical research are envisioned for synthetic biology. In recent years these new strategies have opened up the possibilities to study gene and genome editing, creation of novel tools for functional studies in virus, parasites and pathogenic bacteria. There is also the possibility to re-design organisms to generate vaccine subunits or produce new pharmaceuticals to combat multi-drug resistant pathogens. In this review we provide our opinion on the applicability of synthetic biology strategies for functional studies of pathogenic organisms and some applications such as genome editing and gene network studies to further comprehend virulence factors and determinants in pathogenic organisms. We also discuss what we consider important ethical issues for this field of molecular biology, especially for potential misuse of the new technologies. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members.

PubMed

Ramond, J-B; Makhalanyane, T P; Tuffin, M I; Cowan, D A

2015-04-01

Normalization is a procedure classically employed to detect rare sequences in cellular expression profiles (i.e. cDNA libraries). Here, we present a normalization protocol involving the direct treatment of extracted environmental metagenomic DNA with S1 nuclease, referred to as normalization of metagenomic DNA: NmDNA. We demonstrate that NmDNA, prior to post hoc PCR-based experiments (16S rRNA gene T-RFLP fingerprinting and clone library), increased the diversity of sequences retrieved from environmental microbial communities by detection of rarer sequences. This approach could be used to enhance the resolution of detection of ecologically relevant rare members in environmental microbial assemblages and therefore is promising in enabling a better understanding of ecosystem functioning. This study is the first testing 'normalization' on environmental metagenomic DNA (mDNA). The aim of this procedure was to improve the identification of rare phylotypes in environmental communities. Using hypoliths as model systems, we present evidence that this post-mDNA extraction molecular procedure substantially enhances the detection of less common phylotypes and could even lead to the discovery of novel microbial genotypes within a given environment. © 2014 The Society for Applied Microbiology.

Microbiological performance of dairy processing plants is influenced by scale of production and the implemented food safety management system: a case study.

PubMed

Opiyo, Beatrice Atieno; Wangoh, John; Njage, Patrick Murigu Kamau

2013-06-01

The effects of existing food safety management systems and size of the production facility on microbiological quality in the dairy industry in Kenya were studied. A microbial assessment scheme was used to evaluate 14 dairies in Nairobi and its environs, and their performance was compared based on their size and on whether they were implementing hazard analysis critical control point (HACCP) systems and International Organization for Standardization (ISO) 22000 recommendations. Environmental samples from critical sampling locations, i.e., workers' hands and food contact surfaces, and from end products were analyzed for microbial quality, including hygiene indicators and pathogens. Microbial safety level profiles (MSLPs) were constructed from the microbiological data to obtain an overview of contamination. The maximum MSLP score for environmental samples was 18 (six microbiological parameters, each with a maximum MSLP score of 3) and that for end products was 15 (five microbiological parameters). Three dairies (two large scale and one medium scale; 21% of total) achieved the maximum MSLP scores of 18 for environmental samples and 15 for the end product. Escherichia coli was detected on food contact surfaces in three dairies, all of which were small scale dairies, and the microorganism was also present in end product samples from two of these dairies, an indication of cross-contamination. Microbial quality was poorest in small scale dairies. Most operations in these dairies were manual, with minimal system documentation. Noncompliance with hygienic practices such as hand washing and cleaning and disinfection procedures, which is common in small dairies, directly affects the microbial quality of the end products. Dairies implementing HACCP systems or ISO 22000 recommendations achieved maximum MSLP scores and hence produced safer products.

[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.

Molecular characterization of hepatitis A virus isolates from environmental and clinical samples in Greece

PubMed Central

2010-01-01

Background Hepatitis A virus (HAV) strains detected in environmental and clinical samples were analysed to characterize the genotypes of HAV circulating in Greece. Fifty (50) sewage samples were collected from Patras (South-Western Greece) and Alexandroupolis (North-Eastern Greece) from 2007 until 2009, accordingly. The clinical samples derived from an HAV outbreak involved populations from three neighbouring prefectures of North-Eastern Greece (Xanthi, Rodopi, and Evros). HAV particles were detected by nested RT-PCR, using a previously validated set of primers to amplify a 290-bp fragment encompassing the 5'-NTR. Positive HAV samples were confirmed by sequencing of the PCR product. To determine the relatedness between the different isolated sequences, a phylogenetic tree was constructed. Results Results showed a 100% prevalence of genotype I, and particularly subgenotype IA. The analyzed HAV strains were closely related between them with the percentage of nucleotide identity ranging between 96% and 100%. Conclusions The study revealed the major prevalence of circulating strains of IA genotype in Greece and underlined the usefulness of molecular methods for the detection and typing of viruses in both environmental and clinical samples. The present study is, to our knowledge, the first in Greece to depict the simultaneous molecular characterization of HAV strains isolated from both clinical and environmental samples. PMID:20846383

Impact of transition from microscopy to molecular screening for detection of intestinal protozoa in Dutch patients.

PubMed

Svraka-Latifovic, S; Bouter, S; Naus, H; Bakker, L J; Timmerman, C P; Dorigo-Zetsma, J W

2014-11-01

Detection of intestinal protozoa by PCR methods has been described as being sensitive and specific, and as improving the diagnostic yield. Here we present the outcome of the transition from microscopy to molecular screening for detection of a select group of intestinal protozoa in faeces in our laboratory. Introduction of molecular screening for intestinal protozoa resulted in higher sensitivity, reduced hands-on-time, reduced time-to-results, leading to improved diagnostic efficiency. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

Evaluation of oral microbiology lab curriculum reform.

PubMed

Nie, Min; Gao, Zhen Y; Wu, Xin Y; Jiang, Chen X; Du, Jia H

2015-12-07

According to the updated concept of oral microbiology, the School of Stomatology, Wuhan University, has carried out oral microbiology teaching reforms during the last 5 years. There was no lab curriculum before 2009 except for a theory course of oral microbiology. The school has implemented an innovative curriculum with oral medicine characteristics to strengthen understanding of knowledge, cultivate students' scientific interest and develop their potential, to cultivate the comprehensive ability of students. This study was designed to evaluate the oral microbiology lab curriculum by analyzing student performance and perceptions regarding the curriculum from 2009 to 2013. The lab curriculum adopted modalities for cooperative learning. Students collected dental plaque from each other and isolated the cariogenic bacteria with selective medium plates. Then they purified the enrichment culture medium and identified the cariogenic strains by Gram stain and biochemical tests. Both quantitative and qualitative data for 5 years were analysed in this study. Part One of the current study assessed student performance in the lab from 2009 to 2013. Part Two used qualitative means to assess students' perceptions by an open questionnaire. The 271 study students' grades on oral microbiology improved during the lab curriculum: "A" grades rose from 60.5 to 81.2 %, and "C" grades fell from 28.4 to 6.3 %. All students considered the lab curriculum to be interesting and helpful. Quantitative and qualitative data converge to suggest that the lab curriculum has strengthened students' grasp of important microbiology-related theory, cultivated their scientific interest, and developed their potential and comprehensive abilities. Our student performance and perception data support the continued use of the innovative teaching system. As an extension and complement of the theory course, the oral microbiology lab curriculum appears to improve the quality of oral medicine education and help to

Medical microbiology training needs and trainee experience.

PubMed

Seale, Josephine; Elamin, Wael; Millar, Michael

2014-02-01

Training in microbiology is continuing to evolve. Standardisation of this process has, in part, been achieved through the development of a training curriculum by the Royal College of Pathologists (RCPath). A substantial proportion of microbiology training occurs through telephone consultations. To ascertain the content of these interactions and the extent to which the necessary skills outlined by the curriculum are attainable via these consultations. Records of telephone consultations made by microbiology registrars (SpR) on the Laboratory Information Management System (LIMS) over a 6 month period were analysed with regard to who initiated contact and the type of advice provided. An average of 426 SpR entries per month were made on the LIMS following telephone consultations. These consultations were predominantly initiated by fellow clinicians as opposed to the SpR. The majority (79%) of advice entailed guidance as to the use of antimicrobials which resulted in an alteration of the current regimen in 54% of cases. This study represents the first attempt to quantify the telephone consultations of microbiology trainees. It is concluded that although such interactions provide a means of attaining some of the competencies outlined by the RCPath curriculum, the bias towards antimicrobial advice reflects a discrepancy between the needs of the service users and the broad skill set advocated by the current microbiology training programme. Future modifications will need to take this into account to ensure both the training of SpRs and the microbiology service is fit for purpose.

Proteomics in medical microbiology.

PubMed

Cash, P

2000-04-01

The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

[Microbiological quality of " ice, ice cream. sorbet" sold on the streets of Phnom Penh; April 1996-April 1997].

PubMed

Kruy, S L; Soares, J L; Ping, S; Sainte-Marie, F F

2001-12-01

A study of the microbiological quality of ice lice creams/sorbets sold on the streets of Phnom Penh city was conducted from April 1996 to April 1997. Socio-demographic and environmental characteristics with two ice/ice creams samples were collected from vendors selected in the city. A total of 105 vendors and 210 ice/ice creams samples were randomly selected for the study period. Ice/ice cream vendors in the streets of Phnom Penh were adults (mean age: 28 years old) with a male predominance (86.5%). Mean educational level of vendors was 5 years with no training in mass catering. Most ice creams and sorbets (81.7%) were made using traditional methods. Microbiological analysis performed in the laboratory of Pasteur Institute of Cambodia indicated the poor bacteriological quality of the samples. The proportions of samples classified unsafe according to microbiological criteria were 83.3% for total bacterial count at 30 degrees C, 70% for total coliforms, 30% for faecal coliforms, 12.2% for Staphylococcus aureus and 1.9% for presence of Salmonella spp. These bacterial results suggest that many other food products sold in the streets may be similarly poor. Safety measures should be undertaken to avoid potential threats. Regulation of the street food sector should be part of a larger strategy for enhanced food safety and environmental quality in the city.

TyPol - a new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior.

PubMed

Servien, Rémi; Mamy, Laure; Li, Ziang; Rossard, Virginie; Latrille, Eric; Bessac, Fabienne; Patureau, Dominique; Benoit, Pierre

2014-09-01

Following legislation, the assessment of the environmental risks of 30000-100000 chemical substances is required for their registration dossiers. However, their behavior in the environment and their transfer to environmental components such as water or atmosphere are studied for only a very small proportion of the chemical in laboratory tests or monitoring studies because it is time-consuming and/or cost prohibitive. Therefore, the objective of this work was to develop a new methodology, TyPol, to classify organic compounds, and their degradation products, according to both their behavior in the environment and their molecular properties. The strategy relies on partial least squares analysis and hierarchical clustering. The calculation of molecular descriptors is based on an in silico approach, and the environmental endpoints (i.e. environmental parameters) are extracted from several available databases and literature. The classification of 215 organic compounds inputted in TyPol for this proof-of-concept study showed that the combination of some specific molecular descriptors could be related to a particular behavior in the environment. TyPol also provided an analysis of similarities (or dissimilarities) between organic compounds and their degradation products. Among the 24 degradation products that were inputted, 58% were found in the same cluster as their parents. The robustness of the method was tested and shown to be good. TyPol could help to predict the environmental behavior of a "new" compound (parent compound or degradation product) from its affiliation to one cluster, but also to select representative substances from a large data set in order to answer some specific questions regarding their behavior in the environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular ecology of Listeria spp., Salmonella, Escherichia coli O157:H7 and non-O157 Shiga toxin-producing E. coli in pristine natural environments in Northern Colorado.

PubMed

Ahlstrom, C A; Manuel, C S; Den Bakker, H C; Wiedmann, M; Nightingale, K K

2018-02-01

Molecular subtyping is commonly used in foodborne disease surveillance and microbial source tracking. There is a knowledge gap regarding the molecular ecology of foodborne pathogens in non-food-associated environments. The objective of this study was to isolate and subtype foodborne pathogens from pristine natural environments with minimal anthropogenic inputs. Five locations (wilderness areas) in Northern Colorado were sampled during the spring, summer and fall over a 2-year period. Soil, water, sediment, surface soil and wildlife faecal samples were microbiologically analysed to detect Listeria, Salmonella and Shiga toxin-producing Escherichia coli (STEC), and resultant isolates were subtyped. Three samples tested positive for Listeria monocytogenes and 19 samples contained other Listeria spp. Salmonella was isolated from two samples, five samples contained non-O157 STEC, and E. coli O157:H7 was not detected. Two L. monocytogenes isolates from faecal samples collected from the same wilderness area over a year apart shared the same PFGE pattern, while all other isolates had a unique type. Our data indicate that (i) there was a rare presence of human foodborne pathogens in pristine natural environments in Northern Colorado, (ii) there was genetic diversity between organisms isolated within a given wilderness area, and (iii) the Northern Colorado climate and topography may contribute to the low occurrence of these organisms. Relatively little is known about the molecular ecology of foodborne pathogens in pristine natural environments. While foodborne pathogens were rarely detected in wildlife faecal and environmental samples from the wilderness areas in this study, some isolates shared DNA fingerprint types with human clinical isolates from same region during the same time frame, highlighting the need for environmental isolate subtype data. The availability of molecular subtyping data for non-food-associated foodborne pathogen isolates can facilitate

Microbiology of Fresh Produce: Route of Contamination, Detection Methods, and Remedy.

PubMed

Rajwar, Asmita; Srivastava, Pragati; Sahgal, Manvika

2016-10-25

Fresh fruits and vegetables are an important part of a healthful diet. They provide vitamins, minerals and fiber to help keep our body healthy. Occasionally, fresh fruits and vegetables can become contaminated with harmful bacteria or viruses, which are also known as pathogens. The major family of pathogen associated with food are members of Enterobacteriaceae which commonly form a part of microbiological criteria and their presence is traditionally related to hygiene and safety of foods. Organic fertilizers, irrigation water quality and soil are major source of contamination. For removal of pathogens, various decontamination procedures are also followed to reduce microbial load on the fruits. These are chemical preservatives and irradiation. Microbiological study of fresh produce can be done by various phenotypic, biochemical and molecular techniques so that pathogen can properly be identified. The World Health Organization (WHO) developed global risk communication message and training materials to assist countries in strengthening their food educating programs. There is a need for improved surveillance systems on food-borne pathogens, on food products and on outbreaks so that comparable data are available from a wider range of countries.

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.

Microbiological studies of hot springs in India: a review.

PubMed

Poddar, Abhijit; Das, Subrata K

2018-01-01

The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.

Lower antibiotic costs attributable to clinical microbiology rounds.

PubMed

Huang, Richard S P; Guervil, David J; Hunter, Robert L; Wanger, Audrey

2015-09-01

At our institution, our microbiologist, pharmacist, and infectious disease (ID) team meet to discuss ID patients, and this meeting is referred to as microbiology rounds. We hypothesized that our microbiology rounds reduce antibiotic costs. The study involved a review of 80 patients with an ID consultation order at each of the 3 hospitals: hospital A (HA) (only HA has microbiology rounds), hospital B (HB), and hospital C (HC). Of this population, we included patients with a positive blood culture. Thirty-six patients who met the above criteria were included in the study. The average antibiotic cost/patient/day at HA, HB, and HC were $66.0, $123, and $109, respectively. Also, we found that change in antibiotics was appropriate when compared to the final microbiology results in 90%, 44%, and 40% of the time at HA, HB, and HC, respectively. Herein, we found an association between conducting microbiology rounds and reduction of antibiotic cost. Copyright © 2015 Elsevier Inc. All rights reserved.

[Safety in the Microbiology laboratory].

PubMed

Rojo-Molinero, Estrella; Alados, Juan Carlos; de la Pedrosa, Elia Gómez G; Leiva, José; Pérez, José L

2015-01-01

The normal activity in the laboratory of microbiology poses different risks - mainly biological - that can affect the health of their workers, visitors and the community. Routine health examinations (surveillance and prevention), individual awareness of self-protection, hazard identification and risk assessment of laboratory procedures, the adoption of appropriate containment measures, and the use of conscientious microbiological techniques allow laboratory to be a safe place, as records of laboratory-acquired infections and accidents show. Training and information are the cornerstones for designing a comprehensive safety plan for the laboratory. In this article, the basic concepts and the theoretical background on laboratory safety are reviewed, including the main legal regulations. Moreover, practical guidelines are presented for each laboratory to design its own safety plan according its own particular characteristics. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Molecular characterization of environmental Cryptococcus neoformans VNII isolates in Jos, Plateau State, Nigeria.

PubMed

Nnadi, N E; Enweani, I B; Cogliati, M; Ayanbimpe, G M; Okolo, M O; Kim, E; Sabitu, M Z; Criseo, G; Romeo, O; Scordino, F

2016-12-01

Cryptococcus neoformans and Cryptococcus gattii are encapsulated yeasts able to cause fatal neurological infections in both human and other mammals. Cryptococcosis is the most common fungal infection of the central nervous system and has a huge burden in sub-Saharan Africa and South East Asia. Bird excreta are considered an environmental reservoir for C. neoformans in urban areas, therefore a study aimed at isolating and characterizing this yeast is important in disease management. In this study, one hundred samples of pigeon droppings were collected in Jos, Plateau State, Nigeria. C. neoformans was isolated from three samples and initially identified using standard phenotypic and biochemical tests. Molecular analysis revealed that all three isolates belonged to C. neoformans genotype VNII, mating type α and were assigned to the sequence type ST43 by multilocus sequence typing analysis. This study reports, for the first time, the molecular characterization of C. neoformans in Nigeria, where little is still known about the environmental distribution of the genotypes, serotypes and mating types of this important human pathogen. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Implementation of Rapid Molecular Infectious Disease Diagnostics: the Role of Diagnostic and Antimicrobial Stewardship.

PubMed

Messacar, Kevin; Parker, Sarah K; Todd, James K; Dominguez, Samuel R

2017-03-01

New rapid molecular diagnostic technologies for infectious diseases enable expedited accurate microbiological diagnoses. However, diagnostic stewardship and antimicrobial stewardship are necessary to ensure that these technologies conserve, rather than consume, additional health care resources and optimally affect patient care. Diagnostic stewardship is needed to implement appropriate tests for the clinical setting and to direct testing toward appropriate patients. Antimicrobial stewardship is needed to ensure prompt appropriate clinical action to translate faster diagnostic test results in the laboratory into improved outcomes at the bedside. This minireview outlines the roles of diagnostic stewardship and antimicrobial stewardship in the implementation of rapid molecular infectious disease diagnostics. Copyright © 2017 American Society for Microbiology.

Molecular mechanisms governing differential robustness of development and environmental responses in plants

PubMed Central

Lachowiec, Jennifer; Queitsch, Christine; Kliebenstein, Daniel J.

2016-01-01

Background Robustness to genetic and environmental perturbation is a salient feature of multicellular organisms. Loss of developmental robustness can lead to severe phenotypic defects and fitness loss. However, perfect robustness, i.e. no variation at all, is evolutionarily unfit as organisms must be able to change phenotype to properly respond to changing environments and biotic challenges. Plasticity is the ability to adjust phenotypes predictably in response to specific environmental stimuli, which can be considered a transient shift allowing an organism to move from one robust phenotypic state to another. Plants, as sessile organisms that undergo continuous development, are particularly dependent on an exquisite fine-tuning of the processes that balance robustness and plasticity to maximize fitness. Scope and Conclusions This paper reviews recently identified mechanisms, both systems-level and molecular, that modulate robustness, and discusses their implications for the optimization of plant fitness. Robustness in living systems arises from the structure of genetic networks, the specific molecular functions of the underlying genes, and their interactions. This very same network responsible for the robustness of specific developmental states also has to be built such that it enables plastic yet robust shifts in response to environmental changes. In plants, the interactions and functions of signal transduction pathways activated by phytohormones and the tendency for plants to tolerate whole-genome duplications, tandem gene duplication and hybridization are emerging as major regulators of robustness in development. Despite their obvious implications for plant evolution and plant breeding, the mechanistic underpinnings by which plants modulate precise levels of robustness, plasticity and evolvability in networks controlling different phenotypes are under-studied. PMID:26473020

Environmental effects and aquatic organisms: investigations of molecular mechanisms of carcinogenesis.

PubMed Central

Van Beneden, R J

1997-01-01

Cancers of the reproductive system are among the leading causes of mortality in women in the United States. While both genetic and environmental factors have been implicated in their etiology, the extent of the contribution of environmental factors to human diseases remains controversial. To better address the role of environmental exposures in cancer etiology, there has been an increasing focus on the development of nontraditional, environmentally relevant models. Our research involves the development of one such model. Gonadal tumors have been described in the softshell clam (Mya arenaria) in Maine and the hardshell clam (Mercenaria spp.) from Florida. Prevalence of these tumors is as high as 40% in some populations in eastern Maine and 60% in some areas along the Indian River in Florida. The average tumor prevalence in Maine and Florida is approximately 20 and 11%, respectively. An association has been suggested between the use of herbicides and the incidence of gonadal tumors in the softshell clam in Maine. The role of environmental exposures in the development of the tumors in Mercenaria in Florida is unknown; however, there is evidence that genetic factors may contribute to its etiology. Epidemiologic studies of human populations in these same areas show a higher than average mortality rate due to cancers of the reproductive system in women, including both ovarian and breast cancer. The relationship, if any, among these observations is unknown. Our studies on the molecular basis of this disease in clams may provide additional information on environmental exposures and their possible link to cancer in clams and other organisms, including humans. Images Figure 1. A Figure 1. B PMID:9168012

Coral microbiology

USGS Publications Warehouse

Rosenberg, Eugene; Kellogg, Christina A.; Rohwer, Forest

2007-01-01

In the last 30 years, there has been approximately a 30% loss of corals worldwide, largely due to emerging diseases (Harvell et al., 2002, 2007; Hughes et al., 2003). Coral microbiology is a new field, driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms and to use this knowledge to eventually prevent the spread of coral 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.

How many microbiology consultants are needed?

PubMed Central

Bignardi, G E

1993-01-01

It is difficult to measure medical staff workload and medical staff requirements in microbiology departments. A review of 14 job descriptions for consultant microbiologists showed that the number of hospital beds and the number of specimens are more reliable workload indices than the population figure. Ratios between beds or specimens and medical staff numbers may help to identify understaffed or overstaffed microbiology departments. PMID:8254095

Molecular Methods for the Detection of Mycoplasma and Ureaplasma Infections in Humans

PubMed Central

Waites, Ken B.; Xiao, Li; Paralanov, Vanya; Viscardi, Rose M.; Glass, John I.

2012-01-01

Mycoplasma and Ureaplasma species are well-known human pathogens responsible for a broad array of inflammatory conditions involving the respiratory and urogenital tracts of neonates, children, and adults. Greater attention is being given to these organisms in diagnostic microbiology, largely as a result of improved methods for their laboratory detection, made possible by powerful molecular-based techniques that can be used for primary detection in clinical specimens. For slow-growing species, such as Mycoplasma pneumoniae and Mycoplasma genitalium, molecular-based detection is the only practical means for rapid microbiological diagnosis. Most molecular-based methods used for detection and characterization of conventional bacteria have been applied to these organisms. A complete genome sequence is available for one or more strains of all of the important human pathogens in the Mycoplasma and Ureaplasma genera. Information gained from genome analyses and improvements in efficiency of DNA sequencing are expected to significantly advance the field of molecular detection and genotyping during the next few years. This review provides a summary and critical review of methods suitable for detection and characterization of mycoplasmas and ureaplasmas of humans, with emphasis on molecular genotypic techniques. PMID:22819362

Environmental Shortcourse Final report [Joint US-EC Short Course on Environmental Biotechnology: Microbial Catalysts for the Environment

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

Zylstra, Gerben; van der Meer, Jan Roelof

The Joint US-EC Short Course on Environmental Biotechnology is designed for several purposes. One of the central tenets is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that will set the groundwork for future overseas collaborative interactions. The course is also designed to give the scientists hands-on experience in modern, up-to-date biotechnological methods for the analysis of microbes and their activities pertinent to the remediation of pollutants in the environment. The 2011 course covered multiple theoretical and practical topics in environmental biotechnology. The practical part was centered around amore » full concise experiment to demonstrate the possibility for targeted remediation of contaminated soil. Experiments included chemical, microbiological, and molecular analyses of sediments and/or waters, contaminant bioavailability assessment, seeded bioremediation, gene probing, PCR amplification, microbial community analysis based on 16S rRNA gene diversity, and microarray analyses. Each of these topics is explained in detail. The practical part of the course was complemented with two lectures per day, given by distinguished scientists from the US and from Europe, covering a research area related to what the students are doing in the course.« less

Amid the possible causes of a very famous foxing: molecular and microscopic insight into Leonardo da Vinci's self-portrait.

PubMed

Piñar, Guadalupe; Tafer, Hakim; Sterflinger, Katja; Pinzari, Flavia

2015-12-01

Leonardo da Vinci's self-portrait is affected by foxing spots. The portrait has no fungal or bacterial infections in place, but is contaminated with airborne spores and fungal material that could play a role in its disfigurement. The knowledge of the nature of the stains is of great concern because future conservation treatments should be derived from scientific investigations. The lack of reliable scientific data, due to the non-culturability of the microorganisms inhabiting the portrait, prompted the investigation of the drawing using non-invasive and micro-invasive sampling, in combination with scanning electron microscope (SEM) imaging and molecular techniques. The fungus Eurotium halophilicum was found in foxing spots using SEM analyses. Oxalates of fungal origin were also documented. Both findings are consistent with the hypothesis that tonophilic fungi germinate on paper metabolizing organic acids, oligosaccharides and proteic compounds, which react chemically with the material at a low water activity, forming brown products and oxidative reactions resulting in foxing spots. Additionally, molecular techniques enabled a screening of the fungi inhabiting the portrait and showed differences when different sampling techniques were employed. Swabs samples showed a high abundance of lichenized Ascomycota, while the membrane filters showed a dominance of Acremonium sp. colonizing the drawing. © 2015 The Authors. Environmental Microbiology Reports published by Society for Applied Microbiology and John Wiley & Sons Ltd.

ENVIRONMENTALLY BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

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

J. Robert Paterek; Gemma Husmillo

The overall program objective is to develop and evaluate environmental benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is one or more environmental benign, a.k.a. ''green'' products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Capsicum sp. extracts and pure compounds were screened for their antimicrobial activity against MIC causing bacteria. Studies on the ability of these compounds to dissociate biofilm from the substratum were conducted using microtiter plate assays. Tests usingmore » laboratory scale pipeline simulators continued. Preliminary results showed that the natural extracts possess strong antimicrobial activity being comparable to or even better than the pure compounds tested against strains of sulfate reducers. Their minimum inhibitory concentrations had been determined. It was also found that they possess bactericidal properties at minimal concentrations. Biofilm dissociation activity as assessed by microtiter plate assays demonstrated varying degrees of differences between the treated and untreated group with the superior performance of the extracts over pure compounds. Such is an indication of the possible benefits that could be obtained from these natural products. Confirmatory experiments are underway.« less

[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

Status of the database on microorganism inactivation in environmental media (DIMEM)

USDA-ARS?s Scientific Manuscript database

Inactivation of pathogenic and indicator microorganisms is the essential component of their environmental fate which needs to be considered in environmental microbiology models. Existing data from a large number of inactivation experiments are dispersed across numerous publications with varying avai...

Practical microbiology in schools: a survey of UK teachers.

PubMed

Redfern, James; Burdass, Dariel; Verran, Joanna

2013-11-01

A survey of secondary school teachers investigated practical microbiology in the classroom. The results were heartening (practical microbiology was common), but concerns were expressed regarding equipment, time, cost, and expertise. Microbiologists should engage more with school education to support teachers and maintain the health of microbiology for future generations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Epidemiological transition of colorectal cancer in developing countries: Environmental factors, molecular pathways, and opportunities for prevention

PubMed Central

Bishehsari, Faraz; Mahdavinia, Mahboobeh; Vacca, Michele; Malekzadeh, Reza; Mariani-Costantini, Renato

2014-01-01

Colorectal cancer (CRC) is one of the leading causes of cancer and cancer-related mortality worldwide. The disease has been traditionally a major health problem in industrial countries, however the CRC rates are increasing in the developing countries that are undergoing economic growth. Several environmental risk factors, mainly changes in diet and life style, have been suggested to underlie the rise of CRC in these populations. Diet and lifestyle impinge on nuclear receptors, on the intestinal microbiota and on crucial molecular pathways that are implicated in intestinal carcinogenesis. In this respect, the epidemiological transition in several regions of the world offers a unique opportunity to better understand CRC carcinogenesis by studying the disease phenotypes and their environmental and molecular associations in different populations. The data from these studies may have important implications for the global prevention and treatment of CRC. PMID:24876728

Molecular Characterization of Polio from Environmental Samples: ISSP, The Israeli Sewage Surveillance Protocol.

PubMed

Shulman, Lester M; Manor, Yossi; Hindiyeh, Musa; Sofer, Danit; Mendelson, Ella

2016-01-01

Polioviruses are enteric viruses that cause paralytic poliomyelitis in less than 0.5 % of infections and are asymptomatic in >90 % infections of naïve hosts. Environmental surveillance monitors polio in populations rather than in individuals. When this very low morbidity to infection ratio, drops drastically in highly vaccinated populations, environmental surveillance employing manual or automatic sampling coupled with molecular analysis carried out in well-equipped central laboratories becomes the surveillance method of choice since polioviruses are excreted by infected individuals regardless of whether or not the infection is symptomatic. This chapter describes a high throughput rapid turn-around time method for molecular characterization of polioviruses from sewage. It is presented in five modules: (1) Sewage collection and concentration of the viruses in the sewage; (2) Cell cultures for identification of virus in the concentrated sewage; (3) Nucleic acid extractions directly from sewage and from tissue cultures infected with aliquots of concentrated sewage; (4) Nucleic Acid Amplification for poliovirus serotype identification and intratypic differentiation (discriminating wild and vaccine derived polioviruses form vaccine strains); and (5) Molecular characterization of viral RNA by qRT-PCR, TR-PCR, and Sequence analysis. Monitoring silent or symptomatic transmission of vaccine-derived polioviruses or wild polioviruses is critical for the endgame of poliovirus eradication. We present methods for adapting standard kits and validating the changes for this purpose based on experience gained during the recent introduction and sustained transmission of a wild type 1 poliovirus in Israel in 2013 in a population with an initial IPV vaccine coverage >90 %.

[Publication rates of Turkish medical specialty and doctorate theses on Medical Microbiology, Clinical Microbiology and Infectious Diseases disciplines in international journals].

