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

Aquatic Microbiology Laboratory Manual.

ERIC Educational Resources Information Center

Cooper, Robert C.; And Others

This laboratory manual presents information and techniques dealing with aquatic microbiology as it relates to environmental health science, sanitary engineering, and environmental microbiology. The contents are divided into three categories: (1) ecological and physiological considerations; (2) public health aspects; and (3)microbiology of water…

Computer Modeling of Microbiological Experiments in the Teaching Laboratory: Animation Techniques.

ERIC Educational Resources Information Center

Tritz, Gerald J.

1987-01-01

Discusses the use of computer assisted instruction in the medical education program of the Kirksville College of Osteopathic Medicine (Missouri). Describes the animation techniques used in a series of simulations for microbiology. (TW)

An Investigation of the Effectiveness of Radiotracer Techniques for Instruction in Microbiology.

ERIC Educational Resources Information Center

Hurlburt, Evelyn McClelland

Students in a junior college microbiology course were randomly assigned to one of two laboratory treatments: one using radiotracer techniques to investigate aspects of microbial metabolism, and the other using conventional techniques to investigate the same metabolic features. An achievement test administered at the completion of the unit and six…

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

PubMed

Andreu, Antonia; Matas, Lurdes

2010-10-01

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

Successful Application of Active Learning Techniques to Introductory Microbiology.

ERIC Educational Resources Information Center

Hoffman, Elizabeth A.

2001-01-01

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

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

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.

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.

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.

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

DTIC Science & Technology

2014-05-01

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

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

PubMed Central

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

2003-01-01

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

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…

Imaging mass spectrometry in microbiology

PubMed Central

Watrous, Jeramie D.; Dorrestein, Pieter C.

2013-01-01

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

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.

[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.

Sampling and Data Analysis for Environmental Microbiology

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

Murray, Christopher J.

2001-06-01

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

Restructuring a General Microbiology Laboratory into an Investigative Experience.

ERIC Educational Resources Information Center

Deutch, Charles E.

1994-01-01

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

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.

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

PubMed

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

2014-12-01

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

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

A comparison between polymerase chain reaction (PCR) and traditional techniques for the diagnosis of leptospirosis in bovines.

PubMed

Hernández-Rodríguez, Patricia; Díaz, César A; Dalmau, Ernesto A; Quintero, Gladys M

2011-01-01

Leptospirosis is caused by Leptospira, gram negative spirochaetes whose microbiologic identification is difficult due to their low rate of growth and metabolic activity. In Colombia leptospirosis diagnosis is achieved by serological techniques without unified criteria for what positive titers are. In this study we compared polymerase chain reaction (PCR) with microbiological culture and dark field microscopy for the diagnosis of leptospirosis. Microbiological and molecular techniques were performed on 83 samples of urine taken from bovines in the savannahs surrounding Bogotá in Colombia, with presumptive diagnosis of leptospirosis. 117 samples of urine taken from healthy bovines were used as negative controls. 83 samples were MAT positive with titers ≥ 1:50; 81 with titers ≥ 1:100; and 66 with titers ≥ 1:200. 36% of the total samples (73/200) were Leptospira positives by microbiological culture, 32% (63/200) by dark field microscopy and 37% (74/200) by PCR. Amplicons obtained by PCR were 482 base pair long which are Leptospira specific. An amplicon of 262 base pairs typical of pathogenic Leptospira was observed in 71 out of the 74 PCR positive samples. The remaining 3 samples showed a 240 base pair amplicon which is typical of saprophytic Leptospira. PCR as a Leptospira diagnosis technique was 100% sensitive and 99% specific in comparison to microbiological culture. Kappa value of 0.99 indicated an excellent concordance between these techniques. Sensitivity and specificity reported for MAT when compared to microbiological culture was 0.95 and 0.89 with a ≥ 1:50 cut off. PCR was a reliable method for the rapid and precise diagnosis of leptospirosis when compared to traditional techniques in our study. The research presented here will be helpful to improve diagnosis and control of leptospirosis in Colombia and other endemic countries. Copyright © 2010 Elsevier B.V. All rights reserved.

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.

Individualized Quality Control Plan (IQCP): Is It Value-Added for Clinical Microbiology?

PubMed

Sharp, Susan E; Miller, Melissa B; Hindler, Janet

2015-12-01

The Center for Medicaid and Medicare Services (CMS) recently published their Individualized Quality Control Plan (IQCP [https://www.cms.gov/regulations-and-guidance/legislation/CLIA/Individualized_Quality_Control_Plan_IQCP.html]), which will be the only option for quality control (QC) starting in January 2016 if laboratories choose not to perform Clinical Laboratory Improvement Act (CLIA) [U.S. Statutes at Large 81(1967):533] default QC. Laboratories will no longer be able to use "equivalent QC" (EQC) or the Clinical and Laboratory Standards Institute (CLSI) standards alone for quality control of their microbiology systems. The implementation of IQCP in clinical microbiology laboratories will most certainly be an added burden, the benefits of which are currently unknown. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The need for European professional standards and the challenges facing clinical microbiology.

PubMed

Humphreys, H; Nagy, E; Kahlmeter, G; Ruijs, G J H M

2010-06-01

Microorganisms spread across national boundaries and the professional activities of clinical (medical) microbiologists are critical in minimising their impact. Clinical microbiologists participate in many activities, e.g. diagnosis, antibiotic therapy, and there is a need for a set of professional standards for Europe with a common curriculum, to build upon the current strengths of the specialty and to facilitate the free movement of specialists within the European Union. Such standards will also better highlight the important contribution of clinical microbiologists to healthcare. There is a move to larger centralised microbiology laboratories often located off-site from an acute hospital, driven by the concentration of resources, amalgamation of services, outsourcing of diagnostics, automation, an explosion in the range of staff competencies and accreditation. Large off-site centralised microbiology laboratories are often distant to the patient and may not facilitate the early detection of microbial spread. Ultimately, the needs of patients and the public are paramount in deciding on the future direction of clinical microbiology. Potential conflicts between integration on an acute hospital site and centralisation can be resolved by a common set of professional standards and a team-based approach that puts patients first.

Applications of Flow Cytometry to Clinical Microbiology†

PubMed Central

Álvarez-Barrientos, Alberto; Arroyo, Javier; Cantón, Rafael; Nombela, César; Sánchez-Pérez, Miguel

2000-01-01

Classical microbiology techniques are relatively slow in comparison to other analytical techniques, in many cases due to the need to culture the microorganisms. Furthermore, classical approaches are difficult with unculturable microorganisms. More recently, the emergence of molecular biology techniques, particularly those on antibodies and nucleic acid probes combined with amplification techniques, has provided speediness and specificity to microbiological diagnosis. Flow cytometry (FCM) allows single- or multiple-microbe detection in clinical samples in an easy, reliable, and fast way. Microbes can be identified on the basis of their peculiar cytometric parameters or by means of certain fluorochromes that can be used either independently or bound to specific antibodies or oligonucleotides. FCM has permitted the development of quantitative procedures to assess antimicrobial susceptibility and drug cytotoxicity in a rapid, accurate, and highly reproducible way. Furthermore, this technique allows the monitoring of in vitro antimicrobial activity and of antimicrobial treatments ex vivo. The most outstanding contribution of FCM is the possibility of detecting the presence of heterogeneous populations with different responses to antimicrobial treatments. Despite these advantages, the application of FCM in clinical microbiology is not yet widespread, probably due to the lack of access to flow cytometers or the lack of knowledge about the potential of this technique. One of the goals of this review is to attempt to mitigate this latter circumstance. We are convinced that in the near future, the availability of commercial kits should increase the use of this technique in the clinical microbiology laboratory. PMID:10755996

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

The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology.

PubMed

Ruskova, Lenka; Raclavsky, Vladislav

2011-09-01

Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology. Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization. We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.

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

Natural Attenuation of Perchlorate in Groundwater: Processes, Tools and Monitoring Techniques

DTIC Science & Technology

2008-04-01

attenuation of perchlorate. Tier 3: Microbiological Indicators. For situations where additional lines of evidence are required, Tier 3 offers...USEPA, 1997). Like enhanced bioremediation, MNA requires an in-depth understanding of the microbiology , chemistry, and hydrogeology of the...nitrate, perchlorate (if present), and iron have been depleted in the microbiological treatment zone. Whereas sulfate concentration greater than 20

National collaborative shellfish pollution-indicator study: Site selection. Phase 2. Rept. for 1988-89

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

Leonard, D.L.; Slaughter, E.A.; Corning, B.C.

1990-07-01

Each year, about 16 million areas of estuarine waters are classified for the harvest of molluscan shellfish as open or limited to harvest according to microbiological 'indicator' standards and pollution survey guidelines established by the National Shellfish Sanitation Program. The program was developed in the 1920s in response to typhoid fever outbreaks associated with shellfish consumption. Current microbiological indicator standards in shellfish and shellfish-growing waters are extrpolated from standards set in the 1920s. Results from studies in the last decade have indicated that these microbiological indicator standards and thus classification of shellfish-growing waters may no longer be valid. The Nationalmore » Collaborative Shellfish Pollution Indicator Study is proposed as a four-year study to evaluate the current relationships between indicators of human enteric pathogens and the incidence of shellfish-borne diseases. Tasks forces were established to address specific issues, including site selection, shoreline surveys, and laboratory methodologies.« less

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

PubMed

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

2016-08-01

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

[Microbiological point of care tests].

PubMed

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

2010-11-01

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

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.

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.

Microbiology as a High-School Elective

ERIC Educational Resources Information Center

Peterson, Priscilla

1973-01-01

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

Collection, transport and general processing of clinical specimens in Microbiology laboratory.

PubMed

Sánchez-Romero, M Isabel; García-Lechuz Moya, Juan Manuel; González López, Juan José; Orta Mira, Nieves

2018-02-06

The interpretation and the accuracy of the microbiological results still depend to a great extent on the quality of the samples and their processing within the Microbiology laboratory. The type of specimen, the appropriate time to obtain the sample, the way of sampling, the storage and transport are critical points in the diagnostic process. The availability of new laboratory techniques for unusual pathogens, makes necessary the review and update of all the steps involved in the processing of the samples. Nowadays, the laboratory automation and the availability of rapid techniques allow the precision and turn-around time necessary to help the clinicians in the decision making. In order to be efficient, it is very important to obtain clinical information to use the best diagnostic tools. Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

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.

Internal audit in a microbiology laboratory.

PubMed Central

Mifsud, A J; Shafi, M S

1995-01-01

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

Drinking water quality assessment.

PubMed

Aryal, J; Gautam, B; Sapkota, N

2012-09-01

Drinking water quality is the great public health concern because it is a major risk factor for high incidence of diarrheal diseases in Nepal. In the recent years, the prevalence rate of diarrhoea has been found the highest in Myagdi district. This study was carried out to assess the quality of drinking water from different natural sources, reservoirs and collection taps at Arthunge VDC of Myagdi district. A cross-sectional study was carried out using random sampling method in Arthunge VDC of Myagdi district from January to June,2010. 84 water samples representing natural sources, reservoirs and collection taps from the study area were collected. The physico-chemical and microbiological analysis was performed following standards technique set by APHA 1998 and statistical analysis was carried out using SPSS 11.5. The result was also compared with national and WHO guidelines. Out of 84 water samples (from natural source, reservoirs and tap water) analyzed, drinking water quality parameters (except arsenic and total coliform) of all water samples was found to be within the WHO standards and national standards.15.48% of water samples showed pH (13) higher than the WHO permissible guideline values. Similarly, 85.71% of water samples showed higher Arsenic value (72) than WHO value. Further, the statistical analysis showed no significant difference (P<0.05) of physico-chemical parameters and total coliform count of drinking water for collection taps water samples of winter (January, 2010) and summer (June, 2010). The microbiological examination of water samples revealed the presence of total coliform in 86.90% of water samples. The results obtained from physico-chemical analysis of water samples were within national standard and WHO standards except arsenic. The study also found the coliform contamination to be the key problem with drinking water.

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.

Laboratory Diagnosis of Infective Endocarditis

PubMed Central

Liesman, Rachael M.; Pritt, Bobbi S.; Maleszewski, Joseph J.

2017-01-01

ABSTRACT Infective endocarditis is life-threatening; identification of the underlying etiology informs optimized individual patient management. Changing epidemiology, advances in blood culture techniques, and new diagnostics guide the application of laboratory testing for diagnosis of endocarditis. Blood cultures remain the standard test for microbial diagnosis, with directed serological testing (i.e., Q fever serology, Bartonella serology) in culture-negative cases. Histopathology and molecular diagnostics (e.g., 16S rRNA gene PCR/sequencing, Tropheryma whipplei PCR) may be applied to resected valves to aid in diagnosis. Herein, we summarize recent knowledge in this area and propose a microbiologic and pathological algorithm for endocarditis diagnosis. PMID:28659319

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

PubMed

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

2014-01-01

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

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

PubMed Central

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

2014-01-01

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

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.

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.

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.

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).

Evaluation of heterotrophic plate and chromogenic agar colony counting in water quality laboratories.

PubMed

Hallas, Gary; Monis, Paul

2015-01-01

The enumeration of bacteria using plate-based counts is a core technique used by food and water microbiology testing laboratories. However, manual counting of bacterial colonies is both time and labour intensive, can vary between operators and also requires manual entry of results into laboratory information management systems, which can be a source of data entry error. An alternative is to use automated digital colony counters, but there is a lack of peer-reviewed validation data to allow incorporation into standards. We compared the performance of digital counting technology (ProtoCOL3) against manual counting using criteria defined in internationally recognized standard methods. Digital colony counting provided a robust, standardized system suitable for adoption in a commercial testing environment. The digital technology has several advantages:•Improved measurement of uncertainty by using a standard and consistent counting methodology with less operator error.•Efficiency for labour and time (reduced cost).•Elimination of manual entry of data onto LIMS.•Faster result reporting to customers.

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

PubMed

Duerden, Brian

2005-12-01

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

[Implementation of quality standard UNE-EN ISO/IEC 17043 in the External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology].

PubMed

Poveda Gabaldón, Marta; Ovies, María Rosario; Orta Mira, Nieves; Serrano, M del Remedio Guna; Avila, Javier; Giménez, Alicia; Cardona, Concepción Gimeno

2011-12-01

The quality standard "UNE-EN-ISO 17043: 2010. Conformity assessment. General requirements for proficiency testing" applies to centers that organize intercomparisons in all areas. In the case of clinical microbiology laboratories, these intercomparisons must meet the management and technical standards required to achieve maximum quality in the performance of microbiological analysis and the preparation of test items (sample, product, data or other information used in the proficiency test) to enable them to be accredited. Once accredited, these laboratories can operate as a tool for quality control laboratories and competency assessment. In Spain, accreditation is granted by the Spanish Accreditation Body [Entidad Nacional de Acreditación (ENAC)]. The objective of this review is to explain how to apply the requirements of the standard to laboratories providing intercomparisons in the field of clinical microbiology (the organization responsible for all the tasks related to the development and operation of a proficiency testing program). This requires defining the scope and specifying the technical requirements (personnel management, control of equipment, facilities and environment, the design of the proficiency testing and data analysis for performance evaluation, communication with participants and confidentiality) and management requirements (document control, purchasing control, monitoring of complaints / claims, non-compliance, internal audits and management reviews). Copyright © 2011 Elsevier España S.L. All rights reserved.

Individualized Quality Control Plan (IQCP): Is It Value-Added for Clinical Microbiology?

PubMed Central

Miller, Melissa B.; Hindler, Janet

2015-01-01

The Center for Medicaid and Medicare Services (CMS) recently published their Individualized Quality Control Plan (IQCP [https://www.cms.gov/regulations-and-guidance/legislation/CLIA/Individualized_Quality_Control_Plan_IQCP.html]), which will be the only option for quality control (QC) starting in January 2016 if laboratories choose not to perform Clinical Laboratory Improvement Act (CLIA) [U.S. Statutes at Large 81(1967):533] default QC. Laboratories will no longer be able to use “equivalent QC” (EQC) or the Clinical and Laboratory Standards Institute (CLSI) standards alone for quality control of their microbiology systems. The implementation of IQCP in clinical microbiology laboratories will most certainly be an added burden, the benefits of which are currently unknown. PMID:26447112

Microbiology--Safety Considerations.

ERIC Educational Resources Information Center

Hoffmann, Sheryl K.

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

Surface microbial contamination in hospitals: A pilot study on methods of sampling and the use of proposed microbiologic standards.

PubMed

Claro, Tânia; O'Reilly, Marese; Daniels, Stephen; Humphreys, Hilary

2015-09-01

Contamination of hospital surfaces by bacteria is increasingly recognized. We assessed commonly touched surfaces using contact plates and Petrifilms (3M, St. Paul, MN) and compared the results against proposed microbiology standards. Toilet door handles were the most heavily contaminated (7.97 ± 0.68 colony forming units [CFU]/cm(2)) and exceeded proposed standards on 74% of occasions. Petrifilms detected statistically higher CFU from bedside lockers. Further research is required on the use of standards and methods of sampling. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

DEVELOPMENT OF MICROBIAL METAGENOMIC MARKERS FOR ENVIRONMENTAL MONITORING AND RISK ASSESSMENT

EPA Science Inventory

The microbiological water quality standards established by EPA depend on culturing fecal indicator bacteria to predict the risks associated with water usage. For decades this has been the favored approach to microbiological monitoring in spite of the fact that culture-based meth...

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

PubMed

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

2010-03-01

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

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

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

1989-01-01

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

High-pressure liquid chromatography analysis of antibiotic susceptibility disks.

PubMed Central

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

1979-01-01

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

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-01-01

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

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

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

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-01-01

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

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-01-01

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

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

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

[Do Multiplex PCR techniques displace classical cultures in microbiology?].

PubMed

Auckenthaler, Raymond; Risch, Martin

2015-02-01

Multiplex PCR technologies progressively find their way in clinical microbiology. This technique allows the simultaneous amplification of multiple DNA targets in a single test run for the identification of pathogens up to the species level. Various pathogens of infectious diseases can be detected by a symptom-oriented approach clearly and quickly with high reliability. Essentially multiplex PCR panels are available for clarification of gastrointestinal, respiratory, sexually transmitted infections and meningitis. Today's offer from industry, university hospitals and large private laboratories of Switzerland is tabulated and commented.

Resident training in microbiology.

PubMed

Haller, Barbara L

2007-06-01

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

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.

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.

Diagnostic molecular microbiology: a 2013 snapshot.

PubMed

Fairfax, Marilynn Ransom; Salimnia, Hossein

2013-12-01

Molecular testing has a large and increasing role in the diagnosis of infectious diseases. It has evolved significantly since the first probe tests were FDA approved in the early 1990s. This article highlights the uses of molecular techniques in diagnostic microbiology, including "older," as well as innovative, probe techniques, qualitative and quantitative RT-PCR, highly multiplexed PCR panels, some of which use sealed microfluidic test cartridges, MALDI TOF, and nuclear magnetic resonance. Tests are grouped together by technique and target. Tests with similar roles for similar analytes are compared with respect to benefits, drawbacks, and possible problems. Copyright © 2013 Elsevier Inc. All rights reserved.

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…

The effect of ionizing radiation on microbiological decontamination of medical herbs and biologically active compounds

NASA Astrophysics Data System (ADS)

Migdal, W.; Owczarczyk, B.; Kedzia, B.; Holderna-Kedzia, E.; Segiet-Kujawa, E.

1998-06-01

Several thousand tons of medical herbs are produced annually by pharmaceutical industry in Poland. This product should be of highest quality and microbial purity. Recently, chemical methods of decontamination are recognized as less safe, thus irradiation technique was chosen to replace them in use. In the Institute of Nuclear Chemistry and Technology the national program on the application of irradiation to the decontamination of medical herbs is in progress now. The purpose of the program is to elaborate, on the basis of research work, the facility standards and technological instructions indispensable for the practice of radiation technology.

Bacterial Prevalence and Antibiotic Resistance in Clinical Isolates of Diabetic Foot Ulcers in the Northeast of Tamaulipas, Mexico.

PubMed

Sánchez-Sánchez, Mario; Cruz-Pulido, Wendy Lizeth; Bladinieres-Cámara, Eduardo; Alcalá-Durán, Rodrigo; Rivera-Sánchez, Gildardo; Bocanegra-García, Virgilio

2017-06-01

Diabetic foot ulcers (DFUs) are a serious and common problem in patients with diabetes mellitus and constitute one of the major causes of lower extremity amputation. The microbiological profile of DFUs depends on the acute or chronic character of the wound. Aerobic gram-positive cocci are the predominant organisms isolated from DFUs. Diabetic foot biopsies from patients admitted to the Angiology and Vascular Surgery Hospital of the Northeast, in Reynosa, Tamaulipas from December 2011 to April 2016 were analyzed. The samples were processed using standard microbiology techniques. Antimicrobial susceptibility testing was carried out according to the protocol established by the Clinical & Laboratory Standards Institute (CLSI). We obtained 246 bacterial isolates, based on the results of phenotypic resistance. The least effective antibiotics for gram-positive bacteria were penicillin and dicloxacillin; for gram-negative bacteria, cefalotin and penicillin were the least effective. Levofloxacin, cefalotin, and amikacin were the most effective antibiotics for gram-positive and negative bacteria, respectively. Enterobacter genus was significantly associated with muscle biopsies ( P = .011) and samples without growth were significantly associated with specimens of pyogenic origin ( P = .000). In 215 DFU samples, we found that Staphylococcus aureus was the most commonly isolated pathogen followed by Enterobacter sp. This is consistent with previous reports. Enterobacter species may play an important role in the colonization/infection of certain tissues; however, further studies are needed in this regard.

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.

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.

Antimicrobial activity of biogenic silver nanoparticles, and silver chloride nanoparticles: an overview and comments.

PubMed

Durán, Nelson; Nakazato, Gerson; Seabra, Amedea B

2016-08-01

The antimicrobial impact of biogenic-synthesized silver-based nanoparticles has been the focus of increasing interest. As the antimicrobial activity of nanoparticles is highly dependent on their size and surface, the complete and adequate characterization of the nanoparticle is important. This review discusses the characterization and antimicrobial activity of biogenic synthesized silver nanoparticles and silver chloride nanoparticles. By revising the literature, there is confusion in the characterization of these two silver-based nanoparticles, which consequently affects the conclusion regarding to their antimicrobial activities. This review critically analyzes recent publications on the synthesis of biogenic silver nanoparticles and silver chloride nanoparticles by attempting to correlate the characterization of the nanoparticles with their antimicrobial activity. It was difficult to correlate the size of biogenic nanoparticles with their antimicrobial activity, since different techniques are employed for the characterization. Biogenic synthesized silver-based nanoparticles are not completely characterized, particularly the nature of capped proteins covering the nanomaterials. Moreover, the antimicrobial activity of theses nanoparticles is assayed by using different protocols and strains, which difficult the comparison among the published papers. It is important to select some bacteria as standards, by following international foundations (Pharmaceutical Microbiology Manual) and use the minimal inhibitory concentration by broth microdilution assays from Clinical and Laboratory Standards Institute, which is the most common assay used in antibiotic ones. Therefore, we conclude that to have relevant results on antimicrobial effects of biogenic silver-based nanoparticles, it is necessary to have a complete and adequate characterization of these nanostructures, followed by standard methodology in microbiology protocols.

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories.

PubMed

Gargis, Amy S; Kalman, Lisa; Lubin, Ira M

2016-12-01

Clinical microbiology and public health laboratories are beginning to utilize next-generation sequencing (NGS) for a range of applications. This technology has the potential to transform the field by providing approaches that will complement, or even replace, many conventional laboratory tests. While the benefits of NGS are significant, the complexities of these assays require an evolving set of standards to ensure testing quality. Regulatory and accreditation requirements, professional guidelines, and best practices that help ensure the quality of NGS-based tests are emerging. This review highlights currently available standards and guidelines for the implementation of NGS in the clinical and public health laboratory setting, and it includes considerations for NGS test validation, quality control procedures, proficiency testing, and reference materials. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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/.

Protocol for the validation of microbiological control of cellular products according to German regulators recommendations--Boon and Bane for the manufacturer.

PubMed

Störmer, M; Radojska, S; Hos, N J; Gathof, B S

2015-04-01

In order to generate standardized conditions for the microbiological control of HPCs, the PEI recommended defined steps for validation that will lead to extensive validation as shown in this study, where a possible validation principle for the microbiological control of allogeneic SCPs is presented. Although it could be demonstrated that automated culture improves microbial safety of cellular products, the requirement for extensive validation studies needs to be considered. © 2014 International Society of Blood Transfusion.

Adventures in the Environmental World and Environmental Microbiology Sampling of Air for Pharmaceutical Sterile Compounding.

PubMed

Ligugnana, Roberto

2017-01-01

Chapter <797> issued by the United States Pharmacopeial Convention, Inc. is the standard for sterile compounding. It is designed to reduce the number of patient infections due to contaminated pharmaceutical preparation. This regulation applies to all staff who prepare compounded sterile preparations and all places where they are produced, including hospitals, clinics, pharmacies, and physician's offices. This article provides the history of environmental microbiology and provides a discussion on environmental microbiology sampling of air for pharmaceutical sterile compounding. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

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.

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

PubMed

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

2015-01-01

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

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

PubMed

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

2016-06-01

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

[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.

Feasibility of Representing a Danish Microbiology Model Using FHIR.

PubMed

Andersen, Mie Vestergaard; Kristensen, Ida Hvass; Larsen, Malene Møller; Pedersen, Claus Hougaard; Gøeg, Kirstine Rosenbeck; Pape-Haugaard, Louise B

2017-01-01

Achieving interoperability in health is a challenge and requires standardization. The newly developed HL7 standard: Fast Healthcare Interoperability Resources (FHIR) promises both flexibility and interoperability. This study investigates the feasibility of expressing a Danish microbiology message model content in FHIR to explore whether complex in-use legacy models can be migrated and what challenges this may pose. The Danish microbiology message model (the DMM) is used as a case to illustrate challenges and opportunities accosted with applying the FHIR standard. Mapping of content from DMM to FHIR was done as close as possible to the DMM to minimize migration costs except when the structure of the content did not fit into FHIR. From the DMM a total of 183 elements were mapped to FHIR. 75 (40.9%) elements were modeled as existing FHIR elements and 96 (52.5%) elements were modeled as extensions and 12 (6.6%) elements were deemed unnecessary because of build-in FHIR characteristics. In this study, it was possible to represent the content of a Danish message model using HL7 FHIR.

Effect of production variables on microbiological removal in locally-produced ceramic filters for household water treatment.

PubMed

Lantagne, Daniele; Klarman, Molly; Mayer, Ally; Preston, Kelsey; Napotnik, Julie; Jellison, Kristen

2010-06-01

Diarrhoeal diseases cause an estimated 1.87 million child deaths per year. Point-of-use filtration using locally made ceramic filters improves microbiological quality of stored drinking water and prevents diarrhoeal disease. Scaling-up ceramic filtration is inhibited by lack of universal quality control standards. We investigated filter production variables to determine their affect on microbiological removal during 5-6 weeks of simulated normal use. Decreases in the clay:sawdust ratio and changes in the burnable decreased effectiveness of the filter. Method of silver application and shape of filter did not impact filter effectiveness. A maximum flow rate of 1.7 l(-hr) was established as a potential quality control measure for one particular filter to ensure 99% (2- log(10)) removal of total coliforms. Further research is indicated to determine additional production variables associated with filter effectiveness and develop standardized filter production procedures prior to scaling-up.

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

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.

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

PubMed

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

2011-12-01

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

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

PubMed

Thomson, Richard B

2016-06-01

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

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

PubMed

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

2010-08-01

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

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.

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.

Microbial biodiversity assessment of the European Space Agency's ExoMars 2016 mission.

PubMed

Koskinen, Kaisa; Rettberg, Petra; Pukall, Rüdiger; Auerbach, Anna; Wink, Lisa; Barczyk, Simon; Perras, Alexandra; Mahnert, Alexander; Margheritis, Diana; Kminek, Gerhard; Moissl-Eichinger, Christine

2017-10-25

The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli lander was subject to strict requirements for microbial cleanliness according to the obligatory planetary protection policy. To reach the required cleanliness, the ExoMars 2016 flight hardware was assembled in a newly built, biocontrolled cleanroom complex at Thales Alenia Space in Turin, Italy. In this study, we performed microbiological surveys of the cleanroom facilities and the spacecraft hardware before and during the assembly, integration and testing (AIT) activities. Besides the European Space Agency (ESA) standard bioburden assay, that served as a proxy for the microbiological contamination in general, we performed various alternative cultivation assays and utilised molecular techniques, including quantitative PCR and next generation sequencing, to assess the absolute and relative abundance and broadest diversity of microorganisms and their signatures in the cleanroom and on the spacecraft hardware. Our results show that the bioburden, detected microbial contamination and microbial diversity decreased continuously after the cleanroom was decontaminated with more effective cleaning agents and during the ongoing AIT. The studied cleanrooms and change room were occupied by very distinct microbial communities: Overall, the change room harboured a higher number and diversity of microorganisms, including Propionibacterium, which was found to be significantly increased in the change room. In particular, the so called alternative cultivation assays proved important in detecting a broader cultivable diversity than covered by the standard bioburden assay and thus completed the picture on the cleanroom microbiota. During the whole project, the bioburden stayed at acceptable level and did not raise any concern for the ExoMars 2016 mission. The cleanroom complex at Thales Alenia Space in Turin is an excellent example of how efficient microbiological control is performed.

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.

[ISO 15189 accreditation in clinical microbiology laboratory: general concepts and the status in our laboratory].

PubMed

Akyar, Işin

2009-10-01

One important trend in the laboratory profession and quality management is the global convergence of laboratory operations. The goal of an accredited medical laboratory is to continue "offering useful laboratory service for diagnosis and treatment of the patients and also aid to the health of the nation". An accredited clinical laboratory is managed by a quality control system, it is competent technically and the laboratory service meets the needs of all its patients and physicians by taking the responsibility of all the medical tests and therapies. For this purpose, ISO 15189 international standard has been prepared by 2003. ISO 15189 standard is originated from the arrangement of ISO 17025 and ISO 9001:2000 standards. Many countries such as England, Germany, France, Canada and Australia have preferred ISO 15189 as their own laboratory accreditation programme, meeting all the requirements of their medical laboratories. The accreditation performance of a clinical microbiology laboratory is mainly based on five essential points; preanalytical, analytical, postanalytical, quality control programmes (internal, external, interlaboratory) and audits (internal, external). In this review article, general concepts on ISO 15189 accreditation standards for the clinical microbiology laboratories have been summarized and the status of a private laboratory (Acibadem LabMed, Istanbul) in Turkey has been discussed.

