Board-invited review: Rumen microbiology: Leading the way in microbial ecology

USDA-ARS?s Scientific Manuscript database

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not ...

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…

Emerging applications of fluorescence spectroscopy in medical microbiology field.

PubMed

Shahzad, Aamir; Köhler, Gottfried; Knapp, Martin; Gaubitzer, Erwin; Puchinger, Martin; Edetsberger, Michael

2009-11-26

There are many diagnostic techniques and methods available for diagnosis of medically important microorganisms like bacteria, viruses, fungi and parasites. But, almost all these techniques and methods have some limitations or inconvenience. Most of these techniques are laborious, time consuming and with chances of false positive or false negative results. It warrants the need of a diagnostic technique which can overcome these limitations and problems. At present, there is emerging trend to use Fluorescence spectroscopy as a diagnostic as well as research tool in many fields of medical sciences. Here, we will critically discuss research studies which propose that Fluorescence spectroscopy may be an excellent diagnostic as well as excellent research tool in medical microbiology field with high sensitivity and specificity.

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.

Broad-range PCR: past, present, or future of bacteriology?

PubMed

Renvoisé, A; Brossier, F; Sougakoff, W; Jarlier, V; Aubry, A

2013-08-01

PCR targeting the gene encoding 16S ribosomal RNA (commonly named broad-range PCR or 16S PCR) has been used for 20 years as a polyvalent tool to study prokaryotes. Broad-range PCR was first used as a taxonomic tool, then in clinical microbiology. We will describe the use of broad-range PCR in clinical microbiology. The first application was identification of bacterial strains obtained by culture but whose phenotypic or proteomic identification remained difficult or impossible. This changed bacterial taxonomy and allowed discovering many new species. The second application of broad-range PCR in clinical microbiology is the detection of bacterial DNA from clinical samples; we will review the clinical settings in which the technique proved useful (such as endocarditis) and those in which it did not (such as characterization of bacteria in ascites, in cirrhotic patients). This technique allowed identifying the etiological agents for several diseases, such as Whipple disease. This review is a synthesis of data concerning the applications, assets, and drawbacks of broad-range PCR in clinical microbiology. Copyright © 2013 Elsevier Masson SAS. 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

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

USGS Publications Warehouse

Briggs, Kay Marano

2010-01-01

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

Microbiological sampling of spacecraft cabling, antennas, solar panels and thermal blankets

NASA Technical Reports Server (NTRS)

Koukol, R. C.

1973-01-01

Sampling procedures and techniques described resulted from various flight project microbiological monitoring programs of unmanned planetary spacecraft. Concurrent with development of these procedures, compatibility evaluations were effected with the cognizant spacecraft subsystem engineers to assure that degradation factors would not be induced during the monitoring program. Of significance were those areas of the spacecraft configuration for which special handling precautions and/or nonstandard sample gathering techniques were evolved. These spacecraft component areas were: cabling, high gain antenna, solar panels, and thermal blankets. The compilation of these techniques provides a historical reference for both the qualification and quantification of sampling parameters as applied to the Mariner Spacecraft of the late 1960's and early 1970's.

[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.

External Quality Assessments for Microbiologic Diagnosis of Diphtheria in Europe

PubMed Central

Both, Leonard; Neal, Shona; De Zoysa, Aruni; Mann, Ginder; Czumbel, Ida

2014-01-01

The European Diphtheria Surveillance Network (EDSN) ensures the reliable epidemiological and microbiologic assessment of disease prevalence in the European Union. Here, we describe a survey of current diagnostic techniques for diphtheria surveillance conducted across the European Union and report the results from three external quality assessment (EQA) schemes performed between 2010 and 2014. PMID:25297336

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

PubMed

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

2017-01-01

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

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.

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

PubMed

Kristóf, Katalin; Pongrácz, Júlia

2016-04-01

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

Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

PubMed

Gunar, O V; Sakhno, N G

2015-12-30

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

Modified ecometric technique (four-quadrant sequential streak) to evaluate Campylobacter enrichment broth proficiency in suppressing background microflora

USDA-ARS?s Scientific Manuscript database

Ecometric technique is a semi-quantitative scoring method used for quality control of culture media in microbiological laboratories. The technique involves inoculation with defined populations of specific culture onto solid media via a standardized chronological streaking technique, leading to ever-...

The recording of student performance in the microbiology laboratory as a training, tutorial, and motivational tool.

PubMed

Lipson, Steven M; Gair, Marina

2011-01-01

The laboratory component of a microbiology course consists of exercises which mandate a level of proficiency and manual dexterity equal to and often beyond that recognized among other biology courses. Bacterial growth, maintenance, identification (e.g., Gram stain, biochemical tests, genomics), as well as the continuous need to maintain laboratory safety and sterile technique, are only a few skills/responsibilities critical to the discipline of microbiology. Performance of the Gram stain remains one of the most basic and pivotal skills that must be mastered in the microbiology laboratory. However, a number of students continually have difficulty executing the Gram stain and preparative procedures associated with the test. In order to address this issue, we incorporated real-time digital recording as a supplemental teaching aid in the microbiology laboratory. Our use of the digital movie camera in the teaching setting served to enhance interest, motivate students, and in general, improve student performance.

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

PubMed

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

2004-06-01

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

Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling

PubMed Central

Haruta, Shin; Yoshida, Takehito; Aoi, Yoshiteru; Kaneko, Kunihiko; Futamata, Hiroyuki

2013-01-01

In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature. PMID:23995424

Estimation of Microbial Concentration in Food Products from Qualitative, Microbiological Test Data with the MPN Technique.

PubMed

Fujikawa, Hiroshi

2017-01-01

Microbial concentration in samples of a food product lot has been generally assumed to follow the log-normal distribution in food sampling, but this distribution cannot accommodate the concentration of zero. In the present study, first, a probabilistic study with the most probable number (MPN) technique was done for a target microbe present at a low (or zero) concentration in food products. Namely, based on the number of target pathogen-positive samples in the total samples of a product found by a qualitative, microbiological examination, the concentration of the pathogen in the product was estimated by means of the MPN technique. The effects of the sample size and the total sample number of a product were then examined. Second, operating characteristic (OC) curves for the concentration of a target microbe in a product lot were generated on the assumption that the concentration of a target microbe could be expressed with the Poisson distribution. OC curves for Salmonella and Cronobacter sakazakii in powdered formulae for infants and young children were successfully generated. The present study suggested that the MPN technique and the Poisson distribution would be useful for qualitative microbiological test data analysis for a target microbe whose concentration in a lot is expected to be low.

A novel electronic nose as adaptable device to judge microbiological quality and safety in foodstuff.

PubMed

Sberveglieri, V; Carmona, E Nunez; Comini, Elisabetta; Ponzoni, Andrea; Zappa, Dario; Pirrotta, Onofrio; Pulvirenti, A

2014-01-01

This paper presents different applications, in various foodstuffs, by a novel electronic nose (EN) based on a mixed metal oxide sensors array composed of thin films as well as nanowires. The electronic nose used for this work has been done, starting from the commercial model EOS835 produced by SACMI Scarl. The SENSOR Lab (CNR-INO, Brescia) has produced both typologies of sensors, classical MOX and the new technologies with nanowire. The aim of this work was to test and to illustrate the broad spectrum of potential uses of the EN technique in food quality control and microbial contamination diagnosis. The EN technique was coupled with classical microbiological and chemical techniques, like gas chromatography with mass spectroscopy (GC-MS) with SPME technique. Three different scenarios are presented: (a) detection of indigenous mould in green coffee beans, (b) selection of microbiological spoilage of Lactic Acid Bacteria (LAB), and (c) monitoring of potable water. In each case, the novel EN was able to identify the spoiled product by means of the alterations in the pattern of volatile organic compounds (VOCs), reconstructed by principal component analysis (PCA) of the sensor responses. The achieved results strongly encourage the use of EN in industrial laboratories. Finally, recent trends and future directions are illustrated.

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.

A four-quadrant sequential streak technique to evaluate Campylobacter selective broths for suppressing background flora in broiler carcass rinses

USDA-ARS?s Scientific Manuscript database

The ecometric technique is a semi-quantitative scoring method used in the quality control of culture media in microbiology laboratories. This technique involves inoculation with defined populations of a specific culture onto solid media via a standardized chronological streaking technique, leading ...

Clinical diagnosis of ventilator associated pneumonia revisited: comparative validation using immediate post-mortem lung biopsies.

PubMed

Fàbregas, N; Ewig, S; Torres, A; El-Ebiary, M; Ramirez, J; de La Bellacasa, J P; Bauer, T; Cabello, H

1999-10-01

A study was undertaken to assess the diagnostic value of different clinical criteria and the impact of microbiological testing on the accuracy of clinical diagnosis of suspected ventilator associated pneumonia (VAP). Twenty five deceased mechanically ventilated patients were studied prospectively. Immediately after death, multiple bilateral lung biopsy specimens (16 specimens/patient) were obtained for histological examination and quantitative lung cultures. The presence of both histological pneumonia and positive lung cultures was used as a reference test. The presence of infiltrates on the chest radiograph and two of three clinical criteria (leucocytosis, purulent secretions, fever) had a sensitivity of 69% and a specificity of 75%; the corresponding numbers for the clinical pulmonary infection score (CPIS) were 77% and 42%. Non-invasive as well as invasive sampling techniques had comparable values. The combination of all techniques achieved a sensitivity of 85% and a specificity of 50%, and these values remained virtually unchanged despite the presence of previous treatment with antibiotics. When microbiological results were added to clinical criteria, adequate diagnoses originating from microbiological results which might have corrected false positive and false negative clinical judgements (n = 5) were countered by a similar proportion of inadequate diagnoses (n = 6). Clinical criteria had reasonable diagnostic values. CPIS was not superior to conventional clinical criteria. Non-invasive and invasive sampling techniques had diagnostic values comparable to clinical criteria. An algorithm guiding antibiotic treatment exclusively by microbiological results does not increase the overall diagnostic accuracy and carries the risk of undertreatment.

[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.

Quality of the aetiological diagnosis of ventilator-associated pneumonia in Spain in the opinion of intensive care specialists and microbiologists.

PubMed

Bouza, Emilio; Martínez-Alarcón, José; Maseda, Emilio; Palomar, Mercedes; Zaragoza, Rafael; Pérez-Granda, María Jesús; Muñoz, Patricia; Burillo, Almudena

2017-03-01

Current guidelines for the microbiological diagnosis of ventilator-associated pneumonia (VAP) are imprecise. Based on data provided by intensive care specialists (ICS) and microbiologists, this study defines the clinical practices and microbiological techniques currently used for an aetiological diagnosis of VAP and pinpoints deficiencies. Eighty hospitals in the national health network with intensive care and microbiology departments were sent two questionnaires, one for each department, in order to collect data on VAP diagnosis for the previous year. Out of the 80 hospitals, 35 (43.8%) hospitals participated. These included 673 ICU beds, 32,020 ICU admissions, 173,820 ICU days stay, and generated 27,048 lower respiratory tract specimens in the year. A third of the hospitals (35%) had a microbiology department available 24/7. Most samples (83%) were tracheal aspirates. Gram stain results were immediately reported in around half (47%) of the hospitals. Quantification was made in 75% of hospitals. Molecular techniques and direct susceptibility testing were performed in 12% and one institution, respectively. Mean turnaround time for a microbiological report was 1.7 (SD; 0.7), and 2.2 (SD; 0.6) days for a negative and positive result, respectively. Telephone/in-person information was offered by 65% of the hospitals. Most (89%) ICS considered microbiological information as very useful. No written procedures were available in half the ICUs. Both ICS and microbiologists agreed that present guidelines for the diagnosis of VAP could be much improved, and that a new set of consensus guidelines is urgently required. A need for guidelines to be more effectively implemented was also identified in order to improve outcomes in patients with VAP. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Direct Microscopy: A Useful Tool to Diagnose Oral Candidiasis in Children and Adolescents.

PubMed

Marty, Mathieu; Bourrat, Emmanuelle; Vaysse, Frédéric; Bonner, Mark; Bailleul-Forestier, Isabelle

2015-12-01

Oral candidiasis is one of the most common opportunistic fungal infections of the oral cavity in human. Among children, this condition represents one of the most frequent affecting the mucosa. Although most diagnoses are made based on clinical signs and features, a microbiological analysis is sometimes necessary. We performed a literature review on the diagnosis of oral candidiasis to identify the techniques most commonly employed in routine clinical practice. A Medline-PubMed search covering the last 10 years was performed. Microbiological techniques were used in cases requiring confirmation of the clinical diagnosis. In such cases, direct microscopy was the method most commonly used for diagnosing candidiasis. Direct microscopy appears as the method of choice for confirming clinical diagnosis and could become a routine chair-side technique.

Candida spp. in oral cancer and oral precancerous lesions.

PubMed

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

2013-07-01

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

Application of predictive modelling techniques in industry: from food design up to risk assessment.

PubMed

Membré, Jeanne-Marie; Lambert, Ronald J W

2008-11-30

In this communication, examples of applications of predictive microbiology in industrial contexts (i.e. Nestlé and Unilever) are presented which cover a range of applications in food safety from formulation and process design to consumer safety risk assessment. A tailor-made, private expert system, developed to support safe product/process design assessment is introduced as an example of how predictive models can be deployed for use by non-experts. Its use in conjunction with other tools and software available in the public domain is discussed. Specific applications of predictive microbiology techniques are presented relating to investigations of either growth or limits to growth with respect to product formulation or process conditions. An example of a probabilistic exposure assessment model for chilled food application is provided and its potential added value as a food safety management tool in an industrial context is weighed against its disadvantages. The role of predictive microbiology in the suite of tools available to food industry and some of its advantages and constraints are discussed.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification.

PubMed

Bizzini, A; Greub, G

2010-11-01

Until recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for the identification of microorganisms remained confined to research laboratories. In the last 2 years, the availability of relatively simple to use MALDI-TOF MS devices, which can be utilized in clinical microbiology laboratories, has changed the laboratory workflows for the identification of pathogens. Recently, the first prospective studies regarding the performance in routine bacterial identification showed that MALDI-TOF MS is a fast, reliable and cost-effective technique that has the potential to replace and/or complement conventional phenotypic identification for most bacterial strains isolated in clinical microbiology laboratories. For routine bacterial isolates, correct identification by MALDI-TOF MS at the species level was obtained in 84.1-93.6% of instances. In one of these studies, a protein extraction step clearly improved the overall valid identification yield, from 70.3% to 93.2%. This review focuses on the current state of use of MALDI-TOF MS for the identification of routine bacterial isolates and on the main difficulties that may lead to erroneous or doubtful identifications. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

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.

Clinical diagnosis of ventilator associated pneumonia revisited: comparative validation using immediate post-mortem lung biopsies

PubMed Central

Fabregas, N.; Ewig, S.; Torres, A.; El-Ebiary, M.; Ramirez, J.; de la Bellacasa, J. P.; Bauer, T.; Cabello, H.

1999-01-01

BACKGROUND—A study was undertaken to assess the diagnostic value of different clinical criteria and the impact of microbiological testing on the accuracy of clinical diagnosis of suspected ventilator associated pneumonia (VAP).
METHODS—Twenty five deceased mechanically ventilated patients were studied prospectively. Immediately after death, multiple bilateral lung biopsy specimens (16 specimens/patient) were obtained for histological examination and quantitative lung cultures. The presence of both histological pneumonia and positive lung cultures was used as a reference test.
RESULTS—The presence of infiltrates on the chest radiograph and two of three clinical criteria (leucocytosis, purulent secretions, fever) had a sensitivity of 69% and a specificity of 75%; the corresponding numbers for the clinical pulmonary infection score (CPIS) were 77% and 42%. Non-invasive as well as invasive sampling techniques had comparable values. The combination of all techniques achieved a sensitivity of 85% and a specificity of 50%, and these values remained virtually unchanged despite the presence of previous treatment with antibiotics. When microbiological results were added to clinical criteria, adequate diagnoses originating from microbiological results which might have corrected false positive and false negative clinical judgements (n = 5) were countered by a similar proportion of inadequate diagnoses (n =6).
CONCLUSIONS—Clinical criteria had reasonable diagnostic values. CPIS was not superior to conventional clinical criteria. Non-invasive and invasive sampling techniques had diagnostic values comparable to clinical criteria. An algorithm guiding antibiotic treatment exclusively by microbiological results does not increase the overall diagnostic accuracy and carries the risk of undertreatment.

 PMID:10491448

Demonstrations of Extraterrestrial Life Detection Techniques in the High School Biology Laboratory

ERIC Educational Resources Information Center

Saltinski, Ronald

1969-01-01

Discusses the experimental procedures and equipment for exobiology projects at the high school level. An interdisciplinary approach involving electronic equipment and micro-biological laboratory techniques is used. Photographs and diagrams of equipment are included. Bibliography. (LC)

Virtual Simulations as Preparation for Lab Exercises: Assessing Learning of Key Laboratory Skills in Microbiology and Improvement of Essential Non-Cognitive Skills.

PubMed

Makransky, Guido; Thisgaard, Malene Warming; Gadegaard, Helen

2016-01-01

To investigate if a virtual laboratory simulation (vLAB) could be used to replace a face to face tutorial (demonstration) to prepare students for a laboratory exercise in microbiology. A total of 189 students who were participating in an undergraduate biology course were randomly selected into a vLAB or demonstration condition. In the vLAB condition students could use a vLAB at home to 'practice' streaking out bacteria on agar plates in a virtual environment. In the demonstration condition students were given a live demonstration from a lab tutor showing them how to streak out bacteria on agar plates. All students were blindly assessed on their ability to perform the streaking technique in the physical lab, and were administered a pre and post-test to determine their knowledge of microbiology, intrinsic motivation to study microbiology, and self-efficacy in the field of microbiology prior to, and after the experiment. The results showed that there were no significant differences between the two groups on their lab scores, and both groups had similar increases in knowledge of microbiology, intrinsic motivation to study microbiology, as well as self-efficacy in the field of microbiology. Our data show that vLABs function just as well as face to face tutorials in preparing students for a physical lab activity in microbiology. The results imply that vLABs could be used instead of face to face tutorials, and a combination of virtual and physical lab exercises could be the future of science education.

Mass spectrometry: a revolution in clinical microbiology?

PubMed

Lavigne, Jean-Philippe; Espinal, Paula; Dunyach-Remy, Catherine; Messad, Nourredine; Pantel, Alix; Sotto, Albert

2013-02-01

Recently, different bacteriological laboratory interventions that decrease reporting time have been developed. These promising new broad-based techniques have merit, based on their ability to identify rapidly many bacteria, organisms difficult to grow or newly emerging strains, as well as their capacity to track disease transmission. The benefit of rapid reporting of identification and/or resistance of bacteria can greatly impact patient outcomes, with an improvement in the use of antibiotics, in the reduction of the emergence of multidrug resistant bacteria and in mortality rates. Different techniques revolve around mass spectrometry (MS) technology: matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), PCR combined with electrospray ionization-mass spectrometry (PCR/ESIMS), iPLEX MassArray system and other new evolutions combining different techniques. This report emphasizes the (r)evolution of these technologies in clinical microbiology.

Board-invited review: Rumen microbiology: leading the way in microbial ecology.

PubMed

Krause, D O; Nagaraja, T G; Wright, A D G; Callaway, T R

2013-01-01

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.

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

DTIC Science & Technology

2007-01-01

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

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.

[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.

[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.

Animal experimentation in Japan: regulatory processes and application for microbiological studies.

PubMed

Takahashi-Omoe, H; Omoe, K

2007-07-01

We have conducted animal experimentation as a highly effective technique in biological studies. Also in microbiological studies, we have used experimentation to prevent and treat many infectious diseases in humans and animals. In Japan, the 'Law for the Humane Treatment and Management of Animals', which covers the consideration of the three R principles, refinement, replacement and reduction for an international humane approach to animal experimentation came into effect in June 2006. Looking towards the straightforward operation of the law in animal experimentation, three government ministries established new basic guidelines for experimentation performed in their jurisdictional research and testing facilities. For future microbiological studies involving animals in Japan, we need to perform animal experiments according to the basic guidelines in association with overseas management systems. In this report, we discussed essential actions for the management of animal experimentation in microbiological studies in Japan.

From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology.

PubMed

Nai, Corrado; Meyer, Vera

2018-06-01

Since the onset of microbiology in the late 19th century, scientists have been growing microorganisms almost exclusively as pure cultures, resulting in a limited and biased view of the microbial world. Only a paradigm shift in cultivation techniques - from axenic to mixed cultures - can allow a full comprehension of the (chemical) communication of microorganisms, with profound consequences for natural product discovery, microbial ecology, symbiosis, and pathogenesis, to name a few areas. Three main technical advances during the last decade are fueling the realization of this revolution in microbiology: microfluidics, next-generation 3D-bioprinting, and single-cell metabolomics. These technological advances can be implemented for large-scale, systematic cocultivation studies involving three or more microorganisms. In this review, we present recent trends in microbiology tools and discuss how these can be employed to decode the chemical language that microorganisms use to communicate. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of river pollution data from low-flow period by means of multivariate techniques: a case study from the oil-shale industry region, northeastern Estonia.

PubMed

Truu, Jaak; Heinaru, Eeva; Talpsep, Ene; Heinaru, Ain

2002-01-01

The oil-shale industry has created serious pollution problems in northeastern Estonia. Untreated, phenol-rich leachate from semi-coke mounds formed as a by-product of oil-shale processing is discharged into the Baltic Sea via channels and rivers. An exploratory analysis of water chemical and microbiological data sets from the low-flow period was carried out using different multivariate analysis techniques. Principal component analysis allowed us to distinguish different locations in the river system. The riverine microbial community response to water chemical parameters was assessed by co-inertia analysis. Water pH, COD and total nitrogen were negatively related to the number of biodegradative bacteria, while oxygen concentration promoted the abundance of these bacteria. The results demonstrate the utility of multivariate statistical techniques as tools for estimating the magnitude and extent of pollution based on river water chemical and microbiological parameters. An evaluation of river chemical and microbiological data suggests that the ambient natural attenuation mechanisms only partly eliminate pollutants from river water, and that a sufficient reduction of more recalcitrant compounds could be achieved through the reduction of wastewater discharge from the oil-shale chemical industry into the rivers.

Microbiological quality of natural waters.

PubMed

Borrego, J J; Figueras, M J

1997-12-01

Several aspects of the microbiological quality of natural waters, especially recreational waters, have been reviewed. The importance of the water as a vehicle and/or a reservoir of human pathogenic microorganisms is also discussed. In addition, the concepts, types and techniques of microbial indicator and index microorganisms are established. The most important differences between faecal streptococci and enterococci have been discussed, defining the concept and species included. In addition, we have revised the main alternative indicators used to measure the water quality.

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.

[Agrobacterium rubi strains from blueberry plants are highly diverse].

PubMed

Abrahamovich, Eliana; López, Ana C; Alippi, Adriana M

2014-01-01

The diversity of a collection of Agrobacterium rubi strains isolated from blueberries from different regions of Argentina was studied by conventional microbiological tests and molecular techniques. Results from biochemical and physiological reactions, as well as from rep-PCR and RFLP analysis of PCR-amplified 23S rDNA showed high phenotypic and genotypic intraspecific variation. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España. All rights reserved.

["What an ideal clinical microbiological laboratory should be"--from the position of medical technologist].

PubMed

Nagasawa, M

2000-01-01

The evolution of the microbiology laboratory is necessary for correspondence to the transfiguration of infection and contribution to clinical applications. Especially, the correspondence of emergency tests such as smear strain and antigen detection, the report added value and the infection surveillance in team medical treatment are indispensable. Also, medical technologists need to be knowledge able about techniques related to infection overall, and participation in infection diagnosis and social responsibility are indispensable.

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

PubMed

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

2015-12-01

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

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

DNAemia detection by multiplex PCR and biomarkers for infection in systemic inflammatory response syndrome patients.

PubMed

Fitting, Catherine; Parlato, Marianna; Adib-Conquy, Minou; Memain, Nathalie; Philippart, François; Misset, Benoît; Monchi, Mehran; Cavaillon, Jean-Marc; Adrie, Christophe

2012-01-01

Fast and reliable assays to precisely define the nature of the infectious agents causing sepsis are eagerly anticipated. New molecular biology techniques are now available to define the presence of bacterial or fungal DNA within the bloodstream of sepsis patients. We have used a new technique (VYOO®) that allows the enrichment of microbial DNA before a multiplex polymerase chain reaction (PCR) for pathogen detection provided by SIRS-Lab (Jena, Germany). We analyzed 72 sepsis patients and 14 non-infectious systemic inflammatory response syndrome (SIRS) patients. Among the sepsis patients, 20 had a positive blood culture and 35 had a positive microbiology in other biological samples. Of these, 51.4% were positive using the VYOO® test. Among the sepsis patients with a negative microbiology and the non-infectious SIRS, 29.4% and 14.2% were positive with the VYOO® test, respectively. The concordance in bacterial identification between microbiology and the VYOO® test was 46.2%. This study demonstrates that these new technologies offer great hopes, but improvements are still needed.

A Simple ELISA Exercise for Undergraduate Biology.

ERIC Educational Resources Information Center

Baker, William P.; Moore, Cathy R.

Understanding of immunological techniques such as the Enzyme Linked Immuno Sorbent Assay (ELISA) is an important part of instructional units in human health, developmental biology, microbiology, and biotechnology. This paper describes a simple ELISA exercise for undergraduate biology that effectively simulates the technique using a paper model.…

[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).

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.

Recombinant organisms for production of industrial products

PubMed Central

Adrio, Jose-Luis

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. PMID:21326937

Comparison of an automated Most Probable Number (MPN) technique to traditional plating methods for estimating populations of total aerobes, coliforms and E. coli associated with freshly processed broiler chickens

USDA-ARS?s Scientific Manuscript database

Traditional microbiological techniques for estimating populations of viable bacteria can be laborious and time consuming. The Most Probable Number (MPN) technique is especially tedious as multiple series of tubes must be inoculated at several different dilutions. Recently, an instrument (TEMPOTM) ...

Comparison of destructive and nondestructive sampling techniques of retail chicken carcasses for enumeration of hygiene indicator microorganisms.

PubMed

Cossi, Marcus Vinícius Coutinho; de Almeida, Michelle Vieira; Dias, Mariane Rezende; de Arruda Pinto, Paulo Sérgiode; Nero, Luís Augusto

2012-01-01

The type of sampling technique used to obtain food samples is fundamental to the success of microbiological analysis. Destructive and nondestructive techniques, such as tissue excision and rinsing, respectively, are widely employed in obtaining samples from chicken carcasses. In this study, four sampling techniques used for chicken carcasses were compared to evaluate their performances in the enumeration of hygiene indicator microorganisms. Sixty fresh chicken carcasses were sampled by rinsing, tissue excision, superficial swabbing, and skin excision. All samples were submitted for enumeration of mesophilic aerobes, Enterobacteriaceae, coliforms, and Escherichia coli. The results were compared to determine the statistical significance of differences and correlation (P < 0.05). Tissue excision provided the highest microbial counts compared with the other procedures, with significant differences obtained only for coliforms and E. coli (P < 0.05). Significant correlations (P < 0.05) were observed for all the sampling techniques evaluated for most of the hygiene indicators. Despite presenting a higher recovery ability, tissue excision did not present significant differences for microorganism enumeration compared with other nondestructive techniques, such as rinsing, indicating its adequacy for microbiological analysis of chicken carcasses.

Testing Water for Bacterial Pollution.

ERIC Educational Resources Information Center

Dillner, Harry

This autoinstructional lesson deals with the study of water pollution control. It is a learning activity directed toward high school students of biology and/or ecology. A general knowledge of microbiology techniques is regarded as a prerequisite for the lesson. Behavioral objectives are given. Emphasis is placed on use of techniques and materials…

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.

Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change

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

Hungate, Bruce; Pett-Ridge, Jennifer; Blazewicz, Steven

In this project, we developed an innovative and ground-breaking technique, quantitative stable isotope probing, a technique that uses density separation of nucleic acids as a quantitative measurement technique. This work is substantial because it advances SIP beyond the qualitative technique that has dominate the field for years. The first methods paper was published in Applied and Environmental Microbiology (Hungate et al. 2015), and this paper describes the mathematical model underlying the quantitative interpretation. A second methods paper (Schwartz et al. 2015) provides a conceptual overview of the method and its application to research problems. A third methods paper was justmore » published (Koch et al. 2018), in which we develop the quantitative model combining sequencing and isotope data to estimate actual rates of microbial growth and death in natural populations. This work has met much enthusiasm in scientific presentations around the world. It has met with equally enthusiastic resistance in the peer-review process, though our record of publication to date argues that people are accepting the merits of the approach. The skepticism and resistance are also potentially signs that this technique is pushing the field forward, albeit with some of the discomfort that accompanies extrapolation. Part of this is a cultural element in the field – the field of microbiology is not accustomed to the assumptions of ecosystem science. Research conducted in this project has pushed the philosophical perspective that major advances can occur when we advocate a sound merger between the traditions of strong inference in microbiology with those of grounded scaling in ecosystem science.« less

Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change

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

Hungate, Bruce; PettRidge, Jennifer; Blazewicz, St

In this project, we developed an innovative and groundbreaking technique, quantitative stable isotope probing, a technique that uses density separation of nucleic acids as a quantitative measurement technique. This work is substantial because it advances SIP beyond the qualitative technique that has dominate the field for years. The first methods paper was published in Applied and Environmental Microbiology (Hungate et al. 2015), and this paper describes the mathematical model underlying the quantitative interpretation. A second methods paper (Schwartz et al. 2015) provides a conceptual overview of the method and its application to research problems. A third methods paper was justmore » published (Koch et al. 2018), in which we develop the quantitative model combining sequencing and isotope data to estimate actual rates of microbial growth and death in natural populations. This work has met much enthusiasm in scientific presentations around the world. It has met with equally enthusiastic resistance in the peerreview process, though our record of publication to date argues that people are accepting the merits of the approach. The skepticism and resistance are also potentially signs that this technique is pushing the field forward, albeit with some of the discomfort that accompanies extrapolation. Part of this is a cultural element in the field – the field of microbiology is not accustomed to the assumptions of ecosystem science. Research conducted in this project has pushed the philosophical perspective that major advances can occur when we advocate a sound merger between the traditions of strong inference in microbiology with those of grounded scaling in ecosystem science.« less

Sterilization techniques for biodegradable scaffolds in tissue engineering applications

PubMed Central

Dai, Zheng; Ronholm, Jennifer; Tian, Yiping; Sethi, Benu; Cao, Xudong

2016-01-01

Biodegradable scaffolds have been extensively studied due to their wide applications in biomaterials and tissue engineering. However, infections associated with in vivo use of these scaffolds by different microbiological contaminants remain to be a significant challenge. This review focuses on different sterilization techniques including heat, chemical, irradiation, and other novel sterilization techniques for various biodegradable scaffolds. Comparisons of these techniques, including their sterilization mechanisms, post-sterilization effects, and sterilization efficiencies, are discussed. PMID:27247758

The use of paleo-imaging and microbiological testing in the analysis of antique cultural material: multislice tomography, and microbial analysis of the Trogir Cathedral cope hood depicting St. Martin and a beggar.

PubMed

Cavka, Mislav; Petaros, Anja; Kavur, Lovro; Skrlin, Jasenka; Mlinaric Missoni, Emilija; Jankovic, Ivor; Brkljacic, Boris

2013-01-01

Paleoradiology is the study of biological and other materials from archeological settings through the use of various medical imaging techniques. Although it is most often used in the scientific study of ancient human remains, it can also be used to study metals, ceramics, paper, and clothes. The aim of this study was to test two paleoimaging techniques (MSCT and mammography) in the analysis of an important Croatian liturgical vestment: the hood of a bishop's cope from St. Lawrence's Treasury in Trogir depicting St. Martin and a beggar. To ensure a safe environment for scientists participating in the analysis, a preliminary microbiological analysis was performed, which contributed to the database of microbiological flora found on Croatian archeological remains and relics studied to date. Due to a great amount of metal filaments, the paleoradiological analysis did not produce satisfactory results. However, a digitally enhanced image clearly showed fine metal embroidery of the hood that was not so easily perceived by naked eye. This article argues in favor of expanding paleoradiological studies on materials other than human remains and also of publishing unsatisfactory results, as important lessons for future development of techniques and methods to analyze ancient remains and seek answers about human historical and cultural heritage.

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.

[Isolation of Pseudomonas stutzeri from an odontogenic inflammatory cyst: Diagnostic relevance].

PubMed

Molgatini, Susana; Rey, Eduardo; Basilaki, Jorge; Mosca, Christian; Galante, Rafael; Gliosca, Laura

Pseudomonas stutzeri is distributed widely in the environment, and occupies different ecological niches. However, it is found in clinically relevant infections as an opportunistic pathogen. Isolation of P. stutzeri from an odontogenic inflammatory cyst is an uncommon microbiological finding that has not been reported to date. In the case presented here, the bacterium was isolated from surgical material obtained from excision of an inflammatory odontogenic cyst located in the tooth 1.2, and presenting with concomitant pulp necrosis. Complementary techniques such as radiographs, CAT scans, and histopathological and microbiological studies were used to establish definitive diagnosis. The obtained results allowed classifying the process as an inflammatory cyst infected by P. stutzeri. Biotyping and characterization of the susceptibility profile of the isolated strain allowed adjusting the antibiotic therapy more specifically. The microbiological studies allowed establishing the etiology of the infectious process, adjusting the treatment plan, and re-establishing tissue integrity. Copyright © 2016 Asociación Argentina de Microbiología. All rights reserved.

Experimental methods for studying microbial survival in extraterrestrial environments.

PubMed

Olsson-Francis, Karen; Cockell, Charles S

2010-01-01

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

[Comparison between rapid detection method of enzyme substrate technique and multiple-tube fermentation technique in water coliform bacteria detection].

PubMed

Sun, Zong-ke; Wu, Rong; Ding, Pei; Xue, Jin-Rong

2006-07-01

To compare between rapid detection method of enzyme substrate technique and multiple-tube fermentation technique in water coliform bacteria detection. Using inoculated and real water samples to compare the equivalence and false positive rate between two methods. Results demonstrate that enzyme substrate technique shows equivalence with multiple-tube fermentation technique (P = 0.059), false positive rate between the two methods has no statistical difference. It is suggested that enzyme substrate technique can be used as a standard method for water microbiological safety evaluation.

Sonication technique improves microbiological diagnosis in patients treated with antibiotics before surgery for prosthetic joint infections.

PubMed

Scorzolini, Laura; Lichtner, Miriam; Iannetta, Marco; Mengoni, Fabio; Russo, Gianluca; Panni, Alfredo Schiavone; Vasso, Michele; Vasto, Michele; Bove, Marco; Villani, Ciro; Mastroianni, Claudio M; Vullo, Vincenzo

2014-07-01

Microbiological diagnosis is crucial for the appropriate management of implant-associated orthopedic infections (IAOIs). Sonication of biomaterials for microbiological diagnosis has not yet been introduced in routine clinical practice. Aim of this study was to describe the advantages and feasibility of this procedure in the clinical setting. We prospectively studied 56 consecutive patients undergoing revision because of IAOI and compared the sensitivity of sonication of explanted orthopedic implants with standard cultures. Patients were divided into two groups: those with foreign body infection (FBI, 15 patients) and those with prosthetic joint infection (PJI, 41 patients). Clinical, radiological and microbiological features were recorded. In the PJI group the sensitivity of sonication in detecting bacterial growth was higher than conventional culture (77% vs 34.1% respectively, p<0.002), while no difference was observed in the FBI group (85.7% vs 86% respectively, p>0.05). Coagulase-negative Staphylococci accounted for 90% of the bacteria detected by sonication. Moreover, we found that in the PJI group the sensitivity of sonication was not affected by the timing of antibiotic interruption before surgery. Sonication remains an important tool to improve microbiological diagnosis in PJIs, especially in patients who received previous antimicrobial treatment.

Comparison of an automated Most Probable Number (MPN) technique to traditional plating methods for estimating populations of total aerobes, coliforms and E. coli associated with freshly processed broiler chickens

USDA-ARS?s Scientific Manuscript database

Recently, an instrument (TEMPOTM) has been developed to automate the Most Probable Number (MPN) technique and reduce the effort required to estimate some bacterial populations. We compared the automated MPN technique to traditional microbiological plating methods or PetrifilmTM for estimating the t...

Recombinant organisms for production of industrial products.

PubMed

Adrio, Jose-Luis; Demain, Arnold L

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. © 2010 Landes Bioscience

Optical and force nanoscopy in microbiology.

PubMed

Xiao, Jie; Dufrêne, Yves F

2016-10-26

Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.

The effect of a cannula milk sampling technique on the microbiological diagnosis of bovine mastitis.

PubMed

Friman, M; Hiitiö, H; Niemi, M; Holopainen, J; Pyörälä, S; Simojoki, H

2017-08-01

Two methods of collecting milk samples from mastitic bovine mammary quarters were compared. Samples were taken in a consistent order in which standard aseptic technique sampling was done first, followed by insertion of a sterile cannula through the teat canal and collection of a second sample. Microbiological results of those two sampling techniques were compared. Milk samples were analysed using multiplex real-time polymerase chain reaction (PCR). The cannula technique produced a reduced number of microbial species or groups of species per sample compared with conventional sampling. Staphylococcus spp. were the most common species identified and were detected more often during conventional sampling than with cannula sampling. Staphylococcus spp. identified in milk samples could also have originated from the teat canal without being present in the milk. The number of samples positive for Trueperella pyogenes or yeasts in the conventional samples was twice as high as in the cannula samples, indicating that the presence of Trueperella pyogenes and yeast species should not necessarily be interpreted as being the causative agents of bovine intra-mammary infections (IMI). Copyright © 2017 Elsevier Ltd. All rights reserved.

Towards objective hand hygiene technique assessment: validation of the ultraviolet-dye-based hand-rubbing quality assessment procedure.

PubMed

Lehotsky, Á; Szilágyi, L; Bánsághi, S; Szerémy, P; Wéber, G; Haidegger, T

2017-09-01

Ultraviolet spectrum markers are widely used for hand hygiene quality assessment, although their microbiological validation has not been established. A microbiology-based assessment of the procedure was conducted. Twenty-five artificial hand models underwent initial full contamination, then disinfection with UV-dyed hand-rub solution, digital imaging under UV-light, microbiological sampling and cultivation, and digital imaging of the cultivated flora were performed. Paired images of each hand model were registered by a software tool, then the UV-marked regions were compared with the pathogen-free sites pixel by pixel. Statistical evaluation revealed that the method indicates correctly disinfected areas with 95.05% sensitivity and 98.01% specificity. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

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.

Microbial ecology of the skin in the era of metagenomics and molecular microbiology.

PubMed

Hannigan, Geoffrey D; Grice, Elizabeth A

2013-12-01

The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.

Microbiology of destructive periodontal disease in adolescent patients with congenital neutropenia. A report of 3 cases.

PubMed

van Winkelhoff, A J; Schouten-van Meeteren, A Y; Baart, J A; Vandenbroucke-Grauls, C M

2000-11-01

Congenital neutropenia is one condition that may predispose for destructive periodontal disease at a young age. In this report, we describe the microbiology of 3 adolescent patients with congenital neutropenia two of whom suffered from severe periodontitis. Microbiological testing of the parents was also performed in 1 case. DNA fingerprinting was used to study transmission of putative periodontal pathogens in this case. From 1 patient with periodontitis, Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis were isolated; a 2nd periodontitis patient was infected with P. gingivalis. A 3rd patient had gingivitis only and no A. actinomycetemcomitans or P. gingivalis were found. Using the amplified fragment length polymorphism DNA fingerprinting technique, bacterial transmission between the father and a patient was shown for A. actinomycetemcomitans but not for P. gingivalis.

