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.

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.

STANDARDIZATION AND VALIDATION OF MICROBIOLOGICAL METHODS FOR EXAMINATION OF BIOSOLIDS

EPA Science Inventory

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

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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.

Standard on microbiological management of fluids for hemodialysis and related therapies by the Japanese Society for Dialysis Therapy 2008.

PubMed

Kawanishi, Hideki; Akiba, Takashi; Masakane, Ikuto; Tomo, Tadashi; Mineshima, Michio; Kawasaki, Tadayuki; Hirakata, Hideki; Akizawa, Tadao

2009-04-01

The Committee of Scientific Academy of the Japanese Society for Dialysis Therapy (JSDT) proposes a new standard on microbiological management of fluids for hemodialysis and related therapies. This standard is within the scope of the International Organization for Standardization (ISO), which is currently under revision. This standard is to be applied to the central dialysis fluid delivery systems (CDDS), which are widely used in Japan. In this standard, microbiological qualities for dialysis water and dialysis fluids are clearly defined by endotoxin level and bacterial count. The qualities of dialysis fluids were classified into three levels: standard, ultrapure, and online prepared substitution fluid. In addition, the therapeutic application of each dialysis fluid is clarified. Since high-performance dialyzers are frequently used in Japan, the standard recommends that ultrapure dialysis fluid be used for all dialysis modalities at all dialysis facilities. It also recommends that the dialysis equipment safety management committee at each facility should validate the microbiological qualities of online prepared substitution fluid.

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

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.

[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 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.

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.

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.

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

PubMed

Kristóf, Katalin; Pongrácz, Júlia

2016-04-01

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

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

PubMed

Blake, Christopher J

2007-09-01

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

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

PubMed

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

2007-01-01

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

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.

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.

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.

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 two-hour antibiotic susceptibility test by ATP-bioluminescence.

PubMed

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

2016-01-01

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

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

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.

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 continued value of disk diffusion for assessing antimicrobial susceptibility in clinical laboratories: report from the Clinical and Laboratory Standards Institute Methods Development and Standardization Working Group.

PubMed

Humphries, Romney M; Kircher, Susan; Ferrell, Andrea; Krause, Kevin M; Malherbe, Rianna; Hsiung, Andre; Burnham, C A

2018-05-09

Expedited pathways to antimicrobial agent approval by the United States Food and Drug Administration (FDA) have led to increased delays between drug approval and the availability of FDA-cleared antimicrobial susceptibility testing (AST) devices. Antimicrobial disks for use with disk diffusion testing are among the first AST devices available to clinical laboratories. However, many laboratories are reluctant to implement a disk diffusion method for a variety of reasons, including dwindling proficiency with this method, interruptions to laboratory workflow, uncertainty surrounding the quality and reliability of a disk diffusion test, and perceived need to report an MIC to clinicians. This mini-review provides a report from the Clinical and Laboratory Standards Institute Working Group on Methods Development and Standardization on the current standards and clinical utility of disk diffusion testing. Copyright © 2018 American Society for Microbiology.

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 ...

The Manufacture, Shipping and Receiving and Quality Control of Rodent Bedding Materials

NASA Technical Reports Server (NTRS)

Kraft, Lisbeth M.

1980-01-01

The criteria for rodent bedding and nesting materials are discussed. The literature is reviewed regarding sources of bedding materials, manufacturing methods, quality control, procedures (microbiological, physical and chemical), storage, methods, shipment, methods of use and disposal, current knowledge concerning bedding effects on animals as related to research and testing and legal aspects. Future needs, especially with respect to the promulgation of standards, also are addressed.

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

PubMed

Desjardins, Marc; Fleming, Christine Ann

2014-08-01

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

Microbiological 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.

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

PubMed

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

2012-01-01

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

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

[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.

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

USDA-ARS?s Scientific Manuscript database

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

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…

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.

[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.

[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.

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

PubMed

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

2018-05-01

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

Rapid test for the detection of hazardous microbiological material

NASA Astrophysics Data System (ADS)

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

2009-09-01

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

Measurement uncertainty of the EU methods for microbiological examination of red meat.

PubMed

Corry, Janet E L; Hedges, Alan J; Jarvis, Basil

2007-09-01

Three parallel trials were made of EU methods proposed for the microbiological examination of red meat using two analysts in each of seven laboratories within the UK. The methods involved determination of aerobic colony count (ACC) and Enterobacteriaceae colony count (ECC) using simulated methods and a freeze-dried standardised culture preparation. Trial A was based on a simulated swab test, Trial B a simulated meat excision test and Trial C was a reference test on reconstituted inoculum. Statistical analysis (ANOVA) was carried out before and after rejection of outlying data. Expanded uncertainty values (relative standard deviation x2) for repeatability and reproducibility, based on the log10 cfu/ml, on the ACC ranged from +/-2.1% to +/-2.7% and from +/-5.5% to +/-10.5%, respectively, depending upon the test procedure. Similarly for the ECC, expanded uncertainty estimates for repeatability and reproducibility ranged from +/-4.6% to +/-16.9% and from +/-21.6% to +/-23.5%, respectively. The results are discussed in relation to the potential application of the methods.

[Microbiological diagnosis of viral respiratory infections].

PubMed

Eiros, José M; Ortiz de Lejarazu, Raúl; Tenorio, Alberto; Casas, Inmaculada; Pozo, Francisco; Ruiz, Guillermo; Pérez-Breña, Pilar

2009-03-01

Acute respiratory infection is the most common disease occurring over a person's lifetime, with etiological variations determined mainly by age, environmental circumstances, the healthcare setting, and the underlying pathology. More than 200 different viruses distributed in six viral families have been implicated in the pathogenesis of respiratory tract infection. These facts are generating an increasing diagnostic demand that should be incorporated into the healthcare setting without delay. To meet this demand, the Spanish Society of Infectious Diseases and Clinical Microbiology has updated its Standard Procedure for the microbiological diagnosis of viral respiratory infection. This document contains an update primarily of infections caused by influenza viruses, and secondarily, infections due to other conventional and emerging respiratory viruses. In all cases, the methods for direct virological diagnosis (cell culture, and detection of antigens and nucleic acid) are reviewed, with special reference to techniques for molecular detection and genetic characterization.

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

PubMed

Slosárek, M; Kríz, B

2000-11-01

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

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

USDA-ARS?s Scientific Manuscript database

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

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.

[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.

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.

[Examination of drinking water used in livestock production. Microbiological and physico-chemical methods. Ready to use test kits in field experiments].

PubMed

Sassen, J

2000-08-01

Livestock health care service is very much involved and interested in surveillance of the drinking water as well. However, in order to examine the water immediately "on the fly", test kits have to be provided, which offer results comparable to these obtained in the laboratories according to official prescription. The German Army was confronted with a similar situation during the secently performed mission in crisis regions. At the early state of a mission usually laboratory equipment is not yet established. Therefore a set of test kits was compiled suitable for mobile microbiological examination of drinking water. This set was excessively examined comparison with reference methods. In conclusion it is shown, that the mobile set gains equal or even better results compared to those obtained according to legally prescribed standard procedures.