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

Multicenter Assessment of Gram Stain Error Rates

PubMed Central

Balada-Llasat, Joan-Miquel; Harrington, Amanda; Cavagnolo, Robert

2016-01-01

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. PMID:26888900

Physicochemical and Microbiological Qualities’ Assessment of Popular Bangladeshi Mango Fruit Juice

PubMed Central

Amin, Ruhul; Rahman, Shafkat S.; Hossain, Mahboob; Choudhury, Naiyyum

2018-01-01

Introduction: Mango juice has always been considered as a delicious, nutritious popular drink, but processed juice may not always be safe due to chemical and microbial risks. Determination of physicochemical and microbiological qualities of some packed mango juices of Bangladesh will help consumers to know the present scenario. Material and Methods: Six commercially available different juice samples were collected from the market. Carbohydrate profiles were determined using HPLC, crude protein content was calculated using the Kjeldahl method and other parameters were determined by standard AOAC methods. Standard culture techniques were followed to assess the total viable count (TVC), E. coli and other fecal coliforms. Results: The highest quantity of monosaccharide (58.88%) was recorded in the AC1ME5 brand, while the lowest in Homemade (5.648%) and MN1GL2 (9.867%). The maximum content of acidity recorded was 0.24% and minimum 0.21%. The TSS content of all samples varied from 19% to 12%. The highest quantity 6.87% and the lowest 3.62% of reducing sugar were recorded. Most of the mango juices were low in protein and very low/negligible in fat content. Total viable count of different types of fruit juices varied from 1×103 - 3×103 CFU/ml. No significant amount of E. coli and fecal coliform was detected. Conclusion: It can be concluded that the locally available mango juices contain a safe level of nutritional and microbial elements for human consumption, but not highly satisfactory. PMID:29785220

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.

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.

How Well Does Physician Selection of Microbiologic Tests Identify Clostridium difficile and other Pathogens in Paediatric Diarrhoea? Insights Using Multiplex PCR-Based Detection

PubMed Central

Stockmann, Chris; Rogatcheva, Margarita; Harrel, Brian; Vaughn, Mike; Crisp, Rob; Poritz, Mark; Thatcher, Stephanie; Korgenski, Ernest K; Barney, Trenda; Daly, Judy; Pavia, Andrew T

2014-01-01

The objective of this study was to compare the aetiologic yield of standard of care microbiologic testing ordered by physicians with that of a multiplex PCR platform. Stool specimens obtained from children and young adults with gastrointestinal illness were evaluated by standard laboratory methods and a developmental version of the FilmArray Gastrointestinal Diagnostic System (FilmArray GI Panel), a rapid multiplex PCR platform that detects 23 bacterial, viral, and protozoal agents. Results were classified according to the microbiologic tests requested by the treating physician. A median of 3 (range 1-10) microbiologic tests were performed by the clinical laboratory during 378 unique diarrhoeal episodes. A potential aetiologic agent was identified in 46% of stool specimens by standard laboratory methods and in 65% of specimens tested using the FilmArray GI Panel (P<0.001). For those patients who only had Clostridium difficile testing requested, an alternative pathogen was identified in 29% of cases with the FilmArray GI Panel. Notably, 11 (12%) cases of norovirus were identified among children who only had testing for C. difficile ordered. Among those who had C. difficile testing ordered in combination with other tests, an additional pathogen was identified in 57% of stool specimens with the FilmArray GI Panel. For patients who had no C. difficile testing performed, the FilmArray GI Panel identified a pathogen in 63% of cases, including C. difficile in 8%. Physician-specified laboratory testing may miss important diarrhoeal pathogens. Additionally, standard laboratory testing is likely to underestimate co-infections with multiple infectious diarrhoeagenic agents. PMID:25599941

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.

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.

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

Improved Sepsis Alert With a Telephone Call From the Clinical Microbiology Laboratory: A Clinical Trial.

PubMed

Bunsow, Eleonora; González-Del Vecchio, Marcela; Sanchez, Carlos; Muñoz, Patricia; Burillo, Almudena; Bouza, Emilio

2015-09-01

Early sepsis attention is a standard of care in many institutions and the role of different specialists is well recognized. However, the impact of a telephone call from a specialist in Clinical Microbiology upon blood cultures request has not been assessed to the best of our knowledge. We performed telephone calls followed by an interview with physicians and nurses in charge of adult patients (> 18 years old) whose blood cultures had just been received in the Microbiology Laboratory in a tertiary hospital. Patients were randomly classified in 2 different groups: group A (telephone call performed) and group B (no telephone call). At the end of the telephonic intervention, recommendations on the use of microbiology and biochemical tests as well as on the management and antibiotic therapy of sepsis were made if required. We included 300 patients. Of those fulfilling standard criteria of sepsis, 30.3% of the nurses and 50% of the physicians immediately recognized it. Advice to optimize the use of biochemical and microbiological tests was provided in 36% of the cases and to improve antimicrobial therapy in 57.6%. The median number of days of antibiotic use in groups A and B were, respectively, 6 days (IQR: 2-12) vs 9 days (IQR: 4-16) P = 0.008 and the median number of prescribed daily doses of antimicrobials (6 [IQR: 3-17] vs 10 [IQR: 5-22] P = 0.016) were lower in group A. We estimate a reduction, only in the use of antibiotic, of 1.8 million Euros per year. A telephone call with management advice, immediately after the arrival of blood cultures in the Microbiology Laboratory improves the recognition of sepsis and the use of diagnostic resources and reduces antimicrobial consumption and expenses.

Improved Sepsis Alert With a Telephone Call From the Clinical Microbiology Laboratory

PubMed Central

Bunsow, Eleonora; Vecchio, Marcela González-Del; Sanchez, Carlos; Muñoz, Patricia; Burillo, Almudena; Bouza, Emilio

2015-01-01

Abstract Early sepsis attention is a standard of care in many institutions and the role of different specialists is well recognized. However, the impact of a telephone call from a specialist in Clinical Microbiology upon blood cultures request has not been assessed to the best of our knowledge. We performed telephone calls followed by an interview with physicians and nurses in charge of adult patients (> 18 years old) whose blood cultures had just been received in the Microbiology Laboratory in a tertiary hospital. Patients were randomly classified in 2 different groups: group A (telephone call performed) and group B (no telephone call). At the end of the telephonic intervention, recommendations on the use of microbiology and biochemical tests as well as on the management and antibiotic therapy of sepsis were made if required. We included 300 patients. Of those fulfilling standard criteria of sepsis, 30.3% of the nurses and 50% of the physicians immediately recognized it. Advice to optimize the use of biochemical and microbiological tests was provided in 36% of the cases and to improve antimicrobial therapy in 57.6%. The median number of days of antibiotic use in groups A and B were, respectively, 6 days (IQR: 2–12) vs 9 days (IQR: 4–16) P = 0.008 and the median number of prescribed daily doses of antimicrobials (6 [IQR: 3–17] vs 10 [IQR: 5–22] P = 0.016) were lower in group A. We estimate a reduction, only in the use of antibiotic, of 1.8 million Euros per year. A telephone call with management advice, immediately after the arrival of blood cultures in the Microbiology Laboratory improves the recognition of sepsis and the use of diagnostic resources and reduces antimicrobial consumption and expenses. PMID:26426609

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

PubMed

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

2015-07-01

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

[Implementation of the technical requirements of the UNE-EN-ISO 15189 quality standard in a mycobacterial laboratory].

PubMed

Guna Serrano, M del Remedio; Ocete Mochón, M Dolores; Lahiguera, M José; Bresó, M Carmen; Gimeno Cardona, Concepción

2013-02-01

The UNE-EN-ISO 15189:2007 standard defines the requirements for quality and competence that must be met by medical laboratories. These laboratories should use this international standard to develop their own quality management systems and to evaluate their own competencies; in turn, this standard will be used by accreditation bodies to confirm or recognize the laboratories' competence. In clinical microbiology laboratories, application of the standard implies the implementation of the technical and specific management requirements that must be met to achieve optimal quality when carrying out microbiological tests. In Spain, accreditation is granted by the Spanish Accreditation Body (Entidad Nacional de Acreditación). This review aims to discuss the practical application of the standard's technical requirements in mycobacterial laboratory. Firstly, we define the scope of accreditation. Secondly, we specify how the items of the standard on personnel management, control of equipment, environmental facilities, method validation, internal controls and customer satisfaction surveys were developed and implemented in our laboratory. Copyright © 2013 Elsevier España, S.L. 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 DNA hybridization techniques in the assessment of diarrheal disease among refugess in Thailand. [Shigella; Escherichia coli; Campylobacter; Cryptosporidium

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

Taylor, D.N.; Echeverria, P.; Pitarangsi, C.

1988-01-01

The epidemiology and etiology of acute diarrheal disease were determined in a Hmong refugee camp on the Thai-Laotian border from April 11 to May 14, 1985. DNA hybridization techniques were used to detect Shigella species, enteroinvasive Escherichia coli, and enterotoxigenic E. coli. A monoclonal enzyme-linked immunosorbent assay was used to detect rotavirus, and standard microbiology was used to detect other enteropathogens. The age-specific diarrheal disease rates were 47 episodes per month per 1000 children less than five years old and 113 episodes per month per 1000 children less than one year old. Rotavirus, enterotoxigenic E. coli, Campylobacter, and Cryptosporidium weremore » the predominant pathogens in children less than two years old. The DNA probe hybridized with 94% of 31 specimens identified as enterotoxigenic E. coli by the standard assays and with none of the specimens in which the standard assays were negative. The probe for Shigella and enteroinvasive E. coli hybridized in eight of 10 stools that contained Shigella and four of 314 stools from which Shigella and enteroinvasive E. coli were not isolated. The use of DNA probes allows specimens to be collected in remote areas with a minimum amount of equipment and technical expertise so that they can be easily transported to a central laboratory for further processing.« less

Microbiological and other hazards from seafoods with special reference to Vibrio parahaemolyticus

PubMed Central

Barrow, G. I.

1974-01-01

The salient features of some of the more important microbiological health hazards to man from seafoods are reviewed briefly. They include poisoning, indirectly from toxins produced by certain marine algae or more directly by Clostridium botulinum, as well as infection with the marine bacterium Vibrio parahaemolyticus. Local culinary habits play a significant role in such kinds of illness, and food well cooked shortly before consumption is always preferable. Since established customs die hard, safety ultimately depends, not so much on arbitrary microbiological standards, but on hygienic production, correct storage and distribution, and on education in intelligent eating habits. PMID:4467856

[Analysis of the results of the SEIMC External Quality Control Program. Year 2011].

PubMed

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

2013-02-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica [SEIMC]) includes controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology, and molecular microbiology. This article presents the most relevant conclusions and lessons from the 2011 controls. Overall, the results obtained in 2011 confirm the excellent skill and good technical standards found in previous years. Nevertheless, erroneous results can be obtained in any laboratory and in clinically relevant determinations. The results of this program highlight the need to implement both internal and external controls, such as those offered by the SEIMC program, in order to ensure maximal quality of microbiological tests. Copyright © 2013 Elsevier España, S.L. All rights reserved.

The Engaged Microbiologist: Bringing the Microbiological Sciences to the K-12 Community.

PubMed

Westenberg, David J

2016-03-01

Exposing K-12 students to cutting edge science that impacts their daily lives can bring classroom lessons to life. Citizen-science projects are an excellent way to bring high-level science to the classroom and help satisfy one of the cornerstone concepts of the Next Generation Science Standards (NGSS), "engaging in practices that scientists and engineers actually use." This can be a daunting task for teachers who may lack the background or resources to integrate these projects into the classroom. This is where scientific societies such as the American Society for Microbiology (ASM) can play a critical role. ASM encourages its members to engage with the K-12 community by providing networking opportunities and resources for ASM members and K-12 teachers to work together to bring microbiology into the classroom. Journal of Microbiology & Biology Education.

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.

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.

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.

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.

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.

The Individualized Quality Control Plan - Coming Soon to Clinical Microbiology Laboratories Everywhere!

PubMed

Anderson, Nancy

2015-11-15

As of January 1, 2016, microbiology laboratories can choose to adopt a new quality control option, the Individualized Quality Control Plan (IQCP), under the Clinical Laboratory Improvement Amendments of 1988 (CLIA). This voluntary approach increases flexibility for meeting regulatory requirements and provides laboratories the opportunity to customize QC for their testing in their unique environments and by their testing personnel. IQCP is an all-inclusive approach to quality based on risk management to address potential errors in the total testing process. It includes three main steps, (1) performing a risk assessment, (2) developing a QC plan, and (3) monitoring the plan through quality assessment. Resources are available from the Centers for Medicare & Medicaid Services, Centers for Disease Control and Prevention, American Society for Microbiology, Clinical and Laboratory Standards Institute, and accrediting organizations, such as the College of American Pathologists and Joint Commission, to assist microbiology laboratories implementing IQCP.

The Engaged Microbiologist: Bringing the Microbiological Sciences to the K–12 Community

PubMed Central

Westenberg, David J.

2016-01-01

Exposing K–12 students to cutting edge science that impacts their daily lives can bring classroom lessons to life. Citizen-science projects are an excellent way to bring high-level science to the classroom and help satisfy one of the cornerstone concepts of the Next Generation Science Standards (NGSS), “engaging in practices that scientists and engineers actually use.” This can be a daunting task for teachers who may lack the background or resources to integrate these projects into the classroom. This is where scientific societies such as the American Society for Microbiology (ASM) can play a critical role. ASM encourages its members to engage with the K–12 community by providing networking opportunities and resources for ASM members and K–12 teachers to work together to bring microbiology into the classroom. Journal of Microbiology & Biology Education PMID:27047585

Assessing Clinical Microbiology Practice Guidelines: American Society for Microbiology Ad Hoc Committee on Evidence-Based Laboratory Medicine Practice Guidelines Assessment.

PubMed

Nachamkin, Irving; Kirn, Thomas J; Westblade, Lars F; Humphries, Romney

2017-11-01

As part of the American Society for Microbiology (ASM) Evidence-Based Laboratory Medicine Practice Guidelines Committee of the Professional Practice Committee, an ad hoc committee was formed in 2014 to assess guidelines published by the committee using an assessment tool, Appraisal of Guidelines for Research Evaluation II (AGREE II). The AGREE II assessment helps reviewers determine whether published guidelines are robust, transparent, and clear in presenting practice recommendations in a standardized manner. Identifying strengths and weaknesses of practice guidelines by ad hoc assessments helps with improving future guidelines through the participation of key stakeholders. This minireview describes the development of the ad hoc committee and results from their review of several ASM best practices guidelines and a non-ASM practice guideline from the Emergency Nurses Association. Copyright © 2017 American Society for Microbiology.

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

PubMed

Ikutegbe, Victoria; Sikoki, Francis

2014-10-15

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

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.

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

PubMed Central

2016-01-01

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

Microbiological standards and handling codes for chilled and frozen foods. A review.

PubMed

ELLIOTT, R P; MICHENER, H D

1961-09-01

The usefulness of microbiological standards for frozen foods is now a controversy in the trade and scientific literature. Most reviewers have given arguments both for and against, and have concluded that they should be applied with great caution. Such standards have the advantage of putting questions of safety on a convenient numerical basis. Canadian workers have reported that promulgation of standards has invariably raised the hygienic level of the products controlled. Bacteriological standards have often been associated with the question of safety to the consumer. Everyone recognizes that food poisoning bacteria are a potential danger in any food. But many have argued that the history of food poisoning outbreaks from frozen foods is excellent and that there is no need for standards; on the other hand, proponents of standards have pointed to the incomplete investigation and reporting of outbreaks, and have argued that there may be more outbreaks than we realize. They have pointed to laboratory studies that have shown grossly mishandled precooked frozen foods to be truly dangerous. Some have proposed that pathogens should be absent from foods; but others have questioned that a microbiological standard can accomplish this end. Some pathogens, such as Salmonella or Staphylococcus have been shown to be so ubiquitous that their presence in some commercial foods is unavoidable. Also, sampling and analytical methods have been described as inadequate to guarantee that pathogens present will be detected. Some have argued that control at the source is a better way-through inspections of the plant operation, by enforcement of handling codes, or by processing procedures such as pasteurization, which would be more certain to result in a pathogen-free food.A most important part of any of the proposed standards is a "total count" of viable aerobic bacteria. English workers have found that foods causing poisoning outbreaks usually had total viable counts above 10 million per gram. On the other hand, these same workers found Salmonella on meats with very low total viable count. The assumption by many that low total count indicates safety has been shown to be not always true. Furthermore, high counts of nonpathogenic organisms, such as psychrophilic saprophytes would have no public health significance. The relation between bacterial level and quality is open to less controversy. Some authorities have pointed to bacterial level as a measure of sanitation, adequacy of refrigeration, or speed of handling. Others have indicated that to determine which of these factors caused a high count would be impossible with only a total count on the product as a guide. Some investigators have said a high count affects flavor adversely before actual spoilage is evident, and this may be a factor in competition on today's market. It is well established that initial bacterial level will affect the shelf-life of a chilled product. Methods of analysis are more nearly adequate for counts than for pathogens, but they need improvement, and should be clearly specified as part of any bacteriological standard. Foods with high count could sometimes be brought into compliance merely by storing them for a sufficient period frozen, or by heating them slightly. This has been cited by some authors as a disadvantage of bacteriological standards. The enterococci and the coliform group (except Escherichia coli) have been shown to be ubiquitous and therefore should not be used alone to indicate fecal contamination. Although E. coli has greater significance, its source should be determined each time it is found. Various reviewers have expressed the need for caution in the application of standards. The principal precautionary arguments we have found are as follows:1) A single set of microbiological standards should not be applied to foods as a miscellaneous group, such as "frozen foods" or "precooked foods."2) Microbiological standards should be applied first to the more hazardous types of foods on an individual basis, after sufficient data are accumulated on expected bacterial levels, with consideration of variations in composition, processing procedures, and time of frozen storage.3) When standards are chosen, there should be a definite relation between the standard and the hazard against which it is meant to protect the public.4) Methods of sampling and analysis should be carefully studied for reliability and reproducibility among laboratories, and chosen methods should be specified in detail as part of the standard.5) Tolerances should be included in the standard to account for inaccuracies of sampling and analysis.6) At first, the standard should be applied on a tentative basis to allow for voluntary compliance before becoming a strictly enforced regulation.7) Microbiological standards will be expensive to enforce.8) If standards are unwisely chosen they will not stand in courts of law.

[Microbiological assessment of the Gouda-type cheese-making process in a Venezuelan industry].

PubMed

Dáivila, Jacqueline; Reyes, Genara; Corzo, Otoniel

2006-03-01

The adoption of the Hazard Analysis and Critical Control Point (HACCP) system is necessary to assure the safety of the product in the cheese-making industry. The compliment of pre-requisite programs as Good Manufacture Practices (GMPs) and Sanitation Standard Operating Procedures (SSOPs) are required before the implementation of the HACCP plan. GMPs are the standards related to equipments, tools, personnel, etc. SSOPs are the procedures related to hygiene and sanitation of the plant and workers. The aim of this study was to assess the compliment of the pre-requisite programs and the microbiological conditions of the Gouda type cheese-making process in a Venezuelan processing plant before designing a HACCP plan. Samples were: (a) raw milk, pasteurized milk, curd and ripened cheese, (b) water, (c) environment of the production areas and ripening premises, (d) equipments before and after sanitation, (e) food handlers. Microbiological analyses were done according to COVENIN standards. This study showed that even though pasteurization process was effective to kill pathogen bacteria of the raw milk and the water was safe, however there are deficient manufacture practices in the hygiene as well as in sanitation of the plant and food handlers. Prerequisite programs (GMP-SSOP) of this industry need to be well established, controlled and evaluated.

Donor Derived Candida stellimalicola in a Clinical Specimen: Preservation Fluid Contamination During Pancreas Procurement.

PubMed

Dupont, Damien; Huguenin, Antoine; Tisserand, Elodie; Reiter, Véronique; Morelon, Emmanuel; Badet, Lionel; Villena, Isabelle; Wallon, Martine; Toubas, Dominique

2018-06-01

We report here a case of possible donor-derived Candida stellimalicola infection after pancreas transplantation. Candida stellimalicola, an environmental non-filamentous yeast, was isolated from both the peritoneal fluid of the graft donor and the preservation fluid of the transplanted pancreas. Interestingly, this strain exhibited high minimum inhibitory concentrations to azoles. These results justified the use of echinocandins as therapy instead of fluconazole. This switch permitted a favorable outcome. To our knowledge, this is the first report of C. stellimalicola from clinical samples and therefore the first reported case of a possible human infection. This case report highlights the need for standardized microbiological procedures in solid organ transplant settings. Moreover, it underlines the importance of using molecular identification technique when routine techniques do not allow successful identification of the pathogen. It is of utmost importance to determine sensitivity profile, even in the absence of species-level identification, because resistance to fluconazole is not uncommon, especially in emergent species.

A new method for long-term storage of titred microbial standard solutions suitable for microbiologic quality control activities of pharmaceutical companies.

PubMed

Chiellini, Carolina; Mocali, Stefano; Fani, Renato; Ferro, Iolanda; Bruschi, Serenella; Pinzani, Alessandro

2016-08-01

Commercially available lyophilized microbial standards are expensive and subject to reduction in cell viability due to freeze-drying stress. Here we introduce an inexpensive and straightforward method for in-house microbial standard preparation and cryoconservation that preserves constant cell titre and cell viability over 14 months.

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.

21 CFR 120.6 - Sanitation standard operating procedures.

Code of Federal Regulations, 2010 CFR

2010-04-01

... garments; (3) Prevention of cross contamination from insanitary objects to food, food packaging material... health conditions that could result in the microbiological contamination of food, food packaging... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Sanitation standard operating procedures. 120.6...

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.

[Municipal landfill site in Krzyz near Tarnów as source of microbiological factors harmful to environment and human health].

PubMed

Fraczek, Krzysztof; Barabasz, Wiesław

2004-01-01

The present study aimed to evaluate microbiological pollution of air with microorganisms belonging to different taxonomic and physiological groups, and to examine whether the effect of the municipal landfill site in Krzyz changes at various study sites located: in so called "zero zone" (operating landfill), at different distances from the landfill and in Tarnów. Microbiological studies of atmospheric air were carried out from May 1998 to April 2001. Measurements were taken at 10 study sites located at the operating municipal landfill site in Krzyz, inside and outside of its protection zone. Microbial air pollution standard (PN-89/Z-04111/02 and PN-89/Z-04111/03) were used to evaluate the impact of municipal landfill site on the atmospheric environment. The standards were most often exceeded by hemolytic bacteria, (277 cases out of 360 measurements) i.e. 76.9%, and Actinomycetes (213 cases out of 360 measurements) i.e 59.1%, while by fungi (26 cases out of 360 measurements) i.e 7.2% and bacteria (42 cases out of 360 measurements) i.e 11.6% in a lesser degree. The standards were most often exceeded in operating land fill site sector, at the gateway to the land fill site and in partially reclaimed sector. Fewest cases of standard exceedance were recorded in control site (located outside the landfill site), near built-up area and before the entrance to the land fill site.

Evaluation of Petrifilms(TM) as a diagnostic test to detect bovine mastitis organisms in Kenya.

PubMed

Gitau, George K; Bundi, Royford M; Vanleeuwen, John; Mulei, Charles M

2013-03-01

The study purpose was to validate Petrifilms(TM) (3M Microbiology, 2005) against standard culture methods in the diagnosis of bovine mastitis organisms in Kenya. On 128 smallholder dairy cattle farms in Kenya, between June 21, 2010 and August 31, 2010, milk samples from 269 cows that were positive on California Mastitis Test (CMT) were cultured using standard laboratory culture methods and Petrifilms(TM) (Aerobic Count and Coliform Count -3M Microbiology, 2005), and results were compared. Staphylococcus aureus was the most common bacterium isolated (73 % of samples). Clinical mastitis was found in only three cows, and there were only two Gram-negative isolates, making it impossible to examine the agreement between the two tests for Gram-negative- or clinical mastitis samples. The observed agreement between the standard culture and Petrifilm(TM) (3M Microbiology, 2005) results for Gram-positive isolates was 85 %, and there was fair agreement beyond that expected due to chance alone, with a kappa (κ) of 0.38. Using culture results as a gold standard, the Petrifilms(TM) had a sensitivity of 90 % for Gram-positive samples and specificity of 51 %. With 87 % of CMT-positive samples resulting in Gram-positive pathogens cultured, there was a positive predictive value of 93 % and a negative predictive value of 43 %. Petrifilms(TM) should be considered for culture of mastitis organisms in developing countries, especially when Gram-positive bacteria are expected.

[Methods for evaluating diagnostic tests in Enfermedades Infecciosas y Microbiología Clínica].

PubMed

Ramos, J M; Hernández, I

1998-04-01

In the field of infectious diseases and clinical microbiology, the evaluation of diagnostic tests (DT) is an important research area. The specific difficulties of this type of research has motivated that have not caught the severity methodological of others areas of clinical research. This article try to asses and characterize the methodology of articles about DT published in Enfermedades Infecciosas y Microbiología Clínica (EIMC) journal. Forty-five articles was selected in the EIMC journal during the 1990-1996 period, because of determinate the sensitivity and specificity of different DT. Methodological standards, extensively accepted was used. In all of articles, except one (98%) the gold standard was specified yours use, however in 4 studies (9%) include the DT in the gold standard (incorporation bias). The correct description of DT was reported in 75% of cases, but only in 11% cases the reproducibility of test was evaluated. The description of source of reference population, standard of inclusion and spectrum of composition was described in 58, 33 and 40% of articles, respectively. In 33% of studies presented workup bias, only 6% commented blind-analysis of results, and 11% presented indeterminate test results. Half of the studies reported test indexes for clinical subgroups, only one article (2%) provided numerical precision for test indexes, and only 7% reported receiver operating characteristics curves. The methodological quality of DT research in the EIMC journal may improve in different aspects of design and presentation of results.

Finding an optimal strategy for measuring the quality of groundwater as a source for drinking water

NASA Astrophysics Data System (ADS)

van Driezum, Inge; Saracevic, Ernis; Scheibz, Jürgen; Zessner, Matthias; Kirschner, Alexander; Sommer, Regina; Farnleitner, Andreas; Blaschke, Alfred Paul

2015-04-01

A good chemical and microbiological water quality is of great importance in riverbank filtration systems that are used as public water supplies. Water quality is ideally monitored frequently at the drinking water well using a steady pumping rate. Monitoring source water (like groundwater) however, can be more challenging. First of all, piezometers should be drilled in the correct layer of the aquifer. Secondly, the sampling design should include all preferred parameters (microbiological and chemical parameters) and should also take the hydrological conditions into account. In this study, we made use of different geophysical techniques (ERT and FDEM) to select the optimal placement of the piezometers. We also designed a sampling strategy which can be used to sample fecal indicators, biostability parameters, standard chemical parameters and a wide range of micropollutants. Several time series experiments were carried out in the study site Porous GroundWater Aquifer (PGWA) - an urban floodplain extending on the left bank of the river Danube downstream of the City of Vienna, Austria. The upper layer of the PGWA consist of silt and has a thickness from 1 to 6 meter. The underlying confined aquifer consists of sand and gravel and has a thickness of in between 3 and 15 meter. Hydraulic conductivities range from 5 x 10-2 m/s up to 5 x 10-5 m/s. Underneath the aquifer are alternating sand and clay/silt layers. As fecal markers Escherichia coli, enterococci and aerobic spores were measured. Biostability was measured using leucine incorporation. Additionally, several micropollutants and standard chemical parameters were measured. Results showed that physical and chemical parameters stayed stable in all monitoring wells during extended purging. A similar trend could be observed for E coli and enterococci. In the wells close to the river, aerobic spores and leucine incorporation decreased after 30 min. of pumping, whereas the well close to the backwater showed a different pattern. Overall, purging for 45 minutes was the optimal sampling procedure for the microbiological parameters. Samples for the detection of micropollutants were taken after 15 min. purging.

Laboratory Diagnosis of Sepsis? No SIRS, Not Just Yet.

PubMed

Dunne, W Michael

2015-08-01

In order to maximize the benefit of prompt antimicrobial therapy and avoid the risk associated with inappropriate use of antimicrobial agents, patients with suspected sepsis must be rapidly differentiated from patients with systemic inflammatory response syndrome (SIRS). In combination with standard microbiological testing, a number of biomarkers have been recently evaluated for this purpose, and the performance characteristics of the most promising of these are reviewed. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

[Hygiene in airline catering. I. Microbiologic study of meals distributed on aircrafts].

PubMed

Castellani, P; Frugoni, G

1983-08-25

A preliminary microbiological survey, conducted in the Italian national airlines Catering Department is reported. Precooked,, frozen meals reheated on medium and long distance flights were examined. The results indicate that hygiene standards are satisfactorily maintained. The presence of staphylococcus aureus in some samples highlights the importance of preventive and prophylactic measures in healthy carriers. In view of the growing concern about Salmonella poisoning in airline passengers the absence of this bacterium is extremely satisfying.

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

PubMed Central

Tebbutt, G. M.

1991-01-01

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

A health-sanitary evaluation of lacteal desserts for consumption in Santa Cruz de Tenerife.

PubMed

Rodríguez, C; Alvarez, R; Hardisson, A; Arias, A; Sierra, A

1994-01-01

The consumption of lacteal desserts in the province of Santa Cruz de Tenerife is notably high. However, there are no legal standards in Spain regarding microbiological quality. For this reason, we have decided that it would be of interest to carry out a health-sanitary study of these products, with the aim of discovering their microbial content. 330 samples of lacteal desserts on sale in the province of Santa Cruz de Tenerife have undergone analysis. They have been divided into three groups: cream caramel (egg and vanilla) (80), mousse (60) and the third group, known as "other desserts", which includes custard and the rest of lacteal desserts not included in the previous groupings (190). Neither E. coli, Salmonella spp., Shigella spp., nor Staphylococcus aureus have been detected in any of the samples analysed. In spite of the fact that the results obtained do not reflect high microbiological contamination, we consider it necessary to lay down legal standards, with reference values, for these lacteal products, which will guarantee good microbiological quality.

PubMed Central

Ceriale, E.; Messina, G.; Lenzi, D.; Manzi, P.