PubMed

Sipahi, Oğuz Reşat; Caglayan Serin, Derya; Pullukcu, Hüsnü; Tasbakan, Meltem; Köseli Ulu, Demet; Yamazhan, Tansu; Arda, Bilgin; Sipahi, Hilal; Ulusoy, Sercan

2014-04-01

Writing a thesis is mandatory for getting a postgraduate medical degree in Turkey. Publication of the results of the thesis in an indexed journal makes the results available to researchers, however publication rate is usually low. The aim of this retrospective observational study was to investigate the publication rate of Turkish Infectious Diseases and Clinical Microbiology, Medical Microbiology specialty theses and Microbiology doctorate theses in international peer-review journals. On August 17th 2007, the thesis database of the Council of Higher Education of the Republic of Turkey (YOK) where all specialization and doctorate theses are recorded obligatorily, was searched for Infectious Diseases and Clinical Microbiology and Medical Microbiology specialty and Microbiology doctorate theses. Assuming that publication of a thesis would last at least six months, theses dated to February 2007 and after were excluded. The publication rate of those theses was found out by searching Science Citation Index-Expanded database for thesis author and supervisor between August 17-September 12, 2007. Chi-square test was used for statistical analysis. Our search yielded a total of 834 theses dated from 1997 to 2007, however 10 of them were excluded, since they were dated to February 2007 or after. It was found that the overall publication rate was 11.4% (94/824). The publication rates for Microbiology doctorate, Medical Microbiology and Infectious Diseases and Clinical Microbiology specialty theses were 13.7% (34/249), 10.7% (33/309) and 10.2% (27/266), respectively, with no statistical significance (p> 0.05). It was determined that nine (9.6%) of the 94 published theses belonged to 1997-2001 period, whereas 85 (80.4%) were in 2002-2007 period (p< 0.05). The probable reason for this increase was thought to be related with the updated criteria of YOK carried out in 2000 for academic promotions, nevertheless the publication rate of the investigated theses in international peer

Microbiological and environmental issues in show caves.

PubMed

Saiz-Jimenez, Cesareo

2012-07-01

Cultural tourism expanded in the last half of the twentieth century, and the interest of visitors has come to include caves containing archaeological remains. Some show caves attracted mass tourism, and economical interests prevailed over conservation, which led to a deterioration of the subterranean environment and the rock art. The presence and the role of microorganisms in caves is a topic that is often ignored in cave management. Knowledge of the colonisation patterns, the dispersion mechanisms, and the effect on human health and, when present, over rock art paintings of these microorganisms is of the utmost importance. In this review the most recent advances in the study of microorganisms in caves are presented, together with the environmental implications of the findings.

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

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.

DEVELOPMENT OF MOLECULAR MARKERS OF RESPONSE TO ASSESS THE SENSITIVITY OF CHILDREN TO ENVIRONMENTAL CHEMICALS

EPA Science Inventory

Development of Molecular Markers of Response to Assess the Sensitivity of Children to Environmental Chemicals

J.Allen, C. Blackman, M. Blaze, D. Delker, D. DeMarini, C. Doerr, R. Grindstaff, S.
Hester, C. Jones, A. Kligerman, G. Knapp, M. Kohan, C. Nelson, R. Owen, J. P...

Microbiology--Safety Considerations.

ERIC Educational Resources Information Center

Hoffmann, Sheryl K.

This paper discusses the risk assessment associated with microbiology instruction based on grade level, general control measures, appropriate activities for middle school and high school students, the preparation and sterilization of equipment, and safe handling techniques. Appended are instructions and figures on making wire loops and the…

Testing the performance of microbiological safety cabinets used in microbiology laboratories in South Korea.

PubMed

Hwang, S H; Yi, T W; Cho, K H; Lee, I M; Yoon, C S

2011-09-01

To test a performance of the microbiological safety cabinets (MSCs) according to the type of MSCs in microbial laboratories. Tests were carried out to assess the performance of 31 MSCs in 14 different facilities, including six different biological test laboratories in six hospitals and eight different laboratories in three universities. The following tests were performed on the MSCs: the downflow test, intake velocity test, high-efficiency particulate air filter leak test and the airflow smoke pattern test. These performance tests were carried out in accordance with the standard procedures. Only 23% of Class II A1 (8), A2 (19) and unknown MSCs (4) passed these performance tests. The main reasons for the failure of MSCs were inappropriate intake velocity (65%), leakage in the HEPA filter sealing (50%), unbalanced airflow smoke pattern in the cabinets (39%) and inappropriate downflow (27%). This study showed that routine checks of MSCs are important to detect and strengthen the weak spots that frequently develop, as observed during the evaluation of the MSCs of various institutions. Routine evaluation and maintenance of MSCs are critical for optimizing performance. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Microbiological, clinical and molecular findings of non-typhoidal Salmonella bloodstream infections associated with malaria, Oriental Province, Democratic Republic of the Congo.

PubMed

Falay, Dadi; Kuijpers, Laura Maria Francisca; Phoba, Marie-France; De Boeck, Hilde; Lunguya, Octavie; Vakaniaki, Emmanuel; Bertrand, Sophie; Mattheus, Wesley; Ceyssens, Pieter-Jan; Vanhoof, Raymond; Devlieger, Hugo; Van Geet, Chris; Verheyen, Erik; Ngbonda, Dauly; Jacobs, Jan

2016-06-10

In sub-Saharan Africa, non-typhoidal Salmonella (NTS) can cause bloodstream infections, referred to as invasive non-typhoidal Salmonella disease (iNTS disease); it can occur in outbreaks and is often preceded by malaria. Data from Central Africa is limited. Clinical, microbiological and molecular findings of NTS recovered in a blood culture surveillance project (2009-2014) were analyzed. In March-July 2012 there was an epidemic increase in malaria infections in the Oriental Province of the Democratic Republic of the Congo (DRC). In one referral hospital, overall hospital admissions in June 2012 were 2.6 times higher as compared to the same period in the years before and after (336 versus an average of 128 respectively); numbers of malaria cases and blood transfusions were nearly three- and five-fold higher respectively (317 versus 112 and 250 versus 55). Case fatality rates (in-hospital deaths versus all admissions) peaked at 14.6 %. Salmonella Typhimurium and Salmonella Enteritidis together accounted for 88.9 % of pathogens isolated from blood cultures collected during an outreach visit to the affected districts in June 2012. Children infected with Salmonella Enteritidis (33 patient files available) tended to be co-infected with Plasmodium falciparum more often than children infected with Salmonella Typhimurium (40 patients files available) (81.8 % versus 62.5 %). Through the microbiological surveillance project (May 2009-May 2014) 113 unique NTS isolates were collected (28.5 % (113/396) of pathogens); most (95.3 %) were recovered from children < 15 years. Salmonella Typhimurium (n = 54) and Salmonella Enteritidis (n = 56) accounted for 47.8 % and of 49.6 % NTS isolates respectively. Multilocus variable-number tandem-repeat analysis (MLVA) revealed more heterogeneity for Salmonella Typhimurium than for Salmonella Enteritidis. Most (82/96, 85.4 %) NTS isolates that were available for antibiotic susceptibility testing were multidrug resistant

The role of biomineralization in microbiologically influenced corrosion

NASA Technical Reports Server (NTRS)

Little, B.; Wagner, P.; Hart, K.; Ray, R.; Lavoie, D.; Nealson, K.; Aguilar, C.

1998-01-01

Synthetic iron oxides (goethite, alpha-FeO.OH; hematite, Fe2O3; and ferrihydrite, Fe(OH)3) were used as model compounds to simulate the mineralogy of surface films on carbon steel. Dissolution of these oxides exposed to pure cultures of the metal-reducing bacterium, Shewanella putrefaciens, was followed by direct atomic absorption spectroscopy measurement of ferrous iron coupled with microscopic analyses using confocal laser scanning and environmental scanning electron microscopies. During an 8-day exposure the organism colonized mineral surfaces and reduced solid ferric oxides to soluble ferrous ions. Elemental composition, as monitored by energy dispersive x-ray spectroscopy, indicated mineral replacement reactions with both ferrihydrite and goethite as iron reduction occurred. When carbon steel electrodes were exposed to S. putrefaciens, microbiologically influenced corrosion was demonstrated electrochemically and microscopically.

Microbiology Learning and Education Online.

PubMed

Guarner, Jeannette; Niño, Silvia M

2016-05-01

The ubiquity of devices that connect to the Internet has exploded, allowing for easy dissemination of information. Many teachers from kindergarten to universities use the information obtained online or post material they want their students to access. Online media readily places articles, books, videos, and games at our fingertips. The public in general also gathers health information from the Internet. The following review will explore what has been published regarding microbiology education and learning online and the use of electronic media by microbiologists for scientific purposes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

Verification of performance specifications for a US Food and Drug Administration-approved molecular microbiology test: Clostridium difficile cytotoxin B using the Becton, Dickinson and Company GeneOhm Cdiff assay.

PubMed

Schlaberg, Robert; Mitchell, Michael J; Taggart, Edward W; She, Rosemary C

2012-01-01

US Food and Drug Administration (FDA)-approved diagnostic tests based on molecular genetic technologies are becoming available for an increasing number of microbial pathogens. Advances in technology and lower costs have moved molecular diagnostic tests formerly performed for research purposes only into much wider use in clinical microbiology laboratories. To provide an example of laboratory studies performed to verify the performance of an FDA-approved assay for the detection of Clostridium difficile cytotoxin B compared with the manufacturer's performance standards. We describe the process and protocols used by a laboratory for verification of an FDA-approved assay, assess data from the verification studies, and implement the assay after verification. Performance data from the verification studies conducted by the laboratory were consistent with the manufacturer's performance standards and the assay was implemented into the laboratory's test menu. Verification studies are required for FDA-approved diagnostic assays prior to use in patient care. Laboratories should develop a standardized approach to verification studies that can be adapted and applied to different types of assays. We describe the verification of an FDA-approved real-time polymerase chain reaction assay for the detection of a toxin gene in a bacterial pathogen.

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology †

PubMed Central

Briggs, Amy G.; Hughes, Lee E.; Brennan, Robert E.; Buchner, John; Horak, Rachel E. A.; Amburn, D. Sue Katz; McDonald, Ann H.; Primm, Todd P.; Smith, Ann C.; Stevens, Ann M.; Yung, Sunny B.; Paustian, Timothy D.

2017-01-01

Misconceptions, or alternative conceptions, are incorrect understandings that students have incorporated into their prior knowledge. The goal of this study was the identification of misconceptions in microbiology held by undergraduate students upon entry into an introductory, general microbiology course. This work was the first step in developing a microbiology concept inventory based on the American Society for Microbiology’s Recommended Curriculum Guidelines for Undergraduate Microbiology. Responses to true/false (T/F) questions accompanied by written explanations by undergraduate students at a diverse set of institutions were used to reveal misconceptions for fundamental microbiology concepts. These data were analyzed to identify the most difficult core concepts, misalignment between explanations and answer choices, and the most common misconceptions for each core concept. From across the core concepts, nineteen misconception themes found in at least 5% of the coded answers for a given question were identified. The top five misconceptions, with coded responses ranging from 19% to 43% of the explanations, are described, along with suggested classroom interventions. Identification of student misconceptions in microbiology provides a foundation upon which to understand students’ prior knowledge and to design appropriate tools for improving instruction in microbiology. PMID:29854046

Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review.

PubMed

Liu, Zhifeng; Liu, Yujie; Zeng, Guangming; Shao, Binbin; Chen, Ming; Li, Zhigang; Jiang, Yilin; Liu, Yang; Zhang, Yu; Zhong, Hua

2018-07-01

The molecular docking has been employed successfully to study the mechanism of biodegradation in the environmental remediation in the past few years, although medical science and biology are the main application areas for it. Molecular docking is a very convenient and low cost method to understand the reaction mechanism of proteins or enzymes with ligands with a high accuracy. This paper mainly provides a review for the application of molecular docking between organic pollutants and enzymes. It summarizes the fundamental knowledge of molecular docking, such as its theory, available softwares and main databases. Moreover, five types of pollutants, including phenols, BTEX (benzene, toluene, ethylbenzene, and xylenes), nitrile, polycyclic aromatic hydrocarbons (PAHs), and high polymer (e.g., lignin and cellulose), are discussed from molecular level. Different removal mechanisms are also explained in detail via docking technology. Even though this method shows promising application in the research of biodegradation, further studies are still needed to relate with actual condition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Transforming clinical microbiology with bacterial genome sequencing.

PubMed

Didelot, Xavier; Bowden, Rory; Wilson, Daniel J; Peto, Tim E A; Crook, Derrick W

2012-09-01

Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

Transforming clinical microbiology with bacterial genome sequencing

PubMed Central

2016-01-01

Whole genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here we review the current status of clinical microbiology and how it has already begun to be transformed by the use of next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. The application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow. PMID:22868263

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.

Subsurface Microbiology and Biogeochemistry

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

Fredrickson, Jim K.; Fletcher, Madilyn

2001-05-01

Jim contributed a chapter to this book, in addition to co-editing it with Madilyn Fletcher. Fredrickson, J. K., and M. Fletcher. (eds.) 2001 Subsurface Microbiology and Biogeochemistry. Wiley-Liss, Inc., New York.

Planning Meeting for Colloquium and Report on: Systems Microbiology: Beyond Microbial Genomics

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

Buckley, Merry R.

to emerge from studying systems microbiology (e.g., environmental, agricultural, energy production, medical)? (3) Who should be working on systems microbiology? Research Issues: (1) What kind of information is needed to understand how biological systems function? (2) What kind of information is currently available? (3) What information is not available? (4) How do we acquire additional information? (5) What defines a microbial species? (6) How do we measure ''noise'' in a biological system? (7) How are biological systems regulated? (8) How can a systems biology approach be applied to microbial communities? Technical Challenges: (1) What are the technical bottlenecks that limit advances in systems microbiology? (2) What are the quantitative issues and problems that need to be addressed? (3) How much data do we need? (4) How do we best get those data? (5) What kind of data do we need? (6) How do we assure the quality of the data? (7) How do we optimize utilization of the data? (8) How do we apply data from one system to another? (9) What are the questions we need to ask to determine functionality? Education, Training, and Communications Issues: (1) Are we currently training scientists to utilize existing and emerging technologies? If not, how do we? (2) Should new collaborations be initiated to study systems microbiology? If so, what are they and who should participate (academics, research foundations, industry, government, etc.)? (3) How can these collaborations be encouraged? (4) How important is international collaboration? Why or why not? (5) What should the public know about the potential of this kind of research? (6) Are there commercial potentials? If so, what are they? (7) What can the scientific community do to better communicate these issues? How? (8) Is there a role for professional societies? If so, what?« less

Current and past strategies for bacterial culture in clinical microbiology.

PubMed

Lagier, Jean-Christophe; Edouard, Sophie; Pagnier, Isabelle; Mediannikov, Oleg; Drancourt, Michel; Raoult, Didier

2015-01-01

A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Environmental microbiology as related to planetary quarantine

NASA Technical Reports Server (NTRS)

Pflug, I. J.

1972-01-01

The experimental design of a study to evaluate the effect of different cleaning methods and storage conditions on the dry heat resistance of Bacillus subtilis var. niger spores is described and the results for the first evaluation are reported. Specifically, the synergistic effect which occurs when spores are subjected simultaneously to dry heat and gamma radiation so as to be able to specify thermoradiation sterilization cycles was investigated. Attempts were made to understand the underlying mechanism(s) that lead to spore death from this combination of stresses. Data cover: (1) the survival of spores on surfaces at various temperatures in a precisely controlled environmental system, (2) the rate of destruction of these spores at ambient temperature when subjected to gamma radiation, and (3) the rate of destruction of spores when they are subjected to combined gamma radiation and thermal stresses.

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.

ENVIRONMENTAL BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

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

J.R. Paterek; G. Husmillo; V. Trbovic

The overall program objective is to develop and evaluate environmental benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is one or more environmental benign, a.k.a. ''green'' products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter were isolation and cultivation of MIC-causing microorganisms from corroded pipeline samples, optimizing parameters in the laboratory-scale corrosion test loop system and testing the effective concentrations of Capsicum sp. extracts to verifymore » the extent of corrosion on metal coupons by batch culture method. A total of 22 strains from the group of heterotrophic, acid producing, denitrifying and sulfate reducing bacteria were isolated from the gas pipeline samples obtained from Northern Indiana Public Service Company in Trenton, Indiana. They were purified and will be sent out for identification. Bacterial strains of interest were used in antimicrobial screenings and test loop experiments. Parameters for the laboratory-scale test loop system such as gas and culture medium flow rate; temperature; inoculation period; and length of incubation were established. Batch culture corrosion study against Desulfovibrio vulgaris showed that one (S{sub 1}M) out of the four Capsicum sp. extracts tested was effective in controlling the corrosion rate in metal coupons by 33.33% when compared to the untreated group.« less

Goals and objectives for molecular pathology education in residency programs. The Association for Molecular Pathology Training and Education Committee.

PubMed

1999-11-01

Increasing knowledge of the molecular basis of disease and advances in technology for analyzing nucleic acids and gene products are changing pathology practice. The explosion of information regarding inherited susceptibility to disease is an important aspect of this transformation. Pathology residency programs are incorporating molecular pathology education into their curricula to prepare newly trained pathologists for the future, yet little guidance has been available regarding the important components of molecular pathology training. We present general goals for pathology training programs for molecular pathology education. These include recommendations to pathology residents for the acquisition of both basic knowledge in human genetics and molecular biology and specific skills relevant to microbiology, molecular oncology, genetics, histocompatibility, and identity determination. The importance of residents gaining facility in integrating data gained via nucleic acid based-technology with other laboratory and clinical information available in the care of patients is emphasized.

Identification of Burkholderia spp. in the Clinical Microbiology Laboratory: Comparison of Conventional and Molecular Methods

PubMed Central

van Pelt, Cindy; Verduin, Cees M.; Goessens, Wil H. F.; Vos, Margreet C.; Tümmler, Burkhard; Segonds, Christine; Reubsaet, Frans; Verbrugh, Henri; van Belkum, Alex

1999-01-01

Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as Burkholderia cepacia (n = 51), B. gladioli (n = 14), Ralstonia pickettii (n = 6), B. multivorans (n = 2), Stenotrophomonas maltophilia (n = 3), and Pseudomonas aeruginosa (n = 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as Burkholderia spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of B. cepacia appeared to be the API 20NE test. None of the biochemical assays successfully grouped the B. gladioli strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different Burkholderia spp. With this method, B. gladioli was also reliably classified in a separate group. For the laboratory diagnosis of B. cepacia, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a Burkholderia phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR

Evaluation of hygiene practices and microbiological status of ready-to-eat vegetable salads in Spanish school canteens.

PubMed

Rodríguez-Caturla, Magdevis Y; Valero, Antonio; Carrasco, Elena; Posada, Guiomar D; García-Gimeno, Rosa M; Zurera, Gonzalo

2012-08-30

This study was conducted in eight Spanish school canteens during the period 2008-2009. Food handlers' practices, kitchen equipment, hygiene/sanitation conditions and handling practices were evaluated using checklists. In parallel, the microbiological quality and safety of ready-to-eat (RTE) vegetable salads were assessed. In addition, food contact surfaces and environmental air quality of different areas were analysed. The study determined the relationship between the microbiological quality of RTE foods and food handling practices, together with the degree of contamination of working surfaces and environmental contamination of processing and distribution areas. Some deficiencies were found regarding the use and change of gloves, hand-washing and cleanliness of working surfaces. The microbial levels detected in the foods examined indicated the absence of pathogens in the samples analysed. Surface counts were higher on cutting boards and faucets, showing insufficient cleanliness procedures. This study constitutes a descriptive analysis of the hygiene/sanitation conditions implemented in food service systems in eight Spanish school canteens. The results should help risk managers to better define control measures to be adopted in order to prevent foodborne infections. Copyright © 2012 Society of Chemical Industry.

Evaluation of an online program to teach microbiology to internal medicine residents.

PubMed

Guarner, Jeannette; Burd, Eileen M; Kraft, Colleen S; Armstrong, Wendy S; Lenorr, Kenya; Spicer, Jennifer O; Martin, Donna; del Rio, Carlos

2015-01-01

Microbiology rounds are an integral part of infectious disease consultation service. During microbiology rounds, we highlight microbiology principles using vignettes. We created case-based, interactive, microbiology online modules similar to the vignettes presented during microbiology rounds. Since internal medicine residents rotating on our infectious disease elective have limited time to participate in rounds and learn microbiology, our objective was to evaluate the use of the microbiology online modules by internal medicine residents. We asked residents to complete 10 of 25 online modules during their infectious disease elective. We evaluated which modules they chose and the change in their knowledge level. Forty-six internal medicine residents completed assessments given before and after accessing the modules with an average of 11/20 (range, 6 to 19) and 16/20 (range, 9 to 20) correct questions, respectively (average improvement, 5 questions; P = 0.0001). The modules accessed by more than 30 residents included those related to Clostridium difficile, anaerobes, Candida spp., Streptococcus pneumoniae, influenza, Mycobacterium tuberculosis, and Neisseria meningitidis. We demonstrated improved microbiology knowledge after completion of the online modules. This improvement may not be solely attributed to completing the online modules, as fellows and faculty may have provided additional microbiology education during the rotation. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

There must be a prokaryote somewhere: microbiology's search for itself

NASA Technical Reports Server (NTRS)

Woese, C. R.

1994-01-01

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.

The roots--a short history of industrial microbiology and biotechnology.

PubMed

Buchholz, Klaus; Collins, John

2013-05-01

Early biotechnology (BT) had its roots in fascinating discoveries, such as yeast as living matter being responsible for the fermentation of beer and wine. Serious controversies arose between vitalists and chemists, resulting in the reversal of theories and paradigms, but prompting continuing research and progress. Pasteur's work led to the establishment of the science of microbiology by developing pure monoculture in sterile medium, and together with the work of Robert Koch to the recognition that a single pathogenic organism is the causative agent for a particular disease. Pasteur also achieved innovations for industrial processes of high economic relevance, including beer, wine and alcohol. Several decades later Buchner, disproved the hypothesis that processes in living cells required a metaphysical 'vis vitalis' in addition to pure chemical laws. Enzymes were shown to be the chemical basis of bioconversions. Studies on the formation of products in microbial fermentations, resulted in the manufacture of citric acid, and chemical components required for explosives particularly in war time, acetone and butanol, and further products through fermentation. The requirements for penicillin during the Second World War lead to the industrial manufacture of penicillin, and to the era of antibiotics with further antibiotics, like streptomycin, becoming available. This was followed by a new class of high value-added products, mainly secondary metabolites, e.g. steroids obtained by biotransformation. By the mid-twentieth century, biotechnology was becoming an accepted specialty with courses being established in the life sciences departments of several universities. Starting in the 1970s and 1980s, BT gained the attention of governmental agencies in Germany, the UK, Japan, the USA, and others as a field of innovative potential and economic growth, leading to expansion of the field. Basic research in Biochemistry and Molecular Biology dramatically widened the field of life

ENVIRONMENTALLY BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

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

John J. Kilbane II; William Bogan

2004-01-31

The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter included the fractionation of extracts prepared from several varieties of pepper plants, and using several solvents, by high performance liquid chromatography (HPLC). A preliminary determination of antimicrobial activities ofmore » the new extracts and fractions using a growth inhibition assay, and evaluation of the extracts ability to inhibit biofilm formation was also performed. The analysis of multiple extracts of pepper plants and fractions of extracts of pepper plants obtained by HPLC illustrated that these extracts and fractions are extremely complex mixtures of chemicals. Gas chromatography-mass spectrometry was used to identify the chemical constituents of these extracts and fractions to the greatest degree possible. Analysis of the chemical composition of various extracts of pepper plants has illustrated the complexity of the chemical mixtures present, and while additional work will be performed to further characterize the extracts to identify bioactive compounds the focus of efforts should now shift to an evaluation of the ability of extracts to inhibit corrosion in mixed culture biofilms, and in pure cultures of bacterial types which are known or believed to be important in corrosion.« less

From genomics to mechanistic insight: a global perspective on molecular deficits induced by environmental agents.

PubMed

Ramos, Kenneth S; Steffen, Marlene C; Falahatpisheh, M H; Nanez, Adrian

2007-06-01

As the postgenomic era continues to unfold, a new wave of scientific investigation is upon us focusing on the application of genomic technologies to study the meanings encrypted on the DNA code and the responses of living organisms to changes in their environment. Recent functional genomics studies in this laboratory have focused on the role of the aryl hydrocarbon receptor, a ubiquitous transcription factor, in genetic programming during renal development. Also of interest is the application of genomics investigations to the study of chronic medical conditions associated with early life exposures to environmental contaminants. Molecular evidence is discussed in this review within the framework of human molecular medicine.

Molecular targets of epigenetic regulation and effectors of environmental influences

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

Choudhuri, Supratim, E-mail: Supratim.Choudhuri@fda.hhs.go; Cui Yue; Klaassen, Curtis D., E-mail: cklaasse@kumc.ed

The true understanding of what we currently define as epigenetics evolved over time as our knowledge on DNA methylation and chromatin modifications and their effects on gene expression increased. The current explosion of research on epigenetics and the increasing documentation of the effects of various environmental factors on DNA methylation, chromatin modification, as well as on the expression of small non-coding RNAs (ncRNAs) have expanded the scope of research on the etiology of various diseases including cancer. The current review briefly discusses the molecular mechanisms of epigenetic regulation and expands the discussion with examples on the role of environment, suchmore » as the immediate environment during development, in inducing epigenetic changes and modulating gene expression.« less

Microbiology in Introductory Biology.

ERIC Educational Resources Information Center

Callery, Michael L.; And Others

1980-01-01

Describes a microbiology unit developed for an introductory college biology course in which the identity of an unknown bacterium is determined. Also described is an interactive taxonomy computer program which aids in the identity of the unknown organism. (CS)

The next generation of microbiological testing of poultry

USDA-ARS?s Scientific Manuscript database

Microbiological testing of food products is a common practice of food processors to ensure compliance with food safety criteria. Sampling on its own is of limited value, but when applied regularly at different stages of the food chain, microbiology testing can be an integral part of a quality contr...

Fungal Rhinosinusitis: Microbiological and Histopathological Perspective

PubMed Central

Singh, Ajay Kumar; Verma, Nitya; Khare, Vineeta; Ahamad, Abrar; Verma, Virendra; Agarwal, S.P

2017-01-01

Introduction On the basis of histopathology Fungal Rhinosinusitis (FRS) is categorized into non-invasive (allergic fungal rhinosinusitis, fungal ball) and invasive (acute invasive, chronic invasive and granulomatous invasive fungal sinusitis). This differentiation helps to decide the treatment. Role of latest molecular methods such as PCR and conventional methods such as KOH microscopy and culture also needs to be evaluated. Therefore, in this study we planned to categorise fungal rhinosinusitis on the basis of histopathology and compare it with other methods such as PCR, culture and KOH microscopy. Aim To analyse fungal rhinosinusitis cases by both histopathologically and microbiologically. Materials and Methods A total of 76 clinically suspected fungal rhinosinusitis cases were included in the study. The tissue of suspected cases were processed and examined by KOH microscopy, histopathologically, culture and PCR. Histopathological examination was done by PAS, GMS and H&E stain. Results FRS was diagnosed in 37 (48.68%) cases out of 76 clinically suspected cases of FRS. In which 17 (22.3%) cases were positive by direct microscopy, 21 (27.6%) by culture, 27 (35.5%) by PCR and 14 (18.42%) by histopathology. Approximately 14 cases of FRS were classified according to histopathology; 10 (71.3%) as non-invasive FRS. Out of these 10, 9 (64.2%) were classified as AFRS and 1 (7.14%) as fungal ball. Only 4 cases (28.5%) were diagnosed with invasive FRS. Out of these 4 cases, 2 (14.2%) were of chronic invasive fungal rhinosinusitis, 1 (7.14%) was of granulomatous invasive fungal rhinosinusitis and 1 (7.14%) was of acute fulminant invasive fungal rhinosinusitis. Allergic Fungal Rhinosinusitis (AFRS) is the most common type of FRS. Aspergillus flavus was found to be the most common fungi causing FRS. Conclusion Diagnosis should not be based on the single method. It should be done by both histopathological and microbiological methods, especially for those cases which are

Legionnaires' disease from a cooling tower in a community outbreak in Lidköping, Sweden- epidemiological, environmental and microbiological investigation supported by meteorological modelling.

PubMed

Ulleryd, Peter; Hugosson, Anna; Allestam, Görel; Bernander, Sverker; Claesson, Berndt E B; Eilertz, Ingrid; Hagaeus, Anne-Christine; Hjorth, Martin; Johansson, Agneta; de Jong, Birgitta; Lindqvist, Anna; Nolskog, Peter; Svensson, Nils

2012-11-21

An outbreak of Legionnaires' Disease took place in the Swedish town Lidköping on Lake Vänern in August 2004 and the number of pneumonia cases at the local hospital increased markedly. As soon as the first patients were diagnosed, health care providers were informed and an outbreak investigation was launched. Classical epidemiological investigation, diagnostic tests, environmental analyses, epidemiological typing and meteorological methods. Thirty-two cases were found. The median age was 62 years (range 36 - 88) and 22 (69%) were males. No common indoor exposure was found. Legionella pneumophila serogroup 1 was found at two industries, each with two cooling towers. In one cooling tower exceptionally high concentrations, 1.2 × 109 cfu/L, were found. Smaller amounts were also found in the other tower of the first industry and in one tower of the second plant. Sero- and genotyping of isolated L. pneumophila serogroup 1 from three patients and epidemiologically suspected environmental strains supported the cooling tower with the high concentration as the source. In all, two L. pneumophila strains were isolated from three culture confirmed cases and both these strains were detected in the cooling tower, but one strain in another cooling tower as well. Meteorological modelling demonstrated probable spread from the most suspected cooling tower towards the town centre and the precise location of four cases that were stray visitors to Lidköping. Classical epidemiological, environmental and microbiological investigation of an LD outbreak can be supported by meteorological modelling methods.The broad competence and cooperation capabilities in the investigation team from different authorities were of paramount importance in stopping this outbreak.

Legionnaires’ disease from a cooling tower in a community outbreak in Lidköping, Sweden- epidemiological, environmental and microbiological investigation supported by meteorological modelling

PubMed Central

2012-01-01

Background An outbreak of Legionnaires’ Disease took place in the Swedish town Lidköping on Lake Vänern in August 2004 and the number of pneumonia cases at the local hospital increased markedly. As soon as the first patients were diagnosed, health care providers were informed and an outbreak investigation was launched. Methods Classical epidemiological investigation, diagnostic tests, environmental analyses, epidemiological typing and meteorological methods. Results Thirty-two cases were found. The median age was 62 years (range 36 – 88) and 22 (69%) were males. No common indoor exposure was found. Legionella pneumophila serogroup 1 was found at two industries, each with two cooling towers. In one cooling tower exceptionally high concentrations, 1.2 × 109 cfu/L, were found. Smaller amounts were also found in the other tower of the first industry and in one tower of the second plant. Sero- and genotyping of isolated L. pneumophila serogroup 1 from three patients and epidemiologically suspected environmental strains supported the cooling tower with the high concentration as the source. In all, two L. pneumophila strains were isolated from three culture confirmed cases and both these strains were detected in the cooling tower, but one strain in another cooling tower as well. Meteorological modelling demonstrated probable spread from the most suspected cooling tower towards the town centre and the precise location of four cases that were stray visitors to Lidköping. Conclusions Classical epidemiological, environmental and microbiological investigation of an LD outbreak can be supported by meteorological modelling methods. The broad competence and cooperation capabilities in the investigation team from different authorities were of paramount importance in stopping this outbreak. PMID:23171054

Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices.