Programmed Lab Experiments for Biochemical Investigation of Quorum-Sensing Signal Molecules in Rhizospheric Soil Bacteria.

PubMed

Nievas, Fiorela L; Bogino, Pablo C; Giordano, Walter

2016-05-06

Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences of lab experiments allow these students to investigate biochemical problems whose solution is feasible within the context of their knowledge and experience. We previously designed and reported a programmed lab experiment that familiarizes microbiology students with techniques for detection and characterization of quorum-sensing (QS) and quorum-quenching (QQ) signal molecules. Here, we describe a sequence of experiments designed to expand the understanding and capabilities of biochemistry students using techniques for extraction and identification of QS and QQ signal molecules from peanut rhizospheric soil bacteria, including culturing and manipulation of bacteria under sterile conditions. The program provides students with an opportunity to perform useful assays, draw conclusions from their results, and discuss possible extensions of the study. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:256-262, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Review of Telemicrobiology

PubMed Central

Rhoads, Daniel D.; Mathison, Blaine A.; Bishop, Henry S.; da Silva, Alexandre J.; Pantanowitz, Liron

2016-01-01

Context Microbiology laboratories are continually pursuing means to improve quality, rapidity, and efficiency of specimen analysis in the face of limited resources. One means by which to achieve these improvements is through the remote analysis of digital images. Telemicrobiology enables the remote interpretation of images of microbiology specimens. To date, the practice of clinical telemicrobiology has not been thoroughly reviewed. Objective Identify the various methods that can be employed for telemicrobiology, including emerging technologies that may provide value to the clinical laboratory. Data Sources Peer-reviewed literature, conference proceedings, meeting presentations, and expert opinions pertaining to telemicrobiology have been evaluated. Results A number of modalities have been employed for telemicroscopy including static capture techniques, whole slide imaging, video telemicroscopy, mobile devices, and hybrid systems. Telemicrobiology has been successfully implemented for applications including routine primary diagnois, expert teleconsultation, and proficiency testing. Emerging areas include digital culture plate reading, mobile health applications and computer-augmented analysis of digital images. Conclusions Static image capture techniques to date have been the most widely used modality for telemicrobiology, despite the fact that other newer technologies are available and may produce better quality interpretations. Increased adoption of telemicrobiology offers added value, quality, and efficiency to the clinical microbiology laboratory. PMID:26317376

A review on microbiological decontamination of fresh produce with nonthermal plasma.

PubMed

Pignata, C; D'Angelo, D; Fea, E; Gilli, G

2017-06-01

Food safety is a critical public health issue for consumers and the food industry because microbiological contamination of food causes considerable social and economic burdens on health care. Most foodborne illness comes from animal production, but as of the mid-1990s in the United States and more recently in the European Union, the contribution of fresh produce to foodborne outbreaks has rapidly increased. Recent studies have suggested that sterilization with nonthermal plasma could be a viable alternative to the traditional methods for the decontamination of heat-sensitive materials or food because this technique proves capable of eliminating micro-organisms on surfaces without altering the substrate. In the last 10 years, researchers have used nonthermal plasma in a variety of food inoculated with many bacterial species. All of these experiments were conducted exclusively in a laboratory and, to our knowledge, this technique has not been used in an industrial setting. Thus, the purpose of this review is to understand whether this technology could be used at the industrial level. The latest researches using nonthermal plasma on fresh produce were analysed. These evaluations have focused on the log reduction of micro-organisms and the treatment time. © 2017 The Society for Applied Microbiology.

An exploration of the perceptions, developmental reasoning levels, differences in learning processes, and academic achievement levels of students in introductory college microbiology

NASA Astrophysics Data System (ADS)

Poole, Barbara Ann Matherly

1997-11-01

This study explored the relationship between the grades students earned in introductory college microbiology and American College Testing scores, sex, race, age, GED or high school diploma, full-time or part-time student status, developmental reasoning levels, memory tactics, and expected achievement. The study also explored student perceptions at the beginning and the end of the microbiology courses for science preparation, expected achievement, relevancy of microbiology, and expectations for the course. Archival records for 121 freshman level and 119 sophomore level microbiology students were accessed to obtain final grades, ACT scores, sex, race, age, GED or high school diploma and full-time or part-time status. The same information was obtained for the 113 freshman level and the 85 sophomore level students who participated in the study. The study groups were given the Group Assessment of Logical Thinking to assess their level of formal reasoning ability, the Inventory of Learning Processes-Revised to assess three memory techniques, an initial perception survey, and an exit perception survey. Academic achievement in microbiology could not be predicted using composites of the predictor variables. There were significant relationships between the GALT scores and the predicted grades with both the freshman and the sophomore final grades. The Self-Efficacy Fact Retention scores and the Literal Memorization scores had significant relationships to the final grades of the freshmen but not the sophomores. There was not a significant relationship between the Deep Semantic scores and the final grades in either group. Students indicated that high school science had given them only a medium to low level of preparation for college microbiology. The sophomores felt that previous college science classes had given them a much better preparation for microbiology than did the freshmen students. Both groups expressed the importance of the laboratory experience to the understanding of science and also the relevancy of microbiology both to their chosen professions and to their own personal lives.

Investigation of compounds essential for the origin of life

NASA Technical Reports Server (NTRS)

Dayhoff, M. O.; Hunt, L. T.

1983-01-01

Nucleic acid sequencing as a technique to determine the chemical and biological evolution of certain prokaryotic metabolic pathways is discussed. Protein in data and a microbiological organization of the prokaryotes is included.

Molecular characterization of Streptococcus agalactiae strains isolated from fishes in Malaysia.

PubMed

Amal, M N A; Zamri-Saad, M; Siti-Zahrah, A; Zulkafli, A R; Nur-Nazifah, M

2013-07-01

The aim of this study was to characterize Streptococcus agalactiae strains that were isolated from fishes in Malaysia using random amplified polymorphic DNA (RAPD) and repetitive extragenic palindromic PCR (REP-PCR) techniques. A total of 181 strains of Strep. agalactiae isolated from red hybrid tilapia (Oreochromis sp.) and golden pompano (Trachinotus blochii) were characterized using RAPD and REP-PCR techniques. Both the fingerprinting techniques generated reproducible band patterns, differing in the number and molecular mass amplicons. The RAPD technique displayed greater discriminatory power by its production of more complex binding pattern and divided all the strains into 13 groups, compared to 9 by REP-PCR technique. Both techniques showed the availability to differentiate the genetic profiles of the strains according to their geographical location of origin. Three strains of Strep. agalactiae that were recovered from golden pompano showed a genetic dissimilarity from the strains isolated from red hybrid tilapia, while the strain of ATCC 27956 that recovered from bovine displayed a unique profile for both methods. Both techniques possess excellent discriminative capabilities and can be used as a rapid means of comparing Strep. agalactiae strains for future epidemiological investigation. Framework as the guideline in traceability of this disease and in the search for potential local vaccine candidates for streptococcosis in this country. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

Strengths and limitations of molecular subtyping in a community outbreak of Legionnaires' disease.

PubMed

Kool, J L; Buchholz, U; Peterson, C; Brown, E W; Benson, R F; Pruckler, J M; Fields, B S; Sturgeon, J; Lehnkering, E; Cordova, R; Mascola, L M; Butler, J C

2000-12-01

An epidemiological and microbiological investigation of a cluster of eight cases of Legionnaires' disease in Los Angeles County in November 1997 yielded conflicting results. The epidemiological part of the investigation implicated one of several mobile cooling towers used by a film studio in the centre of the outbreak area. However, water sampled from these cooling towers contained L. pneumophila serogroup 1 of another subtype than the strain that was recovered from case-patients in the outbreak. Samples from two cooling towers located downwind from all of the case-patients contained a Legionella strain that was indistinguishable from the outbreak strain by four subtyping techniques (AP-PCR, PFGE, MAb, and MLEE). It is unlikely that these cooling towers were the source of infection for all the case-patients, and they were not associated with risk of disease in the case-control study. The outbreak strain also was not distinguishable, by three subtyping techniques (AP-PCR, PFGE, and MAb), from a L. pneumophila strain that had caused an outbreak in Providence, RI, in 1993. Laboratory cross-contamination was unlikely because the initial subtyping was done in different laboratories. In this investigation, microbiology was helpful for distinguishing the outbreak cluster from unrelated cases of Legionnaires' disease occurring elsewhere. However, multiple subtyping techniques failed to distinguish environmental sources that were probably not associated with the outbreak. Persons investigating Legionnaires' disease outbreaks should be aware that microbiological subtyping does not always identify a source with absolute certainty.

Designing Cancer-Killing Artificial Viruses to Improve Student Understanding of Microbiology

PubMed Central

Kuniyuki, Andy; Sharp, Gwen

2011-01-01

Our objective was to assess the effectiveness of a “learning by designing” group project used in a lower-division Microbiology course. Students used knowledge gained from the course to design an artificial virus that would kill cancer cells. The assignment required groups to integrate the individual course topics into a unified, complex understanding of the field of microbiology. Throughout the course, students and the instructor collaborated in creating a rubric to evaluate the groups’ final presentations. This paper reports the results of an assessment of the project by comparing the instructor’s and the students’ scores for the presentations. Students’ and the instructor’s scores were correlated; the Pearson coefficient of 0.52 was statistically significant. The results indicate that students gained sufficient knowledge to accurately evaluate proposed designs. Additionally, the overall course grade distribution improved compared to the semester before the project was introduced. Finally, in order to engage students in thinking about their own learning process, they completed a reflection assignment that required them to discuss the changes in their understanding of microbiology over the course of the semester. Our assessment indicates that a design project can serve as an effective and useful learning technique in undergraduate Microbiology courses, though modifications are suggested. PMID:23653757

Microcoupon Assay Of Adhesion And Growth Of Bacterial Films

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Koenig, David W.

1994-01-01

Microbiological assay technique facilitates determination of some characteristics of sessile bacteria like those that attach to and coat interior walls of water-purification systems. Biofilms cause sickness and interfere with purification process. Technique enables direct measurement of rate of attachment of bacterial cells, their metabolism, and effects of chemicals on them. Used to quantify effects of both bactericides and growth-stimulating agents and in place of older standard plate-count and tube-dilution techniques.

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

PubMed

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

2011-07-01

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

[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.

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

PubMed

Wang, Jack T H; Daly, Joshua N; Willner, Dana L; Patil, Jayee; Hall, Roy A; Schembri, Mark A; Tyson, Gene W; Hugenholtz, Philip

2015-05-01

Clinical microbiology testing is crucial for the diagnosis and treatment of community and hospital-acquired infections. Laboratory scientists need to utilize technical and problem-solving skills to select from a wide array of microbial identification techniques. The inquiry-driven laboratory training required to prepare microbiology graduates for this professional environment can be difficult to replicate within undergraduate curricula, especially in courses that accommodate large student cohorts. We aimed to improve undergraduate scientific training by engaging hundreds of introductory microbiology students in an Authentic Large-Scale Undergraduate Research Experience (ALURE). The ALURE aimed to characterize the microorganisms that reside in the healthy human oral cavity-the oral microbiome-by analyzing hundreds of samples obtained from student volunteers within the course. Students were able to choose from selective and differential culture media, Gram-staining, microscopy, as well as polymerase chain reaction (PCR) and 16S rRNA gene sequencing techniques, in order to collect, analyze, and interpret novel data to determine the collective oral microbiome of the student cohort. Pre- and postsurvey analysis of student learning gains across two iterations of the course (2012-2013) revealed significantly higher student confidence in laboratory skills following the completion of the ALURE (p < 0.05 using the Mann-Whitney U-test). Learning objectives on effective scientific communication were also met through effective student performance in laboratory reports describing the research outcomes of the project. The integration of undergraduate research in clinical microbiology has the capacity to deliver authentic research experiences and improve scientific training for large cohorts of undergraduate students.

[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.

Planetary quarantine. Space research and technology

NASA Technical Reports Server (NTRS)

1973-01-01

Planetary quarantine strategies for advanced spacecraft consider effects of satellite encounter, Jupiter atmosphere entry, space radiation, and cleaning and decontamination techniques on microbiological growth probability. Analytical restructuring is developed for microbial burden prediction and planetary contamination.

Laboratory Techniques for the Blind

ERIC Educational Resources Information Center

Tombaugh, Dorothy

1972-01-01

Describes modifications of laboratory procedures for the BSCS Green Version biology, including dissection, microbiology, animal behavior, physiology, biochemistry, and genetics that make the methods suitable for direct experimentation by blind students. Discusses models as substitutes for microscopy. (AL)

Viking planetary quarantine procedures and implementation

NASA Technical Reports Server (NTRS)

Howell, R.

1974-01-01

Some of the techniques and methodology that were used on Viking to implement planetary quarantine requirements are reported. Special attention was given to techniques and approaches used to implement sterilization of the Viking probe. Quarantine procedures for unmanned planetary missions and procedures for microbiological contamination of space hardware are included. A probability of contamination of the biological instruments onboard by terrestrial organisms was examined.

Comparison of the biopsy and cytobrush techniques for diagnosis of subclinical endometritis in mares

PubMed Central

2014-01-01

Background Endometritis is a major cause of infertility in the mare. Therefore, the diagnosis of this disease is very important in veterinary practice. The objective of this study was to compare bacteriological and cytological results obtained from the mare uterus using biopsy (EB) and cytobrush (CB) techniques and relating these findings to the presence of polymorphonuclear cells (PMNs) in endometrial tissue as the gold standard for detection of endometritis. In particular, we tested the hypothesis that endometrial cytology and microbiology data obtained from material collected using the EB and CB techniques are similar, so that the CB technique could preferentially be used to detect subclinical endometritis in clinical practice. Methods A total of 69 mares suspected of subclinical endometritis because of previous reproductive history and 15 maiden mares were enrolled in this study. Material collected from both EB and CB was smeared on sterile glass slides for cytological examinations and on culture media for microbiological examinations. Bacteriological cultures and cytological samples were classified as negative (no growth or mixed cultures of more than three microorganisms; <2% PMNs) or positive (pure growth of microorganisms; >2% PMNs) for endometritis. Results Positive growth was observed in 43% of CB samples and in 54% of EB samples (difference not significant). The growth of β-hemolytic streptococci was always connected with positive cytology. This relationship was not observed for growth of E. coli or for non-pathogenic flora. The sensitivity of bacterial growth and cytology from EB was 0.63 and 0.73 respectively. The sensitivities of bacterial growth and cytology from CB were 0.50 and 0.71 respectively. Conclusion Microbiological and cytological results obtained from CB are similar to those obtained from EB and based on these findings the CB technique may be recommended for collection of materials from the mare’s uterus in clinical practice. PMID:24708825

Cystic Fibrosis: Microbiology and Host Response.

PubMed

Zemanick, Edith T; Hoffman, Lucas R

2016-08-01

The earliest descriptions of lung disease in people with cystic fibrosis (CF) showed the involvement of 3 interacting pathophysiologic elements in CF airways: mucus obstruction, inflammation, and infection. Over the past 7 decades, our understanding of CF respiratory microbiology and inflammation has evolved with the introduction of new treatments, increased longevity, and increasingly sophisticated laboratory techniques. This article reviews the current understanding of infection and inflammation and their roles in CF lung disease. It also discusses how this constantly evolving information is used to inform current therapeutic strategies, measures and predictors of disease severity, and research priorities. Copyright © 2016 Elsevier Inc. All rights reserved.

[A microbiological investigation of the effectiveness of Micro Megas E-spray].

PubMed

Kardel, K; Hegna, I K; Kardel, M

1976-06-01

The disinfecting effect of Micro Megas E-spray was tested using a microbiological technique which also included a practical test. Contra-angels and straight handpieces which were sprayed after being used for treatment on patients, and then dried and incubated in a liquid medium, showed a marked growth of microorganisms. The spray had a weak and barely significant growth inhibiting effect on contaminated, simulated instrument surfaces. using Pseudomonas aeruginosa, Escherichia coli and Staphylococcus aureus as test bacteria. It is concluded that the spray is not suitable for distinfection of contra-angels and straight handpieces.

Literature Reference for Cryptosporidium spp. (Applied and Environmental Microbiology. 1999. 65(9): 3936–3941)

EPA Pesticide Factsheets

Procedures are described for analysis of animal samples using tissue culture techniques that may be adapted for assessment of solid, particulate, liquid and water samples contaminated with Cryptosporidium parvum.

[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.

Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution.

PubMed

Ishii, Satoshi; Sadowsky, Michael J

2009-04-01

A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.

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.

Characterization of Outer Space Radiation Induced Changes in Extremophiles Utilizing Deep Space Gateway Opportunities

NASA Astrophysics Data System (ADS)

Venkateswaran, K.; Wang, C.; Smith, D.; Mason, C.; Landry, K.; Rettberg, P.

2018-02-01

Extremophilic microbial survival, adaptation, biological functions, and molecular mechanisms associated with outer space radiation can be tested by exposing them onto Deep Space Gateway hardware (inside/outside) using microbiology and molecular biology techniques.

Development and test of flexible film coupon strips for use as a sampling technique

NASA Technical Reports Server (NTRS)

Aldridge, C.

1969-01-01

Film consisting of a gelatin base serves as a flexible, water soluble microbiological assay coupon for clean room use. It is nontoxic to microorganisms and capable of remaining unchanged during periods of storage.

[Microbiological investigation of endoscopes at Brest Hospital over a period from 2007 to 2009].

PubMed

Saliou, P; Garlantézec, R; Baron, R; Quiot, J-J; Cholet, F; Le Floch, M-F; Lejeune, B

2011-04-01

The aim of this study is to evaluate the quality of disinfection of endoscopes at Brest hospital over a period from 2007 to 2009. Retrospective study of microbiological investigations of endoscopes done at Brest hospital from 2007 to 2009. The interpretation of the microbiological investigations is based on the recommendations of the Comité technique national des infections nosocomiales et infections liées aux soins (CTINILS) of 2007. Most of the controls realized over the period deal with gastroenterological endoscopes (63.4 %) and bronchial endoscopes (21.8 %). Most of the controls (66.8 %) are conformed to the target level. Only 26.7 % of the controls get the level of action. Globally, the rate of level of action significantly increases (p=0.004) from 2007 (21.2 %) to 2009 (35.6 %). This increase is relatively important in gastroenterology endoscopy (46.8 % in 2009 versus 24.1 % in 2007) whereas the rate decreases in bronchial endoscopy (14.8 % in 2009 versus 25.9 % in 2007). In gastroenterological endoscopy, rates vary with the type of endoscopes and the context of controls, but there is no significant difference between manual disinfection and automated disinfection. The most frequent germ found in gastroenterological and bronchial endoscopies is Pseudomonas aeruginosa. Our results show that it is very difficult to insure a perfect disinfection of endoscopes. Difficulties met are certainly related with the complexity of the endoscopes and of the techniques of disinfection. Infections of patients are very infrequent in endoscopy, which takes the question of the pertinence of the threshold used for microbiological investigations. Copyright © 2010. Published by Elsevier SAS.

Using qPCR for Water Microbial Risk Assessments

EPA Science Inventory

Microbial risk assessment (MRA) has traditionally utilized microbiological data that was obtained by culture-based techniques that are expensive and time consuming. With the advent of PCR methods there is a realistic opportunity to conduct MRA studies economically, in less time,...

STANDARDIZATION AND VALIDATION OF MICROBIOLOGICAL METHODS FOR EXAMINATION OF BIOSOLIDS

EPA Science Inventory

The objective of this presentation is to discuss pathogens of concern in biosolids, the analytical techniques used to evaluate microorganisms in biosolids, and to discuss standardization and validation of analytical protocols for microbes within a complex matrix. Implications of ...

21 CFR 866.5090 - Antimitochondrial antibody immunological test system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... immunochemical techniques the antimitochondrial antibodies in human serum. The measurements aid in the diagnosis of diseases that produce a spectrum of autoantibodies (antibodies produced against the body's own... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test...

21 CFR 866.5090 - Antimitochondrial antibody immunological test system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... immunochemical techniques the antimitochondrial antibodies in human serum. The measurements aid in the diagnosis of diseases that produce a spectrum of autoantibodies (antibodies produced against the body's own... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test...

21 CFR 866.5090 - Antimitochondrial antibody immunological test system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... immunochemical techniques the antimitochondrial antibodies in human serum. The measurements aid in the diagnosis of diseases that produce a spectrum of autoantibodies (antibodies produced against the body's own... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test...

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,...

Characterization of the corrosion resistance of biologically active solutions: The effects of anodizing and welding

NASA Technical Reports Server (NTRS)

Walsh, Daniel W.

1991-01-01

An understanding of fabrication processes, metallurgy, electrochemistry, and microbiology is crucial to the resolution of microbiologically influenced corrosion (MIC) problems. The object of this effort was to use AC impedance spectroscopy to characterize the corrosion resistance of Type II anodized aluminum alloy 2219-T87 in sterile and biologically active media and to examine the corrosion resistance of 316L, alloy 2219-T87, and titanium alloy 6-4 in the welded and unwelded conditions. The latter materials were immersed in sterile and biologically active media and corrosion currents were measured using the polarization resistance (DC) technique.

CYSTIC FIBROSIS: MICROBIOLOGY AND HOST RESPONSE

PubMed Central

Zemanick, Edith T.

2016-01-01

THE EARLIEST DESCRIPTIONS OF LUNG DISEASE IN PEOPLE WITH CYSTIC FIBROSIS (CF) DEMONSTRATED THE INVOLVEMENT OF THREE INTERACTING PATHOPHYSIOLOGICAL ELEMENTS IN CF AIRWAYS: MUCUS OBSTRUCTION, INFLAMMATION, AND INFECTION. OVER THE PAST 7 DECADES, OUR UNDERSTANDING OF CF RESPIRATORY MICROBIOLOGY AND INFLAMMATION HAS EVOLVED WITH THE INTRODUCTION OF NEW TREATMENTS, WITH INCREASED LONGEVITY, AND WITH INCREASINGLY SOPHISTICATED LABORATORY TECHNIQUES. IN THIS CHAPTER, WE WILL REVIEW THE CURRENT STATE OF UNDERSTANDING OF THE ROLES OF INFECTION AND INFLAMMATION AND THEIR ROLES IN DRIVING LUNG DISEASE. WE WILL ALSO DISCUSS HOW THIS CONSTANTLY EVOLVING INFORMATION IS USED TO INFORM CURRENT THERAPEUTIC STRATEGIES, MEASURES AND PREDICTORS OF DISEASE SEVERITY, AND RESEARCH PRIORITIES. PMID:27469179

Update in Infectious Diseases 2017.

PubMed

Candel, F J; Peñuelas, M; Lejárraga, C; Emilov, T; Rico, C; Díaz, I; Lázaro, C; Viñuela-Prieto, J M; Matesanz, M

2017-09-01

Antimicrobial resistance in complex models of continuous infection is a current issue. The update 2017 course addresses about microbiological, epidemiological and clinical aspects useful for a current approach to infectious disease. During the last year, nosocomial pneumonia approach guides, recommendations for management of yeast and filamentous fungal infections, review papers on the empirical approach to peritonitis and extensive guidelines on stewardship have been published. HIV infection is being treated before and more intensively. The implementation of molecular biology, spectrometry and inmunology to traditional techniques of staining and culture achieve a better and faster microbiological diagnosis. Finally, the infection is increasingly integrated, assessing non-antibiotic aspects in the treatment.

Molecular diagnostics in medical microbiology: yesterday, today and tomorrow.

PubMed

van Belkum, Alex

2003-10-01

Clinical microbiology is clearly on the move, and various new diagnostic technologies have been introduced into laboratory practice over the past few decades. However, Henri D Isenberg recently stated that molecular biology techniques promised to revolutionise the diagnosis of infectious disease, but that, to date, this promise is still in its infancy. Molecular diagnostics have now surpassed these early stages and have definitely reached puberty. Currently, a second generation of automated molecular approaches is already within the microbiologists' reach. Quantitative amplification tests in combination with genomics, transcriptomics, proteomics and related methodologies will pave the way to further enhancement of innovative microbial detection and identification.

Definition of a near real time microbiological monitor for space vehicles

NASA Technical Reports Server (NTRS)

Kilgore, Melvin V., Jr.; Zahorchak, Robert J.; Arendale, William F.

1989-01-01

Efforts to identify the ideal candidate to serve as the biological monitor on the space station Freedom are discussed. The literature review, the evaluation scheme, descriptions of candidate monitors, experimental studies, test beds, and culture techniques are discussed. Particular attention is given to descriptions of five candidate monitors or monitoring techniques: laser light scattering, primary fluorescence, secondary fluorescence, the volatile product detector, and the surface acoustic wave detector.

Transfer of plasmid DNA to clinical coagulase-negative staphylococcal pathogens by using a unique bacteriophage.

PubMed

Winstel, Volker; Kühner, Petra; Krismer, Bernhard; Peschel, Andreas; Rohde, Holger

2015-04-01

Genetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a unique Staphylococcus aureus strain via a specific S. aureus bacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinical Staphylococcus epidermidis isolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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 materials were developed and placed on the BSCS Web site (http://www.bscs.org).« 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

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.

What's growing on General Practitioner's stethoscope?

PubMed

Carducci, A; Cargnelutti, M; Tassinari, F; Bizzarro, A; Cordio, G; Carletti, S; Maccarini, L; Pelissero, G

2016-01-01

Non-critical medical devices, as stethoscopes, have long been considered as vectors in microorganisms' transmission. Cleaning standards for non-critical medical equipment are often unclear. This study was designed to assess the attitude of General Practitioners (GPs) towards cleaning their stethoscope and the degree of microbiological contamination of doctor's instrument in outpatient setting. Observational, crossover study. A structured questionnaire was administered to GPs to test their knowledge about medical instrument's cleanliness recommendations and the surface of the diaphragm of their stethoscopes was analyzed for bacteriological isolates using mass spectrometry technique. Most of GPs declared they don't know cleaning recommendations for non-critical medical devices and a relevant bacterial growth was identified on the majority of the stethoscopes' membranes. Almost all microbiological isolates resulted typically found in cutaneous flora. We can't state that the GP's stethoscopes feature a risk of transmission for microbiological pathogens; anyway, because of the level of contamination we observed, cleaning recommendations to disinfect instruments on a regular basis should be better indicated.

Polymerase Chain Reaction/Rapid Methods Are Gaining a Foothold in Developing Countries.

PubMed

Ragheb, Suzan Mohammed; Jimenez, Luis

Detection of microbial contamination in pharmaceutical raw materials and finished products is a critical factor to guarantee their safety, stability, and potency. Rapid microbiological methods-such as polymerase chain reaction-have been widely applied to clinical and food quality control analysis. However, polymerase chain reaction applications to pharmaceutical quality control have been rather slow and sporadic. Successful implementation of these methods in pharmaceutical companies in developing countries requires important considerations to provide sensitive and robust assays that will comply with good manufacturing practices. In recent years several publications have encouraged the application of molecular techniques in the microbiological assessment of pharmaceuticals. One of these techniques is polymerase chain reaction (PCR). The successful application of PCR in the pharmaceutical industry in developing countries is governed by considerable factors and requirements. These factors include the setting up of a PCR laboratory and the choice of appropriate equipment and reagents. In addition, the presence of well-trained analysts and establishment of quality control and quality assurance programs are important requirements. The pharmaceutical firms should take into account these factors to allow better chances for regulatory acceptance and wide application of this technique. © PDA, Inc. 2014.

21 CFR 866.5200 - Carbonic anhydrase B and C immunological test system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... immunochemical techniques specific carbonic anhydrase protein molecules in serum and other body fluids. Measurements of carbonic anhydrase B and C aid in the diagnosis of abnormal hemoglobin metabolism. (b...

21 CFR 866.5200 - Carbonic anhydrase B and C immunological test system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... immunochemical techniques specific carbonic anhydrase protein molecules in serum and other body fluids. Measurements of carbonic anhydrase B and C aid in the diagnosis of abnormal hemoglobin metabolism. (b...

21 CFR 866.5890 - Inter-alpha trypsin inhibitor immunological test system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... measure by immunochemical techniques the inter-alpha trypsin inhibitor (a protein) in serum and other body fluids. Measurement of inter-alpha trypsin inhibitor may aid in the diagnosis of acute bacterial...

21 CFR 866.5200 - Carbonic anhydrase B and C immunological test system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... immunochemical techniques specific carbonic anhydrase protein molecules in serum and other body fluids. Measurements of carbonic anhydrase B and C aid in the diagnosis of abnormal hemoglobin metabolism. (b...

21 CFR 866.5890 - Inter-alpha trypsin inhibitor immunological test system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... measure by immunochemical techniques the inter-alpha trypsin inhibitor (a protein) in serum and other body fluids. Measurement of inter-alpha trypsin inhibitor may aid in the diagnosis of acute bacterial...

21 CFR 866.5890 - Inter-alpha trypsin inhibitor immunological test system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... measure by immunochemical techniques the inter-alpha trypsin inhibitor (a protein) in serum and other body fluids. Measurement of inter-alpha trypsin inhibitor may aid in the diagnosis of acute bacterial...

21 CFR 866.5890 - Inter-alpha trypsin inhibitor immunological test system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... measure by immunochemical techniques the inter-alpha trypsin inhibitor (a protein) in serum and other body fluids. Measurement of inter-alpha trypsin inhibitor may aid in the diagnosis of acute bacterial...

21 CFR 866.5200 - Carbonic anhydrase B and C immunological test system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test... immunochemical techniques specific carbonic anhydrase protein molecules in serum and other body fluids. Measurements of carbonic anhydrase B and C aid in the diagnosis of abnormal hemoglobin metabolism. (b...

Medical Laboratory Technician--Microbiology (AFSC 90470).

ERIC Educational Resources Information Center

Thompson, Joselyn H.

This four-volume student text is designed for use by Air Force personnel enrolled in a self-study extension course for medical laboratory technicians. Covered in the individual volumes are laboratory procedures in clinical bacteriology (the history of bacteriology; aseptic techniques and sterilization procedures; bacterial morphology and…

Investigations Into Life Science.

ERIC Educational Resources Information Center

Mentzer, Dean Samuel

This laboratory manual, containing 44 exercises, is intended to be used as part of an audio-tutorial approach to laboratory work in a life-science course for student nurses. Exercises include basic techniques of miscroscopy, microbiology, electrophysiology, routine biochemical analyses of blood and urine, and microscopic examination of prepared…

Superresolution microscopy for microbiology

PubMed Central

Coltharp, Carla; Xiao, Jie

2014-01-01

Summary This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of super-resolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission-depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate super-resolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments. PMID:22947061

Development of imaging techniques to study the pathogenesis of biosafety level 2/3 infectious agents.

PubMed

Rella, Courtney E; Ruel, Nancy; Eugenin, Eliseo A

2014-12-01

Despite significant advances in microbiology and molecular biology over the last decades, several infectious diseases remain global concerns, resulting in the death of millions of people worldwide each year. According to the Center for Disease Control (CDC) in 2012, there were 34 million people infected with HIV, 8.7 million new cases of tuberculosis, 500 million cases of hepatitis, and 50-100 million people infected with dengue. Several of these pathogens, despite high incidence, do not have reliable clinical detection methods. New or improved protocols have been generated to enhance detection and quantitation of several pathogens using high-end microscopy (light, confocal, and STORM microscopy) and imaging software. In the current manuscript, we discuss these approaches and the theories behind these methodologies. Thus, advances in imaging techniques will open new possibilities to discover therapeutic interventions to reduce or eliminate the devastating consequences of infectious diseases. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease.

PubMed

Hoggard, Michael; Wagner Mackenzie, Brett; Jain, Ravi; Taylor, Michael W; Biswas, Kristi; Douglas, Richard G

2017-01-01

Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered. Copyright © 2016 American Society for Microbiology.

Promoting science for all by way of student interest in a transformative undergraduate microbiology laboratory for nonmajors.

PubMed

Marbach-Ad, Gili; McGinnis, J Randy; Dai, Amy H; Pease, Rebecca; Schalk, Kelly A; Benson, Spencer

2009-01-01

In this study, we investigated a pedagogical innovation in an undergraduate microbiology course, Microbes and Society, for non-microbiology majors and education majors. The aim was to improve students' understanding by connecting their science experience to their areas of interest. Based on this idea of teaching, we redesigned the laboratory portion of a microbiology course. We had students in the laboratory component choose their areas of interest and use the areas as a framework for understanding science and how it influences and shapes the world around them. This course was part of a longitudinal project (Project Nexus) which prepares, supports, and sustains upper elementary and middle-level specialist science teachers. We used a battery of data collection instruments. We analyzed all data in several dimensions including using active-learning techniques, forming linkages between science and teaching, and connecting science and society. Our hypothesis was that we could promote science for all by connecting the diverse students' areas of interest in science to the laboratory's curriculum. We assessed the success of achieving our goal by using researchers' observations, the instructors' perspectives, and students' feedback. Our findings suggested that this course was appreciated by the students, especially education majors, who recognized the innovations as engaging and worthwhile.

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

PubMed

Lech, Tomasz

2016-05-01

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

Promoting Science for All by Way of Student Interest in a Transformative Undergraduate Microbiology Laboratory for Nonmajors†

PubMed Central

Marbach-Ad, Gili; McGinnis, J. Randy; Dai, Amy H.; Pease, Rebecca; Schalk, Kelly A.; Benson, Spencer

2009-01-01

In this study, we investigated a pedagogical innovation in an undergraduate microbiology course, Microbes and Society, for non-microbiology majors and education majors. The aim was to improve students’ understanding by connecting their science experience to their areas of interest. Based on this idea of teaching, we redesigned the laboratory portion of a microbiology course. We had students in the laboratory component choose their areas of interest and use the areas as a framework for understanding science and how it influences and shapes the world around them. This course was part of a longitudinal project (Project Nexus) which prepares, supports, and sustains upper elementary and middle-level specialist science teachers. We used a battery of data collection instruments. We analyzed all data in several dimensions including using active-learning techniques, forming linkages between science and teaching, and connecting science and society. Our hypothesis was that we could promote science for all by connecting the diverse students’ areas of interest in science to the laboratory’s curriculum. We assessed the success of achieving our goal by using researchers’ observations, the instructors’ perspectives, and students’ feedback. Our findings suggested that this course was appreciated by the students, especially education majors, who recognized the innovations as engaging and worthwhile. PMID:23653691

Characterisation and identification of bacteria using SERS.

PubMed

Jarvis, Roger M; Goodacre, Royston

2008-05-01

Within microbiology Raman spectroscopy is considered as a very important whole-organism fingerprinting technique, which is used to characterise, discriminate and identify microorganisms and assess how they respond to abiotic or biotic stress. Enhancing the sensitivity of Raman spectroscopy is very beneficial for the rapid analysis of bacteria (and indeed biological systems in general), where the ultimate goal is to achieve this without the need for lengthy cell culture. Bypassing this step would provide significant benefits in many areas such as medical, environmental and industrial microbiology, microbial systems biology, biological warfare countermeasures and bioprocess monitoring. In this tutorial review we will report on the advances made in bacterial studies, a relatively new and exciting application area for SERS.

Spoilage of chicken skin at 2 degrees C: electron microscopic study.

PubMed Central

Thomas, C J; McMeekin, T A

1981-01-01

Microscopic techniques were used in conjunction with normal microbiological procedures to examine the development of the spoilage microflora on the skin of chicken carcasses held at 2 degrees C. Pigmented and nonpigmented psychrotrophic pseudomonads were the major spoilage bacteria isolated at all stages of storage examined. The spoilage microflora grow within a liquid film covering the skin surface, as well as in feather follicle shafts. Penetration and disruption of skin tissue were not observed even after onset of organoleptic spoilage. Bacteria were not attached to the skin by extracellular bridging substances. These data suggest a nonspecific histological-microbiological relationship between he spoilage association and the skin substrate. Images PMID:7195190

Some Antifungal Properties of Sorbic Acid Extracted from Berries of Rowan (Sorbus Aucuparia).

ERIC Educational Resources Information Center

Brunner, Ulrich

1985-01-01

The food preservative sorbic acid can be extracted from Eurasian mountain ash berries (commercially available) and used to show antifungal properties in microbiological investigations. Techniques for extraction, purification, ultraviolet analysis, and experiments displaying antifungal activity are described. A systematic search for similar…

Soil and Water – What is Detectable through Microbiological Sample Preparation Techniques

EPA Science Inventory

The concerns of a potential terrorist’s use of biological agents in soil and ground water are articulated by comparisons to major illnesses in this Country involving contaminated drinking water sources. Objectives are focused on the importance of sample preparation in the rapid, ...

A Simple Method for Encouraging Active Participation in Small-Group Discussion Sessions

ERIC Educational Resources Information Center

Lee, Adrian

1977-01-01

A format for a small-group teaching session is described that could be modified for any subject in a medical curriculum. The technique discussed uses subgroups and a simple recording chart that have been successful in teaching microbiology to medical students. (LBH)

The value of molecular techniques to diagnose Ureaplasma urealyticum and Nocardia farcinica pleuropneumonia in a patient with diffuse large B-cell lymphoma.

PubMed

Canouï, Etienne; Blanc, Kim; Loubinoux, Julien; Valade, Sandrine; Hamard, Cécile; Lefebvre, Aurélie; Amorim, Sandy; Bébéar, Cécile; Rodriguez-Nava, Veronica; Lebeaux, David; Launay, Odile; Alifano, Marco; Rabbat, Antoine; Kernéis, Solen

2017-11-01

An unusual case of pleural empyema related to Nocardia farcinica and Ureaplasma urealyticum, occurring after autologous haematopoietic stem cell transplantation in a 30-year-old patient with lymphoma, is reported. This case illustrates the role of repeated and comprehensive microbiological investigations and the contribution of molecular techniques in reaching the aetiological diagnosis. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Summer Workshop in Metagenomics: One Week Plus Eight Students Equals Gigabases of Cloned DNA †

PubMed Central

Rios-Velazquez, Carlos; Williamson, Lynn L.; Cloud-Hansen, Karen A.; Allen, Heather K.; McMahon, Mathew D.; Sabree, Zakee L.; Donato, Justin J.; Handelsman, Jo

2011-01-01

We designed a week-long laboratory workshop in metagenomics for a cohort of undergraduate student researchers. During this course, students learned and utilized molecular biology and microbiology techniques to construct a metagenomic library from Puerto Rican soil. Pre-and postworkshop assessments indicated student learning gains in technical knowledge, skills, and confidence in a research environment. Postworkshop construction of additional libraries demonstrated retention of research techniques by the students. PMID:23653755

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.

Laboratory Diagnosis and Characterization of Fungal Disease in Patients with Cystic Fibrosis (CF): A Survey of Current UK Practice in a Cohort of Clinical Microbiology Laboratories.