2017-01-01

Summary Introduction. Contamination of hospital surfaces plays an important role in the transmission of several healthcare-associated microorganisms, therefore methods for evaluating hospital surfaces' cleaning gain particular importance. Among these, there are visual inspection, quantitative microbiology, fluorescent markers and adenosine triphosphate (ATP) bioluminescence. The latter seems to provide interesting features, detecting the presence of ATP on surface (as Relative Light Units, RLU), a proxy of organic matter and microbial contamination. Several studies have investigated the effectiveness of this technology; with this research, we aim to summarize the most significant results. Methods. A systematic review was conducted. The keywords (namely, "ATP", "bioluminescence", "hospital" and "surfaces") were searched in PubMed/MEDLINE and Scopus databases, in order to find relevant data, from January 2000 to October 2014. After the selection, we globally considered 27 articles. Results. Most of the studies were conducted in United Kingdom and in USA. Different threshold RLU benchmark values were identified by analyzed studies. Fourteen of these researches compared the ATP bioluminescence with microbiological methods, 11 identified a significant correlation between the two methods, although poor or not complete for 5. Discussion. ATP bioluminescence is not a standardized methodology: each tool has different benchmark values, not always clearly defined. At the moment, we can say that the technique could be used to assess, in real time, hospital surfaces where cleanliness is required, but not sterility. PMID:28900359

A quantitative method to evaluate the donor corneal tissue quality used in a comparative study between two hypothermic preservation media.

PubMed

Parekh, Mohit; Salvalaio, Gianni; Ferrari, Stefano; Amoureux, Marie-Claude; Albrecht, Cecile; Fortier, Denis; Ponzin, Diego

2014-12-01

To standardize a new evaluation technique for calculating the overall quality (OQ) of the donor cornea and validate it using a comparative study of corneas preserved in Optisol-GS and Cornea Cold®. Thirty pairs of donor corneas were selected for a 4 week in vitro comparative study using masked observers. Physiological parameters like thickness, transparency, viable endothelial cell density (VECD) and morphology were transformed to numerical range (0-4) to obtain the OQ. Microbiological examination was performed using Bactec instrument. Students t test showed statistically better results (p < 0.05) from week 3 for thickness, week 2 for transparency and week 1 for morphology and VECD; statistical significance (p < 0.05) was found for OQ from week 2 for the corneas preserved in Cornea Cold® compared to Optisol-GS. Epithelial quality was similar regardless of the medium. Microbiological examination showed absence of aerobic and anaerobic microorganisms in both media. OQ method is efficient, consistent and easy, now validated for comparative studies. Further refinement is necessary for its use at eye-banks, bio-banks and research or transplantation purposes. Cornea Cold® is a promising hypothermic corneal storage medium with preservation time ≤21 days. This permits higher flexibility, evaluation accuracy, longer duration for surgical preparation and ease of transportation.

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

USGS Publications Warehouse

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

2000-01-01

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

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.…

Quality in the molecular microbiology laboratory.

PubMed

Wallace, Paul S; MacKay, William G

2013-01-01

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

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

[Analysis of the results of the SEIMC External Quality Control Program. Year 2012].

PubMed

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

2014-02-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) include controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology and molecular microbiology. This article presents the most relevant conclusions and lessons from the 2012 controls. As a whole, the results obtained in 2012 confirm the excellent skill and good technical standards found in previous editions. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. Once again, the results of this program highlighted the need to implement both internal and external controls in order to assure the maximal quality of the microbiological tests. Copyright © 2014 Elsevier España, S.L. All rights reserved.

[Bacteriological quality of drinking water in the City of Merida, Mexico].

PubMed

Flores-Abuxapqui, J J; Suárez-Hoil, G J; Puc-Franco, M A; Heredia-Navarrete, M R; Vivas-Rosel, M D; Franco-Monsreal, J

1995-01-01

With the aim of knowing the microbiological quality of drinking water in Merida, Yucatan, 383 paired samples of drinking water (two per house) were studied. Three hundred sixty four (95%) city water system samples and 283 (73.89%) tap water samples met the microbiological standards for drinking water. It was concluded that microbiological quality of drinking water from the city water system is satisfactory, except for the water system district Merida III, which has a significant aerobic plate count contamination level (21.7% of the samples). Domestic storage systems preserve water quality, with the exception of district Merida I, which has the highest level of contamination (4.8% of the samples) possibly from sewage water and fecal sources.

[Analysis of the results of the SEIMC External Quality Control Program. Year 2014].

PubMed

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

2016-07-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) include controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology and molecular microbiology. This article presents the most relevant conclusions and lessons from the 2014 controls. As a whole, the results obtained in 2014 confirm the excellent skill and good technical standards found in previous editions. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. Once again, the results of the SEIMC program highlighted the need to implement both internal and external controls in order to assure the maximal quality of the microbiological tests. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

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.

Comparative Analysis of Subtyping Methods against a Whole- Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

DTIC Science & Technology

2015-01-01

enterica serovar En- teritidis. Food Microbiology 34:164 –173. http://dx.doi.org/10.1016/j.fm .2012.11.012. 11. Dewaele I, Rasschaert G, Bertrand S...MVLST showed the potential to trace major lineages and ecological origins of S. enterica serotype Enteritidis. Our results suggested that whole-genome...in Journal of Clinical Microbiology , Vol. 53 (1) (2015), (3 (1). DoD Components reserve a royalty-free, nonexclusive and irrevocable right to

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…

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.

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.

Rapid classification of heavy metal-exposed freshwater bacteria by infrared spectroscopy coupled with chemometrics using supervised method

NASA Astrophysics Data System (ADS)

Gurbanov, Rafig; Gozen, Ayse Gul; Severcan, Feride

2018-01-01

Rapid, cost-effective, sensitive and accurate methodologies to classify bacteria are still in the process of development. The major drawbacks of standard microbiological, molecular and immunological techniques call for the possible usage of infrared (IR) spectroscopy based supervised chemometric techniques. Previous applications of IR based chemometric methods have demonstrated outstanding findings in the classification of bacteria. Therefore, we have exploited an IR spectroscopy based chemometrics using supervised method namely Soft Independent Modeling of Class Analogy (SIMCA) technique for the first time to classify heavy metal-exposed bacteria to be used in the selection of suitable bacteria to evaluate their potential for environmental cleanup applications. Herein, we present the powerful differentiation and classification of laboratory strains (Escherichia coli and Staphylococcus aureus) and environmental isolates (Gordonia sp. and Microbacterium oxydans) of bacteria exposed to growth inhibitory concentrations of silver (Ag), cadmium (Cd) and lead (Pb). Our results demonstrated that SIMCA was able to differentiate all heavy metal-exposed and control groups from each other with 95% confidence level. Correct identification of randomly chosen test samples in their corresponding groups and high model distances between the classes were also achieved. We report, for the first time, the success of IR spectroscopy coupled with supervised chemometric technique SIMCA in classification of different bacteria under a given treatment.

Near-infrared spectroscopy for the detection and quantification of bacterial contaminations in pharmaceutical products.

PubMed

Quintelas, Cristina; Mesquita, Daniela P; Lopes, João A; Ferreira, Eugénio C; Sousa, Clara

2015-08-15

Accurate detection and quantification of microbiological contaminations remains an issue mainly due the lack of rapid and precise analytical techniques. Standard methods are expensive and time-consuming being associated to high economic losses and public health threats. In the context of pharmaceutical industry, the development of fast analytical techniques able to overcome these limitations is crucial and spectroscopic techniques might constitute a reliable alternative. In this work we proved the ability of Fourier transform near infrared spectroscopy (FT-NIRS) to detect and quantify bacteria (Bacillus subtilis, Escherichia coli, Pseudomonas fluorescens, Salmonella enterica, Staphylococcus epidermidis) from 10 to 10(8) CFUs/mL in sterile saline solutions (NaCl 0.9%). Partial least squares discriminant analysis (PLSDA) models showed that FT-NIRS was able to discriminate between sterile and contaminated solutions for all bacteria as well as to identify the contaminant bacteria. Partial least squares (PLS) models allowed bacterial quantification with limits of detection ranging from 5.1 to 9 CFU/mL for E. coli and B. subtilis, respectively. This methodology was successfully validated in three pharmaceutical preparations (contact lens solution, cough syrup and topic anti-inflammatory solution) proving that this technique possess a high potential to be routinely used for the detection and quantification of bacterial contaminations. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Does vaginal irrigation with saline solution in women with infectious vaginitis contribute to the clinical and microbiological results of antibiotic therapy?

PubMed

Derbent, Aysel Uysal; Ulukanlıgil, Mustafa; Keskin, Esra Aktepe; Soylu, Gül; Kafalı, Hasan

2012-01-01

To compare the clinical and microbiological results between patients with infectious vaginitis receiving vaginal irrigation with saline or no irrigation before standard antibiotic therapy. Women with vaginitis (n = 109) were randomized to receive vaginal irrigation with saline or no irrigation before standard antibiotic therapy. The vaginal symptoms perceived by subjects and clinical findings were assessed with a standardized scale during four follow-up visits, and Gram stain Nugent scores and vaginal fluid cultures were analyzed at each visit. Vaginal discharge (z = 7.159; p < 0.001), pruritus (z = 5.169; p < 0.001), itching (z = 2.969; p < 0.003) and odor scores (z = 2.303; p < 0.021) were significantly reduced in the study group compared to the control group between the first visit and 3-5 days after irrigation, before the start of antibiotic therapy. The second and third visits (15 and 30-45 days after antibiotic therapy) showed that the patients' symptoms and amounts of visible vaginal discharge did not differ between the two groups. Moreover, the microbiological cures of patients in each group did not differ at these visits (z = 0.447; p = 0.655). Vaginal irrigation with saline significantly reduces self-reported symptoms in the short term but has no effect on long-term clinical and laboratory results in women with infectious vaginitis. Copyright © 2012 S. Karger AG, Basel.

Meat, the metabolites: an integrated metabolite profiling and lipidomics approach for the detection of the adulteration of beef with pork

PubMed Central

Trivedi, Drupad K.; Hollywood, Katherine A.; Rattray, Nicholas J. W.; Ward, Holli; Trivedi, Dakshat K.; Greenwood, Joseph; Ellis, David I.

2016-01-01

Adulteration of high quality food products with sub-standard and cheaper grades is a world-wide problem taxing the global economy. Currently, many traditional tests suffer from poor specificity, highly complex outputs and a lack of high-throughput processing. Metabolomics has been successfully used as an accurate discriminatory technique in a number of applications including microbiology, cancer research and environmental studies and certain types of food fraud. In this study, we have developed metabolomics as a technique to assess the adulteration of meat as an improvement on current methods. Different grades of beef mince and pork mince, purchased from a national retail outlet were combined in a number of percentage ratios and analysed using GC-MS and UHPLC-MS. These techniques were chosen because GC-MS enables investigations of metabolites involved in primary metabolism whilst UHPLC-MS using reversed phase chromatography provides information on lipophilic species. With the application of chemometrics and statistical analyses, a panel of differential metabolites were found for identification of each of the two meat types. Additionally, correlation was observed between metabolite content and percentage of fat declared on meat products’ labelling. PMID:26911805

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

PubMed

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

2005-01-01

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

The microbiological examination of ready-to-eat organic vegetables from retail establishments in the United Kingdom.

PubMed

Sagoo, S K; Little, C L; Mitchell, R T

2001-12-01

A microbiological study of uncooked ready-to-eat organic vegetables was undertaken to determine the microbiological quality of these vegetables on retail sale in the UK. Organic vegetables were collected and examined according to a standardized protocol. The majority (3185 of 3200; 99.5%) of samples were found to be of satisfactory/acceptable quality whilst only 15 (0.5%) were of unsatisfactory quality. Unsatisfactory results were due to Escherichia coli and Listeria spp. (not L. monocytogenes) levels in excess of 102 cfu g-1. The absence of pathogens (L. monocytogenes, Salmonella, Campylobacter and E. coli O157) and the low incidence (1.5%) of E. coli and Listeria spp. associated with these organic vegetables indicates that overall agricultural, hygiene, harvesting and production practices were good. There has been a significant expansion of the UK organic market since 1998/99. Of the various commodity sectors making up the organic market, fruit and vegetables is the largest sector and this has been reflected in an increased interest in their microbiological safety. This is the first study to provide information on the microbiological quality of organic vegetables.

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

PubMed

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

2011-09-01

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

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.

[Comparative study of combined local treatment (sulfadimidine, metronidazole and nystatin) and the standard monotherapy in uncomplicated bacterial vaginosis].

PubMed

Milánkovits, Márton; Baksay, László; Plachy, János

2002-12-22

Comparative, in vivo, human, prospective, single blind, clinical and microbiological diagnoses based and randomised study of the treatment of uncomplicated bacterial vaginosis with two forms of combined (metronidazole + nystatin + sulfadimidin) vaginal suppositories (laminated and mixed containing the same ingredients) and the standard preparations available in the Hungarian market (Dalacin vaginal cream and Klion vaginal suppository). The examinations involved 60 volunteers and were performed in the Gynecological Outpatient Clinic of the Council of Erd, the microbiological samples were examined at Saint Rókus Hospital in Budapest. The combined treatment was better tolerated and resulted in normal vaginal pH significantly more often at the same rate of recovery. The combined treatment is simultaneously effective in cases of the most prevalent coinfections too.

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...

The Lebanese Society for Infectious Diseases and Clinical Microbiology (LSIDCM) guidelines for adult community-acquired pneumonia (Cap) in Lebanon.

PubMed

Moghnieh, Rima; Yared Sakr, Nadine; Kanj, Souha S; Musharrafieh, Umayya; Husni, Rula; Jradeh, Mona; Al-Awar, Ghassan; Matar, Madona; Jureij, Wafa; Antoine, Saad; Azar, Eid; Abi Hanna, Pierre; Minari, Afaf; Hammoud, Jamale; Kfoury, Joumana; Mahfouz, Tahsin; Abou Chakra, Diaa; Zaatari, Mohamad; Tabbarah, Zuhayr A

2014-01-01

Adult community-acquired pneumonia (CAP) is a common cause of morbidity and mortality which is managed by different disciplines in a heterogeneous fashion. Development of consensus guidelines to standardize these wide variations in care has become a prime objective. The Lebanese Society of Infectious Diseases and Clinical Microbiology (LSIDCM) convened to set Lebanese national guidelines for the management of CAP since it is a major and a prevalent disease affecting the Lebanese population. These guidelines, besides being helpful in direct clinical practice, play a major role in establishing stewardship programs in hospitals in an effort to contain antimicrobial resistance on the national level. These guidelines are intended for primary care practitioners and emergency medicine physicians. They constitute an appropriate starting point for specialists' consultation being based on the available local epidemiological and resistance data. This document includes the following: 1/ Rationale and scope of the guidelines; 2/ Microbiology of CAP based on Lebanese data; 3/ Clinical presentation and diagnostic workup of CAP; 4/ Management and prevention strategies based on the IDSA/ATS Consensus Guidelines, 2007, and the ESCMID Guidelines, 2011, and tailored to the microbiological data in Lebanon; 5/ Comparison to regional guidelines. The recommendations made in this document were graded based on the strength of the evidence as in the 2007 IDSA/ATS Consensus Guidelines. Hopefully, these guidelines will be an important step towards standardization of CAP care in Lebanon and set the agenda for further research in this area.

MALDI-TOF MS in the Microbiology Laboratory: Current Trends.

PubMed

Schubert, Sören; Kostrzewa, Markus

2017-01-01

Within less than a decade matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a gold standard for microbial identification in clinical microbiology laboratories. Besides identification of microorganisms the typing of single strains as well as the antibiotic and antimycotic resistance testing has come into focus in order to speed up the microbiological diagnostic. However, the full potential of MALDI-TOF MS has not been tapped yet and future technological advancements will certainly expedite this method towards novel applications and enhancement of current practice. So, the following chapter shall be rather a brainstorming and forecast of how MALDI-TOF MS will develop to influence clinical diagnostics and microbial research in the future. It shall open up the stage for further discussions and does not claim for overall validity.

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.

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

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.

Development, optimization and validation of a rapid colorimetric microplate bioassay for neomycin sulfate in pharmaceutical drug products.

PubMed

Francisco, Fabiane Lacerda; Saviano, Alessandro Morais; Pinto, Terezinha de Jesus Andreoli; Lourenço, Felipe Rebello

2014-08-01

Microbiological assays have been used to evaluate antimicrobial activity since the discovery of the first antibiotics. Despite their limitations, microbiological assays are widely employed to determine antibiotic potency of pharmaceutical dosage forms, since they provide a measure of biological activity. The aim of this work is to develop, optimize and validate a rapid colorimetric microplate bioassay for the potency of neomycin in pharmaceutical drug products. Factorial and response surface methodologies were used in the development and optimization of the choice of microorganism, culture medium composition, amount of inoculum, triphenyltetrazolium chloride (TTC) concentration and neomycin concentration. The optimized bioassay method was validated by the assessment of linearity (range 3.0 to 5.0μg/mL, r=0.998 and 0.994 for standard and sample curves, respectively), precision (relative standard deviation (RSD) of 2.8% and 4.0 for repeatability and intermediate precision, respectively), accuracy (mean recovery=100.2%) and robustness. Statistical analysis showed equivalency between agar diffusion microbiological assay and rapid colorimetric microplate bioassay. In addition, microplate bioassay had advantages concerning the sensitivity of response, time of incubation, and amount of culture medium and solutions required. Copyright © 2014 Elsevier B.V. All rights reserved.

Implementing a Quality Management System in the Medical Microbiology Laboratory.

PubMed

Carey, Roberta B; Bhattacharyya, Sanjib; Kehl, Sue C; Matukas, Larissa M; Pentella, Michael A; Salfinger, Max; Schuetz, Audrey N

2018-07-01

This document outlines a comprehensive practical approach to a laboratory quality management system (QMS) by describing how to operationalize the management and technical requirements described in the ISO 15189 international standard. It provides a crosswalk of the ISO requirements for quality and competence for medical laboratories to the 12 quality system essentials delineated by the Clinical and Laboratory Standards Institute. The quality principles are organized under three main categories: quality infrastructure, laboratory operations, and quality assurance and continual improvement. The roles and responsibilities to establish and sustain a QMS are outlined for microbiology laboratory staff, laboratory management personnel, and the institution's leadership. Examples and forms are included to assist in the real-world implementation of this system and to allow the adaptation of the system for each laboratory's unique environment. Errors and nonconforming events are acknowledged and embraced as an opportunity to improve the quality of the laboratory, a culture shift from blaming individuals. An effective QMS encourages "systems thinking" by providing a process to think globally of the effects of any type of change. Ultimately, a successful QMS is achieved when its principles are adopted as part of daily practice throughout the total testing process continuum. Copyright © 2018 American Society for Microbiology.

Potency Determination of Antidandruff Shampoos in Nystatin International Unit Equivalents

PubMed Central

Anusha Hewage, D. B. G.; Pathirana, W.; Pinnawela, Amara

2008-01-01

A convenient standard microbiological potency determination test for the antidandruff shampoos was developed by adopting the pharmacopoeial microbiological assay procedure of the drug nystatin. A standard curve was drawn consisting of the inhibition zone diameters vs. logarithm of nystatin concentrations in international units using the fungus Saccharomyces cerevisiae (yeast) strain National Collection of Type Culture (NCTC) 1071606 as the test organism. From the standard curve the yeast inhibitory potencies of the shampoos in nystatin international unit equivalents were determined from the respective inhibition zones of the test samples of the shampoos. Under test conditions four shampoo samples showed remarkable fungal inhibitory potencies of 10227, 10731, 12396 and 18211 nystatin international unit equivalents/ml while two shampoo samples had extremely feeble inhibitory potencies 4.07 and 4.37 nystatin international unit equivalents/ml although the latter two products claimed antifungal activity. The potency determination method could be applied to any antidandruff shampoo with any one or a combination of active ingredients. PMID:21394271

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

EPA Pesticide Factsheets

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

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.

Emerging and Underrecognized Complications of Illicit Drug Use

PubMed Central

Wurcel, Alysse G.; Merchant, Elisabeth A.; Clark, Roger P.; Stone, David R.

2015-01-01

Illicit drug use can result in a wide range of medical complications. As the availability, synthesis, and popularity of illicit drugs evolve over time, new syndromes associated with their use may mimic infections. Some of these symptoms are anticipated drug effects, and others are complications of adulterants mixed with drugs or complications from the method of using drugs. Some illicit drugs are associated with rare infections, which are difficult to diagnosis with standard microbiological techniques. The goal of this review is to orient a wide range of clinicians—including general practitioners, emergency medicine providers, and infectious diseases specialists—to complications of illicit drug use that may be underrecognized. Improving awareness of infectious and noninfectious complications of illicit drug can expedite diagnosis and medical treatment of persons who use drugs and facilitate targeted harm reduction counseling to prevent future complications. PMID:26270683

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.

A procedure for estimating Bacillus cereus spores in soil and stream-sediment samples - A potential exploration technique

USGS Publications Warehouse

Watterson, J.R.

1985-01-01

The presence of bacterial spores of the Bacillus cereus group in soils and stream sediments appears to be a sensitive indicator of several types of concealed mineral deposits, including vein-type gold deposits. The B. cereus assay is rapid, inexpensive, and inherently reproducible. The test, currently under investigation for its potential in mineral exploration, is recommended for use on a research basis. Among the aerobic spore-forming bacilli, only B. cereus and closely related strains produce an opaque zone in egg-yolk emulsion agar. This characteristic, also known as the Nagler of lecitho-vitellin reaction, has long been used to rapidly indentify and estimate presumptive B. cereus. The test is here adapted to permit rapid estimation of B. cereus spores in soil and stream-sediment samples. Relative standard deviation was 10.3% on counts obtained from two 40-replicate pour-plate determinations. As many as 40 samples per day can be processed. Enough procedural detail is included to permit investigation of the test in conventional geochemical laboratories using standard microbiological safety precautions. ?? 1985.

Microbiologic evaluation of microfiber mops for surface disinfection.

PubMed

Rutala, William A; Gergen, Maria F; Weber, David J

2007-11-01

Recently, health care facilities have started to use a microfiber mopping technique rather than a conventional, cotton string mop to clean floors. The effectiveness of microfiber mops to reduce microbial levels on floors was investigated. We compared the efficacy of microfiber mops with that of conventional, cotton string mops in 3 test conditions (cotton mop and standard wringer bucket, microfiber mop and standard wringer bucket, microfiber system). Twenty-four rooms were evaluated for each test condition. RODAC plates containing D/E Neutralizing Agar were used to assess "precleaning" and "postcleaning" microbial levels. The microfiber system demonstrated superior microbial removal compared with cotton string mops when used with a detergent cleaner (95% vs 68%, respectively). The use of a disinfectant did not improve the microbial elimination demonstrated by the microfiber system (95% vs 95%, respectively). However, use of disinfectant did significantly improve microbial removal when a cotton string mop was used (95% vs 68%, respectively). The microfiber system demonstrated superior microbial removal compared with cotton string mops when used with a detergent cleaner. The use of a disinfectant did not improve the microbial elimination demonstrated by the microfiber system.

The Montpellier Leishmania Collection, from a Laboratory Collection to a Biological Resource Center: A 39-Year-Long Story.

PubMed

Pratlong, Francine; Balard, Yves; Lami, Patrick; Talignani, Loïc; Ravel, Christophe; Dereure, Jacques; Lefebvre, Michèle; Serres, Ghislaine; Bastien, Patrick; Dedet, Jean-Pierre

2016-12-01

We report the development of a laboratory collection of Leishmania that was initiated in 1975 and, after 39 years, has become an international Biological Resource Center (BRC-Leish, Montpellier, France, BioBank No. BB-0033-00052), which includes 6353 strains belonging to 36 Leishmania taxa. This is a retrospective analysis of the technical and organizational changes that have been adopted over time to take into account the technological advances and related modifications in the collection management and quality system. The technical improvements concerned the culture and cryopreservation techniques, strain identification by isoenzymatic and molecular techniques, data computerization and quality management to meet the changes in international standards, and in the cryogenic and microbiological safety procedures. The BRC is working toward obtaining the NF-S 96-900 certification in the coming years. Our long-term expertise in Leishmania storage and typing and collection maintenance should encourage field epidemiologists and clinical practitioners in endemic countries to secure their own strain collection with the help of the French BRC-Leish.

The Montpellier Leishmania Collection, from a Laboratory Collection to a Biological Resource Center: A 39-Year-Long Story

PubMed Central

Pratlong, Francine; Balard, Yves; Lami, Patrick; Talignani, Loïc; Ravel, Christophe; Dereure, Jacques; Lefebvre, Michèle; Serres, Ghislaine; Bastien, Patrick

2016-01-01

We report the development of a laboratory collection of Leishmania that was initiated in 1975 and, after 39 years, has become an international Biological Resource Center (BRC-Leish, Montpellier, France, BioBank No. BB-0033-00052), which includes 6353 strains belonging to 36 Leishmania taxa. This is a retrospective analysis of the technical and organizational changes that have been adopted over time to take into account the technological advances and related modifications in the collection management and quality system. The technical improvements concerned the culture and cryopreservation techniques, strain identification by isoenzymatic and molecular techniques, data computerization and quality management to meet the changes in international standards, and in the cryogenic and microbiological safety procedures. The BRC is working toward obtaining the NF-S 96-900 certification in the coming years. Our long-term expertise in Leishmania storage and typing and collection maintenance should encourage field epidemiologists and clinical practitioners in endemic countries to secure their own strain collection with the help of the French BRC-Leish. PMID:27379470

The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next?

PubMed

Mitra, Anita; MacIntyre, David A; Marchesi, Julian R; Lee, Yun S; Bennett, Phillip R; Kyrgiou, Maria

2016-11-01

The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth study of vaginal microbial community structure to a level of detail not possible with standard culture-based microbiological techniques. The human papillomavirus (HPV) causes both cervical intraepithelial neoplasia (CIN) and cervical cancer. Although the virus is highly prevalent, only a small number of women have a persistent HPV infection and subsequently develop clinically significant disease. There is emerging evidence which leads us to conclude that increased diversity of vaginal microbiota combined with reduced relative abundance of Lactobacillus spp. is involved in HPV acquisition and persistence and the development of cervical precancer and cancer. In this review, we summarise the current literature and discuss potential mechanisms for the involvement of vaginal microbiota in the evolution of CIN and cervical cancer. The concept of manipulation of vaginal bacterial communities using pre- and probiotics is also discussed as an exciting prospect for the field of cervical pathology.

Meropenem/colistin synergy testing for multidrug-resistant Acinetobacter baumannii strains by a two-dimensional gradient technique applicable in routine microbiology.

PubMed

van Belkum, Alex; Halimi, Diane; Bonetti, Eve-Julie; Renzi, Gesuele; Cherkaoui, Abdessalam; Sauvonnet, Véronique; Martelin, Roland; Durand, Géraldine; Chatellier, Sonia; Zambardi, Gilles; Engelhardt, Anette; Karlsson, Åsa; Schrenzel, Jacques

2015-01-01

Precise assessment of potential therapeutic synergy, antagonism or indifference between antimicrobial agents currently depends on time-consuming and hard-to-standardize in vitro chequerboard titration methods. We here present a method based on a novel two-dimensional antibiotic gradient technique named Xact™. We used a test comprising a combination of perpendicular gradients of meropenem and colistin in a single quadrant. We compared test outcomes with those obtained with classical chequerboard microbroth dilution testing in a study involving 27 unique strains of multidrug-resistant Acinetobacter baumannii from diverse origins. We were able to demonstrate 92% concordance between the new technology and classical chequerboard titration using the A. baumannii collection. Two strains could not be analysed by Xact™ due to their out-of-range MIC of meropenem (>128 mg/L). The new test was shown to be diagnostically useful, easy to implement and less labour intensive than the classical method. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Post-photorefractive keratectomy contact lens microbiological findings of individuals who work in a hospital environment.

PubMed

Pereira, Carlos Eduardo Gonçalves; Hida, Richard Yudi; Silva, Cely Barreto; de Andrade, Marizilda Rita; Fioravanti-Lui, Giovana Arlene; Lui-Netto, Adamo

2015-05-01

To describe the microbiological findings from bandage contact lenses in patients who work in a hospital environment submitted to photorefractive keratectomy (PRK). This prospective comparative case series enrolled 43 eyes of 22 volunteers (28.05 ± 3.50 years). Fourteen individuals (n = 27) were health care professionals who work in health care facilities or community physician's offices. Eight individuals (n = 16) were patients who do not work in hospital environment. Photorefractive keratectomy was performed using standard technique, and a silicone hydrogel bandage contact lens was placed on the cornea and evaluated for adequate fit. Seven days after surgery, the bandage lenses were removed and imprinted in the following culture media: blood agar, chocolate agar, anaerobic-selective agar, and Sabouraud agar. When microbial growth was detected, the microorganism was identified, colony-forming units were quantified, and morphology and Gram-staining properties were analyzed. All isolates were tested for susceptibility to various antibiotics. Significance was assessed by Fisher exact test. Microbial growth was detected in 16.27% of all contact lenses samples. No fungi or anaerobes were found. Microbial growth was only observed in bandage lenses removed from patients who work in hospital environments. Most microorganisms found were sensitive to all antibiotics tested. These results suggest that working in hospital environments increase contamination of the contact lenses after PRK.

CRENAME, A Molecular Microbiology Method Enabling Multiparametric Assessment of Potable/Drinking Water.

PubMed

Bissonnette, Luc; Maheux, Andrée F; Bergeron, Michel G

2017-01-01

The microbial assessment of potable/drinking water is done to ensure that the resource is free of fecal contamination indicators or waterborne pathogens. Culture-based methods for verifying the microbial safety are limited in the sense that a standard volume of water is generally tested for only one indicator (family) or pathogen.In this work, we describe a membrane filtration-based molecular microbiology method, CRENAME (Concentration Recovery Extraction of Nucleic Acids and Molecular Enrichment), exploiting molecular enrichment by whole genome amplification (WGA) to yield, in less than 4 h, a nucleic acid preparation which can be repetitively tested by real-time PCR for example, to provide multiparametric presence/absence tests (1 colony forming unit or microbial particle per standard volume of 100-1000 mL) for bacterial or protozoan parasite cells or particles susceptible to contaminate potable/drinking water.

Candida bloodstream infection: a clinical microbiology laboratory perspective.