PubMed

Peck, Vincent; Quiza, Liliana; Buffet, Jean-Philippe; Khdhiri, Mondher; Durand, Audrey-Anne; Paquette, Alain; Thiffault, Nelson; Messier, Christian; Beaulieu, Nadyre; Guertin, Claude; Constant, Philippe

2016-05-01

The impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high-throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Introduction to Clinical Microbiology for the General Dentist.

PubMed

Rams, Thomas E; van Winkelhoff, Arie J

2017-04-01

Clinical oral microbiology may help dental professionals identify infecting pathogenic species and evaluate their in vitro antimicrobial susceptibility. Saliva, dental plaque biofilms, mucosal smears, abscess aspirates, and soft tissue biopsies are sources of microorganisms for laboratory testing. Microbial-based treatment end points may help clinicians better identify patients in need of additional or altered dental therapies before the onset of clinical treatment failure, and help improve patient oral health outcomes. Microbiological testing appears particularly helpful in periodontal disease treatment planning. Further research and technological advances are likely to increase the availability and clinical utility of microbiological analysis in modern dental practice. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbiological Spoilage of Cereal Products

NASA Astrophysics Data System (ADS)

Cook, Frederick K.; Johnson, Billie L.

A wide range of cereal products, including bakery items, refrigerated dough, fresh pasta products, dried cereal products, snack foods, and bakery mixes, are manufactured for food consumption. These products are subject to physical, chemical, and microbiological spoilage that affects the taste, aroma, leavening, appearance, and overall quality of the end consumer product. Microorganisms are ubiquitous in nature and have the potential for causing food spoilage and foodborne disease. However, compared to other categories of food products, bakery products rarely cause food poisoning. The heat that is applied during baking or frying usually eliminates pathogenic and spoilage microorganisms, and low moisture contributes to product stability. Nevertheless, microbiological spoilage of these products occurs, resulting in substantial economic losses.

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

Microbiology facilities aboard Space Station Freedom (SSF)

NASA Technical Reports Server (NTRS)

Cioletti, L. A.; Mishra, S. K.; Richard, Elizabeth E.; Taylor, R.

1990-01-01

A comprehensive microbiological facility is being designed for use on board Space Station Freedom (SSF). Its purpose will be to conduct microbial surveillance of the SSF environment and to examine clinical specimens. Air, water, and internal surfaces will be periodically monitored to satisfy requirements for a safe environment. Crew health will remain a principle objective for every mission. This paper will review the Microbiology Subsystem capabilities planned for SSF application.

Evaluation of an Online Program To Teach Microbiology to Internal Medicine Residents

PubMed Central

Burd, Eileen M.; Kraft, Colleen S.; Armstrong, Wendy S.; Lenorr, Kenya; Spicer, Jennifer O.; Martin, Donna; del Rio, Carlos

2014-01-01

Microbiology rounds are an integral part of infectious disease consultation service. During microbiology rounds, we highlight microbiology principles using vignettes. We created case-based, interactive, microbiology online modules similar to the vignettes presented during microbiology rounds. Since internal medicine residents rotating on our infectious disease elective have limited time to participate in rounds and learn microbiology, our objective was to evaluate the use of the microbiology online modules by internal medicine residents. We asked residents to complete 10 of 25 online modules during their infectious disease elective. We evaluated which modules they chose and the change in their knowledge level. Forty-six internal medicine residents completed assessments given before and after accessing the modules with an average of 11/20 (range, 6 to 19) and 16/20 (range, 9 to 20) correct questions, respectively (average improvement, 5 questions; P = 0.0001). The modules accessed by more than 30 residents included those related to Clostridium difficile, anaerobes, Candida spp., Streptococcus pneumoniae, influenza, Mycobacterium tuberculosis, and Neisseria meningitidis. We demonstrated improved microbiology knowledge after completion of the online modules. This improvement may not be solely attributed to completing the online modules, as fellows and faculty may have provided additional microbiology education during the rotation. PMID:25392364

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)

Geographic variation in the aetiology, epidemiology and microbiology of bronchiectasis.

PubMed

Chandrasekaran, Ravishankar; Mac Aogáin, Micheál; Chalmers, James D; Elborn, Stuart J; Chotirmall, Sanjay H

2018-05-22

Bronchiectasis is a disease associated with chronic progressive and irreversible dilatation of the bronchi and is characterised by chronic infection and associated inflammation. The prevalence of bronchiectasis is age-related and there is some geographical variation in incidence, prevalence and clinical features. Most bronchiectasis is reported to be idiopathic however post-infectious aetiologies dominate across Asia especially secondary to tuberculosis. Most focus to date has been on the study of airway bacteria, both as colonisers and causes of exacerbations. Modern molecular technologies including next generation sequencing (NGS) have become invaluable tools to identify microorganisms directly from sputum and which are difficult to culture using traditional agar based methods. These have provided important insight into our understanding of emerging pathogens in the airways of people with bronchiectasis and the geographical differences that occur. The contribution of the lung microbiome, its ethnic variation, and subsequent roles in disease progression and response to therapy across geographic regions warrant further investigation. This review summarises the known geographical differences in the aetiology, epidemiology and microbiology of bronchiectasis. Further, we highlight the opportunities offered by emerging molecular technologies such as -omics to further dissect out important ethnic differences in the prognosis and management of bronchiectasis.

ENVIRONMENTALLY BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

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

J. Robert Paterek; Gemma Husmillo; Amrutha Daram

The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter includes the application of new methods of Capsicum sp. (pepper) extraction by soxhlet method and analysis of a new set of extracts by thin layer chromatography (TLC) and highmore » performance liquid chromatography (HPLC); isolation and cultivation of MIC-causing microorganisms from corroded pipeline samples; and evaluation of antimicrobial activities of the old set of pepper extracts in comparison with major components of known biocides and corrosion inhibitors. Twelve new extracts from three varieties of Capsicum sp. (Serrano, Habanero, and Chile de Arbol) were obtained by soxhlet extraction using 4 different solvents. Results of TLC done on these extracts showed the presence of capsaicin and some phenolic compounds, while that of HPLC detected capsaicin and dihydrocapsaicin peaks. More tests will be done to determine specific components. Additional isolates from the group of heterotrophic, acid-producing, denitrifying and sulfate-reducing bacteria were obtained from the pipeline samples submitted by gas companies. Isolates of interest will be used in subsequent antimicrobial testing and test-loop simulation system experiments. Results of antimicrobial screening of Capsicum sp. extracts and components of known commercial biocides showed comparable activities when tested against two strains of sulfate-reducing bacteria.« less

Molecular and microbiological report of a hospital outbreak of NDM-1-carrying Enterobacteriaceae in Mexico.

PubMed

Bocanegra-Ibarias, Paola; Garza-González, Elvira; Morfín-Otero, Rayo; Barrios, Humberto; Villarreal-Treviño, Licet; Rodríguez-Noriega, Eduardo; Garza-Ramos, Ulises; Petersen-Morfin, Santiago; Silva-Sanchez, Jesus

2017-01-01

To characterize the microbiological, molecular and epidemiological data of an outbreak of carbapenem-resistant Enterobacteriaceae (CRE) in a tertiary-care hospital in Mexico. From September 2014 to July 2015, all CRE clinical isolates recovered during an outbreak in the Hospital Civil "Fray Antonio Alcalde" in Jalisco, Mexico were screened for antimicrobial susceptibility, carbapenemase production, carbapenemase-encoding genes, and plasmid profiles. Horizontal transfer of imipenem resistance; and clonal diversity by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST); as well as biofilm production and the presence of 14 virulence genes were analyzed in selected isolates. Fifty-two carbapenem-resistant isolates corresponding to 5 species were detected, i.e., Klebsiella pneumoniae (n = 46), Enterobacter cloacae (n = 3), Escherichia coli (n = 1), Providencia rettgeri (n = 1) and Citrobacter freundii (n = 1) with carbapenemase encoding genes blaNDM-1 (n = 48), blaVIM (n = 3), blaIMP (n = 1) and blaKPC (n = 1) detected in these isolates. The blaNDM-1 gene was detected in plasmids from 130- to 170-kb in K. pneumoniae (n = 46); E. cloacae (n = 3), E. coli (n = 1) and P. rettgeri (n = 1). The transfer of plasmids harboring the blaNDM-1 gene was obtained in eight transconjugants. One plasmid restriction pattern was detected, with the blaNDM-1 identified in different restriction fragments. Predominant clone A of K. pneumoniae isolates archived 28/46 (60%) isolates and belongs to ST392. Besides, ST307, ST309, ST846, ST2399, and ST2400 were detected for K. pneumoniae; as well as E. cloacae ST182 and E. coli ST10. The fimA and uge genes were more likely to be identified in K. pneumoniae carbapenem-susceptible isolates (p = <0.001) and biofilm production was more liable to be observed in carbapenem-resistant isolates (p = <0.05). Four Enterobacteriaceae species harboring the blaNDM-1 gene were detected in a nosocomial outbreak in Mexico; horizontal

Workshop on the Application of Genomic Tools for the Rapid Molecular Characterization of Bacterial Isolates in Food-borne Disease Outbreak Investigations Ottawa, ON, February 24-25, 2014

DTIC Science & Technology

2014-05-01

techniques in regulatory food microbiology testing. When testing is conducted to verify compliance with food regulations, detection and typing are...8 Implementation of Molecular Techniques in Regulatory Food Microbiology Testing ................................ 8 From A,C,G,T to PFGE, to MLST... food -borne isolates, as well as some case studies highlighting the role of genomics in the resolution of critical regulatory food microbiology issues

Curricular Guidelines in Microbiology.

ERIC Educational Resources Information Center

Wilett, Norman P.; And Others

1984-01-01

The American Association of Dental Schools' guidelines for curriculum development in microbiology outline the scope of the subject, interrelationships with other disciplines and specialties, primary educational goals, prerequisites, core content, specific behavioral objectives in each subarea, sequencing, and faculty and facilities requirements.…

The Effect of Having at Least One Previous Course in Microbiology upon the Test Scores of Students in a Veterinary Microbiologic Curriculum

ERIC Educational Resources Information Center

Brown, John; And Others

1977-01-01

A comparative analysis of two groups of students indicated that unless individuals had special reasons for taking courses in microbiology before entering the College of Veterinary Medicine, these courses would be of no special benefit in the one-year microbiologic sequence. (LBH)

Next Generation Microbiology Requirements

NASA Technical Reports Server (NTRS)

Ott, C. M.; Oubre, C. M.; Elliott, T. F.; Castro, V. A.; Pierson, D. L.

2012-01-01

As humans continue to explore deep into space, microorganisms will travel with them. The primary means to mitigate the risk of infectious disease are a combination of prudent spacecraft design and rigorous operational controls. The effectiveness of these methods are evaluated by microbiological monitoring of spacecraft, food, water, and the crew that is performed preflight, in-flight, and post-flight. Current NASA requirements associated with microbiological monitoring are based on culture-based methodology where microorganisms are grown on a semi-solid growth medium and enumerated. Subsequent identification of the organisms requires specialized labor and large equipment, which historically has been performed on Earth. Requirements that rely strictly on culture-based units limit the use of non-culture based monitoring technology. Specifically, the culture-based "measurement criteria" are Colony Forming Units (CFU, representing the growth of one microorganism at a single location on the agar medium) per a given volume, area, or sample size. As the CFU unit by definition is culture-based, these requirements limit alternative technologies for spaceflight applications. As spaceflight missions such as those to Mars extend further into space, culture-based technology will become difficult to implement due to the (a) limited shelf life of the culture media, (b) mass/volume necessary to carry these consumables, and (c) problems associated with the production of biohazardous material in the habitable volume of the spacecraft. In addition, an extensive amount of new knowledge has been obtained during the Space Shuttle, NASA-Mir, and International Space Station Programs, which gave direction for new or modified microbial control requirements for vehicle design and mission operations. The goal of this task is to develop and recommend a new set of requirements for vehicle design and mission operations, including microbiological monitoring, based upon "lessons learned" and new

Microbiological quality and safety assessment of lettuce production in Brazil.

PubMed

Ceuppens, Siele; Hessel, Claudia Titze; de Quadros Rodrigues, Rochele; Bartz, Sabrina; Tondo, Eduardo César; Uyttendaele, Mieke

2014-07-02

The microbiological quality and safety of lettuce during primary production in Brazil were determined by enumeration of hygiene indicators Escherichia coli, coliforms and enterococci and detection of enteric pathogens Salmonella and E. coli O157:H7 in organic fertilizers, soil, irrigation water, lettuce crops, harvest boxes and worker's hands taken from six different lettuce farms throughout the crop growth cycle. Generic E. coli was a suitable indicator for the presence of Salmonella and E. coli O157:H7, while coliforms and enterococci were not. Few pathogens were detected: 5 salmonellae and 2 E. coli O157:H7 from 260 samples, of which only one was lettuce and the others were manure, soil and water. Most (5/7) pathogens were isolated from the same farm and all were from organic production. Statistical analysis revealed the following environmental and agro-technical risk factors for increased microbial load and pathogen prevalence in lettuce production: high temperature, flooding of lettuce fields, application of contaminated organic fertilizer, irrigation with water of inferior quality and large distances between the field and toilets. Control of the composting process of organic fertilizers and the irrigation water quality appear most crucial to improve and/or maintain the microbiological quality and safety during the primary production of lettuce. Copyright © 2014 Elsevier B.V. All rights reserved.

[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.

Design Criteria for Microbiological Facilities at Fort Detrick. Volume I: Introduction.

ERIC Educational Resources Information Center

Army Biological Labs., Fort Detrick, MD. Industrial Health and Safety Div.

Volume I of a two volume manual serves as an introduction to design criteria for microbiological facilities. It is addressed to management personnel responsible for planning, budgeting, and making policy decisions for construction or remodeling of microbiological research laboratories. This volume is also concerned with--(1) microbiological safety…

The Danish Microbiology Database (MiBa) 2010 to 2013.

PubMed

Voldstedlund, M; Haarh, M; Mølbak, K

2014-01-09

The Danish Microbiology Database (MiBa) is a national database that receives copies of reports from all Danish departments of clinical microbiology. The database was launched in order to provide healthcare personnel with nationwide access to microbiology reports and to enable real-time surveillance of communicable diseases and microorganisms. The establishment and management of MiBa has been a collaborative process among stakeholders, and the present paper summarises lessons learned from this nationwide endeavour which may be relevant to similar projects in the rapidly changing landscape of health informatics.

Summer Undergraduate Research Program: Environmental studies

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

McMillan, J.

1994-12-31

The purpose of the summer undergraduate internship program for research in environmental studies is to provide an opportunity for well-qualified students to undertake an original research project as an apprentice to an active research scientist in basic environmental research. The students are offered research topics at the Medical University in the scientific areas of pharmacology and toxicology, epidemiology and risk assessment, environmental microbiology, and marine sciences. Students are also afforded the opportunity to work with faculty at the University of Charleston, SC, on projects with an environmental theme. Ten well-qualified students from colleges and universities throughout the eastern United Statesmore » were accepted into the program.« less

Evaluation of the 3M™ Molecular Detection Assay (MDA) 2 - Salmonella for the Detection of Salmonella spp. in Select Foods and Environmental Surfaces: Collaborative Study, First Action 2016.01.

PubMed

Bird, Patrick; Flannery, Jonathan; Crowley, Erin; Agin, James R; Goins, David; Monteroso, Lisa

2016-07-01

The 3M™ Molecular Detection Assay (MDA) 2 - Salmonella uses real-time isothermal technology for the rapid and accurate detection of Salmonella spp. from enriched select food, feed, and food-process environmental samples. The 3M MDA 2 - Salmonella was evaluated in a multilaboratory collaborative study using an unpaired study design. The 3M MDA 2 - Salmonella was compared to the U.S. Food and Drug Administration Bacteriological Analytical Manual Chapter 5 reference method for the detection of Salmonella in creamy peanut butter, and to the U.S. Department of Agriculture, Food Safety and Inspection Service Microbiology Laboratory Guidebook Chapter 4.08 reference method "Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg and Catfish Products and Carcass and Environmental Samples" for the detection of Salmonella in raw ground beef (73% lean). Technicians from 16 laboratories located within the continental United States participated. Each matrix was evaluated at three levels of contamination: an uninoculated control level (0 CFU/test portion), a low inoculum level (0.2-2 CFU/test portion), and a high inoculum level (2-5 CFU/test portion). Statistical analysis was conducted according to the probability of detection (POD) statistical model. Results obtained for the low inoculum level test portions produced difference in collaborator POD values of 0.03 (95% confidence interval, -0.10 to 0.16) for raw ground beef and 0.06 (95% confidence interval, -0.06 to 0.18) for creamy peanut butter, indicating no statistically significant difference between the candidate and reference methods.

[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.

Total internal reflection ellipsometry and SPR detection of low molecular weight environmental toxins

NASA Astrophysics Data System (ADS)

Nabok, A. V.; Tsargorodskaya, A.; Hassan, A. K.; Starodub, N. F.

2005-06-01

The environmental toxins, such as herbicides simazine and atrazine, and T2 mycotoxin were registered with the optical methods of surface plasmon resonance (SPR) and recently developed total internal reflection ellipsometry (TIRE). The immune assay approach was exploited for in situ registration of the above low molecular weight toxins with specific antibodies immobilised onto the gold surface via (poly)allylamine hydrochloride layer using electrostatic self-assembly (ESA) technique. The comparison of two methods of SPR and TIRE shows a higher sensitivity of the latter.

Molecular basis of natural variation and environmental control of trichome patterning

PubMed Central

Hauser, Marie-Theres

2014-01-01

Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

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.

Microbiological quality of retail spices in Tehran, Iran.

PubMed

Koohy-Kamaly-Dehkordy, Paliz; Nikoopour, Houshang; Siavoshi, Farideh; Koushki, Mohammadreza; Abadi, Alireza

2013-05-01

The microbiological quality of 351 samples of nine types of spices including black pepper, caraway, cinnamon, cow parsnip, curry powder, garlic powder, red pepper, sumac, and turmeric, collected from retail shops in Tehran during 2007, was determined. The numbers of aerobic mesophilic bacteria, Escherichia coli, and molds exceeded Iran's National Standard limits, at 63.2% (>5 × 10(5) CFU/g), 23.4% (>0.3 MPN/g), and 21.9% (>5 × 10(3) CFU/g) of the studied samples, respectively. Coliform contamination was more than 10(3) MPN/g in 24.8% of samples. High contamination of retail spices is considered an indication of environmental or fecal contamination due to unhygienic practices in their production. Use of spices with high microbial content could increase the chance of food spoilage and transmission of foodborne pathogens. Accordingly, application of food safety measurements to reduce microbial counts in spices is strongly recommended.

Microbiological contamination in water filtration plants in Islamabad.

PubMed

Hisam, Aliya; Ur Rahman, Mahmood; Kadir, Ehsan; Tariq, Naseer Alam; Masood, Sumaira

2014-05-01

To determine the frequency of microbiological contamination of water in different water filtration plants in Islamabad. Descriptive cross-sectional study. Water Filtration Plants (WFP) in different sectors of Islamabad, from April to September 2012. Water samples were collected in sterilized bottles according to the standard water sampling protocol from site and transported to Pakistan Council for Research in Water Resources (PCRWR) for analysis. Microbiological quality of water was determined in terms of total coliforms (< 2.0 MPN/100 ml) and Escherichia coli (< 2.0 MPN/100 ml). Microbiological contaminated water was defined the sample which had more than 2.0 MPN per 100 ml of either total coliforms or Escherichia (E.) coli. Thirty two WFP were analyzed for microbiological contamination. E. coli was present in 8 (25.0%) water samples, while 24 (75.0%) water samples were free from it. Total coliforms were present in 13 (40.6%) of the samples of WFP, while 19 (59.3%) samples were free from total coliform. Faecal coliforms were present in 8 (25.0%) and absent in 24 (75.0%) samples. Both E. coli and total coliform were present in 8 (25.0%) samples. Nine (59.3) WFP were free from E. coli, total coliform and faecal coliform. Statistically, no significant association was found (p > 0.05) between microbiological contamination and the sectors. Less than half of the water samples of the WFP were contaminated while certain sectors showed more frequent contamination than others.

Promoting active learning of graduate student by deep reading in biochemistry and microbiology pharmacy curriculum.

PubMed

Peng, Ren

2017-07-08

To promote graduate students' active learning, deep reading of high quality papers was done by graduate students enrolled in biochemistry and microbiology pharmacy curriculum offered by college of life science, Jiangxi Normal University from 2013 to 2015. The number of graduate students, who participated in the course in 2013, 2014, and 2015 were eleven, thirteen and fifteen, respectively. Through deep reading of papers, presentation, and group discussion in the lecture, these graduate students have improved their academic performances effectively, such as literature search, PPT document production, presentation management, specialty document reading, academic inquiry, and analytical and comprehensive ability. The graduate students also have increased their understanding level of frontier research, scientific research methods, and experimental methods. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):305-312, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

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

Transforming a sequence of microbiology courses using student profile data.

PubMed

Buxeda, R J; Moore, D A

2000-05-01

A study was performed in the General Microbiology and Industrial Microbiology courses to increase research awareness at an early stage of the educational process and to establish collaboration between students in an Industrial Microbiology program and industry. In both courses, the professor helped students determine their learning styles and then used these data to design activities in order to accomplish the above objectives. In both the treatment and the control sections, students learned about strategies to optimize learning based on their learning styles. A cooperative learning format was introduced to promote active learning and team-building skills. The diverse learning styles data profile was used by students during cooperative learning activities for effective team integration. In the General Microbiology course, a mentor-mentee structure was introduced to expose students to research in microbiology by visiting research facilities on campus. This structure was an addition to the regular curriculum, which meets American Society for Microbiology curriculum recommendations. The results suggest an increase in interest in research by students. In the Industrial Microbiology course, a strategy was introduced to establish collaboration with industry in which students visit the workplace and identify microbial processes, microbiologist roles, and skills needed by microbiologists. Evaluation of these topics using pre- and posttest data indicates a significant increase in acquired knowledge relevant to daily workplace environments with the reformed course. In both courses, students gain information early in their academic experience to help them consider participation in research experiences while providing them with real-world experience toward the end of their academic careers, when they see the need for it.

A commentary on the role of molecular technology and automation in clinical diagnostics

PubMed Central

O’Connor, Ciara; Fitzgibbon, Marie; Powell, James; Barron, Denis; O’Mahony, Jim; Power, Lorraine; O’Connell, Nuala H; Dunne, Colum

2014-01-01

Historically, the identification of bacterial or yeast isolates has been based on phenotypic characteristics such as growth on defined media, colony morphology, Gram stain, and various biochemical reactions, with significant delay in diagnosis. Clinical microbiology as a medical specialty has embraced advances in molecular technology for rapid species identification with broad-range 16S rDNA polymerase chain reaction (PCR) and matrix-assisted laser desorption and/or ionization time of flight (MALDI-TOF) mass spectrometry demonstrated as accurate, rapid, and cost-effective methods for the identification of most, but not all, bacteria and yeasts. Protracted conventional incubation times previously necessary to identify certain species have been mitigated, affording patients quicker diagnosis with associated reduction in exposure to empiric broad-spectrum antimicrobial therapy and shortened hospital stay. This short commentary details such molecular advances and their implications in the clinical microbiology setting. PMID:24658184

A commentary on the role of molecular technology and automation in clinical diagnostics.

PubMed

O'Connor, Ciara; Fitzgibbon, Marie; Powell, James; Barron, Denis; O'Mahony, Jim; Power, Lorraine; O'Connell, Nuala H; Dunne, Colum

2014-01-01

Historically, the identification of bacterial or yeast isolates has been based on phenotypic characteristics such as growth on defined media, colony morphology, Gram stain, and various biochemical reactions, with significant delay in diagnosis. Clinical microbiology as a medical specialty has embraced advances in molecular technology for rapid species identification with broad-range 16S rDNA polymerase chain reaction (PCR) and matrix-assisted laser desorption and/or ionization time of flight (MALDI-TOF) mass spectrometry demonstrated as accurate, rapid, and cost-effective methods for the identification of most, but not all, bacteria and yeasts. Protracted conventional incubation times previously necessary to identify certain species have been mitigated, affording patients quicker diagnosis with associated reduction in exposure to empiric broad-spectrum antimicrobial therapy and shortened hospital stay. This short commentary details such molecular advances and their implications in the clinical microbiology setting.

Restructuring a General Microbiology Laboratory into an Investigative Experience.

ERIC Educational Resources Information Center

Deutch, Charles E.

1994-01-01

Describes an investigative laboratory sequence based upon the isolation and characterization of soil bacteria to aid microbiology teachers in providing students with activities that expose them to basic techniques of microbiology as well as demonstrates the scientific process and the experimental analysis of microorganisms. (ZWH)

A review of 'green' strategies to prevent or mitigate microbiologically influenced corrosion.

PubMed

Little, Brenda; Lee, Jason; Ray, Richard

2007-01-01

Two approaches to control microbiologically influenced corrosion (MIC) have been developed that do not require the use of biocides. These strategies include the following: i) use of biofilms to inhibit or prevent corrosion, and ii) manipulation (removal or addition) of an electron acceptor, (e.g. oxygen, sulphate or nitrate) to influence the microbial population. In both approaches the composition of the microbial community is affected by small perturbations in the environment (e.g. temperature, nutrient concentration and flow) and the response of microorganisms cannot be predicted with certainty. The following sections will review the literature on the effectiveness of these environmentally friendly, "green," strategies for controlling MIC.

Twenty-first-century medical microbiology services in the UK.

PubMed

Duerden, Brian

2005-12-01

With infection once again a high priority for the UK National Health Service (NHS), the medical microbiology and infection-control services require increased technology resources and more multidisciplinary staff. Clinical care and health protection need a coordinated network of microbiology services working to consistent standards, provided locally by NHS Trusts and supported by the regional expertise and national reference laboratories of the new Health Protection Agency. Here, I outline my thoughts on the need for these new resources and the ways in which clinical microbiology services in the UK can best meet the demands of the twenty-first century.

Molecular typing of environmental Cryptococcus neoformans/C. gattii species complex isolates from Manaus, Amazonas, Brazil.

PubMed

Alves, Gleica Soyan Barbosa; Freire, Ana Karla Lima; Bentes, Amaury Dos Santos; Pinheiro, José Felipe de Souza; de Souza, João Vicente Braga; Wanke, Bodo; Matsuura, Takeshi; Jackisch-Matsuura, Ani Beatriz

2016-08-01

Cryptococcus neoformans and Cryptococcus gattii are the main causative agents of cryptococcosis, a systemic fungal disease that affects internal organs and skin, and which is acquired by inhalation of spores or encapsulated yeasts. It is currently known that the C. neoformans/C. gattii species complex has a worldwide distribution, however, some molecular types seem to prevail in certain regions. Few environmental studies of Cryptococcus have been conducted in the Brazilian Amazon. This is the first ecological study of the pathogenic fungi C. neoformans/C. gattii species complex in the urban area of Manaus, Amazonas, Brazil. A total of 506 samples from pigeon droppings (n = 191), captive bird droppings (n = 60) and tree hollows (n = 255) were collected from June 2012 to January 2014 at schools and public buildings, squares, pet shops, households, the zoo and the bus station. Samples were plated on niger seed agar (NSA) medium supplemented with chloramphenicol and incubated at 25°C for 5 days. Dark-brown colonies were isolated and tested for thermotolerance at 37°C, cycloheximide resistance and growth on canavanine-glycine-bromothymol blue agar. Molecular typing was done by PCR-RFLP. Susceptibility to the antifungal drugs amphotericin B, fluconazole, itraconazole and ketoconazole was tested using Etest(®) strips. In total, 13 positive samples were obtained: one tree hollow (C. gattiiVGII), nine pigeon droppings (C. neoformansVNI) and three captive bird droppings (C. neoformansVNI). The environmental cryptococcal isolates found in this study were of the same molecular types as those responsible for infections in Manaus. © 2016 Blackwell Verlag GmbH.

Molecular Biology for the Environment: an EC-US hands-on Course in Environmental Biotechnology

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

Victor de Lorenzo; Juan Luis Ramos; Jerome Kukor

One of the central goals of this activity is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that should result in future collaborations. The course is designed to give scientists hands-on experience in modern, up-to-date biotechnological methods at the interface between molecular biology and environmental biotechnology for the analysis of microorganisms and their activities with regard to the remediation of pollutants in the environment.

Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations

PubMed Central

Lamendella, Regina; Li, Kent C.; Oerther, Daniel

2013-01-01

Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental waters. In order to address this, we studied the diversity of 9,340 partial (>600 bp in length) Bacteroidales 16S rRNA gene sequences from 13 fecal sources and nine feces-contaminated watersheds. The compositions of major Bacteroidales populations were analyzed to determine which host and environmental sequences were contributing to each group. This information allowed us to identify populations which were both exclusive to swine fecal sources and detected in swine-contaminated waters. Phylogenetic and diversity analyses revealed that some markers previously believed to be highly specific to swine populations are shared by multiple hosts, potentially explaining the cross-amplification signals obtained with nontargeted hosts. These data suggest that while many Bacteroidales populations are cosmopolitan, others exhibit a preferential host distribution and may be able to survive different environmental conditions. This study further demonstrates the importance of elucidating the diversity patterns of targeted bacterial groups to develop more inclusive fecal source tracking applications. PMID:23160126

Microbiological testing of Skylab foods.

NASA Technical Reports Server (NTRS)

Heidelbaugh, N. D.; Mcqueen, J. L.; Rowley, D. B.; Powers , E. M.; Bourland, C. T.

1973-01-01

Review of some of the unique food microbiology problems and problem-generating circumstances the Skylab manned space flight program involves. The situations these problems arise from include: extended storage times, variations in storage temperatures, no opportunity to resupply or change foods after launch of the Skylab Workshop, first use of frozen foods in space, first use of a food-warming device in weightlessness, relatively small size of production lots requiring statistically valid sampling plans, and use of food as an accurately controlled part in a set of sophisticated life science experiments. Consideration of all of these situations produced the need for definite microbiological tests and test limits. These tests are described along with the rationale for their selection. Reported test results show good compliance with the test limits.

Clinical microbiology of coryneform bacteria.