Microbial contamination of mobile phones in a health care setting in Alexandria, Egypt

PubMed Central

Selim, Heba Sayed; Abaza, Amani Farouk

2015-01-01

Aim: This study aimed at investigating the microbial contamination of mobile phones in a hospital setting. Methods: Swab samples were collected from 40 mobile phones of patients and health care workers at the Alexandria University Students’ Hospital. They were tested for their bacterial contamination at the microbiology laboratory of the High Institute of Public Health. Quantification of bacteria was performed using both surface spread and pour plate methods. Isolated bacterial agents were identified using standard microbiological methods. Methicillin-resistant Staphylococcus aureus was identified by disk diffusion method described by Bauer and Kirby. Isolated Gram-negative bacilli were tested for being extended spectrum beta lactamase producers using the double disk diffusion method according to the Clinical and Laboratory Standards Institute recommendations. Results: All of the tested mobile phones (100%) were contaminated with either single or mixed bacterial agents. The most prevalent bacterial contaminants were methicillin-resistant S. aureus and coagulase-negative staphylococci representing 53% and 50%, respectively. The mean bacterial count was 357 CFU/ml, while the median was 13 CFU/ml using the pour plate method. The corresponding figures were 2,192 and 1,720 organisms/phone using the surface spread method. Conclusions: Mobile phones usage in hospital settings poses a risk of transmission of a variety of bacterial agents including multidrug-resistant pathogens as methicillin-resistant S. aureus. The surface spread method is an easy and useful tool for detection and estimation of bacterial contamination of mobile phones. PMID:25699226

Competency Assessment of Microbiology Medical Laboratory Technologists in Ontario, Canada

PubMed Central

Fleming, Christine Ann

2014-01-01

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

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

PubMed

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

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

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

PubMed

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

2006-07-01

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

Comparative evaluation of chromogenic agar CM1046 and mFC agar for detection of E. coli and thermotolerant coliform bacteria from water samples.

PubMed

Wohlsen, T D

2011-08-01

The equivalence of Oxoid (CM 1046) Brilliance((TM)) E. coli/coliform selective agar to mFC agar, as used in the Australian/New Zealand Standard Method to detect thermotolerant coliforms and Escherichia coli in water samples, was assessed. A total of 244 water samples were analysed in parallel over a 5-month period. Sewage effluent samples (n = 131, sites = 43), freshwater (n = 62, sites = 18) and marine/brackish water samples (n = 51, sites = 23) were analysed. The Wilcoxon matched-pairs signed-ranks test showed a varying degree of statistical difference between the two methods. All matrices had a higher recovery in the trial method. Enterococci faecalis, Aeromonas spp. and Vibrio spp. did not grow on the CM1046 agar, and Pseudomonas aeruginosa and Enterobacter aerogenes were inhibited. The use of CM 1046 for the detection and enumeration of E. coli and thermotolerant coliforms in water samples is a suitable alternative to the AS/NZS Standard Method. The use of CM1046 agar was less labour intensive and time consuming, as no secondary confirmation steps were required. Confirmed results could be reported within 24 h of sample analysis, as compared to 48 h with the reference method. Public health concerns can be addressed in a more efficient manner. © 2011 Unitywater. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

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.

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.

[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.

Microbial contamination of mobile phones in a health care setting in Alexandria, Egypt.

PubMed

Selim, Heba Sayed; Abaza, Amani Farouk

2015-01-01

This study aimed at investigating the microbial contamination of mobile phones in a hospital setting. Swab samples were collected from 40 mobile phones of patients and health care workers at the Alexandria University Students' Hospital. They were tested for their bacterial contamination at the microbiology laboratory of the High Institute of Public Health. Quantification of bacteria was performed using both surface spread and pour plate methods. Isolated bacterial agents were identified using standard microbiological methods. Methicillin-resistant Staphylococcus aureus was identified by disk diffusion method described by Bauer and Kirby. Isolated Gram-negative bacilli were tested for being extended spectrum beta lactamase producers using the double disk diffusion method according to the Clinical and Laboratory Standards Institute recommendations. All of the tested mobile phones (100%) were contaminated with either single or mixed bacterial agents. The most prevalent bacterial contaminants were methicillin-resistant S. aureus and coagulase-negative staphylococci representing 53% and 50%, respectively. The mean bacterial count was 357 CFU/ml, while the median was 13 CFU/ml using the pour plate method. The corresponding figures were 2,192 and 1,720 organisms/phone using the surface spread method. Mobile phones usage in hospital settings poses a risk of transmission of a variety of bacterial agents including multidrug-resistant pathogens as methicillin-resistant S. aureus. The surface spread method is an easy and useful tool for detection and estimation of bacterial contamination of mobile phones.

Applicability of rapid and on-site measured enzyme activity for surface water quality monitoring in an agricultural catchment

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Farnleitner, Andreas H.; Sommer, Regina; Kumpan, Monika; Zessner, Matthias

2014-05-01

For the near real time and on-site detection of microbiological fecal pollution of water, the measurement of beta-D- Glucuronidase (GLUC) enzymatic activity has been suggested as a surrogate parameter and has been already successfully operated for water quality monitoring of ground water resources (Ryzinska-Paier et al. 2014). Due to possible short measure intervals of three hours, this method has high potential as a water quality monitoring tool. While cultivation based standard determination takes more than one working day (Cabral 2010) the potential advantage of detecting the GLUC activity is the high temporal measuring resolution. Yet, there is still a big gap of knowledge on the fecal indication capacity of GLUC (specificity, sensitivity, persistence, etc.) in relation to potential pollution sources and catchment conditions (Cabral 2010, Ryzinska-Paier et al. 2014). Furthermore surface waters are a big challenge for automated detection devices in a technical point of view due to the high sediment load during event conditions. This presentation shows results gained form two years of monitoring in an experimental catchment (HOAL) dominated by agricultural land use. Two enzymatic measurement devices are operated parallel at the catchment outlet to test the reproducibility and precision of the method. Data from continuous GLUC monitoring under both base flow and event conditions is compared with reference samples analyzed by standardized laboratory methods for fecal pollution detection (e.g. ISO 16649-1, Colilert18). It is shown that rapid enzymatic on-site GLUC determination can successfully be operated from a technical point of view for surface water quality monitoring under the observed catchment conditions. The comparison of enzyme activity with microbiological standard analytics reveals distinct differences in the dynamic of the signals during event conditions. Cabral J. P. S. (2010) "Water Microbiology. Bacterial Pathogens and Water" International Journal of Environmental Research and Public Health 7 (10): 3657-3703. Ryzinska-Paier, G., T. Lendenfeld, K. Correa, P. Stadler, A.P. Blaschke, R. L. Mach, H. Stadler, AKT Kirschner und A.H. Farnleitner (2014) A sensitive and robust method for automated on-line monitoring of enzymatic activities in water and water resources. Water Sci. Technol. in press

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

Rapid microbiological assay of serum vitamin B12 by electronic counter

PubMed Central

Stuart, J.; Sklaroff, S. A.

1966-01-01

A new method of measuring the growth of Lactobacillus leichmannii is reported. Its adoption for the estimation of serum vitamin B12 levels shortens the incubation period required to five hours at 45°C. The method is compared statistically with a standard method of estimation, requiring incubation at 37°C., by duplicate determinations on 106 hospital patients. The significance of the apparently decreased accuracy of the new method at low serum levels is discussed, and a re-appraisal of the optimum growth temperature of Lactobacillus leichmannii suggested. PMID:5904982

Rapid microbiological assay of serum vitamin B 12 by electronic counter.