PubMed

Pongrácz, Júlia; Kristóf, Katalin

2014-09-01

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

Assessing Clinical Microbiology Practice Guidelines: American Society for Microbiology Ad Hoc Committee on Evidence-Based Laboratory Medicine Practice Guidelines Assessment

PubMed Central

Kirn, Thomas J.; Westblade, Lars F.; Humphries, Romney

2017-01-01

ABSTRACT As part of the American Society for Microbiology (ASM) Evidence-Based Laboratory Medicine Practice Guidelines Committee of the Professional Practice Committee, an ad hoc committee was formed in 2014 to assess guidelines published by the committee using an assessment tool, Appraisal of Guidelines for Research Evaluation II (AGREE II). The AGREE II assessment helps reviewers determine whether published guidelines are robust, transparent, and clear in presenting practice recommendations in a standardized manner. Identifying strengths and weaknesses of practice guidelines by ad hoc assessments helps with improving future guidelines through the participation of key stakeholders. This minireview describes the development of the ad hoc committee and results from their review of several ASM best practices guidelines and a non-ASM practice guideline from the Emergency Nurses Association. PMID:28835476

Surveillance of Environmental and Procedural Measures of Infection Control in the Operating Theatre Setting

PubMed Central

Raggi, Alessandra; Sanna, Tiziana; Mazzetti, Magda; Orsi, Alessandra; Zanni, Angela; Farruggia, Patrizia

2017-01-01

The microbiological contamination of operating theatres and the lack of adherence to best practices by surgical staff represent some of the factors affecting Surgical Site Infections (SSIs). The aim of the present study was to assess the microbiological quality of operating settings and the staff compliance to the SSI evidence-based control measures. Ten operating rooms were examined for microbiological contamination of air and surfaces, after cleaning procedures, in “at rest” conditions. Furthermore, 10 surgical operations were monitored to assess staff compliance to the recommended practices. None of the air samples exceeded microbiological reference standards and only six of the 200 surface samples (3.0%) were slightly above recommended levels. Potentially pathogenic bacteria and moulds were never detected. Staff compliance to best practices varied depending on the type of behaviour investigated and the role of the operator. The major not compliant behaviours were: pre-operative skin antisepsis, crowding of the operating room and hand hygiene of the anaesthetist. The good environmental microbiological quality observed is indicative of the efficacy of the cleaning-sanitization procedures adopted. The major critical point was staff compliance to recommended practices. Awareness campaigns are therefore necessary, aimed at improving the organisation of work so as to facilitate compliance to operative protocols. PMID:29283367

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.

Microbiological contamination in water filtration plants in Islamabad.

PubMed

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

2014-05-01

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

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

Evaluation of syndromic patient management algorithm for urethral discharge.

PubMed

Djajakusumah, T; Sudigdoadi, S; Keersmaekers, K; Meheus, A

1998-06-01

To determine feasibility, validity, and cost effectiveness of the syndromic approach to male patients with urethral discharge in Bandung, Indonesia. The WHO algorithm on urethral discharge with no microscopy available was evaluated. Patients presented with a complaint of urethral discharge and if discharge was confirmed the algorithm was applied. Treatment covered gonococcal and chlamydial infection (ciprofloxacin 500 mg single oral dose plus doxycycline 100 mg, twice daily orally for 7 days). The gold standard for validation was gonococcal culture and chlamydia antigen detection. 140 male patients with a complaint of urethral discharge were enrolled; 119 had confirmed discharge and entered the decision tree: 107 were followed and 104 (97%) were clinically cured. Of the three patients with persistent discharge, one had a purulent urethral discharge, diagnosed as gonococcal urethritis and he was probably reinfected; two patients had a serous discharge and microbiological tests were negative. Overall, 106 out of 107 patients (99%) were microbiologically cured. Sensitivity of the algorithm is 100% and its positive predictive value (PPV) is 75% or 97% if validated against gold standard microbiological tests or Gram stain, respectively. Cost per patient is rupiah (Rp)5.894 ($US2.56) for the algorithm compared with Rp43.024 ($18.70) for full microbiological diagnosis. The cost estimate for an algorithm of urethral discharge with microscopy available is Rp6.432 ($2.80) The "symptom and sign" algorithm is fully adapted to the prevailing situation in primary healthcare settings, is acceptable to healthcare workers and patients (who are effectively treated at their first visit), is highly cost effective, is 100% sensitive (no false negatives, which is not the case with microbiological diagnosis), and has a high PPV, between 75% and 97%. It is an excellent patient management tool and a sound basis for partner notification so that it should have a major impact on STD/HIV control and prevention in both men and women.

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.

Water Supplies: Microbiological Analysis

EPA Science Inventory

Producing high-quality drinking water that is free of harmful microorganisms and maintaining its purity through distribution systems are essential for public health. Drinking water quality standards and guidelines for microbial contaminants vary within and among countries but typ...

7 CFR 58.653 - Microbiological requirements for sherbet.

Code of Federal Regulations, 2011 CFR

2011-01-01

... requirements for sherbet. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count and shall contain not more than 10 coliform organisms per gram in...

7 CFR 58.653 - Microbiological requirements for sherbet.

Code of Federal Regulations, 2010 CFR

2010-01-01

... requirements for sherbet. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count and shall contain not more than 10 coliform organisms per gram in...

7 CFR 58.653 - Microbiological requirements for sherbet.

Code of Federal Regulations, 2013 CFR

2013-01-01

... requirements for sherbet. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count and shall contain not more than 10 coliform organisms per gram in...

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.

Mycoplasma testing of cell substrates and biologics: Review of alternative non-microbiological techniques.

PubMed

Volokhov, Dmitriy V; Graham, Laurie J; Brorson, Kurt A; Chizhikov, Vladimir E

2011-01-01

Mycoplasmas, particularly species of the genera Mycoplasma and Acholeplasma, are known to be occasional microbial contaminants of cell cultures that produce biologics. This presents a serious concern regarding the risk of mycoplasma contamination for research laboratories and commercial facilities developing and manufacturing cell-derived biological and biopharmaceutical products for therapeutic use. Potential undetected contamination of these products or process intermediates with mycoplasmas represents a potential safety risk for patients and a business risk for producers of biopharmaceuticals. To minimize these risks, monitoring for adventitious agents, such as viruses and mycoplasmas, is performed during the manufacture of biologics produced in cell culture substrates. The "gold standard" microbiological assay, currently recommended by the USP, EP, JP and the US FDA, for the mycoplasma testing of biologics, involves the culture of viable mycoplasmas in broth, agar plates and indicator cells. Although the procedure enables highly efficient mycoplasma detection in cell substrates and cell-derived products, the overall testing strategy is time consuming (a minimum of 28 days) and requires skilled interpretation of the results. The long time period required for these conventional assays does not permit their use for products with short shelf-lives or for timely 'go/no-go' decisions during routine in-process testing. PCR methodology has existed for decades, however PCR based and other alternative methods for mycoplasma detection have only recently been considered for application to biologics manufacture. The application of alternative nucleic acid-based, enzyme-based and/or recombinant cell-culture methods, particularly in combination with efficient sample preparation procedures, could provide advantages over conventional microbiological methods in terms of analytical throughput, simplicity, and turnaround time. However, a challenge to the application of alternative methods for detection of mycoplasmas remains whether these alternative methods can provide a limit of detection comparable or superior to those of the culture methods. An additional challenge is that nucleic acid amplification technique (NAT) methods do not allow for accurate discrimination between viable and non-viable mycoplasma contaminants, which might lead to false-positive results (e.g. from inactivated raw materials, etc.). Our review provides an overview of these alternative methods and discusses the pros and cons of their application for the testing of mycoplasmas in biologics and cell substrates. Published by Elsevier Ltd.

Surgical Space Suits Increase Particle and Microbiological Emission Rates in a Simulated Surgical Environment.

PubMed

Vijaysegaran, Praveen; Knibbs, Luke D; Morawska, Lidia; Crawford, Ross W

2018-05-01

The role of space suits in the prevention of orthopedic prosthetic joint infection remains unclear. Recent evidence suggests that space suits may in fact contribute to increased infection rates, with bioaerosol emissions from space suits identified as a potential cause. This study aimed to compare the particle and microbiological emission rates (PER and MER) of space suits and standard surgical clothing. A comparison of emission rates between space suits and standard surgical clothing was performed in a simulated surgical environment during 5 separate experiments. Particle counts were analyzed with 2 separate particle counters capable of detecting particles between 0.1 and 20 μm. An Andersen impactor was used to sample bacteria, with culture counts performed at 24 and 48 hours. Four experiments consistently showed statistically significant increases in both PER and MER when space suits are used compared with standard surgical clothing. One experiment showed inconsistent results, with a trend toward increases in both PER and MER when space suits are used compared with standard surgical clothing. Space suits cause increased PER and MER compared with standard surgical clothing. This finding provides mechanistic evidence to support the increased prosthetic joint infection rates observed in clinical studies. Copyright © 2017 Elsevier Inc. All rights reserved.

The characterization and certification of a quantitative reference material for Legionella detection and quantification by qPCR.

PubMed

Baume, M; Garrelly, L; Facon, J P; Bouton, S; Fraisse, P O; Yardin, C; Reyrolle, M; Jarraud, S

2013-06-01

The characterization and certification of a Legionella DNA quantitative reference material as a primary measurement standard for Legionella qPCR. Twelve laboratories participated in a collaborative certification campaign. A candidate reference DNA material was analysed through PCR-based limiting dilution assays (LDAs). The validated data were used to statistically assign both a reference value and an associated uncertainty to the reference material. This LDA method allowed for the direct quantification of the amount of Legionella DNA per tube in genomic units (GU) and the determination of the associated uncertainties. This method could be used for the certification of all types of microbiological standards for qPCR. The use of this primary standard will improve the accuracy of Legionella qPCR measurements and the overall consistency of these measurements among different laboratories. The extensive use of this certified reference material (CRM) has been integrated in the French standard NF T90-471 (April 2010) and in the ISO Technical Specification 12 869 (Anon 2012 International Standardisation Organisation) for validating qPCR methods and ensuring the reliability of these methods. © 2013 The Society for Applied Microbiology.

Application of an oligonucleotide microarray-based nano-amplification technique for the detection of fungal pathogens.

PubMed

Lu, Weiping; Gu, Dayong; Chen, Xingyun; Xiong, Renping; Liu, Ping; Yang, Nan; Zhou, Yuanguo

2010-10-01

The traditional techniques for diagnosis of invasive fungal infections in the clinical microbiology laboratory need improvement. These techniques are prone to delay results due to their time-consuming process, or result in misidentification of the fungus due to low sensitivity or low specificity. The aim of this study was to develop a method for the rapid detection and identification of fungal pathogens. The internal transcribed spacer two fragments of fungal ribosomal DNA were amplified using a polymerase chain reaction for all samples. Next, the products were hybridized with the probes immobilized on the surface of a microarray. These species-specific probes were designed to detect nine different clinical pathogenic fungi including Candida albicans, Candida tropocalis, Candida glabrata, Candida parapsilosis, Candida krusei, Candida lusitaniae, Candida guilliermondii, Candida keyfr, and Cryptococcus neoformans. The hybridizing signals were enhanced with gold nanoparticles and silver deposition, and detected using a flatbed scanner or visually. Fifty-nine strains of fungal pathogens, including standard and clinically isolated strains, were correctly identified by this method. The sensitivity of the assay for Candida albicans was 10 cells/mL. Ten cultures from clinical specimens and 12 clinical samples spiked with fungi were also identified correctly. This technique offers a reliable alternative to conventional methods for the detection and identification of fungal pathogens. It has higher efficiency, specificity and sensitivity compared with other methods commonly used in the clinical laboratory.

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)

Diagnostic procedures in tularaemia with special focus on molecular and immunological techniques.

PubMed

Splettstoesser, W D; Tomaso, H; Al Dahouk, S; Neubauer, H; Schuff-Werner, P

2005-08-01

Tularaemia is a severe bacterial zoonosis caused by the highly infectious agent Francisella tularensis. It is endemic in countries of the northern hemisphere ranging from North America to Europe, Asia and Japan. Very recently, Francisella-like strains causing disease in humans were described from tropical northern Australia. In the last decade, efforts have been made to develop sensitive and specific immunological and molecular techniques for the laboratory diagnosis of tularaemia and also for the definite identification of members of the species F. tularensis and its four subspecies. Screening for the keyword 'Francisella' a Medline search over the last decade was performed and articles describing diagnostic methods for tularaemia and its causative agent were selected. Besides classical microbiological techniques (cultivation, biochemical profiling, susceptibility testing) several new immunological and molecular approaches to identify F. tularensis have been introduced employing highly specific antibodies and various polymerase chain reaction (PCR)-based methods. Whereas direct antigen detection by enzyme-linked immunosorbent assay (ELISA) or immunofluorescence might allow early presumptive diagnosis of tularaemia, these methods--like all PCR techniques--still await further evaluation. Therefore, diagnosis of tularaemia still relies mainly on the demonstration of specific antibodies in the host. ELISA and immunoblot methods started to replace the standard tube or micro-agglutination assays. However, the diagnostic value of antibody detection in the very early clinical phase of tularaemia is limited. Francisella tularensis is regarded as a 'highest priority' biological agent (category 'A' according to the CDC, Atlanta, GA, USA), thus rapid and reliable diagnosis of tularaemia is required not only for a timely onset of therapy, the handling of outbreak investigations but also for the surveillance of endemic foci. Only very recently, evaluated test kits for serological diagnosis of human tularaemia became available, while the introduction of standardized molecular techniques for detection and typing is still missing.

Faecal indicator bacteria enumeration in beach sand: A comparison study of extraction methods in medium to coarse sands

USGS Publications Warehouse

Boehm, A.B.; Griffith, J.; McGee, C.; Edge, T.A.; Solo-Gabriele, H. M.; Whitman, R.; Cao, Y.; Getrich, M.; Jay, J.A.; Ferguson, D.; Goodwin, K.D.; Lee, C.M.; Madison, M.; Weisberg, S.B.

2009-01-01

Aims: The absence of standardized methods for quantifying faecal indicator bacteria (FIB) in sand hinders comparison of results across studies. The purpose of the study was to compare methods for extraction of faecal bacteria from sands and recommend a standardized extraction technique. Methods and Results: Twenty-two methods of extracting enterococci and Escherichia coli from sand were evaluated, including multiple permutations of hand shaking, mechanical shaking, blending, sonication, number of rinses, settling time, eluant-to-sand ratio, eluant composition, prefiltration and type of decantation. Tests were performed on sands from California, Florida and Lake Michigan. Most extraction parameters did not significantly affect bacterial enumeration. anova revealed significant effects of eluant composition and blending; with both sodium metaphosphate buffer and blending producing reduced counts. Conclusions: The simplest extraction method that produced the highest FIB recoveries consisted of 2 min of hand shaking in phosphate-buffered saline or deionized water, a 30-s settling time, one-rinse step and a 10 : 1 eluant volume to sand weight ratio. This result was consistent across the sand compositions tested in this study but could vary for other sand types. Significance and Impact of the Study: Method standardization will improve the understanding of how sands affect surface water quality. ?? 2009 The Society for Applied Microbiology.

Setting a standard: the limulus amebocyte lysate assay and the assessment of microbial contamination on spacecraft surfaces.

PubMed

Morris, Heather C; Monaco, Lisa A; Steele, Andrew; Wainwright, Norm

2010-10-01

Historically, colony-forming units as determined by plate cultures have been the standard unit for microbiological analysis of environmental samples, medical diagnostics, and products for human use. However, the time and materials required make plate cultures expensive and potentially hazardous in the closed environments of future NASA missions aboard the International Space Station and missions to other Solar System targets. The Limulus Amebocyte Lysate (LAL) assay is an established method for ensuring the sterility and cleanliness of samples in the meat-packing and pharmaceutical industries. Each of these industries has verified numerical requirements for the correct interpretation of results from this assay. The LAL assay is a rapid, point-of-use, verified assay that has already been approved by NASA Planetary Protection as an alternate, molecular method for the examination of outbound spacecraft. We hypothesize that standards for molecular techniques, similar to those used by the pharmaceutical and meat-packing industries, need to be set by space agencies to ensure accurate data interpretation and subsequent decision making. In support of this idea, we present research that has been conducted to relate the LAL assay to plate cultures, and we recommend values obtained from these investigations that could assist in interpretation and analysis of data obtained from the LAL assay.

Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces.

PubMed

Lourenço, Anália; Coenye, Tom; Goeres, Darla M; Donelli, Gianfranco; Azevedo, Andreia S; Ceri, Howard; Coelho, Filipa L; Flemming, Hans-Curt; Juhna, Talis; Lopes, Susana P; Oliveira, Rosário; Oliver, Antonio; Shirtliff, Mark E; Sousa, Ana M; Stoodley, Paul; Pereira, Maria Olivia; Azevedo, Nuno F

2014-04-01

The minimum information about a biofilm experiment (MIABiE) initiative has arisen from the need to find an adequate and scientifically sound way to control the quality of the documentation accompanying the public deposition of biofilm-related data, particularly those obtained using high-throughput devices and techniques. Thereby, the MIABiE consortium has initiated the identification and organization of a set of modules containing the minimum information that needs to be reported to guarantee the interpretability and independent verification of experimental results and their integration with knowledge coming from other fields. MIABiE does not intend to propose specific standards on how biofilms experiments should be performed, because it is acknowledged that specific research questions require specific conditions which may deviate from any standardization. Instead, MIABiE presents guidelines about the data to be recorded and published in order for the procedure and results to be easily and unequivocally interpreted and reproduced. Overall, MIABiE opens up the discussion about a number of particular areas of interest and attempts to achieve a broad consensus about which biofilm data and metadata should be reported in scientific journals in a systematic, rigorous and understandable manner. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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.

Microbiological assay for the analysis of certain macrolides in pharmaceutical dosage forms.

PubMed

Mahmoudi, A; Fourar, R E-A; Boukhechem, M S; Zarkout, S

2015-08-01

Clarithromycin (CLA) and roxithromycin (ROX) are macrolide antibiotics with an expanded spectrum of activity that are commercially available as tablets. A microbiological assay, applying the cylinder-plate method and using a strain of Micrococcus luteus ATCC 9341 as test organism, has been used and validated for the quantification of two macrolide drugs; CLA and ROX in pure and pharmaceutical formulations. The validation of the proposed method was carried out for linearity, precision, accuracy and specificity. The linear dynamic ranges were from 0.1 to 0.5μg/mL for both compounds. Logarithmic calibration curve was obtained for each macrolide (r>0.989) with statistically equal slopes varying from 3.275 to 4.038, and a percentage relative standard deviation in the range of 0.24-0.92%. Moreover, the method was applied successfully for the assay of the studied drugs in pharmaceutical tablet dosage forms. Recovery from standard addition experiments in commercial products was 94.71-96.91% regarding clarithromycin and 93.94-98.12% regarding roxithromycin, with a precision (%RSD) 1.32-2.11%. Accordingly, this microbiological assay can be used for routine quality control analysis of titled drugs in tablet formulations. Copyright © 2015 Elsevier B.V. All rights reserved.

[Spatial and seasonal characterization of the drinking water from various sources in a peri-urban town of Salta].

PubMed

Rodriguez-Alvarez, María S; Moraña, Liliana B; Salusso, María M; Seghezzo, Lucas

Drinking water monitoring plans are important to characterize both treated and untreated water used for drinking purposes. Access to drinking water increased in recent years as a response to the Millennium Development Goals set for 2015. The new Sustainable Development Goals aim to ensure universal access to safe drinking water by 2030. Within the framework of these global goals, it is crucial to monitor local drinking water systems. In this paper, treated and untreated water from different sources currently consumed in a specific town in Salta, northern Argentina, was thoroughly assessed. Monitoring extended along several seasons and included the physical, chemical and microbiological variables recommended by the Argentine Food Code. On the one hand, treated water mostly complies with these standards, with some non-compliances detected during the rainy season. Untreated water, on the other hand, never meets microbiological standards and is unfit for human consumption. Monitoring seems essential to detect anomalies and help guarantee a constant provision of safe drinking water. New treatment plants are urgently needed to expand the water grid to the entire population. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Effect of metronidazole versus standard care on length of stay of patients admitted with severe infectious mononucleosis: a randomized controlled trial.

PubMed

Lennon, P; O'Neill, J P; Fenton, J E

2014-07-01

Metronidazole may be of use in the treatment of infectious mononucleosis (IM). Our aim is to show that metronidazole shortens hospital stay for patients with severe IM. A single-centre randomized controlled trial was undertaken in patients admitted with severe IM, who were with a similar group treated by the standard care. Patients were blinded to which treatment arm they were in. Forty-two of these patients were enrolled in the trial. The primary endpoint was the difference in length of stay. This was significantly less in the metronidazole group (3.67 days v 4.67) (p 0.032). This study demonstrates that metronidazole has a role to play in severe infectious mononucleosis. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Evolution of microbiological analytical methods for dairy industry needs

PubMed Central

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

2014-01-01

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

Harmonisation of microbial sampling and testing methods for distillate fuels

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

Hill, G.C.; Hill, E.C.

1995-05-01

Increased incidence of microbial infection in distillate fuels has led to a demand for organisations such as the Institute of Petroleum to propose standards for microbiological quality, based on numbers of viable microbial colony forming units. Variations in quality requirements, and in the spoilage significance of contaminating microbes plus a tendency for temporal and spatial changes in the distribution of microbes, makes such standards difficult to implement. The problem is compounded by a diversity in the procedures employed for sampling and testing for microbial contamination and in the interpretation of the data obtained. The following paper reviews these problems andmore » describes the efforts of The Institute of Petroleum Microbiology Fuels Group to address these issues and in particular to bring about harmonisation of sampling and testing methods. The benefits and drawbacks of available test methods, both laboratory based and on-site, are discussed.« less

Evolution of microbiological analytical methods for dairy industry needs.

PubMed

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

2014-01-01

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

The Czech External Quality Control system in medical microbiology and parasitology.

PubMed

Slosárek, M; Kríz, B

2000-11-01

The External Quality Control (EQC) system in activities of laboratories engaged in medical microbiology and parasitology was established in the Czech Republic in 1993 when to the first laboratories which applied coded serum samples were sent for diagnosis of viral hepatitis and bacterial strains for identification. In the course of years the number of control areas increased and in 2000 there were 31 and the number of those interested in participation in EQC increased from 79 in 1993 to 434 in 2000. This year a total of 13,239 samples will be sent to laboratories. Gradually thus almost all microbiological and parasitological laboratories concerned with examination of clinical material became involved. Seven-year experience with EQC in the Czech Republic revealed that gradually the results of various examinations became more accurate, that methods became standardized and the most suitable examination sets are used.

[Analysis of the results of the SEIMC External Quality Control Program. Year 2013].

PubMed

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

2015-07-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) include controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology, molecular microbiology and HIV-1, HCV and HBV viral loads. This manuscript presents the analysis of results obtained of the participants from the 2013 SEIMC External Quality Control Programme, except viral loads controls, that they are summarized in a manuscript abroad. As a whole, the results obtained in 2013 confirm the excellent skill and good technical standards found in previous editions. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. Once again, the results of this program highlighted the need to implement both internal and external controls in order to assure the maximal quality of the microbiological tests. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

Wavelength-normalized spectroscopic analysis of Staphylococcus aureus and Pseudomonas aeruginosa growth rates.

PubMed

McBirney, Samantha E; Trinh, Kristy; Wong-Beringer, Annie; Armani, Andrea M

2016-10-01

Optical density (OD) measurements are the standard approach used in microbiology for characterizing bacteria concentrations in culture media. OD is based on measuring the optical absorbance of a sample at a single wavelength, and any error will propagate through all calculations, leading to reproducibility issues. Here, we use the conventional OD technique to measure the growth rates of two different species of bacteria, Pseudomonas aeruginosa and Staphylococcus aureus. The same samples are also analyzed over the entire UV-Vis wavelength spectrum, allowing a distinctly different strategy for data analysis to be performed. Specifically, instead of only analyzing a single wavelength, a multi-wavelength normalization process is implemented. When the OD method is used, the detected signal does not follow the log growth curve. In contrast, the multi-wavelength normalization process minimizes the impact of bacteria byproducts and environmental noise on the signal, thereby accurately quantifying growth rates with high fidelity at low concentrations.

Estimation of the Rate of Unrecognized Cross-Contamination with Mycobacterium tuberculosis in London Microbiology Laboratories

PubMed Central

Ruddy, M.; McHugh, T. D.; Dale, J. W.; Banerjee, D.; Maguire, H.; Wilson, P.; Drobniewski, F.; Butcher, P.; Gillespie, S. H.

2002-01-01

Isolates from patients with confirmed tuberculosis from London were collected over 2.5 years between 1995 and 1997. Restriction fragment length polymorphism (RFLP) analysis was performed by the international standard technique as part of a multicenter epidemiological study. A total of 2,779 samples representing 2,500 individual patients from 56 laboratories were examined. Analysis of these samples revealed a laboratory cross-contamination rate of between 0.54%, when only presumed cases of cross-contamination were considered, and 0.93%, when presumed and possible cases were counted. Previous studies suggest an extremely wide range of laboratory cross-contamination rates of between 0.1 and 65%. These data indicate that laboratory cross-contamination has not been a common problem in routine practice in the London area, but in several incidents patients did receive full courses of therapy that were probably unnecessary. PMID:12409381

Studies on the disposable obstetrical dressings sterilized by radiation and the effect of its application

NASA Astrophysics Data System (ADS)

Haiqiao, Wang; Sujing, Sun

1993-10-01

In order to attain an optimum sterilization treatment to obstetric dressings, a new product made by us, with 60Coγ-ray, the effects of radiation on standard bacteria pseudomonas aeruginosa ATcc27853, Escherichia coli ATcc25922, Staphylococcus aureus ATcc25923, Clostridium PB6KA, short Bacillus E60163202 and HBSAg were studied. Results showed that at the absorbed dose of 10 kGy, all the bacteria, bacillus and HBSAg were killed off, and sterilized with the dose, the dressings can completely accord with the demands of hygiene, which was further confirmed by microbiological and poisonous tests and the effects of clinical application. In Nov. 1988, the dressings was awarded the excellent prize in the 1st international exhibition of patent, new technique and new equipment in Guangzhou; its effective application is also reported in the paper.

[Effect of Invasive Herb Species on the Structure of Soil Yeast Complexes in Mixed Forests Exemplified by Impatiens parviflora DC].

PubMed

Glushakova, A M; Kachalkin, A V; Chernov, I Yu

2015-01-01

Yeast abundance and diversity in a mixed forest sod-podzol soil under Impatiens parviflora DC plants was studied in comparison with unimpaired aboriginal herbaceous plants typical of the Mid-Russian secondary, after-forest meadow. The study was carried out throughout the vegetation period. Standard microbiological plating techniques revealed 36 yeast species. Typical pedobiotic (Cryptococcus podzolicus, Wickerhamomyces anomalus) and eurybiotic yeast species (Rhodotorula mucilaginosa) predominated in both biotopes. The relative abundance of the autochthonous soil yeast species Cryptococcus podzolicus was higher in the soil under aboriginal herbs than under Impatiens parviflora. Sites with aboriginal vegetation were also characterized by high abundance of the pedogamous species Schwanniomyces castelli and Torulaspora delbrueckii. The share of yeastlike Trichosporon fungi with high hydrolytic activity was considerably higher under adventitious plants Impatiens parviflora, as well as in the previously studied soil under Heracleum sosnowskyi.

Quick counting method for estimating the number of viable microbes on food and food processing equipment.

PubMed

Winter, F H; York, G K; el-Nakhal, H

1971-07-01

A rapid method for estimating the extent of microbial contamination on food and on food processing equipment is described. Microbial cells are rinsed from food or swab samples with sterile diluent and concentrated on the surface of membrane filters. The filters are incubated on a suitable bacteriological medium for 4 hr at 30 C, heated at 105 C for 5 min, and stained. The membranes are then dried at 60 C for 15 min, rendered transparent with immersion oil, and examined microscopically. Data obtained by the rapid method were compared with counts of the same samples determined by the standard plate count method. Over 60 comparisons resulted in a correlation coefficient of 0.906. Because the rapid technique can provide reliable microbiological count information in extremely short times, it can be a most useful tool in the routine evaluation of microbial contamination of food processing facilities and for some foods.

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.

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

PubMed

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

2017-06-01

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

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

PubMed

Desjardins, Marc; Fleming, Christine Ann

2014-08-01

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

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

DTIC Science & Technology

1986-12-12

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

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.

Microbiological findings of vulvovaginitis in prepubertal girls.

PubMed

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

2014-01-01

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

Promoting microbiology education through the iGEM synthetic biology competition.

PubMed

Kelwick, Richard; Bowater, Laura; Yeoman, Kay H; Bowater, Richard P

2015-08-01

Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research. Synthetic biology projects have developed into wide-ranging training and educational experiences through iGEM, the International Genetically Engineered Machines competition. Elements of the competition are judged against specific criteria and teams can win medals and prizes across several categories. Collaboration is an important element of iGEM, and all DNA constructs synthesized by iGEM teams are made available to all researchers through the Registry for Standard Biological Parts. An overview of microbiological developments in the iGEM competition is provided. This review is targeted at educators that focus on microbiology and synthetic biology, but will also be of value to undergraduate and postgraduate students with an interest in this exciting subject area. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Utility of percutaneous joint aspiration and synovial biopsy in identifying culture-positive infected hip arthroplasty.

PubMed

Cross, M Connor; Kransdorf, Mark J; Chivers, F Spencer; Lorans, Roxanne; Roberts, Catherine C; Schwartz, Adam J; Beauchamp, Christopher P

2014-02-01

Percutaneous synovial biopsy has recently been reported to have a high diagnostic value in the preoperative identification of periprosthetic infection of the hip. We report our experience with this technique in the evaluation of patients undergoing revision hip arthroplasty, comparing results of preoperative synovial biopsy with joint aspiration in identifying an infected hip arthroplasty by bacteriological analysis. We retrospectively reviewed the results of the 110 most recent revision hip arthroplasties in which preoperative synovial biopsy and joint aspiration were both performed. Revision surgery for these patients occurred during the period from September 2005 to March 2012. Using this study group, results from preoperative cultures were compared with preoperative laboratory studies and the results of intraoperative cultures. Synovial aspiration was done using an 18- or 20-gauge spinal needle. Synovial biopsy was done coaxially following aspiration using a 22-gauge Chiba needle or 21-gauge Sure-Cut needle. Standard microbiological analysis was performed on preoperative synovial fluid aspirate and synovial biopsy. Intraoperative tissue biopsy bacteriological analysis results at surgical revision were accepted as the "gold standard" for the presence or absence of infection. Seventeen of 110 (15 %) of patients had intraoperative culture-positive periprosthetic infection. Of these 17 cases, there were ten cases where either the synovial fluid aspiration and/or the synovial biopsy were true positive (sensitivity of 59 %, specificity of 100 %, positive predictive value of 100 % and accuracy of 94 %). There were seven cases where aspiration and biopsy results were both falsely negative, but no false-positive results. Similar results were found for synovial fluid aspiration alone. The results of synovial biopsy alone resulted in the identification of seven infected joints with no false-positive result (sensitivity of 41 %, specificity of 100 %, positive predictive value of 100 %, and accuracy of 91 %). Standard microbiological analyses performed on percutaneous synovial biopsy specimen during the preoperative evaluation of patients undergoing revision hip arthroplasty did not improve detection of culture-positive periprosthetic infection as compared to synovial fluid aspiration alone.