PubMed

Boyle, Maeve; Moore, John E; Whitehouse, Joanna L; Bilton, Diana; Downey, Damian G

2018-03-02

There is much uncertainty as to how fungal disease is diagnosed and characterized in patients with cystic fibrosis (CF). A 19-question anonymous electronic questionnaire was developed and distributed to ascertain current practice in clinical microbiology laboratories providing a fungal laboratory service to CF centres in the UK. Analyses of responses identified the following: (1) current UK laboratory practice, in general, follows the current guidelines, but the scope and diversity of what is currently being delivered by laboratories far exceeds what is detailed in the guidelines; (2) there is a lack of standardization of fungal tests amongst laboratories, outside of the current guidelines; (3) both the UK CF Trust Laboratory Standards for Processing Microbiological Samples from People with Cystic Fibrosis and the US Cumulative Techniques and Procedures in Clinical Microbiology (Cumitech) Guidelines 43 Cystic Fibrosis Microbiology need to be updated to reflect both new methodological innovations, as well as better knowledge of fungal disease pathophysiology in CF; (4) there is a need for clinical medicine to decide upon a stratification strategy for the provision of new fungal assays that will add value to the physician in the optimal management of CF patients; (5) there is also a need to rationale what assays should be performed at local laboratory level and those which are best served at National Mycology Reference Laboratory level; and (6) further research is required in developing laboratory assays, which will help ascertain the clinical importance of 'old' fungal pathogens, as well as 'emerging' fungal pathogens.

[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.

Phosphorus Mobility in the Landscape: First Steps to Linking Hydrology and Microbiology

NASA Astrophysics Data System (ADS)

Saia, S. M.; Walter, M. T.; Regan, J.

2011-12-01

Numerous resources are spent each year to control phosphorus (P) nonpoint source pollution around the world. Despite these efforts, high P levels in freshwater bodies are still a persistent issue. Eutrophication and subsequent algal bloom die-offs, brought about by excess P, can harm local economies as well as human and ecosystem health. To overcome this disconnect between nutrient management strategies and observed P concentrations, scientists must advance research beyond the physical and chemical mechanisms commonly included in P transport experiments. Microbiological techniques (e.g. PCR and flow cytometry) are making it easier to tease out the influence of specific microorganisms on nutrient transport. Polyphosphate accumulating organisms (PAOs) are often used in wastewater treatment plants (WWTP) to remove P from effluent water but have rarely been studied in natural settings. In this study, we combined field and laboratory column experiments to identifying the influence of changing water content and temperature on PAO-facilitated P mobility. In the field, we collected a gridded network of soil samples and measured the temperature, water content, and P concentrations (bioavailable and total P) for each. We also quantified PAO presence using qPCR techniques. In the lab, we added various concentrations of WWTP sludge (with PAO present) to autoclaved soils. We measured dissolved P concentrations in effluent water with respect to moisture content and temperature. Based on the results to these experiments, we hope to draw attention to the importance of microbiological controls on P mobility in freshwater ecosystems.

A Systems Approach to Biology (SAB).

ERIC Educational Resources Information Center

Bush, Kenneth H.; And Others

This pupil's study guide is intended to be used with audio-taped biology modules. Each of the units (on laboratory techniques, plant and animal diversity, chemistry, cells, energy, microbiology, genetics, and development) contains an abstract providing an overview of the unit, the rationale and performance objectives for each module, questions to…

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

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.

Tuberculous otitis media with facial paralysis: a clinical and microbiological diagnosis-a case report.

PubMed

Quaranta, Nicola; Petrone, Paolo; Michailidou, Alexandra; Miragliotta, Luisa; Santantonio, Marilina; Del Prete, Raffaele; Mosca, Adriana; Miragliotta, Giuseppe

2011-01-01

The tuberculosis of the ear is rare, and in most cases the clinical picture resembles that of a chronic otitis media. The diagnosis is often delayed, and this can lead to irreversible complications such as hearing loss and/or facial paralysis. In view of its rare occurrence, we report a case of primary tuberculous otitis media in a 87-year-old female patient. The diagnosis was made on the basis of both histological and microbiological findings. In particular, gene amplification techniques such as real-time polymerase chain reaction are useful method for rapid diagnosis and detecting tuberculous bacilli usually present at very low number. Early diagnosis is essential for the prompt institution of antituberculous therapy.

Tuberculous Otitis Media with Facial Paralysis: A Clinical and Microbiological Diagnosis—A Case Report

PubMed Central

Quaranta, Nicola; Petrone, Paolo; Michailidou, Alexandra; Miragliotta, Luisa; Santantonio, Marilina; Del Prete, Raffaele; Mosca, Adriana; Miragliotta, Giuseppe

2011-01-01

The tuberculosis of the ear is rare, and in most cases the clinical picture resembles that of a chronic otitis media. The diagnosis is often delayed, and this can lead to irreversible complications such as hearing loss and/or facial paralysis. In view of its rare occurrence, we report a case of primary tuberculous otitis media in a 87-year-old female patient. The diagnosis was made on the basis of both histological and microbiological findings. In particular, gene amplification techniques such as real-time polymerase chain reaction are useful method for rapid diagnosis and detecting tuberculous bacilli usually present at very low number. Early diagnosis is essential for the prompt institution of antituberculous therapy. PMID:22570801

Application of MALDI-TOF mass spectrometry in clinical diagnostic microbiology.

PubMed

De Carolis, Elena; Vella, Antonietta; Vaccaro, Luisa; Torelli, Riccardo; Spanu, Teresa; Fiori, Barbara; Posteraro, Brunella; Sanguinetti, Maurizio

2014-09-12

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful technique for identification of microorganisms, changing the workflow of well-established laboratories so that its impact on microbiological diagnostics has been unparalleled. In comparison with conventional identification methods that rely on biochemical tests and require long incubation procedures, MALDI-TOF MS has the advantage of identifying bacteria and fungi directly from colonies grown on culture plates in a few minutes and with simple procedures. Numerous studies on different systems available demonstrate the reliability and accuracy of the method, and new frontiers have been explored besides microbial species level identification, such as direct identification of pathogens from positive blood cultures, subtyping, and drug susceptibility detection.

Diagnosis of clinical bovine mastitis by fine needle aspiration followed by staining and scanning electron microscopy in a Prototheca zopfii outbreak.

PubMed

da Costa, Elizabeth Oliveira; Ribeiro, Márcio Garcia; Ribeiro, Andréa Rentz; Rocha, Noeme Sousa; de Nardi Júnior, Geraldo

2004-07-01

Biopsy by fine needle aspiration together with microbiological examination and scanning electron microscopy were evaluated in diagnosis of clinical bovine mastitis in a Prototheca zopfii outbreak. Fine needle aspiration was performed in 21 mammary quarters from ten Holstein cows presenting clinical mastitis caused by P. zopfii. The algae were previously identified in the microbiological examination of milk collected from these cows. Material aspirated from these 21 mammary glands was submitted to cytological staining (Gram, Giemsa and/or Shor staining). Fine needle aspiration enabled cytological identification of the algae in these 21 mammary glands, from which P. zopfii was isolated in the milk. Simultaneously, five mammary fragments collected by fine needle aspiration from these 21 mammary glands presenting clinical mastitis were also submitted to microbiological examination. P. zopfii was also isolated from these five fragments. Scanning electron microscopy technique also identified three of these five P zopfii strains isolated from mammary fragments collected by cytological aspiration. These results suggest that fine needle aspiration may be an alternative method for the diagnosis of clinical mastitis.

2009 Gordon Research Conference, Applied and Environmental Microbiology

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

Dubilier, Nicole

The topic of the 2009 Gordon Conference on Applied and Environmental Microbiology is: From Single Cells to the Environment. The Conference will present and discuss cutting-edge research on applied and environmental microbiology with a focus on understanding interactions between microorganisms and the environment at levels ranging from single cells to complex communities. The Conference will feature a wide range of topics such as single cell techniques (including genomics, imaging, and NanoSIMS), microbial diversity at scales ranging from clonal to global, environmental 'meta-omics', biodegradation and bioremediation, metal - microbe interactions, animal microbiomes and symbioses. The Conference will bring together investigators whomore » are at the forefront of their field, and will provide opportunities for junior scientists and graduate students to present their work in poster format and exchange ideas with leaders in the field. Some poster presenters will be selected for short talks. The collegial atmosphere of this Conference, with extensive discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings, provides an ideal setting for scientists from different disciplines to exchange ideas, brainstorm and discuss cross-disciplinary collaborations.« less

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.

Super-long Anabiosis of Ancient Microorganisms in Ice and Terrestrial Models for Development of Methods to Search for Life on Mars, Europa and other Planetary Bodies

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Duxbury, N. S.; Bobin, N. E.; Fukuchi, M.; Hoover, R. B.; Kanda, H.; Mitskevich, I. N.; Mulyukin, A. L.; Naganuma, T.; Poglazova, M. N.;

Role of microbiological culture and polymerase chain reaction (PCR) of actinomyces in medication-related osteonecrosis of the jaw (MRONJ).

PubMed

Panya, Sappasith; Fliefel, Riham; Probst, Florian; Tröltzsch, Matthias; Ehrenfeld, Michael; Schubert, Sören; Otto, Sven

2017-03-01

We hypothesized that local infection plays a critical role in the pathogenesis of medication-related osteonecrosis of the jaw (MRONJ). Recent developments in molecular methods have revolutionized new approaches for the rapid detection of microorganisms including those difficult to culture. The aim of our study is to identify the bacterial profiles in MRONJ by microbiological culture and polymerase chain reactions (PCR). A retrospective analysis was performed on MRONJ patients from 2008 to 2014. The bacterial profile from MRONJ bone samples was determined using microbiological culture and PCR. Ninety five patients fulfilled the inclusion criteria with mean age of 69.85 ± 8.71 years. A female predilection was detected. The mandible was more commonly affected than maxilla. Tooth extraction was the frequent triggering factor. Breast cancer was the primary cause for administration and intravenous bisphosphonates were the most commonly administrated antiresorptive drugs. The majority of patients were classified as stage 2. Posterior teeth were most commonly affected. Based on bone culture results, the most common microorganism were both actinomyces and mixed flora. PCR confirmed the presence of actinomyces in 55 patients. Our data suggest that PCR might be an innovative method for detection of microorganisms difficult to culture using traditional microbiological techniques. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Faecal coliform bacteria in Febros river (northwest Portugal): temporal variation, correlation with water parameters, and species identification.

PubMed

Cabral, João Paulo; Marques, Cristina

2006-07-01

Febros river water was sampled weekly, during 35 successive weeks, and analyzed for microbiological (total coliforms, faecal coliforms, faecal streptococci and enterococci) and chemical-physical (ammonia and temperature) parameters. All microbiological parameters were highly correlated with each other and with ammonia, suggesting that the simultaneous determination of all variables currently in use in the evaluation of the microbiological quality of waters is probably redundant, and could be simplified, and that ammonia should be tested as a sentinel parameter of the microbiological pollution load of Febros river. From the strains isolated from positive tubes of the faecal coliforms test (multiple tube fermentation technique) and retested in this assay, Escherichia coli, Klebsiella oxytoca and Klebsiella pneumoniae subsp. pneumoniae strains were positive, indicating that the faecal coliforms test is not totally specific for Escherichia coli, and can detect other bacteria. Considering that these Klebsiella spp. are not necessarily of faecal origin, it was concluded that the faecal coliforms test can overestimate true faecal pollution. From the strains isolated from positive tubes of the faecal coliforms procedure, only Escherichia coli strains were clearly positive in the beta-D-glucuronidase test. All other species were negative or very weakly positive, suggesting that the assay of the beta-D-glucuronidase activity is less prone to false positives than the faecal coliforms test in the quantification of Escherichia coli in environmental waters.

Mass spectrometry. [in organic chemistry

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Shackleton, C. H. L.; Howe, I.; Chizhov, O. S.

1978-01-01

A review of mass spectrometry in organic chemistry is given, dealing with advances in instrumentation and computer techniques, selected topics in gas-phase ion chemistry, and applications in such fields as biomedicine, natural-product studies, and environmental pollution analysis. Innovative techniques and instrumentation are discussed, along with chromatographic-mass spectrometric on-line computer techniques, mass spectral interpretation and management techniques, and such topics in gas-phase ion chemistry as electron-impact ionization and decomposition, photoionization, field ionization and desorption, high-pressure mass spectrometry, ion cyclotron resonance, and isomerization reactions of organic ions. Applications of mass spectrometry are examined with respect to bio-oligomers and their constituents, biomedically important substances, microbiology, environmental organic analysis, and organic geochemistry.

A Comparison of Heat versus Methanol Fixation for Gram Staining Bacteria

ERIC Educational Resources Information Center

Minnerath, Jeanne M.; Roland, Jenna M.; Rossi, Lucas C.; Weishalla, Steven R.; Wolf, Melissa M.

2009-01-01

Gram staining bacteria is a fundamental technique introduced in general biology and microbiology laboratory courses. Two common problems students encounter when Gram staining bacteria are (1) having a difficult time locating bacterial cells on the microscope slide and (2) over-decolorizing bacterial cells during the staining procedure such that…

Differentiation of live and dead salmonella cells using fourier transform infrared (FTIR) spectroscopy and principle component analysis (PCA) technique

USDA-ARS?s Scientific Manuscript database

Various technologies have been developed for pathogen detection using optical, electrochemical, biochemical and physical properties. Conventional microbiological methods need time from days to week to get the result. Though this method is very sensitive and accurate, a rapid detection of pathogens i...

Outcomes of a Research-Driven Laboratory and Literature Course Designed to Enhance Undergraduate Contributions to Original Research

ERIC Educational Resources Information Center

Rasche, Madeline E.

2004-01-01

This work describes outcomes of a research-driven advanced microbiology laboratory and literature research course intended to enhance undergraduate preparation for and contributions to original research. The laboratory section was designed to teach fundamental biochemistry and molecular biology techniques in the context of an original research…

A Survey of Current Literature on Sampling, Sample Handling, and Long Term Storage for Environmental Materials.

ERIC Educational Resources Information Center

Maienthal, E. J.; Becker, D. A.

This report presents the results of an extensive literature survey undertaken to establish optimum sampling, sample handling and long-term storage techniques for a wide variety of environmental samples to retain sample integrity. The components of interest are trace elements, organics, pesticides, radionuclides and microbiologicals. A bibliography…

Unit: Micro-Organisms and Man, Inspection Pack, National Trial Print.

ERIC Educational Resources Information Center

Australian Science Education Project, Toorak, Victoria.

This unit, intended for students in grades eight or nine, is a revised version of ED 053 990. The teacher's guide lists the aims of the unit, behavioral objectives, suitable references and audio-visual aids, required apparatus and materials, and provides teaching notes for each activity, including comments concerning microbiological techniques.…

In Situ Analysis of Bacterial Lipopeptide Antibiotics by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging.

PubMed

Debois, Delphine; Ongena, Marc; Cawoy, Hélène; De Pauw, Edwin

2016-01-01

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a technique developed in the late 1990s enabling the two-dimensional mapping of a broad variety of biomolecules present at the surface of a sample. In many applications including pharmaceutical studies or biomarker discovery, the distribution of proteins, lipids or drugs, and metabolites may be visualized within tissue sections. More recently, MALDI MSI has become increasingly applied in microbiology where the versatility of the technique is perfectly suited to monitor the metabolic dynamics of bacterial colonies. The work described here is focused on the application of MALDI MSI to map secondary metabolites produced by Bacilli, especially lipopeptides, produced by bacterial cells during their interaction with their environment (bacteria, fungi, plant roots, etc.). This chapter addresses the advantages and challenges that the implementation of MALDI MSI to microbiological samples entails, including detailed protocols on sample preparation (from both microbiologist and mass spectrometrist points of view), matrix deposition, and data acquisition and interpretation. Lipopeptide images recorded from confrontation plates are also presented.

Rifaximin Stability: A Look at UV, IR, HPLC, and Turbidimetry Methods.

PubMed

Kogawa, Ana Carolina; Salgado, Hérida Regina Nunes

2018-03-01

The study of the stability of medicines is mandated by the International Conference on Harmonization and the World Health Organization. Rifaximin, an antimicrobial marketed in the form of tablets, has no record of stability studies. Thus, the objective of the present work was to investigate the behavior and stability of rifaximin tablets for 6 months under simultaneous conditions of temperature and humidity by UV, IR, HPLC, and turbidimetry techniques. After 6 months of stability study, rifaximin tablets were shown to obey zero-order kinetics when analyzed by physicochemical methods and second-order kinetics when analyzed by a microbiological method. However, the UV method was not suitable for the evaluation of rifaximin. IR, HPLC, and turbidimetry methods can already be used to evaluate the stability of rifaximin tablets. It is important to analyze products with more than one type of method before releasing results mainly in the case of antimicrobial products in which the association of physicochemical and microbiological techniques must be a rule. Rifaximin tablets can be considered stable after 6 months under conditions of 40 ± 2°C and 75 ± 5% relative humidity.

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.

PubMed

Buttigieg, Pier Luigi; Ramette, Alban

2014-12-01

The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.

Human Milk Processing: A Systematic Review of Innovative Techniques to Ensure the Safety and Quality of Donor Milk.

PubMed

Peila, Chiara; Emmerik, Nikki E; Giribaldi, Marzia; Stahl, Bernd; Ruitenberg, Joost E; van Elburg, Ruurd M; Moro, Guido E; Bertino, Enrico; Coscia, Alessandra; Cavallarin, Laura

2017-03-01

Pasteurization, performed at 62.5°C for 30 minutes (holder pasteurization), is currently recommended in all international human milk banks guidelines, but it affects some human milk bioactive and nutritive components. The present systematic review is aimed at critically reviewing evidence on the suitability of human milk processing techniques other than holder pasteurization, both thermal and nonthermal, to ensure microbiological safety, and on the effects of these techniques on biologically active donor milk components. A systematic review of English and non-English articles using Medline, PubMed, Embase, SCOPUS, and CAB Abstracts, with no restriction in publication date was performed. Search terms included: human, breast, donor, or banked milk, breastmilk, breast fed, breastfed, breastfeed; HTST, Flash, High Pressure, UV, ultrasonic or nonthermal; process, pasteuris, pasteuriz. Only primary research articles published in peer-reviewed journals were included, providing or not a comparison with holder pasteurized human milk, provided that the pasteurization technique was clearly described, and not intended for domestic use. Additional studies were identified by searching bibliographies of relevant articles. Twenty-six studies were identified as being relevant. Two examined both High Pressure Processing and High-Temperature-Short-Time pasteurization; 10 only examined High Pressure Processing; 10 only examined High-Temperature-Short-Time; 2 articles examined ultraviolet irradiation; 2 articles examined (thermo-)ultrasonic processing. The results indicate that data about safety for microbiological control are still scarce for most of the novel technologies, and that consensus on processing conditions is necessary for nonthermal technologies, before any conclusions on the qualitative and nutritional advantages of these techniques can be drawn.

Percutaneous CT-Guided Biopsies of the Cervical Spine: Technique, Histopathologic and Microbiologic Yield, and Safety at a Single Academic Institution.

PubMed

Wiesner, E L; Hillen, T J; Long, J; Jennings, J W

2018-05-01

Cervical spine biopsies can be challenging due to the anatomy and the adjacent critical structures. Percutaneous image-guided biopsies can obviate the need for an open biopsy, however there have been few studies looking at the approaches, safety, and efficacy of percutaneous cervical spine biopsies. This retrospective study evaluated technical considerations, histopathologic and microbiologic yield, and safety in CT-guided cervical bone biopsies. A retrospective review of cervical bone and/or bone/disc biopsies performed from January 2010 to January 2017 was included in this study. Clinical diagnosis and indication, patient demographics, biopsy location, biopsy needle type, technical approach, lesion size, dose-length product, conscious sedation details, complications, and diagnostic histopathologic and/or microbiologic yield were recorded for each case and summarized. A total of 73 patients underwent CT-guided cervical bone biopsies. Fifty-three percent (39/73) were for clinical/imaging concern for infection and 47% (34/73) were for primary tumors or metastatic disease. Thirty-four percent (25/73) were of the inferior cervical spine (ie, C6 and C7). A sufficient sample was obtained for histopathologic and microbiologic analyses in 96% (70/73) of the biopsies. Forty-six percent (18/39) of those samples taken for infection had positive cultures. Two intraprocedural complications occurred in which the patients became hypotensive during the procedure without long-term complications. Percutaneous CT-guided biopsy of the cervical spine is an effective and safe procedure with high diagnostic yield and can obviate open procedures for histopathologic and microbiologic analyses of patients with clinical and imaging findings concerning for infection or primary and metastatic osseous lesions. © 2018 by American Journal of Neuroradiology.

A European perspective on intravascular catheter-related infections: report on the microbiology workload, aetiology and antimicrobial susceptibility (ESGNI-005 Study).

PubMed

Bouza, E; San Juan, R; Muñoz, P; Pascau, J; Voss, A; Desco, M

2004-09-01

The laboratory workload, microbiological techniques and aetiology of catheter-related infections in European hospitals are mostly unknown. The present study (ESGNI-005) comprised a 1-day (22 October 2001), laboratory-based, point-prevalence survey based on a questionnaire completed by microbiology laboratories in European (European Union (EU) and non-EU) hospitals. Also included were questions requesting retrospective information for the year 2000. In total, 151 hospitals from 26 European countries participated, of which 78.1% were teaching institutions. Overall, the estimated population served by these institutions was 121,363,800, and the estimated number of admissions during 2000 was 6,712,050. The total number of catheter tips processed during 2000 was 142,727, or 21/1,000 admissions, of which 23.7% were considered to be positive in the institutions using semiquantitative or quantitative techniques. Overall, EU centres received significantly more catheter tip samples/1,000 admissions and had a significantly higher rate of 'positivity' (p < 0.0001) than non-EU centres. Of the institutions surveyed, 11.4% (7.2% in EU countries and 23.7% in non-EU countries; p 0.04) used only qualitative techniques for catheter tip sample processing. On the day of the study, 167 microorganisms were recovered from significant catheter tip cultures (122 patients), of which Gram-positive bacteria represented 70.7%, Gram-negative bacteria 22.2%, and yeasts 7.2%. The five most common microorganisms were coagulase-negative staphylococci, Staphylococcus aureus, Candida spp., Enterococcus spp. and Pseudomonas spp. Overall, 19% of catheter tip cultures were polymicrobial. In the case of S. aureus, 40% of isolates were resistant to oxacillin, as were 63.4% of coagulase-negative staphylococcus isolates. Of 37 Gram-negative isolates, 35% were resistant to cefotaxime, 31% to ceftazidime, and 27% to ciprofloxacin. Imipenem and cefepime had the lowest reported rates of resistance (11%).

Chemical and biological techniques for identifying irradiated foods and food constituents-carbonyls and 2-deoxygluconic acid

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

Schubert, J.; Esterbauer, H.

1973-01-01

From international colloquium: the identification of irradiated foodstuffs; Karlsruhe, Germany (24 Oct 1973). New microbiological and chemical procedures are described for the detection, concentration, and identification of compounds produced in irradiated foods. The microbiological method employs an equation, by which inhibition of cell growth is expressed in a simple, economic, and consistent manner for identification of different classes of growth inhibitors using a single growth index, namely, concentration of substance at which time needed for log phase cells to double is ten times the controls. The chemical procedure permits carbonyl compounds to be spectrophotometrically determined in the presence of carbohydratesmore » without prior separation. The G(carbonyl) yields have been measured in irradiated hexoses and disaccharide solutions in the presence and absence of OH scavengers (KI and formate) and e/sub aq/ scavengers (N/sub 2/O). It has been demonstrated that the cytotoxic carbonyls produced upon carbohydrate irradiation are dicarbonyl sugars which convert to alpha , BETA -unsaturated carbonyl sugars by enolization or dehydration upon heating. Carbonyl yields in various irradiated foods are reported (e.g., strawberries: G = 2.2 and beef, G = 0.8). Both the carbonyl and microbiological techniques are uniquely applicable to the identification of non- volative compounds produced in irradiated foods. By anion exchange, we can rapidly separate enolizable carbonyls and 2-deoxygluconic acid from neutrnl sugars and obtain concentration factors of 50-fold and greater, thus enabling us to differentiate irradiated from nonirradiated foods at low radiation doses (approximately 1 Krad). (GE)« less

Biological Risks and Laboratory-Acquired Infections: A Reality That Cannot be Ignored in Health Biotechnology

PubMed Central

Coelho, Ana Cláudia; García Díez, Juan

2015-01-01

Advances and research in biotechnology have applications over a wide range of areas, such as microbiology, medicine, the food industry, agriculture, genetically modified organisms, and nanotechnology, among others. However, research with pathogenic agents, such as virus, parasites, fungi, rickettsia, bacterial microorganisms, or genetic modified organisms, has generated concern because of their potential biological risk – not only for people, but also for the environment due to their unpredictable behavior. In addition, concern for biosafety is associated with the emergence of new diseases or re-emergence of diseases that were already under control. Biotechnology laboratories require biosafety measures designed to protect their staff, the population, and the environment, which may be exposed to hazardous organisms and materials. Laboratory staff training and education is essential, not only to acquire a good understanding about the direct handling of hazardous biological agents but also knowledge of the epidemiology, pathogenicity, and human susceptibility to the biological materials used in research. Biological risk can be reduced and controlled by the correct application of internationally recognized procedures such as proper microbiological techniques, proper containment apparatus, adequate facilities, protective barriers, and special training and education of laboratory workers. To avoid occupational infections, knowledge about standardized microbiological procedures and techniques and the use of containment devices, facilities, and protective barriers is necessary. Training and education about the epidemiology, pathogenicity, and biohazards of the microorganisms involved may prevent or decrease the risk. In this way, the scientific community may benefit from the lessons learned in the past to anticipate future problems. PMID:25973418

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.

Review of water disinfection techniques

NASA Technical Reports Server (NTRS)

Colombo, Gerald V.; Sauer, Richard L.

1987-01-01

Throughout the history of manned space flight the supply of potable water to the astronauts has presented unique problems. Of particular concern has been the microbiological quality of the potable water. This has required the development of both preflight water system servicing procedures to disinfect the systems and inflight disinfectant addition and monitoring devices to ensure continuing microbiological control. The disinfectants successfully used to date have been aqueous chlorine or iodine. Because of special system limitations the use of iodine has been the most successful for inflight use and promises to be the agent most likely to be used in the future. Future spacecraft potable, hygiene, and experiment water systems will utilize recycled water. This will present special problems for water quality control. NASA is currently conducting research and development to solve these problems.

Microbiologic assay of space hardware.

NASA Technical Reports Server (NTRS)

Favero, M. S.

1971-01-01

Review of the procedures used in the microbiological examination of space hardware. The general procedure for enumerating aerobic and anaerobic microorganisms and spores is outlined. Culture media and temperature-time cycles used for incubation are reviewed, along with assay systems designed for the enumeration of aerobic and anaerobic spores. The special problems which are discussed are involved in the precise and accurate enumeration of microorganisms on surfaces and in the neutralization of viable organisms buried inside solid materials that could be released to a planet's surface if the solid should be fractured. Special attention is given to sampling procedures including also the indirect techniques of surface assays of space hardware such as those using detachable or fallout strips. Some data on comparative levels of microbial contamination on lunar and planetary spacecraft are presented.

Identification of a novel 16S rRNA gene variant of Actinomyces funkei from six patients with purulent infections.

PubMed

Hinić, V; Straub, C; Schultheiss, E; Kaempfer, P; Frei, R; Goldenberger, D

2013-07-01

Little is known about the clinical significance and laboratory diagnosis of Actinomyces funkei. In this report we describe six clinical cases where A. funkei was isolated from purulent, polymicrobial infections. Conventional identification procedures were compared with molecular methods including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique. Analysis of the full 16S rRNA gene sequence of the six investigated strains revealed differences from the A. funkei type strain. DNA-DNA hybridization showed that the clinical strains represent a novel 16S rRNA gene variant within the species of A. funkei. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Control of microbial contamination.

NASA Technical Reports Server (NTRS)

Mcdade, J. J.

1971-01-01

Two specific applications are discussed of microbial contamination control in planetary quarantine. Under the first concept, using the clean room to control environmental microorganisms, the objective is to reduce the microbial species and keep the numbers of microorganisms within an enclosure at a low level. The clean room concept is aimed at obtaining a product that has a controlled and reduced level of microbial contamination. Under the second concept, using the microbiological barrier to control microbial contamination of a specific product, the barrier techniques are designed to prevent the entry of any microorganisms into a sterile work area. Thus the assembly of space flight hardware within the confines of a microbiological barrier is aimed at obtaining a sterile product. In theory and practice, both approaches are shown to be applicable to the planetary quarantine program.

Microbiological Analysis of Surfaces of Leonardo Da Vinci's Atlantic Codex: Biodeterioration Risk.

PubMed

Tarsitani, Gianfranco; Moroni, Catia; Cappitelli, Francesca; Pasquariello, Giovanna; Maggi, Oriana

2014-01-01

Following the discovery of discoloration on some pages of the Atlantic Codex (AC) of Leonardo da Vinci kept in the Biblioteca Ambrosiana in Milan, some investigations have been carried out to verify the presence of microorganisms, such as bacteria and fungi. To verify the presence of microorganisms a noninvasive method of sampling has been used that was efficient and allowed us to highlight the microbial facies of the material that was examined using conventional microbiological techniques. The microclimatic conditions in the storage room as well as the water content of the volume were also assessed. The combined observations allowed the conclusion that the discoloration of suspected biological origin on some pages of AC is not related to the presence or current attack of microbial agents.

Microbiological Analysis of Surfaces of Leonardo Da Vinci's Atlantic Codex: Biodeterioration Risk

PubMed Central

Moroni, Catia; Pasquariello, Giovanna; Maggi, Oriana

2014-01-01

Following the discovery of discoloration on some pages of the Atlantic Codex (AC) of Leonardo da Vinci kept in the Biblioteca Ambrosiana in Milan, some investigations have been carried out to verify the presence of microorganisms, such as bacteria and fungi. To verify the presence of microorganisms a noninvasive method of sampling has been used that was efficient and allowed us to highlight the microbial facies of the material that was examined using conventional microbiological techniques. The microclimatic conditions in the storage room as well as the water content of the volume were also assessed. The combined observations allowed the conclusion that the discoloration of suspected biological origin on some pages of AC is not related to the presence or current attack of microbial agents. PMID:25574171

Towards the innovation for microbiology curriculum change: students' perception.

PubMed

Saha, Rumpa; Das, Shukla; Kaur, Iqbal R

2012-08-01

For a medical curriculum to be an effective means of learning for today's students, it has to be designed with knowledge of their priorities, needs and abilities. This can be best achieved by inviting students' view-point during curriculum planning. The present study thus elicits opinion of the medical students through a randomly issued set of questionnaires, towards the present microbiology curriculum in order to quantitate from their view-point, the weakness as well as the strengths of the existing curriculum. Their evaluation reveals that they welcome new techniques like problem-based learning but at the same time emphasise the need to integrate what is taught in close association with clinical circumstance. Hence it is important to understand the minds and needs of our students before implementing the syllabus content across to the consumers.

An Experimental Guide for Personnel Training Requirements of Technicians in Future Food Irradiation Technology Industries. Final Report.

ERIC Educational Resources Information Center

Stiles, Philip G.

With increasing requirements for food free from microbiological health hazards plus extended shelf life of refrigerated and nonrefrigerated foods, many persons will need fundamental training in irradiation techniques and methods of handling irradiated food. Special training needs and criteria for training were defined by conducting interviews with…

Fun Microbiology: Using a Plant Pathogenic Fungus To Demonstrate Koch's Postulates.

ERIC Educational Resources Information Center

Mitchell, James K.; Orsted, Kathy M.; Warnes, Carl E.

1997-01-01

Describes an experiment using a plant pathogenic fungus in which students learn to follow aseptic techniques, grow and produce spores of a fungus, use a hemacytometer for enumerating spores, prepare serial dilutions, grow and inoculate plants, isolate a pure culture using agar streak plates, and demonstrate the four steps of Koch's postulates.…

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…

Infrared and NIR Raman spectroscopy in medical microbiology

NASA Astrophysics Data System (ADS)

Naumann, Dieter

1998-04-01

FTIR and FT-NIR Raman spectra of intact microbial cells are highly specific, fingerprint-like signatures which can be used to (i) discriminate between diverse microbial species and strains, (ii) detect in situ intracellular components or structures such as inclusion bodies, storage materials or endospores, (iii) detect and quantify metabolically released CO2 in response to various different substrate, and (iv) characterize growth-dependent phenomena and cell-drug interactions. The characteristic information is extracted from the spectral contours by applying resolution enhancement techniques, difference spectroscopy, and pattern recognition methods such as factor-, cluster-, linear discriminant analysis, and artificial neural networks. Particularly interesting applications arise by means of a light microscope coupled to the spectrometer. FTIR spectra of micro-colonies containing less than 103 cells can be obtained from colony replica by a stamping technique that transfers micro-colonies growing on culture plates to a special IR-sample holder. Using a computer controlled x, y- stage together with mapping and video techniques, the fundamental tasks of microbiological analysis, namely detection, enumeration, and differentiation of micro- organisms can be integrated in one single apparatus. FTIR and NIR-FT-Raman spectroscopy can also be used in tandem to characterize medically important microorganisms. Currently novel methodologies are tested to take advantage of the complementary information of IR and Raman spectra. Representative examples on medically important microorganisms will be given that highlight the new possibilities of vibrational spectroscopies.

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.

Characterization, thermal stability studies, and analytical method development of Paromomycin for formulation development.

PubMed

Khan, Wahid; Kumar, Neeraj

2011-06-01

Paromomycin (PM) is an aminoglycoside antibiotic, first isolated in the 1950s, and approved in 2006 for treatment of visceral leishmaniasis. Although isolated six decades back, sufficient information essential for development of pharmaceutical formulation is not available for PM. The purpose of this paper was to determine thermal stability and development of new analytical method for formulation development of PM. PM was characterized by thermoanalytical (DSC, TGA, and HSM) and by spectroscopic (FTIR) techniques and these techniques were used to establish thermal stability of PM after heating PM at 100, 110, 120, and 130 °C for 24 h. Biological activity of these heated samples was also determined by microbiological assay. Subsequently, a simple, rapid and sensitive RP-HPLC method for quantitative determination of PM was developed using pre-column derivatization with 9-fluorenylmethyl chloroformate. The developed method was applied to estimate PM quantitatively in two parenteral dosage forms. PM was successfully characterized by various stated techniques. These techniques indicated stability of PM for heating up to 120 °C for 24 h, but when heated at 130 °C, PM is liable to degradation. This degradation is also observed in microbiological assay where PM lost ∼30% of its biological activity when heated at 130 °C for 24 h. New analytical method was developed for PM in the concentration range of 25-200 ng/ml with intra-day and inter-day variability of < 2%RSD. Characterization techniques were established and stability of PM was determined successfully. Developed analytical method was found sensitive, accurate, and precise for quantification of PM. Copyright © 2010 John Wiley & Sons, Ltd. Copyright © 2010 John Wiley & Sons, Ltd.

Microbial consortia of gorgonian corals from the Aleutian islands

USGS Publications Warehouse

Gray, Michael A.; Stone, R.P.; McLaughlin, M.R.; Kellogg, C.A.

2011-01-01

Gorgonians make up the majority of corals in the Aleutian archipelago and provide critical fish habitat in areas of economically important fisheries. The microbial ecology of the deep-sea gorgonian corals Paragorgea arborea, Plumarella superba, and Cryogorgia koolsae was examined with culture-based and 16S rRNA gene-based techniques. Six coral colonies (two per species) were collected. Samples from all corals were cultured, and clone libraries were constructed from P. superba and C. koolsae. Cultured bacteria were dominated by the Gammaproteobacteria, especially Vibrionaceae, with other phyla comprising <6% of the isolates. The clone libraries showed dramatically different bacterial communities between corals of the same species collected at different sites, with no clear pattern of conserved bacterial consortia. Two of the clone libraries (one from each coral species) were dominated by Tenericutes, with Alphaproteobacteria dominating the remaining sequences. The other libraries were more diverse and had a more even distribution of bacterial phyla, showing more similarity between genera than within coral species. Here we report the first microbiological characterization of P. arborea, P. superba, and C. koolsae. FEMS Microbiology Ecology ?? 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

Quantification of HTLV-1 Clonality and TCR Diversity

PubMed Central

Laydon, Daniel J.; Melamed, Anat; Sim, Aaron; Gillet, Nicolas A.; Sim, Kathleen; Darko, Sam; Kroll, J. Simon; Douek, Daniel C.; Price, David A.; Bangham, Charles R. M.; Asquith, Becca

2014-01-01

Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological “species” in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations. PMID:24945836

Management of established pressure ulcer infections in spinal cord injury patients.

PubMed

Dinh, A; Bouchand, F; Davido, B; Duran, C; Denys, P; Lortat-Jacob, A; Rottman, M; Salomon, J; Bernard, L

2018-06-21

Pressure ulcers are frequently observed in spinal cord injury (SCI) patients. They can be life-threatening and are a major medico-economic burden. Despite their frequency, their pathophysiology and optimal management are still poorly understood. Most available data comes from non-comparative studies, especially in terms of antimicrobial use. We performed a critical review of the literature and opinions of infectious disease specialists based in a French expert center for this disease. We mainly focused on antimicrobial treatments prescribed in this situation. These infections are usually clinically diagnosed. Microbiological samples are not the gold standard for this assessment. Furthermore, reliable microbiological identification is a major challenge but should help select antimicrobial treatment. Imaging technique could be helpful but cannot replace the physical examination. The choice of antimicrobials must consider the potential ecological collateral damages in this vulnerable population. Antimicrobial therapy should be as short as possible, adapted to the microbiological identification, and must have suitable bioavailability. Management of infected pressure ulcers is a major concern in disabled patients already highly exposed to antimicrobial treatment and multidrug-resistant organisms colonization. Extensive data is required. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

A professional development model for medical laboratory scientists working in the microbiology laboratory.

PubMed

Amerson, Megan H; Pulido, Lila; Garza, Melinda N; Ali, Faheem A; Greenhill, Brandy; Einspahr, Christopher L; Yarsa, Joseph; Sood, Pramilla K; Hu, Peter C

2012-01-01

The University of Texas M.D. Anderson Cancer Center, Division of Pathology and Laboratory Medicine is committed to providing the best pathology and medicine through: state-of-the art techniques, progressive ground-breaking research, education and training for the clinical diagnosis and research of cancer and related diseases. After surveying the laboratory staff and other hospital professionals, the Department administrators and Human Resource generalists developed a professional development model for Microbiology to support laboratory skills, behavior, certification, and continual education within its staff. This model sets high standards for the laboratory professionals to allow the labs to work at their fullest potential; it provides organization to training technologists based on complete laboratory needs instead of training technologists in individual areas in which more training is required if the laboratory needs them to work in other areas. This model is a working example for all microbiology based laboratories who want to set high standards and want their staff to be acknowledged for demonstrated excellence and professional development in the laboratory. The PDM model is designed to focus on the needs of the laboratory as well as the laboratory professionals.

Fitting distributions to microbial contamination data collected with an unequal probability sampling design.

PubMed

Williams, M S; Ebel, E D; Cao, Y

2013-01-01

The fitting of statistical distributions to microbial sampling data is a common application in quantitative microbiology and risk assessment applications. An underlying assumption of most fitting techniques is that data are collected with simple random sampling, which is often times not the case. This study develops a weighted maximum likelihood estimation framework that is appropriate for microbiological samples that are collected with unequal probabilities of selection. A weighted maximum likelihood estimation framework is proposed for microbiological samples that are collected with unequal probabilities of selection. Two examples, based on the collection of food samples during processing, are provided to demonstrate the method and highlight the magnitude of biases in the maximum likelihood estimator when data are inappropriately treated as a simple random sample. Failure to properly weight samples to account for how data are collected can introduce substantial biases into inferences drawn from the data. The proposed methodology will reduce or eliminate an important source of bias in inferences drawn from the analysis of microbial data. This will also make comparisons between studies and the combination of results from different studies more reliable, which is important for risk assessment applications. © 2012 No claim to US Government works.