PubMed

Stuart, J; Sklaroff, S A

1966-01-01

A new method of measuring the growth of Lactobacillus leichmannii is reported. Its adoption for the estimation of serum vitamin B(12) levels shortens the incubation period required to five hours at 45 degrees C. The method is compared statistically with a standard method of estimation, requiring incubation at 37 degrees C., by duplicate determinations on 106 hospital patients. The significance of the apparently decreased accuracy of the new method at low serum levels is discussed, and a re-appraisal of the optimum growth temperature of Lactobacillus leichmannii suggested.

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.

Microbiology of Fresh Comminuted Turkey Meat

DTIC Science & Technology

1976-04-12

823 Reprinted from J. Milk Food Technol. Vol. 39. No. 12. Pages 823-829 (December. 1976) Cooyright 1976, International Association of Milk , Food, and...most probable number (MPN) method (13). niacin, and riboflavin (29). Canadian officials have proposed microbial standards The literature contains...onto Mueller-Hinton agar plates containing 5% various retail markets in the San Francisco Bay Area. They were defibrinated sheep blood. Representative

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.

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

Performance characteristics of two bioassays and high-performance liquid chromatography for determination of flucytosine in serum.

PubMed Central

St-Germain, G; Lapierre, S; Tessier, D

1989-01-01

We compared the accuracy and precision of two microbiological methods and one high-pressure liquid chromatography (HPLC) procedure used to measure the concentrations of flucytosine in serum. On the basis of an analysis of six standards, all methods were judged reliable within acceptable limits for clinical use. With the biological methods, a slight loss of linearity was observed in the 75- to 100-micrograms/ml range. Compared with the bioassays, the HPLC method did not present linearity problems and was more precise and accurate in the critical zone of 100 micrograms/ml. On average, results obtained with patient sera containing 50 to 100 micrograms of flucytosine per ml were 10.6% higher with the HPLC method than with the bioassays. Standards for the biological assays may be prepared in serum or water. PMID:2802566

Chapter A7. Section 7.2. Fecal Indicator Viruses

USGS Publications Warehouse

Bushon, Rebecca N.

2003-01-01

More than 100 types of human pathogenic viruses may be present in fecal-contaminated waters. Coliphages are used as indicators of virus-related fecal contamination and of the microbiological quality of waters. This report provides information on the equipment, sampling protocols, and laboratory methods that are in standard use by U.S. Geological Survey (USGS) personnel for the collection of data on fecal indicator viruses.

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.

Microbiological Quality and Food Safety of Plants Grown on ISS Project

NASA Technical Reports Server (NTRS)

Wheeler, Raymond M. (Compiler)

2014-01-01

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

[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.

Comparative evaluation of matrix-assisted laser desorption ionisation-time of flight mass spectrometry and conventional phenotypic-based methods for identification of clinically important yeasts in a UK-based medical microbiology laboratory.

PubMed

Fatania, Nita; Fraser, Mark; Savage, Mike; Hart, Jason; Abdolrasouli, Alireza

2015-12-01

Performance of matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) was compared in a side-by side-analysis with conventional phenotypic methods currently in use in our laboratory for identification of yeasts in a routine diagnostic setting. A diverse collection of 200 clinically important yeasts (19 species, five genera) were identified by both methods using standard protocols. Discordant or unreliable identifications were resolved by sequencing of the internal transcribed spacer region of the rRNA gene. MALDI-TOF and conventional methods were in agreement for 182 isolates (91%) with correct identification to species level. Eighteen discordant results (9%) were due to rarely encountered species, hence the difficulty in their identification using traditional phenotypic methods. MALDI-TOF MS enabled rapid, reliable and accurate identification of clinically important yeasts in a routine diagnostic microbiology laboratory. Isolates with rare, unusual or low probability identifications should be confirmed using robust molecular methods. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Bacterial meningitis in children under 15 years of age in Nepal.

PubMed

Shrestha, Rajani Ghaju; Tandukar, Sarmila; Ansari, Shamshul; Subedi, Akriti; Shrestha, Anisha; Poudel, Rekha; Adhikari, Nabaraj; Basnyat, Shital Raj; Sherchand, Jeevan Bahadur

2015-08-19

Bacterial meningitis in children is a life-threatening problem resulting in severe morbidity and mortality. For the prompt initiation of antibacterial therapy, rapid and reliable diagnostic methods are of utmost importance. Therefore, this study was designed to find out the rate of bacterial pathogens of meningitis from suspected cases by performing conventional methods and latex agglutination. A descriptive type of study was carried out from May 2012 to April 2013. Cerebrospinal fluid (CSF) specimens from 252 suspected cases of meningitis were subjected for Gram staining, bacterial culture and latex agglutination test. The identification of growth of bacteria was done following standard microbiological methods recommended by American Society for Microbiology. Antibiotic sensitivity testing was done by modified Kirby-Bauer disk diffusion method. From the total 252 suspected cases, 7.2 % bacterial meningitis was revealed by Gram staining and culture methods whereas latex agglutination method detected 5.6 %. Gram-negative organisms contributed the majority of the cases (72.2 %) with Haemophilus influenzae as the leading pathogen for meningitis. Overall, 33.3 % mortality rate was found. In conclusion, a significant rate of bacterial meningitis was found in this study prompting concern for national wide surveillance.

[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.

[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.

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

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...

Methods for Recovering Microorganisms from Solid Surfaces Used in the Food Industry: A Review of the Literature

PubMed Central

Ismaïl, Rached; Aviat, Florence; Michel, Valérie; Le Bayon, Isabelle; Gay-Perret, Perrine; Kutnik, Magdalena; Fédérighi, Michel

2013-01-01

Various types of surfaces are used today in the food industry, such as plastic, stainless steel, glass, and wood. These surfaces are subject to contamination by microorganisms responsible for the cross-contamination of food by contact with working surfaces. The HACCP-based processes are now widely used for the control of microbial hazards to prevent food safety issues. This preventive approach has resulted in the use of microbiological analyses of surfaces as one of the tools to control the hygiene of products. A method of recovering microorganisms from different solid surfaces is necessary as a means of health prevention. No regulation exists for surface microbial contamination, but food companies tend to establish technical specifications to add value to their products and limit contamination risks. The aim of this review is to present the most frequently used methods: swabbing, friction or scrubbing, printing, rinsing or immersion, sonication and scraping or grinding and describe their advantages and drawbacks. The choice of the recovery method has to be suitable for the type and size of the surface tested for microbiological analysis. Today, quick and cheap methods have to be standardized and especially easy to perform in the field. PMID:24240728

Methods for recovering microorganisms from solid surfaces used in the food industry: a review of the literature.