PubMed Central

Funke, G; von Graevenitz, A; Clarridge, J E; Bernard, K A

1997-01-01

Coryneform bacteria are aerobically growing, asporogenous, non-partially-acid-fast, gram-positive rods of irregular morphology. Within the last few years, there has been a massive increase in the number of publications related to all aspects of their clinical microbiology. Clinical microbiologists are often confronted with making identifications within this heterogeneous group as well as with considerations of the clinical significance of such isolates. This review provides comprehensive information on the identification of coryneform bacteria and outlines recent changes in taxonomy. The following genera are covered: Corynebacterium, Turicella, Arthrobacter, Brevibacterium, Dermabacter. Propionibacterium, Rothia, Exiguobacterium, Oerskovia, Cellulomonas, Sanguibacter, Microbacterium, Aureobacterium, "Corynebacterium aquaticum," Arcanobacterium, and Actinomyces. Case reports claiming disease associations of coryneform bacteria are critically reviewed. Minimal microbiological requirements for publications on disease associations of coryneform bacteria are proposed. PMID:8993861

Molecularly imprinted polymers based stir bar sorptive extraction for determination of cefaclor and cefalexin in environmental water.

PubMed

Peng, Jun; Liu, Donghao; Shi, Tian; Tian, Huairu; Hui, Xuanhong; He, Hua

2017-07-01

Although stir bar sportive extraction was thought to be a highly efficiency and simple pretreatment approach, its wide application was limited by low selectivity, short service life, and relatively high cost. In order to improve the performance of the stir bar, molecular imprinted polymers and magnetic carbon nanotubes were combined in the present study. In addition, two monomers were utilized to intensify the selectivity of molecularly imprinted polymers. Fourier transform infrared spectroscopy, scanning electron microscopy, and selectivity experiments showed that the molecularly imprinted polymeric stir bar was successfully prepared. Then micro-extraction based on the obtained stir bar was coupled with HPLC for determination of trace cefaclor and cefalexin in environmental water. This approach had the advantages of stir bar sportive extraction, high selectivity of molecular imprinted polymers, and high sorption efficiency of carbon nanotubes. To utilize this pretreatment approach, pH, extraction time, stirring speed, elution solvent, and elution time were optimized. The LOD and LOQ of cefaclor were found to be 3.5 ng · mL -1 and 12.0 ng · mL -1 , respectively; the LOD and LOQ of cefalexin were found to be 3.0 ng · mL -1 and 10.0 ng · mL -1 , respectively. The recoveries of cefaclor and cefalexin were 86.5 ~ 98.6%. The within-run precision and between-run precision were acceptable (relative standard deviation <7%). Even when utilized in more than 14 cycles, the performance of the stir bar did not decrease dramatically. This demonstrated that the molecularly imprinted polymeric stir bar based micro-extraction was a convenient, efficient, low-cost, and a specific method for enrichment of cefaclor and cefalexin in environmental samples.

Microbiology studies in the Space Shuttle

NASA Technical Reports Server (NTRS)

Taylor, G. R.

1976-01-01

Past space microbiology studies have evaluated three general areas: microbe detection in extraterrestrial materials; monitoring of autoflora and medically important species on crewmembers, equipment, and cabin air; and in vitro evaluations of isolated terrestrial species carried on manned and unmanned spaceflights. These areas are briefly reviewed to establish a basis for presenting probable experiment subjects applicable to the Space Shuttle era. Most extraterrestrial life detection studies involve visitations to other heavenly bodies. Although this is not applicable to the first series of Shuttle flights, attempts to capture meteors and spores in space could be important. Human pathogen and autoflora monitoring will become more important with increased variety among crewmembers. Inclusion of contaminated animal and plant specimens in the space lab will necessitate inflight evaluation of cross-contamination and infection potentials. The majority of Shuttle microbiology studies will doubtless fall into the third study area. Presence of a space lab will permit a whole range of experimentation under conditions similar to these experienced in earth-based laboratories. The recommendations of various study groups are analyzed, and probable inflight microbiological experiment areas are identified for the Life Sciences Shuttle Laboratory.

Ultrasonic non invasive techniques for microbiological instrumentation

NASA Astrophysics Data System (ADS)

Elvira, L.; Sierra, C.; Galán, B.; Resa, P.

2010-01-01

Non invasive techniques based on ultrasounds have advantageous features to study, characterize and monitor microbiological and enzymatic reactions. These processes may change the sound speed, viscosity or particle distribution size of the medium where they take place, which makes possible their analysis using ultrasonic techniques. In this work, two different systems for the analysis of microbiological liquid media based on ultrasounds are presented. In first place, an industrial application based on an ultrasonic monitoring technique for microbiological growth detection in milk is shown. Such a system may improve the quality control strategies in food production factories, being able to decrease the time required to detect possible contaminations in packed products. Secondly, a study about the growing of the Escherichia coli DH5 α in different conditions is presented. It is shown that the use of ultrasonic non invasive characterization techniques in combination with other conventional measurements like optical density provides complementary information about the metabolism of these bacteria.

What is a microbiologist? A survey exploring the microbiology workforce.

PubMed

Redfern, James; Verran, Joanna

2015-12-01

Microbiology has a long tradition of making inspirational, world-changing discovery. Microbiology now plays essential roles in many disciplines, leading to some microbiologists raising concern over the apparent loss of identity. An electronic survey was undertaken to capture the scientific identity (based on scientific discipline) of people for whom microbiology forms a part of their profession, in addition to information regarding their first degree (title, country and year in which the degree was completed) and the sector in which they currently work. A total of 447 responses were collected, representing 52 countries from which they gained their first degree. Biology was the most common first degree title (of 32 titles provided), while microbiologist was the most common scientific identity (of 26 identities provided). The data collected in this study gives a snapshot of the multidisciplinarity, specialism and evolving nature of the microbiology academic workforce. While the most common scientific identity chosen in this study was that of a microbiologist, it appears that the microbiological workforce is contributed to by a range of different disciplines, highlighting the cross-cutting, multidisciplined and essential role microbiology has within scientific endeavour. Perhaps, we should be less concerned with labels, and celebrate the success with which our discipline has delivered. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Making Microbiology Even Smaller!

ERIC Educational Resources Information Center

Young, Linda Mull; Motz, Vicki Abrams

2013-01-01

We outline protocols for producing slant-minis (SLINIs) and mini-deeps (MEEPs) and examples of their use in simple microbiology experiments suitable for high school students. The principal benefits of these protocols are decreased cost associated with significantly reduced media use; easier, less expensive disposal of waste; and increased safety…

Molecular properties and prebiotic effect of inulin obtained from artichoke (Cynara scolymus L.).

PubMed

López-Molina, Dorotea; Navarro-Martínez, María Dolores; Rojas Melgarejo, Francisco; Hiner, Alexander N P; Chazarra, Soledad; Rodríguez-López, José Neptuno

2005-06-01

A high molecular weight inulin has been prepared from artichoke (Cynara scolymus L.) agroindustrial wastes using environmentally benign aqueous extraction procedures. Physico-chemical analysis of the properties of artichoke inulin was carried out. Its average degree of polymerization was 46, which is higher than for Jerusalem artichoke, chicory, and dahlia inulins. GC-MS confirmed that the main constituent monosaccharide in artichoke inulin was fructose and its degradation by inulinase indicated that it contained the expected beta-2,1-fructan bonds. The FT-IR spectrum was identical to that of chicory inulin. These data indicate that artichoke inulin will be suitable for use in a wide range of food applications. The health-promoting prebiotic effects of artichoke inulin were demonstrated in an extensive microbiological study showing a long lasting bifidogenic effect on Bifidobacterium bifidum ATCC 29521 cultures and also in mixed cultures of colonic bacteria.

Medical Devices; Immunology and Microbiology Devices; Classification of the Assayed Quality Control Material for Clinical Microbiology Assays. Final order.

PubMed

2017-07-27

The Food and Drug Administration (FDA, Agency, or we) is classifying the assayed quality control material for clinical microbiology assays into class II (special controls). The special controls that will apply to the device are identified in this order and will be part of the codified language for the assayed quality control material for clinical microbiology assays' classification. The Agency is classifying the device into class II (special controls) to provide a reasonable assurance of safety and effectiveness of the device.

Rein and Zheng Elected to American Academy of Microbiology | Poster

Cancer.gov

By Nancy Parrish, Staff Writer Earlier this year, Alan Rein, Ph.D., and Zhi-Ming (Thomas) Zheng, M.D., Ph.D., were elected to fellowship in the American Academy of Microbiology, the honorific leadership group within the American Society for Microbiology (ASM). They were among 88 microbiologists who were elected to the academy “through a highly selective, peer-review process, based on their records of scientific achievement and original contributions that have advanced microbiology,” according to the society’s website.

Chapter 12. Canyons microbiology studies

USGS Publications Warehouse

Kellogg, Christina A.; Lawler, Stephanie N.

2017-01-01

Off the eastern coast of the United States, several deep canyons cut through the continental shelf, acting like funnels to move sediment from the shelf out to the deep seafloor. Exposed rock outcrops and ledges along the walls of these canyons provide important habitat for deepsea corals and sponges. Although a few scientific expeditions have visited these canyons in the 1970s (Hecker and Blechschmidt 1979, Hecker et al. 1980), their purpose was mainly to map the contours and capture photographs of the bottom using manned submersibles and towed cameras. Our knowledge of the biodiversity in these complex ecosystems is limited; we know little about the macrofauna (e.g., fishes, crabs, sponges, and deepsea corals) and even less about the microbiota.The research described in this report was conducted from 2011 to 2015 as part of the Bureau of Ocean Energy Management (BOEM) study, entitled “Atlantic Deepwater Canyons” study. This work used molecular and microbiological techniques to examine the microbial ecology and diversity associated with Baltimore and Norfolk canyons. Specifically, this work focused on the microbial ecology of four species of octocorals (Acanthogorgia aspera, Anthothela grandiflora, Paramuricea placomus, and Primnoa resedaeformis), the microbial diversity in sediments within and outside the canyons, and a settling plate experiment designed to characterize microbial biofilm formation on a variety of hard substrates.

Observations on Microbiology Laboratory Instruction for Allied Health Students.

ERIC Educational Resources Information Center

Benathen, Isaiah A.

1993-01-01

The purposes of this paper are (1) to demonstrate that medical microbiology laboratory exercises should be presented with a focus on medical applications, not just traditional microbiology and (2) that exercises devoted to differential diagnostic decision making can be used to enhance the problem solving of students. (PR)

Using Biocatalysis to Integrate Organic Chemistry into a Molecular Biology Laboratory Course

ERIC Educational Resources Information Center

Beers, Mande; Archer, Crystal; Feske, Brent D.; Mateer, Scott C.

2012-01-01

Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We…

Revolutionizing clinical microbiology laboratory organization in hospitals with in situ point-of-care.

PubMed

Cohen-Bacrie, Stéphan; Ninove, Laetitia; Nougairède, Antoine; Charrel, Rémi; Richet, Hervé; Minodier, Philippe; Badiaga, Sékéné; Noël, Guilhem; La Scola, Bernard; de Lamballerie, Xavier; Drancourt, Michel; Raoult, Didier

2011-01-01

Clinical microbiology may direct decisions regarding hospitalization, isolation and anti-infective therapy, but it is not effective at the time of early care. Point-of-care (POC) tests have been developed for this purpose. One pilot POC-lab was located close to the core laboratory and emergency ward to test the proof of concept. A second POC-lab was located inside the emergency ward of a distant hospital without a microbiology laboratory. Twenty-three molecular and immuno-detection tests, which were technically undemanding, were progressively implemented, with results obtained in less than four hours. From 2008 to 2010, 51,179 tests yielded 6,244 diagnoses. The second POC-lab detected contagious pathogens in 982 patients who benefited from targeted isolation measures, including those undertaken during the influenza outbreak. POC tests prevented unnecessary treatment of patients with non-streptococcal tonsillitis (n = 1,844) and pregnant women negative for Streptococcus agalactiae carriage (n = 763). The cerebrospinal fluid culture remained sterile in 50% of the 49 patients with bacterial meningitis, therefore antibiotic treatment was guided by the molecular tests performed in the POC-labs. With regard to enterovirus meningitis, the mean length-of-stay of infected patients over 15 years old significantly decreased from 2008 to 2010 compared with 2005 when the POC was not in place (1.43±1.09 versus 2.91±2.31 days; p = 0.0009). Altogether, patients who received POC tests were immediately discharged nearly thrice as often as patients who underwent a conventional diagnostic procedure. The on-site POC-lab met physicians' needs and influenced the management of 8% of the patients that presented to emergency wards. This strategy might represent a major evolution of decision-making regarding the management of infectious diseases and patient care.

Revolutionizing Clinical Microbiology Laboratory Organization in Hospitals with In Situ Point-of-Care

PubMed Central

Cohen-Bacrie, Stéphan; Ninove, Laetitia; Nougairède, Antoine; Charrel, Rémi; Richet, Hervé; Minodier, Philippe; Badiaga, Sékéné; Noël, Guilhem; La Scola, Bernard; de Lamballerie, Xavier; Drancourt, Michel; Raoult, Didier

2011-01-01

Background Clinical microbiology may direct decisions regarding hospitalization, isolation and anti-infective therapy, but it is not effective at the time of early care. Point-of-care (POC) tests have been developed for this purpose. Methods and Findings One pilot POC-lab was located close to the core laboratory and emergency ward to test the proof of concept. A second POC-lab was located inside the emergency ward of a distant hospital without a microbiology laboratory. Twenty-three molecular and immuno-detection tests, which were technically undemanding, were progressively implemented, with results obtained in less than four hours. From 2008 to 2010, 51,179 tests yielded 6,244 diagnoses. The second POC-lab detected contagious pathogens in 982 patients who benefited from targeted isolation measures, including those undertaken during the influenza outbreak. POC tests prevented unnecessary treatment of patients with non-streptococcal tonsillitis (n = 1,844) and pregnant women negative for Streptococcus agalactiae carriage (n = 763). The cerebrospinal fluid culture remained sterile in 50% of the 49 patients with bacterial meningitis, therefore antibiotic treatment was guided by the molecular tests performed in the POC-labs. With regard to enterovirus meningitis, the mean length-of-stay of infected patients over 15 years old significantly decreased from 2008 to 2010 compared with 2005 when the POC was not in place (1.43±1.09 versus 2.91±2.31 days; p = 0.0009). Altogether, patients who received POC tests were immediately discharged nearly thrice as often as patients who underwent a conventional diagnostic procedure. Conclusions The on-site POC-lab met physicians' needs and influenced the management of 8% of the patients that presented to emergency wards. This strategy might represent a major evolution of decision-making regarding the management of infectious diseases and patient care. PMID:21811599

Use of Case Studies to Introduce Undergraduate Students to Principles of Food Microbiology, Molecular Biology, and Epidemiology of Food-Borne Disease

ERIC Educational Resources Information Center

Ponder, Monica A.; Sumner, Susan

2009-01-01

Mock outbreaks of infectious disease offer the ability to introduce principles of food microbiology, ecology, and epidemiology to undergraduate students using an inquiry driven process. Students were presented with an epidemiological case study detailing patient history, clinical presentation, and foods recently consumed. The students then had to…

Medical Microbiology: Deficits and Remedies

ERIC Educational Resources Information Center

Gabridge, Michael G.

1974-01-01

Microbiology is a typical medical science in which basic information can have direct application. Yet, surveys and questionnaires of recent medical school graduates indicate a serious lack of retentiion in regard to basic biological science. (Author)

The value of case-based teaching vignettes in clinical microbiology rounds.

PubMed

Spicer, Jennifer O; Kraft, Colleen S; Burd, Eileen M; Armstrong, Wendy S; Guarner, Jeannette

2014-03-01

To describe the implementation and evaluation of a case-based microbiology curriculum during daily microbiology rounds. Vignettes consist of short cases with images and questions that facilitate discussion among microbiologists, pathologists, infectious disease physicians, and trainees (residents and fellows). We performed a survey to assess the value of these vignettes to trainees. Motivation to come to rounds on time increased from 60% to 100%. Trainees attending rounds after implementation of the vignettes perceived the value of microbiology rounds to be significantly higher compared with those who attended rounds before implementation (P = .04). Pathology residents found that vignettes were helpful for retaining knowledge (8.3 of 10 points). The vignettes have enhanced the value of microbiology rounds by serving as a formalized curriculum exposing trainees from multiple specialties to various microbiology topics. Emphasis on interdisciplinary interactions between clinical and laboratory personnel was highlighted with this case-based curriculum.

Topic Outlines in Microbiology: An Instructor's Guide for Junior and Community Colleges.

ERIC Educational Resources Information Center

American Society for Microbiology, Washington, DC.

This resource guide presents subject matter organized in outline form for four topical areas: introductory microbiology; medical microbiology; microbial genetics; and microbial physiology. The first two units comprise the two most frequently taught microbiology courses in community and junior colleges. The outlines for microbial genetics and…

Regulation of migration in Mythimna separata (Walker) in China: A review integrating environmental, physiological, hormonal, genetic, and molecular factors

USDA-ARS?s Scientific Manuscript database

Each year the oriental armyworm, Mythimna separata, undertakes a seasonal, long-distance, multigeneration roundtrip migration between Southern and Northern China. The developmental decision to migrate is facultative and controlled by environmental, physiological, hormonal, genetic, and molecular fac...

Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.

PubMed

Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

2014-01-01

As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

Microbiology of organic and conventionally grown fresh produce.

PubMed

Maffei, Daniele F; Batalha, Erika Y; Landgraf, Mariza; Schaffner, Donald W; Franco, Bernadette D G M

2016-12-01

Fresh produce is a generalized term for a group of farm-produced crops, including fruits and vegetables. Organic agriculture has been on the rise and attracting the attention of the food production sector, since it uses eco-agricultural principles that are ostensibly environmentally-friendly and provides products potentially free from the residues of agrochemicals. Organic farming practices such as the use of animal manure can however increase the risk of contamination by enteric pathogenic microorganisms and may consequently pose health risks. A number of scientific studies conducted in different countries have compared the microbiological quality of produce samples from organic and conventional production and results are contradictory. While some have reported greater microbial counts in fresh produce from organic production, other studies do not. This manuscript provides a brief review of the current knowledge and summarizes data on the occurrence of pathogenic microorganisms in vegetables from organic production. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Microbiological findings of vulvovaginitis in prepubertal girls.

PubMed

Bumbulienė, Žana; Venclavičiūtė, Karolina; Ramašauskaite, Diana; Arlauskiene, Audrone; Bumbul, Elžbieta; Drąsutiene, Gražina

2014-01-01

To compare vaginal culture results between prepubertal girls with and without vulvovaginitis, and obtain an overview of the most commonly encountered microbes. Prospective descriptive study. Outpatient clinic of Vilnius University Hospital Santariskiu Klinikos during September 2011-December 2012. 115 prepubertal girls with vulvovaginitis symptoms and additionally 20 age-matched asymptomatic girls. Each girl had a vaginal smear carried out using a sterile swab from the introitus or lower third of the vagina. All samples were referred to the microbiology laboratory where standard microbiological diagnostic procedures were performed. Positive microbiological findings were seen in all 115 (100%) symptomatic girls and in 12 (60%) control group girls (p<0.001). Pathogenic bacteria were found only in symptomatic girls. Statistically significant differences in bacteria culture results (pure or mixed) and growth of isolated bacteria colonies between patients versus healthy girls were found (p<0.05). The dominant bacteria in the target group, accounting for 66% of all isolated microbes, were Escherichia coli, Enterococcus faecalis, Staphylococcus coagulase negative, Streptococcus α haemolyticus and A group Streptococcus β haemolyticus. The bacteria of faecal origin were isolated from 61 (53%) girls with vulvovaginitis and from 5 (25%) girls without vaginal inflammation (p<0.05). Instances of Candida species were extremely rare (2.6%). Positive microbiological findings, mixed bacteria cultures and a high growth of bacteria colonies are found significantly more often in girls with vulvovaginitis. The main causative premenarchal vulvovaginitis agents are faecal in origin.

[Applications of MALDI-TOF-MS in clinical microbiology laboratory].

PubMed

Carbonnelle, Etienne; Nassif, Xavier

2011-10-01

For twenty years, mass spectrometry (MS) has emerged as a particularly powerful tool for analysis and characterization of proteins in research. It is only recently that this technology, especially MALDI-TOF-MS (Matrix Assisted Laser Desorption Ionization Time-Of-Flight) has entered the field of routine microbiology. This method has proven to be reliable and safe for the identification of bacteria, yeasts, filamentous fungi and dermatophytes. MALDI-TOF-MS is a rapid, precise and cost-effective method for identification, compared to conventional phenotypic techniques or molecular biology. Its ability to analyse whole microorganisms with few sample preparation has greatly reduced the time to identification (1-2 min). Furthermore, this technology can be used to identify bacteria directly from clinical samples as blood culture bottles or urines. Future applications will be developed in order to provide direct information concerning virulence or resistance protein markers. © 2011 médecine/sciences – Inserm / SRMS.

Ten years of R&D and full automation in molecular diagnosis.

PubMed

Greub, Gilbert; Sahli, Roland; Brouillet, René; Jaton, Katia

2016-01-01

A 10-year experience of our automated molecular diagnostic platform that carries out 91 different real-time PCR is described. Progresses and future perspectives in molecular diagnostic microbiology are reviewed: why automation is important; how our platform was implemented; how homemade PCRs were developed; the advantages/disadvantages of homemade PCRs, including the critical aspects of troubleshooting and the need to further reduce the turnaround time for specific samples, at least for defined clinical settings such as emergencies. The future of molecular diagnosis depends on automation, and in a novel perspective, it is time now to fully acknowledge the true contribution of molecular diagnostic and to reconsider the indication for PCR, by also using these tests as first-line assays.

Multiple molecular effect pathways of an environmental oestrogen in fish.

PubMed

Filby, Amy L; Thorpe, Karen L; Tyler, Charles R

2006-08-01

Complex interrelationships in the signalling of oestrogenic effects mean that environmental oestrogens present in the aquatic environment have the potential to disrupt physiological function in fish in a more complex manner than portrayed in the present literature. Taking a broader approach to investigate the possible effect pathways and the likely consequences of environmental oestrogen exposure in fish, the effects of 17beta-oestradiol (E(2)) were studied on the expression of a suite of genes which interact to mediate growth, development and thyroid and interrenal function (growth hormone GH (gh), GH receptor (ghr ), insulin-like growth factor (IGF-I) (igf1), IGF-I receptor (igf1r ), thyroid hormone receptors-alpha (thra) and -beta (thrb) and glucocorticoid receptor (gr )) together with the expression analyses of sex-steroid receptors and ten other genes centrally involved in sexual development and reproduction in fathead minnow (fhm; Pimephales promelas). Exposure of adult fhm to 35 ng E(2)/l for 14 days induced classic oestrogen biomarker responses (hepatic oestrogen receptor 1 and plasma vitellogenin), and impacted on the reproductive axis, feminising "male" steroidogenic enzyme expression profiles and suppressing genes involved in testis differentiation. However, E(2) also triggered a cascade of responses for gh, ghr, igf1, igf1r, thra, thrb and gr in the pituitary, brain, liver, gonad and gill, with potential consequences for the functioning of many physiological processes, not just reproduction. Molecular responses to E(2) were complex, with most genes showing differential responses between tissues and sexes. For example, igf1 expression increased in brain but decreased in gill on exposure to E(2), and responded in an opposite way in males compared with females in liver, gonad and pituitary. These findings demonstrate the importance of developing a deeper understanding of the endocrine interactions for unravelling the mechanisms of environmental oestrogen

Towards a rational strategy for monitoring of microbiological quality of ambient waters

PubMed Central

Poma, Hugo Ramiro; Cacciabue, Dolores Gutiérrez; Garcé, Beatriz; Gonzo, Elio Emilio; Rajal, Verónica Beatriz

2012-01-01

Water is one of the main sources of human exposure to microbiological hazards. Although legislation establishes regulatory standards in terms of fecal indicator bacteria to assess the microbiological quality of water, these do not necessarily predict the presence of pathogens such as parasites and viruses. Better surveillance and management strategies are needed to assess the risk of pathogens waterborne transmission. We established a baseline dataset to characterize river water quality, identify changes over time, and design a rational monitoring strategy. Data from a year-long monthly monitoring campaign of the polluted Arenales River (Argentina), were analyzed to statistically correlate physicochemical and microbiological variables, the seasonal and longitudinal variation of the water quality and determine the similarity between study sites. The measured variables (sixteen) reflected the deterioration in the river quality through the city. Different viruses and parasites found did not correlate with the concentration of total and thermotolerant coliforms. There was significant seasonal variation for temperature, turbidity, conductivity, dissolved oxygen, enterococci, and norovirus. Strong correlations between some variables were found; we selected eight variables (dissolved oxygen, conductivity, turbidity, total and thermotolerant coliforms, Enterococcus, and adenovirus and Microsporidium as viral and parasitological indicators, respectively) for future monitoring. There was similarity between the monitoring locations, which were grouped into four clusters validated by cophenetic correlation and supported by discriminant analysis. This allowed us to reduce the number of sites, from eleven down to five. Sixty seven percent of the total variance and the correlation structure between variables was explained using five principal components. All these analyses led to a new long-term systematic monitoring scheme A rational monitoring strategy based on the selection of

Environmental Fate and Effects of Organotin Biocides: A Molecular and Microbiological Assessment.

DTIC Science & Technology

1986-12-12

GROUP__ biocides, antifouling compounds, environment, tributyltin , 08 organotin, tin, standards, biodegradation, organometals !9.\\ASTRACT (Continue on...and effects of the toxic tributyltin species, an active agent in new ship antifouling coatings. -44-4eiped- vltratrace’butyltin measurement’ ehdl c d...Standards Gaithersburg, MD 20899 Introduction New tributyltin -based antifouling paints, some types already widely used in the private sector, offer

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

76 FR 48169 - Advancing Regulatory Science for Highly Multiplexed Microbiology/Medical Countermeasure Devices...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-08

...] Advancing Regulatory Science for Highly Multiplexed Microbiology/ Medical Countermeasure Devices; Public... Regulatory Science for Highly Multiplexed Microbiology/Medical Countermeasure Devices.'' The purpose of the public meeting is to discuss performance evaluation of highly multiplexed microbiology/medical...

Veterinary Microbiology, 3rd Edition

USDA-ARS?s Scientific Manuscript database

Veterinary Microbiology, Third Edition is organized into four sections and begins with an updated and expanded introductory section on infectious disease pathogenesis, diagnosis and clinical management. The second section covers bacterial and fungal pathogens, and the third section describes viral d...

American Society for Microbiology resources in support of an evidence-based approach to teaching microbiology.

PubMed

Merkel, Susan M

2016-08-01

Numerous national reports have addressed the need for changing how science courses in higher education are taught, so that students develop a deeper understanding of critical concepts and the analytical and cognitive skills needed to address future challenges. This review presents some evidence-based approaches to curriculum development and teaching. Results from discipline-based education research indicate that it is critically important for educators to formulate learning goals, provide frequent and authentic assessments and actively engage students in their learning. Professional societies can play a role in helping to put these changes into practice. To this end, the American Society for Microbiology has developed a number of educational programs and resources, which are described here to encourage the implementation of student-centered learning in microbiology education. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[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.

Technical Tension Between Achieving Particulate and Molecular Organic Environmental Cleanliness: Data from Astromaterial Curation Laboratories

NASA Technical Reports Server (NTRS)

Allton, J. H.; Burkett, P. J.

2011-01-01

NASA Johnson Space Center operates clean curation facilities for Apollo lunar, Antarctic meteorite, stratospheric cosmic dust, Stardust comet and Genesis solar wind samples. Each of these collections is curated separately due unique requirements. The purpose of this abstract is to highlight the technical tensions between providing particulate cleanliness and molecular cleanliness, illustrated using data from curation laboratories. Strict control of three components are required for curating samples cleanly: a clean environment; clean containers and tools that touch samples; and use of non-shedding materials of cleanable chemistry and smooth surface finish. This abstract focuses on environmental cleanliness and the technical tension between achieving particulate and molecular cleanliness. An environment in which a sample is manipulated or stored can be a room, an enclosed glovebox (or robotic isolation chamber) or an individual sample container.

Microbiological Water Quality of Impoundments: A Literature Review.

DTIC Science & Technology

1982-12-01

A123-470 MICROBIOLOGICAL WATER QUALITY OF IMPOUNDMENTS:A i/i LITERATURE REYIEU(U) TEX S UNJY AT DALLAS RICHRDSON G BURTON DEC 82 NES/MP/E-82-6...REPORT G PERIOD COVERED . MICROBIOLOGICAL WATER QUALITY OF IMPOUNDMENTS: Final report A LITERATURE REVIEW 6. PERFORMING ORG. REPORT NUMBER 7. AUTHOR...Va. 22151. IS. KEY WORDS (Continue an reverse side It necessary mid Identify by black numnber) Bacteria Water quality S Impoundments Water sampling

76 FR 71982 - Advancing Regulatory Science for Highly Multiplexed Microbiology/Medical Countermeasure Devices...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-21

...] Advancing Regulatory Science for Highly Multiplexed Microbiology/ Medical Countermeasure Devices; Public... Multiplexed Microbiology/ Medical Countermeasure Devices'' that published in the Federal Register of August 8... the October 13, 2011, meeting, including the performance evaluation of highly multiplexed microbiology...

Perceptions of Prospective Biology Teachers on Scientific Argumentation in Microbiology Inquiry Lab Activities

NASA Astrophysics Data System (ADS)

Roviati, E.; Widodo, A.; Purwianingsih, W.; Riandi, R.

2017-09-01

Inquiry laboratory activity and scientific argumentation in science education should be promoted and explicitly experienced by prospective biology teacher students in classes, including in microbiology courses. The goal of this study is to get information about perceptions of prospective biology teachers on scientific argumentation in microbiology inquiry lab activities. This study reported the result of a survey research to prospective biology teachers about how their perception about microbiology lab classes and their perception about inquiry and argumentation in microbiology lab activities should be. The participants of this study were 100 students of biology education department from an institute in Cirebon, West Java taking microbiology lecture during the fifth semester. The data were collected using questionnaire to explore the perceptions and knowledge of prospective biology teachers about microbiology, inquiry lab activities and argumentation. The result showed that students thought that the difficulties of microbiology as a subject were the lack of references and the way lecturer teaching. The students’ perception was that argumentation and inquiry should be implemented in microbiology courses and lab activities. Based on the data from questionnaire, It showed that prospective biology teacher students had very little knowledge about scientific argumentation and its implementation in science education. When the participants made arguments based on the problems given, they showed low quality of arguments.

[Influence of new technologies in modern microbiology].