Determination of the folate content in cladodes of nopal (Opuntia ficus indica) by microbiological assay utilizing Lactobacillus casei (ATCC 7469) and enzyme-linked immunosorbent assay.

PubMed

Ortiz-Escobar, Tania Breshkovskaya; Valverde-González, Maria Elena; Paredes-López, Octavio

2010-05-26

Prickly pear cactus has been an important food source in Mexico since ancient times due to its economical and ecological benefits and potential nutraceutical value. Nevertheless, studies on the nutritional aspects and health benefits have been scarce. The purpose of this study was to assess, apparently for the first time, the folate contents of cladodes of nopal by a microbiological assay, using Lactobacillus casei (ATCC 7469) in extracts that were enzymatically treated to release the bound vitamin, employing single, dual, and trienzymatic procedures, and using the enzyme-linked immunosorbent assay (ELISA). We used Opuntia cladodes of different length sizes. The microbiological assay showed some differences among enzyme treatments and sizes of nopal; the trienzyme treatment (alpha-amylase-protease-conjugase) was more efficient in determining the folate content in nopal, giving 5.0 ng/g in the small size cladodes at 54 h of testing time, while ELISA showed no significant differences in the folate content among sizes of cladodes (5.5-5.62 ng/g at 0 min testing time). Both techniques may be used for the assessment of folate content in cladodes, but ELISA is more rapid and reliable.

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

PubMed Central

2016-01-01

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum, Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereus strain was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days. PMID:26896133

Microbial consortia of gorgonian corals from the Aleutian islands.

PubMed

Gray, Michael A; Stone, Robert P; McLaughlin, Molly R; Kellogg, Christina A

2011-04-01

Gorgonians make up the majority of corals in the Aleutian archipelago and provide critical fish habitat in areas of economically important fisheries. The microbial ecology of the deep-sea gorgonian corals Paragorgea arborea, Plumarella superba, and Cryogorgia koolsae was examined with culture-based and 16S rRNA gene-based techniques. Six coral colonies (two per species) were collected. Samples from all corals were cultured, and clone libraries were constructed from P. superba and C. koolsae. Cultured bacteria were dominated by the Gammaproteobacteria, especially Vibrionaceae, with other phyla comprising <6% of the isolates. The clone libraries showed dramatically different bacterial communities between corals of the same species collected at different sites, with no clear pattern of conserved bacterial consortia. Two of the clone libraries (one from each coral species) were dominated by Tenericutes, with Alphaproteobacteria dominating the remaining sequences. The other libraries were more diverse and had a more even distribution of bacterial phyla, showing more similarity between genera than within coral species. Here we report the first microbiological characterization of P. arborea, P. superba, and C. koolsae. FEMS Microbiology Ecology © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis.

PubMed

Korsak, N; Taminiau, B; Hupperts, C; Delhalle, L; Nezer, C; Delcenserie, V; Daube, G

2017-04-17

The aim of this study was to investigate the influence of the slaughter technique (Halal vs Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological procedures and 16S rDNA metagenetics. The purpose was also to investigate the neck area to identify bacteria originating from the digestive or the respiratory tract. Twenty bovine carcasses (10 from each group) were swabbed at the slaughterhouse, where both slaughtering methods are practiced. Two swabbing areas were chosen: one "legal" zone of 1600cm 2 (composed of zones from rump, flank, brisket and forelimb) and locally on the neck area (200cm 2 ). Samples were submitted to classical microbiology for aerobic Total Viable Counts (TVC) at 30°C and Enterobacteriaceae counts, while metagenetic analysis was performed on the same samples. The classical microbiological results revealed no significant differences between both slaughtering practices; with values between 3.95 and 4.87log CFU/100cm 2 and 0.49 and 1.94log CFU/100cm 2 , for TVC and Enterobacteriaceae respectively. Analysis of pyrosequencing data showed that differences in the bacterial population abundance between slaughtering methods were mainly observed in the "legal" swabbing zone compared to the neck area. Bacterial genera belonging to the Actinobacteria phylum were more abundant in the "legal" swabbing zone in "Halal" samples, while Brevibacterium and Corynebacterium were encountered more in "Halal" samples, in all swabbing areas. This was also the case for Firmicutes bacterial populations (families of Aerococcaceae, Planococcaceae). Except for Planococcoceae, the analysis of Operational Taxonomic Unit (OTU) abundances of bacteria from the digestive or respiratory tract revealed no differences between groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis of taxonomy at the genus level taxonomy highlights differences between swabbing areas. Although not clearly proven in this study, differences in hygiene practices used during both slaughtering protocols could explain the differences in contamination between carcasses from both slaughtering groups. Copyright © 2016 Elsevier B.V. All rights reserved.

Culturing marine bacteria – an essential prerequisite for biodiscovery

PubMed Central

Joint, Ian; Mühling, Martin; Querellou, Joël

2010-01-01

Summary The potential for using marine microbes for biodiscovery is severely limited by the lack of laboratory cultures. It is a long‐standing observation that standard microbiological techniques only isolate a very small proportion of the wide diversity of microbes that are known in natural environments from DNA sequences. A number of explanations are reviewed. The process of establishing laboratory cultures may destroy any cell‐to‐cell communication that occurs between organisms in the natural environment and that are vital for growth. Bacteria probably grow as consortia in the sea and reliance on other bacteria for essential nutrients and substrates is not possible with standard microbiological approaches. Such interactions should be considered when designing programmes for the isolation of marine microbes. The benefits of novel technologies for manipulating cells are reviewed, including single cell encapsulation in gel micro‐droplets. Although novel technologies offer benefits for bringing previously uncultured microbes into laboratory culture, many useful bacteria can still be isolated using variations of plating techniques. Results are summarized for a study to culture bacteria from a long‐term observatory station in the English Channel. Bacterial biodiversity in this assemblage has recently been characterized using high‐throughput sequencing techniques. Although Alphaproteobacteria dominated the natural bacterial assemblage throughout the year, Gammaproteobacteria were the most frequent group isolated by plating techniques. The use of different gelling agents and the addition of ammonium to seawater‐based agar did lead to the isolation of a higher proportion of Alphaproteobacteria. Variation in medium composition was also able to increase the recovery of other groups of particular interest for biodiscovery, such as Actinobacteria. PMID:21255353

A quick and effective method of limb preparation with health, safety and efficiency benefits.

PubMed

Naderi, N; Maw, K; Thomas, M; Boyce, D E; Shokrollahi, K

2012-03-01

Pre-operative limb preparation (PLP) usually involves lifting the limb and holding it in a fixed 'static' posture for several minutes. This is hazardous to theatre staff. Furthermore, 'painting' the limb can be time consuming and difficult areas such as between toes and fingers may remain unsterile. We demonstrate the time efficiency and asepsis achieved using the 'sterile bag' preparation technique. An additional advantage is the ability to prepare and anaesthetise a limb prior to theatre, increasing efficiency substantially for units with a large throughput of cases, such as day-case hand surgery lists. We monitored the duration of PLP in 20 patients using the 'sterile bag' technique compared to 20 patients using a conventional 'painting' method. Additionally, microbiology samples acquired from prepared upper limbs of 27 sequential patients operated on by a single surgeon over a two-month period were sent for culture immediately prior to commencement of surgery. The mean duration of the 'sterile bag' PLP was significantly lower than that of the conventional method (24 seconds vs 85 seconds, p=0.045). The technique can take as little as ten seconds (n=1). Final microbiology reports showed no growth for any of the 27 patients from whom a culture sample was taken. The sterile bag technique is effective in achieving asepsis, has the potential to increase theatre efficiency and reduces manual handling hazards compared to the conventional method. It is now taught to all theatre staff in our hospital during manual handling training. It can be undertaken in approximately ten seconds with practice for the upper limb.

Impact of Roadway Stormwater Runoff on Microbial Contamination in the Receiving Stream.

PubMed

Wyckoff, Kristen N; Chen, Si; Steinman, Andrew J; He, Qiang

2017-09-01

Stormwater runoff from roadways has increasingly become a regulatory concern for water pollution control. Recent work has suggested roadway stormwater runoff as a potential source of microbial pollutants. The objective of this study was to determine the impact of roadway runoff on the microbiological quality of receiving streams. Microbiological quality of roadway stormwater runoff and the receiving stream was monitored during storm events with both cultivation-dependent fecal bacteria enumeration and cultivation-independent high-throughput sequencing techniques. Enumeration of total coliforms as a measure of fecal microbial pollution found consistently lower total coliform counts in roadway runoff than those in the stream water, suggesting that roadway runoff was not a major contributor of microbial pollutants to the receiving stream. Further characterization of the microbial community in the stormwater samples by 16S ribosomal RNA gene-based high-throughput amplicon sequencing revealed significant differences in the microbial composition of stormwater runoff from the roadways and the receiving stream. The differences in microbial composition between the roadway runoff and stream water demonstrate that roadway runoff did not appear to have a major influence on the stream in terms of microbiological quality. Thus, results from both fecal bacteria enumeration and high-throughput amplicon sequencing techniques were consistent that roadway stormwater runoff was not the primary contributor of microbial loading to the stream. Further studies of additional watersheds with distinct characteristics are needed to validate these findings. Understanding gained in this study could support the development of more effective strategies for stormwater management in sensitive watersheds. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

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

PubMed

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

2015-11-06

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

Improvements to a PCR-based serogrouping scheme for Salmonella enterica from dairy farm samples

USDA-ARS?s Scientific Manuscript database

The PCR method described by Herrera-León, et al. (Research in Microbiology 158:122-127, 2007) has proved to be a simple and useful technique for characterizing isolates of Salmonella enterica enterica belonging to serogroups B, C1, C2, D1, and E1, groups which encompass a majority of the isolates fr...

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

Application of the microbiological method DEFT/APC to detect minimally processed vegetables treated with gamma radiation

NASA Astrophysics Data System (ADS)

Araújo, M. M.; Duarte, R. C.; Silva, P. V.; Marchioni, E.; Villavicencio, A. L. C. H.

2009-07-01

Marketing of minimally processed vegetables (MPV) are gaining impetus due to its convenience, freshness and apparent health effect. However, minimal processing does not reduce pathogenic microorganisms to safe levels. Food irradiation is used to extend the shelf life and to inactivate food-borne pathogens. In combination with minimal processing it could improve safety and quality of MPV. A microbiological screening method based on the use of direct epifluorescent filter technique (DEFT) and aerobic plate count (APC) has been established for the detection of irradiated foodstuffs. The aim of this study was to evaluate the applicability of this technique in detecting MPV irradiation. Samples from retail markets were irradiated with 0.5 and 1.0 kGy using a 60Co facility. In general, with a dose increment, DEFT counts remained similar independent of the irradiation while APC counts decreased gradually. The difference of the two counts gradually increased with dose increment in all samples. It could be suggested that a DEFT/APC difference over 2.0 log would be a criteria to judge if a MPV was treated by irradiation. The DEFT/APC method could be used satisfactorily as a screening method for indicating irradiation processing.

Spectrometric microbiological analyzer

NASA Astrophysics Data System (ADS)

Schlager, Kenneth J.; Meissner, Ken E.

1996-04-01

Currently, there are four general approaches to microbiological analysis, i.e., the detection, identification and quantification of micro-organisms: (1) Traditional culturing and staining procedures, metabolic fermentations and visual morphological characteristics; (2) Immunological approaches employing microbe-specific antibodies; (3) Biotechnical techniques employing DNA probes and related genetic engineering methods; and (4) Physical measurement techniques based on the biophysical properties of micro-organisms. This paper describes an instrumentation development in the fourth of the above categories, physical measurement, that uses a combination of fluorometric and light scatter spectra to detect and identify micro-organisms at the species level. A major advantage of this approach is the rapid turnaround possible in medical diagnostic or water testing applications. Fluorometric spectra serve to define the biochemical characteristics of the microbe, and light scatter spectra the size and shape morphology. Together, the two spectra define a 'fingerprint' for each species of microbe for detection, identification and quantification purposes. A prototype instrument has been developed and tested under NASA sponsorship based on fluorometric spectra alone. This instrument demonstrated identification and quantification capabilities at the species level. The paper reports on test results using this instrument, and the benefits of employing a combination of fluorometric and light scatter spectra.

Bio-analytical applications of microbial fuel cell-based biosensors for onsite water quality monitoring.

PubMed

ElMekawy, A; Hegab, H M; Pant, D; Saint, C P

2018-01-01

Globally, sustainable provision of high-quality safe water is a major challenge of the 21st century. Various chemical and biological monitoring analytics are presently utilized to guarantee the availability of high-quality water. However, these techniques still face some challenges including high costs, complex design and onsite and online limitations. The recent technology of using microbial fuel cell (MFC)-based biosensors holds outstanding potential for the rapid and real-time monitoring of water source quality. MFCs have the advantages of simplicity in design and efficiency for onsite sensing. Even though some sensing applications of MFCs were previously studied, e.g. biochemical oxygen demand sensor, recently numerous research groups around the world have presented new practical applications of this technique, which combine multidisciplinary scientific knowledge in materials science, microbiology and electrochemistry fields. This review presents the most updated research on the utilization of MFCs as potential biosensors for monitoring water quality and considers the range of potentially toxic analytes that have so far been detected using this methodology. The advantages of MFCs over established technology are also considered as well as future work required to establish their routine use. © 2017 The Society for Applied Microbiology.

[Wound microbial sampling methods in surgical practice, imprint techniques].

PubMed

Chovanec, Z; Veverková, L; Votava, M; Svoboda, J; Peštál, A; Doležel, J; Jedlička, V; Veselý, M; Wechsler, J; Čapov, I

2012-12-01

The wound is a damage of tissue. The process of healing is influenced by many systemic and local factors. The most crucial and the most discussed local factor of wound healing is infection. Surgical site infection in the wound is caused by micro-organisms. This information is known for many years, however the conditions leading to an infection occurrence have not been sufficiently described yet. Correct sampling technique, correct storage, transportation, evaluation, and valid interpretation of these data are very important in clinical practice. There are many methods for microbiological sampling, but the best one has not been yet identified and validated. We aim to discuss the problem with the focus on the imprint technique.

[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.

Nano-Optics for Chemical and Materials Characterization

NASA Astrophysics Data System (ADS)

Beversluis, Michael; Stranick, Stephan

2007-03-01

Light microscopy can provide non-destructive, real-time, three-dimensional imaging with chemically-specific contrast, but diffraction frequently limits the resolution to roughly 200 nm. Recently, structured illumination techniques have allowed fluorescence imaging to reach 50 nm resolution [1]. Since these fluorescence techniques were developed for use in microbiology, a key challenge is to take the resolution-enhancing features and apply them to contrast mechanisms like vibrational spectroscopy (e.g., Raman and CARS microscopy) that provide morphological and chemically specific imaging.. We are developing a new hybrid technique that combines the resolution enhancement of structured illumination microscopy with scanning techniques that can record hyperspectral images with 100 nm spatial resolution. We will show such superresolving images of semiconductor nanostructures and discuss the advantages and requirements for this technique. Referenence: 1. M. G. L. Gustafsson, P. Natl. Acad. Sci. USA 102, 13081-13086 (2005).

Biological sand filters: low-cost bioremediation technique for production of clean drinking water.

PubMed

Lea, Michael

2014-05-01

Approximately 1.1 billion people in rural and peri-urban communities of developing countries do not have access to safe drinking water. The mortality from diarrheal-related diseases amounts to ∼2.2 million people each year from the consumption of unsafe water. Most of them are children under 5 years of age--250 deaths an hour from microbiologically contaminated water. There is conclusive evidence that one low-cost household bioremediation intervention, use of biological sand filters, is capable of dramatically improving the microbiological quality of drinking water. This unit will describe this relatively new and proven bioremediation technology's ability to empower at-risk populations to use naturally occurring biological principles and readily available materials as a sustainable way to achieve the health benefits of safe drinking water. Copyright © 2014 John Wiley & Sons, Inc.

A great leap forward in microbial ecology.

PubMed

Okabe, Satoshi; Oshiki, Mamoru; Kamagata, Yoichi; Yamaguchi, Nobuyasu; Toyofuku, Masanori; Yawata, Yutaka; Tashiro, Yosuke; Nomura, Nobuhiko; Ohta, Hiroyuki; Ohkuma, Moriya; Hiraishi, Akira; Minamisawa, Kiwamu

2010-01-01

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

Biological sand filters: low-cost bioremediation technique for production of clean drinking water.

PubMed

Lea, Michael

2008-05-01

Approximately 1.1 billion people in rural and peri-urban communities of developing countries do not have access to safe drinking water. The mortality from diarrheal-related diseases amounts to approximately 2.2 million people each year from the consumption of unsafe water. Most of them are children under 5 years of age-250 deaths an hour from microbiologically contaminated water. There is conclusive evidence that one low-cost household bioremediation intervention, biological sand filters, are capable of dramatically improving the microbiological quality of drinking water. This unit will describe this relatively new and proven bioremediation technology's ability to empower at-risk populations to use naturally occurring biology and readily available materials as a sustainable way to achieve the health benefits of safe drinking water. Copyright 2008 by John Wiley & Sons, Inc.

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

PubMed

Blake, Christopher J

2007-09-01

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

Evaluation of gram-chromotrope kinyoun staining technique: its effectiveness in detecting microsporidial spores in fecal specimens.

PubMed

Salleh, Fatmah M; Al-Mekhlafi, Abdulsalam M; Nordin, Anisah; Yasin, 'Azlin M; Al-Mekhlafi, Hesham M; Moktar, Norhayati

2011-01-01

This study was conducted to evaluate the modification of the usual Gram-chromotrope staining technique developed in-house known as Gram-chromotrope Kinyoun (GCK) in comparison with the Weber Modified Trichrome (WMT) staining technique; as the reference technique. Two hundred and ninety fecal specimens received by the Microbiology Diagnostic Laboratory of Hospital Universiti Kebangsaan Malaysia were examined for the presence of microsporidial spores. The sensitivity and specificity of GCK compared to the reference technique were 98% and 98.3%, respectively. The positive and negative predictive values were 92.5% and 99.6%, respectively. The agreement between the reference technique and the GCK staining technique was statistically significant by Kappa statistics (K = 0.941, P < 0.001). It is concluded that the GCK staining technique has high sensitivity and specificity in the detection of microsporidial spores in fecal specimens. Hence, it is recommended to be used in the diagnosis of intestinal microsporidiosis. Copyright © 2011 Elsevier Inc. All rights reserved.

[Proteomics in infectious diseases].

PubMed

Quero, Sara; Párraga-Niño, Noemí; García-Núñez, Marian; Sabrià, Miquel

2016-04-01

Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of "Omics" sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Raman Spectroscopy of Microbial Pigments

PubMed Central

Edwards, Howell G. M.; Oren, Aharon

2014-01-01

Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions. PMID:24682303

Careers in Microbiology...Horizons Unlimited

ERIC Educational Resources Information Center

Goldschmidt Millicent C.; Whitt, Dixie

1978-01-01

A broad range of present microbiological work is discussed in order to indicate the many possible careers now open in microbiology. Some areas are immunology, environmental microbiology, agricultural, industrial, and food microbiology, and space microbiology. An employment outlook is also given. (MDR)

Microbiology of processed edible insect products - Results of a preliminary survey.

PubMed

Grabowski, Nils Th; Klein, Günter

2017-02-21

Little is known of the microbiology of processed insect products. The present survey analysed a total of n=38 samples of deep-fried and spiced (Acheta domesticus, Locusta migratoria, and Omphisa fuscidentalis), cooked in soy sauce ("tsukudani"; Oxya yezoensis, Vespula flaviceps, and Bombyx mori), dried (A. domesticus, L. migatoria, Alphitobius diaperinus, Tenebrio molitor, B. mori, Hermetia illucens, and Musca domestica), powdered (H. illucens, T. molitor) and other (incl. deep-frozen B. mori and honeybee pollen) insect products microbiologically (total bacterial count [TBC], Enterobacteriaceae, staphylococci, bacilli, and yeasts and moulds counts, salmonellae, Listeria monocytogenes, and Escherichia coli). Although each product type revealed a microbiological profile of its own, dried and powdered insects ("class I") displayed markedly higher counts than the deep-fried and cooked ones ("class II"). Thresholds between class I and II products were estimated at 4.0 (TBC), 1.0 (Enterobacteriaceae, yeasts and moulds), 2.5 (staphylococci), and 3.0lgcfu/g (bacilli). All samples were negative for salmonellae, L. monocytogenes, E. coli and Stapyhlococcus aureus, but dried and powdered insects, as well as pollen, contained B. cereus, coliforms, Serratia liquefaciens, Listeria ivanovii, Mucor spp., Aspergillus spp., Penicillium spp., and Cryptococcus neoformans. Comparing the results with the hygiene criteria for edible insects proposed by Belgium and the Netherlands, class I products failed to comply with many bacterial count limits despite the absence of classical food pathogens. Therefore, class I products should always be consumed after another heating step as indicated by the manufacturer, until drying techniques are able to ensure lower bacterial counts. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbiological and clinical effects of probiotics and antibiotics on nonsurgical treatment of chronic periodontitis: a randomized placebo- controlled trial with 9-month follow-up

PubMed Central

Morales, Alicia; Gandolfo, Alessandro; Bravo, Joel; Carvajal, Paola; Silva, Nora; Godoy, Claudia; Garcia-Sesnich, Jocelyn; Hoare, Anilei; Diaz, Patricia; Gamonal, Jorge

2018-01-01

ABSTRACT Objective The aim of this double-blind, placebo-controlled and parallel- arm randomized clinical trial was to evaluate the effects of Lactobacillus rhamnosus SP1-containing probiotic sachet and azithromycin tablets as an adjunct to nonsurgical therapy in clinical parameters and in presence and levels of Tannerella forsythia, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. Material and Methods Forty-seven systemically healthy volunteers with chronic periodontitis were recruited and monitored clinically and microbiologically at baseline for 3, 6 and 9 months after therapy. Subgingival plaque samples were collected from four periodontal sites with clinical attachment level ≥1 mm, probing pocket depth ≥4 mm and bleeding on probing, one site in each quadrant. Samples were cultivated and processed using the PCR technique. Patients received nonsurgical therapy including scaling and root planing (SRP) and were randomly assigned to a probiotic (n=16), antibiotic (n = 16) or placebo (n = 15) group. L. rhamnosus SP1 was taken once a day for 3 months. Azithromycin 500mg was taken once a day for 5 days. Results All groups showed improvements in clinical and microbiological parameters at all time points evaluated. Probiotic and antibiotic groups showed greater reductions in cultivable microbiota compared with baseline. The placebo group showed greater reduction in number of subjects with P. gingivalis compared with baseline. However, there were no significant differences between groups. Conclusions The adjunctive use of L. rhamnosus SP1 sachets and azithromycin during initial therapy resulted in similar clinical and microbiological improvements compared with the placebo group. PMID:29364340

[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.

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.

An Overview of Microbiology Research in Japan, with Notes on Medical History, Education and Health Care.

DTIC Science & Technology

1981-07-01

Kyogoku: infrared spectroscopy , Raman spectroscop , and nuclear magnetic resonance spectroscopy of protein and protein models; resonance Raman spectra...Research projects - tritium labeling techniques; heavy metal accumulations in deciduous teeth; chemistry of the mycotoxin fusarenon; EM of phage P22 DNA...fluorescence correlation spectroscopy . - Biological Activities of Biopolymers - Dr. M. Kageyama, Director: Analysis of Pseudomonas aeruginosa bacteriocins

The human urinary microbiome and how it relates to urogynecology.

PubMed

Schneeweiss, Jenifer; Koch, Marianne; Umek, Wolfgang

2016-09-01

Recent studies applying molecular techniques have demonstrated the presence of a urinary microbiota not detected by standard microbiological techniques. These have been found in the urine of healthy individuals and in those suffering from clinical symptoms. The present article reviews the findings of these studies to date, describing the molecular techniques, and specifically outlining any differences in microbiomes in relation to urogynecological disease. Further, the role of commensal bacteria in the lower urinary tract is considered. An extensive literature search was conducted to identify articles on the microbiome of the female urinary tract in health and disease. We searched the electronic meta-databases Ovid MEDLINE® 1946-2015 and Embase 1974-2015. The keywords "microbiome, microbiota, bacterial colonization, microbiology, commensal bacteria, and bacteriuria" were searched in combination with "lower urinary tract symptoms, urogenital symptoms, urinary tract infection, overactive bladder and urinary incontinence." A total of 426 papers were retrieved; 33 were included in this paper. The microbiome of the female lower urinary tract shows variance between individuals and between age groups. There are significant differences between the microbiota in the lower urinary tract of individuals with urological symptoms and those without, relating to type and proportion of commensal Lactobacillus spp. There is only weak evidence to suggest that Lactobacillus might be applied as a therapeutic measure. It is still unclear what role microbiota plays in female urinary tract health. The discovery of bacteria in the urine of healthy individuals may have implications for future therapies for lower urinary tract symptoms.

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

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

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.

Application of Microbiological Method Direct Epifluorescence Filter Techique/Aerobic Plate Count Agar in the Identification of Irradiated Herbs and Spices

PubMed Central

Di Schiavi, Maria Teresa; Foti, Marina; Mosconi, Maria Cristina; Mattiolo, Giuseppina; Cavallina, Roberta

2014-01-01

Irradiation is a preservation technology used to improve the safety and hygienic quality of food. Aim of this study was to assess the applicability and validity of the microbiological screening method direct epifluorescence filter technique (DEFT)/aerobic plate count (APC) (EN 13783:2001) for the identification of irradiated herbs and spices. Tests on non-irradiated and irradiated samples of dried herbs and spices were performed. The method was based on the comparison of APC and count obtained using DEFT. In accordance with the standard reference, this method is not applicable to samples with APC<103 colony forming units (CFU)/g and this is its main limit. The results obtained in our laboratories showed that in 50% of cases of non-irradiated samples and in 96% of the samples treated with ionising radiation, the method was not applicable due to a value of CFU/g <103. PMID:27800348

[Microbiological verification of a self control plan for a hospital food service].

PubMed

Torre, I; Pennino, F; Crispino, M

2006-01-01

During the past years, it has been an increment of food related infectious diseases. In order to avoid micro biological food contamination, adherence to good manufacturing is required through control measures of food safety practices. Updated national and European regulations underline the need to apply the HACCP system, overcoming the old concept of sample control on the end user product. This work shows results of microbiological controls made along the whole productive chain. Measurements are made using biomolecular techniques (PFGE) in order to assess the management of the micro biological risk of the self control plan applied to a hospital food service of Naples. The use of the PFGE applied on some micro-organisms gram negative potentially pathogen, underlines the circulation, continued in time, of these micro-organisms within the cooking area. In addition, cross contamination between several matrixes of samples has been detected.

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.

[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.

Prevalence of Legionella spp. in water systems of hospitals and hotels in South Western Greece.

PubMed

Fragou, K; Kokkinos, P; Gogos, C; Alamanos, Y; Vantarakis, A

2012-01-01

The aim of the present study was to determine the prevalence of Legionella spp. in water systems of hospitals and hotels located in South Western Greece, to study the molecular epidemiology of the isolated strains and their possible association with bacterial contamination (total count and Pseudomonas aeruginosa), the water pH, and temperature. A prevalence survey for Legionella spp. by culturing techniques in water distribution systems of eight hospitals and nine hotels occurred in South Western Greece. Water sampling and microbiological analysis were carried out following the ISO methods. Legionella pneumophila was detected in 33% and 36% of the distribution systems of hospitals and hotels, respectively. Our survey results suggest a frequent prevalence of elevated concentrations of Legionella spp. in water systems of hospitals and hotels. Our investigation has confirmed the need to regularly monitor the microbiological condition of water systems in hospitals and hotels.

Microbiological investigations on the water of a thermal bath at Budapest.

PubMed

Szuróczki, Sára; Kéki, Zsuzsa; Káli, Szandra; Lippai, Anett; Márialigeti, Károly; Tóth, Erika

2016-06-01

Thermal baths are unique aquatic environments combining a wide variety of natural and anthropogenic ecological factors, which also appear in their microbiological state. There is limited information on the microbiology of thermal baths in their complexity, tracking community shifts from the thermal wells to the pools. In the present study, the natural microbial community of well and pool waters in Gellért bath was studied in detail by cultivation-based techniques. To isolate bacteria, 10% R2A and minimal synthetic media (with "bath water") with agar-agar and gellan gum were used after prolonged incubation time; moreover, polyurethane blocks covered with media were also applied. Strains were identified by sequencing their 16S rRNA gene after grouping them by amplified rDNA restriction analysis. From each sample, the dominance of Alphaproteobacteria was characteristic though their diversity differed among samples. Members of Actinobacteria, Firmicutes, Beta- and Gamma-proteobacteria, Deinococcus-Thermus, and Bacteroidetes were also identified. Representatives of Deinococcus-Thermus phylum appeared only in the pool water. The largest groups in the pool water belonged to the Tistrella and Chelatococcus genera. The most dominant member in the well water was a new taxon, its similarity to Hartmannibacter diazotrophicus as closest relative was 93.93%.

[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.

Pulmonary infections in critical/intensive care - rapid diagnosis and optimizing antimicrobial usage.

PubMed

Douglas, Ivor S

2017-05-01

Diagnosis of pulmonary infection, including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) in the critically ill patient remains a common and therapeutically challenging diagnosis with significant attributable morbidity, mortality, and cost. Current clinical approaches to surveillance, early detection and, conventional culture-based microbiology are inadequate for optimal targeted antibiotic treatment and stewardship. Efforts to enhance diagnosis of HAP and VAP and the impact of these novel approaches on rational antimicrobial selection and stewardship are the focus of recent studies reviewed here. Recent consensus guidelines for diagnosis and management of HAP and VAP are relatively silent on the potential role of novel rapid microbiological techniques and reply heavily on conventional culture strategies of noninvasively obtained (including endotracheal aspirate samples). Novel rapid microbiological diagnostics, including nucleic acid amplification, mass spectrometry, and fluorescence microscopy-based technologies are promising approaches for the future. Exhaled breath biomarkers, including measurement of VOC represent a future approach. Further validation of novel diagnostic technology platforms will be required to evaluate their utility for enhancing diagnosis and guiding treatment of pulmonary infections in the critically ill. However, the integration of novel diagnostics for rapid microbial identification, resistance phenotyping, and antibiotic sensitivity testing into usual care practice could significantly transform the care of patients and potentially inform improved targeted antimicrobial selection, de-escalation, and stewardship.

[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.

Surgical site infections due to rapidly growing mycobacteria in puducherry, India.

PubMed

Kannaiyan, Kavitha; Ragunathan, Latha; Sakthivel, Sulochana; Sasidar, A R; Muralidaran; Venkatachalam, G K

2015-03-01

Rapidly growing Mycobacteria are increasingly recognized, nowadays as an important pathogen that can cause wide range of clinical syndromes in humans. We herein describe unrelated cases of surgical site infection caused by Rapidly growing Mycobacteria (RGM), seen during a period of 12 months. Nineteen patients underwent operations by different surgical teams located in diverse sections of Tamil Nadu, Pondicherry, Karnataka, India. All patients presented with painful, draining subcutaneous nodules at the infection sites. Purulent material specimens were sent to the microbiology laboratory. Gram stain and Ziehl-Neelsen staining methods were used for direct examination. Culture media included blood agar, chocolate agar, MacConkey agar, Sabourauds agar and Lowenstein-Jensen medium for Mycobacteria. Isolated microorganisms were identified and further tested for antimicrobial susceptibility by standard microbiologic procedures. Mycobacterium fortuitum and M.chelonae were isolated from the purulent drainage obtained from wounds by routine microbiological techniques from all the specimens. All isolates analyzed for antimicrobial susceptibility pattern were sensitive to clarithromycin, linezolid and amikacin but were variable to ciprofloxacin, rifampicin and tobramycin. Our case series highlights that a high level of clinical suspicion should be maintained for patients presenting with protracted soft tissue lesions with a history of trauma or surgery as these infections not only cause physical but also emotional distress that affects both the patients and the surgeon.

Emerging bacterial pathogens: the past and beyond.

PubMed

Vouga, M; Greub, G

2016-01-01

Since the 1950s, medical communities have been facing with emerging and reemerging infectious diseases, and emerging pathogens are now considered to be a major microbiologic public health threat. In this review, we focus on bacterial emerging diseases and explore factors involved in their emergence as well as future challenges. We identified 26 major emerging and reemerging infectious diseases of bacterial origin; most of them originated either from an animal and are considered to be zoonoses or from water sources. Major contributing factors in the emergence of these bacterial infections are: (1) development of new diagnostic tools, such as improvements in culture methods, development of molecular techniques and implementation of mass spectrometry in microbiology; (2) increase in human exposure to bacterial pathogens as a result of sociodemographic and environmental changes; and (3) emergence of more virulent bacterial strains and opportunistic infections, especially affecting immunocompromised populations. A precise definition of their implications in human disease is challenging and requires the comprehensive integration of microbiological, clinical and epidemiologic aspects as well as the use of experimental models. It is now urgent to allocate financial resources to gather international data to provide a better understanding of the clinical relevance of these waterborne and zoonotic emerging diseases. Copyright © 2015. Published by Elsevier Ltd.

Evaluation of fluorescence in situ hybridisation (FISH) for the detection of fungi directly from blood cultures and cerebrospinal fluid from patients with suspected invasive mycoses.

PubMed

Da Silva, Roberto Moreira; Da Silva Neto, João Ricardo; Santos, Carla Silvana; Frickmann, Hagen; Poppert, Sven; Cruz, Kátia Santana; Koshikene, Daniela; De Souza, João Vicente Braga

2015-01-31

The aim of this study was to evaluate the diagnostic performance of in-house FISH (fluorescence in situ hybridisation) procedures for the direct identification of invasive fungal infections in blood cultures and cerebrospinal fluid (CSF) samples and to compare these FISH results with those obtained using traditional microbiological techniques and PCR targeting of the ITS1 region of the rRNA gene. In total, 112 CSF samples and 30 positive blood cultures were investigated by microscopic examination, culture, PCR-RFLP and FISH. The sensitivity of FISH for fungal infections in CSF proved to be slightly better than that of conventional microscopy (India ink) under the experimental conditions, detecting 48 (instead of 46) infections in 112 samples. The discriminatory powers of traditional microbiology, PCR-RFLP and FISH for fungal bloodstream infections were equivalent, with the detection of 14 fungal infections in 30 samples. However, the mean times to diagnosis after the detection of microbial growth by automated blood culture systems were 5 hours, 20 hours and 6 days for FISH, PCR-RFLP and traditional microbiology, respectively. The results demonstrate that FISH is a valuable tool for the identification of invasive mycoses that can be implemented in the diagnostic routine of hospital laboratories.

Salmonella rarely detected in Mississippi coastal waters and sediment.

PubMed

Carr, M R; Wang, S Y; McLean, T I; Flood, C J; Ellender, R D

2010-12-01

Standards for the rapid detection of individual pathogens from environmental samples have not been developed, but in their absence, the use of molecular-based detection methods coupled with traditional microbiology techniques allows for rapid and accurate pathogen detection from environmental waters and sediment. The aim of this research was to combine the use of enrichment with PCR for detection of Salmonella in Mississippi coastal waters and sediment and observe if that presence correlated with levels of enterococci and climatological variables. Salmonella were primarily found in samples that underwent nutrient enrichment and were present more frequently in freshwater than marine waters. Salmonella were detected infrequently in marine and freshwater sediments. There was a significant positive correlation between the presence of detectable Salmonella and the average enterococcal count. An inverse relationship, however, was observed between the frequency of detection and the levels of salinity, turbidity and sunlight exposure. Results from this study indicated the presence of Salmonella in Mississippi coastal waters, and sediments are very low with significant differences between freshwater and marine environments. Using pathogenic and novel nonpathogenic molecular markers, Salmonella do not appear to be a significant pathogenic genus along the Mississippi Coast. © 2010 The Authors. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology.

Raman sorting and identification of single living micro-organisms with optical tweezers

NASA Astrophysics Data System (ADS)

Xie, Changan; Chen, De; Li, Yong-Qing

2005-07-01

We report on a novel technique for sorting and identification of single biological cells and food-borne bacteria based on laser tweezers and Raman spectroscopy (LTRS). With this technique, biological cells of different physiological states in a sample chamber were identified by their Raman spectral signatures and then they were selectively manipulated into a clean collection chamber with optical tweezers through a microchannel. As an example, we sorted the live and dead yeast cells into the collection chamber and validated this with a standard staining technique. We also demonstrated that bacteria existing in spoiled foods could be discriminated from a variety of food particles based on their characteristic Raman spectra and then isolated with laser manipulation. This label-free LTRS sorting technique may find broad applications in microbiology and rapid examination of food-borne diseases.

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

PubMed

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

2014-12-01

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

[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.

How risky are pinholes in gloves? A rational appeal for the integrity of gloves for isolators.

PubMed

Gessler, Angela; Stärk, Alexandra; Sigwarth, Volker; Moirandat, Claude

2011-01-01

Isolators provide a high degree of protection for the product and/or the environment and operators in pharmaceutical production, as well as for analytical and sterility testing. Gloves allow for performing testing and for easy access to the process. Due to their nature-thin plastic, highly flexible-and their risk of puncture or rupture, they are regarded as one of the main potential sources of contamination. Glove integrity testing is therefore a main issue and has been addressed by many regulations such as those imposed by the USP, U.S. Food and Drug Administration, and Pharmaceutical Inspection Convention. This paper presents a short overview of different glove integrity test procedures and their ability to detect leaking gloves. Additionally, extensive microbiological tests have been performed to give more evidence and cross-correlation to physical testing. Most of the physical tests have limitations either in detecting pinholes and/or they are difficult to implement for routine testing. Microbiological tests are only applicable for evaluation and validation purposes, but not for routine testing, because they are time-consuming and do not allow immediate action. Routine visual verification of gloves by trained personnel turns out to be a very reliable technique. Additional microbiological tests supported by microbiological environmental monitoring helped to develop a new concept presented here on how to handle gloves with pinholes. It is proposed not to automatically consider a pinhole in a glove as a breach in isolator integrity, but to consider any action in view of controlling and monitoring the effective bioload on the outside of the gloves. With the combination of semi-automatic physical testing with independent protocol, visual inspection, and control of bioload through microbiological environmental monitoring potential contamination, risks can be minimized and maximum safety maintained. Isolators are enclosure designs to protect critical handling and process steps in pharmaceutical environments. They provide a high degree of protection for product and/or environment and operators against particles, potentially hazardous active principles, and microbial load. Gloves mounted on windows and doors of the isolator allow for manipulation, performing testing, and access to the process. Due to their nature and their use with risk of puncture or rupture, they are regarded as a potential source for contamination. Glove integrity testing has therefor been addressed by regulations such as those imposed by the USP and the Food and Drug Administration. This paper presents a short overview of various glove integrity test procedures and their ability to detect leaking gloves. Most of the tests have limitations either in detecting pinholes and/or they are difficult to implement for routine testing. Routine visual verification of gloves by trained personnel turns out to be a very reliable technique. Additional microbiological tests led to a new concept presented here on how to handle gloves with pinholes and how to take action. With this approach, risks can be minimized and maximum safety maintained by controlling and monitoring the effective bioload on the outside of the gloves.