PubMed

Ismaïl, Rached; Aviat, Florence; Michel, Valérie; Le Bayon, Isabelle; Gay-Perret, Perrine; Kutnik, Magdalena; Fédérighi, Michel

2013-11-14

Various types of surfaces are used today in the food industry, such as plastic, stainless steel, glass, and wood. These surfaces are subject to contamination by microorganisms responsible for the cross-contamination of food by contact with working surfaces. The HACCP-based processes are now widely used for the control of microbial hazards to prevent food safety issues. This preventive approach has resulted in the use of microbiological analyses of surfaces as one of the tools to control the hygiene of products. A method of recovering microorganisms from different solid surfaces is necessary as a means of health prevention. No regulation exists for surface microbial contamination, but food companies tend to establish technical specifications to add value to their products and limit contamination risks. The aim of this review is to present the most frequently used methods: swabbing, friction or scrubbing, printing, rinsing or immersion, sonication and scraping or grinding and describe their advantages and drawbacks. The choice of the recovery method has to be suitable for the type and size of the surface tested for microbiological analysis. Today, quick and cheap methods have to be standardized and especially easy to perform in the field.

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota.

PubMed

Grégory, Dubourg; Chaudet, Hervé; Lagier, Jean-Christophe; Raoult, Didier

2018-03-01

Describing the human hut gut microbiota is one the most exciting challenges of the 21 st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.

Detecting 16S rRNA Methyltransferases in Enterobacteriaceae by Use of Arbekacin.

PubMed

McGann, Patrick; Chahine, Sarah; Okafor, Darius; Ong, Ana C; Maybank, Rosslyn; Kwak, Yoon I; Wilson, Kerry; Zapor, Michael; Lesho, Emil; Hinkle, Mary

2016-01-01

16S rRNA methyltransferases confer resistance to most aminoglycosides, but discriminating their activity from that of aminoglycoside-modifying enzymes (AMEs) is challenging using phenotypic methods. We demonstrate that arbekacin, an aminoglycoside refractory to most AMEs, can rapidly detect 16S methyltransferase activity in Enterobacteriaceae with high specificity using the standard disk susceptibility test. Copyright © 2015, American Society for Microbiology. 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.

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

PubMed

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

2016-08-01

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

Bioluminescence lights the way to food safety

NASA Astrophysics Data System (ADS)

Brovko, Lubov Y.; Griffiths, Mansel W.

2003-07-01

The food industry is increasingly adopting food safety and quality management systems that are more proactive and preventive than those used in the past which have tended to rely on end product testing and visual inspection. The regulatory agencies in many countries are promoting one such management tool, Hazard Analysis Critical Control Point (HACCP), as a way to achieve a safer food supply and as a basis for harmonization of trading standards. Verification that the process is safe must involve microbiological testing but the results need not be generated in real-time. Of all the rapid microbiological tests currently available, the only ones that come close to offering real-time results are bioluminescence-based methods. Recent developments in application of bioluminescence for food safety issues are presented in the paper. These include the use of genetically engineered microorganisms with bioluminescent and fluorescent phenotypes as a real time indicator of physiological state and survival of food-borne pathogens in food and food processing environments as well as novel bioluminescent-based methods for rapid detection of pathogens in food and environmental samples. Advantages and pitfalls of the methods are discussed.

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

Rectal swab sampling followed by an enrichment culture-based real-time PCR assay to detect Salmonella enterocolitis in children.

PubMed

Lin, L-H; Tsai, C-Y; Hung, M-H; Fang, Y-T; Ling, Q-D

2011-09-01

Although routine bacterial culture is the traditional reference standard method for the detection of Salmonella infection in children with diarrhoea, it is a time-consuming procedure that usually only gives results after 3-4 days. Some molecular detection methods can improve the turn-around time to within 24 h, but these methods are not applied directly from stool or rectal swab specimens as routine diagnostic methods for the detection of gastrointestinal pathogens. In this study, we tested the feasibility of a bacterial enrichment culture-based real-time PCR assay method for detecting and screening for diarrhoea in children caused by Salmonella. Our results showed that the minimum real-time PCR assay time required to detect enriched bacterial culture from a swab was 3 h. In all children with suspected Salmonella diarrhoea, the enrichment culture-based real-time PCR achieved 85.4% sensitivity and 98.1% specificity, as compared with the 53.7% sensitivity and 100% specificity of detection with the routine bacterial culture method. We suggest that rectal swab sampling followed by enrichment culture-based real-time PCR is suitable as a rapid method for detecting and screening for Salmonella in paediatric patients. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

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.

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.

[Analysis of the results of the HIV-1, HCV and HBV viral load of SEIMC External Quality Control Program. Year 2014].

PubMed

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

2016-07-01

Human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV) and hepatitis C virus (HCV) viral load determinations are among the most relevant markers for the follow up of patients infected with these viruses. External quality control tools are crucial to ensure the accuracy of results obtained by microbiology laboratories. This article summarizes the results obtained from the 2014 SEIMC (Spanish Society of Infectious Diseases and Clinical Microbiology) External Quality Control Programme for HIV-1, HCV, and HBV viral loads. In the HIV-1 program, a total of 5 standards were sent. One standard consisted in seronegative human plasma, while the remaining 4 contained plasma from 3 different viremic patients, in the range of 2-5 log10 copies/mL; 2 of these standards were identical aiming to determine repeatability. A significant proportion of the laboratories (30.8% on average) obtained values out of the accepted range (mean ± 0.25 log10 copies/mL), depending on the standard and on the method used for quantification. Repeatability was excellent, with up to 95.8% of laboratories reporting results within the limits (Δ < 0.5 log10 copies/mL). The HBV and HCV program consisted of 2 standards with different viral load contents. Most of the participants, 83.7% in the case of HCV and 87.9% in the HBV, obtained all the results within the accepted range (mean ± 1.96 standard deviations log10 IU/mL). Data from this analysis reinforce the utility of proficiency programmes to ensure the quality of the results obtained by a particular laboratory, as well as the importance of the post-analytical phase on the overall quality. Due to the remarkable interlaboratory variability, it is advisable to use the same method and the same laboratory for patient follow up. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

The advantages of the application of amnion membrane in the treatment of burns.

PubMed

Andonovska, D; Dzokic, Gj; Spasevska, L; Trajkovska, T; Popovska, K; Todorov, I; Petrovski, P; Kondov, G; Sapova, B; Marcikic, G; Atanasova, E; Obocki, E; Ugrinovska, J; Andonovski, D; Andonovski, D; Vasilevska, V; Mircevska-Zogovska, E