PubMed

Pumarola, Tomás

2010-10-01

The influence of new technologies in modern microbiology is directly related to their automation, the real driving force of change. Automation has occurred since the beginning of clinical microbiology, but from the 1980s has experienced huge development, which is being projected through the immediate future to all areas of the speciality. Automation has become a prime organizational tool. However, its main disadvantage is that it has no limits, which in association with the current economicallyoriented criteria, is encouraging initiatives to integrate the various laboratory specialities into one production center and, eventually, to outsource its activity. This process could significantly reduce the quality of clinical microbiology and the training of future specialists, or even worst, lead to the eventual disappearance of the speciality, at least as it is known today. The future development of highly automated and integrated laboratories is an irreversible process. To preserve the quality of the speciality and of specialist training, rather than fight directly against this process, we must, as microbiologists, actively participate with creativity and leadership. Copyright © 2010 Elsevier España S.L. All rights reserved.

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.

7 CFR 58.528 - Microbiological requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Requirements for Cottage Cheese Bearing Usda Official Identification § 58.528 Microbiological requirements. Compliance shall be...

Random Amplified Polymorphic DNA PCR in the Teaching of Molecular Epidemiology

ERIC Educational Resources Information Center

Reinoso, Elina B.; Bettera, Susana G.

2016-01-01

In this article, we describe a basic practical laboratory designed for fifth-year undergraduate students of Microbiology as part of the Epidemiology course. This practice provides the students with the tools for molecular epidemiological analysis of pathogenic microorganisms using a rapid and simple PCR technique. The aim of this work was to assay…

Goals and Objectives for Molecular Pathology Education in Residency Programs

PubMed Central

1999-01-01

Increasing knowledge of the molecular basis of disease and advances in technology for analyzing nucleic acids and gene products are changing pathology practice. The explosion of information regarding inherited susceptibility to disease is an important aspect of this transformation. Pathology residency programs are incorporating molecular pathology education into their curricula to prepare newly trained pathologists for the future, yet little guidance has been available regarding the important components of molecular pathology training. We present general goals for pathology training programs for molecular pathology education. These include recommendations to pathology residents for the acquisition of both basic knowledge in human genetics and molecular biology and specific skills relevant to microbiology, molecular oncology, genetics, histocompatibility, and identity determination. The importance of residents gaining facility in integrating data gained via nucleic acid based-technology with other laboratory and clinical information available in the care of patients is emphasized. PMID:11272908

An Option in Applied Microbiology.

ERIC Educational Resources Information Center

Lee, William E., III

1988-01-01

Describes a program option for undergraduate chemical engineering students interested in biotechnology. Discusses how this program is deployed at the University of Southern Florida. Lists courses which apply to this program. Discusses the goals of teaching applied microbiology to engineering majors. (CW)

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)

[Applications of MALDI-TOF technology in clinical microbiology].

PubMed

Suarez, S; Nassif, X; Ferroni, A

2015-02-01

Until now, the identification of micro-organisms has been based on the cultural and biochemical characteristics of bacterial and fungal species. Recently, Mass Spectrometry type Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF MS) was developed in clinical microbiology laboratories. This new technology allows identification of micro-organisms directly from colonies of bacteria and fungi within few minutes. In addition, it can be used to identify germs directly from positive blood culture bottles or directly from urine samples. Other ways are being explored to expand the use of MALDI-TOF in clinical microbiology laboratories. Indeed, some studies propose to detect bacterial antibiotic resistance while others compare strains within species for faster strain typing. The main objective of this review is to update data from the recent literature for different applications of MALDI-TOF technique in microbiological diagnostic routine. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Microbiological quality of Argentinian paprika.

PubMed

Melo González, María G; Romero, Stella M; Arjona, Mila; Larumbe, Ada G; Vaamonde, Graciela

The aim of this study was to evaluate the microbiological quality of paprika produced in Catamarca, Argentina. Microbiological analyses were carried out for the enumeration of total aerobic mesophilic bacteria, coliforms, yeasts and molds, and the detection of Salmonella in samples obtained from different local producers during three consecutive years. The mycobiota was identified paying special attention to the mycotoxigenic molds. Standard plate counts of aerobic mesophilic bacteria ranged from 2.7×10 5 to 3.7×10 7 CFU/g. Coliform counts ranged from <10 to 8.1×10 4 CFU/g. Salmonella was not detected in any of the samples tested. Fungal counts (including yeasts and molds) ranged between 2×10 2 and 1.9×10 5 CFU/g. These results showed a high level of microbial contamination, exceeding in several samples the maximum limits set in international food regulations. The study of the mycobiota demonstrated that Aspergillus was the predominant genus and Aspergillus niger (potential producer of ochratoxin A) the most frequently isolated species, followed by Aspergillus flavus (potential producer of aflatoxins). Other species of potential toxigenic fungi such as Aspergillus ochraceus, Aspergillus westerdijkiae, Penicillium chrysogenum, Penicillium crustosum, Penicillium commune, Penicillium expansum and Alternaria tenuissima species group were encountered as part of the mycobiota of the paprika samples indicating a risk of mycotoxin contamination. A. westerdijkiae was isolated for the first time in Argentina. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Environmental Forensics: Molecular Insight into Oil Spill Weathering Helps Advance High Magnetic Field FT-ICR Mass Spectrometry

NASA Astrophysics Data System (ADS)

McKenna, Amy

2013-03-01

The depletion of terrestrial global oil reserves has shifted oil exploration into offshore and ultra-deep water (> 5000 ft) oil reserves to meet global energy demands. Deep water reservoirs are currently in production in many parts of the world, including the Gulf of Mexico, but production is complicated by the water depth and thick salt caps that challenge reservoir characterization / production. The explosion aboard the Deepwater Horizon in April 2010 resulted in an estimated total release of ~5 million barrels (BP claims that they collected ~1M barrels, for a net release of 4 M) of light, sweet crude oil into the Gulf of Mexico and shifted attention toward the environmental risks associated with offshore oil production. The growing emphasis on deep water and ultra-deep water oil production poses a significant environmental threat, and increased regulations require that oil companies minimize environmental impact to prevent oil spills, and mitigate environmental damage when spills occur. Every oil spill is unique. The molecular transformations that occur to petroleum after contact with seawater depend on the physical and chemical properties of the spilled oil, environmental conditions, and deposition environment. Molecular-level knowledge of the composition, distribution, and total mass of released hydrocarbons is essential to disentangle photo- and bio-degradation, source identification, and long-term environmental impact of hydrocarbons released into the environment. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is unsurpassed in its ability to characterize complex mixtures at the level of elemental composition assignment. Only FT-ICR mass spectrometry can routinely achieve the required minimum resolving power necessary to elucidate molecular-level characterization of crude oil. Conversely, the spectral complexity of petroleum facilitates identification of systematic errors in the accumulation, transfer, excitation, and detection

Application of the MALDI Biotyper to clinical microbiology: progress and potential.

PubMed

Kostrzewa, Markus

2018-03-01

The introduction of the MALDI Biotyper in laboratories substantially changed microbiology practice, this has been called a revolution. The system accelerated diagnostic while costs were reduced and accuracy was increased. In just a few years MALDI-TOF MS became the first-line identification tool for microorganisms. Ten years after its introduction, more than 2000 MALDI Biotyper systems are installed in laboratories which are performing routine diagnostic, and the number is still increasing. Areas covered: This article summarises changes in clinical microbiology introduced by the MALDI Biotyper and its effects, as it has been published in peer reviewed articles found in PubMed. Further, the potential of novel developments to increase the value of the system is described. Expert commentary: The MALDI Biotyper has significantly improved clinical microbiology in the area of microorganism identification. Now new developments and applications, e.g. for typing and resistance testing, might further increase its value in clinical microbiology. The systems might get the central diagnostic analyser which is getting integrated into the widely automated microbiology laboratories of the future.

The clinical, radiological, microbiological, and molecular profile of the skin‐penetration site of transfemoral amputees treated with bone‐anchored prostheses

PubMed Central

Lennerås, Maria; Tsikandylakis, Georgios; Trobos, Margarita; Omar, Omar; Vazirisani, Forugh; Palmquist, Anders; Berlin, Örjan; Brånemark, Rickard

2016-01-01

Abstract The breach of the skin barrier is a critical issue associated with the treatment of individuals with transfemoral amputation (TFA) using osseointegrated, percutaneous titanium implants. Thirty TFA patients scheduled for abutment exchange or removal were consecutively enrolled. The aims were to determine the macroscopic skin signs, the presence of bacteria and the gene expression in abutment‐adherent cells and to conduct correlative and comparative analyses between the different parameters. Redness and a granulation ring were present in 47% of the patients. Bacteria were detected in 27/30 patients, commonly in the bone canal. Staphylococcus aureus, coagulase‐negative staphylococci, streptococci, and Enterococcus faecalis were the most common. A positive correlation was found between TNF‐α expression and the detection of S. aureus. Staphylococcus aureus together with other bacterial species revealed a positive relationship with MMP‐8 expression. A negative correlation was demonstrated between the length of the residual femur bone and the detection of a granulation ring and E. faecalis. A positive correlation was revealed between fixture loosening and pain and the radiological detection of endosteal bone resorption. Fixture loosening was also correlated with the reduced expression of interleukin‐10 and osteocalcin. It is concluded that several relationships exist between clinical, radiological, microbiological, and molecular assessments of the percutaneous area of TFAs. Further long term studies on larger patient cohorts are required to determine the precise cause‐effect relationships and unravel the role of host‐bacteria interactions in the skin, bone canal and on the abutment for the longevity of percutaneous implants as treatment of TFA. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 578–589, 2017. PMID:27750392

Isolation and identification of Salmonella spp. in environmental water by molecular technology in Taiwan

NASA Astrophysics Data System (ADS)

Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Shen, Tsung Yu; Kao, Po Min; Shen, Shu Min; Chen, Jung Sheng

2013-04-01

Salmonella spp. is one of the most important causal agents of waterborne diseases. The taxonomy of Salmonella is very complicated and its genus comprises more than 2,500 serotypes. The detection of Salmonella in environmental water samples by routines culture methods using selective media and characterization of suspicious colonies based on biochemical tests and serological assay are generally time consuming. To overcome this drawback, it is desirable to use effective method which provides a higher discrimination and more rapid identification about Salmonella in environmental water. The aim of this study is to investigate the occurrence of Salmonella using molecular technology and to identify the serovars of Salmonella isolates from 70 environmental water samples in Taiwan. The analytical procedures include membrane filtration, non-selective pre-enrichment, selective enrichment of Salmonella. After that, we isolated Salmonella strains by selective culture plates. Both selective enrichment and culture plates were detected by Polymerase Chain Reaction (PCR). Finally, the serovars of Salmonella were confirmed by using biochemical tests and serological assay. In this study, 15 water samples (21.4%) were identified as Salmonella by PCR. The positive water samples will further identify their serotypes by culture method. The presence of Salmonella in environmental water indicates the possibility of waterborne transmission in drinking watershed. Consequently, the authorities need to provide sufficient source protection and to maintain the system for disease prevention. Keywords: Salmonella spp., serological assay, PCR

Environmental microbiology as a mosaic of explored ecosystems and issues.

PubMed

Faure, Denis; Bonin, Patricia; Duran, Robert

2015-09-01

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

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.

[Bibliometric analysis of the Spanish scientific production in Infectious Diseases and Microbiology].

PubMed

Ramos, José Manuel; González-Alcaide, Gregorio; Gutiérrez, Félix

2016-03-01

The bibliometric analysis of production and impact of documents by knowledge area is a quantitative and qualitative indicator of research activity in this field. The aim of this article is to determine the contribution of Spanish research institutions in Infectious Diseases and Microbiology in recent years. Documents published in the journals included in the categories "Infectious Diseases" and "Microbiology" of the Web of Science (Science Citation Index Expanded) of the ISI Web of Knowledge from the year 2000-2013 were analysed. In Infectious Diseases, Spain ranked fourth worldwide, and contributed 5.7% of the 233,771 documents published in this specialty. In Microbiology, Spain was in sixth place with a production rate of 5.8% of the 149,269 documents of this category. The Spanish production increased over the study period, both in Infectious Diseases and Microbiology, from 325 and 619 documents in 2000 to 756 and 1245 documents in 2013, with a growth rate of 131% and 45.8%, respectively. The journal with the largest number of documents published was Enfermedades Infecciosas y Microbiología Clínica, with 8.6% and 8.2% of papers published in the categories of Infectious Diseases and Microbiology, respectively, and was the result of international collaborations, especially with institutions in the United States. The "index h" was 116 and 139 in Infectious Diseases and Microbiology, placing Spain in fifth place in both categories within countries of the European Union. In recent years, Spanish research in Infectious Diseases and Microbiology has reached a good level of production and international visibility, reaching a global leadership position. Copyright © 2015. Published by Elsevier España, S.L.U.

Microbiology in Schools Advisory Committee (MISAC)

ERIC Educational Resources Information Center

Bainbridge, B. W.

1972-01-01

Summarizes the work of the committee, lists its membership, and provides the addresses of (English) suppliers of microbiological equipment and (British) sources of microbial cultures, including bacteria, fungi, and freshwater plankton. (AL)

Microbiological Lessons Learned from the Space Shuttle

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Bruce, Rebekah; Castro, Victoria A.; Mehta, Satish K.

2011-01-01

After 30 years of being the centerpiece of NASA s human spacecraft, the Space Shuttle will retire. This highly successful program provided many valuable lessons for the International Space Station (ISS) and future spacecraft. Major microbiological risks to crewmembers include food, water, air, surfaces, payloads, animals, other crewmembers, and ground support personnel. Adverse effects of microorganisms are varied and can jeopardize crew health and safety, spacecraft systems, and mission objectives. Engineering practices and operational procedures can minimize the negative effects of microorganisms. To minimize problems associated with microorganisms, appropriate steps must begin in the design phase of new spacecraft or space habitats. Spacecraft design must include requirements to control accumulation of water including humidity, leaks, and condensate on surfaces. Materials used in habitable volumes must not contribute to microbial growth. Use of appropriate materials and the implementation of robust housekeeping that utilizes periodic cleaning and disinfection will prevent high levels of microbial growth on surfaces. Air filtration can ensure low levels of bioaerosols and particulates in the breathing air. The use of physical and chemical steps to disinfect drinking water coupled with filtration can provide safe drinking water. Thorough preflight examination of flight crews, consumables, and the environment can greatly reduce pathogens in spacecraft. The advances in knowledge of living and working onboard the Space Shuttle formed the foundation for environmental microbiology requirements and operations for the International Space Station (ISS) and future spacecraft. Research conducted during the Space Shuttle Program resulted in an improved understanding of the effects of spaceflight on human physiology, microbial properties, and specifically the host-microbe interactions. Host-microbe interactions are substantially affected by spaceflight. Astronaut immune

ProbeZT: Simulation of transport coefficients of molecular electronic junctions under environmental effects using Büttiker's probes

NASA Astrophysics Data System (ADS)

Korol, Roman; Kilgour, Michael; Segal, Dvira

2018-03-01

We present our in-house quantum transport package, ProbeZT. This program provides linear response coefficients: electrical and electronic thermal conductances, as well as the thermopower of molecular junctions in which electrons interact with the surrounding thermal environment. Calculations are performed based on the Büttiker probe method, which introduces decoherence, energy exchange and dissipation effects phenomenologically using virtual electrode terminals called probes. The program can realize different types of probes, each introducing various environmental effects, including elastic and inelastic scattering of electrons. The molecular system is described by an arbitrary tight-binding Hamiltonian, allowing the study of different geometries beyond simple one-dimensional wires. Applications of the program to study the thermoelectric performance of molecular junctions are illustrated. The program also has a built-in functionality to simulate electron transport in double-stranded DNA molecules based on a tight-binding (ladder) description of the junction.

Low-Volatility Model Demonstrates Humidity Affects Environmental Toxin Deposition on Plastics at a Molecular Level.

PubMed

Hankett, Jeanne M; Collin, William R; Yang, Pei; Chen, Zhan; Duhaime, Melissa

2016-02-02

Despite the ever-increasing prevalence of plastic debris and endocrine disrupting toxins in aquatic ecosystems, few studies describe their interactions in freshwater environments. We present a model system to investigate the deposition/desorption behaviors of low-volatility lake ecosystem toxins on microplastics in situ and in real time. Molecular interactions of gas-phase nonylphenols (NPs) with the surfaces of two common plastics, poly(styrene) and poly(ethylene terephthalate), were studied using quartz crystal microbalance and sum frequency generation vibrational spectroscopy. NP point sources were generated under two model environments: plastic on land and plastic on a freshwater surface. We found the headspace above calm water provides an excellent environment for NP deposition and demonstrate significant NP deposition on plastic within minutes at relevant concentrations. Further, NP deposits and orders differently on both plastics under humid versus dry environments. We attributed the unique deposition behaviors to surface energy changes from increased water content during the humid deposition. Lastly, nanograms of NP remained on microplastic surfaces hours after initial NP introduction and agitating conditions, illustrating feasibility for plastic-bound NPs to interact with biota and surrounding matter. Our model studies reveal important interactions between low-volatility environmental toxins and microplastics and hold potential to correlate the environmental fate of endocrine disrupting toxins in the Great Lakes with molecular behaviors.

Development of standardized inspections in restaurants using visual assessments and microbiological sampling to quantify the risks.

PubMed Central

Tebbutt, G. M.

1991-01-01

The relationship between visual inspections carried out by environmental health officers and microbiological examination was studied in 89 restaurants. Using 30 variables a standardized inspection procedure was developed and each of the premises was assessed in six main areas-structure and design, cleaning and cleanliness, personal hygiene, risk of contamination, temperature control, and training and knowledge about food hygiene. Selected foods and specimens from hands, surfaces, and wiping cloths were examined. There were significant associations between all six areas of the inspections. The structure and design were significantly related to the combined score from all the other areas (P less than 0.001). There were no highly significant associations between microbiological examination and visual assessments. The microbial contamination of wiping cloths, however, was related to the cleaning and cleanliness (P = 0.005). Microbial sampling provided additional information to inspections and was a valuable aid. Further development of this risk-assessment approach could provide an effective system for monitoring potential health risks in high-risk food premises. PMID:1936161

Definite (microbiologically confirmed) tuberculous meningitis: predictors and prognostic impact.

PubMed

Jha, Sneh Kumar; Garg, Ravindra Kumar; Jain, Amita; Malhotra, Hardeep Singh; Verma, Rajesh; Sharma, Praveen Kumar

2015-12-01

Microbiological confirmation cannot be obtained in approximately two-third patients with tuberculous meningitis. In this study, we sought to identify epidemiological, clinical, cerebrospinal fluid, and imaging parameters that could indicate the possibility of microbiological confirmation among patients with suspected tuberculous meningitis. In this prospective observational study, patients with tuberculous meningitis were evaluated for clinical, laboratory (cerebrospinal fluid microscopy, culture, and polymerase chain reaction), and neuroimaging parameters. All patients received anti-tuberculosis drugs and corticosteroids. The patients were followed for a period of 6 months. Among 118 cases of tuberculous meningitis, there were 43 (36 %) definite (microbiologically confirmed) cases, 59 (50 %) probable and 16 (14 %) possible cases. Among 43 definite cases, tuberculosis polymerase chain reaction (PCR) was positive in 42 (35 %) patients, culture was positive in 1 case and microscopy, after Ziehl-Neelsen staining, was positive in 3 cases. Three factors, modified Barthel index score at admission ≤12 (p = 0.008), cerebrospinal fluid total cell count >100/mm(3) (p = 0.016), and basal exudates on imaging (p = 0.015), were significantly associated with definite tuberculous meningitis. Among 20 patients who died within 6 months, 13 belonged to definite tuberculous meningitis group (p < 0.001). Stage III tuberculous meningitis (p = 0.004), baseline-modified Barthel index score ≤12 (p = 0.013), and positive tuberculosis PCR (p = 0.007) were independently associated with poor outcome on multivariate analysis. Severe disability, cerebrospinal fluid cells >100 mm(3), and basal exudates are significantly related to the presence of microbiologically confirmed definite tuberculous meningitis. Microbiologically confirmed tuberculous meningitis is associated with poorer outcome.

Engineering strategies for the design of plant nutrient delivery systems for use in space: approaches to countering microbiological contamination

NASA Technical Reports Server (NTRS)

Gonzales, A. A.; Schuerger, A. C.; Barford, C.; Mitchell, R.

1996-01-01

Microbiological contamination of crops within space-based plant growth research chambers has been postulated as a potentially significant problem. Microbial infestations; fouling of Nutrient Delivery System (NDS) fluid loops; and the formation of biofilms have been suggested as the most obvious and important manifestations of the problem. Strict sanitation and quarantine procedures will reduce, but not eliminate, microbial species introduced into plant growth systems in space habitats. Microorganisms transported into space most likely will occur as surface contaminants on spacecraft components, equipment, the crew, and plant-propagative materials. Illustrations of the potential magnitude of the microbiological contamination issue will be drawn from the literature and from documentation of laboratory and commercial field experience. Engineering strategies for limiting contamination and for the development of countermeasures will be described. Microbiological control technologies and NDS hardware will be discussed. Configurations appropriate for microgravity research facilities, as well as anticipated bio-regenerative life support system implementations, will be explored. An efficiently designed NDS, capable of adequately meeting the environmental needs of crop plants in space, is considered to be critical in both the research and operational domains. Recommended experiments, tests, and technology developments, structured to allow the development of prudent engineering solutions also will be presented.

Engineering Strategies for the Design of Plant Nutrient Delivery Systems for Use in Space: Approaches to Countering Microbiological Contamination

NASA Technical Reports Server (NTRS)

Gonzales, A. A.; Schuerger, A. C.; Mitchell, R.; Harper, Lynn D. (Technical Monitor)

1994-01-01

Microbiological contamination of crops within space-based crop growth research chambers has been postulated as a potentially significant problem. Microbial infestations; fouling of Nutrient Delivery System (NDS) fluid loops; and the formation of biofilms, have been suggested as the most obvious and important manifestations of the problem. Strict sanitation and quarantine procedures will reduce, but not eliminate, microbial species introduced into plant growing systems in space habitats. Microorganisms transported into space will most likely occur as contaminants on spacecraft components, equipment, the crew, and plant-propagative materials. Illustrations of the potential magnitude of the microbiological contamination issue will be drawn from the literature and from documentation of laboratory and commercial field experience. Engineering strategies for limiting contamination and for the development of countermeasures will be described. Microbiological control technologies and NDS hardware will be discussed. Configurations appropriate for microgravity research facilities, as well as anticipated bio-regenerative life support system implementations, will be explored. An efficiently designed NDS, capable of adequately meeting the environmental needs of crop plants in space, is considered to be critical in both the research and operational domains. Recommended experiments, tests and technology developments, structured to allow the development of prudent engineering solutions, will also be presented.

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.

[Isolation of Sporothrix pallida complex in clinical and environmental samples from Chile].

PubMed

Cruz Choappa, Rodrigo M; Vieille Oyarzo, Peggy I; Carvajal Silva, Laura C

2014-01-01

The isolation of S. pallida complex from medical samples and home garden soil of a patient in Chile is here in reported. Fungi of the Sporothrix schenckii complex can cause various infections. In Chile, the medical and environmental isolates of these this complex are rare. The aim of this study was to identify an unusual agent in a case of onychomycosis and to detect its presence in the patient's home garden. For this purpose, clinical samples were obtained by scraping the patient's subungueal first right toe nail as well as by taking soil samples from different areas of her home garden. Species identification was performed by morphophysiology and one of the strains isolated from the patient's toe nail was sent to CBS for molecular confirmation (14.062). S. pallida complex was identified both from the patient's toe nail and samples taken from her home garden. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España. All rights reserved.

Soil Microbiology, Ecology, and Biochemistry

USDA-ARS?s Scientific Manuscript database

The 4th edition of Soil Microbiology, Ecology, and Biochemistry Edited by Eldor Paul continues in the vein of the 3rd edition by providing an excellent, broad-reaching introduction to soil biology. The new edition improves on the previous by providing extensive supplementary materials, links to outs...

[Microbiological diagnosis of infections of the skin and soft tissues].

PubMed

Burillo, Almudena; Moreno, Antonio; Salas, Carlos

2007-11-01

Skin and soft tissue infections are often seen in clinical practice, yet their microbiological diagnosis is among the most complex of laboratory tasks. The diagnosis of a skin and a soft tissue infection is generally based on clinical criteria and not microbiological results. A microbiological diagnosis is reserved for cases in which the etiology of infection is required, e.g., when the infection is particularly severe, when less common microorganisms are suspected as the causative agent (e.g. in immunocompromised patients), when response to antimicrobial treatment is poor, or when a longstanding wound does not heal within a reasonable period of time. We report the indications, sampling and processing techniques, and interpretation criteria for various culture types, including quantitative cultures from biopsy or tissue specimens and semiquantitative and qualitative cultures performed on all types of samples. For non-invasive samples taken from open wounds, application of the Q index to Gram stains is a cost-effective way to standardize sample quality assessment and interpretation of the pathogenic involvement of the different microorganisms isolated from cultures. All these issues are covered in the SEIMC microbiological procedure number 22: Diagnóstico microbiológico de las infecciones de piel y tejidos blandos (Microbiological diagnosis of infections of the skin and soft tissues) (2nd ed., 2006, www.seimc.org/protocolos/microbiologia).

Extending Molecular Signatures of Climatic and Environmental Change to the Mesozoic

NASA Astrophysics Data System (ADS)

Brassell, S. C.

2007-12-01

The distributions, abundances and isotopic compositions of molecular constituents in sediments depend on their source organisms and the combination of environmental and climatic parameters that constrain or control their biosynthesis. Many such relationships are well documented and understood, thereby providing proxies of proven utility in paleoclimatic reconstructions. Thus, the temperature dependence in the extent of unsaturation in alkenones derived from prymnesiophyte algae, and in the proportion of ring structures in glycerol dibiphytanyl glycerol tetraethers (GDGTs) synthesized by crenarchaeota enables determination of sea surface paleotemperatures from sedimentary records. This molecular approach presumes temporal uniformity in the controlling factors on biosynthesis of these lipids, and their survival in the geological record, notwithstanding the challenge of establishing ancient calibrations for such proxies. Thus, alkenone records from marine sediments document cooling at the Eocene/Oligocene boundary but cannot assess changes in ocean temperatures during the Cretaceous, unlike GDGTs, which record fluctuations in ocean temperatures during the Early Cretaceous, and even survive in Jurassic strata. Other molecular measures offer less precise, yet informative, indications of climate. For example, the occurrence of sterol ethers in Valanginian sediments from the mid-Pacific suggests some cooling at that time, since these compounds are only known to occur elsewhere in cold waters or upwelling systems. Molecular compositions can also attest to levels of oxygenation in marine systems. In particular, the occurrence of 13C-depleted isorenieratane indicates the presence of photosynthetic green sulfur bacteria, and therefore anoxic conditions, albeit perhaps short-lived. Intermittent occurrences of isorenieratane often alternate with the appearance of 2-methylhopanoids, which provide separate distinct evidence for variations in oxygenation, linked to circumstances

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.

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.

A Comprehensive Survey of Preclinical Microbiology Curricula Among US Medical Schools.

PubMed

Melber, Dora J; Teherani, Arianne; Schwartz, Brian S

2016-07-15

A strong foundational understanding of microbiology is crucial for the 21st century physician. Given recent major advances in medical microbiology, curricular changes will likely be needed. Before transforming curricula, we must first obtain a comprehensive understanding of contemporary medical student microbiology education. We disseminated a 38-question survey to microbiology course directors and curriculum deans at 142 US medical schools accredited by the Liason Committee on Medical Education. Survey questions focused on course leadership, curricular structure, course content, and educator perceptions about microbiology education locally and nationally. One hundred and four (73%) of 142 schools completed the survey. Ninety-four (90%) schools identified a course director. Of these, 48% were led by microbiologists alone, 23% co-led by a microbiologist and a clinician, 20% by a clinician alone, and 8% by a laboratory medicine physician with or without a co-director. At 55 (53%) schools, the curricula were organized in a single block or course and at 47 (45%) it was integrated into other curricula. Areas of emerging importance, such as antimicrobial stewardship, global health, infection control, and the microbiome, were addressed at 66%, 65%, 64%, and 47% of institutions, respectively. Respondents reported the following concerns: challenges integrating microbiology into other courses, reduced total teaching hours, and difficulty balancing basic and clinical science topics. Preclinical microbiology course directors report significant challenges in meeting the needs of changing curriculum structure and content. Enhanced local collaboration between microbiologists and clinicians, as well as national collaboration among relevant societies to design best practices and support research, may be strategies for future success. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e

Integration of Diagnostic Microbiology in a Model of Total Laboratory Automation.

PubMed

Da Rin, Giorgio; Zoppelletto, Maira; Lippi, Giuseppe

2016-02-01

Although automation has become widely utilized in certain areas of diagnostic testing, its adoption in diagnostic microbiology has proceeded much more slowly. To describe our real-world experience of integrating an automated instrument for diagnostic microbiology (Walk-Away Specimen Processor, WASPLab) within a model of total laboratory automation (TLA). The implementation process was divided into 2 phases. The former period, lasting approximately 6 weeks, entailed the installation of the WASPLab processor to operate as a stand-alone instrumentation, whereas the latter, lasting approximately 2 weeks, involved physical connection of the WASPLab with the automation. Using the WASPLab instrument in conjunction with the TLA model, we obtained a time savings equivalent to the work of 1.2 full-time laboratory technicians for diagnostic microbiology. The connection of WASPLab to TLA allowed its management by a generalist or clinical chemistry technician, with no need for microbiology skills on the part of either worker. Hence, diagnostic microbiology could be performed by the staff that is already using the TLA, extending their activities to include processing urgent clinical chemistry and hematology specimens. The time to result was also substantially improved. According to our experience, using the WASPLab instrument as part of a TLA in diagnostic microbiology holds great promise for optimizing laboratory workflow and improving the quality of testing. © American Society for Clinical Pathology, 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

BiOutils: an interface to connect university laboratories with microbiology classes in schools.

PubMed

Caine, Massimo; Zuchuat, Sandrine; Weber, Aurélia; Ducret, Verena; Linder, Patrick; Perron, Karl

2015-10-01

The contribution of microbiology to the scientific advances of modern experimental biology has very often made the difference. Despite this, its role as an independent discipline has slowly started to fade away. This situation has been worsening due to (i) a marginal role of microbiology in academic curricula and (ii) a low or misplaced interest by the public at large towards this field of study. In order to counter this phenomenon, microbiology researchers and passionate scientists have made several efforts to engage and inform the broad public and academic policymakers about the importance of microbiology as an independent discipline. One of the approaches used in this direction is to support the teaching of microbiology in schools. BiOutils, a science communication platform based within a microbiology lab, has been committed to this goal since its creation in 2007. In this article, we describe how the platform is able to work in synergy with school teachers, providing engaging activities that can be performed in schools' classrooms. Our aim is to provide a perspective on how every microbiology lab with little costs and efforts can support the teaching of a discipline that will remain independent thanks to the fascination that they will be able to transmit. © FEMS 2015. All rights reserved.