[Chronic postoperative endophthalmitis caused by Propionibacterium acnes].

PubMed

Kocur, I; Baráková, D; Kuchynka, P; Fiser, I

1998-07-01

There is a report of three cases of chronic postoperative endophthalmitis following cataract operations. In two patients there was proven Propionibacterium acnes. There is presented a technique to obtain specimens for microbiological examination and an overview of clinical experience in treatment of the mentioned less common types of endophthalmitis. Early surgical treatment as well as intraocular injection of vancomycin can help to restore a good visual acuity despite of longlasting inflammation.

The Majority of US Combat Casualty Soft-Tissue Wounds are not Infected or Colonized Upon Arrival or during Treatment at a Continental US Military Medical Facility

DTIC Science & Technology

2010-01-01

comparison in chronic wounds. Ostomy Wound Manage 2001;47:34-7. 8. Pallua N, Fuchs PC. Hafemann B, et al. A new technique for quanti- tative bacterial...chronic wounds. Ostomy Wound Manage 1997;43:20-30. 10. Steer JA, Papini RPG, Wilson APR, et al. Quantitative microbiology in the management of bum

The study of marine corrosion of copper alloys in chlorinated condenser cooling circuits: the role of microbiological components.

PubMed

Carvalho, Maria L; Doma, Jemimah; Sztyler, Magdalena; Beech, Iwona; Cristiani, Pierangela

2014-06-01

The present paper reports the on-line monitoring of corrosion behavior of the CuNi 70:30 and Al brass alloys exposed to seawater and complementary offline microbiological analyses. An electrochemical equipment with sensors specifically set for industrial application and suitable to estimate the corrosion (by linear polarization resistance technique), the biofilm growth (by the BIOX electrochemical probe), the chlorination treatment and other physical-chemical parameters of the water has been used for the on-line monitoring. In order to identify and better characterize the bacteria community present on copper alloys, tube samples were collected after a long period (1year) and short period (2days) of exposition to treated natural seawater (TNSW) and natural seawater (NSW). From the collected samples, molecular techniques such as DNA extraction, polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE) and identification by sequencing were performed to better characterize and identify the microbial biodiversity present in the samples. The monitoring data confirmed the significant role played by biofouling deposition against the passivity of these Cu alloys in seawater and the positive influence of antifouling treatments based on low level dosages. Molecular analysis indicated biodiversity with the presence of Marinobacter, Alteromonas and Pseudomonas species. Copyright © 2013 Elsevier B.V. All rights reserved.

Bleeding Efficiency, Microbiological Quality and Oxidative Stability of Meat from Goats Subjected to Slaughter without Stunning in Comparison with Different Methods of Pre-Slaughter Electrical Stunning

PubMed Central

Sabow, Azad Behnan; Zulkifli, Idrus; Goh, Yong Meng; Ab Kadir, Mohd Zainal Abidin; Kaka, Ubedullah; Imlan, Jurhamid Columbres; Abubakar, Ahmed Abubakar; Adeyemi, Kazeem Dauda; Sazili, Awis Qurni

2016-01-01

The influence of pre-slaughter electrical stunning techniques and slaughter without stunning on bleeding efficiency and shelf life of chevon during a 14 d postmortem aging were assessed. Thirty two Boer crossbred bucks were randomly assigned to four slaughtering techniques viz slaughter without stunning (SWS), low frequency head-only electrical stunning (LFHO; 1 A for 3 s at a frequency of 50 Hz), low frequency head-to-back electrical stunning (LFHB; 1 A for 3 s at a frequency of 50 Hz) and high frequency head-to-back electrical stunning (HFHB; 1 A for 3 s at a frequency of 850 Hz). The SWS, LFHO and HFHB goats had higher (p<0.05) blood loss and lower residual hemoglobin in muscle compared to LFHB. The LFHB meat had higher (p<0.05) TBARS value than other treatments on d 7 and 14 d postmortem. Slaughtering methods had no effect on protein oxidation. Higher bacterial counts were observed in LFHB meat compared to those from SWS, LFHO and HFHB after 3 d postmortem. Results indicate that the low bleed-out in LFHB lowered the lipid oxidative stability and microbiological quality of chevon during aging. PMID:27035716

Bleeding Efficiency, Microbiological Quality and Oxidative Stability of Meat from Goats Subjected to Slaughter without Stunning in Comparison with Different Methods of Pre-Slaughter Electrical Stunning.

PubMed

Sabow, Azad Behnan; Zulkifli, Idrus; Goh, Yong Meng; Ab Kadir, Mohd Zainal Abidin; Kaka, Ubedullah; Imlan, Jurhamid Columbres; Abubakar, Ahmed Abubakar; Adeyemi, Kazeem Dauda; Sazili, Awis Qurni

2016-01-01

The influence of pre-slaughter electrical stunning techniques and slaughter without stunning on bleeding efficiency and shelf life of chevon during a 14 d postmortem aging were assessed. Thirty two Boer crossbred bucks were randomly assigned to four slaughtering techniques viz slaughter without stunning (SWS), low frequency head-only electrical stunning (LFHO; 1 A for 3 s at a frequency of 50 Hz), low frequency head-to-back electrical stunning (LFHB; 1 A for 3 s at a frequency of 50 Hz) and high frequency head-to-back electrical stunning (HFHB; 1 A for 3 s at a frequency of 850 Hz). The SWS, LFHO and HFHB goats had higher (p<0.05) blood loss and lower residual hemoglobin in muscle compared to LFHB. The LFHB meat had higher (p<0.05) TBARS value than other treatments on d 7 and 14 d postmortem. Slaughtering methods had no effect on protein oxidation. Higher bacterial counts were observed in LFHB meat compared to those from SWS, LFHO and HFHB after 3 d postmortem. Results indicate that the low bleed-out in LFHB lowered the lipid oxidative stability and microbiological quality of chevon during aging.

Risk factors and biofilm detection on central venous catheters of patients attended at tertiary hospital.

PubMed

Pérez-Zárate, Pamela; Aragón-Piña, Antonio; Soria-Guerra, Ruth Elena; González-Amaro, Ana María; Pérez-Urizar, José; Pérez-González, Luis Fernando; Martinez-Gutierrez, Fidel

2015-11-01

To determinate the significance of risk factors with the presence of biofilm on catheters of patients attended at tertiary hospital cares. A total of 126 patients were included, data collection by observing the handling of the CVC, clinical history and microbiological isolation methods of CVCs tips (Roll-plate, sonication and scanning electron microscopy) were evaluated. Certain factors, such as the lack of proper hand washing, the use of primary barriers and preparing medications in the same hospital service, showed an important relationship between biofilm formation in CVCs. The sonication method presented that most of the samples had isolation of multispecies 29 samples (64%); in contrast with the roll-plate method, just one sample (3%) was isolated. The importance of the strict aseptic techniques of insertion and of the handlings of CVC was highlighted, the failure of both techniques was related to the biofilm formation and was evidenced using the scanning electron microscopy. Since this tool is not available in most hospitals, we present the correlation of those evidences with other standard microbiological methods and risk factors, which are necessary for the sensible detection of the different steps of the biofilm formation on CVC and their correct interpretation with clinical evidences. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Microbiological Surveillance of Measles and Rubella in Spain. Laboratory Network].

PubMed

Echevarría, Juan Emilio; Fernández García, Aurora; de Ory, Fernando

2015-01-01

The Laboratory is a fundamental component on the surveillance of measles and rubella. Cases need to be properly confirmed to ensure an accurate estimation of the incidence. Strains should be genetically characterized to know the transmission pattern of these viruses and frequently, outbreaks and transmission chains can be totally discriminated only after that. Finally, the susceptibility of the population is estimated on the basis of sero-prevalence surveys. Detection of specific IgM response is the base of the laboratory diagnosis of these diseases. It should be completed with genomic detection by RT-PCR to reach an optimal efficiency, especially when sampling is performed early in the course of the disease. Genotyping is performed by genomic sequencing according to reference protocols of the WHO. Laboratory surveillance of measles and rubella in Spain is organized as a net of regional laboratories with different capabilities. The National Center of Microbiology as National Reference Laboratory (NRL), supports regional laboratories ensuring the availability of all required techniques in the whole country and watching for the quality of the results. The NRL is currently working in the implementation of new molecular techniques based on the analysis of genomic hypervariable regions for the strain characterization at sub-genotypic levels and use them in the surveillance.

Improving industrial yeast strains: exploiting natural and artificial diversity.

PubMed

Steensels, Jan; Snoek, Tim; Meersman, Esther; Picca Nicolino, Martina; Voordeckers, Karin; Verstrepen, Kevin J

2014-09-01

Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity. © 2014 The Authors. FEMS Microbiology Reviews published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.

Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM).

PubMed

Behrens, Sebastian; Kappler, Andreas; Obst, Martin

2012-11-01

Environmental microbiology research increasingly focuses on the single microbial cell as the defining entity that drives environmental processes. The interactions of individual microbial cells with each other, the environment and with higher organisms shape microbial communities and control the functioning of whole ecosystems. A single-cell view of microorganisms in their natural environment requires analytical tools that measure both cell function and chemical speciation at the submicrometre scale. Here we review the technical capabilities and limitations of high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission (soft) X-ray microscopy (STXM) and give examples of their applications. Whereas NanoSIMS can be combined with isotope-labelling, thereby localizing the distribution of cellular activities (e.g. carbon/nitrogen fixation/turnover), STXM provides information on the location and chemical speciation of metabolites and products of redox reactions. We propose the combined use of both techniques and discuss the technical challenges of their joint application. Both techniques have the potential to enhance our understanding of cellular mechanisms and activities that contribute to microbially mediated processes, such as the biogeochemical cycling of elements, the transformation of contaminants and the precipitation of mineral phases. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Molecular identification of black-pigmented bacteria from subgingival samples of cats suffering from periodontal disease.

PubMed

Pérez-Salcedo, L; Laguna, E; Sánchez, M C; Marín, M J; O'Connor, A; González, I; Sanz, M; Herrera, D

2015-04-01

To characterise the black-pigmented bacterial species found in the subgingival samples of cats with periodontal disease using molecular-based microbiological techniques. Sixty-five subgingival samples obtained from 50 cats with periodontal disease were analysed by polymerase chain reaction amplified ribosomal DNA restriction analysis and cloning and sequencing of the 16S rRNA genes. Among the 65 subgingival samples, eight phylogenetic profiles were obtained, of which the most prevalent species were: Porphyromonas gulae (40%), P. gingivalis/P. gulae (36 · 9%), P. gulae/Porphyromonas sp. UQD 406 (9 · 2%), Odoribacter denticanis (6 · 2%), P. gulae/Porphyromonas sp. UQD 348 (1 · 5%) and P. circumdentaria (1 · 5%). When compared with the species resulting from biochemical diagnosis, the identification of P. gulae was congruent in 70% of the cases, while colonies identified as P. intermedia-like corresponded in 80% of cases to P. gulae. The use of molecular-based microbiological diagnostic techniques resulted in a predominance of Porphyromonas spp. in the subgingival plaque of cats suffering from periodontal disease. Further characterisation of these bacteria identified P. gulae, O. denticanis and P. circumdentaria. The more frequently detected phylogenetic profiles corresponded to P. gingivalis and P. gulae. © 2015 British Small Animal Veterinary Association.

Uncharted Microbial World: Microbes and Their Activities in the Environment

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

Harwood, Caroline; Buckley, Merry

Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymiedmore » many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable systems with features like clear physical boundaries, limited microbial diversity, and manipulability with the goal of understanding fundamental principles that may apply to more complex systems. A great deal of microbial genetic and phenotypic diversity remains to be explored, and the commercial and medical potential locked up in these unknowns should compel the field to move forward. Future microbiology research will build on the successes of the past using new techniques and approaches. Uncultivated microbes hold great promise for industry, medicine, and the recycling of precious resources, and research and technology must make inroads in overcoming the barriers that prevent their study. In many cases, we will no longer be able to rely on isolated, pure cultures of microorganisms, but must use communities of microorganisms, which presently are poorly understood. Indeed, community-level studies can benefit from deconstructing microbial communities and analyzing the component members separately, but this is not feasible in every system. The effects of perturbation on microbial communities also require study. Humans rely on the services of microbes in innumerable ways, but we have little or no predictive understanding of how microbial communities respond to disturbance. Research must address current limitations in detecting microscale interactions among microbes by enhancing current technologies and fostering new microscopic tools, biosensors, and gas sensors for appropriate small scales. Genomics, which has enabled great progress in microbiology research of individual species, must be applied to communities of microorganisms. This will require improved methods of DNA extraction and amplification from environmental samples and improved strategies for DNA sequence assembly. In the future, genome sequencing efforts should continue the exploration of evolutionarily diverse microbes, as well as help reveal the mechanisms by which closely related microbes evolve. Technological advances have spurred every great leap in microbial biology, and in order to move forward, new methods for revealing the activities of microorganisms must be continually developed. Today, researchers need access to better techniques for enriching and isolating novel microorganisms, particularly approaches that enable them to mimic the low nutrient conditions to which many environmental microbes are adapted. Other outstanding needs include methods for performing in situ work and bioinformatics tools. Finally, there are several ways that training and education in microbiology are failing to adequately prepare the next generation of scientists for the challenges ahead. Training in some of the long-established disciplines, including enrichment and isolation, physiology, enzymology, and biochemistry, needs to be revitalized.« less

Free-standing few-layered graphene oxide films: selective, steady and lasting permeation of organic molecules with adjustable speeds

NASA Astrophysics Data System (ADS)

Huang, Tao; An, Qi; Luan, Xinglong; Zhang, Qian; Zhang, Yihe

2016-01-01

A variety of small molecules with diameters around 1 nm possess a range of functions, such as antibiotic, antimicrobic, anticoagulant, pesticidal and chemotherapy effects, making these molecules especially useful in various applications ranging from medical treatment to environmental microbiological control. However, the long-term steady delivery (release or permeation) of these small molecules with adjustable and controllable speeds has remained an especially challenging task. In this study, we prepared covalently cross-linked free-standing few-layered GO films using a layer-by-layer technique in combination with photochemical cross-linkages, and achieved a controlled release of positively charged, negatively charged, and zwitterionic small molecules with adjustable and controllable speeds. The steady delivery of the small molecule lasted up to 9 days. Other functionalities, such as graphene-enhanced Raman spectra and electrochemical properties that could also be integrated or employed in delivery systems, were also studied for our films. We expect the special molecular delivery properties of our films to lead to new possibilities in drug/fertilizer delivery and environmental microbiological control applications.A variety of small molecules with diameters around 1 nm possess a range of functions, such as antibiotic, antimicrobic, anticoagulant, pesticidal and chemotherapy effects, making these molecules especially useful in various applications ranging from medical treatment to environmental microbiological control. However, the long-term steady delivery (release or permeation) of these small molecules with adjustable and controllable speeds has remained an especially challenging task. In this study, we prepared covalently cross-linked free-standing few-layered GO films using a layer-by-layer technique in combination with photochemical cross-linkages, and achieved a controlled release of positively charged, negatively charged, and zwitterionic small molecules with adjustable and controllable speeds. The steady delivery of the small molecule lasted up to 9 days. Other functionalities, such as graphene-enhanced Raman spectra and electrochemical properties that could also be integrated or employed in delivery systems, were also studied for our films. We expect the special molecular delivery properties of our films to lead to new possibilities in drug/fertilizer delivery and environmental microbiological control applications. Electronic supplementary information (ESI) available: AFM images of GO and GO films, UV-vis spectra of delayed release, and permeation fidelities. See DOI: 10.1039/c5nr08129g

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

PubMed

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

2018-05-01

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

Consensus of microbiology reporting of ear swab results to primary care clinicians in patients with otitis externa.

PubMed

Geyer, M; Howell-Jones, R; Cunningham, R; McNulty, C

2011-01-01

Otitis externa is a ubiquitous inflammatory disease; although it arises most commonly from an infection, there is no consensus in the UK for the reporting of ear swab culture results. This study aims to review current microbiology laboratory reporting of ear swab specimens to primary care and reach an evidence-based consensus for a reporting policy. Fifty consecutive ear swab reports were reviewed from each of 12 laboratories in the South West region to determine and discuss reporting practice. The Health Protection Agency (HPA) GP Microbiology Laboratory Use Group reviewed the underlying evidence and worked towards a consensus of expert microbiology opinion for laboratory reporting of ear swab results using a modified version of the Delphi technique. A total of 487 reports from primary care were reviewed (54% female; 46% male). Cultures most commonly yielded Pseudomonas species (36%), Staphylococcus species (21%), Streptococcus species (15%) and fungi (11%). Five reporting policies were agreed: Policy 1: Common pathogens such as group A beta-haemolytic streptococci, Streptococcus pneumoniae, Staphylococcus aureus - Always reported by name with antibiotic susceptibilities. Policy 2: Pseudomonas species - Always reported, but antibiotic susceptibilities only reported in severe disease. Policy 3: Aspergillus, Candida, coliforms and Proteus species, as well as non-group A streptococci and anaerobes - Only reported if moderate numbers of colonies and it is the predominant organism present; if appropriate report antibiotic susceptibilities. Policy 4: Coagulase-negative staphylococci, diphtheroids and enterococci - Not reported by name; generic terms used and antibiotic susceptibilities not reported. Policy 5: When antibiotic susceptibilities reported these must include susceptibility to a topical antibiotic. It is suggested that laboratories should consider adopting this evidence-based reporting consensus for ear swab culture results from primary care patients with otitis externa.

Recovery of hygiene water by multifiltration. [in space shuttle orbiters

NASA Technical Reports Server (NTRS)

Putnam, David F.; Jolly, Clifford D.; Colombo, Gerald V.; Price, Don

1989-01-01

A multifiltration hygiene water reclamation process that utilizes adsorption and particulate filtration techniques is described and evaluated. The applicability of the process is tested using a simulation of a 4-man subsystem operation for 240 days. It is proposed the process has a 10 year life, weighs 236 kg, and uses 88 kg of expendable filters and adsorption beds to process 8424 kg of water. The data reveal that the multifiltration is an efficient nonphase change technique for hygiene water recovery and that the chemical and microbiological purity of the product water is within the standards specified for the Space Station hygiene water.

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...

Microbial Cell Imaging

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

Doktycz, Mitchel John; Sullivan, Claretta; Mortensen, Ninell P

Atomic force microscopy (AFM) is finding increasing application in a variety of fields including microbiology. Until the emergence of AFM, techniques for ivnestigating processes in single microbes were limited. From a biologist's perspective, the fact that AFM can be used to generate high-resolution images in buffers or media is its most appealing feature as live-cell imaging can be pursued. Imaging living cells by AFM allows dynamic biological events to be studied, at the nanoscale, in real time. Few areas of biological research have as much to gain as microbiology from the application of AFM. Whereas the scale of microbes placesmore » them near the limit of resolution for light microscopy. AFM is well suited for the study of structures on the order of a micron or less. Although electron microscopy techniques have been the standard for high-resolution imaging of microbes, AFM is quickly gaining favor for several reasons. First, fixatives that impair biological activity are not required. Second, AFM is capable of detecting forces in the pN range, and precise control of the force applied to the cantilever can be maintained. This combination facilitates the evaluation of physical characteristics of microbes. Third, rather than yielding the composite, statistical average of cell populations, as is the case with many biochemical assays, the behavior of single cells can be monitored. Despite the potential of AFM in microbiology, there are several limitations that must be considered. For example, the time required to record an image allows for the study of gross events such as cell division or membrane degradation from an antibiotic but precludes the evaluation of biological reactions and events that happen in just fractions of a second. Additionally, the AFM is a topographical tool and is restricted to imaging surfaces. Therefore, it cannot be used to look inside cells as with opticla and transmission electron microscopes. other practical considerations are the limitation on the maximum scan size (roughly 100 x 100 {mu}m) and the restricted movement of the cantilever in the Z (or height) direction. In most commercial AFMs, the Z range is restricted to roughly 10 {mu}m such that the height of cells to be imaged must be seriously considered. Nevertheless, AFM can provide structural-functional information at nanometer resolution and do so in physiologically relevant environments. Further, instrumentation for scanning probe microscopy continues to advance. Systems for high-speed imaging are becoming available, and techniques for looking inside the cells are being demonstrated. The ability to combine AFM with other imaging modalities is likely to have an even greater impact on microbiological studies. AFM studies of intact microbial cells started to appear in the literature in the 1990s. For example, AFM studies of Saccharomyces cerevisiae examined buddings cars after cell division and detailed changes related to cell growth processes. Also, the first AFM studies of bacterial biofilms appeared. In the late 1990s, AFM studies of intact fungal spores described clear changes in spore surfaces upon germination, and studies of individual bacterial cells were also described. These early bacterial imaging studies examined changes in bacterial morphology due to antimicrobial peptides exposure and bacterial adhesion properties. The majority of these early studies were carried out on dried samples and took advantage of the resolving power of AFM. The lack of cell mounting procedures presented an impediment for cell imaging studies. Subsequently, several approaches to mounting microbial cells have been developed, and these techniques are described later. Also highlighted are general considerations for microbial imaging and a description of some of the various applications of AFM to microbiology.« less

Methods for understanding microbial community structures and functions in microbial fuel cells: a review.

PubMed

Zhi, Wei; Ge, Zheng; He, Zhen; Zhang, Husen

2014-11-01

Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output. Copyright © 2014 Elsevier Ltd. All rights reserved.

Food Safety Evaluation Based on Near Infrared Spectroscopy and Imaging: A Review.

PubMed

Fu, Xiaping; Ying, Yibin

2016-08-17

In recent years, due to the increasing consciousness of food safety and human health, much progress has been made in developing rapid and nondestructive techniques for the evaluation of food hazards, food authentication, and traceability. Near infrared (NIR) spectroscopy and imaging techniques have gained wide acceptance in many fields because of their advantages over other analytical techniques. Following a brief introduction of NIR spectroscopy and imaging basics, this review mainly focuses on recent NIR spectroscopy and imaging applications for food safety evaluation, including (1) chemical hazards detection; (2) microbiological hazards detection; (3) physical hazards detection; (4) new technology-induced food safety concerns; and (5) food traceability. The review shows NIR spectroscopy and imaging to be effective tools that will play indispensable roles for food safety evaluation. In addition, on-line/real-time applications of these techniques promise to be a huge growth field in the near future.

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 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.

Development of a micromanipulation method for single cell isolation of prokaryotes and its application in food safety.

PubMed

Hohnadel, Marisa; Maumy, Myriam; Chollet, Renaud

2018-01-01

For nearly a century, conventional microbiological methods have been standard practice for detecting and identifying pathogens in food. Nevertheless, the microbiological safety of food has improved and various rapid methods have been developed to overcome the limitations of conventional methods. Alternative methods are expected to detect low cell numbers, since the presence in food of even a single cell of a pathogenic organism may be infectious. With respect to low population levels, the performance of a detection method is assessed by producing serial dilutions of a pure bacterial suspension to inoculate representative food matrices with highly diluted bacterial cells (fewer than 10 CFU/ml). The accuracy of data obtained by multiple dilution techniques is not certain and does not exclude some colonies arising from clumps of cells. Micromanipulation techniques to capture and isolate single cells from environmental samples were introduced more than 40 years ago. The main limitation of the current micromanipulation technique is still the low recovery rate for the growth of a single cell in culture medium. In this study, we describe a new single cell isolation method and demonstrate that it can be used successfully to grow various types of microorganism from picked individual cells. Tests with Gram-positive and Gram-negative organisms, including cocci, rods, aerobes, anaerobes, yeasts and molds showed growth recovery rates from 60% to 100% after micromanipulation. We also highlight the use of our method to evaluate and challenge the detection limits of standard detection methods in food samples contaminated by a single cell of Salmonella enterica.

A Calorimeter Design for Rapidly Estimating the Level of Foodborne Microorganisms

DTIC Science & Technology

1975-12-01

of control, could produce a severe public health crisis and impair troop efficiency. Rapid microbiological quality measuring techniques are urgently...would more effectively use the volume of the calorimeter sample chamber. Then we could increase the volume, make it easy to add the growth medium and...from this paper are also represented in Table III. His results were criticized by Forest & Walker (1962P who claimed that the effect observed was due

Surface Analytical Techniques for Microbiologically Influenced Corrosion. A Review

DTIC Science & Technology

1994-01-01

chemical process, oil and gas. and power generation industries and the U.S. pitting of stainle steels is 1h military have acknowledged the occurrence...ony on metal surface. photosynthetic biofilm may influence ennoblement of the open circuit potential of type 316L stainless steel so that it approaches...at depths within an estuarine biofilm on type 304 stainless steel . fur-oxidizing. iron-red ing. sulfate- -producing, and hydr en-producing b

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

PubMed

Shintani, Hideharu

2016-01-01

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

Microbiology of animal bite wound infections.

PubMed

Abrahamian, Fredrick M; Goldstein, Ellie J C

2011-04-01

The microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. Bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. Bacteria may also originate from the victim's own skin or the physical environment at the time of injury. Our review has focused on bite wound infections in humans from dogs, cats, and a variety of other animals such as monkeys, bears, pigs, ferrets, horses, sheep, Tasmanian devils, snakes, Komodo dragons, monitor lizards, iguanas, alligators/crocodiles, rats, guinea pigs, hamsters, prairie dogs, swans, and sharks. The medical literature in this area has been made up mostly of small case series or case reports. Very few studies have been systematic and are often limited to dog or cat bite injuries. Limitations of studies include a lack of established or inconsistent criteria for an infected wound and a failure to utilize optimal techniques in pathogen isolation, especially for anaerobic organisms. There is also a lack of an understanding of the pathogenic significance of all cultured organisms. Gathering information and conducting research in a more systematic and methodical fashion through an organized research network, including zoos, veterinary practices, and rural clinics and hospitals, are needed to better define the microbiology of animal bite wound infections in humans.

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.

Microbiology of Animal Bite Wound Infections

PubMed Central

Abrahamian, Fredrick M.; Goldstein, Ellie J. C.

2011-01-01

Summary: The microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. Bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. Bacteria may also originate from the victim's own skin or the physical environment at the time of injury. Our review has focused on bite wound infections in humans from dogs, cats, and a variety of other animals such as monkeys, bears, pigs, ferrets, horses, sheep, Tasmanian devils, snakes, Komodo dragons, monitor lizards, iguanas, alligators/crocodiles, rats, guinea pigs, hamsters, prairie dogs, swans, and sharks. The medical literature in this area has been made up mostly of small case series or case reports. Very few studies have been systematic and are often limited to dog or cat bite injuries. Limitations of studies include a lack of established or inconsistent criteria for an infected wound and a failure to utilize optimal techniques in pathogen isolation, especially for anaerobic organisms. There is also a lack of an understanding of the pathogenic significance of all cultured organisms. Gathering information and conducting research in a more systematic and methodical fashion through an organized research network, including zoos, veterinary practices, and rural clinics and hospitals, are needed to better define the microbiology of animal bite wound infections in humans. PMID:21482724

Detection of intracellular bacteria in exfoliated urothelial cells from women with urge incontinence.

PubMed

Cheng, Ying; Chen, Zhuoran; Gawthorne, Jayde A; Mukerjee, Chinmoy; Varettas, Kerry; Mansfield, Kylie J; Schembri, Mark A; Moore, Kate H

2016-10-01

The role of subclinical infection in patients with urge incontinence has been largely ignored. The aim of this study was to test for the presence of intracellular bacteria in exfoliated urothelial cells obtained from the urine of patients with detrusor overactivity or mixed incontinence +/- a history of UTI, and compare this to a control group of patients with stress incontinence and no history of infection. Bacterial cystitis was assessed by routine microbiology and compared to microscopic analysis of urine by Wright staining. Subsequent analysis of urothelial cells by confocal microscopy was performed to determine the existence of intracellular bacteria. Bacterial cystitis was seen in 13% of patients based on routine microbiology. Wright staining of concentrated urothelial cells demonstrated the presence of bacteria in 72% of samples. Filamentous bacterial cells were observed in 51% of patients and were significantly more common in patients with detrusor overactivity. Intracellular Escherichia coli were observed by confocal microscopy. This study supports the possibility that a subset of patients with urge incontinence may have unrecognised chronic bacterial colonisation, maintained via an intracellular reservoir. In patients with negative routine microbiology, application of the techniques used in this study revealed evidence of infection, providing further insights into the aetiology of urge incontinence. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

[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.

[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.

Microbiology Education in Nursing Practice.

PubMed

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

2017-01-01

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

Microbiology Education in Nursing Practice†

PubMed Central

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

2017-01-01

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

Application of polymerase chain reaction for detection of Vibrio parahaemolyticus associated with tropical seafoods and coastal environment.

PubMed

Dileep, V; Kumar, H S; Kumar, Y; Nishibuchi, M; Karunasagar, Indrani; Karunasagar, Iddya

2003-01-01

To study the incidence of Vibrio parahaemolyticus in seafoods, water and sediment by molecular techniques vs conventional microbiological methods. Of 86 samples analysed, 28 recorded positive for V. parahaemolyticus by conventional microbiological method, while 53 were positive by the toxR-targeted PCR, performed directly on enrichment broth lysates. While one sample of molluscan shellfish was positive for tdh gene, trh gene was detected in three enrichment broths of molluscan shellfish. Direct application of PCR to enrichment broths will be useful for the rapid and sensitive detection of potentially pathogenic strains of V. parahemolyticus in seafoods. Vibrio parahaemolyticus is an important human pathogen responsible for food-borne gastroenteritis world-wide. As, both pathogenic and non-pathogenic strains of V. parahaemolyticus exist in the seafood, application of PCR specific for the virulence genes (tdh & trh) will help in detection of pathogenic strains of V. parahaemolyticus and consequently reduce the risk of food-borne illness.

Microbiological levels of randomly selected food contact surfaces in hotels located in Spain during 2007-2009.

PubMed

Doménech-Sánchez, Antonio; Laso, Elena; Pérez, María José; Berrocal, Clara Isabel

2011-09-01

The aim of this study was to survey the microbial levels of food contact surfaces in hotels. Microbiological levels of 4611 surfaces (chopping machines, kitchenware, knives, worktops, and cutting boards) from 280 different facilities in Spain were determined in a 3-year period. The contact-plate technique was used throughout the survey. Overall, the mean of the log of total aerobic count cm(-2) was 0.62, better than those reported for child-care and assisted living facilities. Significant differences were detected among different types of surfaces, time of sampling, season, and year. The majority (74%) of food contact surfaces sampled in Spanish hotels was within the recommended standard of <1.3 log CFU cm(-2), and differences depend on several factors. Our results set a representative picture of the actual situation in our resorts and establish the basis for the development of educational programs to improve food handlers' knowledge of foodborne diseases and their transmission via food contact surfaces.

Construction and evaluation of an online microbiology course for nonscience majors.

PubMed

Hughes, Lee

2008-01-01

The development of web-based technologies provides a new method for course delivery. As with any new technique, evaluation is a necessary tool to determine if the method is consistent with expectations. This study describes the conversion of a nonscience majors' microbiology lecture course to online delivery and evaluates the hypothesis that the online course can be as effective as the traditional course. Course examination scores are compared between the face-to-face and online sections over a 3-year period. On all but one of the course examinations, no significant difference is found for those students in these two distinctly different course types. The success rate, as defined by those students earning grades of C or better, is high for both course types, although the traditional course success rate is slightly higher. Student evaluations of the courses are also positive, though some differences are noted. Overall, student performance in the online course is equivalent to that in the traditional course.

Raman spectroscopic studies on bacteria

NASA Astrophysics Data System (ADS)

Maquelin, Kees; Choo-Smith, Lin-P'ing; Endtz, Hubert P.; Bruining, Hajo A.; Puppels, Gerwin J.

2000-11-01

Routine clinical microbiological identification of pathogenic micro-organisms is largely based on nutritional and biochemical tests. Laboratory results can be presented to a clinician after 2 - 3 days for most clinically relevant micro- organisms. Most of this time is required to obtain pure cultures and enough biomass for the tests to be performed. In the case of severely ill patients, this unavoidable time delay associated with such identification procedures can be fatal. A novel identification method based on confocal Raman microspectroscopy will be presented. With this method it is possible to obtain Raman spectra directly from microbial microcolonies on the solid culture medium, which have developed after only 6 hours of culturing for most commonly encountered organisms. Not only does this technique enable rapid (same day) identifications, but also preserves the sample allowing it to be double-checked with traditional tests. This, combined with the speed and minimal sample handling indicate that confocal Raman microspectroscopy has much potential as a powerful new tool in clinical diagnostic microbiology.

Bromelain, a cysteine protease from pineapple (Ananas comosus) stem, is an inhibitor of fungal plant pathogens.

PubMed

López-García, B; Hernández, M; Segundo, B S

2012-07-01

This study aimed to evaluate the effect of bromelain, a cysteine protease isolated from pineapple (Ananas comosus), on growth of several agronomically important fungal pathogens. Purification of bromelain from pineapple stems was carried out by chromatography techniques, and its antimicrobial activity was tested against the fungal pathogens Fusarium verticillioides, Fusarium oxysporum and Fusarium proliferatum by broth microdilution assay. A concentration of 0.3 μmol l(-1) of bromelain was sufficient for 90% growth inhibition of F. verticillioides. The capability of bromelain to inhibit fungal growth is related to its proteolytic activity. The study demonstrates that stem bromelain exhibits a potent antifungal activity against phytopathogens and suggests its potential use as an effective agent for crop protection. The results support the use of a natural protease that accumulates at high levels in pineapple stems as alternative to the use of chemical fungicides for crop protection. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

Multifrequency impedance measurement technique for wireless characterization of microbiological cell cultures

NASA Astrophysics Data System (ADS)

Wissenwasser, J.; Vellekoop, M. J.; Kapferer, W.; Lepperdinger, G.; Heer, R.

2011-11-01

An impedance measurement system with probe signal frequencies up to 50 kHz with AC-probe voltages below 30 mV rms was integrated for wireless and battery-free monitoring of microbiological cell cultures. The here presented modular design and the use of state-of-the-art components greatly eases adoptions to a wide range of biotechnological applications without the need of bulky LCR-meters or potentiostats. The device had a power consumption of less than 2.5 mA at a 3.3 V single power supply and worked trouble-free within the humid environment of a cell culture incubator. Measurements on lumped RC-elements showed an error of less than 1% for absolute values and less than 1° regarding the phase of the complex impedance. The performance of sensor devices with interdigitated electrode structures for the measurement of adherent cell cultures was tested in the presence of phosphate-buffered saline solution in the humid atmosphere of an incubator for biological cell cultures.

Experimental investigation of microbiologically influenced corrosion of selected steels in sugarcane juice environment.

PubMed

Wesley, Sunil Bala; Maurya, Devendra Prasad; Goyal, Hari Sharan; Negi, Sangeeta

2013-12-01

In the current study, ferritic stainless grades AISI 439 and AISI 444 were investigated as possible construction materials for machinery and equipment in the cane-sugar industry. Their performance in corrosive cane-sugar juice environment was compared with the presently used low carbon steel AISI 1010 and austenitic stainless steel AISI 304. The Tafel plot electrochemical technique was used to evaluate general corrosion performance. Microbiologically influenced corrosion (MIC) behaviour in sugarcane juice environment was studied. Four microbial colonies were isolated from the biofilms on the metal coupon surfaces on the basis of their different morphology. These were characterized as Brevibacillus parabrevis, Bacillus azotoformans, Paenibacillus lautus and Micrococcus sp. The results of SEM micrographs showed that AISI 439 and AISI 304 grades had suffered maximum localized corrosion. MIC investigations revealed that AISI 444 steel had the best corrosion resistance among the tested materials. However from the Tafel plots it was evident that AISI 1010 had the least corrosion resistance and AISI 439 the best corrosion resistance.

Open-source do-it-yourself multi-color fluorescence smartphone microscopy

PubMed Central

Sung, Yulung; Campa, Fernando; Shih, Wei-Chuan

2017-01-01

Fluorescence microscopy is an important technique for cellular and microbiological investigations. Translating this technique onto a smartphone can enable particularly powerful applications such as on-site analysis, on-demand monitoring, and point-of-care diagnostics. Current fluorescence smartphone microscope setups require precise illumination and imaging alignment which altogether limit its broad adoption. We report a multi-color fluorescence smartphone microscope with a single contact lens-like add-on lens and slide-launched total-internal-reflection guided illumination for three common tasks in investigative fluorescence microscopy: autofluorescence, fluorescent stains, and immunofluorescence. The open-source, simple and cost-effective design has the potential for do-it-yourself fluorescence smartphone microscopy. PMID:29188104

Multidisciplinary approach for in-deep assessment of joint prosthesis failure.

PubMed

Tessarolo, F; Caola, I; Piccoli, F; Dorigotti, P; Demattè, E; Molinari, M; Malavolta, M; Barbareschi, M; Caciagli, P; Nollo, G

2009-01-01

In spite of advancement in biomaterials and biomechanics, in development of new osteo-integrative materials and coatings, and in macro- micro- component design, a non negligible fraction of the implanted prosthesis fails before the expected lifetime. A prospective observational clinical study has been conducted to define and apply a set of experimental techniques to in-deep assess the failure of joint prosthesis. Microbiological, histological and micro-structural techniques were implemented to specifically address phenomena occurring at the tissue-implant interface. Results obtained from 27 cases of prosthetic joint failure are discussed in terms of sensitivity and specificity. A procedural flow-chart is finally proposed for the assessment of joint prosthesis failure.

Technology Assessment and Strategy for Development of a Rapid Field Water Microbiology Test Kit

DTIC Science & Technology

1991-09-01

fresh and marine waters (Santiago- Mercado and Hazen 1987; Valdes-Collazo et al. 1987; Perez-Rosas and Hazen 1988; Bermudez and Hazen 1988; Rivera et al...Santiago- Mercado and Hazen 1987; Valdes-Collazo et al. 1987). Investigators are constantly improving the coltform-MF technique as it is the... Mercado and Hazen 1987; Valdes-Collazo et al. 1987; Perez-Rosas and Hazen 1988; Bermudez and Hazen 1988; Rivera et al. 1988). The tropical conditions

A Technical Review of Electrochemical Techniques Applied to Microbiologically Influenced Corrosion

DTIC Science & Technology

1991-01-01

these cases. Additional problems can arise from the effects of the sweep rate which is used to determine R. according to equation (2). If the sweep ...small amplitude cyclic voltametry and ESCA.43 From the frequency dependence of the impedance data it was concluded that two relaxations were associated...the correct sweep rate and the elimination of the ohmic drop during the experiment are important considerations as discussed elsewhere. 5° The use of

Correlation and simple linear regression.

PubMed

Eberly, Lynn E

2007-01-01

This chapter highlights important steps in using correlation and simple linear regression to address scientific questions about the association of two continuous variables with each other. These steps include estimation and inference, assessing model fit, the connection between regression and ANOVA, and study design. Examples in microbiology are used throughout. This chapter provides a framework that is helpful in understanding more complex statistical techniques, such as multiple linear regression, linear mixed effects models, logistic regression, and proportional hazards regression.

Colored cosmetic contact lenses: an unsafe trend in the younger generation.