2008-07-01

A crucial and important factor for successful treatment of burns is the early covering of the burned area with skin substitutes. The covering of the burn requires material that restores the epidermal function and integrates itself into the process of healing. Biological dressings are the golden standard for the temporary covering of burns. All biological skin substitutes are susceptible to early graft reaction and the only exception is the amnion membrane. The importance of the amnion membrane as a biological dressing for burns amounts to: a barrier to bacterial colonization, hastens the epithelisation, and control of water loss. Amnioplasty is a method of application of amnion membrane on the recipient site. In this comparative study, 60 patients with dermal and sub-dermal burns were included. Research was made on an examination group of 30 patients with burns where the method of amnioplasty was applied, and for this amnion membrane conserved in 76% alcohol was used. The control group was made up of 30 patients with burns treated conventionally, and standard methods for the local treatment of burns were applied: exposition, occlusive dressing and initial excision with skin grafting. Pathohistological and microbiological analyses of the bioptical material were made. The degree of the burns was determined through a pathohistological analysis of the bioptical material taken the third day, and in some of the subjects where re-epithelialization was determined on the seventh day, the further re-epithelialization was observed clinically. Pathohistological examination enabled discrimination between bacterial colonization and the invasive bacterial infection. Furthermore, the type of bacterial colonization and infection was determined, which was confirmed with microbiological analysis. The analysis of the results from the microbiological and pathohistological researches of the bioptical material according to the bacterial colonization and infection showed that, although between the examined and the control group there was no statistically important difference, the value of p = 0.067 is close to the statistically important value of p < 0.05. The results of the pathohistological examination of the bioptical material taken the seventh day and analysed according to the re-epithelialization showed that there was a significant difference between the two groups of p < 0.035. It should be mentioned that, although according to the microbiological examinations of the bioptical material a statistically significant difference was not achieved, clinical significance was achieved. The obtained significance of p < 0.035 compared to the re-epithelialization in both groups approved the application of the method of amnioplasty. The histological analysis of the bioptical material not only determines the degree of the burns specifically, but facilitates the choice of method for further treatment, observes the speed of the re-epithelialization and plays an important part in the correct diagnosis and the early start of the specific therapy, important in preventing sepsis. The application of amnion membrane as a biological dressing speeds the re-epithelialization and prevents invasive bacterial infection. Pathohistological examination of the burns is recommended to be established as a standard method in clinical practice.

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

PubMed

Zhang, Shuangfei; Hu, Zhong; Wang, Hui

2018-01-01

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

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

PubMed Central

Zhang, Shuangfei; Hu, Zhong; Wang, Hui

2018-01-01

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

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

PubMed

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

2017-12-01

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

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

Current studies on bacterospermia the leading cause of male infertility: a protégé and potential threat towards mans extinction

PubMed Central

Isaiah, Ibeh Nnana; Nche, Bikwe Thomas; Nwagu, Ibeh Georgina; Nnanna, Ibeh Isaiah

2011-01-01

Background: The current rise of male infertility associated with bacterospermia and urogenital infection has been on the increase amongst adult married males in Benin metropolis and a major cause of concern to male fertility and reproduction in Nigeria. Aim: To microbiologically isolate and study the infectious agent that has led to male infertility and also to study the percentage occurrence of bacteropsermia and urogenital caused infertility in adult married males in Benin metropolis Material and Method: using standard microbiological methods of isolating and identifying the organism, specimen was collected and processed which includes the susceptibility profile of isolates and sperm quality. In this study a total of 140 sperm samples was collected from patient who were referred from the consultant outpatient department of the University of Benin Teaching Hospital and then evaluated bacteriologically using standard bacterial cultural methods Results: Among the total cases, 92 (65.7%) showed at least one pathogen. Staphylococcus aureus (28.3%), Staphylococcus Saprophyticus (13.0%), Pseudomonas aerouginosa (6.5%), Escherichia Coli (19.6%) Proteus mirabilis (10.8%) Klebsiella spp (10.8%) and Proteus vulgaris (10.8%). Conclusion: There was an outstanding significant relationship between bacteriospermia and the rate of total motility and morphologically abnormal sperms, The percentage of morphologically normal sperm was lower in this study. Staphylococcus aureus Staphylococcus saprohyticus and Escherichia coli were the most common pathogen having negative effects on sperm motility and morphology in this study. PMID:22363079

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.

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.

Comparative efficiency of different methods of gluten extraction in indigenous varieties of wheat.

PubMed

Imran, Samra; Hussain, Zaib; Ghafoor, Farkhanda; Nagra, Saeedahmad; Ziai, Naheeda Ashbeal

2013-06-01

The present study investigated six varieties of locally grown wheat (Lasani, Sehar, Miraj-08, Chakwal-50, Faisalabad-08 and Inqlab) procured from Punjab Seed Corporation, Lahore, Pakistan for their proximate contents. On the basis of protein content and ready availability, Faisalabad-08 (FD-08) was selected to be used for the assessment of comparative efficiency of various methods used for gluten extraction. Three methods, mechanical, chemical and microbiological were used for the extraction of gluten from FD-08. Each method was carried out under ambient conditions using a drying temperature of 55 degrees C. Mechanical method utilized four different processes viz:- dough process, dough batter process, batter process and ethanol washing process using standard 150 mesh. The starch thus obtained was analyzed for its proximate contents. Dough batter process proved to be the most efficient mechanical method and was further investigated using 200 and 300 mesh. Gluten content was determined using sandwich omega-gliadin enzyme-linked immunosorbent assay (ELISA).The results of dough batter process using 200 mesh indicated a starch product with gluten content of 678 ppm. Chemical method indicated high gluten content of more than 5000 ppm and the microbiological method reduced the gluten content from 2500 ppm to 398 ppm. From the results it was observed that no gluten extraction method is viable to produce starch which can fulfill the criteria of a gluten free product (20 ppm).

[Rapid bioluminescent antibiotic susceptibility assay].

PubMed

Frundzhian, V G; Ugarova, N N; Blatun, L A; Terekhova, R P; Rusanova, E V

2009-01-01

Rapid testing of pathogen susceptibility to antibiotics is of great practical value for rational chemotherapy of pyoinflammatory deseases and postoperative complications of microbial etiology. The standard microbiological methods, i.e., the disk diffusion method and the method of serial dilutions are labour- and time-consuming (not less than 18-36 hours). The method of the authors is based on measuring bioluminescence resulting from interaction of adenosine-5'-triphosphate (ATP) and ATP reagent, a standard reaction mixture of firefly luciferase (an enzyme) and luciferin. The bioluminescence intensity is proportional to the ATP concentration in the reaction mixture and the ATP concentration is proportional to the number of the pathogen viable cells in the sample. The bioluminescence intensity value in the pathogen suspension aliquots with and without (control) the antibiotic were compared after the incubation for 5 hours and the coefficient of the microbial cell growth inhibition was calculated. Satisfactory correlation (R2 > 88%) of the results of the bioluminescent assay and the assay with the disk diffusion method and the method of serial dilutions was observed.

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

PubMed Central

Reuter, Sandra; Ellington, Matthew J.; Cartwright, Edward J. P.; Köser, Claudio U.; Török, M. Estée; Gouliouris, Theodore; Harris, Simon R.; Brown, Nicholas M.; Holden, Matthew T. G.; Quail, Mike; Parkhill, Julian; Smith, Geoffrey P.; Bentley, Stephen D.; Peacock, Sharon J.

2014-01-01

IMPORTANCE The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. CONCLUSIONS AND RELEVANCE The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance. PMID:23857503

Identification of Low-Level Vancomycin Resistance in Staphylococcus aureus in the Era of Informatics.

PubMed

Ford, Bradley A

2016-04-01

Vancomycin-intermediateStaphylococcus aureus(VISA) and heteroresistant VISA (hVISA) are pathogens for which accurate antimicrobial susceptibility testing (AST) would rule out standard treatment with vancomycin. Unfortunately, AST for vancomycin is relatively slow and standard methods are unable to reliably detect VISA and hVISA. An article in this issue (C. A. Mather, B. J. Werth, S. Sivagnanam, D. J. SenGupta, and S. M. Butler-Wu, J Clin Microbiol 54:883-890, 2016, doi:http://dx.doi.org/10.1128/JCM.02428-15) describes a rapid whole-cell matrix-assisted laser desorption ionization-time of flight proxy susceptibility method that highlights current innovations and challenges with rapid AST, VISA/hVISA identification, and clinical bioinformatics. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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 testing of pharmaceuticals and cosmetics in Egypt.