MICROBIOLOGICAL QUALITY OF FOOD SUPPLEMENTS.

PubMed

Ratajczak, Magdalena; Kubicka, Marcelina M; Kamińska, Dorota; Długaszewska, Jolanta

2015-01-01

Many specialists note that the food offered today - as a result of very complex technological processing - is devoid of many components that are important for the organism and the shortages have to be supplemented. The simplest for it is to consume diet supplements that provide the missing element in a concentrated form. In accordance with the applicable law, medicinal products include all substances or mixtures of substances that are attributed with properties of preventing or treating diseases with humans or animals. Permits to admit supplements to the market are issued by the Chief Sanitary Inspector and the related authorities; permits for medicines are issued by the Chief Pharmaceutical Inspector and the Office for Registration of Medicinal Products, Medical Devices and Biocidal Products. Therefore, admittance of a supplement to the market is less costly and time consuming_than admittance of a medicine. Supplements and medicines may contain the same component but medicines will have a larger concentration than supplements. Sale of supplements at drug stores and in the form of tablets, capsules, liquids or powders makes consumer often confusing supplements with medicines. Now there are no normative documents specifying limits of microbiological impurities in diet supplements. In Polish legislation, diet supplements are subject to legal acts concerning food. Medicines have to comply with microbiological purity requirements specified in the Polish Pharmacopeia. As evidenced with the completed tests, the proportion of diet supplement samples with microbiological impurities is 6.5%. Sales of diet supplements have been growing each year, they are consumed by healthy people but also people with immunology deficiencies and by children and therefore consumers must be certain that they buy safe products.

The Development of a Post-Baccalaureate Certificate Program in Molecular Diagnostics

PubMed Central

Williams, Gail S.; Brown, Judith D.; Keagle, Martha B.

2000-01-01

A post-baccalaureate certificate program in diagnostic molecular sciences was created in 1995 by the Diagnostic Genetic Sciences Program in the School of Allied Health at the University of Connecticut. The required on-campus lecture and laboratory courses include basic laboratory techniques, health care issues, cell biology, immunology, human genetics, research, management, and molecular diagnostic techniques and laboratory in molecular diagnostics. These courses precede a 6-month, full-time practicum at an affiliated full-service molecular laboratory. The practicum includes amplification and blotting methods, a research project, and a choice of specialized electives including DNA sequencing, mutagenesis, in situ hybridization methods, or molecular diagnostic applications in microbiology. Graduates of the program are immediately eligible to sit for the National Credentialing Agency examination in molecular biology to obtain the credential Clinical Laboratory Specialist in Molecular Biology (CLSp(MB). This description of the University of Connecticut program may assist other laboratory science programs in creating similar curricula. PMID:11232107

The pharmacological activity of medical herbs after microbiological decontamination by irradiation

NASA Astrophysics Data System (ADS)

Owczarczyk, H. B.; Migdał, W.; K ȩdzia, B.

2000-03-01

In the Institute of Nuclear Chemistry and Technology research on microbiological decontamination of medicinal herbs by irradiation has been carried out since 1996. It was shown that using ionizing radiation (a dose of 10 kGy) can obtain satisfactory results of microbiological decontamination of these products. The content of essential biologically active substances such as essential oils, flavonoids, glycosides, anthocyans, antra-compounds, poliphenoloacids, triterpene saponins, oleanosides and plants mucus did not change significantly after irradiation. Pharmacological activity of medicinal herbs has been found satisfactory after microbiological decontamination by irradiation.

Cellular and molecular effects of developmental exposure to diethylstilbestrol: implications for other environmental estrogens.

PubMed Central

Newbold, R

1995-01-01

Concerns have been raised regarding the role of environmental and dietary estrogens as possible contributors to an increased incidence of various abnormalities in estrogen-target tissues of both sexes. These abnormalities include breast cancer, endometriosis, fibroids, and uterine adenocarcinoma in females, as well as alterations in sex differentiation, decreased sperm concentrations, benign prostatic hyperplasia, prostatic cancer, testicular cancer, and reproductive problems in males. Whether these concerns are valid remains to be determined; however, studies with the potent synthetic estrogen diethylstilbestrol (DES) suggest that exogenous estrogen exposure during critical stages of development can result in permanent cellular and molecular alterations in the exposed organism. These alterations manifest themselves in the female and male as structural, functional, or long-term pathological changes including neoplasia. Although DES has potent estrogenic activity, it may be used as a model compound to study the effects of weaker environmental estrogens, many of which may fit into the category of endocrine disruptors. PMID:8593881

[Pilot tests using molecular diagnostic assay cervicovaginal infection during pregnancy].

PubMed

Beltrán-Montoya, J; Escudero-Gontes, S; Martínez-Huerta, N E; Ávila-Vergara, M A; Morales-Hernández, V; Canchola-Sotelo, C; Palacios-González, B; Vadillo-Ortega, F

2016-08-01

The prevalence of cervicovaginal infections during pregnancy has been associated with adverse perinatal outcomes however, the actual approach used for diagnosis is not effective. The aim of this study was to compare the diagnosis of vaginal infections in pregnant women using clinical, molecular diagnostic and traditional microbiological culture in a pilot study, to determine the prevalence and association with the development of preterm labor. We performed a nested cross-sectional study composed by 54 women in a cohort of pregnant women in Mexico City. Cervicovaginal infections were evaluated by clinical methods, microbiology culture and a commercially available molecular biology test. Prevalence of cervicovaginal infections during pregnancy was estimated between 28% and 50% according to methodologies. Considering the clinical diagnosis of preterm labor as the gold standard, all diagnostic tests were poor as predictors of preterm labor. Traditional approaches to establish the significance of cervicovaginal infection in pregnancy are exhausted, so be sought new ways to understand this complex relationship. Meanwhile it is recommended to continue to use traditional methods to identify infections during pregnancy in both knowledge of new methods aimed at understanding these relationships are sophisticated.

[The journal of the Spanish Society of Microbiology, 1945-1995].

PubMed

Isamat, D; Navarrete, A; Fernández de Castillo, A

1996-03-01

The official journal of the Spanish Society for Microbiology (SEM) was first published in 1947, under the name Microbiología Española. Until 1984 the journal was published by the SEM jointly with the Institute (from the National Research Council, CSIC). In 1985 SEM started by itself to publish a new journal named Microbiología SEM, which may be considered the continuation of the former. From 1985 on the journal has increased both the quality and variety of its articles. At the beginning, most articles were in Spanish. Gradually, articles in English have been majority, to increase international readership. Currently the journal is published quarterly, with more than 500 pages per year.

Recent publications in medical microbiology and immunology: a retrospective.

PubMed

Doerr, H W; Cinatl, J

2012-02-01

A look back is done to some clinical and basic research activities recently published in medical microbiology and immunology. The review covers clinical experiences and in vitro experiments to understand the emergency, pathogenicity, epidemic spread, and vaccine-based prevention of avian and swine-origin flu. Some new developments and concepts in diagnosis, (molecular) epidemiology, and therapy of AIDS, viral hepatitis C, and herpesvirus-associated diseases are outlined. Regulation of immune system has been discussed in a special issue 2010 including some aspects of CNS affections (measles). Mycobacterial infection and its prevention by modern recombinant vaccines have reached new interest, as well as new concepts of vaccination and prophylaxis against several other bacteria. Adaptation to host niches enables immune escape (example brucella) and determines virulence (example N. meningitidis). Chlamydia pneumoniae, previously considered to trigger atherosclerosis, is hypothetically associated to Alzheimer disease, while CMV, another putative trigger of atherosclerosis, gains evidence of oncomodulation in CNS tumor diseases. In terms of globalization, exotic virus infections are increasingly imported from southern countries.

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.

77 FR 16126 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-19

.... FDA-2012-N-0159] Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for... convened a meeting of the Microbiology Devices Panel of the Medical Devices Advisory Committee (Microbiology Devices Panel) on June 29, 2011 (Ref. 2). Although not a formal reclassification meeting, panel...

Microbiological contamination in counterfeit and unapproved drugs

PubMed Central

2014-01-01

Background Counterfeit and unapproved medicines are inherently dangerous and can cause patient injury due to ineffectiveness, chemical or biological contamination, or wrong dosage. Growth of the counterfeit medical market in developed countries is mainly attributable to life-style drugs, which are used in the treatment of non-life-threatening and non-painful conditions, such as slimming pills, cosmetic-related pharmaceuticals, and drugs for sexual enhancement. One of the main tasks of health authorities is to identify the exact active pharmaceutical ingredients (APIs) in confiscated drugs, because wrong API compounds, wrong concentrations, and/or the presence of chemical contaminants are the main risks associated with counterfeit medicines. Serious danger may also arise from microbiological contamination. We therefore performed a market surveillance study focused on the microbial burden in counterfeit and unapproved medicines. Methods Counterfeit and unapproved medicines confiscated in Canada and Austria and controls from the legal market were examined for microbial contaminations according to the US and European pharmacopoeia guidelines. The microbiological load of illegal and legitimate samples was statistically compared with the Wilcoxon rank-sum test. Results Microbial cultivable contaminations in counterfeit and unapproved phosphodiesterase type 5 inhibitors were significantly higher than in products from the legal medicines market (p < 0.0001). Contamination levels exceeding the USP and EP limits were seen in 23% of the tested illegal samples in Canada. Additionally, microbiological contaminations above the pharmacopoeial limits were detected in an anabolic steroid and an herbal medicinal product in Austria (6% of illegal products tested). Conclusions Our results show that counterfeit and unapproved pharmaceuticals are not manufactured under the same hygienic conditions as legitimate products. The microbiological contamination of illegal medicinal

Microbiological contamination in counterfeit and unapproved drugs.

PubMed

Pullirsch, Dieter; Bellemare, Julie; Hackl, Andreas; Trottier, Yvon-Louis; Mayrhofer, Andreas; Schindl, Heidemarie; Taillon, Christine; Gartner, Christian; Hottowy, Brigitte; Beck, Gerhard; Gagnon, Jacques

2014-06-26

Counterfeit and unapproved medicines are inherently dangerous and can cause patient injury due to ineffectiveness, chemical or biological contamination, or wrong dosage. Growth of the counterfeit medical market in developed countries is mainly attributable to life-style drugs, which are used in the treatment of non-life-threatening and non-painful conditions, such as slimming pills, cosmetic-related pharmaceuticals, and drugs for sexual enhancement. One of the main tasks of health authorities is to identify the exact active pharmaceutical ingredients (APIs) in confiscated drugs, because wrong API compounds, wrong concentrations, and/or the presence of chemical contaminants are the main risks associated with counterfeit medicines. Serious danger may also arise from microbiological contamination. We therefore performed a market surveillance study focused on the microbial burden in counterfeit and unapproved medicines. Counterfeit and unapproved medicines confiscated in Canada and Austria and controls from the legal market were examined for microbial contaminations according to the US and European pharmacopoeia guidelines. The microbiological load of illegal and legitimate samples was statistically compared with the Wilcoxon rank-sum test. Microbial cultivable contaminations in counterfeit and unapproved phosphodiesterase type 5 inhibitors were significantly higher than in products from the legal medicines market (p < 0.0001). Contamination levels exceeding the USP and EP limits were seen in 23% of the tested illegal samples in Canada. Additionally, microbiological contaminations above the pharmacopoeial limits were detected in an anabolic steroid and an herbal medicinal product in Austria (6% of illegal products tested). Our results show that counterfeit and unapproved pharmaceuticals are not manufactured under the same hygienic conditions as legitimate products. The microbiological contamination of illegal medicinal products often exceeds USP and EP limits

Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity.

PubMed

Barrera-Redondo, Josué; Ramírez-Barahona, Santiago; Eguiarte, Luis E

2018-05-01

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Random amplified polymorphic DNA PCR in the teaching of molecular epidemiology.

PubMed

Reinoso, Elina B; Bettera, Susana G

2016-07-08

In this article, we describe a basic practical laboratory designed for fifth-year undergraduate students of Microbiology as part of the Epidemiology course. This practice provides the students with the tools for molecular epidemiological analysis of pathogenic microorganisms using a rapid and simple PCR technique. The aim of this work was to assay RAPD-PCR technique in order to infer possible epidemiological relationships. The activity gives students an appreciation of the value of applying a simple molecular biological method as RAPD-PCR to a discipline-specific question. It comprises a three-session laboratory module to genetically assay DNAs from strains isolated from a food outbreak. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):391-396, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Microbiology as a High-School Elective

ERIC Educational Resources Information Center

Peterson, Priscilla

1973-01-01

Describes a course in microbiology offered as a high school science elective. The laboratory-oriented course has proved to be very popular and provides students with the basic techniques for handling equipment and working safely with bacteria. (JR)

Molecular Descriptors

NASA Astrophysics Data System (ADS)

Consonni, Viviana; Todeschini, Roberto

In the last decades, several scientific researches have been focused on studying how to encompass and convert - by a theoretical pathway - the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities, or other experimental properties. Molecular descriptors are formally mathematical representations of a molecule obtained by a well-specified algorithm applied to a defined molecular representation or a well-specified experimental procedure. They play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, toxicology, ecotoxicology, health research, and quality control. Evidence of the interest of the scientific community in the molecular descriptors is provided by the huge number of descriptors proposed up today: more than 5000 descriptors derived from different theories and approaches are defined in the literature and most of them can be calculated by means of dedicated software applications. Molecular descriptors are of outstanding importance in the research fields of quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs), where they are the independent chemical information used to predict the properties of interest. Along with the definition of appropriate molecular descriptors, the molecular structure representation and the mathematical tools for deriving and assessing models are other fundamental components of the QSAR/QSPR approach. The remarkable progress during the last few years in chemometrics and chemoinformatics has led to new strategies for finding mathematical meaningful relationships between the molecular structure and biological activities, physico-chemical, toxicological, and environmental properties of chemicals. Different approaches for deriving molecular descriptors here reviewed and some of the most relevant descriptors are presented in

Microbiological quality and bacterial diversity of the tropical oyster Crassostrea rhizophorae in a monitored farming system and from natural stocks.

PubMed

Silva Neta, M T; Maciel, B M; Lopes, A T S; Marques, E L S; Rezende, R P; Boehs, G

2015-12-02

Microbiological evaluation is one of the most important parameters for analyzing the viability of an oyster farming system, which addresses public health and ecological concerns. Here, the microbiological quality of the oyster Crassostrea rhizophorae cultivated in a monitored environment and from natural beds in Bahia, northeastern Brazil, was determined. Bacterial diversity in oysters was measured by polymerase chain reaction-denaturing gradient gel electrophoresis. Sequence analysis revealed that most bacterial species showed similarity with uncultured or unidentified bacteria from environmental samples, and were clustered into the phylum Proteobacteria. Diverse bacteria from cultivated (monitored) oyster samples were grouped in the same cluster with a high similarity index (above 79%). Microbiological analyses revealed that these oysters did not contain pathogens. These results reflect the natural balance of the microbial communities essential to the maintenance of health and in inhibiting pathogen colonization in the oyster. On the other hand, bacterial diversity of samples from native stocks in extractive areas displayed a similarity index varying between 55 and 77%, and all samples were clustered separately from each other and from the cluster of samples derived from the cultivation area. Microbiological analyses showed that oysters from the extractive area were not fit for human consumption. This reflected a different composition of the microbial community in this area, probably resulting from anthropic impact. Our study also demonstrated that low temperatures and high rainfall limits the bacterial concentration in tropical oysters. This is the first study analyzing the total bacterial community profiles of the oyster C. rhizophorae.

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.

Guidelines to implement quality management systems in microbiology laboratories for tissue banking.

PubMed

Vicentino, W; Rodríguez, G; Saldías, M; Alvarez, I

2009-10-01

Human tissues for implants are a biomedical product that is being used more frequently by many medical disciplines. There are infections in the patients related to the implanted tissues. The early detection of infections transmitted by blood and the microbiological study of tissues before their clinical use are strategies in tissue banks to prevent these situations. This work sought to contribute to establish the bases for the operation of a laboratory applied to the microbiological quality control of tissues. Based on classical microbiological principles, we defined the operation of microbiological control and tissues sterilization since 2003. We determine lists of acceptable microorganisms for every tissue, criteria for the interpretation of results, and a diagnostic algorithm of microbiological quality. We observed that the circumstances of donor death can be a determinant of the quality. The environment and the operator should be investigated as probable sources of contamination in outbreaks. The criteria of work based on a solid methodology must help to avoid the transmission of infections between donor and recipient. This is a critical point in the quality management of a tissue bank.

Challenges of microarray applications for microbial detection and gene expression profiling in food

USDA-ARS?s Scientific Manuscript database

Microarray technology represents one of the latest advances in molecular biology. The diverse types of microarrays have been applied to clinical and environmental microbiology, microbial ecology, and in human, veterinary, and plant diagnostics. Since multiple genes can be analyzed simultaneously, ...

Muddy puddles - the microbiology of puddles located outside tertiary university teaching hospitals.

PubMed

Furukawa, M; McCaughan, J; Stirling, J; Millar, B C; Bell, J; Goldsmith, C E; Reid, A; Misawa, N; Moore, J E

2018-04-01

In the British Isles, the frequency of rain results in the formation of puddles on footpaths and roads in/around hospitals. No data are available demonstrating the microbiological composition of such puddles and therefore a study was undertaken to examine the microbiology of puddles in the grounds of two tertiary university-teaching hospitals (18 sites) and compared with control puddles from non-hospital rural environments (eight sites), estimating (i) total viable count; (ii) identification of organisms in puddles; (iii) enumeration of Escherichia coli: (iv) detection of Extended Spectrum β-Lactamase producing organisms and (v) direct antimicrobial susceptibility testing. A mean count of 2·3 × 10 3  CFU per ml and 1·0 × 10 9  CFU per ml was obtained for hospital and non-hospital puddles respectively. Isolates (n = 77; 54 hospital and 23 non-hospital) were isolated comprising of 23 species among 17 genera (hospital sites), where the majority (10/16; 62·5%) of genera identified were Gram-negative approximately, a fifth (20·6%) were shared by hospital and non-hospital rural samples. Escherichia coli was detected in half of the hospital puddles and under-half (37·5%) of the rural puddles extended spectrum β-lactamase organisms were not detected in any samples examined. Rainwater puddles from the hospital and non-hospital environments contain a diverse range of bacteria, which are capable of causing infections. This study demonstrated the presence of a wide diversity of bacterial taxa associated with rainwater puddles around hospitals, many of which are capable of causing human disease. Of clinical significance is the presence of Pseudomonas aeruginosa isolated from a hospital puddle, particularly for patients with cystic fibrosis. The presence of potentially disease-causing bacteria in puddles in and around hospitals identifies a new potential environmental reservoir of bacteria. Furthermore work is now needed to define their potential of entering or

Microbiology in Scotland and Northern England.

ERIC Educational Resources Information Center

Hottle, George A.

This document presents a report of medical microbiological research at the universities of Edinburgh, Glasgow, Aberdeen and Newcastle. The article further stresses the difficulties of the scientists as they face their three-fold responsibilities of teaching, diagnostic work and research. (HS)

Predictive microbiology in food packaging applications

USDA-ARS?s Scientific Manuscript database

Predictive microbiology including growth, inactivation, surface transfer (or cross-contamination), and survival, plays important roles in understanding microbial food safety. Growth models may involve the growth potential of a specified pathogen under different stresses, e.g., temperature, pH, wate...

Microbiology on Space Station Freedom

NASA Technical Reports Server (NTRS)

Pierson, Duane L. (Editor); Mcginnis, Michael R. (Editor); Mishra, S. K. (Editor); Wogan, Christine F. (Editor)

1991-01-01

This panel discussion convened in Houston, Texas, at the Lunar and Planetary Institute, on November 6 to 8, 1989, to review NASA's plans for microbiology on Space Station Freedom. A panel of distinguished scientists reviewed, validated, and recommended revisions to NASA's proposed acceptability standards for air, water, and internal surfaces on board Freedom. Also reviewed were the proposed microbiology capabilities and monitoring plan, disinfection procedures, waste management, and clinical issues. In the opinion of this advisory panel, ensuring the health of the Freedom's crews requires a strong goal-oriented research effort to determine the potential effects of microorganisms on the crewmembers and on the physical environment of the station. Because there are very few data addressing the fundamental question of how microgravity influences microbial function, the panel recommended establishing a ground-based microbial model of Freedom, with subsequent evaluation using in-flight shuttle data. Sampling techniques and standards will be affected by both technological advances in microgravity-compatible instrumentation, and by changes in the microbial population over the life of the station.

Rein and Zheng Elected to American Academy of Microbiology | Poster

Cancer.gov

By Nancy Parrish, Staff Writer Earlier this year, Alan Rein, Ph.D., and Zhi-Ming (Thomas) Zheng, M.D., Ph.D., were elected to fellowship in the American Academy of Microbiology, the honorific leadership group within the American Society for Microbiology (ASM). They were among 88 microbiologists who were elected to the academy “through a highly selective, peer-review process,

Decontamination of laboratory microbiological waste by steam sterilization.

PubMed Central

Rutala, W A; Stiegel, M M; Sarubbi, F A

1982-01-01

A steam sterilizer (autoclave) was tested to determine the operating parameters that affected sterilization of microbiological waste. Tests involved standardized loads (5, 10 ad 15 lb [ca. 2.27, 4.54, and 6.80 kg, respectively]) contaminated petri plates in autoclave bags placed in polypropylene or stainless steel containers. Thermal and biological data were obtained by using a digital potentiometer and a biological indicator containing spores of Bacillus stearothermophilus, respectively. The transfer of heat was more efficient when smaller loads of microbiological waste were tested and stainless steel rather than polypropylene containers were used. A single bag with the sides rolled down to expose the top layer of petri plates allowed heat to pass better than did a single bag with the top constricted by a twist-tie. The presence of water in the autoclave bag did not significantly improve heat-up time in stainless steel or polypropylene containers. The results of biological tests substantiated the temperature data. When 10 or 15 lb of microbiological waste was exposed to various test conditions, the only condition that ensured the destruction of B. stearothermophilus involved the use of a stainless steel container (with or without water) for 90 min. Autoclaving for 45 min resulted in the destruction of bacteria included in 10 lb (136 +/- 3 plates) or 15 lb (205 +/- 6 plates) of microbiological waste when stainless steel containers with or without water or polypropylene containers with water used, whereas 60 min was required to kill all bacteria if polypropylene containers without water were used. PMID:7103486

Microbial Biotechnology 2020; microbiology of fossil fuel resources.

PubMed

Head, Ian M; Gray, Neil D

2016-09-01

This roadmap examines the future of microbiology research and technology in fossil fuel energy recovery. Globally, the human population will be reliant on fossil fuels for energy and chemical feedstocks for at least the medium term. Microbiology is already important in many areas relevant to both upstream and downstream activities in the oil industry. However, the discipline has struggled for recognition in a world dominated by geophysicists and engineers despite widely known but still poorly understood microbially mediated processes e.g. reservoir biodegradation, reservoir souring and control, microbial enhanced oil recovery. The role of microbiology is even less understood in developing industries such as shale gas recovery by fracking or carbon capture by geological storage. In the future, innovative biotechnologies may offer new routes to reduced emissions pathways especially when applied to the vast unconventional heavy oil resources formed, paradoxically, from microbial activities in the geological past. However, despite this potential, recent low oil prices may make industry funding hard to come by and recruitment of microbiologists by the oil and gas industry may not be a high priority. With regards to public funded research and the imperative for cheap secure energy for economic growth in a growing world population, there are signs of inherent conflicts between policies aimed at a low carbon future using renewable technologies and policies which encourage technologies which maximize recovery from our conventional and unconventional fossil fuel assets. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

The microbiological quality of pasteurized milk sold by automatic vending machines.

PubMed

Angelidis, A S; Tsiota, S; Pexara, A; Govaris, A

2016-06-01

The microbiological quality of pasteurized milk samples (n = 39) collected during 13 weekly intervals from three automatic vending machines (AVM) in Greece was investigated. Microbiological counts (total aerobic (TAC), total psychrotrophic (TPC), Enterobacteriaceae (EC), and psychrotrophic aerobic bacterial spore counts (PABSC)) were obtained at the time of sampling and at the end of shelf-life (3 days) after storage of the samples at 4 or 8°C. TAC were found to be below the 10(7 ) CFU ml(-1) limit of pasteurized milk spoilage both during sampling as well as when milk samples were stored at either storage temperature for 3 days. Enterobacteriaceae populations were below 1 CFU ml(-1) in 69·2% of the samples tested at the time of sampling, whereas the remaining samples contained low numbers, typically less than 10 CFU ml(-1) . All samples tested negative for the presence of Listeria monocytogenes. Analogous microbiological data were also obtained by sampling and testing prepackaged, retail samples of pasteurized milk from two dairy companies in Greece (n = 26). From a microbiological standpoint, the data indicate that the AVM milk samples meet the quality standards of pasteurized milk. However, the prepackaged, retail milk samples yielded better results in terms of TAC, TPC and EC, compared to the AVM samples at the end of shelf-life. Recently, Greek dairy farmers organized in cooperatives launched the sale of pasteurized milk via AVM and this study reports on the microbiological quality of this product. The data show that AVM milk is sold at proper refrigeration temperatures and meets the quality standards of pasteurized milk throughout the manufacturer's specified shelf-life. However, based on the microbiological indicators tested, the keeping quality of the tested prepackaged, retail samples of pasteurized milk at the end of shelf-life upon storage under suboptimal refrigeration temperature (8°C) was better. © 2016 The Society for Applied

Space Station Freedom Environmental Health Care Program

NASA Technical Reports Server (NTRS)

Richard, Elizabeth E.; Russo, Dane M.

1992-01-01

The paper discusses the environmental planning and monitoring aspects of the Space Station Freedom (SSF) Environmental Health Care Program, which encompasses all phases of the SSF assembly and operation from the first element entry at MB-6 through the Permanent Manned Capability and beyond. Environmental planning involves the definition of acceptability limits and monitoring requirements for the radiation dose barothermal parameters and potential contaminants in the SSF air and water and on internal surfaces. Inflight monitoring will be implemented through the Environmental Health System, which consists of five subsystems: Microbiology, Toxicology, Water Quality, Radiation, and Barothermal Physiology. In addition to the environmental data interpretation and analysis conducted after each mission, the new data will be compared to archived data for statistical and long-term trend analysis and determination of risk exposures. Results of these analyses will be used to modify the acceptability limits and monitoring requirements for the future.

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

PubMed Central

Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

2016-01-01

Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice. PMID:26763956

Microbiology and Safety of Table Eggs

USDA-ARS?s Scientific Manuscript database

This chapter describes the microbiology of table eggs, effects of processing, regulatory influences, relative risk of egg-borne disease, and the role of retail and consumer practices in outbreaks. Effects of washing, refrigeration, and facility sanitation in US commercial facilities will be describe...

Molecular typing of environmental and clinical strains of Vibrio vulnificus isolated in the northeastern USA.

PubMed

Reynaud, Yann; Pitchford, Steven; De Decker, Sophie; Wikfors, Gary H; Brown, Christopher L

2013-01-01

Vibrio vulnificus is a ubiquitous marine bacterium that is responsible for infections and some seafood-related illnesses and deaths in the United States, mainly in individuals with compromised health status in the Gulf of Mexico region. Most phylogenetic studies focus on V. vulnificus strains isolated in the southern United States, but almost no genetic data are available on northeastern bacterial isolates of clinical or environmental origin. Our goal in this study was to examine the genetic diversity of environmental strains isolated from commercially-produced oysters and in clinical strains of known pathogenicity in northeastern United States. We conducted analyses of a total of eighty-three strains of V. vulnificus, including 18 clinical strains known to be pathogenic. A polyphasic, molecular-typing approach was carried out, based upon established biotypes, vcg, CPS, 16S rRNA types and three other genes possibly associated with virulence (arylsulfatase A, mtlABC, and nanA). An established Multi Locus Sequence Typing (MLST) method was also performed. Phylogenetic analyses of these markers and MLST results produced similar patterns of clustering of strains into two main lineages (we categorized as 'LI' and 'LII'), with clinical and environmental strains clustering together in both lineages. Lineage LII was comprised primarily but not entirely of clinical bacterial isolates. Putative virulence markers were present in both clinical and environmental strains. These results suggest that some northeastern environmental strains of V. vulnificus are phylogenetically close to clinical strains and probably are capable of virulence. Further studies are necessary to assess the risk of human illness from consuming raw oysters harvested in the northeastern US.

Culture-Independent Analysis of Aerosol Microbiology in a Metropolitan Subway System

PubMed Central

Robertson, Charles E.; Baumgartner, Laura K.; Harris, J. Kirk; Peterson, Kristen L.; Stevens, Mark J.; Frank, Daniel N.

2013-01-01

The goal of this study was to determine the composition and diversity of microorganisms associated with bioaerosols in a heavily trafficked metropolitan subway environment. We collected bioaerosols by fluid impingement on several New York City subway platforms and associated sites in three sampling sessions over a 1.5-year period. The types and quantities of aerosolized microorganisms were determined by culture-independent phylogenetic analysis of small-subunit rRNA gene sequences by using both Sanger (universal) and pyrosequencing (bacterial) technologies. Overall, the subway bacterial composition was relatively simple; only 26 taxonomic families made up ∼75% of the sequences determined. The microbiology was more or less similar throughout the system and with time and was most similar to outdoor air, consistent with highly efficient air mixing in the system. Identifiable bacterial sequences indicated that the subway aerosol assemblage was composed of a mixture of genera and species characteristic of soil, environmental water, and human skin commensal bacteria. Eukaryotic diversity was mainly fungal, dominated by organisms of types associated with wood rot. Human skin bacterial species (at 99% rRNA sequence identity) included the Staphylococcus spp. Staphylococcus epidermidis (the most abundant and prevalent commensal of the human integument), S. hominis, S. cohnii, S. caprae, and S. haemolyticus, all well-documented human commensal bacteria. We encountered no organisms of public health concern. This study is the most extensive culture-independent survey of subway microbiota so far and puts in place pre-event information required for any bioterrorism surveillance activities or monitoring of the microbiological impact of recent subway flooding events. PMID:23542619

Culture-independent analysis of aerosol microbiology in a metropolitan subway system.