Microbiological methods for the water recovery systems test, revision 1.1

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

Can sterile and pyrogen-free on-line substitution fluid be routinely delivered? A multicentric study on the microbiological safety of on-line haemodiafiltration.

PubMed

Vaslaki, L; Karátson, A; Vörös, P; Major, L; Pethö, F; Ladányi, E; Weber, C; Mitteregger, R; Falkenhagen, D

2000-01-01

Microbial contamination is characterized not only by the presence of bacteria, but also by high concentrations of biologically active by-products. They are potentially able to cross ultrafiltration and dialysis membranes and stimulate immunocompetent blood cells to synthesize cytokines. In turn, cytokine induction causes acute symptoms and has been incriminated in the long-term complications of haemodialysis patients. Infusion of large volumes of substitution fluids following ultrafiltration of microbially contaminated dialysis fluids may place patients on on-line therapies at particular risk. In this study we evaluated 30 machines with a two-stage ultrafiltration system in routine clinical haemodiafiltration settings in six centres for 6 months. Microbiological safety was assessed monthly and at the last use of the filters by determining microbial counts, endotoxin concentration and cytokine-inducing activity. No pyrogenic episodes were observed during the study period. Double-filtration of standard dialysis fluid (range, <1-895 cfu/ml, 0.0028-4.6822 IU/ml) resulted in sterile substitution fluids with endotoxin concentrations well below the Ph.Eur. standard for haemofiltration solutions (range, 0.0014-0.0281 vs 0.25 IU/ml). Moreover, they did not differ from commercial haemofiltration solutions and depyrogenated saline. Likewise, there was no difference in the cytokine-inducing activity between the solutions tested. The high microbiological quality of the ultrafiltered dialysis fluid, which was in the same range as substitution fluid, translates into both the absence of cytokine induction by dialyser back-transport and a redundant safety mode of the on-line system by a second filtration step. On-line HDF treatment can routinely be provided with ultra-pure dialysis fluids and sterile substitution fluids at pyrogen-free levels. The online preparation of substitution fluids thus can be considered microbiologically safe.

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.

The Effect of Preoperative Antimicrobial Prophylaxis on Intraoperative Culture Results in Patients with a Suspected or Confirmed Prosthetic Joint Infection: a Systematic Review.

PubMed

Wouthuyzen-Bakker, Marjan; Benito, Natividad; Soriano, Alex

2017-09-01

Obtaining reliable cultures during revision arthroplasty is important to adequately diagnose and treat a prosthetic joint infection (PJI). The influence of antimicrobial prophylaxis on culture results remains unclear. Since withholding prophylaxis increases the risk for surgical site infections, clarification on this topic is critical. A systematic review was performed with the following research question: in patients who undergo revision surgery of a prosthetic joint, does preoperative antimicrobial prophylaxis affect the culture yield of intraoperative samples in comparison with nonpreoperative antimicrobial prophylaxis? Seven articles were included in the final analysis. In most studies, standard diagnostic culture techniques were used. In patients with a PJI, pooled analysis showed a culture yield of 88% (145/165) in the prophylaxis group versus 95% (344/362) in the nonprophylaxis group ( P = 0.004). Subanalysis of patients with chronic PJIs showed positive cultures in 88% (78/89) versus 91% (52/57), respectively ( P = 0.59). In patients with a suspected chronic infection, a maximum difference of 4% in culture yield between the prophylaxis and nonprophylaxis groups was observed. With the use of standard culture techniques, antimicrobial prophylaxis seems to affect cultures in a minority of patients. Along with the known risk of surgical site infections due to inadequate timing of antimicrobial prophylaxis, we discourage the postponement of prophylaxis until tissue samples are obtained in revision surgery. Future studies are necessary to conclude whether the small percentage of false-negative cultures after prophylaxis can be further reduced with the use of more-sensitive culture techniques, like sonication. Copyright © 2017 American Society for Microbiology.

[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.

Chemical, Physicochemical, Nutritional, Microbiological, Sensory and Rehydration Characteristics of Instant Whole Beans (Phaseolus vulgaris).

PubMed

Ulloa, José Armando; Ibarra-Zavala, Silvia Jazmin; Ramírez-Salas, Silvia Patricia; Rosas-Ulloa, Petra; Ramírez-Ramírez, José Carmen; Ulloa-Rangel, Blanca Estela

2015-03-01

Instant whole beans obtained by drying at 25 °C were evaluated for their chemical, physicochemical, nutritional, microbiological, sensory and rehydration characteristics. The proximal composition of instant whole beans was typical of this kind of food, whereas a w and L* , a* and b* values were 0.639, 98.55, -0.28 and -1.52, respectively. In instant whole beans, 75% of the essential amino acids had a value greater or equal to the reference standard for adult humans; the protein quality in terms of chemical score was 95%. Microbiological counts of aerobic mesophilic bacteria, moulds, yeasts and total coliforms of rehydrated instant whole beans were <10 CFU/g, whereas the scores for colour, flavour, texture and overall acceptability were 7.22, 7.68, 7.24 and 7.34, respectively, on a 1-9 hedonic scale. The logarithmic and Pilosof models showed close fits (R 2 >0.99) to the experimental data for drying of cooked beans and rehydration of instant whole beans, respectively. In the light of the chemical, physicochemical, nutritional, microbiological, sensory and rehydration characteristics of instant whole beans found in this study, drying at 25 °C is recommended for the production of such food.

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

PubMed

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

2014-01-01

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

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

PubMed Central

Inostroza-Ponta, Mario; Valente, Patricia

2014-01-01

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

Microbial source tracking: a forensic technique for microbial source identification?

PubMed

Stapleton, Carl M; Wyer, Mark D; Kay, David; Crowther, John; McDonald, Adrian T; Walters, Martin; Gawler, Andrew; Hindle, Terry

2007-05-01

As the requirements of the Water Framework Directive (WFD) and the US Clean Water Act (USCWA) for the maintenance of microbiological water quality in 'protected areas' highlight, there is a growing recognition that integrated management of point and diffuse sources of microbial pollution is essential. New information on catchment microbial dynamics and, in particular, the sources of faecal indicator bacteria found in bathing and shellfish harvesting waters is a pre-requisite for the design of any 'programme of measures' at the drainage basin scale to secure and maintain compliance with existing and new health-based microbiological standards. This paper reports on a catchment-scale microbial source tracking (MST) study in the Leven Estuary drainage basin, northwest England, an area for which quantitative faecal indicator source apportionment empirical data and land use information were also collected. Since previous MST studies have been based on laboratory trials using 'manufactured' samples or analyses of spot environmental samples without the contextual microbial flux data (under high and low flow conditions) and source information, such background data are needed to evaluate the utility of MST in USCWA total maximum daily load (TMDL) assessments or WFD 'Programmes of Measures'. Thus, the operational utility of MST remains in some doubt. The results of this investigation, using genotyping of Bacteroidetes using polymerase chain reaction (PCR) and male-specific ribonucleic acid coliphage (F + RNA coliphage) using hybridisation, suggest some discrimination is possible between livestock- and human-derived faecal indicator concentrations but, in inter-grade areas, the degree to which the tracer picture reflected the land use pattern and probable faecal indicator loading were less distinct. Interestingly, the MST data was more reliable on high flow samples when much of the faecal indicator flux from catchment systems occurs. Whilst a useful supplementary tool, the MST information did not provide quantitative source apportionment for the study catchment. Thus, it could not replace detailed empirical measurement of microbial flux at key catchment outlets to underpin faecal indicator source apportionment. Therefore, the MST techniques reported herein currently may not meet the standards required to be a useful forensic tool, although continued development of the methods and further catchment scale studies could increase confidence in such methods for future application.

Annual Surveillance Summary: Acinetobacter Infections in the Military Health System, 2015

DTIC Science & Technology

2017-05-01

pharmacy data to assess prescription practices, the Standard Inpatient Data Record to determine healthcare-associated exposures, Defense Manpower ...7 Results ...System (CHCS) microbiology data were used to identify positive Acinetobacter species laboratory results . A unique Acinetobacter species infection

[The influence of "hygienic minimum" course on quality of catering establishments].

PubMed

Venus, Miroslav; Petrovcić, Darija

2010-01-01

The aim of this article was to define the quality of catering establishments in Virovitica Podravina county before and after the course of "hygienic minimum". Research was realized through interview and assessment of microbiological swabs of the same catering establishments before and after the course of "hygienic minimum". All procedures were performed according to Regulations on standard specification in microbiological cleanness and methods of its determining. Twenty-five catering establishments from a group of restaurants and bars were analyzed. In all of them we found improvement in the most of examined parameters. So, implementation of the course through the existing program has proven to be justified.

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,...

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,...

Diversity of thermophilic populations during thermophilic aerobic digestion of potato peel slurry.

PubMed

Ugwuanyi, J O; Harvey, L M; McNeil, B

2008-01-01

To study the diversity of thermophiles during thermophilic aerobic digestion (TAD) of agro-food waste slurries under conditions similar to full-scale processes. Population diversity and development in TAD were studied by standard microbiological techniques and the processes monitored by standard fermentation procedures. Facultative thermophiles were identified as Bacillus coagulans and B. licheniformis, while obligate thermophiles were identified as B. stearothermophilus. They developed rapidly to peaks of 10(7) to 10(8) in

A ten-year follow-up of human leptospirosis in Uruguay: an unresolved health problem.

PubMed

Schelotto, Felipe; Hernández, Elba; González, Sabina; Del Monte, Alicia; Ifran, Silvana; Flores, Karina; Pardo, Lorena; Parada, Daniel; Filippini, Mercedes; Balseiro, Victoria; Geymonat, Juan Pablo; Varela, Gustavo

2012-01-01

Leptospira spp. are delicate bacteria that cannot be studied by usual microbiological methods. They cause leptospirosis, a zoonotic disease transmitted to humans through infected urine of wild or domestic animals. We studied the incidence of this disease in the Uruguayan population, its epidemiologic and clinical features, and compared diagnostic techniques. After examining 6,778 suspect cases, we estimated that about 15 infections/100,000 inhabitants occurred yearly, affecting mainly young male rural workers. Awareness about leptospirosis has grown among health professionals, and its lethality has consequently decreased. Bovine infections were probably the principal source of human disease. Rainfall volumes and floods were major factors of varying incidence. Most patients had fever, asthenia, myalgias or cephalalgia, with at least one additional abnormal clinical feature. 30-40% of confirmed cases presented abdominal signs and symptoms, conjunctival suffusion and altered renal or urinary function. Jaundice was more frequent in patients aged > 40 years. Clinical infections followed an acute pattern and their usual outcome was complete recovery. Laboratory diagnosis was based on indirect micro-agglutination standard technique (MAT). Second serum samples were difficult to obtain, often impairing completion of diagnosis. Immunofluorescence was useful as a screening test and for early detection of probable infections.

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

PubMed

Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

2014-01-01

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

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.

Streptococcus endophthalmitis outbreak after intravitreal injection of bevacizumab: one-year outcomes and investigative results.

PubMed

Goldberg, Roger A; Flynn, Harry W; Miller, Darlene; Gonzalez, Serafin; Isom, Ryan F

2013-07-01

To report the 1-year clinical outcomes of an outbreak of Streptococcus endophthalmitis after intravitreal injection of bevacizumab, including visual acuity outcomes, microbiological testing, and compound pharmacy investigations by the Food and Drug Administration (FDA). Retrospective consecutive case series. Twelve eyes of 12 patients who developed endophthalmitis after receiving intravitreal bevacizumab prepared by a single compounding pharmacy. Medical records of patients were reviewed; phenotypic and DNA analyses were performed on microbes cultured from patients and from unused syringes. An inspection report by the FDA based on site visits to the pharmacy that prepared the bevacizumab syringes was summarized. Visual acuity, interventions received, time to intervention, microbiological consistency, and FDA inspection findings. Between July 5 and 8, 2011, 12 patients developed endophthalmitis after intravitreal bevacizumab from syringes prepared by a single compounding pharmacy. All patients received initial vitreous tap and injection, and 8 patients (67%) subsequently underwent pars plana vitrectomy (PPV). After 12 months follow-up, outcomes have been poor. Seven patients (58%) required evisceration or enucleation, and only 1 patient regained pre-injection visual acuity. Molecular testing using real-time polymerase chain reaction, partial sequencing of the groEL gene, and multilocus sequencing of 7 housekeeping genes confirmed the presence of a common strain of Streptococcus mitis/oralis in vitreous specimens and 7 unused syringes prepared by the compounding pharmacy at the same time. An FDA investigation of the compounding pharmacy noted deviations from standard sterile technique, inconsistent documentation, and inadequate testing of equipment required for safe preparation of medications. In this outbreak of endophthalmitis, outcomes have been generally poor, and PPV did not improve visual results at 1-year follow-up. Molecular testing confirmed a common strain of S. mitis/oralis. Contamination seems to have occurred at the compounding pharmacy, where numerous problems in sterile technique were noted by public health investigators. Copyright © 2013 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Streptococcus Endophthalmitis Outbreak after Intravitreal Injection of Bevacizumab: One-year Outcomes and Investigative Results

PubMed Central

Goldberg, Roger A.; Flynn, Harry W.; Miller, Darlene; Gonzalez, Serafin; Isom, Ryan F.

2013-01-01

Purpose To report the one-year clinical outcomes of an outbreak of Streptococcus endophthalmitis after intravitreal injection of bevacizumab, including visual acuity outcomes, microbiological testing and compound pharmacy investigations by the Food and Drug Administration (FDA). Design Retrospective consecutive case series. Participants 12 eyes of 12 patients who developed endophthalmitis after receiving intravitreal bevacizumab prepared by a single compounding pharmacy. Methods Medical records of patients were reviewed; phenotypic and DNA analyses were performed on microbes cultured from patients and from unused syringes. An inspection report by the FDA based on site-visits to the pharmacy that prepared the bevacizumab syringes was summarized. Main Outcome Measures Visual acuity, interventions received, time-to-intervention; microbiological consistency; FDA inspection findings. Results Between July 5 and July 8, 2011, 12 patients developed endophthalmitis after intravitreal bevacizumab from syringes prepared by a single compounding pharmacy. All patients received initial vitreous tap and injection, and eight (67%) subsequently underwent pars plana vitrectomy (PPV). After twelve months follow-up, outcomes have been poor: 7 patients (58%) required evisceration or enucleation, and only one patient regained pre-injection visual acuity. Molecular testing using real time polymerase chain reaction, partial sequencing of the groEL gene, and multilocus sequencing of 7 housekeeping genes confirmed the presence of a common strain of Streptococcus mitis/oralis in vitreous specimens and seven unused syringes prepared by the compounding pharmacy at the same time. An FDA investigation of the compounding pharmacy noted deviations from standard sterile technique, inconsistent documentation, and inadequate testing of equipment required for safe preparation of medications. Conclusions In this outbreak of endophthalmitis, outcomes have been generally poor and PPV did not improve visual results at one year follow-up. Molecular testing confirmed a common strain of Streptococcus mitis/oralis. Contamination appears to have occurred at the compounding pharmacy, where numerous problems in sterile technique were noted by public health investigators. PMID:23453511

Nutritional and microbiological quality of commercial and homemade blenderized whole food enteral diets for home-based enteral nutritional therapy in adults.

PubMed

Vieira, Maricy Machado Cavalca; Santos, Valdirene Francisca Neves; Bottoni, Andrea; Morais, Tania Beninga

2018-02-01

Serious nutritional and contamination risks may be involved in the preparation of blenderized tube-feeding diets and in the handling of commercial diets. Their nutritional and microbiological quality in home settings is unknown. The objective of this study was to assess the nutritional and microbiological quality of commercial enteral and homemade blenderized whole foods diets intended to adult patients in home nutritional therapy. In a cross sectional study, 66 samples of commercial (CD) and noncommercial (NCD) enteral diets were collected at the homes of patients in home enteral nutritional therapy, 33 of each type. Commercial diets were either powder (PCD; n = 13) or liquid (LCD; n = 20). The samples were analyzed in laboratory to assess their nutritional and microbiological quality. Anthropometric data of mid upper arm circumference (MUAC) and triceps skinfold (TST) thickness were obtained from the patients' medical records. NCD presented significantly lower values for protein, fat, fiber, carbohydrate and energy while water content was significantly higher. PCD and LCD did not show any statistically significant differences between them. In the NCD, the values measured for macronutrients and energy corresponded to less than 50% of the prescribed values (except for fat). In CD, protein value was about 20% more than the prescribed value; fat and energy values corresponded to approximately 100% of the prescription, while carbohydrate corresponded to 92%. Regardless the type of the diet, prevalence of undernutrition was high in both groups though patients of the NCD presented a higher percentage. Samples of NCD complied significantly less with the microbiological standards; only 6.0% complied with the standard for coliform bacteria. Escherichia coli was detected in 10, 2, and 2 samples of NCD, PCD and LCD, respectively. Homemade blenderized enteral diets showed low values of energy and macronutrients, delivered less than 50% of the prescribed values and had high levels of bacterial contamination. Copyright © 2016 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. 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

Decontamination of laboratory microbiological waste by steam sterilization.

PubMed Central

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

1982-01-01

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

[Analysis of the results of the 2010 External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology for HIV-1, HCV, and HBV viral loads].

PubMed

Orta Mira, Nieves; Serrano, María del Remedio Guna; Martínez, José-Carlos Latorre; Ovies, María Rosario; Poveda, Marta; de Gopegui, Enrique Ruiz; Cardona, Concepción Gimeno

2011-12-01

Human immunodeficiency virus type 1 (HIV-1) and hepatitis B (HBV) and C virus (HCV) viral load determinations are among the most important markers for the follow-up of patients infected with these viruses. External quality control tools are crucial to ensure the accuracy of the results obtained by microbiology laboratories. This article summarized the results obtained in the 2010 External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology for HIV-1, HCV, and HBV viral loads and HCV genotyping. In the HIV-1 program, a total of five standards were sent. One standard consisted of seronegative human plasma, while the remaining four contained plasma from three different viremic patients, in the range of 3-5 log(10) copies/mL; two of these standards were identical, with the aim of determining repeatability. A significant proportion of the laboratories (22.6% on average) obtained values out of the accepted range (mean ± 0.2 log(10)copies/mL), depending on the standard and on the method used for quantification. Repeatability was very good, with up to 95% of laboratories reporting results within the limits (Δ<0.5 log(10)copies/mL). The HBV and HCV program consisted of two standards with different viral load contents. Most of the participants, 86.1% in the case of HCV and 87.1% in HBV, obtained all the results within the accepted range (mean ± 1.96 SD log(10)UI/mL). Post-analytical errors due to mistranscription of the results were detected in these controls. Data from this analysis reinforce the utility of proficiency programs to ensure the quality of the results obtained by a particular laboratory, as well as the importance of the post-analytical phase in overall quality. Due to interlaboratory variability, use of the same method and the same laboratory for patient follow-up is advisable. Copyright © 2011 Elsevier España S.L. All rights reserved.

Brewing for Students: An Inquiry-Based Microbiology Lab †

PubMed Central

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

2015-01-01

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

Microbiological quality of drinking rainwater in the inland region of Pajeú, Pernambuco, Northeast Brazil.

PubMed

Xavier, Rogério Pereira; Siqueira, Leonardo Pereira; Vital, Fernando Antonio Chaves; Rocha, Francisca Janaina Soares; Irmão, João Inácio; Calazans, Glícia Maria Torres

2011-01-01

Despite all efforts to store and reduce its consumption, water is becoming less inexhaustible and its quality is falling faster. Considering that water is essential to animal life, it is necessary to adopt measures to ensure its sanitary conditions in order to be fit for consumption. The aim of this study was to analyze the microbiological quality of drinking rainwater used by rural communities of Tuparetama, a small town located in Northeast Brazil. The study covered seven rural communities, totaling 66 households. In each household two samples were collected, one from a tank and the other from a clay pot located inside the home, resulting in 132 samples (tank plus clay pot). Approximately 90% of samples were below the standard recommended by the current legislation, being considered unfit for human consumption. Part of this high microbiological contamination of drinking rainwater could be related to the lack of sanitary education and of an adequate sewerage sanitation system.

Brewing for Students: An Inquiry-Based Microbiology Lab.

PubMed

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

2015-12-01

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

7 CFR 58.643 - Frequency of sampling.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Frequency of sampling. 58.643 Section 58.643 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Procedures § 58.643 Frequency of sampling. (a) Microbiological. Representative samples shall be taken from...

7 CFR 58.643 - Frequency of sampling.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Frequency of sampling. 58.643 Section 58.643 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Procedures § 58.643 Frequency of sampling. (a) Microbiological. Representative samples shall be taken from...

Identification of micro-organisms

NASA Technical Reports Server (NTRS)

Taylor, G. R.; Zaloguev, S. N.

1979-01-01

Manual presents detailed laboratory procedures for identifying aerobic or microaerobic bacteria, yeast or yeastible organisms, and filamentous fungi and conducting other microbiological or immunological evaluations of samples taken from human subjects. Standardized procedures should be useful to researchers and clinicians in laboratories, hospitals and other biological test facilities.

Teratology Studies of Lewisite and Sulfur Mustard Agents: Effects of Lewisite in Rats and Rabbits

DTIC Science & Technology

1987-12-31

virus of mice (PCM), rat corona virus /sialodacryoadenitis virus (RCV/SDA), H-1 virus and Kilham rat virus (KRV) by Microbiological Associates...Pneumonia virus of mice RCV/SDA = Rat corona virus /sialodacryoadenitis virus RH = Relative humidity SC = Subcutaneous SD = Standard deviation SE = Standard... cat , rabbit and human but apparently did not cross the placental membranes readily. The accumulation of a sufficient quantity of arsenate to induce a

Report on the Project for Establishment of the Standardized Korean Laboratory Terminology Database, 2015.

PubMed

Jung, Bo Kyeung; Kim, Jeeyong; Cho, Chi Hyun; Kim, Ju Yeon; Nam, Myung Hyun; Shin, Bong Kyung; Rho, Eun Youn; Kim, Sollip; Sung, Heungsup; Kim, Shinyoung; Ki, Chang Seok; Park, Min Jung; Lee, Kap No; Yoon, Soo Young

2017-04-01

The National Health Information Standards Committee was established in 2004 in Korea. The practical subcommittee for laboratory test terminology was placed in charge of standardizing laboratory medicine terminology in Korean. We aimed to establish a standardized Korean laboratory terminology database, Korea-Logical Observation Identifier Names and Codes (K-LOINC) based on former products sponsored by this committee. The primary product was revised based on the opinions of specialists. Next, we mapped the electronic data interchange (EDI) codes that were revised in 2014, to the corresponding K-LOINC. We established a database of synonyms, including the laboratory codes of three reference laboratories and four tertiary hospitals in Korea. Furthermore, we supplemented the clinical microbiology section of K-LOINC using an alternative mapping strategy. We investigated other systems that utilize laboratory codes in order to investigate the compatibility of K-LOINC with statistical standards for a number of tests. A total of 48,990 laboratory codes were adopted (21,539 new and 16,330 revised). All of the LOINC synonyms were translated into Korean, and 39,347 Korean synonyms were added. Moreover, 21,773 synonyms were added from reference laboratories and tertiary hospitals. Alternative strategies were established for mapping within the microbiology domain. When we applied these to a smaller hospital, the mapping rate was successfully increased. Finally, we confirmed K-LOINC compatibility with other statistical standards, including a newly proposed EDI code system. This project successfully established an up-to-date standardized Korean laboratory terminology database, as well as an updated EDI mapping to facilitate the introduction of standard terminology into institutions. © 2017 The Korean Academy of Medical Sciences.

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

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

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.

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

PubMed

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

2014-01-01

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

Chemical, Physicochemical, Nutritional, Microbiological, Sensory and Rehydration Characteristics of Instant Whole Beans (Phaseolus vulgaris)

PubMed Central

Ibarra-Zavala, Silvia Jazmin; Ramírez-Salas, Silvia Patricia; Rosas-Ulloa, Petra; Ramírez-Ramírez, José Carmen; Ulloa-Rangel, Blanca Estela

2015-01-01

Summary Instant whole beans obtained by drying at 25 °C were evaluated for their chemical, physicochemical, nutritional, microbiological, sensory and rehydration characteristics. The proximal composition of instant whole beans was typical of this kind of food, whereas aw and L*, a* and b* values were 0.639, 98.55, –0.28 and –1.52, respectively. In instant whole beans, 75% of the essential amino acids had a value greater or equal to the reference standard for adult humans; the protein quality in terms of chemical score was 95%. Microbiological counts of aerobic mesophilic bacteria, moulds, yeasts and total coliforms of rehydrated instant whole beans were <10 CFU/g, whereas the scores for colour, flavour, texture and overall acceptability were 7.22, 7.68, 7.24 and 7.34, respectively, on a 1–9 hedonic scale. The logarithmic and Pilosof models showed close fits (R2>0.99) to the experimental data for drying of cooked beans and rehydration of instant whole beans, respectively. In the light of the chemical, physicochemical, nutritional, microbiological, sensory and rehydration characteristics of instant whole beans found in this study, drying at 25 °C is recommended for the production of such food. PMID:27904331

Effects of antineoplastic drugs on Lactobacillus casei and radioisotopic assays for serum folate

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

Carmel, R.

1978-02-01

Microbiologic assay, usually employing Lactobacillus casei, remains the standard assay for serum folate to date. Among its disadvantages have been falsely low results in patients receiving bacteriostatic agents such as antibiotics. This study examined whether commonly used antineoplastic drugs had similar effect. Methotrexate and 5-fluorouracil depressed microbiologic serum folate levels. No effect was found for adriamycin, bleomycin, BCNU, cyclophosphamide, cytosine arabinoside, vincristine, vinblastine, mechlorethamine, mithramycin, hydroxyurea, and hydrocortisone. None of the drugs affected radioassay except methotrexate, which produced falsely high folate results. Thus, it appears that L. casei assay for folate becomes unreliable in patients receiving 5-fluorouracil and radioisotopic assaymore » becomes unreliable in those receiving methotrexate.« less

Superbugs on Duodenoscopes: the Challenge of Cleaning and Disinfection of Reusable Devices.

PubMed

Humphries, Romney M; McDonnell, Gerald

2015-10-01

Inadequate flexible endoscope reprocessing has been associated with infection outbreaks, most recently caused by carbapenem-resistant Enterobacteriaceae. Lapses in essential device reprocessing steps such as cleaning, disinfection/sterilization, and storage have been reported, but some outbreaks have occurred despite claimed adherence to established guidelines. Recommended changes in these guidelines include the use of sterilization instead of high-level disinfection or the use of routine microbial culturing to monitor efficacy of reprocessing. This review describes the current standards for endoscope reprocessing, associated outbreaks, and the complexities associated with both microbiological culture and sterilization approaches to mitigating the risk of infection associated with endoscopy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

7 CFR 58.528 - Microbiological requirements.

Code of Federal Regulations, 2011 CFR

2011-01-01

... based on 3 out of 5 consecutive samples taken at the time of packaging. (a) Coliform. Not more than 10..., GENERAL SPECIFICATIONS FOR APPROVED PLANTS AND STANDARDS FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Requirements for Cottage...

7 CFR 58.528 - Microbiological requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... based on 3 out of 5 consecutive samples taken at the time of packaging. (a) Coliform. Not more than 10..., GENERAL SPECIFICATIONS FOR APPROVED PLANTS AND STANDARDS FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Requirements for Cottage...

7 CFR 58.528 - Microbiological requirements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... based on 3 out of 5 consecutive samples taken at the time of packaging. (a) Coliform. Not more than 10..., GENERAL SPECIFICATIONS FOR APPROVED PLANTS AND STANDARDS FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Requirements for Cottage...

7 CFR 58.528 - Microbiological requirements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... based on 3 out of 5 consecutive samples taken at the time of packaging. (a) Coliform. Not more than 10..., GENERAL SPECIFICATIONS FOR APPROVED PLANTS AND STANDARDS FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Requirements for Cottage...

Alternative antimicrobial commercial egg washing procedures

USDA-ARS?s Scientific Manuscript database

Commercial table eggs are washed prior to packaging. Standard wash procedures use an alkaline pH and warm water. If a cool water method could be developed that would still provide a microbiologically safe egg, the industry may save energy costs associated with water heating. Four wash procedures ...

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

Limitation in the detection of Listeria monocytogenes in food in the presence of competing Listeria innocua.

PubMed

Oravcová, K; Trncíková, T; Kuchta, T; Kaclíková, E

2008-02-01

Detectability of Listeria monocytogenes at 10(0) CFU per food sample in the presence of Listeria innocua using standard microbiological detection was evaluated and compared with the real-time PCR-based method. Enrichment in half-Fraser broth followed by subculture in Fraser broth according to EN ISO 11290-1 was used. False-negative detection of 10(0) CFU L. monocytogenes was obtained in the presence of 10(1) CFU L. innocua per sample using the standard detection method in contrast to more than 10(5) CFU L. innocua per sample using real-time PCR. Identification of L. monocytogenes on the chromogenic medium by the standard procedure was impossible if L. innocua was able to overgrow L. monocytogenes by more than three orders of magnitude after the enrichment in model samples. These results were confirmed using naturally contaminated food samples. Standard microbiological method was insufficient for the reliable detection of 10(0) CFU L. monocytogenes in the presence of more than 10(0) CFU of L. innocua per sample. On the other hand, if the growth of L. monocytogenes was sufficient to reach the concentration equal to the detection limit of PCR, the amount of the other microflora present in the food sample including L. innocua was not relevant for success of the PCR detection of L. monocytogenes. After the enrichment, the PCR detection is more convenient than the standard one as PCR detection is not compromised by other present microflora.

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)

Combined ultrasound-guided cutting-needle biopsy and standard pleural biopsy for diagnosis of malignant pleural effusions.