PubMed

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

2015-12-09

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

The 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.

Current studies on bacterospermia the leading cause of male infertility: a protégé and potential threat towards mans extinction.

PubMed

Isaiah, Ibeh Nnana; Nche, Bikwe Thomas; Nwagu, Ibeh Georgina; Nnanna, Ibeh Isaiah

2011-12-01

The current rise of male infertility associated with bacterospermia and urogenital infection has been on the increase amongst adult married males in Benin metropolis and a major cause of concern to male fertility and reproduction in Nigeria. To microbiologically isolate and study the infectious agent that has led to male infertility and also to study the percentage occurrence of bacteropsermia and urogenital caused infertility in adult married males in Benin metropolis using standard microbiological methods of isolating and identifying the organism, specimen was collected and processed which includes the susceptibility profile of isolates and sperm quality. In this study a total of 140 sperm samples was collected from patient who were referred from the consultant outpatient department of the University of Benin Teaching Hospital and then evaluated bacteriologically using standard bacterial cultural methods Among the total cases, 92 (65.7%) showed at least one pathogen. Staphylococcus aureus (28.3%), Staphylococcus Saprophyticus (13.0%), Pseudomonas aerouginosa (6.5%), Escherichia Coli (19.6%) Proteus mirabilis (10.8%) Klebsiella spp (10.8%) and Proteus vulgaris (10.8%). There was an outstanding significant relationship between bacteriospermia and the rate of total motility and morphologically abnormal sperms, The percentage of morphologically normal sperm was lower in this study. Staphylococcus aureus Staphylococcus saprohyticus and Escherichia coli were the most common pathogen having negative effects on sperm motility and morphology in this study.

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

PubMed

Sathasivan, Arumugam; Fisher, Ian; Kastl, George

2005-07-15

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

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.

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.

[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.

Microbiological contamination of dried and lyophilized garlic as a potential source of food spoilage.

PubMed

Kłębukowska, Lucyna; Zadernowska, Anna; Chajęcka-Wierzchowska, Wioleta

2015-03-01

Garlic is valued more for its flavoring and used in a wide variety of foods. In food technology, fresh garlic is not used, but instead its processed forms, most often dried and lyophilized, are utilized. The quality and safety of the final product largely depends on their microbiological quality. This research has provided information about effect of garlic fixation methods and provided information about effect of microbiological contamination of garlic used as a spice for quality of garlic mayonnaise sauce. The authors decided to undertake studies following a report from one of the manufacturers of garlic sauces on product defects which originated in dried garlic used in the production process. Samples of garlic (n = 26) were examinated using standard cultural methods (counts of fungi, lactic acid bacteria-LAB, spore-producing Bacillus sp. and the presence of anaerobic saccharolytic and proteolytic clostridia), automated system TEMPO (total viable count, Enterobacteriaceae), immunoenzymatic method using VIDAS tests (occurrence of Salmonella sp. and Listeria monocytogenes). The number of total viable count was ranged from 3.51 to 6.85 log CFU/g. Enterobacteriaceae were detected only in one sample. Comparably low values were recorded for fungi (1.30 to 3.47 log CFU/g). The number of LAB was ranged from 2.34 to 5.49 log CFU/g. Clostridium sp. were detected in 22 samples. Salmonella sp. and Listeria monocytogenes were not detected. It was found that garlic, regardless of th preservation procedure, might be a source of contamination of garlic mayonnaise sauce especially with lactic acid bacteria and Clostridium sp. spores.

Evaluation of Three MALDI-TOF Mass Spectrometry Libraries for the Identification of Filamentous Fungi in Three Clinical Microbiology Laboratories in Manitoba, Canada.

PubMed

Stein, Markus; Tran, Vanessa; Nichol, Kimberly A; Lagacé-Wiens, Philippe; Pieroni, Peter; Adam, Heather J; Turenne, Christine; Walkty, Andrew J; Normand, Anne-Cécile; Hendrickx, Marijke; Piarroux, Renaud; Karlowsky, James A

2018-06-12

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify bacterial pathogens and yeasts, but not for the identification of moulds. Recent progress in extraction protocols and the composition of comparative libraries support potential application of MALDI-TOF MS for mould identification in clinical microbiology laboratories. We evaluated the performance of the Bruker Microflex ™ MALDI-TOF MS instrument (Billerica, MA, USA) to identify clinical isolates and reference strains of moulds using three libraries, the Bruker mould library, the National Institutes of Health (NIH) library, and the Mass Spectrometry Identification (MSI) online library, and compared those results to conventional (morphological) and molecular (18S/ITS; gold standard) identification methods. All three libraries demonstrated greater accuracy in genus identification (≥94.9%) than conventional methods (86.4%). MALDI-TOF MS identified 73.3% of isolates to species-level compared to only 31.7% by conventional methods. The MSI library demonstrated the highest rate of species-level identification (72.0%) compared to NIH (19.5%) and Bruker (13.6%) libraries. Greater than 20% of moulds remained unidentified to species-level by all three MALDI-TOF MS libraries primarily because of library limitations or imperfect spectra. The overall identification rate of each MALDI-TOF MS library depended on the number of species and the number of spectra representing each species in the library. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The right to food, food donation and microbiological problems of food safety: an experience in the territory of Florence.

PubMed

Bonaccorsi, Guglielmo; Lorini, Chiara; Pieralli, Francesca; Pieri, Luca; Sala, Antonino; Tanini, Tommaso; Nasali, Marco; Dall'Olio, Beatrice; Santomauro, Francesca

2016-01-01

The aim of this study is to understand whether the freezing without a rapid blast chiller represents a storage method for food at the end of shelf life that guarantees microbiological food safety, so to be considered an effective tool for the appropriate management of food in charitable organizations. The study has been performed on 90 food samples, among those that a charitable foodservice trust receives by the large-scale distribution. The products have been frozen using a domestic refrigerator. The indicators used were: total aerobic microbial count, Escherichia coli, Salmonella spp, Staphylococcus aureus, Campylobacter spp, sulphite reducing clostridia. The results show that the preservation of the chosen fresh products at the end of shelf life in refrigerators, frozen without the use of chillers, is a potential management strategy to avoid the loss of edible food, while maintaining the safety standards.

Comparison of Minocycline Susceptibility Testing Methods for Carbapenem-Resistant Acinetobacter baumannii.