PubMed

Robertson, Charles E; Baumgartner, Laura K; Harris, J Kirk; Peterson, Kristen L; Stevens, Mark J; Frank, Daniel N; Pace, Norman R

2013-06-01

The goal of this study was to determine the composition and diversity of microorganisms associated with bioaerosols in a heavily trafficked metropolitan subway environment. We collected bioaerosols by fluid impingement on several New York City subway platforms and associated sites in three sampling sessions over a 1.5-year period. The types and quantities of aerosolized microorganisms were determined by culture-independent phylogenetic analysis of small-subunit rRNA gene sequences by using both Sanger (universal) and pyrosequencing (bacterial) technologies. Overall, the subway bacterial composition was relatively simple; only 26 taxonomic families made up ~75% of the sequences determined. The microbiology was more or less similar throughout the system and with time and was most similar to outdoor air, consistent with highly efficient air mixing in the system. Identifiable bacterial sequences indicated that the subway aerosol assemblage was composed of a mixture of genera and species characteristic of soil, environmental water, and human skin commensal bacteria. Eukaryotic diversity was mainly fungal, dominated by organisms of types associated with wood rot. Human skin bacterial species (at 99% rRNA sequence identity) included the Staphylococcus spp. Staphylococcus epidermidis (the most abundant and prevalent commensal of the human integument), S. hominis, S. cohnii, S. caprae, and S. haemolyticus, all well-documented human commensal bacteria. We encountered no organisms of public health concern. This study is the most extensive culture-independent survey of subway microbiota so far and puts in place pre-event information required for any bioterrorism surveillance activities or monitoring of the microbiological impact of recent subway flooding events.

The role of microbiological testing in systems for assuring the safety of beef.

PubMed

Brown, M H; Gill, C O; Hollingsworth, J; Nickelson, R; Seward, S; Sheridan, J J; Stevenson, T; Sumner, J L; Theno, D M; Usborne, W R; Zink, D

2000-12-05

The use of microbiological testing in systems for assuring the safety of beef was considered at a meeting arranged by the International Livestock Educational Foundation as part of the International Livestock Congress, TX, USA, during February, 2000. The 11 invited participants from industry and government research organizations concurred in concluding that microbiological testing is necessary for the implementation and maintenance of effective Hazard Analysis Critical Control Point (HACCP) systems, which are the only means of assuring the microbiological safety of beef; that microbiological testing for HACCP purposes must involve the enumeration of indicator organisms rather than the detection of pathogens; that the efficacy of process control should be assessed against performance criteria and food safety objectives that refer to the numbers of indicator organisms in product; that sampling procedures should allow indicator organisms to be enumerated at very low numbers; and that food safety objectives and microbiological criteria are better related to variables, rather than attributes sampling plans.

Molecular epidemiology of acute leukemia in children: causal model, interaction of three factors-susceptibility, environmental exposure and vulnerability period.

PubMed

Mejía-Aranguré, Juan Manuel

Acute leukemias have a huge morphological, cytogenetic and molecular heterogeneity and genetic polymorphisms associated with susceptibility. Every leukemia presents causal factors associated with the development of the disease. Particularly, when three factors are present, they result in the development of acute leukemia. These phenomena are susceptibility, environmental exposure and a period that, for this model, has been called the period of vulnerability. This framework shows how the concepts of molecular epidemiology have established a reference from which it is more feasible to identify the environmental factors associated with the development of leukemia in children. Subsequently, the arguments show that only susceptible children are likely to develop leukemia once exposed to an environmental factor. For additional exposure, if the child is not susceptible to leukemia, the disease does not develop. In addition, this exposure should occur during a time window when hematopoietic cells and their environment are more vulnerable to such interaction, causing the development of leukemia. This model seeks to predict the time when the leukemia develops and attempts to give a context in which the causality of childhood leukemia should be studied. This information can influence and reduce the risk of a child developing leukemia. Copyright © 2016 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

Molecular epidemiology in environmental health: the potential of tumor suppressor gene p53 as a biomarker.

PubMed Central

Semenza, J C; Weasel, L H

1997-01-01

One of the challenges in environmental health is to attribute a certain health effect to a specific environmental exposure and to establish a cause-effect relationship. Molecular epidemiology offers a new approach to addressing these challenges. Mutations in the tumor suppressor gene p53 can shed light on past environmental exposure, and carcinogenic agents and doses can be distinguished on the basis of mutational spectra and frequency. Mutations in p53 have successfully been used to establish links between dietary aflatoxin exposure and liver cancer, exposure to ultraviolet light and skin cancer, smoking and cancers of the lung and bladder, and vinyl chloride exposure and liver cancer. In lung cancer, carcinogens from tobacco smoke have been shown to form adducts with DNA. The location of these adducts correlates with those positions in the p53 gene that are mutated in lung cancer, confirming a direct etiologic link between exposure and disease. Recent investigations have also explored the use of p53 as a susceptibility marker for cancer. Furthermore, studies in genetic toxicology have taken advantage of animals transgenic for p53 to screen for carcinogens in vivo. In this review, we summarize recent developments in p53 biomarker research and illustrate applications to environmental health. PMID:9114284

Molecular Ecological Basis of Grasshopper (Oedaleus asiaticus) Phenotypic Plasticity under Environmental Selection

PubMed Central

Qin, Xinghu; Hao, Kun; Ma, Jingchuan; Huang, Xunbing; Tu, Xiongbing; Ali, Md. Panna; Pittendrigh, Barry R.; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Whitman, Douglas W.; Zhang, Zehua

2017-01-01

While ecological adaptation in insects can be reflected by plasticity of phenotype, determining the causes and molecular mechanisms for phenotypic plasticity (PP) remains a crucial and still difficult question in ecology, especially where control of insect pests is involved. Oedaleus asiaticus is one of the most dominant pests in the Inner Mongolia steppe and represents an excellent system to study phenotypic plasticity. To better understand ecological factors affecting grasshopper phenotypic plasticity and its molecular control, we conducted a full transcriptional screening of O. asiaticus grasshoppers reared in four different grassland patches in Inner Mongolia. Grasshoppers showed different degrees of PP associated with unique gene expressions and different habitat plant community compositions. Grasshopper performance variables were susceptible to habitat environment conditions and closely associated with plant architectures. Intriguingly, eco-transcriptome analysis revealed five potential candidate genes playing important roles in grasshopper performance, with gene expression closely relating to PP and plant community factors. By linking the grasshopper performances to gene profiles and ecological factors using canonical regression, we first demonstrated the eco-transcriptomic architecture (ETA) of grasshopper phenotypic traits (ETAGPTs). ETAGPTs revealed plant food type, plant density, coverage, and height were the main ecological factors influencing PP, while insect cuticle protein (ICP), negative elongation factor A (NELFA), and lactase-phlorizin hydrolase (LCT) were the key genes associated with PP. Our study gives a clear picture of gene-environment interaction in the formation and maintenance of PP and enriches our understanding of the transcriptional events underlying molecular control of rapid phenotypic plasticity associated with environmental variability. The findings of this study may also provide new targets for pest control and highlight the

Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean.

PubMed

Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

2011-10-01

Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species.

Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

PubMed Central

Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

2011-01-01

Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species. PMID:21427750

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.

[The history of commensalism: a contemporary history of microbiology].

PubMed

Poreau, Brice

2014-01-01

Commensalism is a biological association between two species, with one species, the commensal, getting an advantage, whereas the other one, the host, gets no advantage neither disadvantage. This concept is theorized in the 1860's by Pierre-Joseph Van Beneden. Van Beneden is a physician in the 1850's, nevertheless, he is well known as a zoologist. The concept of commensalism developed by Van Beneden is employed in many scientific fields, not only in zoology, but also, in microbiology. Although the use of a possible play of the commensal bacterial microflora is exposed at the end of the 19th century, it is only during the second part of the 20th century that this way is studied. Commensalism in animal microbiology is studied first and then it is studied in human. The aim of this article is to present the history of commensalism as a main part of the history of microbiology.

Molecular simulations for energy, environmental and pharmaceutical applications of nanoporous materials: from zeolites, metal-organic frameworks to protein crystals.

PubMed

Jiang, Jianwen; Babarao, Ravichandar; Hu, Zhongqiao

2011-07-01

Nanoporous materials have widespread applications in chemical industry, but the pathway from laboratory synthesis and testing to practical utilization of nanoporous materials is substantially challenging and requires fundamental understanding from the bottom up. With ever-growing computational resources, molecular simulations have become an indispensable tool for material characterization, screening and design. This tutorial review summarizes the recent simulation studies in zeolites, metal-organic frameworks and protein crystals, and provides a molecular overview for energy, environmental and pharmaceutical applications of nanoporous materials with increasing degree of complexity in building blocks. It is demonstrated that molecular-level studies can bridge the gap between physical and engineering sciences, unravel microscopic insights that are otherwise experimentally inaccessible, and assist in the rational design of new materials. The review is concluded with major challenges in future simulation exploration of novel nanoporous materials for emerging applications.

Antimicrobial Stewardship: How the Microbiology Laboratory Can Right the Ship.

PubMed

Morency-Potvin, Philippe; Schwartz, David N; Weinstein, Robert A

2017-01-01

Antimicrobial stewardship is a bundle of integrated interventions employed to optimize the use of antimicrobials in health care settings. While infectious-disease-trained physicians, with clinical pharmacists, are considered the main leaders of antimicrobial stewardship programs, clinical microbiologists can play a key role in these programs. This review is intended to provide a comprehensive discussion of the different components of antimicrobial stewardship in which microbiology laboratories and clinical microbiologists can make significant contributions, including cumulative antimicrobial susceptibility reports, enhanced culture and susceptibility reports, guidance in the preanalytic phase, rapid diagnostic test availability, provider education, and alert and surveillance systems. In reviewing this material, we emphasize how the rapid, and especially the recent, evolution of clinical microbiology has reinforced the importance of clinical microbiologists' collaboration with antimicrobial stewardship programs. Copyright © 2016 American Society for Microbiology.

Predictive Microbiology and Food Safety Applications

USDA-ARS?s Scientific Manuscript database

Mathematical modeling is the science of systematic study of recurrent events or phenomena. When models are properly developed, their applications may save costs and time. For microbial food safety research and applications, predictive microbiology models may be developed based on the fact that most ...

78 FR 4830 - National Advisory Committee on Microbiological Criteria for Foods; Reestablishment

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-23

... DEPARTMENT OF AGRICULTURE Food Safety and Inspection Service [Docket No. FSIS-2012-0040] National Advisory Committee on Microbiological Criteria for Foods; Reestablishment AGENCY: Food Safety and... Committee on Microbiological Criteria for Foods (NACMCF). The Committee is being reestablished in...

The periodontal abscess (I). Clinical and microbiological findings.

PubMed

Herrera, D; Roldán, S; González, I; Sanz, M

2000-06-01

Little information is available regarding the diagnosis and microbiology of periodontal abscesses. The aim of this descriptive clinical and microbiological study was to provide more information in order to help in the characterisation of the periodontal abscess associated to periodontitis. 29 consecutive patients with a periodontal abscess were studied by the assessment of clinical variables, including both subjective (pain, edema, redness and swelling) and objective (bleeding on probing, suppuration, probing pocket depth, tooth mobility and cervical lymphadenopathy) parameters. Microbiological samples were taken for anaerobic microbiology and processed by means of culture. Systemic involvement was also studied through the analysis of blood and urine samples using conventional laboratory standards. 62% of the abscesses affected untreated periodontitis patients, and 69% were associated with a molar tooth. More than 75% of the abscesses had moderate-severe scores related to edema, redness and swelling, and 90% of the patients reported pain. Bleeding occurred in all abscesses, while suppuration on sampling was detected in 66%. Mean associated pocket depth was 7.28 mm, and 79% of teeth presented some degree of mobility. Cervical lymphadenopathy was seen in 10% of patients, while elevated leucocyte counts were observed in 31.6%. The absolute number of neutrophils was elevated in 42% of the patients. High prevalences of putative periodontal pathogens were found, including Fusobacterium nucleatum, Peptostreptococcus micros, Porphyromonas gingivalis, Prevotella intermedia and Bacteroides forsythus. The periodontal abscess has clear clinical characteristics and is usually associated with severe periodontal destruction. This condition may cause systemic involvement and the lesion generally has a large bacterial mass with a high prevalence of well-recognised periodontal pathogens.

Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound

USGS Publications Warehouse

Harvey, J.B.J.; Hoy, M.S.; Rodriguez, R.J.

2009-01-01

Non-native marine species have been and continue to be introduced into Puget Sound via several vectors including ship's ballast water. Some non-native species become invasive and negatively impact native species or near shore habitats. We present a new methodology for the development and testing of taxon specific PCR primers designed to assess environmental samples of ocean water for the presence of native and non-native bivalves, crustaceans and algae. The intergenic spacer regions (IGS; ITS1, ITS2 and 5.8S) of the ribosomal DNA were sequenced for adult samples of each taxon studied. We used these data along with those available in Genbank to design taxon and group specific primers and tested their stringency against artificial populations of plasmid constructs containing the entire IGS region for each of the 25 taxa in our study, respectively. Taxon and group specific primer sets were then used to detect the presence or absence of native and non-native planktonic life-history stages (propagules) from environmental samples of ballast water and plankton tow net samples collected in Puget Sound. This methodology provides an inexpensive and efficient way to test the discriminatory ability of taxon specific oligonucleotides (PCR primers) before creating molecular probes or beacons for use in molecular ecological applications such as probe hybridizations or microarray analyses. This work addresses the current need to develop molecular tools capable of diagnosing the presence of planktonic life-history stages from non-native marine species (potential invaders) in ballast water and other environmental samples. ?? 2008 Elsevier B.V.

Molecular Tracing to Find Source of Protracted Invasive Listeriosis Outbreak, Southern Germany, 2012-2016.

PubMed

Kleta, Sylvia; Hammerl, Jens Andre; Dieckmann, Ralf; Malorny, Burkhard; Borowiak, Maria; Halbedel, Sven; Prager, Rita; Trost, Eva; Flieger, Antje; Wilking, Hendrik; Vygen-Bonnet, Sabine; Busch, Ulrich; Messelhäußer, Ute; Horlacher, Sabine; Schönberger, Katharina; Lohr, Dorothee; Aichinger, Elisabeth; Luber, Petra; Hensel, Andreas; Al Dahouk, Sascha

2017-10-01

We investigated 543 Listeria monocytogenes isolates from food having a temporal and spatial distribution compatible with that of the invasive listeriosis outbreak occurring 2012-2016 in southern Germany. Using forensic microbiology, we identified several products from 1 manufacturer contaminated with the outbreak genotype. Continuous molecular surveillance of food isolates could prevent such outbreaks.

Frontiers in Microbiology: Envisioning a Curriculum Unit for High School Biology

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

Mark Bloom

Microbiology is undergoing a quiet revolution. Techniques such as polymerase chain reaction, high throughput DNA sequencing, whole genome shotgun sequencing, DNA microarrays, and bioinformatics analyses are greatly aiding our understanding of the estimated one billion species of microbes that inhabit the Earth. Unfortunately, the rapid pace of research in microbiology stands in contrast to the much slower pace of change in educational reform. Biological Sciences Curriculum Study (BSCS) hosted a two-day planning meeting to discuss whether or not a new curriculum unit on microbiology is desirable for the high school audience. Attending the meeting were microbiologists, high school biology teachers,more » and science educators. The consensus of the participants was that an inquiry-based unit dealing with advances in microbiology should be developed for a high school biology audience. Participants established content priorities for the unit, discussed the unit's conceptual flow, brainstormed potential student activities, and discussed the role of educational technology for the unit. As a result of the planning meeting discussions, BSCS staff sought additional funding to develop, disseminate, and evaluate the Frontiers in Microbiology curriculum unit. This unit was intended to be developed as a replacement unit suitable for an introductory biology course. The unit would feature inquiry-based student activities and provide approximately four weeks of instruction. As appropriate, activities would make use of multimedia. The development and production processes would require about two years for completion. Unfortunately, BSCS staff was not able to attract sufficient funding to develop the proposed curriculum unit. Since there were some unexpended funds left over from the planning meeting, BSCS requested and received permission from DOE to use the balance of the funds to prepare background materials about advances in microbiology that would be useful to teachers. These

Comparison of clinical diagnosis and microbiological test results in vaginal infections.

PubMed

Karaca, M; Bayram, A; Kocoglu, M E; Gocmen, A; Eksi, F

2005-01-01

Lower genital tract infections continue to be a problem due to the fact that the clinical diagnosis is usually inadequate, and subsequent care is suboptimal. This study aimed at evaluating the accuracy of clinical diagnosis by comparing it with microbiologic test results, and to determine the causative agents of vaginal infections. Sixty-seven nonpregnant women (18-45 years of age) with the clinical diagnosis of lower genital tract infection were enrolled in the study. Patients were not included if they had a history of vaginal infection during the previous three-month period or intrauterine device. The clinical diagnosis was based on the combinations of symptoms, direct observation of wet mount, homogeneous discharge, vaginal pH > 4.5, and detection of the amine odor after exposure of vaginal secretions to 10% KOH. Vaginal samples were taken with two cotton swabs, one was used for pH determination, and the second was utilized for microbiological tests. Gram staining and cultures with Sabouraud agar and chocolate agar were performed for microbiological diagnosis, and the results were compared. The clinical diagnoses included 26 (38.8%) candidiasis, 18 (26.8%) bacterial vaginosis, three (4.5%) trichomoniasis, and 20 (29.9%) mixed vaginal infections. Of the 26 patients with clinical diagnoses of candidiasis, 12 (46.1%) revealed Candiada albicans, nine (34.6) patients revealed microorganisms other than candida species, and five (19.2%) patients had no growth. Five (27.8%) bacterial vaginosis patients revealed Gardnarella vaginalis and 12 patients (66.6%) did not grow any microorganism. The overall rate of accurate clinical diagnoses confirmed by microbiological test results was 43.2%. Seventeen (43.6) of the 39 microbiological test results correlated with clinical diagnosis, and no growth was observed in 28 (41.8%) cultures. We conclude that the clinical diagnosis of vaginal infection is inadequate and should be confirmed with microbiological testing if the resources

Determining risk for severe leptospirosis by molecular analysis of environmental surface waters for pathogenic Leptospira.

PubMed

Ganoza, Christian A; Matthias, Michael A; Collins-Richards, Devon; Brouwer, Kimberly C; Cunningham, Calaveras B; Segura, Eddy R; Gilman, Robert H; Gotuzzo, Eduardo; Vinetz, Joseph M

2006-08-01

Although previous data indicate that the overall incidence of human leptospirosis in the Peruvian Amazon is similar in urban and rural sites, severe leptospirosis has been observed only in the urban context. As a potential explanation for this epidemiological observation, we tested the hypothesis that concentrations of more virulent Leptospira would be higher in urban than in rural environmental surface waters. A quantitative real-time PCR assay was used to compare levels of Leptospira in urban and rural environmental surface waters in sites in the Peruvian Amazon region of Iquitos. Molecular taxonomic analysis of a 1,200-bp segment of the leptospiral 16S ribosomal RNA gene was used to identify Leptospira to the species level. Pathogenic Leptospira species were found only in urban slum water sources (Fisher's exact test; p = 0.013). The concentration of pathogen-related Leptospira was higher in urban than rural water sources (approximately 10(3) leptospires/ml versus 0.5 x 10(2) leptospires/ml; F = 8.406, p < 0.05). Identical 16S rRNA gene sequences from Leptospira interrogans serovar Icterohaemorrhagiae were found in urban slum market area gutter water and in human isolates, suggesting a specific mode of transmission from rats to humans. In a prospective, population-based study of patients presenting with acute febrile illness, isolation of L. interrogans-related leptospires from humans was significantly associated with urban acquisition (75% of urban isolates); human isolates of other leptospiral species were associated with rural acquisition (78% of rural isolates) (chi-square analysis; p < 0.01). This distribution of human leptospiral isolates mirrored the distribution of leptospiral 16S ribosomal gene sequences in urban and rural water sources. Our findings data support the hypothesis that urban severe leptospirosis in the Peruvian Amazon is associated with higher concentrations of more pathogenic leptospires at sites of exposure and transmission. This

Determining Risk for Severe Leptospirosis by Molecular Analysis of Environmental Surface Waters for Pathogenic Leptospira

PubMed Central

Collins-Richards, Devon; Brouwer, Kimberly C; Cunningham, Calaveras B; Segura, Eddy R; Gilman, Robert H; Gotuzzo, Eduardo; Vinetz, Joseph M

2006-01-01

Background Although previous data indicate that the overall incidence of human leptospirosis in the Peruvian Amazon is similar in urban and rural sites, severe leptospirosis has been observed only in the urban context. As a potential explanation for this epidemiological observation, we tested the hypothesis that concentrations of more virulent Leptospira would be higher in urban than in rural environmental surface waters. Methods and Findings A quantitative real-time PCR assay was used to compare levels of Leptospira in urban and rural environmental surface waters in sites in the Peruvian Amazon region of Iquitos. Molecular taxonomic analysis of a 1,200-bp segment of the leptospiral 16S ribosomal RNA gene was used to identify Leptospira to the species level. Pathogenic Leptospira species were found only in urban slum water sources (Fisher's exact test; p = 0.013). The concentration of pathogen-related Leptospira was higher in urban than rural water sources (~103 leptospires/ml versus 0.5 × 102 leptospires/ml; F = 8.406, p < 0.05). Identical 16S rRNA gene sequences from Leptospira interrogans serovar Icterohaemorrhagiae were found in urban slum market area gutter water and in human isolates, suggesting a specific mode of transmission from rats to humans. In a prospective, population-based study of patients presenting with acute febrile illness, isolation of L. interrogans-related leptospires from humans was significantly associated with urban acquisition (75% of urban isolates); human isolates of other leptospiral species were associated with rural acquisition (78% of rural isolates) (chi-square analysis; p < 0.01). This distribution of human leptospiral isolates mirrored the distribution of leptospiral 16S ribosomal gene sequences in urban and rural water sources. Conclusions Our findings data support the hypothesis that urban severe leptospirosis in the Peruvian Amazon is associated with higher concentrations of more pathogenic leptospires at sites of exposure

76 FR 28689 - Microbiology Devices; Classification of In Vitro Diagnostic Device for Bacillus Species Detection

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-18

.... FDA-2011-N-0103] Microbiology Devices; Classification of In Vitro Diagnostic Device for Bacillus... of the Microbiology Devices Advisory Panel (the Panel). In addition, the proposed rule would... in the Federal Register. 1. Transcript of the FDA Microbiology Devices Panel meeting, March 7, 2002...

76 FR 69034 - Microbiology Devices; Classification of In Vitro Diagnostic Device for Yersinia Species Detection

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-07

... Drug Administration 21 CFR Part 866 Microbiology Devices; Classification of In Vitro Diagnostic Device... CFR Part 866 [Docket No. FDA-2011-N-0729] Microbiology Devices; Classification of In Vitro Diagnostic... of the Microbiology Devices Advisory Panel (the panel). FDA is publishing in this document the...

Molecular method for detection of total coliforms in drinking water samples.

PubMed

Maheux, Andrée F; Boudreau, Dominique K; Bisson, Marc-Antoine; Dion-Dupont, Vanessa; Bouchard, Sébastien; Nkuranga, Martine; Bergeron, Michel G; Rodriguez, Manuel J

2014-07-01

This work demonstrates the ability of a bacterial concentration and recovery procedure combined with three different PCR assays targeting the lacZ, wecG, and 16S rRNA genes, respectively, to detect the presence of total coliforms in 100-ml samples of potable water (presence/absence test). PCR assays were first compared to the culture-based Colilert and MI agar methods to determine their ability to detect 147 coliform strains representing 76 species of Enterobacteriaceae encountered in fecal and environmental settings. Results showed that 86 (58.5%) and 109 (74.1%) strains yielded a positive signal with Colilert and MI agar methods, respectively, whereas the lacZ, wecG, and 16S rRNA PCR assays detected 133 (90.5%), 111 (75.5%), and 146 (99.3%) of the 147 total coliform strains tested. These assays were then assessed by testing 122 well water samples collected in the Québec City region of Canada. Results showed that 97 (79.5%) of the samples tested by culture-based methods and 95 (77.9%), 82 (67.2%), and 98 (80.3%) of samples tested using PCR-based methods contained total coliforms, respectively. Consequently, despite the high genetic variability of the total coliform group, this study demonstrated that it is possible to use molecular assays to detect total coliforms in potable water: the 16S rRNA molecular assay was shown to be as efficient as recommended culture-based methods. This assay might be used in combination with an Escherichia coli molecular assay to assess drinking water quality. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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.

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

Centralization of a regional clinical microbiology service: The Calgary experience

PubMed Central

Church, Deirdre L; Hall, Paula

1999-01-01

Diagnostic laboratory services in Alberta have been dramatically restructured over the past five years. In 1994, Alberta Health embarked on an aggressive laboratory restructuring that cut back approximately 30% of the overall monies previously paid to the laboratory service sector in Calgary. A unique service delivery model consolidated all institutional and community-based diagnostic testing in a company called Calgary Laboratory Services (CLS) in late 1996. CLS was formed by a public/private partnership between the Calgary Regional Health Care Authority (CRHA) and MDS-Kasper Laboratories. By virtue of its customer service base and scope of testing, CLS provides comprehensive regional laboratory services to the entire populace. Regional microbiology services within CLS have been successfully consolidated over the past three years into a centralized high volume laboratory (HVL). Because the HVL is not located in a hospital, rapid response laboratories (RRLs) are operated at each acute care site. Although the initial principle behind the proposed test menus for the RRLs was that only procedures requiring a clinical turnaround time of more than 2 h stay on-site, many other principles had to be used to develop and implement an efficient and clinically relevant RRL model for microbiology. From these guiding principles, a detailed assessment of the needs of each institution and extensive networking with user groups, the functions of the microbiology RRLs were established and a detailed implementation plan drawn up. The experience at CLS with regards to restructuring a regional microbiology service is described herein. A post-hoc analysis provides the pros and cons of directing and operating a regionalized microbiology service. PMID:22346397

Recent applications of hyperspectral imaging in microbiology.

PubMed

Gowen, Aoife A; Feng, Yaoze; Gaston, Edurne; Valdramidis, Vasilis

2015-05-01

Hyperspectral chemical imaging (HSI) is a broad term encompassing spatially resolved spectral data obtained through a variety of modalities (e.g. Raman scattering, Fourier transform infrared microscopy, fluorescence and near-infrared chemical imaging). It goes beyond the capabilities of conventional imaging and spectroscopy by obtaining spatially resolved spectra from objects at spatial resolutions varying from the level of single cells up to macroscopic objects (e.g. foods). In tandem with recent developments in instrumentation and sampling protocols, applications of HSI in microbiology have increased rapidly. This article gives a brief overview of the fundamentals of HSI and a comprehensive review of applications of HSI in microbiology over the past 10 years. Technical challenges and future perspectives for these techniques are also discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

[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.

Artificial Surfaces in Phyllosphere Microbiology.

PubMed

Doan, Hung K; Leveau, Johan H J

2015-08-01

The study of microorganisms that reside on plant leaf surfaces, or phyllosphere microbiology, greatly benefits from the availability of artificial surfaces that mimic in one or more ways the complexity of foliage as a microbial habitat. These leaf surface proxies range from very simple, such as nutrient agars that can reveal the metabolic versatility or antagonistic properties of leaf-associated microorganisms, to the very complex, such as silicon-based casts that replicate leaf surface topography down to nanometer resolution. In this review, we summarize the various uses of artificial surfaces in experimental phyllosphere microbiology and discuss how these have advanced our understanding of the biology of leaf-associated microorganisms and the habitat they live in. We also provide an outlook into future uses of artificial leaf surfaces, foretelling a greater role for microfluidics to introduce biological and chemical gradients into artificial leaf environments, stressing the importance of artificial surfaces to generate quantitative data that support computational models of microbial life on real leaves, and rethinking the leaf surface ('phyllosphere') as a habitat that features two intimately connected but very different compartments, i.e., the leaf surface landscape ('phylloplane') and the leaf surface waterscape ('phyllotelma').

Advanced continuous cultivation methods for systems microbiology.

PubMed

Adamberg, Kaarel; Valgepea, Kaspar; Vilu, Raivo

2015-09-01

Increasing the throughput of systems biology-based experimental characterization of in silico-designed strains has great potential for accelerating the development of cell factories. For this, analysis of metabolism in the steady state is essential as only this enables the unequivocal definition of the physiological state of cells, which is needed for the complete description and in silico reconstruction of their phenotypes. In this review, we show that for a systems microbiology approach, high-resolution characterization of metabolism in the steady state--growth space analysis (GSA)--can be achieved by using advanced continuous cultivation methods termed changestats. In changestats, an environmental parameter is continuously changed at a constant rate within one experiment whilst maintaining cells in the physiological steady state similar to chemostats. This increases the resolution and throughput of GSA compared with chemostats, and, moreover, enables following of the dynamics of metabolism and detection of metabolic switch-points and optimal growth conditions. We also describe the concept, challenge and necessary criteria of the systematic analysis of steady-state metabolism. Finally, we propose that such systematic characterization of the steady-state growth space of cells using changestats has value not only for fundamental studies of metabolism, but also for systems biology-based metabolic engineering of cell factories.

Outbreaks and factors influencing microbiological contamination of fresh produce.

PubMed

Wadamori, Yukiko; Gooneratne, Ravi; Hussain, Malik A

2017-03-01

Fresh fruits and vegetables are nutritionally well-recognised as healthy components in diets. The microbiological foodborne outbreaks associated with the consumption of fresh produce have been increasing. Salmonella spp., Escherichia coli O157:H7, Staphylococcus aureus, Campylobacter spp. and Listeria monocytogenes are the most common pathogens that contaminate fresh produce. This review discusses recent foodborne outbreaks linked to fresh produce, factors that affect microbiological contamination and measures that could be adopted to reduce the foodborne illnesses. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Final Environmental Impact Statement (FEIS)/Final Environmental Impact Report (FEIR). Otis Air National Guard Base, Wastewater Treatment Facility

DTIC Science & Technology

1990-06-01

and G.E. Ness, 1982, Survival of Vibrio cholerae and Escherichia coli in Estuarine Water and Sediments, Applied and Environmental Microbiology, 43...and publications in areas of water and wastewater treatment. David Tomasko, Ph.D., 1985. University of New Mexico . Staff Hydrogeologist. Research...Reserve in California. We are working on EIS’s for the U.S. Air Force Base Closings in realignment in California, New Mexico and Washington, and a very

A SURVEY OF THE MICROBIOLOGICAL QUALITY OF WATER USED IN DENTAL TREATMENT

EPA Science Inventory

In recent years there has been a growing awareness of the microbiological quality of water used in dental water systems. The purpose of this study was to conduct a microbiological survey of dental water units within the Commonwealth of Kentucky. Water samples were collected and ...

Microbiology and Treatment of Acute Apical Abscesses

PubMed Central

Rôças, Isabela N.

2013-01-01

SUMMARY Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium, Parvimonas, Prevotella, Porphyromonas, Dialister, Streptococcus, and Treponema. Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease. PMID:23554416

MICROBIOLOGICAL ASPECTS OF THE ORTHODONTIC TREATMENT.