PubMed

Wang, Jinlin; Zhou, Xinghua; Xie, Xiaohong; Tang, Qing; Shen, Panxiao; Zeng, Yunxiang

2016-11-17

The most efficient approach to diagnose malignant pleural effusions (MPEs) is still controversial and uncertain. This study aimed to evaluate the utility of a combined approach using ultrasound (US)-guided cutting-needle biopsy (CNB) and standard pleural biopsy (SPB) for diagnosing MPE. Pleural effusions were collected from 172 patients for biochemical and microbiological analyses. US-guided CNB and SPB were performed in the same operation sequentially to obtain specimens for histological analysis. US-guided CNB and SPB procedures provided adequate material for histological analysis in 90.7 and 93.0% of cases, respectively, while a combination of the 2 techniques was in 96.5% of cases. The sensitivity, specificity, positive-predictive value (PPV), negative-predictive value (NPV) and diagnostic accuracy of US-guided CNB versus SPB were: 51.2 vs 63.4%, 100 vs 100%, 100 vs 100%, 64.9 vs 72.2% and 74.4 vs 81.3%, respectively. When CNB was combined with SPB, the corresponding values were 88.6, 100, 100, 88.6 and 93.9%, respectively. Whereas sensitivity, NPV and diagnostic accuracy were not significantly different between CNB and SPB, the combination of CNB and SPB significantly improved the sensitivity, NPV and diagnostic accuracy versus each technique alone (p < 0.05). Significant pain (eight patients), moderate haemoptysis (two patients) and chest wall haematomas (two patients) were observed following CNB, while syncope (four patients) and a slight pneumothorax (four patients) were observed following SPB. Use of a combination of US-guided CNB and SPB afforded a high sensitivity to diagnose MPEs, it is a convenient and safe approach.

Infectious complications in children with acute lymphoblastic leukemia treated with the Taiwan Pediatric Oncology Group protocol: A 16-year tertiary single-institution experience.

PubMed

Li, Meng-Ju; Chang, Hsiu-Hao; Yang, Yung-Li; Lu, Meng-Yao; Shao, Pei-Lan; Fu, Chun-Min; Chou, An-Kuo; Liu, Yen-Lin; Lin, Kai-Hsin; Huang, Li-Min; Lin, Dong-Tsamn; Jou, Shiann-Tarng

2017-10-01

Infection is a major complication in pediatric patients with acute lymphoblastic leukemia during chemotherapy. In this study, the infection characteristics were determined and risk factors analyzed based on the Taiwan Pediatric Oncology Group (TPOG) acute lymphoblastic leukemia (ALL) protocol. We retrospectively reviewed fever events during chemotherapy in 252 patients treated during two consecutive clinical trials at a single institution between 1997 and 2012. Patients were classified as standard, high, and very high risk by treatment regimen according to the TPOG definitions. We analyzed the characteristics and risk factors for infection. Fever occurred in 219 patients (86.9%) with a mean of 2.74 episodes per person. The fever events comprised 64% febrile neutropenia, 39% clinically documented infections, and 44% microbiologically documented infections. The microbiologically documented infections were mostly noted during the induction phase and increased in very high risk patients (89 vs. 24% and 46% in standard-risk and high-risk patients, respectively). Younger age and higher risk (high-risk and very high risk groups) were risk factors for fever and microbiologic and bloodstream infections. Female gender and obesity were additive risk factors for urinary tract infection (odds ratios = 3.52 and 3.24, P < 0.001 and P = 0.004, respectively). Infections developed primarily during the induction phase, for which younger age and higher risk by treatment regimen were risk factors. Female gender and obesity were additive risk factors for urinary tract infection. © 2017 Wiley Periodicals, Inc.

Bioinformatic genome comparisons for taxonomic and phylogenic assignments using Aeromonas as a test case

USDA-ARS?s Scientific Manuscript database

Prokaryotic taxonomy is the underpinning of microbiology, providing a framework for the proper identification and naming of organisms. The 'gold standard' of bacterial species delineation is the overall genome similarity as determined by DNA-DNA hybridization (DDH), a technically rigorous yet someti...

Microbiological Validation of the IVGEN System

NASA Technical Reports Server (NTRS)

Porter, David A.

2013-01-01

The principal purpose of this report is to describe a validation process that can be performed in part on the ground prior to launch, and in space for the IVGEN system. The general approach taken is derived from standard pharmaceutical industry validation schemes modified to fit the special requirements of in-space usage.

Competency Assessment of Microbiology Medical Laboratory Technologists in Ontario, Canada

PubMed Central

Fleming, Christine Ann

2014-01-01

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

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

PubMed

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

2000-06-01

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

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

PubMed

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

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

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.

Staffing for infectious diseases, clinical microbiology and infection control in hospitals in 2015: results of an ESCMID member survey.

PubMed

Dickstein, Y; Nir-Paz, R; Pulcini, C; Cookson, B; Beović, B; Tacconelli, E; Nathwani, D; Vatcheva-Dobrevska, R; Rodríguez-Baño, J; Hell, M; Saenz, H; Leibovici, L; Paul, M

2016-09-01

We aimed to assess the current status of infectious diseases (ID), clinical microbiology (CM) and infection control (IC) staffing in hospitals and to analyse modifiers of staffing levels. We conducted an Internet-based survey of European Society of Clinical Microbiology and Infectious Diseases members and affiliates, collecting data on hospital characteristics, ID management infrastructure, ID/IC-related activities and the ratio of physicians per 100 hospital beds. Regression analyses were conducted to examine factors associated with the physician-bed ratio. Five hundred sixty-seven hospital responses were collected between April and June 2015 from 61 countries, 81.2% (384/473) from Europe. A specialized inpatient ward for ID patients was reported in 58.4% (317/543) of hospitals. Rates of antibiotic stewardship programmes (ASP) and surveillance activities in survey hospitals were high, ranging from 88% to 90% for local antibiotic guidelines and 70% to 82% for programmes monitoring hospital-acquired infections. The median ID/CM/IC physician per 100 hospital beds ratio was 1.12 (interquartile range 0.56-2.13). In hospitals performing basic ASP and IC (including local antibiotic guidelines and monitoring device-related or surgical site infections), the ratio was 1.21 (interquartile range 0.57-2.14). Factors independently associated with higher ratios included compliance with European Union of Medical Specialists standards, smaller hospital size, tertiary-care institution, presence of a travel clinic, beds dedicated to ID and a CM unit. More than half of respondents estimated that additional staffing is needed for appropriate IC or ID management. No standard of physician staffing for ID/CM/IC in hospitals is available. A ratio of 1.21/100 beds will serve as an informed point of reference enabling ASP and infection surveillance. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Identification of Highly Pathogenic Microorganisms by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Results of an Interlaboratory Ring Trial

PubMed Central

Lasch, Peter; Wahab, Tara; Weil, Sandra; Pályi, Bernadett; Tomaso, Herbert; Zange, Sabine; Kiland Granerud, Beathe; Drevinek, Michal; Kokotovic, Branko; Wittwer, Matthias; Pflüger, Valentin; Di Caro, Antonino; Stämmler, Maren; Grunow, Roland

2015-01-01

In the case of a release of highly pathogenic bacteria (HPB), there is an urgent need for rapid, accurate, and reliable diagnostics. MALDI-TOF mass spectrometry is a rapid, accurate, and relatively inexpensive technique that is becoming increasingly important in microbiological diagnostics to complement classical microbiology, PCR, and genotyping of HPB. In the present study, the results of a joint exercise with 11 partner institutions from nine European countries are presented. In this exercise, 10 distinct microbial samples, among them five HPB, Bacillus anthracis, Brucella canis, Burkholderia mallei, Burkholderia pseudomallei, and Yersinia pestis, were characterized under blinded conditions. Microbial strains were inactivated by high-dose gamma irradiation before shipment. Preparatory investigations ensured that this type of inactivation induced only subtle spectral changes with negligible influence on the quality of the diagnosis. Furthermore, pilot tests on nonpathogenic strains were systematically conducted to ensure the suitability of sample preparation and to optimize and standardize the workflow for microbial identification. The analysis of the microbial mass spectra was carried out by the individual laboratories on the basis of spectral libraries available on site. All mass spectra were also tested against an in-house HPB library at the Robert Koch Institute (RKI). The averaged identification accuracy was 77% in the first case and improved to >93% when the spectral diagnoses were obtained on the basis of the RKI library. The compilation of complete and comprehensive databases with spectra from a broad strain collection is therefore considered of paramount importance for accurate microbial identification. PMID:26063856

Detection of periodontopathogenic bacteria in pregnant women by traditional anaerobic culture method and by a commercial molecular genetic method.

PubMed

Urbán, Edit; Terhes, Gabriella; Radnai, Márta; Gorzó, István; Nagy, Elisabeth

2010-06-01

To culture facultative and strict anaerobic bacteria is a well-established method for analyzing subgingival plaque samples. Micro-IDent and micro-IDent Plus (HAIN Lifescience GmbH, Nehren, Germany) tests are two commercially available rapid PCR-based methods for the identification and quantification of putative periodontopathogen bacteria. In this study, we compared these commercial PCR-based hybridization methods with conventional anaerobic culture technique. A total of 36 subgingival plaque samples were collected from periodontal pockets of pregnant women with chronic localized periodontitis. Aliquots of these samples were evaluated with species-specific probes provided by micro-IDent and micro-IDent Plus tests simultaneously, and from the same samples anaerobic and capnophylic bacteria were cultured on selective media. The overall agreement between both methods was excellent for Eubacterium nodatum, Tannerella forsythia and Porphyromonas gingivalis (97-92%), fair for Capnocytophaga sp, Eikenella corrodens, Actinobacillus actinomycetemcomitans, and Prevotella intermedia (91-89%) and poor for Fusobacterium nucleatum, Parvimonas micra (Micromonas micros), and Campylobacter rectus (86-78%). Discrepancies in the results may be explained by inability of culture method to distinguish between closely related taxa (e.i P. intermedia/Prevotella. nigrescens), and problems of keeping periodontopathogen bacteria viable, which is required for successful detection by standard culture method. Nucleic acid-based methods may replace cultivation method as frequently used methods in microbiological diagnosis of progressive periodontitis, thus micro-IDent and micro-IDent Plus tests can be recommended where culture of periodontopathogenic bacteria is not performed in routine microbiology laboratories to analyze subgingival plaque samples. 2010 Elsevier Ltd. All rights reserved.

The study and characteristics of ZnO/CdS nanocomposite and its application on nanoantibacterial activities

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

Ali, Tinku; Tripathi, P.; Ahammed, Nashiruddin

We have studied the structural and optical properties of ZnO/CdS nanocomposite and its application on nanoantibacterial activities. In this paper, we have used X-ray diffraction, Transmission electron microscope (TEM) and Energy dispersive X-ray spectroscopy (EDX) techniques in order to know about the structural and optical properties of synthesized ZnO/CdS nanocomposite. After TEM and EDX analysis it has been confirmed that the shape of this nanocomposite is hexagonal and it has no impurity. The optical absorption spectra of pure ZnO and ZnO/CdS nanocomposite have been presented by UV-Visible Spectrometer and the estimated band gap from absorption peak has been found tomore » be 3.36 and 3.74 eV respectively. Antibacterial activity of ZnO/CdS nanocomposite was evaluated by using standard zone of inhibition (ZOI) microbiology assay. The synthesized ZnO/CdS showed promising antibacterial activity against Staphylococcus aureus in dose dependent manner.« less

[Molecular characterization of resistance mechanisms: methicillin resistance Staphylococcus aureus, extended spectrum β-lactamases and carbapenemases].

PubMed

Oteo, Jesús; Belén Aracil, María

2015-07-01

Multi-drug resistance in bacterial pathogens increases morbidity and mortality in infected patients and it is a threat to public health concern by their high capacity to spread. For both reasons, the rapid detection of multi-drug resistant bacteria is critical. Standard microbiological procedures require 48-72 h to provide the antimicrobial susceptibility results, thus there is emerging interest in the development of rapid detection techniques. In recent years, the use of selective and differential culture-based methods has widely spread. However, the capacity for detecting antibiotic resistance genes and their low turnaround times has made molecular methods a reference for diagnosis of multidrug resistance. This review focusses on the molecular methods for detecting some mechanisms of antibiotic resistance with a high clinical and epidemiological impact: a) Enzymatic resistance to broad spectrum β-lactam antibiotics in Enterobacteriaceae, mainly extended spectrum β-lactamases (ESBL) and carbapenemases; and b) methicillin resistance in Staphylococcus aureus. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

The Role of In Vitro Susceptibility Testing in the Management of Candida and Aspergillus.

PubMed

Ostrosky-Zeichner, Luis; Andes, David

2017-08-15

Antifungal susceptibility testing has evolved from a research technique to a standardized and well-validated tool for the clinical management of fungal infections and for epidemiological studies. Genetic mutations and phenotypic resistance in vitro have been shown to correlate with clinical outcomes and treatment failures, and this in turn has led to the creation of clinical breakpoints and, more recently, epidemiological cutoff values for clinically relevant fungal pathogens. Resistance mechanisms for Candida and Aspergillus species have been extensively described and their corresponding genetic mutations can now be readily detected. Epidemiological studies have been able to detect the emergence of regional clonal and nonclonal resistance in several countries. The clinical microbiology laboratory is expected to transition from culture and traditional susceptibility testing to molecular methods for detection, identification, and resistance profiling over the next 5-10 years. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Comparative study of Gram stain, potassium hydroxide smear, culture and nested PCR in the diagnosis of fungal keratitis.

PubMed

Badiee, Parisa; Nejabat, Mahmood; Alborzi, Abdolvahab; Keshavarz, Fatemeh; Shakiba, Elaheh

2010-01-01

This study seeks to evaluate the efficacy and practicality of the molecular method, compared to the standard microbiological techniques for diagnosing fungal keratitis (FK). Patients with eye findings suspected of FK were enrolled for cornea sampling. Scrapings from the affected areas of the infected corneas were obtained and were divided into two parts: one for smears and cultures, and the other for nested PCR analysis. Of the 38 eyes, 28 were judged to have fungal infections based on clinical and positive findings in the culture, smear and responses to antifungal treatment. Potassium hydroxide, Gram staining, culture and nested PCR results (either positive or negative) matched in 76.3, 42.1, 68.4 and 81.6%, respectively. PCR is a sensitive method but due to the lack of sophisticated facilities in routine laboratory procedures, it can serve only complementarily and cannot replace conventional methods. Copyright © 2010 S. Karger AG, Basel.

Arthroscopic management of the painful total elbow arthroplasty.

PubMed

Phadnis, Joideep; Bain, Gregory I

2016-01-01

Failure of total elbow arthroplasty is more common than after other major joint arthroplasties and is often a result of aseptic loosening, peri-prosthetic infection, fracture and instability. Infection can be a devastating complication, yet there are no established guidelines for the pre-operative diagnosis of total elbow peri-prosthetic infection. This is because pre-operative clinical, radiographic and biochemical tests are often unreliable. Using three case examples, a standardized protocol for the clinical and arthroscopic assessment of the painful total elbow arthroplasty is described. This is used to provide a mechanical and microbiological diagnosis of the patient's pain. There have been no complications resulting from the use of this technique in the three patients described, nor in any other patient to date. The staged protocol described in the present study, utilizing arthroscopic assessment, has refined the approach to the painful total elbow arthroplasty because it directly influences the definitive surgical management of the patient. It is recommended that other surgeons follow the principles outlined in the present study when faced with this challenging problem.

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.

Microbiological Water Quality in Relation to Water-Contact Recreation, Cuyahoga River, Cuyahoga Valley National Park, Ohio, 2000 and 2002

USGS Publications Warehouse

Bushon, Rebecca N.; Koltun, G.F.

2004-01-01

The microbiological water quality of a 23-mile segment of the Cuyahoga River within the Cuyahoga Valley National Park was examined in this study. This segment of the river receives discharges of contaminated water from stormwater, combined-sewer overflows, and incompletely disinfected wastewater. Frequent exceedances of Ohio microbiological water-quality standards result in a health risk to the public who use the river for water-contact recreation. Water samples were collected during the recreational season of May through October at four sites on the Cuyahoga River in 2000, at three sites on the river in 2002, and from the effluent of the Akron Water Pollution Control Station (WPCS) both years. The samples were collected over a similar range in streamflow in 2000 and 2002. Samples were analyzed for physical and chemical constituents, as well as the following microbiological indicators and pathogenic organisms: Escherichia coli (E. coli), Salmonella, F-specific and somatic coliphage, enterovirus, infectious enterovirus, hepatitis A virus, Clostridium perfringens (C. perfringens), Cryptosporidium, and Giardia. The relations of the microorganisms to each other and to selected water-quality measures were examined. All microorganisms analyzed for, except Cryptosporidium, were detected at least once at each sampling site. Concentrations of E. coli exceeded the Ohio primary-contact recreational standard (298 colonies per 100 milliliters) in approximately 87 percent of the river samples and generally were higher in the river samples than in the effluent samples. C. perfringens concentrations were positively and significantly correlated with E. coli concentrations in the river samples and generally were higher in the effluent samples than in the river samples. Several of the river samples that met the Ohio E. coli secondary-contact recreational standard (576 colonies per 100 milliliters) had detections of enterovirus, infectious enterovirus, hepatitis A virus, and Salmonella, indicating that there are still risks even when the E. coli standard is not exceeded. River samples in which the secondary-contact recreational standard for E. coli was exceeded showed a higher percentage of the co-occurrence of pathogenic organisms than samples that met the standard. This indicates that in this study area, E. coli is a useful indicator of human health risk. Detections of hepatitis A virus tended to be associated with higher median concentrations of somatic coliphage, F-specific coliphage, and infectious enterovirus. In addition, geometric mean C. perfringens concentrations tended to be higher in samples where hepatitis A virus was present than in samples where hepatitis A virus was absent. Hepatitis A virus was not detected in samples collected upstream from the Akron WPCS; all downstream detections had coincident detections in the Akron WPCS effluent, suggesting that Akron WPCS was a principal source of hepatitis A virus at the downstream sites. Geometric mean concentrations of E. coli were calculated on the basis of analytical results from at least five samples collected at each river site during May, July, and September of 2000. In each case, the Ohio geometric-mean primary-contact recreational standard of 126 col/100 mL was exceeded. E. coli concentrations were significantly correlated with streamflow and increased with streamflow at sites upstream and downstream from the Akron WPCS. This indicates that E. coli loads from sources upstream from the Akron WPCS have the potential to appreciably influence the frequency of attainment of recreational water-quality standards at downstream locations.

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…

[Microbiological characteristics of selected liquid soaps for hands washing].

PubMed

Tyski, Stefan; Bocian, Ewa; Zawistowska, Anna; Mrówka, Agnieszka; Kruszewska, Hanna; Grzybowska, Wanda; Zareba, Tomasz

2013-01-01

According to common belief, supported by the authority of the World Health Organization - WHO, the common (social) hand washing is the simplest, cheapest and the most effective way of reduction the hospital-acquired infections. For this purpose products of"liquid soaps", present in a large number on the market, are most often applied. Microbiological status (microbiological purity and antimicrobial activity) of"liquid soaps" available on the Polish market is not known, because relevant routinely studies have not been performed. Only the antibacterial and / or antifungal activity of certain formulations is sometimes assessed, especially when the manufacturer suggests the standardized application of the products for surgical or hygienic procedures. The aim of this study was to determine the microbiological quality, especially microbiological purity and antimicrobial activity of the selected hands washing products, presents on the Polish market. The 12 selected commercial products, available on the market in Poland, dedicated for hands washing were included into study. Microbiological purity test was carried out in accordance with the Polish Pharmacopoeia (FP) monograph (FP monograph numbers correspond to numbers of the European Pharmacopoeia monograph- Ph. Eur.) No 2.6.12 "Microbiological examination of non-sterile products: microbial enumaration tests", and the monograph of FP No. 2.6.13 "Microbiological examination of non-sterile products: test for specified microorganisms". The following physico-chemical properties of soaps were examined: the pH of the formulations was measured according to the monograph FP No. 2.2.3. "Potentiometric determination of pH", the density of products was assayed according to the monograph FPNo. 2.2.5. "Relative density" and determination the water activity was performed by monograph FP No 2.9.39 "Water-solid interactions: determination of sorption-desorption isotherms and of water activity". Next, antibacterial and antifungal protection was determined in accordance with the monograph FP No 5.1.3. "Efficacy of antimicrobial preservation". The study of antimicrobial activity was carried out in accordance with PN-EN 1040 "Chemical disinfectants and antiseptics - Quantitative suspension test for the evaluation of basic bactericidal activity of chemical disinfectants and antiseptics - Test method and requirements (phase 1)". Finally, using the "time-kill" method the survival of microorganisms after different contact times of the products with bacteria and fungi were determined. All the examined products showed a very high microbiological purity. None of the formulations was characterized by a high acidity or alkalinity. All the analyzed products were slightly thicker than water, but such density of the preparation does not seem to be important parameter in the growth of microorganisms. The results of water activity estimation - the parameter indicating the presence of free, not chemically bound water stimulating microbes growth - do not show that low water content in the preparation may inhibit bacteria and fungi growth. Taking into consideration the antimicrobial protection of the products demonstrated in the tests carried out in accordance within FP monograph No 5.1.3. and PN-EN 1040, and analysing curves indicating killing rate of bacteria and fungi obtained by "time-kill" method, the microorganisms contaminating the products generally should not multiply in their environment, and gradually they die - what can take many hours or even days. The cases of bacterial infections connected with the usage of non-medical liguid soaps, applied in the health care units and described in the literature, should be considered as related rather to contamination of plastic packaging and dosage system, then to contamination of preparation itself inside the package. It was proved, that in all tested products amount of contaminating microbes diminishes in time. The dynamics of this process depends on the microorganisms character - bacteria dies quicker then fungi. The special attention should be given to washing, cleaning and disinfection of preparation dispensing systems, to avoid microbial contamination of product doses applied directly on the hands. It should be emphasized that only formulations containing antimicrobial agents in an appropriate amount, eliminate microorganisms from the skin surface fast and effectively. In case of hygienic and surgical procedures following the standardized manner in order to obtain required reduction rate of microorganisms in a short time - only products complying with appropriate EN standards are suitable. For these puroposes, the popular "liquid soaps" should not be used.

Raw ready-to-eat seafood safety: microbiological quality of the various seafood species available in fishery, hyper and online markets.

PubMed

Kim, H W; Hong, Y J; Jo, J I; Ha, S D; Kim, S H; Lee, H J; Rhee, M S

2017-01-01

Microbiological quality of 206 raw ready-to-eat seafood samples was investigated according to species (gizzard shad, halibut, rockfish, tuna, oyster and squid) and distribution channels (fishery, hyper and online market). Enumeration of aerobic plate count and total coliforms (TC) and pathogenic bacteria (Bacillus cereus, Staphylococcus aureus and Vibrio parahaemolyticus) was performed, and level of microbiological quality was classified into four groups: satisfactory, acceptable, unsatisfactory and unacceptable. Qualitative analysis was also performed for Escherichia coli and eight foodborne pathogens (B. cereus, E. coli O157:H7, Listeria monocytogenes, Salmonella spp., S. aureus, Vibrio cholerae, V. parahaemolyticus, and Vibrio vulnificus). Raw ready-to-eat seafood products revealed 0·5% at an unsatisfactory level and 4·9% at an unacceptable level due to ≥4 log CFU g -1 of TC in squid and ≥3 log CFU g -1 of V. parahaemolyticus in gizzard shad respectively. Gizzard shad was shown to be potentially hazardous, as its sashimi is eaten with its skin attached. Bacillus cereus, E. coli, S. aureus, V. parahaemolyticus and V. vulnificus were qualitatively detected. Samples from the fishery market showed higher detection rate especially in V. parahaemolyticus (21·6%) and V. vulnificus (1·7%) which indicates the need to improve microbiological safety of raw ready-to-eat seafood products in fishery market. Raw ready-to-eat seafood products like sashimi can be easily contaminated with various bacteria from aquatic environments and human reservoirs, which subsequently bring about a risk in food poisoning due to no heating process before consumption. The results of this study provide comprehensive microbiological data on various species of raw ready-to-eat seafood from various distribution channels. It may contribute to establish reasonable standard and effective strategies to ensure a good microbiological quality of raw ready-to-eat seafood for the safety of meals, like sashimi and sushi. © 2016 The Society for Applied Microbiology.

Do biological-based strategies hold promise to biofouling control in MBRs?

PubMed

Malaeb, Lilian; Le-Clech, Pierre; Vrouwenvelder, Johannes S; Ayoub, George M; Saikaly, Pascal E

2013-10-01

Biofouling in membrane bioreactors (MBRs) remains a primary challenge for their wider application, despite the growing acceptance of MBRs worldwide. Research studies on membrane fouling are extensive in the literature, with more than 200 publications on MBR fouling in the last 3 years; yet, improvements in practice on biofouling control and management have been remarkably slow. Commonly applied cleaning methods are only partially effective and membrane replacement often becomes frequent. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective control strategies. Biofouling is driven by microorganisms and their associated extra-cellular polymeric substances (EPS) and microbial products. Microorganisms and their products convene together to form matrices that are commonly treated as a black box in conventional control approaches. Biological-based antifouling strategies seem to be a promising constituent of an effective integrated control approach since they target the essence of biofouling problems. However, biological-based strategies are in their developmental phase and several questions should be addressed to set a roadmap for translating existing and new information into sustainable and effective control techniques. This paper investigates membrane biofouling in MBRs from the microbiological perspective to evaluate the potential of biological-based strategies in offering viable control alternatives. Limitations of available control methods highlight the importance of an integrated anti-fouling approach including biological strategies. Successful development of these strategies requires detailed characterization of microorganisms and EPS through the proper selection of analytical tools and assembly of results. Existing microbiological/EPS studies reveal a number of implications as well as knowledge gaps, warranting future targeted research. Systematic and representative microbiological studies, complementary utilization of molecular and biofilm characterization tools, standardized experimental methods and validation of successful biological-based antifouling strategies for MBR applications are needed. Specifically, in addition, linking these studies to relevant operational conditions in MBRs is an essential step to ultimately develop a better understanding and more effective and directed control strategy for biofouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

PubMed

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

2012-01-01

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

Modeling and evaluation of compliance to water quality regulations in bathing areas on the Daoulas catchment and estuary (France).

PubMed

Bougeard, M; Le Saux, J C; Jouan, M; Durand, G; Pommepuy, M

2010-01-01

The microbiological quality of waters in estuaries determines their acceptability for recreational uses. Microbiological contamination often results from urban wastewater discharges or non-point source pollution (manure spreading), and can cause bathing zones to be closed. European regulations (EC/7/2006) have proposed standards (500 E. coli/100 ml) for the acceptability areas for bathing. In this study, two models were associated to simulate contamination: SWAT on a catchment and MARS 2D in the downstream estuary. After river flow calibration and validation, two scenarios were simulated in SWAT, and E. coli fluxes obtained at the main outlet of the catchment were then introduced into MARS 2D to follow E. coli concentrations in the estuary. An annual evaluation of compliance to bathing area water quality standards was then calculated, linked with daily rainfall classes. Water quality in the estuary was below the standard on 13 days, including 5 days with rainfall superior to 10 mm, due to faecal contamination from soil leaching by rain, and 5 days with rainfall ranging from 0.1 to 5 mm/day, due to the high frequency of this level of rainfall. To conclude, this study allowed us to demonstrate the efficiency of models to gain a better understanding on water quality degradation factors.

The Effect of Exit-Site Antibacterial Honey Versus Nasal Mupirocin Prophylaxis on the Microbiology and Outcomes of Peritoneal Dialysis-Associated Peritonitis and Exit-Site Infections: A Sub-Study of the Honeypot Trial.

PubMed

Zhang, Lei; Badve, Sunil V; Pascoe, Elaine M; Beller, Elaine; Cass, Alan; Clark, Carolyn; de Zoysa, Janak; Isbel, Nicole M; McTaggart, Steven; Morrish, Alicia T; Playford, E Geoffrey; Scaria, Anish; Snelling, Paul; Vergara, Liza A; Hawley, Carmel M; Johnson, David W

2015-12-01

♦ The HONEYPOT study recently reported that daily exit-site application of antibacterial honey was not superior to nasal mupirocin prophylaxis for preventing overall peritoneal dialysis (PD)-related infection. This paper reports a secondary outcome analysis of the HONEYPOT study with respect to exit-site infection (ESI) and peritonitis microbiology, infectious hospitalization and technique failure. ♦ A total of 371 PD patients were randomized to daily exit-site application of antibacterial honey plus usual exit-site care (N = 186) or intranasal mupirocin prophylaxis (in nasal Staphylococcus aureus carriers only) plus usual exit-site care (control, N = 185). Groups were compared on rates of organism-specific ESI and peritonitis, peritonitis- and infection-associated hospitalization, and technique failure (PD withdrawal). ♦ The mean peritonitis rates in the honey and control groups were 0.41 (95% confidence interval [CI] 0.32 - 0.50) and 0.41 (95% CI 0.33 - 0.49) episodes per patient-year, respectively (incidence rate ratio [IRR] 1.01, 95% CI 0.75 - 1.35). When specific causative organisms were examined, no differences were observed between the groups for gram-positive (IRR 0.99, 95% CI 0.66 - 1.49), gram-negative (IRR 0.71, 95% CI 0.39 - 1.29), culture-negative (IRR 2.01, 95% CI 0.91 - 4.42), or polymicrobial peritonitis (IRR 1.08, 95% CI 0.36 - 3.20). Exit-site infection rates were 0.37 (95% CI 0.28 - 0.45) and 0.33 (95% CI 0.26 - 0.40) episodes per patient-year for the honey and control groups, respectively (IRR 1.12, 95% CI 0.81 - 1.53). No significant differences were observed between the groups for gram-positive (IRR 1.10, 95% CI 0.70 - 1.72), gram-negative (IRR: 0.85, 95% CI 0.46 - 1.58), culture-negative (IRR 1.88, 95% CI 0.67 - 5.29), or polymicrobial ESI (IRR 1.00, 95% CI 0.40 - 2.54). Times to first peritonitis-associated and first infection-associated hospitalization were similar in the honey and control groups. The rates of technique failure (PD withdrawal) due to PD-related infection were not significantly different between the groups. ♦ Compared with standard nasal mupirocin prophylaxis, daily topical exit-site application of antibacterial honey resulted in comparable rates of organism-specific peritonitis and ESI, infection-associated hospitalization, and infection-associated technique failure in PD patients. Copyright © 2015 International Society for Peritoneal Dialysis.