PubMed

Wang, Peng; Bowler, Sarah L; Kantz, Serena F; Mettus, Roberta T; Guo, Yan; McElheny, Christi L; Doi, Yohei

2016-12-01

Treatment options for infections due to carbapenem-resistant Acinetobacter baumannii are extremely limited. Minocycline is a semisynthetic tetracycline derivative with activity against this pathogen. This study compared susceptibility testing methods that are used in clinical microbiology laboratories (Etest, disk diffusion, and Sensititre broth microdilution methods) for testing of minocycline, tigecycline, and doxycycline against 107 carbapenem-resistant A. baumannii clinical isolates. Susceptibility rates determined with the standard broth microdilution method using cation-adjusted Mueller-Hinton (MH) broth were 77.6% for minocycline and 29% for doxycycline, and 92.5% of isolates had tigecycline MICs of ≤2 μg/ml. Using MH agar from BD and Oxoid, susceptibility rates determined with the Etest method were 67.3% and 52.3% for minocycline, 21.5% and 18.7% for doxycycline, and 71% and 29.9% for tigecycline, respectively. With the disk diffusion method using MH agar from BD and Oxoid, susceptibility rates were 82.2% and 72.9% for minocycline and 34.6% and 34.6% for doxycycline, respectively, and rates of MICs of ≤2 μg/ml were 46.7% and 23.4% for tigecycline. In comparison with the standard broth microdilution results, very major rates were low (∼2.8%) for all three drugs across the methods, but major error rates were higher (∼5.6%), especially with the Etest method. For minocycline, minor error rates ranged from 14% to 37.4%. For tigecycline, minor error rates ranged from 6.5% to 69.2%. The majority of minor errors were due to susceptible results being reported as intermediate. For minocycline susceptibility testing of carbapenem-resistant A. baumannii strains, very major errors are rare, but major and minor errors overcalling strains as intermediate or resistant occur frequently with susceptibility testing methods that are feasible in clinical laboratories. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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.

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

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)

[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.

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

[Laboratory diagnosis of mucormycosis].

PubMed

Garcia-Hermoso, Dea

2013-03-01

Mucormycosis are deep infections caused by ubiquitous filamentous fungi of the order of Mucorales. The disease occurs mostly in immunocompromised, diabetic or solid organ transplant recipients. There are currently no specific diagnostic guidelines for mucormycosis. The histological examination and culture of the clinical sample remain the most useful approaches for diagnosis. Furthermore, alternative methods to the fungal culture are yet to be standardized. Here we review the current microbiological approaches used for the diagnosis and identification of Mucorales. © 2013 médecine/sciences – Inserm / SRMS.

Microbial ecology laboratory procedures manual NASA/MSFC

NASA Technical Reports Server (NTRS)

Huff, Timothy L.

1990-01-01

An essential part of the efficient operation of any microbiology laboratory involved in sample analysis is a standard procedures manual. The purpose of this manual is to provide concise and well defined instructions on routine technical procedures involving sample analysis and methods for monitoring and maintaining quality control within the laboratory. Of equal importance is the safe operation of the laboratory. This manual outlines detailed procedures to be followed in the microbial ecology laboratory to assure safety, analytical control, and validity of results.

Environmental Consequences of the Failure of the New Orleans Levee System During Hurricane Katrina; Microbiological Analysis

DTIC Science & Technology

2007-06-01

Love, G. Lovelace, J. Stewart, and B. Robinson. 2005. Methods to detect and genotype coliphages in water and shellfish. Methodology for a demonstra... Water fecal coliform counts (colony forming units (cfu) per 100 mL of water ) ranged from 100 to 490,000 (mean=21,381, standard deviation =74,541...100) in St. Bernard Parish and the Lower Ninth Ward polders. The LADEQ primary contact recreational water quality criterion for fecal coliforms is

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

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.

A PCR procedure for the detection of Giardia intestinalis cysts and Escherichia coli in lettuce.

PubMed

Ramirez-Martinez, M L; Olmos-Ortiz, L M; Barajas-Mendiola, M A; Giono Cerezo, S; Avila, E E; Cuellar-Mata, P

2015-06-01

Giardia intestinalis is a pathogen associated with foodborne outbreaks and Escherichia coli is commonly used as a marker of faecal contamination. Implementation of routine identification methods of G. intestinalis is difficult for the analysis of vegetables and the microbiological detection of E. coli requires several days. This study proposes a PCR-based assay for the detection of E. coli and G. intestinalis cysts using crude DNA isolated from artificially contaminated lettuce. The G. intestinalis and E. coli PCR assays targeted the β-giardin and uidA genes, respectively, and were 100% specific. Forty lettuces from local markets were analysed by both PCR and light microscopy and no cysts were detected, the calculated detection limit was 20 cysts per gram of lettuce; however, by PCR, E. coli was detected in eight of ten randomly selected samples of lettuce. These data highlight the need to validate procedures for routine quality assurance. These PCR-based assays can be employed as alternative methods for the detection of G. intestinalis and E. coli and have the potential to allow for the automation and simultaneous detection of protozoa and bacterial pathogens in multiple samples. Significance and impact of the study: There are few studies for Giardia intestinalis detection in food because methods for its identification are difficult for routine implementation. Here, we developed a PCR-based method as an alternative to the direct observation of cysts in lettuce by light microscopy. Additionally, Escherichia coli was detected by PCR and the sanitary quality of lettuce was evaluated using molecular and standard microbiological methods. Using PCR, the detection probability of Giardia cysts inoculated onto samples of lettuce was improved compared to light microscopy, with the advantage of easy automation. These methods may be employed to perform timely and affordable detection of foodborne pathogens. © 2015 The Society for Applied Microbiology.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

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

1988-01-01

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

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

PubMed

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

2011-07-01

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

Audit of laboratory mycology services for the management of patients with fungal infections in the northwest of England.

PubMed

Hassan, I A; Critten, P; Isalska, B; Denning, D W

2006-07-01

Fungal infection is increasingly recognised as an important cause of morbidity and mortality, especially in immunocompromised patients. Little information exists on laboratory services available and the methods used by general microbiology laboratories to diagnose these important infections. To investigate the services microbiology laboratories in northwest England provide towards the diagnosis and management of superficial and deep fungal infections. A questionnaire was sent to laboratories to get a holistic view of the support given to clinicians looking after patients with fungal infections. The aim was not to investigate details of each laboratory's standard operating procedures. The completed questionnaires, which formed the basis of this report, were returned by all 21 laboratories which were recruited. This study was conducted between March 2004 and September 2004. Services were provided to District General Hospitals and to six tertiary centres, including eight teaching hospitals by 16 laboratories. Their bed capacity was 250-1300 beds. Total specimens (including bacterial and viral) processed annually were 42 000-500,000 whereas fungal ones were 560-5400. In most microbiology laboratories of northwest England, clinicians were aware of the potential of fungal pathogens to cause infections especially in immunocompromised patients. Additional measures such as prolonged incubation of samples were introduced to improve fungal yield from patients at high risk. It is necessary to train and educate laboratory and medical staff about the role of serology and molecular methods in diagnosis and management of patients with fungal infection.

Comparison of Uriswab to alternative methods for urine culture collection and transport: confirmation of standard culture methodology for investigation of urinary tract infections.