PubMed

Singh, Shwetambari; Satani, Dipali; Patel, Amit; Vhankade, Ravinder

2012-07-01

To identify the microbiological profile and evaluate the clinical course and outcomes in patients who developed severe infectious keratitis after colored cosmetic contact lens wear. This case series includes 13 patients who developed severe infectious keratitis after colored cosmetic contact lens wear. A detailed history regarding contact lens availability and storage and handling techniques was taken. All patients underwent standard diagnostic microbiological evaluation followed by culture-guided topical antimicrobial therapy. Of 13 patients, 8 were male and 5 were female, with mean age at presentation of 19 ± 3.8 years. All patients were emmetropic, and lenses were worn solely for cosmetic purposes. Seven lenses were dispensed without prescription or fitting from an unlicensed optical shop, 5 patients had shared lenses with friends/relatives, and 1 patient obtained the lens from the garbage. None of the patients followed the recommended contact lens handling and storage techniques. The causative microorganisms included Pseudomonas aeruginosa (54%), Staphylococcus aureus (25%), and Staphylococcus epidermidis (17%), with 1 case of viral keratitis. In 62% of cases, ulcer size was ≥5 × 5 mm and posttreatment corrected visual acuity was 6/24 or less. All patients responded well to topical antimicrobials, and none required surgical intervention. Over-the-counter use of decorative lenses as a cosmetic aid is rapidly increasing. Easy and unmonitored availability of these cosmetic lenses is followed by severe sight-threatening complications in young emmetropic individuals.

Sexual networks: the integration of social and genetic data.

PubMed

Day, S; Ward, H; Ison, C; Bell, G; Weber, J

1998-12-01

New methods for studying sexual networks are presented, drawing upon routine procedures followed in genitourinary medicine clinics in the UK for tracing partners and identifying strains of infection. The routine social procedures were developed to incorporate a structured interview. The routine microbiological diagnosis of gonorrhoea was augmented by phenotyping and the development of new genetic techniques for the fine discrimination of gonococcal strains (opa-typing). Selected results from a study in Sheffield, UK show that each method has limitations, when conducted separately, but these are minimised when the methods are combined. Moreover, the use of simple and routine methods of data collection resolve issues of scale and sample that have beset other network studies, as they provide a means of covering a larger and defined population. Popular concepts about these methods are discussed in the conclusion. The integrated approach employed in our research raises questions both about social methods, 'of people who lie, particularly when they talk about sex', and about microbiological methods, 'of genes that tell the truth' and bypass what people say and think altogether. We argue that these stereotypes are misleading insofar as they suggest that genetic techniques can substitute for the social, and we suggest that even the finest discrimination of organisms at the genetic level will never obviate the need for their interpretation in the light of social data.

Enlightening the life sciences: the history of halobacterial and microbial rhodopsin research.

PubMed

Grote, Mathias; O'Malley, Maureen A

2011-11-01

The history of research on microbial rhodopsins offers a novel perspective on the history of the molecular life sciences. Events in this history play important roles in the development of fields such as general microbiology, membrane research, bioenergetics, metagenomics and, very recently, neurobiology. New concepts, techniques, methods and fields have arisen as a result of microbial rhodopsin investigations. In addition, the history of microbial rhodopsins sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches. The story begins with the late nineteenth century discovery of microorganisms on salted fish and leads into ecological and taxonomical studies of halobacteria in hypersaline environments. These programmes were built on by the discovery of bacteriorhodopsin in organisms that are part of what is now known as the archaeal genus Halobacterium. The transfer of techniques from bacteriorhodopsin studies to the metagenomic discovery of proteorhodopsin in 2000 further extended the field. Microbial rhodopsins have also been used as model systems to understand membrane protein structure and function, and they have become the target of technological applications such as optogenetics and nanotechnology. Analysing the connections between these historical episodes provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Emerging Rapid Resistance Testing Methods for Clinical Microbiology Laboratories and Their Potential Impact on Patient Management

PubMed Central

Frickmann, Hagen; Zautner, Andreas E.

2014-01-01

Atypical and multidrug resistance, especially ESBL and carbapenemase expressing Enterobacteriaceae, is globally spreading. Therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. Consequently, rapid antibiotic resistance testing is essential. Various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. PCR- and sequencing-based approaches are the most expensive but the most frequently applied modes of testing, suitable for the detection of resistance genes even from primary material. Next generation sequencing, based either on assessment of allelic single nucleotide polymorphisms or on the detection of nonubiquitous resistance mechanisms might allow for sequence-based bacterial resistance testing comparable to viral resistance testing on the long term. Fluorescence in situ hybridization (FISH), based on specific binding of fluorescence-labeled oligonucleotide probes, provides a less expensive molecular bridging technique. It is particularly useful for detection of resistance mechanisms based on mutations in ribosomal RNA. Approaches based on MALDI-TOF-MS, alone or in combination with molecular techniques, like PCR/electrospray ionization MS or minisequencing provide the fastest resistance results from pure colonies or even primary samples with a growing number of protocols. This review details the various approaches of rapid resistance testing, their pros and cons, and their potential use for the diagnostic laboratory. PMID:25343142

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.

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...

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

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...

[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.

Characterization of rumen bacterial diversity and fermentation parameters in concentrate fed cattle with and without forage.

PubMed

Petri, R M; Forster, R J; Yang, W; McKinnon, J J; McAllister, T A

2012-06-01

To determine the effects of the removal of forage in high-concentrate diets on rumen fermentation conditions and rumen bacterial populations using culture-independent methods. Detectable bacteria and fermentation parameters were measured in the solid and liquid fractions of digesta from cattle fed two dietary treatments, high concentrate (HC) and high concentrate without forage (HCNF). Comparison of rumen fermentation conditions showed that duration of time spent below pH 5·2 and rumen osmolality were higher in the HCNF treatment. Simpson's index of 16S PCR-DGGE images showed a greater diversity of dominant species in the HCNF treatment. Real-time qPCR showed populations of Fibrobacter succinogenes (P = 0·01) were lower in HCNF than HC diets. Ruminococcus spp., F. succinogenes and Selenomonas ruminantium were at higher (P ≤ 0·05) concentrations in the solid vs the liquid fraction of digesta regardless of diet. The detectable bacterial community structure in the rumen is highly diverse. Reducing diet complexity by removing forage increased bacterial diversity despite the associated reduction in ruminal pH being less conducive for fibrolytic bacterial populations. Quantitative PCR showed that removal of forage from the diet resulted in a decline in the density of some, but not all fibrolytic bacterial species examined. Molecular techniques such as DGGE and qPCR provide an increased understanding of the impacts of dietary changes on the nature of rumen bacterial populations, and conclusions derived using these techniques may not match those previously derived using traditional laboratory culturing techniques. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Membrane filtration immobilization technique-a simple and novel method for primary isolation and enrichment of bacteriophages.

PubMed

Ghugare, G S; Nair, A; Nimkande, V; Sarode, P; Rangari, P; Khairnar, K

2017-02-01

To develop a method for the isolation and enrichment of bacteriophages selectively against specific bacteria coupled with a membrane filtration technique. Rapid isolation and concentration of host-specific bacteriophages was achieved by exposure of the sample suspected to contain bacteriophages to a specific host immobilized on a 0·45 μm membrane in a membrane filtration unit. The principle behind this method is the exploitation of host-specific interaction of bacteriophages with their host and maximizing this interaction using a classic membrane filtration method. This provides a chance for each bacteriophage in the sample to interact with the specific host on the membrane filter fitted with a vacuum pump. Specific bacteriophages of the host are retained on the membrane along with its host cells due to the effect of adsorption and these adsorbed bacteriophages (along with their hosts) on the filter disc are then amplified and enriched in regular nutritive broth tryptose soya broth by incubation. With the help of the plaque assay method, host-specific phages of various bacterial species were isolated, segregated and enriched. The phage concentration method coupled with membrane filtration immobilization of host bacteria was able to isolate and enrich the host-specific bacteriophages by several fold using a lower quantity of an environmental water sample, or other phage suspensions. Enrichment of phages from single plaques was also achieved. The isolation and detection of host-specific bacteriophages from a low density bacteriophage water sample in a single step by the use of a simple and basic microbiological technique can be achieved. Enrichment of phages from low phage titre suspensions is also achieved very effectively. © 2016 The Society for Applied Microbiology.

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 493.909 - 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 493.821 - 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 493.909 - 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...

78 FR 58322 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-23

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group, Microbiology and Infectious Diseases B Subcommittee, Microbiology..., 301-402-9523, [email protected] . Name of Committee: Microbiology, Infectious Diseases and AIDS...

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 493.821 - 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 493.909 - 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...

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...

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 866.2900 - 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 866.2350 - 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 866.2900 - 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 866.2350 - 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 866.2900 - 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...

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...

Immunomicrobiological monitoring of orovaccinal therapy in acute intestinal infections.

PubMed

Corridori, S; Negretti, F

1983-01-01

A double blind study in 42 patients (treated and controls) affected by acute uncomplicated salmonellosis was performed. The treatment consisted of an oral inactivated tetravaccine at the dose of 1 ampoule twice a day for 15 consecutive days. Microbiological and serological techniques (determination of intestinal secretory IgA by means of immunofluorescence, titration of copro and serum antibodies, quali-quantitative coprocultures) have shown that the administration of oral vaccine improved both the clinical and the immunomicrobiological picture in treated patients.

Medical Parasitology Taxonomy Update: January 2012 to December 2015.

PubMed

Simner, P J

2017-01-01

Parasites of medical importance have long been classified taxonomically by morphological characteristics. However, molecular-based techniques have been increasingly used and relied on to determine evolutionary distances for the basis of rational hierarchal classifications. This has resulted in several different classification schemes for parasites and changes in parasite taxonomy. The purpose of this Minireview is to provide a single reference for diagnostic laboratories that summarizes new and revised clinically relevant parasite taxonomy from January 2012 through December 2015. Copyright © 2016 American Society for Microbiology.

[Etiological diagnosis of acute pneumopathies. Evaluative study. 100 cases in a pneumologic center].

PubMed

Denjean, A; Geslin, P; Hirsch, A; Lemoine, J L

1977-05-14

This study involved 100 patients with acute pneumonia and hospitalised in a specialised service: 12 bacterial pneumonia, 40 viral pneumonia (i.e. 52% of the total). Only precise viral and bactérial studies could improve these results. Given the poor results obtained using the microbiological techniques available here, the authors suggest the inclusion in all subsequent studies of aetiological diagnosis of a quantitative examination of sputum bacterial flora and examination for the detection of bacterial exoantigens.

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.

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…

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…

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...

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...

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…

Assessment on Experimental Bacterial Biofilms and in Clinical Practice of the Efficacy of Sampling Solutions for Microbiological Testing of Endoscopes

PubMed Central

Aumeran, C.; Thibert, E.; Chapelle, F. A.; Hennequin, C.; Lesens, O.

2012-01-01

Opinions differ on the value of microbiological testing of endoscopes, which varies according to the technique used. We compared the efficacy on bacterial biofilms of sampling solutions used for the surveillance of the contamination of endoscope channels. To compare efficacy, we used an experimental model of a 48-h Pseudomonas biofilm grown on endoscope internal tubing. Sampling of this experimental biofilm was performed with a Tween 80-lecithin-based solution, saline, and sterile water. We also performed a randomized prospective study during routine clinical practice in our hospital sampling randomly with two different solutions the endoscopes after reprocessing. Biofilm recovery expressed as a logarithmic ratio of bacteria recovered on bacteria initially present in biofilm was significantly more effective with the Tween 80-lecithin-based solution than with saline solution (P = 0.002) and sterile water (P = 0.002). There was no significant difference between saline and sterile water. In the randomized clinical study, the rates of endoscopes that were contaminated with the Tween 80-lecithin-based sampling solution and the saline were 8/25 and 1/25, respectively (P = 0.02), and the mean numbers of bacteria recovered were 281 and 19 CFU/100 ml (P = 0.001), respectively. In conclusion, the efficiency and therefore the value of the monitoring of endoscope reprocessing by microbiological cultures is dependent on the sampling solutions used. A sampling solution with a tensioactive action is more efficient than saline in detecting biofilm contamination of endoscopes. PMID:22170930

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air.

PubMed

Piñar, Guadalupe; Piombino-Mascali, Dario; Maixner, Frank; Zink, Albert; Sterflinger, Katja

2013-11-01

The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and - as a result of salt emanating from the walls - on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors. © 2013 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

Microbiological testing of raw, boxed beef in the context of hazard analysis critical control point at a high-line-speed abattoir.

PubMed

Jericho, K W; Kozub, G C; Gannon, V P; Taylor, C M

2000-12-01

The efficacy of cold storage of raw, bagged, boxed beef was assessed microbiologically at a high-line-speed abattoir (270 carcasses per h). At the time of this study, plant management was in the process of creating a hazard analysis critical control point plan for all processes. Aerobic bacteria, coliforms, and type 1 Escherichia coli were enumerated (5 by 5-cm excision samples, hydrophobic grid membrane filter technology) before and after cold storage of this final product produced at six fabrication tables. In addition, the temperature-function integration technique (TFIT) was used to calculate the potential number of generations of E. coli during the first 24 or 48 h of storage of the boxed beef. Based on the temperature histories (total of 60 boxes, resulting from 12 product cuts, five boxes from each of two fabrication tables on each of 6 sampling days, and six types of fabrication tables), TFIT did not predict any growth of E. coli (with or without lag) for the test period. This was verified by E. coli mean log10 values of 0.65 to 0.42 cm2 (P > 0.05) determined by culture before and after the cooling process, respectively. Counts of aerobic bacteria and coliforms were significantly reduced (P < 0.001 and P < 0.05, respectively) during the initial period of the cooling process. There were significant microbiological differences (P < 0.05) between table-cut units.

Wound Microbiology and Associated Approaches to Wound Management

PubMed Central

Bowler, P. G.; Duerden, B. I.; Armstrong, D. G.

2001-01-01

The majority of dermal wounds are colonized with aerobic and anaerobic microorganisms that originate predominantly from mucosal surfaces such as those of the oral cavity and gut. The role and significance of microorganisms in wound healing has been debated for many years. While some experts consider the microbial density to be critical in predicting wound healing and infection, others consider the types of microorganisms to be of greater importance. However, these and other factors such as microbial synergy, the host immune response, and the quality of tissue must be considered collectively in assessing the probability of infection. Debate also exists regarding the value of wound sampling, the types of wounds that should be sampled, and the sampling technique required to generate the most meaningful data. In the laboratory, consideration must be given to the relevance of culturing polymicrobial specimens, the value in identifying one or more microorganisms, and the microorganisms that should be assayed for antibiotic susceptibility. Although appropriate systemic antibiotics are essential for the treatment of deteriorating, clinically infected wounds, debate exists regarding the relevance and use of antibiotics (systemic or topical) and antiseptics (topical) in the treatment of nonhealing wounds that have no clinical signs of infection. In providing a detailed analysis of wound microbiology, together with current opinion and controversies regarding wound assessment and treatment, this review has attempted to capture and address microbiological aspects that are critical to the successful management of microorganisms in wounds. PMID:11292638

Effects of Time and Storage Conditions on the Chemical and Microbiologic Stability of Diluted Buprenorphine for Injection

PubMed Central

DenHerder, Johnathan M; Reed, Ralph L; Sargent, Jennifer L; Bobe, Gerd; Stevens, Jan F; Diggs, Helen E

2017-01-01

Buprenorphine is a partial μ-opioid agonist used for analgesia. Due to the small size of laboratory rodents, buprenorphine HCl is typically diluted 10- or 20-fold with a sterile diluent, such as saline, for accurate dosing. Protocols for preparing and storing diluted buprenorphine vary by institution, and little published information is available regarding stability and beyond-use dating of specific buprenorphine preparations. The purpose of this study was to determine the chemical and microbiologic stability of diluted buprenorphine stored for a maximum of 180 d. Buprenorphine HCl was diluted 1:10 into sterile bacteriostatic saline by using aseptic technique. Diluted samples were stored in glass vials or plastic syringes, protected from light, and maintained at refrigerated or room temperature for as long as 180 d. Aerobic and anaerobic cultures on all stored samples were negative for bacterial and fungal growth. According to HPLC analysis, diluted buprenorphine stored in glass vials experienced less than 10% loss when stored for 180 d at either refrigerated or room temperature. However, the concentration of buprenorphine stored in syringes declined rapidly to more than 80% loss at room temperature and 28% loss in the refrigerator after 180 d. According to the results of this study, diluted buprenorphine stored in glass vials retains more than 90% of the initial concentration and is microbiologically stable for 180 d. However, our data suggest that, regardless of the duration, storing diluted buprenorphine in plastic syringes is inadvisable. PMID:28724496

Physical and microbiological stability of an extemporaneous tacrolimus suspension for paediatric use.

PubMed

Han, J; Beeton, A; Long, P F; Wong, I; Tuleu, C

2006-04-01

An extemporaneous suspension of tacrolimus for paediatric use has recently been developed but poor bioavailability and erratic plasma concentrations were observed during clinical use. It was not clear whether this was due to changes in the physical properties of the suspension during storage. The aim of this work was to investigate the physical and microbiological stability over the recommended 8-week shelf-life of this extemporaneous tacrolimus suspension. Suspensions (0.5 mg/mL) were custom made by a special manufacturer under Good Manufacturing Practice conditions. The procedure involved mixing tacrolimus capsule contents into Ora Plus and Simple Syrup (1 : 1) using a mortar and pestle followed by an homogenization step. The particle sizes of the suspensions were measured using a MasterSizer. A light microscope equipped with polarizers was used to visualize any particle size changes or crystal growth. Viable bacterial and fungal contamination was assessed using standard colony count techniques on solid media. The suspensions were kept at 22-26 degrees C and evaluated weekly. The volume mean diameter d((4,3)) from laser diffraction did not change significantly. Light microscopy did not reveal any significant change in particle size or crystal growth. Contamination by viable and culturable micro-organisms could not be detected. The suspension was physically (particle size) and microbiologically stable during the 8-week study period suggesting other factors including poor dosing could be responsible for the pharmacokinetic variation observed during clinical use which warrants further investigation.

pH and bacterial profile of dental plaque in children and adults of a low caries population.

PubMed

Raner, Elisabeth; Lindqvist, Lina; Johansson, Sofia; Hassan, Haidar; Carlén, Anette; Suksu-art, Narong; Dahlén, Gunnar

2014-06-01

This study compares pH and microbiological profile of dental plaque in children and adults of a low caries population. Thirty-nine children, 12-14 years of age and 45 adults between 20 and 39 years of age in 5 Karen villages of the Tak province, Northern Thailand were examined for plaque, calculus, caries (DMFT) and pH measurements in resting plaque and after a sucrose rinse. Information on dietary and oral hygiene habits was obtained through interviews using a fixed questionnaire. Microbiological profile of plaque samples was analyzed with DNA-DNA checkerboard technique. Mean DMFT was 0.77 ± 1.56 and 87% of the adults and 67% of the children were caries free (p < 0.05). The mean resting pH was for both age groups in the range of 7.0-7.1 and significantly higher than a Swedish caries free reference group. Karen adult men had significantly lower pH minimum than females and children (p < 0.05). Supragingival plaque samples showed high levels of low acidogenic and anaerobic species, which dominated over strong acid producers such as streptococci. The study indicates that the Karen children and adults has a plaque physiology and microbiology predominating by low acidogenic anaerobes, which in addition to the low sucrose intake explains the low caries prevalence in this population. Copyright © 2014 Elsevier Ltd. All rights reserved.

Can Particulate Air Sampling Predict Microbial Load in Operating Theatres for Arthroplasty?

PubMed Central

Cristina, Maria Luisa; Spagnolo, Anna Maria; Sartini, Marina; Panatto, Donatella; Gasparini, Roberto; Orlando, Paolo; Ottria, Gianluca; Perdelli, Fernanda

2012-01-01

Several studies have proposed that the microbiological quality of the air in operating theatres be indirectly evaluated by means of particle counting, a technique derived from industrial clean-room technology standards, using airborne particle concentration as an index of microbial contamination. However, the relationship between particle counting and microbiological sampling has rarely been evaluated and demonstrated in operating theatres. The aim of the present study was to determine whether particle counting could predict microbiological contamination of the air in an operating theatre during 95 surgical arthroplasty procedures. This investigation was carried out over a period of three months in 2010 in an orthopedic operating theatre devoted exclusively to prosthetic surgery. During each procedure, the bacterial contamination of the air was determined by means of active sampling; at the same time, airborne particulate contamination was assessed throughout the entire procedure. On considering the total number of surgical operations, the mean value of the total bacterial load in the center of the operating theatre proved to be 35 CFU/m3; the mean particle count was 4,194,569 no./m3 for particles of diameter ≥0.5 µm and 13,519 no./m3 for particles of diameter ≥5 µm. No significant differences emerged between the median values of the airborne microbial load recorded during the two types of procedure monitored. Particulates with a diameter of ≥0.5 µm were detected in statistically higher concentrations (p<0.001) during knee-replacement procedures. By contrast, particulates with a diameter of ≥5 µm displayed a statistically higher concentration during hip-replacement procedures (p<0.05). The results did not reveal any statistically significant correlation between microbial loads and particle counts for either of the particle diameters considered (≥0.5 µm and ≥5 µm). Consequently, microbiological monitoring remains the most suitable method of evaluating the quality of air in operating theatres. PMID:23285189

Can particulate air sampling predict microbial load in operating theatres for arthroplasty?

PubMed

Cristina, Maria Luisa; Spagnolo, Anna Maria; Sartini, Marina; Panatto, Donatella; Gasparini, Roberto; Orlando, Paolo; Ottria, Gianluca; Perdelli, Fernanda

2012-01-01

Several studies have proposed that the microbiological quality of the air in operating theatres be indirectly evaluated by means of particle counting, a technique derived from industrial clean-room technology standards, using airborne particle concentration as an index of microbial contamination. However, the relationship between particle counting and microbiological sampling has rarely been evaluated and demonstrated in operating theatres. The aim of the present study was to determine whether particle counting could predict microbiological contamination of the air in an operating theatre during 95 surgical arthroplasty procedures. This investigation was carried out over a period of three months in 2010 in an orthopedic operating theatre devoted exclusively to prosthetic surgery. During each procedure, the bacterial contamination of the air was determined by means of active sampling; at the same time, airborne particulate contamination was assessed throughout the entire procedure. On considering the total number of surgical operations, the mean value of the total bacterial load in the center of the operating theatre proved to be 35 CFU/m(3); the mean particle count was 4,194,569 no./m(3) for particles of diameter ≥0.5 µm and 13,519 no./m(3) for particles of diameter ≥5 µm. No significant differences emerged between the median values of the airborne microbial load recorded during the two types of procedure monitored. Particulates with a diameter of ≥0.5 µm were detected in statistically higher concentrations (p<0.001) during knee-replacement procedures. By contrast, particulates with a diameter of ≥5 µm displayed a statistically higher concentration during hip-replacement procedures (p<0.05). The results did not reveal any statistically significant correlation between microbial loads and particle counts for either of the particle diameters considered (≥0.5 µm and ≥5 µm). Consequently, microbiological monitoring remains the most suitable method of evaluating the quality of air in operating theatres.

Rapid Diagnosis of Smear-Negative Tuberculosis Using Immunology and Microbiology with Induced Sputum in HIV-Infected and Uninfected Individuals

PubMed Central

Breen, Ronan A. M.; Hardy, Gareth A. D.; Perrin, Felicity M. R.; Lear, Sara; Kinloch, Sabine; Smith, Colette J.; Cropley, Ian; Janossy, George; Lipman, Marc C. I.

2007-01-01

Rationale and Objectives Blood-based studies have demonstrated the potential of immunological assays to detect tuberculosis. However lung fluid sampling may prove superior as it enables simultaneous microbiological detection of mycobacteria to be performed. Until now this has only been possible using the expensive and invasive technique of broncho-alveolar lavage. We sought to evaluate an immunoassay using non-invasive induced-sputum to diagnose active tuberculosis. Methods and Results Prospective cohort study of forty-two spontaneous sputum smear-negative or sputum non-producing adults under investigation for tuberculosis. CD4 lymphocytes specific to purified-protein-derivative of Mycobacterium tuberculosis actively synthesising interferon-gamma were measured by flow cytometry and final diagnosis compared to immunoassay using a cut-off of 0.5%. Sixteen subjects (38%) were HIV-infected (median CD4 count [range] = 332 cells/µl [103–748]). Thirty-eight (90%) were BCG-vaccinated. In 27 subjects diagnosed with active tuberculosis, the median [range] percentage of interferon-gamma synthetic CD4+ lymphocytes was 2.77% [0–23.93%] versus 0% [0–2.10%] in 15 negative for active infection (p<0.0001). Sensitivity and specificity of the immunoassay versus final diagnosis of active tuberculosis were 89% (24 of 27) and 80% (12 of 15) respectively. The 3 positive assays in the latter group occurred in subjects diagnosed with quiescent/latent tuberculosis. Assay performance was unaffected by HIV-status, BCG-vaccination or disease site. Combining this approach with traditional microbiological methods increased the diagnostic yield to 93% (25 of 27) alongside acid-fast bacilli smear and 96% (26 of 27) alongside tuberculosis culture. Conclusions These data demonstrate for the first time that a rapid immunological assay to diagnose active tuberculosis can be performed successfully in combination with microbiological methods on a single induced-sputum sample. PMID:18092001

Methods for preservation and extension of shelf life.

PubMed

Gould, G W

1996-11-01

There is potential for spoilage of all foods at some rate or other following harvest, slaughter or manufacture and spoilage may occur at any of the stages between the acquisition of raw materials and the eventual consumption of a food product. These stages include processing, packaging, distribution, retail display, transport, storage and use by the consumer. They are under varying degrees of control that aim to deliver a satisfactory shelf life, to ensure that the finally-consumed product is of high quality and to ensure that it is safe. Spoilage may be caused by a wide range of reactions including some that are essentially physical, some that are chemical, some enzymic and some microbiological. The various forms of microbiological spoilage are preventable to a large degree by a wide range of preservation techniques, most of which act by preventing or inhibiting microbial growth (e.g., chilling, freezing, drying, curing, conserving, vacuum packing, modified atmosphere packing, acidifying, fermenting and adding preservatives). A smaller number of techniques act by inactivating microorganisms (e.g., pasteurization, sterilization and irradiation). Additional techniques restrict the access of microorganisms to products (e.g., aseptic processing and packaging. A major trend is that new and emerging preservation techniques which are coming into use or are under development include more that act by inactivation (e.g., ultrahigh pressure, electroporation, manothermosonication and addition of bacteriolytic enzymes). A further trend is towards the use of procedures that deliver products that are less heavily preserved, have higher quality, are more natural, freer from additives and nutritionally healthier. Less severe preservation procedures are therefore being developed that make use of preservative factors in combinations to deliver (a) less damage to product quality (hurdle technologies); (b) new methods of heating that are better controlled and therefore deliver milder heat to products; (c) cook-chill combinations that deliver longer high quality shelf lives: (d) modified atmosphere packaging to retain quality longer; and (e) use of antimicrobial systems that are more natural. Many of the existing and emerging preservation techniques act by interfering with the homeostatic mechanisms that microorganisms have evolved in order to survive extreme environmental stresses.

Quantitative proteomics in the field of microbiology.

PubMed

Otto, Andreas; Becher, Dörte; Schmidt, Frank

2014-03-01

Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Lymph nodes fine needle cytology in the diagnosis of infectious diseases: clinical settings.

PubMed

Natella, Valentina; Cozzolino, Immacolata; Sosa Fernandez, Laura Virginia; Vigliar, Elena

2012-01-01

Lymph node reactive hyperplasia, caused by specific infectious etiologic factors, represents the most frequent cause of enlarged peripheral lymph nodes. The main infectious agents are viruses, pyogenic bacteria, mycobacteria, fungi and protozoa that may determine unspecific or specific pathological entities, such as cat-scratch disease, toxoplasmosis or infectious mononucleosis. Lymph node fine needle cytology (FNC) is a safe, simple, cost-effective and efficient technique that quickly provides information about the cell population and the nature of the process. FNC can also provide suitable material for ancillary techniques, such as flow cytometry, immunocytochemistry, molecular biology and microbiological examinations. This study focuses on the cytological features of benign lymphadenopathy of infectious origin and their possible contribution to the clinical setting definition of corresponding patients.

Mass spectrometry applied to the identification of Mycobacterium tuberculosis and biomarker discovery.

PubMed

López-Hernández, Y; Patiño-Rodríguez, O; García-Orta, S T; Pinos-Rodríguez, J M

2016-12-01

An adequate and effective tuberculosis (TB) diagnosis system has been identified by the World Health Organization as a priority in the fight against this disease. Over the years, several methods have been developed to identify the bacillus, but bacterial culture remains one of the most affordable methods for most countries. For rapid and accurate identification, however, it is more feasible to implement molecular techniques, taking advantage of the availability of public databases containing protein sequences. Mass spectrometry (MS) has become an interesting technique for the identification of TB. Here, we review some of the most widely employed methods for identifying Mycobacterium tuberculosis and present an update on MS applied for the identification of mycobacterial species. © 2016 The Society for Applied Microbiology.

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

PubMed Central

RIVERA-PEREZ, JESSICA I.; SANTIAGO-RODRIGUEZ, TASHA M.; TORANZOS, GARY A.

2017-01-01

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses. PMID:27726770

Activity-Based Protein Profiling of Microbes

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

Sadler, Natalie C.; Wright, Aaron T.

Activity-Based Protein Profiling (ABPP) in conjunction with multimodal characterization techniques has yielded impactful findings in microbiology, particularly in pathogen, bioenergy, drug discovery, and environmental research. Using small molecule chemical probes that react irreversibly with specific proteins or protein families in complex systems has provided insights in enzyme functions in central metabolic pathways, drug-protein interactions, and regulatory protein redox, for systems ranging from photoautotrophic cyanobacteria to mycobacteria, and combining live cell or cell extract ABPP with proteomics, molecular biology, modeling, and other techniques has greatly expanded our understanding of these systems. New opportunities for application of ABPP to microbial systems include:more » enhancing protein annotation, characterizing protein activities in myriad environments, and reveal signal transduction and regulatory mechanisms in microbial systems.« less

Nocardia transvalensis Disseminated Infection in an Immunocompromised Patient with Idiopathic Thrombocytopenic Purpura

PubMed Central

García-Méndez, Jorge; Carrillo-Casas, Erika M.; Rangel-Cordero, Andrea; Leyva-Leyva, Margarita; Xicohtencatl-Cortes, Juan; Arenas, Roberto; Hernández-Castro, Rigoberto

2016-01-01

Nocardia transvalensis complex includes a wide range of microorganisms with specific antimicrobial resistance patterns. N. transvalensis is an unusual Nocardia species. However, it must be differentiated due to its natural resistance to aminoglycosides while other Nocardia species are susceptible. The present report describes a Nocardia species involved in an uncommon clinical case of a patient with idiopathic thrombocytopenic purpura and pulmonary nocardiosis. Microbiological and molecular techniques based on the sequencing of the 16S rRNA gene allowed diagnosis of Nocardia transvalensis sensu stricto. The successful treatment was based on trimethoprim-sulfamethoxazole and other drugs. We conclude that molecular identification of Nocardia species is a valuable technique to guide good treatment and prognosis and recommend its use for daily bases diagnosis. PMID:27313917

Nocardia transvalensis Disseminated Infection in an Immunocompromised Patient with Idiopathic Thrombocytopenic Purpura.

PubMed

García-Méndez, Jorge; Carrillo-Casas, Erika M; Rangel-Cordero, Andrea; Leyva-Leyva, Margarita; Xicohtencatl-Cortes, Juan; Arenas, Roberto; Hernández-Castro, Rigoberto

2016-01-01

Nocardia transvalensis complex includes a wide range of microorganisms with specific antimicrobial resistance patterns. N. transvalensis is an unusual Nocardia species. However, it must be differentiated due to its natural resistance to aminoglycosides while other Nocardia species are susceptible. The present report describes a Nocardia species involved in an uncommon clinical case of a patient with idiopathic thrombocytopenic purpura and pulmonary nocardiosis. Microbiological and molecular techniques based on the sequencing of the 16S rRNA gene allowed diagnosis of Nocardia transvalensis sensu stricto. The successful treatment was based on trimethoprim-sulfamethoxazole and other drugs. We conclude that molecular identification of Nocardia species is a valuable technique to guide good treatment and prognosis and recommend its use for daily bases diagnosis.

Pre-Medical Preparation in Microbiology among Applicants and Matriculants in Osteopathic Medical School in the United States

PubMed Central

Ramos, Raddy L.; Guercio, Erik; Martinez, Luis R.

2017-01-01

It is recognized that medical school curricula contain significant microbiology-related content as part of the training of future physicians who will be responsible stewards of antimicrobials. Surprisingly, osteopathic and allopathic medical schools do not require pre-medical microbiology coursework, and the extent to which medical students have completed microbiology coursework remains poorly understood. In this report, we show that fewer than 3% of applicants and matriculants to osteopathic medical school (OMS) have completed an undergraduate major or minor in microbiology, and fewer than 17% of applicants and matriculants to OMS have completed one or more microbiology-related courses. These data demonstrate limited pre-medical microbiology-related knowledge among osteopathic medical students, which may be associated with an increase in perceived stress when learning this content or during clinical rotations as well as a potential lack of interest in pursuing a career in infectious diseases. PMID:29854054

Pre-Medical Preparation in Microbiology among Applicants and Matriculants in Osteopathic Medical School in the United States.

PubMed

Ramos, Raddy L; Guercio, Erik; Martinez, Luis R

2017-01-01

It is recognized that medical school curricula contain significant microbiology-related content as part of the training of future physicians who will be responsible stewards of antimicrobials. Surprisingly, osteopathic and allopathic medical schools do not require pre-medical microbiology coursework, and the extent to which medical students have completed microbiology coursework remains poorly understood. In this report, we show that fewer than 3% of applicants and matriculants to osteopathic medical school (OMS) have completed an undergraduate major or minor in microbiology, and fewer than 17% of applicants and matriculants to OMS have completed one or more microbiology-related courses. These data demonstrate limited pre-medical microbiology-related knowledge among osteopathic medical students, which may be associated with an increase in perceived stress when learning this content or during clinical rotations as well as a potential lack of interest in pursuing a career in infectious diseases.

Nonlinear dynamic phase contrast microscopy for microfluidic and microbiological applications

NASA Astrophysics Data System (ADS)

Denz, C.; Holtmann, F.; Woerdemann, M.; Oevermann, M.

2008-08-01

In live sciences, the observation and analysis of moving living cells, molecular motors or motion of micro- and nano-objects is a current field of research. At the same time, microfluidic innovations are needed for biological and medical applications on a micro- and nano-scale. Conventional microscopy techniques are reaching considerable limits with respect to these issues. A promising approach for this challenge is nonlinear dynamic phase contrast microscopy. It is an alternative full field approach that allows to detect motion as well as phase changes of living unstained micro-objects in real-time, thereby being marker free, without contact and non destructive, i.e. fully biocompatible. The generality of this system allows it to be combined with several other microscope techniques such as conventional bright field or fluorescence microscopy. In this article we will present the dynamic phase contrast technique and its applications in analysis of micro organismic dynamics, micro flow velocimetry and micro-mixing analysis.

Molecular ecology of hydrothermal vent microbial communities.

PubMed

Jeanthon, C

2000-02-01

The study of the structure and diversity of hydrothermal vent microbial communities has long been restricted to the morphological description of microorganisms and the use of enrichment culture-based techniques. Until recently the identification of the culturable fraction required the isolation of pure cultures followed by testing for multiple physiological and biochemical traits. However, peculiar inhabitants of the hydrothermal ecosystem such as the invertebrate endosymbionts and the dense microbial mat filaments have eluded laboratory cultivation. Substantial progress has been achieved in recent years in techniques for the identification of microorganisms in natural environments. Application of molecular approaches has revealed the existence of unique and previously unrecognized microorganisms. These have provided fresh insight into the ecology, diversity and evolution of mesophilic and thermophilic microbial communities from the deep-sea hydrothermal ecosystem. This review reports the main discoveries made through the introduction of these powerful techniques in the study of deep-sea hydrothermal vent microbiology.

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...

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.

[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.

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)

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.

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.

Rapid detection of bacteria in drinking water and water contamination case studies

NASA Astrophysics Data System (ADS)

Deininger, Rolf A.; Lee, Jiyoung; Clark, Robert M.

2011-12-01

Water systems are inherently vulnerable to physical, chemical and biologic threats that might compromise a systems' ability to reliably deliver safe water. The ability of a water supply to provide water to its customers can be compromised by destroying or disrupting key physical elements of the water system. However, contamination is generally viewed as the most serious potential terrorist threat to water systems. Chemical or biologic agents could spread throughout a distribution system and result in sickness or death among the consumers and for some agents the presence of the contaminant might not be known until emergency rooms report an increase in patients with a particular set of symptoms. Even without serious health impacts, just the knowledge that a water system had been breached could seriously undermine consumer confidence in public water supplies. Therefore, the ability to rapidly detect contamination, especially microbiological contamination, is highly desirable. The authors summarize water contamination case studies and discuss a technique for identifying microbiological contamination based on ATP bioluminescence. This assay allows an estimation of bacterial populations within minutes and can be applied using a local platform. Previous ATP-based methods requires one hour, one liter of water, and has a sensitivity of 100000 cells for detection. The improved method discussed here is 100 times more sensitive, requires one-hundredth of the sample volume, and is over 10 times faster than standard method. This technique has a great deal of potential for application in situations in which a water system has been compromised.

Dual phylogenetic staining protocol for simultaneous analysis of yeast and bacteria in artworks

NASA Astrophysics Data System (ADS)

González-Pérez, Marina; Brinco, Catarina; Vieira, Ricardo; Rosado, Tânia; Mauran, Guilhem; Pereira, António; Candeias, António; Caldeira, Ana Teresa

2017-02-01

The detection and analysis of metabolically active microorganisms are useful to determine those directly involved in the biodeterioration of cultural heritage (CH). Fluorescence in situ hybridization with oligonucleotide probes targeted at rRNA (RNA-FISH) has demonstrated to be a powerful tool for signaling them. However, more efforts are required for the technique to become a vital tool for the analysis of CH's microbiological communities. Simultaneous analysis of microorganisms belonging to different kingdoms, by RNA-FISH in-suspension approach, could represent an important progress: it could open the door for the future use of the technique to analyze the microbial communities by flow cytometry, which has shown to be a potent tool in environmental microbiology. Thus, in this work, various already implemented in-suspension RNA-FISH protocols for ex situ analysis of yeast and bacteria were investigated and adapted for allowing the simultaneous detection of these types of microorganisms. A deep investigation of the factors that can affect the results was carried out, focusing particular attention on the selection of the fluorochromes used for labelling the probe set. The resultant protocol, involving the use of EUK516-6-FAM/EUB338-Cy3 probes combination, was validated using artificial consortia and gave positive preliminary results when applied in samples from a real case study: the Paleolithic archaeological site of Escoural Cave (Alentejo, Portugal). This approach represents the first dual-staining RNA-FISH in-suspension protocol developed and applied for the simultaneous investigation of CH biodeteriogenic agents belonging to different kingdoms.

Detection and quantification of Alicyclobacillus acidoterrestris by electrical impedance in apple juice.