Assessment of microbiology students' progress with an audience response system.

PubMed

Chaudhry, M Ahmad

2011-01-01

The development of new approaches to teaching of large lecture courses is needed. Today's classroom has a wide range of students including high-achieving motivated learners, students struggling to understand basic concepts, and learning-challenged students. Many of these students can be lost in large classes under the shadow of the high-achieving extroverted students who dominate classroom question-and-answer sessions. Measuring a student's understanding and achievement of content standards becomes difficult until an assessment has been done. To close this gap, an audience response system was introduced in an introductory Principles of Microbiology course. This technology specifically addressed the goal of individualizing instruction to the needs of the students. The evaluation of this project indicated an overall positive impact on student learning.

A Strategy to Establish a Quality Assurance/Quality Control Plan for the Application of Biosensors for the Detection of E. coli in Water.

PubMed

Hesari, Nikou; Kıratlı Yılmazçoban, Nursel; Elzein, Mohamad; Alum, Absar; Abbaszadegan, Morteza

2017-01-03

Rapid bacterial detection using biosensors is a novel approach for microbiological testing applications. Validation of such methods is an obstacle in the adoption of new bio-sensing technologies for water testing. Therefore, establishing a quality assurance and quality control (QA/QC) plan is essential to demonstrate accuracy and reliability of the biosensor method for the detection of E. coli in drinking water samples. In this study, different reagents and assay conditions including temperatures, holding time, E. coli strains and concentrations, dissolving agents, salinity and pH effects, quality of substrates of various suppliers of 4-methylumbelliferyl glucuronide (MUG), and environmental water samples were included in the QA/QC plan and used in the assay optimization and documentation. Furthermore, the procedural QA/QC for the monitoring of drinking water samples was established to validate the performance of the biosensor platform for the detection of E. coli using a culture-based standard technique. Implementing the developed QA/QC plan, the same level of precision and accuracy was achieved using both the standard and the biosensor methods. The established procedural QA/QC for the biosensor will provide a reliable tool for a near real-time monitoring of E. coli in drinking water samples to both industry and regulatory authorities.

A Strategy to Establish a Quality Assurance/Quality Control Plan for the Application of Biosensors for the Detection of E. coli in Water

PubMed Central

Hesari, Nikou; Kıratlı Yılmazçoban, Nursel; Elzein, Mohamad; Alum, Absar; Abbaszadegan, Morteza

2017-01-01

Rapid bacterial detection using biosensors is a novel approach for microbiological testing applications. Validation of such methods is an obstacle in the adoption of new bio-sensing technologies for water testing. Therefore, establishing a quality assurance and quality control (QA/QC) plan is essential to demonstrate accuracy and reliability of the biosensor method for the detection of E. coli in drinking water samples. In this study, different reagents and assay conditions including temperatures, holding time, E. coli strains and concentrations, dissolving agents, salinity and pH effects, quality of substrates of various suppliers of 4-methylumbelliferyl glucuronide (MUG), and environmental water samples were included in the QA/QC plan and used in the assay optimization and documentation. Furthermore, the procedural QA/QC for the monitoring of drinking water samples was established to validate the performance of the biosensor platform for the detection of E. coli using a culture-based standard technique. Implementing the developed QA/QC plan, the same level of precision and accuracy was achieved using both the standard and the biosensor methods. The established procedural QA/QC for the biosensor will provide a reliable tool for a near real-time monitoring of E. coli in drinking water samples to both industry and regulatory authorities. PMID:28054956

Microbiological study of ready-to-eat salad vegetables from retail establishments uncovers a national outbreak of salmonellosis.

PubMed

Sagoo, S K; Little, C L; Ward, L; Gillespie, I A; Mitchell, R T

2003-03-01

The increasing availability of bagged prepared salad vegetables reflects consumer demand for fresh, healthy, convenient, and additive-free foods that are safe and nutritious. During May and June 2001 a study of retail bagged prepared ready-to-eat salad vegetables was undertaken to determine the microbiological quality of these vegetables. Examination of the salad vegetables revealed that the vast majority (3,826 of 3,852 samples; 99.3%) were of satisfactory or acceptable microbiological quality according to Public Health Laboratory Service microbiological guidelines, while 20 (0.5%) samples were of unsatisfactory microbiological quality. Unsatisfactory quality was due to Escherichia coli and Listeria spp. (not Listeria monocytogenes) levels in excess of 10(2) CFU/g. However, six (0.2%) samples were of unacceptable microbiological quality because of the presence of Salmonella (Salmonella Newport PT33 [one sample], Salmonella Umbilo [three samples], and Salmonella Durban [one sample]) or because of a L. monocytogenes level of 660 CFU/g, which indicates a health risk. In each case, the retailer involved and the UK Food Standards Agency were immediately informed, and full investigations were undertaken. Nineteen cases of Salmonella Newport PT33 infection were subsequently identified throughout England and Wales. The outbreak strain of Salmonella Newport PT33 isolated from the salad and from humans had a unique plasmid profile. Campylobacter spp. and E. coli O157 were not detected in any of the samples examined. The presence of Salmonella, as well as high levels of L. monocytogenes, is unacceptable. However, minimally processed cut and packaged salad is exposed to a range of conditions during growth, harvest, preparation, and distribution, and it is possible that these conditions may increase the potential for microbial contamination, highlighting the necessity for the implementation of good hygiene practices from farm to fork to prevent contamination and/or bacterial growth in these salad products.

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

PubMed

Kohlmann, Rebekka; Gatermann, Sören G

2016-01-01

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

Comparative study of antibiotic-containing polymethylmetacrylate capsules and beads.

PubMed

Borzsei, László; Mintál, Tibor; Horváth, Aranka; Koós, Zoltán; Kocsis, Béla; Nyárády, József

2006-01-01

This study aimed at making local antibiotic therapy wider in cases of chronic suppurations by administering antibiotics which previously could not be given in this way through the conventional polymethylmetacrylate (PMMA) carrier techniques. Capsules from this material were produced with a pressing machine designed and laid out by us. The characteristics of antibiotic penetration from this novel carrier were compared to those of PMMA beads. The time-dependent outflow of amikacin, clindamycin, pefloxacin, piperacillin + tazobactam, amoxicillin + clavulanic acid and cefotaxime was examined from the capsules and the beads with standard microbiological techniques using the Micrococcus luteus ATCC9341 test strain. The diameter of the inhibitory zones was measured after 24 h incubation at 37 degrees C and converted to mug/ml antibiotic concentrations. Our results revealed that all antibiotics showed longer-lasting and higher concentration outflow from the PMMA capsules than from the beads. Therefore, these capsules can provide a more promising new opportunity for specific local antimicrobial treatment in cases of chronic suppurative bone and soft tissue injuries. In these cases the polymerization has already been completed and the heat does not influence the structure of the antibiotics; therefore, it can be inserted into the capsules in powder or solution form. Copyright 2006 S. Karger AG, Basel.

Agricultural reuse of municipal wastewater through an integral water reclamation management.

PubMed

Intriago, Juan Carlo; López-Gálvez, Francisco; Allende, Ana; Vivaldi, Gaetano Alessandro; Camposeo, Salvatore; Nicolás Nicolás, Emilio; Alarcón, Juan José; Pedrero Salcedo, Francisco

2018-05-01

The DESERT-prototype, a state-of-the-art compact combination of water treatment technologies based on filtration and solar-based renewable energy, was employed to reclaim water for agricultural irrigation. Water reclaimed through the DESERT-prototype (PW) from a secondary effluent of a wastewater treatment plant, as well as conventional irrigation water (CW) and the secondary effluent (SW) itself, were employed to cultivate baby romaine lettuces in a greenhouse in Murcia (Spain), by means of drip and sprinkler irrigation methods, thus establishing six treatments. Assessments of physicochemical and microbiological quality of irrigation water, as well as agronomic and microbiological quality of crops from all treatments, showed that results associated to PW complied in all cases with relevant standards and guidelines. In contrast, results linked to SW and CW presented certain non-compliance cases of water and crop microbiological quality. These assessments lead to conclude that the DESERT-prototype is an appropriate technology for safe water reclamation oriented to agricultural production, that can be complemented by a proper irrigation method in reaching safety targets. Copyright © 2018 Elsevier Ltd. All rights reserved.

Data on microbiological quality assessment of rural drinking water supplies in Tiran County, Isfahan province, Iran.

PubMed

Jafari, Khadijeh; Mohammadi, Ali Akbar; Heidari, Zahra; Asghari, Farzaneh Baghal; Radfard, Majid; Yousefi, Mahmood; Shams, Mahmoud

2018-06-01

A lack of access to safe drinking water can lead to adverse health effects such as infection, disease, and undesirable aesthetic problems. The current study focused on the investigation of groundwater quality in Tiran's villages (Isfahan province, Iran). To determine essential microbiological quality, water samples were collected from 46 randomly-selected water wells during a one-year period. The parameters of pH and chlorine were measured on-site. Turbidity was measured at 420 nm using a DR5000 spectrophotometer. Microbiological tests including general thermoforms, Escherichia coli , and thermophiles were carried out according to the National Iranian Standard Method 3759. Data showed that 1.8% of the villages under study had contaminated water resources. The turbidity values for 94.5% of the resources were within recommended limits (<5NTU). In 20.6% of the samples, the residual free chlorine was in the range of 0 to 0.2 mg/L, 8.79% of samples had values greater than the recommended limits, and18.5% had no free residual chlorine.

[Invasive pulmonary aspergillosis].

PubMed

Blanchard, E; Gabriel, F; Jeanne-Leroyer, C; Servant, V; Dumas, P-Y

2018-02-01

Invasive pulmonary aspergillosis (IPA) is an important cause of morbidity and mortality in a wide range of patients. Early recognition and diagnosis have become a major focus in improving the management and outcomes of this life-threatening disease. IPA typically occurs during a period of severe and prolonged neutropenia. However, solid organ transplant recipients, patients under immunosuppressive therapy or hospitalized in intensive care units are also at risk. The diagnosis is suspected in the presence of a combination of clinical, biological and CT scan evidence. The microbiological diagnostic strategy should be adapted to the patient's profile. Conventional methods with culture and species identification remain the standard but early diagnosis has been improved by the use of biomarkers such as galactomannan antigen in serum or in bronchoalveolar lavage. The epidemiology of IPA should change with the increased use of antifungal prophylactic regimens and the arrival of targeted therapies. Other microbiological tools, such as PCR and other biomarkers, are currently being assessed. IPA must be considered in a wide range of patients. Its prognosis remains poor despite progress in the microbiological diagnosis and therapeutic management. Copyright © 2018 SPLF. Published by Elsevier Masson SAS. All rights reserved.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-11-01

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

Assessment of a food microbiology senior undergraduate course as a potential food safety distance education course for poultry science majors.

PubMed

O'Bryan, C A; Dittmar, R S; Chalova, V I; Kundinger, M M; Crandall, P G; Ricke, S C

2010-11-01

Distance education courses have become popular due to the increased number of commuter students as well as people already in the workforce who need further education for advancement within their careers. A graduate-level Web-based course entitled Special Topics-Poultry Food Safety Microbiology was developed from an existing senior undergraduate advanced food microbiology course in the Poultry Science Department at Texas A&M University. Conversion of standard lecture material into a distance education course can provide unique challenges to maintain comparable course content in an asynchronous manner. The overall objective for this course was to examine bacterial activities including ecology in food, animals, raw and processed meat, eggs, and human pathogenesis. Students were surveyed at the end of the class and the majority agreed that they would be willing to take the course as an online course, although they were not willing to pay an extra fee for an online course. The majority of students used the online version of the course as a supplement to the classroom rather than as a substitute.

Rapid test for the detection of hazardous microbiological material

NASA Astrophysics Data System (ADS)

Mordmueller, Mario; Bohling, Christian; John, Andreas; Schade, Wolfgang

2009-09-01

After attacks with anthrax pathogens have been committed since 2001 all over the world the fast detection and determination of biological samples has attracted interest. A very promising method for a rapid test is Laser Induced Breakdown Spectroscopy (LIBS). LIBS is an optical method which uses time-resolved or time-integrated spectral analysis of optical plasma emission after pulsed laser excitation. Even though LIBS is well established for the determination of metals and other inorganic materials the analysis of microbiological organisms is difficult due to their very similar stoichiometric composition. To analyze similar LIBS-spectra computer assisted chemometrics is a very useful approach. In this paper we report on first results of developing a compact and fully automated rapid test for the detection of hazardous microbiological material. Experiments have been carried out with two setups: A bulky one which is composed of standard laboratory components and a compact one consisting of miniaturized industrial components. Both setups work at an excitation wavelength of λ=1064nm (Nd:YAG). Data analysis is done by Principal Component Analysis (PCA) with an adjacent neural network for fully automated sample identification.

Microbiological characterization of Serra da Estrela cheese throughout its Appellation d'Origine Protégée region.

PubMed

Tavaria, F K; Malcata, F X

1998-05-01

The purpose of this study was to assess the typical microbiological quality of the most famous Portuguese traditional cheese, Serra da Estrela, and to assess its ripening time and geographical dependence. Ninety-six experimental cheeses manufactured from sixteen batches of milk on eight dairy farms scattered over the Appellation d' Origine Protégée (AOP) region were qualitatively and quantitatively evaluated microbiologically at various ripening times. Viable counts were performed after inoculation on appropriate selective media for aerobic mesophiles and proteolytic and lipolytic microflora, as well as lactococci, lactobacilli, species of Enterobacteriaceae, lactic streptococci, staphylococci, and yeasts. Members of the Enterobacteriaceae and lactic acid bacteria were the predominant microbial groups on all dairy farms throughout maturation; the latter are probably the microbial group responsible for most proteolytic and lipolytic breakdown in Serra da Estrela cheese. The microbial groups whose numbers were most affected by dairy-to-dairy variation were species of Enterobacteriaceae staphylococci, and enterococci, which are the most critical groups in terms of health hazards. It is therefore suggested that tighter control should be implemented at the level of choice of raw materials, in milk-handling practices, and in general throughout the manufacturing process in attempts to standardize production and consistently reduce microbiological risks (even though the distinctiveness of a few final organoleptic characteristics may somehow be reduced.

An assessment of the microbiological quality of liver-based pâté in England 2012-13: comparison of samples collected at retail and from catering businesses.

PubMed

McLAUCHLIN, J; Jørgensen, F; Aird, H; Charlett, A; Elviss, N; Fenelon, D; Fox, A; Willis, C; Amar, C F L

2017-06-01

The purpose of this study was to investigate the microbiological quality of liver pâté. During 2012-13, a total of 870 samples, unrelated to the investigation of food-poisoning outbreaks, were collected either at retail (46%), catering (53%) or the point of manufacture (1%) and were tested using standard methods to detect Salmonella spp. or Campylobacter spp., and to enumerate for Listeria spp., including Listeria monocytogenes, Clostridium perfringens, coagulase-positive staphylococci including Staphylococcus aureus, Bacillus spp., including Bacillus cereus, Escherichia coli, Enterobacteriaceae, and aerobic colony counts (ACCs). Seventy-three percent of samples were of satisfactory microbiological quality, 18% were borderline and 9% unsatisfactory. Salmonella spp. or Campylobacter spp. was not recovered from any sample. The most common causes of unsatisfactory results were elevated ACCs (6% of the samples) and high Enterobacteriaceae counts (4% of samples). The remaining unsatisfactory results were due to elevated counts of: E. coli (three samples); B. cereus (one sample at 2·6 × 105 cfu/g); or L. monocytogenes (one sample at 2·9 × 103 cfu/g). Pâté from retail was less likely to be contaminated with L. monocytogenes than samples collected from catering and samples from supermarkets were of significantly better microbiological quality than those from catering establishments.

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.

Studies of the Ecological Impact of Repetitive Aerial Applications of Herbicides on the Ecosystem of Test Area C-52A, Eglin AFB, Florida

DTIC Science & Technology

1975-08-01

mosquito Beuthss. Microbiology . Effluents. control was rettlizcd using niosquito fish Identifiers: ’Water pollution effects(Arsimals)- Identifiers...support differences between the control and tesi , animals. It is interesting to note the magnitude of the standard deviations between spleen weights from

Haemophilus haemolyticus Isolates Causing Clinical Disease

PubMed Central

Wang, Xin; Briere, Elizabeth C.; Katz, Lee S.; Cohn, Amanda C.; Clark, Thomas A.; Messonnier, Nancy E.; Mayer, Leonard W.

2012-01-01

We report seven cases of Haemophilus haemolyticus invasive disease detected in the United States, which were previously misidentified as nontypeable Haemophilus influenzae. All cases had different symptoms and presentations. Our study suggests that a testing scheme that includes reliable PCR assays and standard microbiological methods should be used in order to improve H. haemolyticus identification. PMID:22573587

Haemophilus haemolyticus isolates causing clinical disease.

PubMed

Anderson, Raydel; Wang, Xin; Briere, Elizabeth C; Katz, Lee S; Cohn, Amanda C; Clark, Thomas A; Messonnier, Nancy E; Mayer, Leonard W

2012-07-01

We report seven cases of Haemophilus haemolyticus invasive disease detected in the United States, which were previously misidentified as nontypeable Haemophilus influenzae. All cases had different symptoms and presentations. Our study suggests that a testing scheme that includes reliable PCR assays and standard microbiological methods should be used in order to improve H. haemolyticus identification.

42 CFR 493.1406 - Standard; Laboratory director qualifications on or before February 28, 1992.

Code of Federal Regulations, 2014 CFR

2014-10-01

... American Society of Cytology to practice cytopathology or possesses qualifications that are equivalent to... biological science as a major subject and (i) Is certified by the American Board of Medical Microbiology, the... master's degree from an accredited institution with a chemical, physical, or biological science as a...

42 CFR 493.1406 - Standard; Laboratory director qualifications on or before February 28, 1992.

Code of Federal Regulations, 2010 CFR

2010-10-01

... American Society of Cytology to practice cytopathology or possesses qualifications that are equivalent to... biological science as a major subject and (i) Is certified by the American Board of Medical Microbiology, the... master's degree from an accredited institution with a chemical, physical, or biological science as a...

42 CFR 493.1406 - Standard; Laboratory director qualifications on or before February 28, 1992.

Code of Federal Regulations, 2011 CFR

2011-10-01

... American Society of Cytology to practice cytopathology or possesses qualifications that are equivalent to... biological science as a major subject and (i) Is certified by the American Board of Medical Microbiology, the... master's degree from an accredited institution with a chemical, physical, or biological science as a...

42 CFR 493.1406 - Standard; Laboratory director qualifications on or before February 28, 1992.

Code of Federal Regulations, 2013 CFR

2013-10-01

... American Society of Cytology to practice cytopathology or possesses qualifications that are equivalent to... biological science as a major subject and (i) Is certified by the American Board of Medical Microbiology, the... master's degree from an accredited institution with a chemical, physical, or biological science as a...

42 CFR 493.1406 - Standard; Laboratory director qualifications on or before February 28, 1992.

Code of Federal Regulations, 2012 CFR

2012-10-01

... American Society of Cytology to practice cytopathology or possesses qualifications that are equivalent to... biological science as a major subject and (i) Is certified by the American Board of Medical Microbiology, the... master's degree from an accredited institution with a chemical, physical, or biological science as a...

[Antimicrobial susceptibility of animal and food isolates of Salmonella enterica].

PubMed

Junod, Tania; López-Martin, Juana; Gädicke, Paula

2013-03-01

Bacterial resistance to one or more antimicrobiak is worrisome. To determine the susceptibility to antimicrobials of Salmonella entérica isolates from animáis and food, from the Laboratory of Veterinary Microbiology at the University of Concepción. The samples were isolated according to traditional microbiological methods standardized protocols. Resistance was determined by the Kirby-Bauer method and minimal inhibitory concentration (MIC), following Clinical and Laboratory Standards Institute recommendations (2008). Nine serotypes were identified among the 68 isolates. Strains were resistant to one or more antibiotics and 11 patterns of resistance were identified. Multidrug resistance (MDR) was observed in 20.5% of the strains tested. The most common was Oxytetracycline resistance (69.1%). Infood, the predominant serotype was S. Derby (2.9%) and S. Senftenberg (2.9%), which is commonly found infood intended for animal consumption. In samples of animal origin, the predominant serotypes were S. infantis (33.8%) and S. Group E (3.9;-;-) (23.5%). The frequeney of resistance found and the impending risk that these strains could reach humans through the food chain, should prompt a follow-up study of this pathogen.

Combined Effects of Inoculation Level and Sequence on Biochemical and Microbiological Characteristics of Probiotic Doogh

PubMed Central

Rahmati Roudsari, Mohammad; Sohrabvandi, Sara; Homayouni Rad, Aziz; Mortazavian, Amir Mohammad

2013-01-01

The combined effects of inoculation level (4 or 8-fold compared to standard inoculation) and sequence (standard inoculation before fermentation and 3-fold inoculation at the end of fermentation=1+3, Two-fold inoculation before fermentation and the same at the end of fermentation=2+2, 2+6, 4-fold before fermentation=4, 4+4, and 8) of culture inoculum containing probiotics on biochemical and microbiological characteristics of probiotic Doogh during fermentation and over 21 days of refrigerated storage (4˚C) were investigated. The probiotic microorganisms were L. acidophilus LA-5 and Bifidobacterium lactis BB-12. Overall, the treatments 8, 4 and 4+4 resulted in the highest viability at the end of fermentation as well as at early days of refrigerated storage. During the second half of cold storage period, the greatest viability of probiotics was related to the treatment 2+6. The treatment ‘8’ showed the shortest incubation time as well as the highest pH drop rate and acidity increase rate during fermentation and over the storage period. PMID:24250636

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.

Diagnosis of vulvovaginitis: comparison of clinical and microbiological diagnosis.

PubMed

Esim Buyukbayrak, Esra; Kars, Bulent; Karsidag, Ayse Yasemin Karageyim; Karadeniz, Bernan Ilkay; Kaymaz, Ozge; Gencer, Serap; Pirimoglu, Zehra Meltem; Unal, Orhan; Turan, Mehmet Cem

2010-11-01

The purpose of the present study was to compare the current diagnostic clinical and laboratory approaches to women with vulvovaginal discharge complaint. The secondary outcomes were to determine the prevalence of infections in our setting and to look for the relation between vulvovaginal infections and predisposing factors if present. Premenopausal women applying to our gynecology outpatient clinic with vaginal discharge complaint were enrolled prospectively into the study. Each patient evaluated clinically with direct observation of vaginal secretions, wet mount examination, whiff test, vaginal pH testing and chlamydia rapid antigen test. Each patient also evaluated microbiologically with vaginal discharge culture and gram staining. Clinical diagnosis was compared with the microbiological diagnosis (the gold standard). Diagnostic accuracy was measured with sensitivity, specificity, positive (ppv) and negative predictive values (npv). 460 patients were included in the study. 89.8% of patients received a clinical diagnosis whereas only 36% of them had microbiological diagnosis. The sensitivity, specificity, ppv, npv of clinical diagnosis over microbiological culture results were 95, 13, 38, 82%, respectively. The most commonly encountered microorganisms by culture were Candida species (17.4%) and Gardnerella vaginalis (10.2%). Clinically, the most commonly made diagnoses were mixed infection (34.1%), bacterial vaginosis (32.4%) and fungal infection (14.1%). Symptoms did not predict laboratory results. Predisposing factors (DM, vaginal douching practice, presence of IUD and usage of oral contraceptive pills) were not found to be statistically important influencing factors for vaginal infections. Clinical diagnosis based on combining symptoms with office-based testing improves diagnostic accuracy but is insufficient. The most effective approach also incorporates laboratory testing as an adjunct when a diagnosis is in question or treatment is failing.

Semiquantitative analysis of gaps in microbiological performance of fish processing sector implementing current food safety management systems: a case study.

PubMed

Onjong, Hillary Adawo; Wangoh, John; Njage, Patrick Murigu Kamau

2014-08-01

Fish processing plants still face microbial food safety-related product rejections and the associated economic losses, although they implement legislation, with well-established quality assurance guidelines and standards. We assessed the microbial performance of core control and assurance activities of fish exporting processors to offer suggestions for improvement using a case study. A microbiological assessment scheme was used to systematically analyze microbial counts in six selected critical sampling locations (CSLs). Nine small-, medium- and large-sized companies implementing current food safety management systems (FSMS) were studied. Samples were collected three times on each occasion (n = 324). Microbial indicators representing food safety, plant and personnel hygiene, and overall microbiological performance were analyzed. Microbiological distribution and safety profile levels for the CSLs were calculated. Performance of core control and assurance activities of the FSMS was also diagnosed using an FSMS diagnostic instrument. Final fish products from 67% of the companies were within the legally accepted microbiological limits. Salmonella was absent in all CSLs. Hands or gloves of workers from the majority of companies were highly contaminated with Staphylococcus aureus at levels above the recommended limits. Large-sized companies performed better in Enterobacteriaceae, Escherichia coli, and S. aureus than medium- and small-sized ones in a majority of the CSLs, including receipt of raw fish material, heading and gutting, and the condition of the fish processing tables and facilities before cleaning and sanitation. Fish products of 33% (3 of 9) of the companies and handling surfaces of 22% (2 of 9) of the companies showed high variability in Enterobacteriaceae counts. High variability in total viable counts and Enterobacteriaceae was noted on fish products and handling surfaces. Specific recommendations were made in core control and assurance activities associated with sampling locations showing poor performance.

The Association between Symptoms and Microbiologically Defined Response to Tuberculosis Treatment

PubMed Central

Hales, Craig M.; Heilig, Charles M.; Chaisson, Richard; Leung, Chi Chiu; Chang, Kwok Chiu; Goldberg, Stefan V.; Gordin, Fred; Johnson, John L.; Muzanyi, Grace; Saukkonen, Jussi; Vernon, Andrew; Villarino, M. Elsa

2013-01-01

Rationale: The lack of consistent associations between clinical outcomes and microbiological responses to therapy for some infectious diseases has raised questions about the adequacy of microbiological endpoints for tuberculosis treatment trials. Objectives: To evaluate the association between symptoms and microbiological response to tuberculosis treatment. Methods: We performed a retrospective analysis of four clinical trials in which participants had culture-positive tuberculosis, standardized symptom assessment, and follow-up mycobacterial cultures. Two trials (studies 22 and 23) followed participants to identify recurrent tuberculosis; participants in studies 27 and 28 were only followed to treatment completion. Measurements and Main Results: This analysis included 1,978 participants; 39 (2.0%) had culture-confirmed treatment failure, and 75 (3.9%) had culture-confirmed recurrence. Productive cough was associated with indices of increased mycobacterial burden at diagnosis (acid-fast smear grade, severity of radiographic abnormalities). Fever and sweats improved rapidly with treatment, whereas productive cough decreased more slowly and was present in 20% of visits after treatment completion. During treatment, study participants with productive cough more often had concurrent culture positivity compared with those without productive cough (studies 22 and 23: adjusted odds ratio, 1.80; 95% confidence interval [CI], 1.33–2.44). Finally, symptoms during the latter part of treatment and follow-up were associated with culture-confirmed treatment failure and recurrence in studies 22 and 23 (for cough: adjusted hazard ratio, 2.07; 95% CI, 1.23–3.49; for fever: adjusted hazard ratio, 5.05; 95% CI, 2.76–9.19). Conclusions: There are consistent relationships between symptoms and microbiological indices of tuberculosis, including measures of mycobacterial burden at baseline, culture positivity during treatment, and time to culture-confirmed treatment failure and recurrence. PMID:23509328

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

PubMed

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

2013-06-01

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

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

PubMed

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

2018-06-01

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

Cheesecake: a potential vehicle for salmonellosis?

PubMed

Hao, Y Y; Scouten, A J; Brackett, R E

1999-01-01

This study was conducted to investigate the potential hazard of Salmonella Enteritidis surviving during the preparation and baking of cheesecake. Batters prepared with standard- and reduced-fat ingredients were inoculated with a 5-strain cocktail of S. Enteritidis (10 and 10(6) CFU/g) and were then baked according to a typical cheesecake recipe. After baking, the cheesecakes were refrigerated overnight before the survival of S. Enteritidis was determined either by direct plating or after enrichment. Samples (approximately 25 g each) were aseptically cut from the center, mid (6.35 cm from edge), and side (2.54 cm from edge) area of each cake for microbiological analysis. Proximate compositions (fat, moisture, protein, ash, pH, and water activity) of both raw batter and final baked cheesecakes were also determined. S. Enteritidis was able to survive baking of cheesecake when batter was inoculated with a high population (10(6) CFU/g) of S. Enteritidis regardless of whether standard-or reduced-fat ingredients were used. Three of nine standard- and four of nine reduced-fat cheesecake samples contained viable S. Enteritidis. In addition, one sample contained viable S. Enteritidis population detectable by direct plating (approximately 10 CFU per g of cake). This sample was taken from the center of a standard-fat cheesecake that was inoculated with a high population (10(6) CFU/g) of S. Enteritidis. Results of this study suggest that cheesecake prepared with eggs of low microbiological quality or cheesecake improperly handled or stored could serve as a vehicle for salmonellosis.

Comparison of two filtration-elution procedures to improve the standard methods ISO 10705-1 & 2 for bacteriophage detection in groundwater, surface water and finished water samples.

PubMed

Helmi, K; Jacob, P; Charni-Ben-Tabassi, N; Delabre, K; Arnal, C

2011-09-01

To select a reliable method for bacteriophage concentration prior detection by culture from surface water, groundwater and drinking water to enhance the sensitivity of the standard methods ISO 10705-1 & 2. Artificially contaminated (groundwater and drinking water) and naturally contaminated (surface water) 1-litre samples were processed for bacteriophages detection. The spiked samples were inoculated with about 150 PFU of F-specific RNA bacteriophages and somatic coliphages using wastewater. Bacteriophage detection in the water samples was achieved using the standard method without and with a concentration step (electropositive Anodisc membrane or a pretreated electronegative Micro Filtration membrane, MF). For artificially contaminated matrices (drinking and ground waters), recovery rates using the concentration step were superior to 70% whilst analyses without concentration step mainly led to false negative results. Besides, the MF membrane presented higher performances compared with the Anodisc membrane. The concentration of a large volume of water (up to one litre) on a filter membrane avoids false negative results obtained by direct analysis as it allows detecting low number of bacteriophages in water samples. The addition of concentration step before applying the standard method could be useful to enhance the reliability of bacteriophages monitoring in water samples as bio-indicators to highlight faecal pollution. © No claim to French Government works. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

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.