PubMed

Zharmagambetova, A; Tuleutayeva, S; Akhmetova, S; Zharmagambetov, A

2017-03-01

An orthodontic appliance in the mouth worsens conditions for its self-cleaning, complicates the teeth care and makes an environment favorable to the soft tooth deposit, in turn, leads to the teeth enamel demineralization. In literature, the majority of works are devoted to the study of the microbial landscape with fixed orthodontic treatment. Despite the obvious relevance, the formation problem of opportunistic and pathogenic microorganisms when treating dentoalveolar anomalies with a removable orthodontic appliance remains understudied. The research aim was to investigate the influence of the removable type of orthodontic treatment of patients aged 12 with dentoalveolar anomalies on the mouth microbiocenosis. The dental examination and microbiological study was conducted to 100 children aged 12 with dentoalveolar anomalies. The dental examination included assessment of the oral hygiene state by the OHI-S index. The microbiological research was conducted in the following sequence: the bacterioscopy smear of plaque, stained by the Gram and Burri method with the assessment of morphological and tinctorial properties of microorganisms. The statistical data analysis was performed using SPSS v22.0 forWindows program. The dental examination showed that the oral hygiene state varied according to the orthodontic treatment stage. During the orthodontic treatment the OHI-S Index was 2.1 score, indicating a satisfactory oral hygiene level. The microbiological study showed that persistent contaminants were lactobacilli, streptococci, staphylococci, and yeast-like fungi. However, the treatment showed a decrease of normal flora level and the increase in number of Candidaalbicans, Staphylococcusaureus and Streptococcusmutans, that was a trigger in the development of dental caries and periodontal disease. During the orthodontic treatment, children with dentoalveolar anomalies are at high risk of dental caries and periodontal disease.

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.

Environmental surveillance of poliovirus in sewage water around the introduction period for inactivated polio vaccine in Japan.

PubMed

Nakamura, Tomofumi; Hamasaki, Mitsuhiro; Yoshitomi, Hideaki; Ishibashi, Tetsuya; Yoshiyama, Chiharu; Maeda, Eriko; Sera, Nobuyuki; Yoshida, Hiromu

2015-03-01

Environmental virus surveillance was conducted at two independent sewage plants from urban and rural areas in the northern prefecture of the Kyushu district, Japan, to trace polioviruses (PVs) within communities. Consequently, 83 PVs were isolated over a 34-month period from April 2010 to January 2013. The frequency of PV isolation at the urban plant was 1.5 times higher than that at the rural plant. Molecular sequence analysis of the viral VP1 gene identified all three serotypes among the PV isolates, with the most prevalent serotype being type 2 (46%). Nearly all poliovirus isolates exhibited more than one nucleotide mutation from the Sabin vaccine strains. During this study, inactivated poliovirus vaccine (IPV) was introduced for routine immunization on 1 September 2012, replacing the live oral poliovirus vaccine (OPV). Interestingly, the frequency of PV isolation from sewage waters declined before OPV cessation at both sites. Our study highlights the importance of environmental surveillance for the detection of the excretion of PVs from an OPV-immunized population in a highly sensitive manner, during the OPV-to-IPV transition period. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Molecular detection of pathogens in water--the pros and cons of molecular techniques.

PubMed

Girones, Rosina; Ferrús, Maria Antonia; Alonso, José Luis; Rodriguez-Manzano, Jesus; Calgua, Byron; Corrêa, Adriana de Abreu; Hundesa, Ayalkibet; Carratala, Anna; Bofill-Mas, Sílvia

2010-08-01

Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed. (c) 2010 Elsevier Ltd. All rights reserved.

Outbreak!: Teaching Clinical and Diagnostic Microbiology Methodologies with an Interactive Online Game

ERIC Educational Resources Information Center

Clark, Sherri; Smith, Geoffrey Battle

2004-01-01

Outbreak! is an online, interactive educational game that helps students and teachers learn and evaluate clinical microbiology skills. When the game was used in introductory microbiology laboratories, qualitative evaluation by students showed very positive responses and increased learning. Outbreak! allows students to design diagnostic tests and…

ENVIRONMENTAL FACTORS AND CHEMICAL AND MICROBIOLOGICAL CONSTITUENTS RELATED TO THE PRESENECE OF VIRUSES IN GROUND WATER FROM SMALL PUBLIC WATER SUPPLIES IN SOUTHEASTERN MICHIGAN

EPA Science Inventory

Thirty-eight public ground-water-supply wells serving fewer than 3,300 people were sampled from July 1999 through July 2001 in southeastern Michigan to determine (1) the occurrence of viral pathogens and microbiological indicators, (2) the adequacy of indicators as predictors of...

Microbiological testing of pharmaceuticals and cosmetics in Egypt.

PubMed

Zeitoun, Hend; Kassem, Mervat; Raafat, Dina; AbouShlieb, Hamida; Fanaki, Nourhan

2015-12-09

Microbial contamination of pharmaceuticals poses a great problem to the pharmaceutical manufacturing process, especially from a medical as well as an economic point of view. Depending upon the product and its intended use, the identification of isolates should not merely be limited to the United States Pharmacopeia (USP) indicator organisms. Eighty-five pre-used non-sterile pharmaceuticals collected from random consumers in Egypt were examined for the eventual presence of bacterial contaminants. Forty-one bacterial contaminants were isolated from 31 of the tested preparations. These isolates were subjected to biochemical identification by both conventional tests as well as API kits, which were sufficient for the accurate identification of only 11 out of the 41 bacterial contaminants (26.8%) to the species level. The remaining isolates were inconclusively identified or showed contradictory results after using both biochemical methods. Using molecular methods, 24 isolates (58.5%) were successfully identified to the species level. Moreover, polymerase chain reaction (PCR) assays were compared to standard biochemical methods in the detection of pharmacopoeial bacterial indicators in artificially-contaminated pharmaceutical samples. PCR-based methods proved to be superior regarding speed, cost-effectiveness and sensitivity. Therefore, pharmaceutical manufacturers would be advised to adopt PCR-based methods in the microbiological quality testing of pharmaceuticals in the future.

The medically important aerobic actinomycetes: epidemiology and microbiology.

PubMed Central

McNeil, M M; Brown, J M

1994-01-01

The aerobic actinomycetes are soil-inhabiting microorganisms that occur worldwide. In 1888, Nocard first recognized the pathogenic potential of this group of microorganisms. Since then, several aerobic actinomycetes have been a major source of interest for the commercial drug industry and have proved to be extremely useful microorganisms for producing novel antimicrobial agents. They have also been well known as potential veterinary pathogens affecting many different animal species. The medically important aerobic actinomycetes may cause significant morbidity and mortality, in particular in highly susceptible severely immunocompromised patients, including transplant recipients and patients infected with human immunodeficiency virus. However, the diagnosis of these infections may be difficult, and effective antimicrobial therapy may be complicated by antimicrobial resistance. The taxonomy of these microorganisms has been problematic. In recent revisions of their classification, new pathogenic species have been recognized. The development of additional and more reliable diagnostic tests and of a standardized method for antimicrobial susceptibility testing and the application of molecular techniques for the diagnosis and subtyping of these microorganisms are needed to better diagnose and treat infected patients and to identify effective control measures for these unusual pathogens. We review the epidemiology and microbiology of the major medically important aerobic actinomycetes. Images PMID:7923055

Using concept maps to describe undergraduate students’ mental model in microbiology course

NASA Astrophysics Data System (ADS)

Hamdiyati, Y.; Sudargo, F.; Redjeki, S.; Fitriani, A.

2018-05-01

The purpose of this research was to describe students’ mental model in a mental model based-microbiology course using concept map as assessment tool. Respondents were 5th semester of undergraduate students of Biology Education of Universitas Pendidikan Indonesia. The mental modelling instrument used was concept maps. Data were taken on Bacteria sub subject. A concept map rubric was subsequently developed with a maximum score of 4. Quantitative data was converted into a qualitative one to determine mental model level, namely: emergent = score 1, transitional = score 2, close to extended = score 3, and extended = score 4. The results showed that mental model level on bacteria sub subject before the implementation of mental model based-microbiology course was at the transitional level. After implementation of mental model based-microbiology course, mental model was at transitional level, close to extended, and extended. This indicated an increase in the level of students’ mental model after the implementation of mental model based-microbiology course using concept map as assessment tool.

Writing To Facilitate Learning in Microbiology.

ERIC Educational Resources Information Center

Fisher, Linda E.

This paper describes a microbiology course that utilizes writing to facilitate learning of complex concepts, for communicating experimental results, and as a diagnostic tool for the instructor in monitoring the students' understanding of material on an on-going basis. In-class writing assignments that summarize subject units are accompanied by a…

[Medical microbiology laboratories in Dutch hospitals: essential for safe patient care].

PubMed

Bonten, M J M

2008-12-06

The Netherlands Health Care Inspectorate investigated the quality of medical microbiology laboratories in Dutch hospitals. By and large the laboratories fulfilled the requirements for appropriate care, although some processes were unsatisfactory and some were insufficiently formalised. In the Netherlands, laboratories for medical microbiology are integrated within hospitals and medical microbiologists are responsible for the diagnostic processes as well as for co-treatment of patients, infection prevention and research. This integrated model contrasts to the more industrialised model in many other countries, where such laboratories are physically distinct from hospitals with a strong focus on diagnostics. The Inspectorate also concludes that the current position of medical microbiology in Dutch hospitals is necessary for patient safety and that outsourcing of these facilities is considered unacceptable.

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

Epigenetic: a molecular link between testicular cancer and environmental exposures.

PubMed

Vega, Aurelie; Baptissart, Marine; Caira, Françoise; Brugnon, Florence; Lobaccaro, Jean-Marc A; Volle, David H

2012-01-01

In the last decades, studies in rodents have highlighted links between in utero and/or neonatal exposures to molecules that alter endocrine functions and the development of genital tract abnormalities, such as cryptorchidism, hypospadias, and impaired spermatogenesis. Most of these molecules, called endocrine disrupters exert estrogenic and/or antiandrogenic activities. These data led to the hypothesis of the testicular dysgenesis syndrome which postulates that these disorders are one clinical entity and are linked by epidemiological and pathophysiological relations. Furthermore, infertility has been stated as a risk factor for testicular cancer (TC). The incidence of TC has been increasing over the past decade. Most of testicular germ cell cancers develop through a pre-invasive carcinoma in situ from fetal germ cells (primordial germ cell or gonocyte). During their development, fetal germ cells undergo epigenetic modifications. Interestingly, several lines of evidence have shown that gene regulation through epigenetic mechanisms (DNA and histone modifications) plays an important role in normal development as well as in various diseases, including TC. Here we will review chromatin modifications which can affect testicular physiology leading to the development of TC; and highlight potential molecular pathways involved in these alterations in the context of environmental exposures.

Molecularly imprinted solid-phase extraction combined with high performance liquid chromatography for analysis of phenolic compounds from environmental water samples.

PubMed

Feng, Qin-Zhong; Zhao, Li-Xia; Yan, Wei; Lin, Jin-Ming; Zheng, Zhi-Xia

2009-08-15

The molecularly imprinted bulk polymer with 2,4,6-trichlorophenol (2,4,6-TCP) as the template molecule and methylacrylic acid (MAA), ethylene glycol dimethacrylate (EGDMA) as functional monomer and the crosslinker, respectively, has been prepared and applied to the molecularly imprinted solid-phase extraction (MISPE) procedure for selective preconcentration of phenolic compounds from environmental water samples. Various parameters affecting the extraction efficiency of the polymer have been evaluated to optimize the selective preconcentration of the phenolic compounds from aqueous samples. The characteristics of the MISPE method were validated by HPLC. The recoveries ranged between 90% and 98% (RSD: 0.9-2.3%, n=3) for tap water, between 85% and 105% (RSD: 2.6-4.9%, n=3) for river water, between 78% and 98% (RSD: 2.6-5.4%, n=3) for sewage water fortified with 0.4 mg L(-1) of phenol, 4-chlorophenol (4-CP), 2,4-dichlorophenol (2,4-DCP), pentachlorophenol (PCP). It was demonstrated that this MISPE-HPLC method could be applied to direct preconcentration and determination of phenolic compounds in environmental water samples.

Microbiological aspects of vulvovaginitis in prepubertal girls.

PubMed

Ranđelović, Gordana; Mladenović, Vesna; Ristić, Ljiljana; Otašević, Suzana; Branković, Sofija; Mladenović-Antić, Snežana; Bogdanović, Milena; Bogdanović, Dragan

2012-08-01

This study aimed to establish the vaginal introitus microbial flora in girls with and without symptoms of vulvovaginitis, and to present the distribution of isolated microorganisms by age groups in girls with vulvovaginitis. We enrolled 500 girls with vulvovaginitis symptoms, aged 2-12 years, referred by their pediatricians for microbiological examination of the vaginal introitus swabs, and 30 age-matched asymptomatic girls. Similar microbial flora was isolated in both groups, but the symptomatic girls had significantly more common positive microbiological findings compared to controls (p < 0.001). In symptomatic girls, the following pathogenic bacteria were isolated: Streptococcus pyogenes (4.2%), Haemophilus influenzae (0.4%), and Staphylococcus aureus (5.8%). Bacteria of fecal origin were found in vaginal introitus swabs in 33.8% of cases, most commonly Proteus mirabilis (14.4%), Enterococcus faecalis (12.2%), and Escherichia coli (7.0%). The finding of fecal flora was more common compared to controls, reaching a statistical significance (p < 0.05), as well as in girls aged up to 6 years (p < 0.001). Candida species were found in 2.4% of girls with vulvovaginitis symptoms. The microbial ecosystem in girls with clinical signs of vulvovaginitis is complex and variable, and the presence of a microorganism does not necessarily imply that it is the cause of infection. The diagnosis of vulvovaginitis in prepubertal girls requires a complex and comprehensive approach, and microbiological findings should be interpreted in the context of clinical findings.

Preflight and postflight microbiological results from 25 space shuttle crews

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Bassinger, Virginia J.; Molina, Thomas C.; Gunter, Emelie G.; Groves, Theron O.; Cioletti, Louis J.; Mishra, S. K.

1993-01-01

Clinical-microbiological investigations are an important aspect of the crew health stabilization program. To ensure that space crews have neither active nor latent infections, clinical specimens, including throat and nasal swabs and urine samples, are collected at 10 days (L-10) and 2days (L-2) before launch, and immediately after landing (L+0). All samples are examined for the presence of bacteria and fungi. In addition, fecal samples are collected at L-10 and examined for bacteria, fungi and parasites. This paper describes clinical-microbiological findings from 144 astronauts participating in 25 Space Shuttle missions spanning Space Transportation System (STS)-26 to STS-50. The spectrum of microbiological findings from the specimens included 25 bacterial and 11 fungal species. Among the bacteria isolated most frequently were Staphylococcus aureus, Enterobacter aerogenes, Enterococcus faecalis, Escherichia coli, Proteus mirabilis and Streptococcus agalactiae. Candida albicans was the most frequently isolated fungal pathogen.

Molecular characterization of lake sediment WEON by Fourier transform ion cyclotron resonance mass spectrometry and its environmental implications.

PubMed

Zhang, Li; Wang, Shengrui; Xu, Yisheng; Shi, Quan; Zhao, Haichao; Jiang, Bin; Yang, Jiachun

2016-12-01

The compositional properties of water-extractable organic nitrogen (WEON) affect its behavior in lake ecosystems. This work is the first comprehensive study using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) for the characterization of the molecular composition of WEON in lake sediment. In sediments of Erhai Lake in China, this study found complex WEON species, with N-containing compounds in the northern, central, and southern regions contributing 34.47%, 42.44%, and 40.6%, respectively, of total compounds. Additionally, a van Krevelen diagram revealed that lignin components were dominant in sediment WEON structures (68% of the total), suggesting terrestrial sources. Furthermore, this study applied ESI-FT-ICR-MS to the examination of the environmental processes of lake sediment WEON on a molecular level. The results indicated that sediment depth impacted WEON composition and geochemical processes. Compared with other ecosystems, the double bond equivalent (DBE) value was apparently lower in Erhai sediment, indicating the presence of relatively fewer and smaller aromatic compounds. In addition, the presence of a large number of N-containing species and abundant oxidized nitrogen functional compounds that were likely to biodegrade may have further increased the potential releasing risk of WEON from Erhai sediment under certain environmental conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbiological monitoring of guinea pigs reared conventionally at two breeding facilities in Korea.

PubMed

Park, Jong-Hwan; Seok, Seung-Hyeok; Baek, Min-Won; Lee, Hui-Young; Kim, Dong-Jae; Cho, Jung-Sik; Kim, Chuel-Kyu; Hwang, Dae-Youn; Park, Jae-Hak

2006-10-01

In this study, microbiological monitoring of guinea pigs reared conventionally in two facilities was performed twice in 2004, with a three-month-interval between surveys. This study was based on the recommendations of the FELASA Working Group, with some modifications. In serological tests in the first survey, some animals from facility A showed positive results for Encephalitozoon cuniculi, Sendai virus, pneumonia virus of mice (PVM), and Reovirus-3 (Reo-3); facility B showed a positive result only for E. cuniculi. The results of the second survey were similar to the first, except for the presence of Sendai virus; all animals from the two facilities were Sendai virus-negative in the second experiment. No pathogenic bacteria were cultured in the organs of any of the animals in the first survey. However, in the second survey, Bordetella bronchiseptica was cultured from the lung tissue of two 10-week-old animals from facility A. Chlamydial infection was examined by the Macchiavello method, but no animal showed positive results. Tests using fecal flotation or the KOH wet mount method showed no infection of endoparasites, protozoa, ectoparasites, or dermatophytes in any animal in both surveys. However, in the histopathological examination, an infection of protozoa-like organisms was observed in the cecum of some animals from facility A. The present study revealed that microbiological contamination was present in guinea pigs reared conventionally in two facilities in Korea, suggesting that there is a need to improve environmental conditions in order to eradicate microbial contamination.

Sheep milk: physical-chemical characteristics and microbiological quality.

PubMed

Merlin Junior, Ivandré Antonio; Santos, Joice Sifuentes dos; Costa, Ligia Grecco; Costa, Renan Grecco; Ludovico, Agostinho; Rego, Fabiola Cristine de Almeida; Santana, Elsa Helena Walter de

2015-09-01

Sheep milk is the third most consumed milk in Brazil. It is much appreciated for its nutritional status and is important for children that have problems with cow milk. Little information is known about the chemical, physical and microbiological composition of sheep milk from South Brazil. Thus, the aim of this study was to describe chemical and microbiological characteristics of sheep milk produced on two rural properties located in southern Brazil (ParanA and Rio Grande do Sul). The chemical composition of sheep milk was 17.32 g/100 g total solids, 5.86 g/100 g total protein, 4.46 g/100 g casein, 1.08 g/100 g whey protein, 7.28 g/100 g fat, 0.93 g/100 g ash, and 3.41 g/100 g lactose. High somatic cell count (1.7x106 cells/mL), total mesophilic bacterias (16.0 x 106 CFU/mL) and psychrotrophics (5.8 x 106 CFU/mL) were observed. Growth of Staphylococcus aureus, enterobacteria and coliforms occurred in 100% of the samples, and 45% of the samples showed growth of Escherichia coli. The sheep milk physical-chemical and microbiology parameters are similar to those presented in the literature for other countries but somatic cell count presented high levels.

Microbiological implications of periurban agriculture and water reuse in Mexico City.

PubMed

Mazari-Hiriart, Marisa; Ponce-de-León, Sergio; López-Vidal, Yolanda; Islas-Macías, Pilar; Amieva-Fernández, Rosa Isabel; Quiñones-Falconi, Francisco

2008-05-28

Recycled treated or untreated wastewater represents an important health challenge in developing countries due to potential water related microbiological exposure. Our aim was to assess water quality and health implications in a Mexico City periurban agricultural area. A longitudinal study in the Xochimilco wetland area was conducted, and 42 sites were randomly selected from 211, including irrigation water canals and effluents of treatment plants. Sample collection took place during rainy and dry seasons (2000-2001). Microbiological parameters (total coliforms, fecal coliforms, streptococci/enterococci, and bacteria other than Vibrio grown on TCBS), Helicobacter pylori, and physicochemical parameters including trihalomethanes (THM) were determined. Fecal coliforms and fecal streptococci are appropriate indicators of human or animal fecal contamination. Fecal coliform counts surpass Mexican and World Health Organization irrigation water guidelines. Identified microorganisms associated with various pathologies in humans and domestic animals comprise Escherichia coli, Klebsiella spp., Salmonella spp., Enterobacter spp., Enterococcus spp., and Pseudomonas spp; H. pylori was also present in the water. An environmental characteristic of the canal system showed high Total Organic Carbon content and relatively low dissolved oxygen concentration; residual chlorine as a disinfection control is not efficient, but THMs do not represent a problem. During the rainy season, temperature and conductivity were higher; in contrast, pH, dissolved oxygen, ammonia, and residual chlorine were lower. This is related with the continuous load of feces from human and animal sources, and to the aquatic systems, which vary seasonally and exhibit evidence of lower water quality in effluents from treatment plants. There is a need for improvement of wastewater treatment systems, as well as more efficient monitoring, regulation, and enforcement procedures for wastewater disposal into bodies of

70th Anniversary Collection for the Microbiology Society: Journal of Medical Microbiology.

PubMed

Mathee, Kalai; Silver, Lynn L; Tatke, Gorakh

2015-12-01

In the last 70 years, we have seen a radical change in our perception and understanding of the microbial world. During this period, we learned from Woese and Fox there exists a third kingdom called 'Archea' based on the phylogenetic studies of the 16S rRNA that revolutionized microbiology (Woese & Fox, 1977; Woese et al., 1978). Furthermore, we were forced to reckon with the fact that Koch and Pasteur's way of growing cells in test-tubes or flasks planktonically does not necessarily translate to the real-life scenario of bacterial lifestyle, where they prefer to live and function as a closely knit microbial community called biofilm. Thanks are due to Costerton, who led the crusade on the concept of biofilms and expanded its scope of inquiry, which forced scientists and clinicians worldwide to rethink how we evaluate and apply the data. Then progressively, disbelief turned into belief, and now it is universally accepted that the micro-organisms hobnob with the members of their community to communicate and coordinate their behaviour, especially in regard to growth patterns and virulence traits via signalling molecules. Just when we thought that we were losing the battle against bacteria, antimicrobials were discovered. We then witnessed the rise and fall of antibiotics and the development of antibiotic resistance. Due to space and choice limitation, we will focus on the three areas that caused this major paradigm shift (i) antimicrobial resistance (AMR), (ii) biofilm and (iii) quorum sensing (QS), and how the Journal of Medical Microbiology played a major role in advancing the shift.

The evolutionary ecology of molecular replicators

PubMed Central

2016-01-01

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology. PMID:27853598

The evolutionary ecology of molecular replicators.

PubMed

Nee, Sean

2016-08-01

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.

Surveillance of Environmental and Procedural Measures of Infection Control in the Operating Theatre Setting

PubMed Central

Raggi, Alessandra; Sanna, Tiziana; Mazzetti, Magda; Orsi, Alessandra; Zanni, Angela; Farruggia, Patrizia

2017-01-01

The microbiological contamination of operating theatres and the lack of adherence to best practices by surgical staff represent some of the factors affecting Surgical Site Infections (SSIs). The aim of the present study was to assess the microbiological quality of operating settings and the staff compliance to the SSI evidence-based control measures. Ten operating rooms were examined for microbiological contamination of air and surfaces, after cleaning procedures, in “at rest” conditions. Furthermore, 10 surgical operations were monitored to assess staff compliance to the recommended practices. None of the air samples exceeded microbiological reference standards and only six of the 200 surface samples (3.0%) were slightly above recommended levels. Potentially pathogenic bacteria and moulds were never detected. Staff compliance to best practices varied depending on the type of behaviour investigated and the role of the operator. The major not compliant behaviours were: pre-operative skin antisepsis, crowding of the operating room and hand hygiene of the anaesthetist. The good environmental microbiological quality observed is indicative of the efficacy of the cleaning-sanitization procedures adopted. The major critical point was staff compliance to recommended practices. Awareness campaigns are therefore necessary, aimed at improving the organisation of work so as to facilitate compliance to operative protocols. PMID:29283367

[Chronic bacterial prostatitis. Clinical and microbiological study of 332 cases].

PubMed

Heras-Cañas, Víctor; Gutiérrez-Soto, Blanca; Serrano-García, María Luisa; Vázquez-Alonso, Fernando; Navarro-Marí, José María; Gutiérrez-Fernández, José

2016-08-19

Chronic bacterial prostatitis (CBP) is characterized by long-lasting symptoms, frequently associated with psychosomatic disorders. The objective of the study was to study PCB in our environment clinically and microbiologically. Between January 2013 and December 2014 761 patients with suspected CBP were studied. Of these patients 332 (43.6%) underwent a complete microbiological study and the major clinical signs and symptoms were collected. Eighteen point four percent of patients were diagnosed microbiologically with CBP, Enterococcus faecalis being the main aetiologic agent (37.7%), followed by Escherichia coli (22.2%). Ninety-six point seven percent of the CBP had positive semen cultures, while only 22.9% had positive urine post-semen cultures. Data of sensitivity, specificity, positive predictive value and negative predictive value of semen were 96.7%, 95.9%, 84.3% and 99.3%, respectively and urine post-semen 22.9%, 99.3%, 87.5% and 85.1%, respectively. Testicular perineum pain (44.3%), ejaculatory discomfort (27.9%) and haemospermia (26.2%) were highlighted as the patients' main clinical manifestations. Fractionated culture for the microbiological diagnosis of CBP could be simplified by the culture of urine pre-semen and semen, without the need for the culture of urine post-semen. The main aetiologic agent of CBP in our media was Enterococcus faecalis, followed by Escherichia coli. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

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.

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.

CARD-FISH for Environmental Microorganisms: Technical Advancement and Future Applications

PubMed Central

Kubota, Kengo

2013-01-01

Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments. PMID:23124765

Rapid microbiology - raising awareness.

PubMed

Bailie, Jonathan

2016-01-01

A 'high-level overview' of some of the emerging rapid microbiology technologies designed to help healthcare engineering and infection control teams working in hospitals and other healthcare facilities more rapidly identify potentially hazardous levels of waterborne microorganisms in their water systems, enabling them to take prompt remedial action, and a look at the some of the 'pros and cons' of such testing techniques, was given by Nalco technical director, Howard Barnes, the vice-chair of the Legionella Control Association (LCA), at a recent LCA open day. HEJ editor, Jonathan Bailie, reports.

[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.

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.

[Funding for Division of Microbiology in 2014 by National Natural Science Foundation of China].

PubMed

Qiao, Jianjun; Huang, Chenyang; Liu, Lin; Wen, Mingzhang

2015-02-04

In this paper, we provided an overview of proposals submitted and projects funded in 2014 at the Division of Microbiology, Department of Life Sciences, National Natural Science Foundation of China. The traits and problems in different sub-disciplines were analyzed, the background, results and analysis of internet voting before panel meetings in Microbiology discipline were also introduced. The information will provide references for Chinese researchers to apply funding in microbiology discipline in the future.

21 CFR 211.113 - Control of microbiological contamination.

Code of Federal Regulations, 2011 CFR

2011-04-01

... shall include validation of all aseptic and sterilization processes. [43 FR 45077, Sept. 29, 1978, as... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures...

21 CFR 211.113 - Control of microbiological contamination.

Code of Federal Regulations, 2012 CFR

2012-04-01

... shall include validation of all aseptic and sterilization processes. [43 FR 45077, Sept. 29, 1978, as... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures...

21 CFR 211.113 - Control of microbiological contamination.

Code of Federal Regulations, 2014 CFR

2014-04-01

... shall include validation of all aseptic and sterilization processes. [43 FR 45077, Sept. 29, 1978, as... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures...

21 CFR 211.113 - Control of microbiological contamination.

Code of Federal Regulations, 2013 CFR

2013-04-01

... shall include validation of all aseptic and sterilization processes. [43 FR 45077, Sept. 29, 1978, as... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures...

National environmental specimen bank survey. [Location of 657 collections of environmental specimens

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

Van Hook, R.I.; Huber, E.E.

1976-01-01

This report presents the data base developed in the National Environmental Specimen Bank (NESB) Survey. The methodology utilized in developing the mailing lists and in developing and maintaining the data base records also is included. The NESB Survey Data Base is computerized in the Oak Ridge Computerized Hierarchical Information System, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830. The NESB Survey mailing list consisted of 4500 names and addresses. The 657 environmental specimen collections that were located and documented in the NESB Survey Data Base include the following categories: animal, atmospheric, geological, microbiological, plant, and water. However, the majority ofmore » the collections identified are biological in nature. Three indices of the NESB Survey Data Base are included in this report: respondents names and addresses categorized by organizational affiliation; (2) alphabetical listing of respondents; and geographical sampling location for materials in collections.« less

Progress in cultivation-independent phyllosphere microbiology

PubMed Central

Müller, Thomas; Ruppel, Silke

2014-01-01

Most microorganisms of the phyllosphere are nonculturable in commonly used media and culture conditions, as are those in other natural environments. This review queries the reasons for their ‘noncultivability’ and assesses developments in phyllospere microbiology that have been achieved cultivation independently over the last 4 years. Analyses of total microbial communities have revealed a comprehensive microbial diversity. 16S rRNA gene amplicon sequencing and metagenomic sequencing were applied to investigate plant species, location and season as variables affecting the composition of these communities. In continuation to culture-based enzymatic and metabolic studies with individual isolates, metaproteogenomic approaches reveal a great potential to study the physiology of microbial communities in situ. Culture-independent microbiological technologies as well advances in plant genetics and biochemistry provide methodological preconditions for exploring the interactions between plants and their microbiome in the phyllosphere. Improving and combining cultivation and culture-independent techniques can contribute to a better understanding of the phyllosphere ecology. This is essential, for example, to avoid human–pathogenic bacteria in plant food. PMID:24003903

Laboratory Design for Microbiological Safety

PubMed Central

Phillips, G. Briggs; Runkle, Robert S.

1967-01-01

Of the large amount of funds spent each year in this country on construction and remodeling of biomedical research facilities, a significant portion is directed to laboratories handling infectious microorganisms. This paper is intended for the scientific administrators, architects, and engineers concerned with the design of new microbiological facilities. It develops and explains the concept of primary and secondary barriers for the containment of microorganisms. The basic objectives of a microbiological research laboratory, (i) protection of the experimenter and staff, (ii) protection of the surrounding community, and (iii) maintenance of experimental validity, are defined. In the design of a new infectious-disease research laboratory, early identification should be made of the five functional zones of the facility and their relation to each other. The following five zones and design criteria applicable to each are discussed: clean and transition, research area, animal holding and research area, laboratory support, engineering support. The magnitude of equipment and design criteria which are necessary to integrate these five zones into an efficient and safe facility are delineated. Images Fig. 1 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 Fig. 11 Fig. 12 Fig. 13 Fig. 14 Fig. 15 Fig. 16 Fig. 17 Fig. 18 Fig. 19 PMID:4961771

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.