PubMed

Fernández, Pilar; Gabaldón, José Antonio; Periago, Mª Jesús

2017-12-01

Alicyclobacillus acidoterrestris is a thermotolerant bacterium able to grow in fruit juices and drinks, as the spoilage by Alicyclobacillus in the final product does not product any gas, but leads to a "medicine flavor" due to the formation of guaicol. Also, its detection is a challenge for the quality control departments, because it takes several days to get the results of traditional microbiology methods. This study aimed at developing a more accurate electrical impedance technique for the detection of A. acidoterrestris in concentrated apple juice. Samples of apple juice were inoculated with A. acidoterrestris spores isolated from a peach and grape juice. For the spore germination, several heat-shock treatments were tested (80 °C/10 min, 70 °C/20 min and 60 °C/30 min). Direct and indirect electrical impedance was applied to detect and quantify the microorganism in the inoculated apple juice, using BAT broth and Bimedia 002A (pH 4). The 80 °C/10 min treatment was selected for spore activation. The valid electrical impedance technique was the indirect method in BAT broth, which measured the changes in the impedance through the formation of CO 2 . In addition, a positive correlation (r = 0.98, R 2  = 0.97) was observed between the classical microbiology (BAM agar) and the indirect impedance method. Copyright © 2017 Elsevier Ltd. 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.

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

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.

Overcoming the obstacles of implementing infection prevention and control guidelines.

PubMed

Birgand, G; Johansson, A; Szilagyi, E; Lucet, J-C

2015-12-01

Reasons for a successful or unsuccessful implementation of infection prevention and control (IPC) guidelines are often multiple and interconnected. This article reviews key elements from the national to the individual level that contribute to the success of the implementation of IPC measures and gives perspectives for improvement. Governance approaches, modes of communication and formats of guidelines are discussed with a view to improve collaboration and transparency among actors. The culture of IPC influences practices and varies according to countries, specialties and healthcare providers. We describe important contextual aspects, such as relationships between actors and resources and behavioural features including professional background or experience. Behaviour change techniques providing goal-setting, feedback and action planning have proved effective in mobilizing participants and may be key to trigger social movements of implementation. The leadership of international societies in coordinating actions at international, national and institutional levels using multidisciplinary approaches and fostering collaboration among clinical microbiology, infectious diseases and IPC will be essential for success. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Microorganisms isolated from root canals presenting necrotic pulp and their drug susceptibility in vitro.

PubMed

Lana, M A; Ribeiro-Sobrinho, A P; Stehling, R; Garcia, G D; Silva, B K; Hamdan, J S; Nicoli, J R; Carvalho, M A; Farias, L de M

2001-04-01

The knowledge about causative agents involved in endodontic infections is increasing, especially due to the improvement of culture techniques for anaerobic bacteria, showing that these microorganisms are predominant in this pathology. In this study, 31 canals with pulp necrosis were microbiologically analyzed before and after manipulation. Obligate and facultative anaerobes, microaerophilic bacteria and yeasts were recovered from 24, 14, 5 and 2 clinical specimens, respectively. The most frequent genera were Prevotella, Fusobacterium, Lactobacillus, Streptococcus, Clostridium and Peptostreptococcus for bacteria and Candida and Saccharomyces for yeasts. Strong positive associations, using an odds ratio system, were found between Clostridium and Prevotella and between Peptostreptococcus and Fusobacterium. Even after the instrumentation and the use of Ca(OH)2, facultative anaerobes were detected in two root canals and yeasts in three. Microorganisms were isolated from seven canals at the end of the endodontic treatment: facultative anaerobes from five and yeasts from one. The microbiological evaluation of root canals with pulp necrosis suggests the presence of polymicrobial infections, mainly involving obligate anaerobes, and shows that the infection may persist after treatment.

Gas chromatographic/mass spectrometric and microbiological analyses on irradiated chicken

NASA Astrophysics Data System (ADS)

Parlato, A.; Calderaro, E.; Bartolotta, A.; D'Oca, M. C.; Giuffrida, S. A.; Brai, M.; Tranchina, L.; Agozzino, P.; Avellone, G.; Ferrugia, M.; Di Noto, A. M.; Caracappa, S.

2007-08-01

Ionizing radiation is widely used as treatment technique for food preservation. It involves among others reduction of microbial contamination, disinfestations, sprout inhibition and extension of shelf life of food. However, the commercialization of irradiated food requires the availability of reliable methods to identify irradiated foodstuffs. In this paper, we present results on the application to irradiated chicken of this method, based on the detection, in muscle and skin samples, of the peaks of ions 98 Da and 112 Da, in a ratio approximately 4:1, typical of radiation induced 2-dodecylcyclobutanones (2-DCB). Aim of the work was also to study the time stability of the measured parameters in samples irradiated at 3 and 5 kGy, and to verify the efficacy of the treatment from a microbiological point of view. Our results show that, one month after irradiation at 3 kGy, the method is suitable using the skin but not the muscle, while the measured parameters are detectable in both samples irradiated at 5 kGy. The microbial population was substantially reduced even at 3 kGy.

Inflammation Thread Runs across Medical Laboratory Specialities.

PubMed

Nydegger, Urs; Lung, Thomas; Risch, Lorenz; Risch, Martin; Medina Escobar, Pedro; Bodmer, Thomas

2016-01-01

We work on the assumption that four major specialities or sectors of medical laboratory assays, comprising clinical chemistry, haematology, immunology, and microbiology, embraced by genome sequencing techniques, are routinely in use. Medical laboratory markers for inflammation serve as model: they are allotted to most fields of medical lab assays including genomics. Incessant coding of assays aligns each of them in the long lists of big data. As exemplified with the complement gene family, containing C2, C3, C8A, C8B, CFH, CFI, and ITGB2, heritability patterns/risk factors associated with diseases with genetic glitch of complement components are unfolding. The C4 component serum levels depend on sufficient vitamin D whilst low vitamin D is inversely related to IgG1, IgA, and C3 linking vitamin sufficiency to innate immunity. Whole genome sequencing of microbial organisms may distinguish virulent from nonvirulent and antibiotic resistant from nonresistant varieties of the same species and thus can be listed in personal big data banks including microbiological pathology; the big data warehouse continues to grow.

Comparative study on the microbiological features of angular cheilitis in HIV seropositive and HIV seronegative patients from South India

PubMed Central

Krishnan, P Anitha; Kannan, Ranganathan

2013-01-01

Objective: This study was designed to compare the microbiological features of angular cheilitis (AC) in human immunodeficiency virus (HIV) seropositive and HIV seronegative individuals, in a group of south Indians. Materials and Methods: Swabs from oral commissures of 46 patients were obtained and inoculated on to Sabouraud's dextrose agar (SDA) supplemented with chloramphenicol, blood agar (BA) and MacConkey's agar (MCA) plates and cultured. α-hemolytic Streptococci, Staphylococcus albus, Staphylococcus aureus, Candida species, Klebsiella species and Pseudomonas species were cultured. Candidal colonies were further speciated by the conventional biotyping technique. Results: In AC of HIV seropositive patients Candida albicans and Staphylococcus aureus were more prevalent than that in HIV seronegative patients. Incidentally in patients with CD4 cell count less than 200 there was an increase in the incidence of Candidal and Staphylococcus aureus colonization when compared to patients with CD4 cell count higher than 200. Conclusion: The present study suggests a definite difference in the microbial flora of AC in HIV seropositive patients than that of HIV seronegative population. PMID:24574650

Role of direct bioautographic method for detection of antistaphylococcal activity of essential oils.

PubMed

Horváth, Györgyi; Jámbor, Noémi; Kocsis, Erika; Böszörményi, Andrea; Lemberkovics, Eva; Héthelyi, Eva; Kovács, Krisztina; Kocsis, Béla

2011-09-01

The aim of the present study was the chemical characterization of some traditionally used and therapeutically relevant essential oils (thyme, eucalyptus, cinnamon bark, clove, and tea tree) and the optimized microbiological investigation of the effect of these oils on clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA). The chemical composition of the oils was analyzed by TLC, and controlled by gas chromatography (GC) and gas chromatography/mass spectrometry (GC/MS). The antibacterial effect was investigated using a TLC-bioautographic method. Antibacterial activity of thyme, clove and cinnamon oils, as well as their main components (thymol, carvacrol, eugenol, and cinnamic aldehyde) was observed against all the bacterial strains used in this study. The essential oils of eucalyptus and tea tree showed weak activity in the bioautographic system. On the whole, the antibacterial activity of the essential oils could be related to their most abundant components, but the effect of the minor components should also be taken into consideration. Direct bioautography is more cost-effective and better in comparison with traditional microbiological laboratory methods (e.g. disc-diffusion, agar-plate technique).

Inflammation Thread Runs across Medical Laboratory Specialities

PubMed Central

Lung, Thomas; Risch, Lorenz; Risch, Martin; Medina Escobar, Pedro; Bodmer, Thomas

2016-01-01

We work on the assumption that four major specialities or sectors of medical laboratory assays, comprising clinical chemistry, haematology, immunology, and microbiology, embraced by genome sequencing techniques, are routinely in use. Medical laboratory markers for inflammation serve as model: they are allotted to most fields of medical lab assays including genomics. Incessant coding of assays aligns each of them in the long lists of big data. As exemplified with the complement gene family, containing C2, C3, C8A, C8B, CFH, CFI, and ITGB2, heritability patterns/risk factors associated with diseases with genetic glitch of complement components are unfolding. The C4 component serum levels depend on sufficient vitamin D whilst low vitamin D is inversely related to IgG1, IgA, and C3 linking vitamin sufficiency to innate immunity. Whole genome sequencing of microbial organisms may distinguish virulent from nonvirulent and antibiotic resistant from nonresistant varieties of the same species and thus can be listed in personal big data banks including microbiological pathology; the big data warehouse continues to grow. PMID:27493451

Super-chilling (-0.7°C) with high-CO2 packaging inhibits biochemical changes of microbial origin in catfish (Clarias gariepinus) muscle during storage.

PubMed

Zhu, Yingchun; Ma, Lizhen; Yang, Hua; Xiao, Yan; Xiong, Youling L

2016-09-01

Controlled freezing-point storage (CFPS) is an emerging preservative technique desirable for fish. In the present study, catfish fillets were stored at -0.7°C under different packaging atmospheres: air (AP), vacuum (VP), and 60% CO2/40% N2 (MAP). Chemical, microbiological, and sensory analyses were performed during storage. Results showed the following descending order of chemical changes (degradation of nucleotides, conversion of protein to volatile-based nitrogen and biogenic amines, and production of trimethylamine nitrogen), as well as loss of sensory properties: 4°C AP>-0.7°C AP≈4°C VP>-0.7°C VP≈4°C MAP>-0.7°C MAP. The chemical changes were well-correlated with microbial growth suggesting the microbiological pathways. Hence, CFPS at -0.7°C in combination with high-CO2 MAP can effectively maintain the quality of fresh catfish meat compared to traditional preservation methods. Copyright © 2016 Elsevier Ltd. All rights reserved.

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).

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

Federating clinical data from six pediatric hospitals: process and initial results for microbiology from the PHIS+ consortium.

PubMed

Gouripeddi, Ramkiran; Warner, Phillip B; Mo, Peter; Levin, James E; Srivastava, Rajendu; Shah, Samir S; de Regt, David; Kirkendall, Eric; Bickel, Jonathan; Korgenski, E Kent; Precourt, Michelle; Stepanek, Richard L; Mitchell, Joyce A; Narus, Scott P; Keren, Ron

2012-01-01

Microbiology study results are necessary for conducting many comparative effectiveness research studies. Unlike core laboratory test results, microbiology results have a complex structure. Federating and integrating microbiology data from six disparate electronic medical record systems is challenging and requires a team of varied skills. The PHIS+ consortium which is partnership between members of the Pediatric Research in Inpatient Settings (PRIS) network, the Children's Hospital Association and the University of Utah, have used "FURTHeR' for federating laboratory data. We present our process and initial results for federating microbiology data from six pediatric hospitals.

76 FR 28443 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

... . Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group, Microbiology and..., Immunology, and Transplantation Research; 93.856, Microbiology and Infectious Diseases Research, National...

77 FR 298 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-04

....gov . Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group; Microbiology... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

78 FR 28858 - National Institute of Allergy and Infectious Diseases Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-16

....gov . Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group; Microbiology... Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and Infectious...

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.

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

Microbiological changes associated with dental prophylaxis.

PubMed

Goodson, J Max; Palys, Michael D; Carpino, Elizabeth; Regan, Elizabeth O; Sweeney, Michael; Socransky, Sigmund S

2004-11-01

Despite the common application of dental prophylaxis as part of patient therapy, there is little reported that describes the microbiological impact of this treatment. The authors gave 20 healthy college-aged subjects three dental prophylaxes with a fluoride-containing prophylaxis paste during a two-week period and instructed them in oral hygiene. They evaluated the microbiological composition of dental plaque samples collected before and after treatment using DNA probe analysis. They analyzed 40 representative bacterial species in seven bacterial complexes by checkerboard DNA-DNA hybridization assay techniques. After three dental prophylaxes, the patients' mean Gingival Index score decreased from 0.82 to 0.77, the mean Plaque Index score decreased from 0.72 to zero, and the total number of bacteria per tooth decreased to approximately one-third of the original number. The authors computed two different measures of bacterial presence. The reduction in bacterial numbers was statistically significant and occurred in many species. Bacterial proportion (DNA percentage or percentage of the bacteria per tooth) did not change significantly. Greater reductions in bacterial count occurred in species that showed high numbers before treatment. The total bacterial count decreased by approximately 72 percent of its original level before prophylaxis was initiated. Professional dental prophylaxis did not target any particular bacteria or bacterial groups but removed bacteria nonspecifically and in proportion to their initial numbers. Repeated dental prophylaxes effect a reduction in bacterial amount that is commensurate with the initial amount, but they do does not alter composition. This suggests that mild gingivitis may be a bacterially nonspecific effect of plaque accumulation and emphasizes the need for regular plaque removal to maintain optimal gingival health.

Microbes in Mascara: Hypothesis-Driven Research in a Nonmajor Biology Lab †

PubMed Central

Burleson, Kathryn M.; Martinez-Vaz, Betsy M.

2011-01-01

In this laboratory exercise, students were taught concepts of microbiology and scientific process through an everyday activity — cosmetic use. The students’ goals for the lab were to develop a hypothesis regarding microbial contamination in cosmetics, learn techniques to culture and differentiate microorganisms from cosmetics, and propose best practices in cosmetics use based on their findings. Prior to the lab, students took a pretest to assess their knowledge of scientific hypotheses, microbiology, and cosmetic safety. In the first week, students were introduced to microbiological concepts and methodologies, and cosmetic terminology and safety. Students completed a hypothesis-writing exercise before formulating and testing their own hypotheses regarding cosmetic contamination. Students provided a cosmetic of their own and, in consultation with their lab group, chose one product for testing. Samples were serially diluted and plated on a variety of selective media. In the second week, students analyzed their plates to determine the presence and diversity of microbes and if their hypotheses were supported. Students completed a worksheet of their results and were given a posttest to assess their knowledge. Average test scores improved from 5.2 (pretest) to 7.8 (posttest), with p-values < 0.0001. Seventy-nine percent (79%) of students correctly identified hypotheses that were not falsifiable or lacked variables, and 89% of students improved their scores on questions concerning safe cosmetic use. Ninety-one percent (91%) of students demonstrated increased knowledge of microbial concepts and methods. Based on our results, this lab is an easy, yet effective, way to enhance knowledge of scientific concepts for nonmajors, while maintaining relevance to everyday life. PMID:23653761

Team-Based Learning in a Pipeline Course in Medical Microbiology for Under-Represented Student Populations in Medicine Improves Learning of Microbiology Concepts.

PubMed

Behling, K C; Murphy, M M; Mitchell-Williams, J; Rogers-McQuade, H; Lopez, O J

2016-12-01

As part of an undergraduate pipeline program at our institution for students from underrepresented minorities in medicine backgrounds, we created an intensive four-week medical microbiology course. Team-based learning (TBL) was implemented in this course to enhance student learning of course content. Three different student cohorts participated in the study, and there were no significant differences in their prior academic achievement based on their undergraduate grade point average (GPA) and pre-course examination scores. Teaching techniques included engaged lectures using an audience response system, TBL, and guided self-directed learning. We hypothesized that more active learning exercises, irrespective of the amount of lecture time, would help students master course content. In year 2 as compared with year 1, TBL exercises were decreased from six to three with a concomitant increase in lecture time, while in year 3, TBL exercises were increased from three to six while maintaining the same amount of lecture time as in year 2. As we hypothesized, there was significant ( p < 0.01) improvement in performance on the post-course examination in years 1 and 3 compared with year 2, when only three TBL exercises were used. In contrast to the students' perceptions that more lecture time enhances learning of course content, our findings suggest that active learning strategies, such as TBL, are more effective than engaged lectures in improving student understanding of course content, as measured by post-course examination performance. Introduction of TBL in pipeline program courses may help achieve better student learning outcomes.

A study of the microbiology of breast abscess in a teaching hospital in Kuwait.

PubMed

Al Benwan, Khalifa; Al Mulla, Ahmed; Rotimi, Vincent O

2011-01-01

To determine the microbiological profile of breast abscess and assess the antibiotic susceptibility of the causative agents. Data obtained from cases of breast abscess over a period of 3.5 years, June 2006 to December 2009, were retrospectively analyzed. Specimens were cultured using optimal aerobic and anaerobic microbiological techniques. The antibiotic susceptibility test was carried out using the methods recommended by the Clinical and Laboratory Standards Institute. One specimen per patient was analyzed. Of the 114 patients, 107 (93.8%) non-lactating and 7 (6.1%) lactating women were diagnosed with breast abscess during this period. Of the 114 specimens, 83 (73%) yielded bacterial growth. Of these, 115 pathogens were isolated with an average of 1.4 pathogens per abscess. Eighteen (22%) of the 83 specimens yielded mixed bacterial growth. There were more Gram-positive pathogens (60, 52%) than anaerobes (32, 28%) and Gram-negative pathogens (22, 19%). The predominant organisms were methicillin-susceptible Staphylococcus aureus (37, 32%), methicillin-resistant S. aureus (MRSA; 11, 10%), Bacteroides spp. (16, 14%), anaerobic streptococci (14, 12%) and Pseudomonas aeruginosa (9, 8%). Of the 48 S. aureus, MRSA accounted for 11 (23%). All MRSA isolates were susceptible to trimethoprim-sulfamethoxazole and vancomycin. S. aureus was the most common pathogenic organism isolated in breast abscesses at Al-Amiri Hospital, Kuwait, of which 23% were MRSA. Nearly a third of the cases were caused by anaerobes, particularly B. fragilis. The data present a basis for the formation of empirical antimicrobial therapeutic policy in the management of breast abscess. Copyright © 2011 S. Karger AG, Basel.

Contribution of sonicate-fluid cultures and broad-range PCR to microbiological diagnosis in vascular graft infections.

PubMed

Kokosar Ulcar, Barbara; Lakic, Nikola; Jeverica, Samo; Pecavar, Blaz; Logar, Mateja; Cerar, Tjasa Kisek; Lejko-Zupanc, Tatjana

2018-06-01

Vascular graft infections (VGI) are associated with considerable morbidity and mortality, and antimicrobial treatment is an important adjunct to surgical treatment. While microbial aetiology of VGI is often difficult to determine, other techniques such as sonication of implanted material may be used to enhance the recovery of biofilm-associated organisms. We performed a retrospective analysis of 22 consecutive patients treated for VGI at University Medical Centre Ljubljana from May 2011 through January 2015. Explanted vascular grafts were flooded with sterile Ringer solution, sonicated for 1 min at a frequency of 40 kHz and inoculated on solid and liquid culture media. Aerobic and anaerobic cultures were performed, incubated for 14 days and any significant bacterial growth was quantitatively evaluated. Additionally, broad-range PCR from sonicate fluid was performed. Microbiological results were compared with the results of preoperatively taken blood cultures and the results of intraoperative tissue cultures (material from peri-graft collection). Identification of the causative organism (irrespective of the method) was achieved in 95.8%. Preoperative blood cultures were positive in 35.3%, intraoperative tissue cultures in 31.8%, sonicate fluid culture in 79.2%, while broad-range PCR from sonicate fluid was positive in 66.7%. In 37.5% the pathogen detected in sonicate fluid culture or broad-range PCR was the only positive microbiological result. Sonicate fluid culture and broad-range PCR from explanted vascular grafts may contribute to optimization of antimicrobial treatment. Optimal timing of antibiotic therapy before explantation should be further assessed to improve diagnostic yield.

Microbiological and clinical assessment of the abutment and non-abutment teeth of partial removable denture wearers.

PubMed

Costa, Luciana; do Nascimento, Cássio; de Souza, Valéria Oliveira Pagnano; Pedrazzi, Vinícius

2017-03-01

The aim of this study was assessing the changes in both clinical and microbiological parameters of healthy individuals after rehabilitation with removable partial denture (RPD). 11 women received unilateral or bilateral free-end saddle RPD in the mandibular arch. Clinical and microbiological parameters of abutment, non-abutment, and antagonist teeth were assessed at baseline (RPD installation) and after 7, 30, 90, and 180days of function. The Checkerboard DNA-DNA hybridization technique was used to identify and quantify up to 43 different microbial species from subgingival biofilm samples. Probing depth, gingival recession, and bleeding on probing were also investigated over time. The total and individual microbial genome counts were shown significantly increased after 180days with no significant differences between abutment, non-abutment, or antagonist teeth. Streptococcus spp., Aggregatibacter actinomycetemcomitans, and other species associated to periodontitis (Peptostreptococcus anaerobius, Prevotella nigrescens, and Tannerella forsythia), as well as opportunistic Candida spp., were recovered in moderate counts. Abutment teeth presented higher values of gingival recession when compared with non-abutment or antagonist teeth, irrespectively time of sampling (p<0.05). No significant differences were found between groups regarding bleeding on probing or probing depth over time. Overall, the microbial counts significantly increased after 6 months of denture loading for both abutment and non-abutment teeth with no significant differences regarding the microbial profile over time. Bleeding on probing and probing depth showed no significant difference between groups over time whereas gingival recession increased in the abutment teeth. Copyright © 2016 Elsevier Ltd. All rights reserved.

Field and Lab-Based Microbiological Investigations of the Marcellus Shale

NASA Astrophysics Data System (ADS)

Wishart, J. R.; Neumann, K.; Edenborn, H. M.; Hakala, A.; Yang, J.; Torres, M. E.; Colwell, F. S.

2013-12-01

The recent exploration of shales for natural gas resources has provided the opportunity to study their subsurface geochemistry and microbiology. Evidence indicates that shale environments are marked by extreme conditions such as high temperature and pressure, low porosity, permeability and connectivity, and the presence of heavy metals and radionuclides. It has been postulated that many of these shales are naturally sterile due to the high pressure and temperature conditions under which they were formed. However, it has been shown in the Antrim and New Albany shales that microbial communities do exist in these environments. Here we review geochemical and microbiological evidence for the possible habitation of the Marcellus shale by microorganisms and compare these conditions to other shales in the U.S. Furthermore, we describe the development of sampling and analysis techniques used to evaluate microbial communities present in the Marcellus shale and associated hydraulic fracturing fluid. Sampling techniques thus far have consisted of collecting flowback fluids from wells and water impoundments and collecting core material from previous drilling expeditions. Furthermore, DNA extraction was performed on Marcellus shale sub-core with a MoBio PowerSoil kit to determine its efficiency. Assessment of the Marcellus shale indicates that it has low porosity and permeability that are not conducive to dense microbial populations; however, moderate temperatures and a natural fracture network may support a microbial community especially in zones where the Marcellus intersects more porous geologic formations. Also, hydraulic fracturing extends this fracture network providing more environments where microbial communities can exist. Previous research which collected flowback fluids has revealed a diverse microbial community that may be derived from hydrofrac fluid production or from the subsurface. DNA extraction from 10 g samples of Marcellus shale sub-core were unsuccessful even when samples were spiked with 8x108 cells/g of shale. This indicated that constituents of shale such as high levels of carbonates, humic acids and metals likely inhibited components of the PowerSoil kit. Future research is focused on refining sample collection and analyses to gain a full understanding of the microbiology of the Marcellus shale and associated flowback fluids. This includes the development of an in situ osmosampler, which will collect temporally relevant fluid and colonized substrate samples. The design of the osmosampler for hydraulic fracturing wells is being adapted from those used to sample marine environments. Furthermore, incubation experiments are underway to study interactions between microbial communities associated with hydraulic fracturing fluid and Marcellus shale samples. In conclusion, evidence suggests that the Marcellus shale is a possible component of the subsurface biosphere. Future studies will be valuable in determining the microbial community structure and function in relation to the geochemistry of the Marcellus shale and its future development as a natural gas resource.

Space Tourism and Safety from Infection

NASA Astrophysics Data System (ADS)

Ilyin, V. K.; Tiurina, D. A.; Usanova, N. A.; Starkova, L. V.; Soloviova, Z. O.; Morozova, Ju. A.; Kirjukhina, N. V.; Webb, A.

This paper highlights the major scenarios of the microbiological changes which occur in the human organism in space missions, i.e. the increasing of the conventional pathogen population share in human microflora and changes in antibiotic susceptibility, and substantiates compatible countermeasures based on probiotics consumption. Special attention is given to the prospects of the consumption of probiotics made of strains which are representative of human commensurate microflora for the support of resistance during a space journey. It is a most important technique and one which will be acceptable for space tourists.

Basis of predictive mycology.

PubMed

Dantigny, Philippe; Guilmart, Audrey; Bensoussan, Maurice

2005-04-15

For over 20 years, predictive microbiology focused on food-pathogenic bacteria. Few studies concerned modelling fungal development. On one hand, most of food mycologists are not familiar with modelling techniques; on the other hand, people involved in modelling are developing tools dedicated to bacteria. Therefore, there is a tendency to extend the use of models that were developed for bacteria to moulds. However, some mould specificities should be taken into account. The use of specific models for predicting germination and growth of fungi was advocated previously []. This paper provides a short review of fungal modelling studies.

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.

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.

Federating Clinical Data from Six Pediatric Hospitals: Process and Initial Results for Microbiology from the PHIS+ Consortium

PubMed Central

Gouripeddi, Ramkiran; Warner, Phillip B.; Mo, Peter; Levin, James E.; Srivastava, Rajendu; Shah, Samir S.; de Regt, David; Kirkendall, Eric; Bickel, Jonathan; Korgenski, E. Kent; Precourt, Michelle; Stepanek, Richard L.; Mitchell, Joyce A.; Narus, Scott P.; Keren, Ron

2012-01-01

Microbiology study results are necessary for conducting many comparative effectiveness research studies. Unlike core laboratory test results, microbiology results have a complex structure. Federating and integrating microbiology data from six disparate electronic medical record systems is challenging and requires a team of varied skills. The PHIS+ consortium which is partnership between members of the Pediatric Research in Inpatient Settings (PRIS) network, the Children’s Hospital Association and the University of Utah, have used “FURTHeR’ for federating laboratory data. We present our process and initial results for federating microbiology data from six pediatric hospitals. PMID:23304298

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

PubMed

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

2012-08-01

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

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

PubMed Central

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

2012-01-01

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

Use of microbiological indicators for assessing hygiene controls for the manufacture of powdered infant formula.

PubMed

Buchanan, Robert L; Oni, Ruth

2012-05-01

Microbiological testing for various indicator microorganisms is used extensively as a means of verifying the effectiveness of efforts to ensure the microbiological quality and safety of a wide variety of foods. However, for each use of an indicator organism the underlying scientific assumptions related to the behavior of the target microorganism, the characteristics of the food matrix, the details of the food manufacturing processes, environment, and distribution system, and the methodological basis for the assay must be evaluated to determine the validity, utility, and efficacy of potential microbiological indicator tests. The recent adoption by the Codex Alimentarius Commission of microbiological criteria for powdered infant formulae and related products provides an excellent example of an evidence-based approach for the establishment of consensus microbiological criteria. The present article reviews these criteria and those of various national governments in relation to emerging principles for the evidence-based establishment of effective indicator organisms.

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.

Application of flow cytometry to wine microorganisms.

PubMed

Longin, Cédric; Petitgonnet, Clément; Guilloux-Benatier, Michèle; Rousseaux, Sandrine; Alexandre, Hervé

2017-04-01

Flow cytometry (FCM) is a powerful technique allowing detection and enumeration of microbial populations in food and during food process. Thanks to the fluorescent dyes used and specific probes, FCM provides information about cell physiological state and allows enumeration of a microorganism in a mixed culture. Thus, this technique is increasingly used to quantify pathogen, spoilage microorganisms and microorganisms of interest. Since one decade, FCM applications to the wine field increase greatly to determine population and physiological state of microorganisms performing alcoholic and malolactic fermentations. Wine spoilage microorganisms were also studied. In this review we briefly describe FCM principles. Next, a deep revision concerning enumeration of wine microorganisms by FCM is presented including the fluorescent dyes used and techniques allowing a yeast and bacteria species specific enumeration. Then, the last chapter is dedicated to fluorescent dyes which are used to date in fluorescent microscopy but applicable in FCM. This chapter also describes other interesting "future" techniques which could be applied to study the wine microorganisms. Thus, this review seeks to highlight the main advantages of the flow cytometry applied to wine microbiology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Colloquium and Report on Systems Microbiology: Beyond Microbial Genomics

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

Merry R. Buckley

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

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.

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.

A manual and an automatic TERS based virus discrimination

NASA Astrophysics Data System (ADS)

Olschewski, Konstanze; Kämmer, Evelyn; Stöckel, Stephan; Bocklitz, Thomas; Deckert-Gaudig, Tanja; Zell, Roland; Cialla-May, Dana; Weber, Karina; Deckert, Volker; Popp, Jürgen

2015-02-01

Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%.Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07033j

Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid.

PubMed

Dickson, Robert P; Erb-Downward, John R; Prescott, Hallie C; Martinez, Fernando J; Curtis, Jeffrey L; Lama, Vibha N; Huffnagle, Gary B

2014-10-01

The diagnosis and management of pneumonia are limited by the use of culture-based techniques of microbial identification, which may fail to identify unculturable, fastidious, and metabolically active viable but unculturable bacteria. Novel high-throughput culture-independent techniques hold promise but have not been systematically compared to conventional culture. We analyzed 46 clinically obtained bronchoalveolar lavage (BAL) fluid specimens from symptomatic and asymptomatic lung transplant recipients both by culture (using a clinical microbiology laboratory protocol) and by bacterial 16S rRNA gene pyrosequencing. Bacteria were identified in 44 of 46 (95.7%) BAL fluid specimens by culture-independent sequencing, significantly more than the number of specimens in which bacteria were detected (37 of 46, 80.4%, P ≤ 0.05) or "pathogen" species reported (18 of 46, 39.1%, P ≤ 0.0001) via culture. Identification of bacteria by culture was positively associated with culture-independent indices of infection (total bacterial DNA burden and low bacterial community diversity) (P ≤ 0.01). In BAL fluid specimens with no culture growth, the amount of bacterial DNA was greater than that in reagent and rinse controls, and communities were markedly dominated by select Gammaproteobacteria, notably Escherichia species and Pseudomonas fluorescens. Culture growth above the threshold of 10(4) CFU/ml was correlated with increased bacterial DNA burden (P < 0.01), decreased community diversity (P < 0.05), and increased relative abundance of Pseudomonas aeruginosa (P < 0.001). We present two case studies in which culture-independent techniques identified a respiratory pathogen missed by culture and clarified whether a cultured "oral flora" species represented a state of acute infection. In summary, we found that bacterial culture of BAL fluid is largely effective in discriminating acute infection from its absence and identified some specific limitations of BAL fluid culture in the diagnosis of pneumonia. We report the first correlation of quantitative BAL fluid culture results with culture-independent evidence of infection. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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)

Acinetobacter Peritoneal Dialysis Peritonitis: A Changing Landscape over Time

PubMed Central

Chao, Chia-Ter; Lee, Szu-Ying; Yang, Wei-Shun; Chen, Huei-Wen; Fang, Cheng-Chung; Yen, Chung-Jen; Chiang, Chih-Kang; Hung, Kuan-Yu; Huang, Jenq-Wen

2014-01-01

Background Acinetobacter species are assuming an increasingly important role in modern medicine, with their persistent presence in health-care settings and antibiotic resistance. However, clinical reports addressing this issue in patients with peritoneal dialysis (PD) peritonitis are rare. Methods All PD peritonitis episodes caused by Acinetobacter that occurred between 1985 and 2012 at a single centre were retrospectively reviewed. Clinical features, microbiological data, and outcomes were analysed, with stratifications based upon temporal periods (before and after 2000). Results Acinetobacter species were responsible for 26 PD peritonitis episodes (3.5% of all episodes) in 25 patients. A. baumannii was the most common pathogen (54%), followed by A. iwoffii (35%), with the former being predominant after 2000. Significantly more episodes resulted from breaks in exchange sterility after 2000, while those from exit site infections decreased (P = 0.01). The interval between the last and current peritonitis episodes lengthened significantly after 2000 (5 vs. 13.6 months; P = 0.05). All the isolates were susceptible to cefepime, fluoroquinolone, and aminoglycosides, with a low ceftazidime resistance rate (16%). Nearly half of the patients (46%) required hospitalisation for their Acinetobacter PD-associated peritonitis, and 27% required an antibiotic switch. The overall outcome was fair, with no mortality and a 12% technique failure rate, without obvious interval differences. Conclusions The temporal change in the microbiology and origin of Acinetobacter PD-associated peritonitis in our cohort suggested an important evolutional trend. Appropriate measures, including technique re-education and sterility maintenance, should be taken to decrease the Acinetobacter peritonitis incidence in PD patients. PMID:25314341

Microbiological Contamination of Drugs during Their Administration for Anesthesia in the Operating Room.

PubMed

Gargiulo, Derryn A; Mitchell, Simon J; Sheridan, Janie; Short, Timothy G; Swift, Simon; Torrie, Jane; Webster, Craig S; Merry, Alan F

2016-04-01

The aseptic techniques of anesthesiologists in the preparation and administration of injected medications have not been extensively investigated, but emerging data demonstrate that inadvertent lapses in aseptic technique may be an important contributor to surgical site and other postoperative infections. A prospective, open, microbiological audit of 303 cases in which anesthesiologists were asked to inject all bolus drugs, except propofol and antibiotics, through a 0.2-µm filter was performed. The authors cultured microorganisms, if present, from the 0.2-µm filter unit and from the residual contents of the syringes used for drawing up or administering drugs. Participating anesthesiologists rated ease of use of the filters after each case. Twenty-three anesthesiologists each anesthetized up to 25 adult patients. The authors isolated microorganisms from filter units in 19 (6.3%) of 300 cases (3 cases were excluded), including Staphylococcus capitis, Staphylococcus warneri, Staphylococcus epidermidis, Staphylococcus haemolyticus, Micrococcus luteus/lylae, Corynebacterium, and Bacillus species. The authors collected used syringes at the end of each case and grew microorganisms from residual drug in 55 of these 2,318 (2.4%) syringes including all the aforementioned microorganisms and also Kocuria kristinae, Staphylococcus aureus, and Staphylococcus hominus. Participants' average rating of ease of use of the filter units was 3.5 out of 10 (0 being very easy and 10 being very difficult). Microorganisms with the potential to cause infection are being injected (presumably inadvertently) into some patients during the administration of intravenous drugs by bolus during anesthesia. The relevance of this finding to postoperative infections warrants further investigation.

Prevention and diagnosis of ventilator-associated pneumonia: a survey on current practices in Southern Spanish ICUs.

PubMed

Sierra, Rafael; Benítez, Encarnación; León, Cristóbal; Rello, Jordi

2005-09-01

To assess the implementation of selected ventilator-associated pneumonia (VAP) prevention strategies, and to learn how VAP is diagnosed in the ICUs of Southern Spain. Multicentric survey. The ICUs of 32 hospitals of the public health-care system of Southern Spain. Directors of ICUs. None. Twenty-eight ICUs (87.5%) returned completed questionnaires. Ventilator circuits were changed every 72 h or longer in 75% of ICUs. Use of heat and moisture exchangers and open endotracheal suction systems were reported in 96% of ICUs. Subglottic secretion drainage was never used, and 57% of ICUs checked endotracheal tube cuff pressure at least daily. Semi-recumbent position was common (93%), and 67.5% of ICUs used frequently noninvasive ventilation. Continuous enteral feeding was reported in all ICUs. Sedative infusions were usually interrupted every day in 11% of ICUs. Seventy-five percent of ICUs had specific guidelines for antibiotic therapy of VAP, but rotation of antibiotics was uncommon (11%). Twenty-nine percent of ICUs diagnosed VAP without microbiological confirmation. The most used technique for microbiologic diagnosis was qualitative culture of endotracheal aspirates (42.8%). The centers with a larger structural complexity reported using VAP therapy guidelines more frequently than the smaller centers, but they did not utilized bronchoscopic techniques for diagnosing VAP. Common prevention and diagnostic procedures in clinical practice, including large teaching institutions, significantly differed from evidence-based recommendations and reports by research groups of excellence. In addition, our study suggests that clinical practice for preventing and diagnosing VAP is variable and many opportunities exist to improve the care of patients receiving mechanical ventilation.

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

Clinical Microbiology Laboratories' Adoption of Culture-Independent Diagnostic Tests Is a Threat to Foodborne-Disease Surveillance in the United States.

PubMed

Shea, Shari; Kubota, Kristy A; Maguire, Hugh; Gladbach, Stephen; Woron, Amy; Atkinson-Dunn, Robyn; Couturier, Marc Roger; Miller, Melissa B

2017-01-01

INTRODUCTIONIn November 2015, the Centers for Disease Control and Prevention (CDC) sent a letter to state and territorial epidemiologists, state and territorial public health laboratory directors, and state and territorial health officials. In this letter, culture-independent diagnostic tests (CIDTs) for detection of enteric pathogens were characterized as "a serious and current threat to public health surveillance, particularly for Shiga toxin-producing Escherichia coli (STEC) and Salmonella" The document says CDC and its public health partners are approaching this issue, in part, by "reviewing regulatory authority in public health agencies to require culture isolates or specimen submission if CIDTs are used." Large-scale foodborne outbreaks are a continuing threat to public health, and tracking these outbreaks is an important tool in shortening them and developing strategies to prevent them. It is clear that the use of CIDTs for enteric pathogen detection, including both antigen detection and multiplex nucleic acid amplification techniques, is becoming more widespread. Furthermore, some clinical microbiology laboratories will resist the mandate to require submission of culture isolates, since it will likely not improve patient outcomes but may add significant costs. Specimen submission would be less expensive and time-consuming for clinical laboratories; however, this approach would be burdensome for public health laboratories, since those laboratories would need to perform culture isolation prior to typing. Shari Shea and Kristy Kubota from the Association of Public Health Laboratories, along with state public health laboratory officials from Colorado, Missouri, Tennessee, and Utah, will explain the public health laboratories' perspective on why having access to isolates of enteric pathogens is essential for public health surveillance, detection, and tracking of outbreaks and offer potential workable solutions which will allow them to do this. Marc Couturier of ARUP Laboratories and Melissa Miller of the University of North Carolina will explain the advantages of CIDTs for enteric pathogens and discuss practical solutions for clinical microbiology laboratories to address these public health needs. Copyright © 2016 American Society for Microbiology.

Short-term clinical and microbiologic effects of pocket debridement with an Er:YAG laser during periodontal maintenance.