ATP bioluminescence: Surface hygiene monitoring in milk preparation room of neonatal intensive care unit

NASA Astrophysics Data System (ADS)

Mohamad, Mahirah; Ishak, Shareena; Jaafar, Rohana; Sani, Norrakiah Abdullah

2018-04-01

ATP Bioluminescence application and standard microbiological analyses were used to evaluate the cleanliness of milk contact surfaces and non-milk contact surfaces in milk preparation room of neonatal intensive care unit (NICU) of Universiti Kebangsaan Malaysia Medical Centre (UKMMC). A total of 44 samples including the breast pump, milk bottle, milk bottle screw top and screw ring, teats, measuring cups, waterless warmer, refrigerator, dishwasher and pasteurizer inner wall were tested on May 2017. 3M Clean and Trace Hygiene Monitoring (UXL100 ATP Test swabs) and the bioluminescence reader Clean-Trace NG Luminometer (3M) were used to measure the Relative Light Unit (RLU) and microbiological analysis using 3M Quick Swab and 3MTM PetrifilmTM for enumeration of aerobic count, Staphylococcus aureus, Enterobacteriaceae, coliform and detection of Escherichia coli (CFU /100cm2 or utensil/item). The RLU values were from 11 to 194 and passed the ATP benchmark for intensive care unit (ICU), < 250 RLU as recommended. Aerobic colony count was only found in waterless warmer (0.05±0.01 mean log CFU/warmer). None of S. aureus, Enterobacteriaceae, E. coli and coliform was detected in all samples. A weak correlation was found between bioluminescence measurements RLU and the microbiological analysis (CFU). However, the use of ATP bioluminescence in monitoring milk preparation room cleanliness can be a useful method for assessing rapidly the surface hygiene as well as to verify the Sanitation Standard Operating Procedure (SSOP) prior to implementation of Hazard Analysis and Critical Control Points (HACCP) in milk preparation room.

Improvement of microbiological qualities of namphrik by gamma irradiation

NASA Astrophysics Data System (ADS)

Chahorm, K.; Neramitmansook, N.; Kongsang, N.; Ko, J.

2017-06-01

Twenty samples of Namphrik from commercial markets were evaluated the microbiological qualities. It was found that 15 samples did not meet Thai Community Product Standard. The total plate count (TPC) in 15 samples were higher than the maximum limits (1.60x104 - 4.4x105 CFU/g). In addition, the other pathogens were higher than the maximum limits such as B. cereus in 11 samples (2.10x103 - 6.10x104 CFU/g) S. aureus in 2 samples (15 - 40 CFU/g) Clostridium perfringens in 4 samples (1.00x102 - 8.8x103 CFU/g) and yeast&mold in 9 samples (3.00 x102 - 9.00x103 CFU/g). To reduce TPC and pathogenic bacteria, the gamma irradiation were applied at 3.28- 4.43 kGy. The results indicated that the irradiation can reduce the TPC around 1.2 - 3.9 log cycles and eliminate pathogens bacteria in the product to make all of 15 samples qualified to the standard. The sensory evaluation was conducted in Namphrik Narok by using difference from control test to determine whether the consumers can differentiate between the non-irradiated and irradiated. The result showed that the consumers can significantly differentiate the color, odor and flavor (p<0.05). However, the preference test showed that there was no significant preferences at p>0.05. Both non-irradiated and irradiated were scored at 6.4 (slightly to moderately preference). Thus the gamma irradiation can be used as a tool to improve the microbiological qualities of the Namphrik Narok product without effecting the consumer preference.

Semiquantitative Culture Analysis during Therapy for Mycobacterium avium Complex Lung Disease.

PubMed

Griffith, David E; Adjemian, Jennifer; Brown-Elliott, Barbara A; Philley, Julie V; Prevots, D Rebecca; Gaston, Christopher; Olivier, Kenneth N; Wallace, Richard J

2015-09-15

Microbiologically based criteria such as sputum culture conversion to negative have traditionally been used to define treatment success for mycobacterial diseases. There are, however, limited data regarding whether nontuberculous mycobacterial sputum culture conversion or semiquantitative culture analysis correlates with subjective or nonmicrobiologic objective indices of treatment response. To determine whether a semiquantitative mycobacterial culture scale correlated with clinical disease status and was predictive of long-term sputum mycobacterial culture conversion to negative in a cohort of patients with nodular/bronchiectatic Mycobacterium avium complex lung disease undergoing therapy. One hundred and eighty patients undergoing standard macrolide-based therapy for M. avium complex lung disease were monitored at standard frequent intervals with symptomatic, radiographic, and microbiologic data collected, including semiquantitative mycobacterial culture analysis. Analyses were used to evaluate clinical and microbiologic predictors of long-term sputum conversion to culture negative. After 12 months of therapy, 148 (82%) patients had sputum conversion to culture negative. Baseline semiquantitative sputum culture scores did not differ between patients with sputum conversion and those without. The change in sputum culture semiquantitative score from baseline to Month 3 was highly predictive of subsequent sputum long-term conversion status indicative of treatment success, as was improvement in cough, and especially early radiographic improvement. Early semiquantitative sputum agar plate culture results can be used to predict symptomatic and radiographic improvement as well as long-term sputum culture conversion to negative in this population. We suggest that semiquantitative sputum culture scores can be a useful tool for evaluating new nontuberculous mycobacterial lung disease therapies.

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%).

[Reflection of estimating postmortem interval in forensic entomology and the Daubert standard].

PubMed

Xie, Dan; Peng, Yu-Long; Guo, Ya-Dong; Cai, Ji-Feng

2013-08-01

Estimating postmortem interval (PMI) is always the emphasis and difficulty in forensic practice. Forensic entomology plays a significant indispensable role. Recently, the theories and technologies of forensic entomology are increasingly rich. But many problems remain in the research and practice. With proposing the Daubert standard, the reliability and accuracy of estimation PMI by forensic entomology need more demands. This review summarizes the application of the Daubert standard in several aspects of ecology, quantitative genetics, population genetics, molecular biology, and microbiology in the practice of forensic entomology. It builds a bridge for basic research and forensic practice to provide higher accuracy for estimating postmortem interval by forensic entomology.

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

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.

Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments.

PubMed

Sinha, Pallavi; Gupta, Anamika; Prakash, Pradyot; Anupurba, Shampa; Tripathi, Rajneesh; Srivastava, G N

2016-03-12

Control of the global burden of tuberculosis is obstructed due to lack of simple, rapid and cost effective diagnostic techniques that can be used in resource poor-settings. To facilitate the early diagnosis of TB directly from clinical specimens, we have standardized and validated the use of nested multiplex PCR, targeting gene fragments IS6110, MTP40 and 32kD α-antigen encoding genes specific for Mycobacterium tuberculosis complex and non-tubercular mycobacteria (NTM), in comparison to smear microscopy, solid culture and single step multiplex PCR. The results were evaluated in comparison to a composite reference standard (CRS) comprising of microbiological results (smear and culture), clinical, radiological and cytopathological findings, clinical treatment and response to anti-tubercular therapy. The nested multiplex PCR (nMPCR) assay was evaluated to test its utility in 600 (535 pulmonary and 65 extra-pulmonary specimens) clinically suspected TB cases. All specimens were processed for smear, culture, single step multiplex PCR and nested multiplex PCR testing. Out of 535 screened pulmonary and 65 extra-pulmonary specimens, 329 (61.5%) and 19 (29.2%) cases were culture positive for M. tuberculosis. Based on CRS, 450 patients had "clinical TB" (definitive-TB, probable-TB and possible-TB). Remaining 150 were confirmed "non-TB" cases. For culture, the sensitivity was low, 79.3% for pulmonary and 54.3% for extra-pulmonary cases. The sensitivity and specificity results for nMPCR test were evaluated taken composite reference standard as a gold standard. The sensitivity of the nMPCR assay was 97.1% for pulmonary and 91.4% for extra-pulmonary TB cases with specificity of 100% and 93.3% respectively. Nested multiplex PCR using three gene primers is a rapid, reliable and highly sensitive and specific diagnostic technique for the detection and differentiation of M. tuberculosis complex from NTM genome and will be useful in diagnosing paucibacillary samples. Nested multiplex PCR assay was found to be better than single step multiplex PCR for assessing the diagnosis of TB.

Assessment of Microbiology Students’ Progress With an Audience Response System

PubMed Central

Chaudhry, M. Ahmad

2011-01-01

The development of new approaches to teaching of large lecture courses is needed. Today’s classroom has a wide range of students including high-achieving motivated learners, students struggling to understand basic concepts, and learning-challenged students. Many of these students can be lost in large classes under the shadow of the high-achieving extroverted students who dominate classroom question-and-answer sessions. Measuring a student’s understanding and achievement of content standards becomes difficult until an assessment has been done. To close this gap, an audience response system was introduced in an introductory Principles of Microbiology course. This technology specifically addressed the goal of individualizing instruction to the needs of the students. The evaluation of this project indicated an overall positive impact on student learning. PMID:23653765

7 CFR 58.648 - Microbiological requirements for ice cream.

Code of Federal Regulations, 2012 CFR

2012-01-01

... requirements for ice cream. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count, and shall contain not more than 10 coliform organisms per gram for plain and not more than 20 coliform per gram in chocolate, fruit, nut or other flavors in three out of...

7 CFR 58.648 - Microbiological requirements for ice cream.

Code of Federal Regulations, 2013 CFR

2013-01-01

... requirements for ice cream. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count, and shall contain not more than 10 coliform organisms per gram for plain and not more than 20 coliform per gram in chocolate, fruit, nut or other flavors in three out of...

7 CFR 58.648 - Microbiological requirements for ice cream.

Code of Federal Regulations, 2011 CFR

2011-01-01

... requirements for ice cream. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count, and shall contain not more than 10 coliform organisms per gram for plain and not more than 20 coliform per gram in chocolate, fruit, nut or other flavors in three out of...

7 CFR 58.648 - Microbiological requirements for ice cream.

Code of Federal Regulations, 2014 CFR

2014-01-01

... requirements for ice cream. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count, and shall contain not more than 10 coliform organisms per gram for plain and not more than 20 coliform per gram in chocolate, fruit, nut or other flavors in three out of...

7 CFR 58.648 - Microbiological requirements for ice cream.

Code of Federal Regulations, 2010 CFR

2010-01-01

... requirements for ice cream. The finished product shall contain not more than 50,000 bacteria per gram as determined by the standard plate count, and shall contain not more than 10 coliform organisms per gram for plain and not more than 20 coliform per gram in chocolate, fruit, nut or other flavors in three out of...

Generic E. coli levels in surface and nontraditional irrigation water in the mid Atlantic in relation to FSMA water quality standards: A CONSERVE study

USDA-ARS?s Scientific Manuscript database

Introduction: The use of surface (pond and river) and nontraditional (reclaimed wastewater, produce wash water) irrigation water (SNIW) could reduce stress on ground water resources. However, it is essential to understand how these irrigation sources may influence the microbiological safety of fresh...

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.

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

PubMed

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

2016-07-01

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

Presence and resistance of Streptococcus agalactiae in vaginal specimens of pregnant and adult non-pregnant women and association with other aerobic bacteria.

PubMed

Numanović, Fatima; Smajlović, Jasmina; Gegić, Merima; Delibegović, Zineta; Bektaš, Sabaheta; Halilović, Emir; Nurkić, Jasmina

2017-02-01

Aim To determine the prevalence rate and resistance profile of Streptococcus agalactiae (S. agalactiae) in vaginal swabs of pregnant and adult non-pregnant women in the Tuzla region, Bosnia and Herzegovina (B&H), as well as its association with other aerobic bacteria. Methods This prospective study included 200 women, 100 pregnant and 100 adult non-pregnant. The research was conducted at the Institute of Microbiology, University Clinical Center Tuzla from October to December 2015. Standard aerobic microbiological techniques were used for isolation and identification of S. agalactiae and other aerobic bacteria. Antimicrobial susceptibility was determined by the disk diffusion and microdilution method(VITEK 2/AES instrument). Results Among 200 vaginal swabs, 17 (8.50%) were positive for S. agalactiae, e. g., 7% (7/100) of pregnant and 10% (10/100) of adult non-pregnant women. In the pregnant group, 71.4% (5/7) of S. agalactiae isolates were susceptible to clindamycin and 85.7%(6/7) to erythromycin. In the adult non-pregnant group, only resistance to clindamycin was observed in one patient (1/10; 10%). S. agalactiae as single pathogen was isolated in 57.14% (4/7) of pregnant and 60% (6/10) of adult non-pregnant S. agalactiae positive women. In mixed microbial cultures S. agalactiae was most frequently associated with Enterococcus faecalis and Escherichia coli. Conclusion The rate of S. agalactiae positive women in the population of pregnant and adult non-pregnant women of Tuzla Canton, B&H is comparable with other European countries. Large studies are needed to develop a common national strategy for the prevention of S. agalactiae infection in B&H, especially during pregnancy. Copyright© by the Medical Assotiation of Zenica-Doboj Canton.

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

PubMed

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

2006-09-01

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

Laboratory-acquired infections of Salmonella enterica serotype Typhi in South Africa: phenotypic and genotypic analysis of isolates.

PubMed

Smith, Anthony Marius; Smouse, Shannon Lucrecia; Tau, Nomsa Pauline; Bamford, Colleen; Moodley, Vineshree Mischka; Jacobs, Charlene; McCarthy, Kerrigan Mary; Lourens, Adré; Keddy, Karen Helena

2017-09-29

Workers in clinical microbiology laboratories are exposed to a variety of pathogenic microorganisms. Salmonella species is among the most commonly reported bacterial causes of laboratory-acquired infections. We report on three cases of laboratory-acquired Salmonella enterica serotype Typhi (Salmonella Typhi) infection which occurred over the period 2012 to 2016 in South Africa. Laboratory investigation included phenotypic and genotypic characterization of isolates. Phenotypic analysis included standard microbiological identification techniques, serotyping and antimicrobial susceptibility testing. Genotypic analysis included the molecular subtyping methodologies of pulsed-field gel electrophoresis analysis, multilocus sequence typing and whole-genome sequencing (WGS); with WGS data analysis including phylogenetic analysis based upon comparison of single nucleotide polymorphism profiles of isolates. All cases of laboratory-acquired infection were most likely the result of lapses in good laboratory practice and laboratory safety. The following critical issues were highlighted. There was misdiagnosis and misreporting of Salmonella Typhi as nontyphoidal Salmonella by a diagnostic laboratory, with associated public health implications. We highlight issues concerning the importance of accurate fluoroquinolone susceptibility testing and interpretation of results according to updated guidelines. We describe potential shortcomings of a single disk susceptibility screening test for fluoroquinolone susceptibility and suggest that confirmatory minimum inhibitory concentration testing should always be performed in cases of invasive Salmonella infections. These antimicrobial susceptibility testing issues resulted in inappropriate ciprofloxacin therapy which may have been responsible for failure in clearance of pathogen from patients. Salmonella Typhi capsular polysaccharide vaccine was not protective in one case, possibly secondarily to a faulty vaccine. Molecular subtyping of isolates proved effective to investigate the genetic relatedness of isolates. Molecular subtyping data interpreted together with epidemiological data allowed us to pinpoint the most likely sources for our cases of laboratory-acquired infection.

Generation and composition of medical wastes from private medical microbiology laboratories.

PubMed

Komilis, Dimitrios; Makroleivaditis, Nikolaos; Nikolakopoulou, Eftychia

2017-03-01

A study on the generation rate and the composition of solid medical wastes (MW) produced by private medical microbiology laboratories (PMML) was conducted in Greece. The novelty of the work is that no such information exists in the literature for this type of laboratories worldwide. Seven laboratories were selected with capacities that ranged from 8 to 88 examinees per day. The study lasted 6months and daily recording of MW weights was done over 30days during that period. The rates were correlated to the number of examinees, examinations and personnel. Results indicated that on average 35% of the total MW was hazardous (infectious) medical wastes (IFMW). The IFMW generation rates ranged from 11.5 to 32.5g examinee -1 d -1 while an average value from all 7 labs was 19.6±9.6g examinee -1 d -1 or 2.27±1.11g examination -1 d -1 . The average urban type medical waste generation rate was 44.2±32.5g examinee -1 d -1 . Using basic regression modeling, it was shown that the number of examinees and examinations can be predictors of the IFMW generation, but not of the urban type MW generation. The number of examinations was a better predictor of the MW amounts than the number of examinees. Statistical comparison of the means of the 7PMML was done with standard ANOVA techniques after checking the normality of the data and after doing the appropriate transformations. Based on the results of this work, it is approximated that 580 tonnes of infectious MW are generated annually by the PMML in Greece. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for the identification of Candida species.

PubMed

Lacroix, C; Gicquel, A; Sendid, B; Meyer, J; Accoceberry, I; François, N; Morio, F; Desoubeaux, G; Chandenier, J; Kauffmann-Lacroix, C; Hennequin, C; Guitard, J; Nassif, X; Bougnoux, M-E

2014-02-01

Candida spp. are responsible for severe infections in immunocompromised patients and those undergoing invasive procedures. The accurate identification of Candida species is important because emerging species can be associated with various antifungal susceptibility spectra. Conventional methods have been developed to identify the most common pathogens, but have often failed to identify uncommon species. Several studies have reported the efficiency of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of clinically relevant Candida species. In this study, we evaluated two commercially available MALDI-TOF systems, Andromas™ and Bruker Biotyper™, for Candida identification in routine diagnosis. For this purpose, we investigated 1383 Candida isolates prospectively collected in eight hospital laboratories during routine practice. MALDI-TOF MS results were compared with those obtained using conventional phenotypic methods. Analysis of rDNA gene sequences with internal transcribed regions or D1-D2 regions is considered the reference standard for identification. Both MALDI-TOF MS systems could accurately identify 98.3% of the isolates at the species level (1359/1383 for Andromas™; 1360/1383 for Bruker Biotyper™) vs. 96.5% for conventional techniques. Furthermore, whereas conventional methods failed to identify rare or emerging species, these were correctly identified by MALDI-TOF MS. Both MALDI-TOF MS systems are accurate and cost-effective alternatives to conventional methods for mycological identification of clinically relevant Candida species and should improve the diagnosis of fungal infections as well as patient management. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Prevention of artificial dental plaque formation in vitro by plant extracts.

PubMed

Smullen, J; Finney, M; Storey, D M; Foster, H A

2012-10-01

A number of previous studies have shown that plant extracts can inhibit formation of dental plaque. The ability of extracts of Rosmarinus officianalis L., Salvia officianalis L., unfermented cocoa, red grape seed and green tea to inhibit plaque bacteria, glucosyltransferase activity, glucan and plaque formation in an in vitro model using bovine teeth was examined. The antimicrobial activity of the plant extracts against oral bacteria was determined using a standard susceptibility agar dilution technique. Inhibition of growth and acid production from glucose and sucrose by Streptococcus mutans in liquid culture was investigated. Prevention of plaque formation on bovine teeth initiated by Strep. mutans was studied using an artificial mouth. The plant extracts inhibited the growth of oral bacteria and prevented acid production by Strep. mutans. Extracts inhibited glucosyltransferase activity and glucan production and inhibited adhesion to glass. Extracts of R. officianalis L. and S. officianalis L. at 0·25 mg ml(-1) reduced plaque growth by >80%. Green tea extract completely inhibited plaque formation but resulted in a greenish discolouration of the teeth which could not be removed by scrubbing. The plant extracts, particularly those from R. officianalis L. and S. officianalis L., inhibited glucosyltranferase activity, glucan production and plaque formation in vitro. The results suggest that the extracts of R. officianalis L. and S. officianalis L. may be useful as antiplaque agents in foods and dental preparations. Bovine teeth can be used as an alternative to hydroxyapatite for studies of plaque formation, but they need to be carefully sterilized before use. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

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…

Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.

PubMed

Tagini, F; Greub, G

2017-11-01

In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.

[Clinical and microbiological profiles of anti-personnel mine injuries in the Medellín area of northwestern Colombia].

PubMed

Restrepo, Ana Cristina; Lópe, Jaime Alberto

2010-01-01

The counts of antipersonnel mine injuries are increasing worldwide, but in Colombia, documentation of the clinical and microbiological characteristics of these lesions is lacking. To determine the clinical and microbiological characteristics of antipersonnel mine injuries for patients admitted for treatment during a 2 and a half year period. The medical records were reviewed for 151 patients hospitalized with injuries caused by antipersonnel mines. The admissions occurred between January 1st 2003 and July 31st 2005 at a highly specialized university hospital, the Pablo Tobón Uribe Hospital in Medellín, Colombia. All patients were male, mean age 24 years old, and all but 8 of them military. The length of stay averaged 20 days and hospital mortality 4%. Multiple lesions occurred in 66.8% of the cases, 88.0% of the injuries affected the limbs, and amputations were mandated in 52.3% of patients. A total of 313 specimens were cultured--68.7% of cultures were positive, and 386 microorganisms were identified. The most prevalent bacteria in the first culture were Pseudomonas aeruginosa and Escherichia coli. In subsequent cultures, P. aeruginosa and Enterococcus faecalis appeared. Most of the patients (93.4%) received standard antibiotic therapy, ampicillin/sulbactam. The clinical and microbiological characteristics of patients were related to their military occupation and the complex injuries produced by the mines. Knowledge of these characteristics will permit the design of better management strategies and empirical treatments.

Microbiological quality of Argentinian paprika.

PubMed

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

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

Microbiological Quality of Seafood Marketed in Taiwan.

PubMed

Wong, Hin-Chung; Jiang, Huai-Yu; Lin, Hsu-Yang; Wang, Yu-Ting

2015-11-01

Seafood is often associated with foodborne illnesses, and Vibrio parahaemolyticus is the most common pathogen implicated in outbreaks in Taiwan. In this study, the microbiological quality of 300 raw or mixed ready-to-eat (RTE) and other cooking-needed seafood samples was examined. The total aerobic and coliform counts of the RTE samples were significantly higher than those of other cooking-needed samples. On average, 55.8 and 29.7% of the RTE samples failed to meet the local microbiological standards for total aerobic (5 log CFU/g) and coliform (3 log most probable number [MPN] per g), counts respectively; the corresponding percentages for the RTE samples from Taipei City were 9.1 and 18.2%, respectively. The total aerobic and coliform counts in the RTE samples from supermarkets and chain restaurants were significantly lower than those from traditional restaurants. The Vibrio species were more frequently identified in the cooking-needed samples than in RTE samples. Low incidences of V. parahaemolyticus (1.4%), V. vulnificus (1.9%), and V. cholerae (0%) were detected in most RTE samples. High densities of V. parahaemolyticus and V. vulnificus (1,200 MPN/g) were detected in a few RTE samples, only one of which contained toxigenic (tdh(+)) V. parahaemolyticus. The results of this investigation reveal that better hygiene of seafood providers such as chain restaurants, supermarkets, and traditional restaurants in Taipei City would effectively improve the microbiological quality of the seafood. The results will facilitate the establishment of measures for controlling the risks associated with seafood in Taiwan.

Clinical accuracy of point-of-care urine culture in general practice.

PubMed

Holm, Anne; Cordoba, Gloria; Sørensen, Tina Møller; Jessen, Lisbeth Rem; Frimodt-Møller, Niels; Siersma, Volkert; Bjerrum, Lars

2017-06-01

To assess the clinical accuracy (sensitivity (SEN), specificity (SPE), positive predictive value and negative predictive value) of two point-of-care (POC) urine culture tests for the identification of urinary tract infection (UTI) in general practice. Prospective diagnostic accuracy study comparing two index tests (Flexicult™ SSI-Urinary Kit or ID Flexicult™) with a reference standard (urine culture performed in the microbiological department). General practice in the Copenhagen area patients. Adult female patients consulting their general practitioner with suspected uncomplicated, symptomatic UTI. (1) Overall accuracy of POC urine culture in general practice. (2) Individual accuracy of each of the two POC tests in this study. (3) Accuracy of POC urine culture in general practice with enterococci excluded, since enterococci are known to multiply in boric acid used for transportation for the reference standard. (4) Accuracy based on expert reading of photographs of POC urine cultures performed in general practice. Standard culture performed in the microbiological department was used as reference standard for all four measures. Twenty general practices recruited 341 patients with suspected uncomplicated UTI. The overall agreement between index test and reference was 0.76 (CI: 0.71-0.80), SEN 0.88 (CI: 0.83-0.92) and SPE 0.55 (CI: 0.46-0.64). The two POC tests produced similar results individually. Overall agreement with enterococci excluded was 0.82 (0.77-0.86) and agreement between expert readings of photographs and reference results was 0.81 (CI: 0.76-0.85). POC culture used in general practice has high SEN but low SPE. Low SPE could be due to both misinterpretation in general practice and an imperfect reference standard. Registration number: ClinicalTrials.gov NCT02323087.

Differentiation of Candida albicans, Candida glabrata, and Candida krusei by FT-IR and chemometrics by CHROMagar™ Candida.

PubMed

Wohlmeister, Denise; Vianna, Débora Renz Barreto; Helfer, Virginia Etges; Calil, Luciane Noal; Buffon, Andréia; Fuentefria, Alexandre Meneghello; Corbellini, Valeriano Antonio; Pilger, Diogo André

2017-10-01

Pathogenic Candida species are detected in clinical infections. CHROMagar™ is a phenotypical method used to identify Candida species, although it has limitations, which indicates the need for more sensitive and specific techniques. Infrared Spectroscopy (FT-IR) is an analytical vibrational technique used to identify patterns of metabolic fingerprint of biological matrixes, particularly whole microbial cell systems as Candida sp. in association of classificatory chemometrics algorithms. On the other hand, Soft Independent Modeling by Class Analogy (SIMCA) is one of the typical algorithms still little employed in microbiological classification. This study demonstrates the applicability of the FT-IR-technique by specular reflectance associated with SIMCA to discriminate Candida species isolated from vaginal discharges and grown on CHROMagar™. The differences in spectra of C. albicans, C. glabrata and C. krusei were suitable for use in the discrimination of these species, which was observed by PCA. Then, a SIMCA model was constructed with standard samples of three species and using the spectral region of 1792-1561cm -1 . All samples (n=48) were properly classified based on the chromogenic method using CHROMagar™ Candida. In total, 93.4% (n=45) of the samples were correctly and unambiguously classified (Class I). Two samples of C. albicans were classified correctly, though these could have been C. glabrata (Class II). Also, one C. glabrata sample could have been classified as C. krusei (Class II). Concerning these three samples, one triplicate of each was included in Class II and two in Class I. Therefore, FT-IR associated with SIMCA can be used to identify samples of C. albicans, C. glabrata, and C. krusei grown in CHROMagar™ Candida aiming to improve clinical applications of this technique. Copyright © 2017 Elsevier B.V. All rights reserved.

Quality of blood culture testing - a survey in intensive care units and microbiological laboratories across four European countries

PubMed Central

2013-01-01

Introduction Blood culture (BC) testing before initiation of antimicrobial therapy is recommended as a standard of care in international sepsis guidelines and has been shown to reduce intensive care unit (ICU) stay, antibiotic use, and costs in hospitalized patients. Whereas microbiological laboratory practice has been highly standardized, shortfalls in the preanalytic procedures in the ICU (that is indication, time-to-incubation, blood volume and numbers of BC sets) have a significant effect on the diagnostic yield. The objective of this study was to gain insights into current practices regarding BC testing in intensive care units. Methods Qualitative survey, data collection by 138 semi-structured telephone interviews in four European countries (Italy, UK, France and Germany) between September and November 2009 in 79 clinical microbiology laboratories (LABs) and 59 ICUs. Results Whereas BC testing is expected to remain the gold standard for sepsis diagnostics in all countries, there are substantial differences regarding preanalytic procedures. The decision to launch BC testing is carried out by physicians vs. ICU nurses in the UK in 92 vs. 8%, in France in 75 vs. 25%, in Italy in 88 vs. 12% and in Germany in 92 vs. 8%. Physicians vs. nurses collect BCs in the UK in 77 vs. 23%, in France in 0 vs. 100%, in Italy in 6 vs. 94% and in Germany in 54 vs. 46%. The mean time from blood collection to incubation in the UK is 2 h, in France 3 h, in Italy 4 h, but 20 h in German remote LABs (2 h in in-house LABs), due to the large number of remote nonresident microbiological laboratories in Germany. There were major differences between the perception of the quality of BC testing between ICUs and LABs. Among German ICU respondents, 62% reported that they have no problems with BC testing, 15% reported time constraints, 15% cost pressure, and only 8% too long time to incubation. However, the corresponding LABs of these German ICUs reported too many false positive results due to preanalytical contaminations (49%), insufficient numbers of incoming BC sets (47%), long transportation time (41%) or cost pressure (18%). Conclusions There are considerable differences in the quality of BC testing across European countries. In Germany, time to incubation is a considerable problem due to the increasing number of remote LABs. This is a major issue of concern to physicians aiming to implement sepsis guidelines in the ICUs. PMID:24144084

Microbial Impact on Success of Human Exploration Missions

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Clinical and economic evaluation of BBL CHROMagar Salmonella (CHROMSal) versus subculture after selenite broth enrichment to CHROMSal and Hektoen enteric agars to detect enteric Salmonella in a large regional microbiology laboratory.

PubMed

Church, Deirdre L; Emshey, Diana; Lloyd, Tracie; Pitout, Johann

2010-09-01

Stool culture for enteric pathogens is one of the most labor-intensive clinical microbiology procedures. Direct plating of stool to BBL CHROMagar Salmonella (CHROMSal) (BD Diagnostics, Sparks, MD) versus subculture after selenite broth enrichment (Sel) to CHROMSal (Sel-CHROMSal) and Hektoen enteric agar (Sel-Hek) (PML Microbiologicals, Eugene, OR) to detect Salmonella were compared. The number of colony picks and biochemical/serotyping tests per plate was recorded. A cost comparison was done. Fifty-one of 2999 (1.7%) stools yielded Salmonella sp., and 80% of isolates grew on CHROMSal by 24 h. CHROMSal demonstrated much less false-positive growth compared to Sel-Hek (P < 0.0001), which reduced biochemical and serotyping tests by 85% and 20%, respectively. Sel-CHROMSal and CHROMSal versus Sel-Hek improved enteric Salmonella detection when compared to a true positive "gold standard" (i.e., recovery by any culture method) with a sensitivity, specificity, positive predictive value, and negative predictive value of 100% and 94.12%, 100% and 99.97%, 100% and 97.96%, and 100% and 99.90%, respectively. CHROMSal use would result in substantial cost and labor savings.

Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

PubMed Central

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

2013-01-01

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

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

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.