PubMed

Tomasi, Cristiano; Schander, Kerstin; Dahlén, Gunnar; Wennström, Jan L

2006-01-01

The erbium-doped:yttrium, aluminum, and garnet (Er:YAG) laser is considered a useful tool for subgingival debridement because the laser treatment creates minimal damage to the root surface and has potential antimicrobial effects. The aim of this randomized controlled clinical trial was to evaluate clinical and microbiologic effects of pocket debridement using an Er:YAG laser in patients during periodontal maintenance. Twenty patients at a recall visit for maintenance were consecutively recruited if presenting at least four teeth with residual probing depth (PD) > or = 5 mm. Two pockets in each of two jaw quadrants were randomly assigned to subgingival debridement using 1) an Er:YAG laser (test) or 2) an ultrasonic scaler (control). The laser beam was set at 160 mJ with a pulse frequency of 10 Hz. Clinical variables were recorded at baseline, 1 month, and 4 months after treatment. Primary clinical outcome variables were changes in PD and clinical attachment level (CAL). Microbiologic analysis of subgingival samples was performed at baseline, 2 days, and 30 days after treatment using a checkerboard DNA-DNA hybridization technique against 12 periodontal disease-associated species. The mean initial PD was 6.0 mm (SD: 1.2) in the test group and 5.8 mm (SD: 0.9) in the control group. At 1 month post-treatment, the PD reduction was significantly greater for test than control sites (0.9 versus 0.5 mm; P <0.05). The CAL gain also was significantly greater (0.5 versus 0.06 mm; P <0.01). At the 4-month examination, no significant differences were detected in PD reduction (1.1 versus 1.0 mm) or CAL gain (0.6 versus 0.4 mm). Both treatments resulted in reduction of the subgingival microflora. No significant differences in microbiologic composition were identified between the treatment groups at various time intervals. Degree of treatment discomfort scored significantly lower for the test than the control treatment modality. The results of the trial failed to demonstrate any apparent advantage of using an Er:YAG laser for subgingival debridement, except less treatment discomfort perceived by the patients.

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...

Microbiological Analysis of the Food Preparation and Dining Facilities at Fort Myer and Bolling Air Force Base

DTIC Science & Technology

1975-02-01

the viewpoint of microbiological safety one would be tempted to conclude that Ft. Myer had a much lower risk hazard than Bolting Air Force Base. The...I TECHNICAL REPORT I I 76·63-FSL MICROBIOLOGICAL ANAL.YSIS OF THE FOOD PREPARATION AND DINING FACILITIES AT FORT MYER AND BOLLING AIR FORCE...RECIPIENT’ S CATALOG NUMBER 75-53-ESL 4. TITLE (and Subtltlo) 5. TYPE OF REPOR T & PERIOD COVERED Microbiological Analysis of the Food Preparation and

[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.

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.

A safety analysis of food waste-derived animal feeds from three typical conversion techniques in China.

PubMed

Chen, Ting; Jin, Yiying; Shen, Dongsheng

2015-11-01

This study was based on the food waste to animal feed demonstration projects in China. A safety analysis of animal feeds from three typical treatment processes (i.e., fermentation, heat treatment, and coupled hydrothermal treatment and fermentation) was presented. The following factors are considered in this study: nutritive values characterized by organoleptic properties and general nutritional indices; the presence of bovine- and sheep-derived materials; microbiological indices for Salmonella, total coliform (TC), total aerobic plate counts (TAC), molds and yeast (MY), Staphylococcus Aureus (SA), and Listeria; chemical contaminant indices for hazardous trace elements such as Cr, Cd, and As; and nitrite and organic contaminants such as aflatoxin B1 (AFB1) and hexachlorocyclohexane (HCH). The present study reveals that the feeds from all three conversion processes showed balanced nutritional content and retained a certain feed value. The microbiological indices and the chemical contaminant indices for HCH, dichlorodiphenyltrichloroethane (DDT), nitrite, and mercury all met pertinent feed standards; however, the presence of bovine- and sheep-derived materials and a few chemical contaminants such as Pb were close to or might exceed the legislation permitted values in animal feeding. From the view of treatment techniques, all feed retained part of the nutritional values of the food waste after the conversion processes. Controlled heat treatment can guarantee the inactivation of bacterial pathogens, but none of the three techniques can guarantee the absence of cattle- and sheep-derived materials and acceptable levels of certain contaminants. The results obtained in this research and the feedstuffs legislation related to animal feed indicated that food waste-derived feed could be considered an adequate alternative to be used in animal diets, while the feeding action should be changed with the different qualities of the products, such as restrictions on the application of ruminants, and recycling as formula feeds. Copyright © 2015 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.

77 FR 28398 - National Institute of Allergy and Infectious Diseases Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-14

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group, Microbiology and Infectious Diseases B Subcommittee. Date: June 7, 2012..., and Transplantation Research; 93.856, Microbiology and Infectious Diseases Research, National...

78 FR 6126 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-29

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group, Microbiology and Infectious Diseases B Subcommittee. Date: February 20-21..., Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and Infectious Diseases Research...

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…

75 FR 28029 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-19

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group; Microbiology and Infectious Diseases B Subcommittee. Date: June 10, 2010....855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and Infectious Diseases...

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.

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.

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.

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.

Biotechnical use of polymerase chain reaction for microbiological analysis of biological samples.

PubMed

Lantz, P G; Abu al-Soud, W; Knutsson, R; Hahn-Hägerdal, B; Rådström, P

2000-01-01

Since its introduction in the mid-80s, polymerase chain reaction (PCR) technology has been recognised as a rapid, sensitive and specific molecular diagnostic tool for the analysis of micro-organisms in clinical, environmental and food samples. Although this technique can be extremely effective with pure solutions of nucleic acids, it's sensitivity may be reduced dramatically when applied directly to biological samples. This review describes PCR technology as a microbial detection method, PCR inhibitors in biological samples and various sample preparation techniques that can be used to facilitate PCR detection, by either separating the micro-organisms from PCR inhibitors and/or by concentrating the micro-organisms to detectable concentrations. Parts of this review are updated and based on a doctoral thesis by Lantz [1] and on a review discussing methods to overcome PCR inhibition in foods [2].

Combined use of atomic force microscopy, X-ray photoelectron spectroscopy, and secondary ion mass spectrometry for cell surface analysis.

PubMed

Dague, Etienne; Delcorte, Arnaud; Latgé, Jean-Paul; Dufrêne, Yves F

2008-04-01

Understanding the surface properties of microbial cells is a major challenge of current microbiological research and a key to efficiently exploit them in biotechnology. Here, we used three advanced surface analysis techniques with different sensitivity, probing depth, and lateral resolution, that is, in situ atomic force microscopy, X-ray photoelectron spectroscopy, and secondary ion mass spectrometry, to gain insight into the surface properties of the conidia of the human fungal pathogen Aspergillus fumigatus. We show that the native ultrastructure, surface protein and polysaccharide concentrations, and amino acid composition of three mutants affected in hydrophobin production are markedly different from those of the wild-type, thereby providing novel insight into the cell wall architecture of A. fumigatus. The results demonstrate the power of using multiple complementary techniques for probing microbial cell surfaces.

Helicobacter pylori Detection and Antimicrobial Susceptibility Testing

PubMed Central

Mégraud, Francis; Lehours, Philippe

2007-01-01

The discovery of Helicobacter pylori in 1982 was the starting point of a revolution concerning the concepts and management of gastroduodenal diseases. It is now well accepted that the most common stomach disease, peptic ulcer disease, is an infectious disease, and all consensus conferences agree that the causative agent, H. pylori, must be treated with antibiotics. Furthermore, the concept emerged that this bacterium could be the trigger of various malignant diseases of the stomach, and it is now a model for chronic bacterial infections causing cancer. Most of the many different techniques involved in diagnosis of H. pylori infection are performed in clinical microbiology laboratories. The aim of this article is to review the current status of these methods and their application, highlighting the important progress which has been made in the past decade. Both invasive and noninvasive techniques will be reviewed. PMID:17428887

First record of Talaromyces udagawae in soil related to decomposing human remains in Argentina.

PubMed

Tranchida, María C; Centeno, Néstor D; Stenglein, Sebastián A; Cabello, Marta N

2016-01-01

The morphologic features of Talaromyces udagawae Stolk and Samson are here described and illustrated. This teleomorphic Ascomycota fungus was isolated from soil obtained in Buenos Aires province (Argentina) from beneath a human cadaver in an advanced state of decomposition. After washing and serial dilution of the soil along with moist-chamber techniques for fungal cultivation, T. udagawae formed very restricted colonies of bright yellow color on different growth media with 8-ascospored asci. The ascospores were ellipsoidal and ornamented. The anamorphic state was not observed. Molecular-genetic techniques identified the species. The present record is the first of the species in Argentina, pointing it as a tool to identify soils where cadaver decomposition occurs. Copyright © 2015 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

75 FR 4094 - National Institute of Allergy And Infectious Diseases; Notice of Closed Meetings

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2010-01-26

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Detection of Pneumonia Associated Pathogens Using a Prototype Multiplexed Pneumonia Test in Hospitalized Patients with Severe Pneumonia

PubMed Central

Schulte, Berit; Eickmeyer, Holm; Heininger, Alexandra; Juretzek, Stephanie; Karrasch, Matthias; Denis, Olivier; Roisin, Sandrine; Pletz, Mathias W.; Klein, Matthias; Barth, Sandra; Lüdke, Gerd H.; Thews, Anne; Torres, Antoni; Cillóniz, Catia; Straube, Eberhard; Autenrieth, Ingo B.; Keller, Peter M.

2014-01-01

Severe pneumonia remains an important cause of morbidity and mortality. Polymerase chain reaction (PCR) has been shown to be more sensitive than current standard microbiological methods – particularly in patients with prior antibiotic treatment – and therefore, may improve the accuracy of microbiological diagnosis for hospitalized patients with pneumonia. Conventional detection techniques and multiplex PCR for 14 typical bacterial pneumonia-associated pathogens were performed on respiratory samples collected from adult hospitalized patients enrolled in a prospective multi-center study. Patients were enrolled from March until September 2012. A total of 739 fresh, native samples were eligible for analysis, of which 75 were sputa, 421 aspirates, and 234 bronchial lavages. 276 pathogens were detected by microbiology for which a valid PCR result was generated (positive or negative detection result by Curetis prototype system). Among these, 120 were identified by the prototype assay, 50 pathogens were not detected. Overall performance of the prototype for pathogen identification was 70.6% sensitivity (95% confidence interval (CI) lower bound: 63.3%, upper bound: 76.9%) and 95.2% specificity (95% CI lower bound: 94.6%, upper bound: 95.7%). Based on the study results, device cut-off settings were adjusted for future series production. The overall performance with the settings of the CE series production devices was 78.7% sensitivity (95% CI lower bound: 72.1%) and 96.6% specificity (95% CI lower bound: 96.1%). Time to result was 5.2 hours (median) for the prototype test and 43.5 h for standard-of-care. The Pneumonia Application provides a rapid and moderately sensitive assay for the detection of pneumonia-causing pathogens with minimal hands-on time. Trial Registration Deutsches Register Klinischer Studien (DRKS) DRKS00005684 PMID:25397673

Developing best practice for fungal specimen management: audit of UK microbiology laboratories.

PubMed

Lasseter, G; Palmer, M; Morgan, J; Watts, J; Yoxall, H; Kibbler, C; McNulty, C

2011-01-01

This study represents an audit of microbiology laboratories in the UK to ascertain whether they are aware of, or follow, the Health Protection Agency (HPA) National Standard Methods Standard Operating Procedure (NSM SOP) for the investigation of dermatological specimens for superficial mycoses, or use a locally adapted version. A questionnaire audit was distributed to 179 NHS microbiology laboratories throughout England, Wales, Scotland and Northern Ireland. The NSM SOP was followed by 92% of laboratories for the microscopy of dermatological samples; light microscopy/ KOH digestion was used by 63% and fluorescence microscopy/KOH digestion by 29% of laboratories. Preliminary reports post-microscopy were issued by 98% of laboratories, with 93% issuing reports within 48 hours. Adherence to the NSM SOP guidelines for culture was low; only 34% of laboratories incubated microscopy-negative specimens for the recommended 14 days, while approximately 60% incubated microscopy-positive specimens for 21 days. The culture medium recommended by the NSM SOP was used in 82% of laboratories. Comments were added to culture reports by 51% of laboratories; most were added manually and comments varied between laboratories. Nail samples were the most common sample received from primary care, followed by skin and hair. These results show no significant difference in the rate of microscopy positives versus culture positives. Microscopy and culture are the easiest and cheapest methods available to UK laboratories for the investigation of suspected superficial fungal infections. Although most laboratories included in this audit claimed to follow the NSM SOP for microscopy and culture, these results show that the techniques used vary throughout the UK. To maximise the service provided to primary care, UK laboratories should use standardise methods based on the NSM SOP.

[A day in Spanish microbiology. Descriptive study of the activity of the clinical microbiology departments].

PubMed

Prieto, J; García-Rodríguez, Ja; Barberán, J; Granizo, Jj; Rodicio, Mp; González, J

2008-12-01

The laboratory is an essential part of the work in the Clinical Microbiology Department. This study has aimed to measure the activity of these laboratories. A survey was self-administered on the activity occurring during one work day by each hospital in October 2007. Thirty six hospitals reported 14,076 tests. Serology was the most frequently reported test (30.3%) followed by urine culture (27.8 %), blood tests (13.2 %), respiratory tract samples (8%), feces (7.1%), urethral (5.8%), skin (5.3%) and cerebrospinal fluid (2.6%). According to species, 73.2% of the isolates were bacteria (22.9 % were positive), 8.9% were virus (17% positive), fungi 8.1% (25.2% positive), and 5.5% mycobacterias (5.9% were positive) and parasite 4.5% (12.5% positive). Susceptibility test were performed by automatic methods (62.3%) followed by diffusion test (27.1%) and E-test (9.1%). A total of 5.6% of the susceptibility tests showed in vitro resistance to antibiotics. Fungi were identified in 108 isolates. Candida and Aspergillus were the most frequent genus (85.1% and 8.3%, respectively). Origins of the samples were: lower respiratory tract (32.4 %), genital tract (24.1 %), urine (10.2 %), blood (10.2 %) and skin (10.2 %). Twelve identification techniques were used, the most frequent being the morphological test (54.8%) and biochemical test (39.7%). Broken down by departments, 20.4% were sent from the ICU, 16.7% from surgery, 29.6% from medicine and 18.5% from primary care. Although the workload of the laboratories has been measured in this work, aspects such as specimen manipulation, clinical advice and research were not considered.

Incorrect diagnosis of Clostridium difficile infection in a university hospital in Japan.

PubMed

Mori, Nobuaki; Yoshizawa, Sadako; Saga, Tomoo; Ishii, Yoshikazu; Murakami, Hinako; Iwata, Morihiro; Collins, Deirdre A; Riley, Thomas V; Tateda, Kazuhiro

2015-10-01

Physicians often fail to suspect Clostridium difficile infection (CDI) and many microbiology laboratories use suboptimal diagnostic techniques. To estimate the extent of and reasons for incorrect diagnosis of CDI in Japan, we investigated toxigenic C. difficile isolated from all stool culture samples and clinical course. Over a 12-month period in 2010, all stool culture samples (n = 975) submitted from inpatients in a university hospital in Japan were cultured for C. difficile and routine microbiological testing was conducted. In total, 177 C. difficile isolates were recovered, and 127 isolates were toxigenic. Among the toxin-A-positive/toxin-B-positive isolates, 12 were also positive for the binary toxin gene. However, clinically important ribotypes, such as 027 and 078, were not identified. A total of 58 (45.7%) cases with toxigenic C. difficile had unformed stool, and the incidence CDI was 1.6 cases per 10,000 patient-days. Of these 58 cases, 40 were not diagnosed in routine testing due to a lack of clinical suspicion (24.1%, 14/58) or a negative C. difficile toxin assay result (44.8%, 26/58). A stool toxin assay was performed in 54 patients (78.2%, 54/69) who did not have unformed stool. The present study demonstrated that a significant number of CDI cases in Japan might be overlooked or misdiagnosed in clinical practice due to a lack of clinical suspicion and limitations of microbiological testing for CDI in Japan. Providing education to promote awareness of CDI among physicians is important to improve the accuracy of diagnosis in Japan. Copyright © 2015 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Multicenter Assessment of Gram Stain Error Rates.

PubMed

Samuel, Linoj P; Balada-Llasat, Joan-Miquel; Harrington, Amanda; Cavagnolo, Robert

2016-06-01

Gram stains remain the cornerstone of diagnostic testing in the microbiology laboratory for the guidance of empirical treatment prior to availability of culture results. Incorrectly interpreted Gram stains may adversely impact patient care, and yet there are no comprehensive studies that have evaluated the reliability of the technique and there are no established standards for performance. In this study, clinical microbiology laboratories at four major tertiary medical care centers evaluated Gram stain error rates across all nonblood specimen types by using standardized criteria. The study focused on several factors that primarily contribute to errors in the process, including poor specimen quality, smear preparation, and interpretation of the smears. The number of specimens during the evaluation period ranged from 976 to 1,864 specimens per site, and there were a total of 6,115 specimens. Gram stain results were discrepant from culture for 5% of all specimens. Fifty-eight percent of discrepant results were specimens with no organisms reported on Gram stain but significant growth on culture, while 42% of discrepant results had reported organisms on Gram stain that were not recovered in culture. Upon review of available slides, 24% (63/263) of discrepant results were due to reader error, which varied significantly based on site (9% to 45%). The Gram stain error rate also varied between sites, ranging from 0.4% to 2.7%. The data demonstrate a significant variability between laboratories in Gram stain performance and affirm the need for ongoing quality assessment by laboratories. Standardized monitoring of Gram stains is an essential quality control tool for laboratories and is necessary for the establishment of a quality benchmark across laboratories. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Skin and soft tissue infections: experience over a five-year period and clinical usefulness of ultrasonography-guided gun biopsy-based culture.

PubMed

Noh, Ji Yun; Cheong, Hee Jin; Song, Joon Young; Hong, Suk-Joo; Myung, Jae Sung; Choi, Won Suk; Jo, Yu Mi; Heo, Jung Yeon; Kim, Woo Joo

2011-12-01

Skin and soft tissue infections (SSTIs) are common clinical diseases, but only a few reports of microbiological data on SSTIs in Korea have been published. In practice, specimens are rarely obtained from infected lesions unless there is visible pus or an abscess pocket. However, identification of the causative pathogen is important, because of emerging drug resistance and the increase in immunocompromised hosts. The medical records of 760 adult cases of community-acquired SSTIs (CA-SSTIs) from September 2003 to August 2008 were reviewed retrospectively. We analyzed epidemio-clinical features and microbiological distributions of CA-SSTIs and evaluated the positive culture rate of several diagnostic methods, including swab, tissue biopsy, blind needle aspiration, ultrasonography (US)-guided needle aspiration, and US-guided gun biopsy. Most CA-SSTIs (76.1%) occurred in previously healthy persons without underlying diseases. Re-infections were identified in 76 (10%) patients and cirrhosis was an independent risk factor for re-infection (odds ratio 3.64, 95% confidence interval 1.36-9.76). The most commonly identified pathogen was methicillin-susceptible Staphylococcus aureus, and 3(rd)-generation cephalosporins were the most commonly used empirical antibiotics (47.9%). US-guided needle aspiration had a high positive culture rate of 73.9% and the positive culture rate of US-guided gun biopsy was 17.5%. Considering the microbiological distribution of CA-SSTIs in Korea, penicillinase-stable penicillin or a 1(st)-generation cephalosporin should be adequate for initial antibiotic treatment. US-guided needle aspiration was a good technique for the identification of causative pathogens, and additive productivity is expected with US-guided gun biopsy culture from lesions without fluid collection.

Microbiological monitoring of marine recreational waters in southern California.

PubMed

Schiff, K C; Weisberg, S B; Dorsey, J H

2001-01-01

An inventory was conducted to assess the number, type, spatial distribution, and costs of microbiological monitoring programs in southern California marine waters from Point Conception to the US/Mexico International Border. The location of each sampling site was determined using global positioning system (GPS), and estimates of geographic coverage were determined using geographic information system (GIS) techniques. Twenty-one programs conducted 87,007 tests annually at 576 sites in the study area. The largest number of sites was sampled in Orange County, whereas the largest number of analyses was performed in Los Angeles County because monitoring programs in this area focused on daily monitoring. Fifteen of the 21 programs were managed by National Pollutant Discharge Elimination System (NPDES) permitted sewage effluent dischargers who sampled both offshore and shoreline waters and typically tested for three indicator bacteria (total coliform, fecal coliform, and enterococcus). Their combined efforts comprised 82% of all of the microbiological indicator analyses conducted on an annual basis. Five of the remaining monitoring organizations were public health agencies, which typically focus their efforts on testing only total coliforms. Laboratory methodology also varied considerably, with NPDES permittees predominantly utilizing membrane filtration while public health agencies generally used multiple tube fermentation or premanufactured test kits. Nearly three quarters of all the effort expended in southern California occurred along the shoreline as opposed to offshore locations. Two thirds of this shoreline effort was focused on high-use sandy beaches and in proximity to perennial fresh-water outlets (storm drains and creeks). Most sampling occurred at a set of fixed sites that were revisited frequently, but only represented about 7% of the total shoreline. We estimated that roughly $3 million is spent annually on monitoring bathing water quality in southern California, exceeding that spent in any other part of the country.

Er:YAG laser in the treatment of periodontal sites with recurring chronic inflammation: a 12-month randomized, controlled clinical trial.

PubMed

Krohn-Dale, Ivar; Bøe, Olav E; Enersen, Morten; Leknes, Knut N

2012-08-01

The objective of this randomized, controlled clinical trial was to compare the clinical and microbiological effects of pocket debridement using erbium-doped: yttrium, aluminium and garnet (Er:YAG) laser with conventional debridement in maintenance patients. Fifteen patients, all smokers, having at least four teeth with residual probing depth (PD) ≥ 5 mm were recruited. Two pockets in two jaw quadrants were randomly assigned to subgingival debridement using an Er:YAG laser (test) or ultrasonic scaler/curette (control) at 3-month intervals. Relative attachment level (RAL), PD, bleeding on probing and dental plaque were recorded at baseline and at 6 and 12 months. Microbiological subgingival samples were taken at the same time points and analysed using a checkerboard DNA-DNA hybridization technique. A significant decrease in PD took place in both treatments from baseline to 12 months (p < 0.01). In the control, the mean initial PD decreased from 5.4 to 4.0 mm at 12 months. For the test, a similar decrease occurred. No significant between-treatment differences were shown at any time point. The mean RAL showed no overall significant inter- or intra-treatment differences (p > 0.05). No significant between-treatment differences were observed in subgingival microbiological composition or total pathogens. The results failed to support that an Er:YAG laser may be superior to conventional debridement in the treatment of smokers with recurring chronic inflammation. This appears to be the first time that repeated Er-YAG laser instrumentation has been compared with mechanical instrumentation of periodontal sites with recurring chronic inflammation over a clinically relevant time period. © 2012 John Wiley & Sons A/S.

High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories ▿

PubMed Central

van Veen, S. Q.; Claas, E. C. J.; Kuijper, Ed J.

2010-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory. PMID:20053859

High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories.

PubMed

van Veen, S Q; Claas, E C J; Kuijper, Ed J

2010-03-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.

Microbiological Quality of Fresh Nopal Juice

PubMed Central

Hernández-Anguiano, Ana María; Landa-Salgado, Patricia; Eslava-Campos, Carlos Alberto; Vargas-Hernández, Mateo; Patel, Jitendra

2016-01-01

The consumption of fresh nopal cactus juice is widely popular among health-conscious consumers in Mexico. The juice is prepared from fresh cladodes that have only been rinsed with tap water and are not subjected to a pasteurization or terminal bacterial reduction process. The aim of this study was to evaluate the microbial quality of commercially available fresh juices (n = 162) made with nopal in Texcoco, State of Mexico, during the summer and spring season. Standard microbiological methods, the PCR technique and the serological method were used for isolation and identification of bacteria. All samples contained total coliforms and 91% were positive for Escherichia coli. Although total coliforms and E. coli were detected throughout the study, their populations were significantly lower (p < 0.05) in winter and spring, respectively. Citrobacter youngae was found in 20% of the samples, an unidentified species of Citrobacter in 10%, C. freundii and Proteus mirabilis in 3%, and Salmonella Javiana in 1%. The presence of these microorganisms, especially Salmonella, in the nopal juices is unacceptable due to its health significance. The information generated in this study is relevant for human health risk assessment associated with the consumption of unpasteurized nopal juices and potential interventions to minimize pathogen contamination. PMID:27973398

Microbiological Quality of Fresh Nopal Juice.

PubMed

Hernández-Anguiano, Ana María; Landa-Salgado, Patricia; Eslava-Campos, Carlos Alberto; Vargas-Hernández, Mateo; Patel, Jitendra

2016-12-10

The consumption of fresh nopal cactus juice is widely popular among health-conscious consumers in Mexico. The juice is prepared from fresh cladodes that have only been rinsed with tap water and are not subjected to a pasteurization or terminal bacterial reduction process. The aim of this study was to evaluate the microbial quality of commercially available fresh juices ( n = 162) made with nopal in Texcoco, State of Mexico, during the summer and spring season. Standard microbiological methods, the PCR technique and the serological method were used for isolation and identification of bacteria. All samples contained total coliforms and 91% were positive for Escherichia coli . Although total coliforms and E. coli were detected throughout the study, their populations were significantly lower ( p < 0.05) in winter and spring, respectively. Citrobacter youngae was found in 20% of the samples, an unidentified species of Citrobacter in 10%, C. freundii and Proteus mirabilis in 3%, and Salmonella Javiana in 1%. The presence of these microorganisms, especially Salmonella , in the nopal juices is unacceptable due to its health significance. The information generated in this study is relevant for human health risk assessment associated with the consumption of unpasteurized nopal juices and potential interventions to minimize pathogen contamination.

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

PubMed

Brůčková, Marie

2012-12-01

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

Anticorrosive Influence of Acetobacter aceti Biofilms on Carbon Steel

NASA Astrophysics Data System (ADS)

France, Danielle Cook

2016-09-01

Microbiologically influenced corrosion (MIC) of carbon steel infrastructure is an emerging environmental and cost issue for the ethanol fuel industry, yet its examination lacks rigorous quantification of microbiological parameters that could reveal effective intervention strategies. To quantitatively characterize the effect of cell concentration on MIC of carbon steel, numbers of bacteria exposed to test coupons were systematically controlled to span four orders of magnitude throughout a seven-day test. The bacterium studied, Acetobacter aceti, has been found in ethanol fuel environments and can convert ethanol to the corrosive species acetic acid. A. aceti biofilms formed during the test were qualitatively evaluated with fluorescence microscopy, and steel surfaces were characterized by scanning electron microscopy. During exposure, biofilms developed more quickly, and test reactor pH decreased at a faster rate, when cell exposure was higher. Resulting corrosion rates, however, were inversely proportional to cell exposure, indicating that A. aceti biofilms are able to protect carbon steel surfaces from corrosion. This is a novel demonstration of corrosion inhibition by an acid-producing bacterium that occurs naturally in corrosive environments. Mitigation techniques for MIC that harness the power of microbial communities have the potential to be scalable, inexpensive, and green solutions to industrial problems.

Conclusions on measurement uncertainty in microbiology.

PubMed

Forster, Lynne I

2009-01-01

Since its first issue in 1999, testing laboratories wishing to comply with all the requirements of ISO/IEC 17025 have been collecting data for estimating uncertainty of measurement for quantitative determinations. In the microbiological field of testing, some debate has arisen as to whether uncertainty needs to be estimated for each method performed in the laboratory for each type of sample matrix tested. Queries also arise concerning the estimation of uncertainty when plate/membrane filter colony counts are below recommended method counting range limits. A selection of water samples (with low to high contamination) was tested in replicate with the associated uncertainty of measurement being estimated from the analytical results obtained. The analyses performed on the water samples included total coliforms, fecal coliforms, fecal streptococci by membrane filtration, and heterotrophic plate counts by the pour plate technique. For those samples where plate/membrane filter colony counts were > or =20, uncertainty estimates at a 95% confidence level were very similar for the methods, being estimated as 0.13, 0.14, 0.14, and 0.12, respectively. For those samples where plate/membrane filter colony counts were <20, estimated uncertainty values for each sample showed close agreement with published confidence limits established using a Poisson distribution approach.

[Mixed invasive fungal infection due to Rhizomucor pusillus and Aspergillus niger in an immunocompetent patient].

PubMed

Pozo-Laderas, Juan Carlos; Pontes-Moreno, Antonio; Robles-Arista, Juan Carlos; Bautista-Rodriguez, M Dolores; Candau-Alvarez, Alberto; Caro-Cuenca, Maria Teresa; Linares-Sicilia, María José

2015-01-01

Mucormycosis infections are rare in immunocompetent patients, and very few cases of mucormycosis associated with aspergillosis in non-haematological patients have been reported. A 17-year-old male, immunocompetent and without any previously known risk factors, was admitted to hospital due to a seizure episode 11 days after a motorcycle accident. He had a complicated clinical course as he had a mixed invasive fungal infection with pulmonary involvement due to Aspergillus niger and disseminated mucormycosis due to Rhizomucor pusillus (histopathological and microbiological diagnosis in several non-contiguous sites). He was treated with liposomal amphotericin B for 7 weeks (total cumulative dose >10 g) and required several surgical operations. The patient survived and was discharged from ICU after 5 months and multiple complications. Treatment with liposomal amphotericin B and aggressive surgical management achieved the eradication of a mixed invasive fungal infection. However, we emphasise the need to maintain a higher level of clinical suspicion and to perform microbiological techniques for early diagnosis of invasive fungal infections in non-immunocompromised patients, in order to prevent spread of the disease and the poor prognosis associated with it. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Informal Trade of Psychoactive Herbal Products in the City of Diadema, SP, Brazil: Quality and Potential Risks

PubMed Central

Soares Neto, Julino Assunção Rodrigues; Kato, Edna Myiake; Galduróz, José Carlos F.; Marques, Luis Carlos; Macrini, Thiago; Rodrigues, Eliana

2013-01-01

The present study aimed to assess the quality and risks involved in the consumption of psychoactive herbal products (PHs) that are available through informal commerce in the city of Diadema, SP, Brazil. Methods of ethnography were used to conduct the fieldwork during which four dealers were selected to record the collection, handling, packaging, types of PHs marketed, and their therapeutic purposes. In addition, lots of the PHs selected were purchased from the dealers and analyzed using microbiology and pharmacognosy techniques. 217 PHs were recorded and categorized into two main groups: stimulants (67%) and depressants (27%) of the central nervous system; sixteen of them were selected, and their 52 lots were acquired. The deficiencies observed in handling and packaging these lots by dealers were confirmed by microbiological analysis; 80.8% of them presented risk according to the indicators defined by the Brazilian Pharmacopoeia. The pharmacognostic analysis confirmed the authenticity of only 9 to 16 PHs analyzed. In addition, descriptions of contraindications, adverse reactions, and drug interactions were found in the literature for the PHs. The results of this study allow the observation of the priorities for the sanitary adequacy of the popular trade of herbs. PMID:23818934

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

Metals and minerals as a biotechnology feedstock: engineering biomining microbiology for bioenergy applications.

PubMed

Banerjee, Indrani; Burrell, Brittany; Reed, Cara; West, Alan C; Banta, Scott

2017-06-01

Developing new feedstocks for the efficient production of biochemicals and biofuels will be a critical challenge as we diversify away from petrochemicals. One possible opportunity is the utilization of sulfide-based minerals in the Earth's crust. Non-photosynthetic chemolithoautotrophic bacteria are starting to be developed to produce biochemicals from CO 2 using energy obtained from the oxidation of inorganic feedstocks. Biomining of metals like gold and copper already exploit the native metabolism of these bacteria and these represent perhaps the largest-scale bioprocesses ever developed. The metabolic engineering of these bacteria could be a desirable alternative to classical heterotrophic bioproduction. In this review, we discuss biomining operations and the challenges and advances in the engineering of associated chemolithoautotrophic bacteria for biofuel production. The co-generation of biofuels integrated with mining operations is a largely unexplored opportunity that will require advances in fundamental microbiology and the development of new genetic tools and techniques for these organisms. Although this approach is presently in its infancy, the production of biochemicals using energy from non-petroleum mineral resources is an exciting new biotechnology opportunity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Executive summary. Management of influenza infection in solid-organ transplant recipients: consensus statement of the Group for the Study of Infection in Transplant Recipients (GESITRA) of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) and the Spanish Network for Research in Infectious Diseases (REIPI).

PubMed

López-Medrano, Francisco; Cordero, Elisa; Gavaldá, Joan; Cruzado, Josep M; Marcos, M Ángeles; Pérez-Romero, Pilar; Sabé, Nuria; Gómez-Bravo, Miguel Ángel; Delgado, Juan Francisco; Cabral, Evelyn; Carratalá, Jordi

2013-10-01

Solid organ transplant (SOT) recipients are at greater risk than the general population for complications and mortality from influenza infection. We have conducted a systematic review to assess the management and prevention of influenza infection in SOT recipients. Recommendations are provided about the procurement of organs from donors with influenza infection. We highlight the importance of the possibility of influenza infection in any SOT recipient presenting upper or lower respiratory symptoms, including pneumonia. The importance of early antiviral treatment of SOT recipients with suspected or confirmed influenza infection and the necessity of annual influenza vaccination are emphasized. The microbiological techniques for diagnosis of influenza infection are reviewed. Guidelines for the use of antiviral prophylaxis are provided. Recommendations for household contacts of SOT recipients with influenza infection and health care workers are also included. Antiviral dose adjustment guidelines are presented for cases of impaired renal function and for pediatric populations. Copyright © 2013 Elsevier España, S.L. All rights reserved.

Hyperspectral image analysis for rapid and accurate discrimination of bacterial infections: A benchmark study.

PubMed

Arrigoni, Simone; Turra, Giovanni; Signoroni, Alberto

2017-09-01

With the rapid diffusion of Full Laboratory Automation systems, Clinical Microbiology is currently experiencing a new digital revolution. The ability to capture and process large amounts of visual data from microbiological specimen processing enables the definition of completely new objectives. These include the direct identification of pathogens growing on culturing plates, with expected improvements in rapid definition of the right treatment for patients affected by bacterial infections. In this framework, the synergies between light spectroscopy and image analysis, offered by hyperspectral imaging, are of prominent interest. This leads us to assess the feasibility of a reliable and rapid discrimination of pathogens through the classification of their spectral signatures extracted from hyperspectral image acquisitions of bacteria colonies growing on blood agar plates. We designed and implemented the whole data acquisition and processing pipeline and performed a comprehensive comparison among 40 combinations of different data preprocessing and classification techniques. High discrimination performance has been achieved also thanks to improved colony segmentation and spectral signature extraction. Experimental results reveal the high accuracy and suitability of the proposed approach, driving the selection of most suitable and scalable classification pipelines and stimulating clinical validations. Copyright © 2017 Elsevier Ltd. All rights reserved.

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)

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 ...

21 CFR 866.1 - Scope.

Code of Federal Regulations, 2014 CFR

2014-04-01

... MICROBIOLOGY DEVICES General Provisions § 866.1 Scope. (a) This part sets forth the classification of immunology and microbiology devices intended for human use that are in commercial distribution. (b) The... immunology and microbiology device that has two or more types of uses (e.g., used both as a diagnostic device...

21 CFR 866.1 - Scope.

Code of Federal Regulations, 2012 CFR

2012-04-01

... MICROBIOLOGY DEVICES General Provisions § 866.1 Scope. (a) This part sets forth the classification of immunology and microbiology devices intended for human use that are in commercial distribution. (b) The... immunology and microbiology device that has two or more types of uses (e.g., used both as a diagnostic device...

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...

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…

21 CFR 866.1 - Scope.

Code of Federal Regulations, 2011 CFR

2011-04-01

... MICROBIOLOGY DEVICES General Provisions § 866.1 Scope. (a) This part sets forth the classification of immunology and microbiology devices intended for human use that are in commercial distribution. (b) The... immunology and microbiology device that has two or more types of uses (e.g., used both as a diagnostic device...

21 CFR 866.1 - Scope.

Code of Federal Regulations, 2010 CFR

2010-04-01

... MICROBIOLOGY DEVICES General Provisions § 866.1 Scope. (a) This part sets forth the classification of immunology and microbiology devices intended for human use that are in commercial distribution. (b) The... immunology and microbiology device that has two or more types of uses (e.g., used both as a diagnostic device...

21 CFR 866.1 - Scope.

Code of Federal Regulations, 2013 CFR

2013-04-01

... MICROBIOLOGY DEVICES General Provisions § 866.1 Scope. (a) This part sets forth the classification of immunology and microbiology devices intended for human use that are in commercial distribution. (b) The... immunology and microbiology device that has two or more types of uses (e.g., used both as a diagnostic device...

77 FR 56660 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-13

... constitute a clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group; Microbiology and Infectious Diseases B Subcommittee. MID-B October..., [email protected] . Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group...

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.

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.

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.

Compliance of clinical microbiology laboratories in the United States with current recommendations for processing respiratory tract specimens from patients with cystic fibrosis.

PubMed

Zhou, Juyan; Garber, Elizabeth; Desai, Manisha; Saiman, Lisa

2006-04-01

Respiratory tract specimens from patients with cystic fibrosis (CF) require unique processing by clinical microbiology laboratories to ensure detection of all potential pathogens. The present study sought to determine the compliance of microbiology laboratories in the United States with recently published recommendations for CF respiratory specimens. Microbiology laboratory protocols from 150 of 190 (79%) CF care sites were reviewed. Most described the use of selective media for Burkholderia cepacia complex (99%), Staphylococcus aureus (82%), and Haemophilus influenzae (89%) and identified the species of all gram-negative bacilli (87%). Only 52% delineated the use of agar diffusion assays for susceptibility testing of Pseudomonas aeruginosa. Standardizing laboratory practices will improve treatment, infection control, and our understanding of the changing epidemiology of CF microbiology.

[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.

Recalls of foods due to microbiological contamination classified by the U.S. Food and Drug Administration, fiscal years 2003 through 2011.

PubMed

Dey, Manashi; Mayo, Jonathan A; Saville, Deborah; Wolyniak, Cecilia; Klontz, Karl C

2013-06-01

Recalls of foods contaminated with pathogens help reduce the transmission of infectious diseases. Here, we summarize the number and nature of foods recalled as a result of microbiological contamination, classified by the U.S. Food and Drug Administration for the period 1 October 2002 through 30 September 2011. Microbiological contamination accounted for 1,395 (42%) of 3,360 recalls of food during this period. Nuts and edible seeds, followed by fishery-seafood products and spices, were the types of products most commonly recalled for microbiological contamination. Salmonella contamination accounted for the greatest number of food products recalled due to microbiological contamination, and was the pathogen most often linked to reported outbreaks involving recalled food products.

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.

Southern promises: a snapshot of the microbiology research landscape in South America based on bibliometric data.

PubMed

Nai, Corrado

2017-09-01

Scientists have a single currency for productivity and impact: published articles. In an effort to map the global research landscape in microbiology, and to obviate the current lack of bibliometric analysis in the field, FEMS-the Federation of European Microbiological Societies-generated a dataset encompassing an exhaustive, worldwide list of microbiology studies for 2013-14, which further includes information as author affiliation, funding agency and number of citations. The manually curated database is useful in assessing the impact and regional productivity of microbiology research at different levels. Here, the data for microbiology research in South America are presented and discussed in detail. Based on the analysis, it emerged that despite great degrees of variation between number of published articles among the countries, a more levelled research productivity was observed when considering further dimensions like population size or number of research institutes. Normalised productivity and impact increase in countries with a 'central research hub', i.e. an institute or university producing a substantial portion of the national output (15% or more). From these observations, a possible strategy to increase impact and productivity in (microbiology) research for emerging countries is outlined. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.