PubMed

Rennie, Robert P; Turnbull, Lee-Ann; Gauchier-Pitts, Kaylee; Bennett, Tracy; Dyrland, Debbie; Blonski, Susan

2016-08-01

The ability to isolate and identify causative agents of urinary tract infections relies primarily on the quality of the urine sample that is submitted to the microbiology. The most important factors are the method of collection, the maintenance of viability of the potential pathogens during transport, and standardization of the culturing of the urine sample. This report is a composite of several investigations comparing collection and transport on urine culture paddles, with a preservative urine sponge (Uriswab), and a comparison of Uriswab with the BD preservative transport tube as methods of preservation of urinary pathogens. Primary studies showed that Uriswab maintained significantly more urinary pathogens than the urine culture paddle with fewer mixed or contaminated cultures. The two preservative transport systems were comparable for maintenance of viability of the pathogens, but there were fewer mixed cultures when samples were collected with Uriswab. This study confirms the importance of a standard volume of 1 μL of urine for culture. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed Central

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

2012-01-01

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

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

Guidelines for the detection of Trichinella larvae at the slaughterhouse in a quality assurance system.

PubMed

Rossi, Patrizia; Pozio, Edoardo

2008-01-01

The European Community Regulation (EC) No. 2075/2005 lays down specific rules on official controls for the detection of Trichinella in fresh meat for human consumption, recommending the pooled-sample digestion method as the reference method. The aim of this document is to provide specific guidance to implement an appropriate Trichinella digestion method by a laboratory accredited according to the ISO/IEC 17025:2005 international standard, and performing microbiological testing following the EA-04/10:2002 international guideline. Technical requirements for the correct implementation of the method, such as the personnel competence, specific equipments and reagents, validation of the method, reference materials, sampling, quality assurance of results and quality control of performance are provided, pointing out the critical control points for the correct implementation of the digestion method.

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.

Susceptibility Testing of Medically Important Parasites.

PubMed

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

2017-07-01

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

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.

PCR/LDR/universal array platforms for the diagnosis of infectious disease.

PubMed

Pingle, Maneesh; Rundell, Mark; Das, Sanchita; Golightly, Linnie M; Barany, Francis

2010-01-01

Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections.

PCR/LDR/Universal Array Platforms for the Diagnosis of Infectious Disease

PubMed Central

Pingle, Maneesh; Rundell, Mark; Das, Sanchita; Golightly, Linnie M.; Barany, Francis

2015-01-01

Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections. PMID:20217576

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.

Microbiology on Space Station Freedom

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

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

Comparing different methods for fast screening of microbiological quality of beach sand aimed at rapid-response remediation.

PubMed

Testolin, Renan C; Almeida, Tito C M; Polette, Marcus; Branco, Joaquim O; Fischer, Larissa L; Niero, Guilherme; Poyer-Radetski, Gabriel; Silva, Valéria C; Somensi, Cleder A; Corrêa, Albertina X R; Corrêa, Rogério; Rörig, Leonardo R; Itokazu, Ana Gabriela; Férard, Jean-François; Cotelle, Sylvie; Radetski, Claudemir M

2017-05-15

There is scientific evidence that beach sands are a significant contributor to the pathogen load to which visitors are exposed. To develop beach quality guidelines all beach zones must be included in microbiological evaluations, but monitoring methods for beach sand quality are relatively longstanding, expensive, laborious and require moderate laboratory infrastructure. This paper aimed to evaluate the microorganism activity in different beach zones applying and comparing a classical method of membrane filtration (MF) with two colorimetric screening methods based on fluorescein (FDA) and tetrazolium (TTC) salt biotransformation to evaluate a new rapid and low-cost method for beach sand microbiological contamination assessments. The colorimetric results can help beach managers to evaluate rapidly and at low cost the microbiological quality of different beach zones in order to decide whether remedial actions need to be adopted to prevent exposure of the public to microbes due to beach sand and/or water contamination. Copyright © 2017. Published by Elsevier Ltd.

[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.

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.

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.

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

Assessment of Physicochemical and Microbiological Quality of Public Swimming Pools in Addis Ababa, Ethiopia

PubMed Central

Yedeme, Kokebe; Legese, Melese Hailu; Gonfa, Almaz; Girma, Somson

2017-01-01

Background: From swimming pools, bathers may acquire many potential pathogens or may be affected by the physicochemical characteristics of water used during bathing. Hence, this study aimed at assessing the physicochemical and microbiological quality of public swimming pools located at different hotels and recreation center in Addis Ababa, Ethiopia. Method: A cross sectional study was carried out from February to May, 2016. Nine hotels and one recreation center which recognized to have public swimming services were included. A total of 60 swimming pool water samples from 10 swimming pools were collected at deeper, shallow and intake point twice on a weekly basis using a 250 ml sterile bottle containing sodium thiosulphate. PH, residual chlorine and temperature of samples were recorded at the time of collection. Sample containing bottles were transported in ice box to microbiological laboratory and analyzed on the same day. Standard cultural and biochemical methods were used for isolation and characterization of the main microbial groups. Total viable count, total coliform count, fecal coliform count and E. coli were determined. Data was analyzed using SPSS Version 20. Results: Average PH and temperature of swimming pool water samples were 7.1 and 29oC respectively. Of all analyzed water samples, 58.4% (n=35/60) of them had PH range of 7.2-7.8, 58.3% (n=35/60) of samples had temperature in the range of 21oC-32oC and 25% (n=15/60) of water samples had residual chlorine in the range of 2-3mg/l. 73.3% (n=44/60) of the samples had a total viable count below 200 MPN/ml and 70% (n-42/60) of the samples had Total Coliform Count values less than 2 MPN/100 ml. Moreover, 66.7% (n=40/60) of the samples had fecal coliform counts falling below 1 MPN /100 ml. E. coli was absent in 70% (n=42/60) of the samples while it was present in 30% (n=18/60) of the samples. Conclusion: PH, residual chlorine and temperature value of majority of the swimming pools’ water samples were within the acceptable limit. Regarding microbial quality, most swimming pools’ water samples complied to the WHO standard. Swimming pools that did not comply to the standard both in physicochemical levels and microbial quality need improvement due to their significant health implication. PMID:28761562

Comparison of a New and Rapid Method: Brucella Coombs Gel Test With Other Diagnostic Tests.

PubMed

Kalem, Fatma; Ergün, Ayşe Gül; Durmaz, Süleyman; Doğan, Metin; Ertuğrul, Ömür; Gündem, Seval

2016-09-01

The aim of this study was to detect reliability of Brucella Coombs gel test (BCGT) by comparing with with ELISA (IgG + IgM), Standard agglutination test, and Brucella immunocapture agglutination methods in serological diagnosis of brucellosis. Brucella Coombs gel test (BCGT), Brucella ELISA (IgG + IgM), Standard agglutination test, and Brucella immunocapture agglutination tests of 78 patients with presumptive diagnosis of brucellosis which were sent to Microbiology Laboratory of Konya Numune Hospital from various regions of Konya were studied. Of 78 patients with ELISA IgG and IgM, STA, BICA and BCGT; 26, 21, 10, 12 and 12 were positive. When compared with BICA, the sensitivity and specifity of BCGT were 100% and 100%, respectively. According to results BCGT can be used as a diagnostic test in routine laboratories after more comprehensive studies in control groups and patients. © 2016 Wiley Periodicals, Inc.

Microbial Assessment and Prevalence of Foodborne Pathogens in Natural Cheeses in Japan

PubMed Central

Enkhtuya, Budbazar; Kusumoto, Akiko

2013-01-01

The production and consumption of domestic natural cheese in Japan is increasing year by year. More than ninety percent of domestic natural cheese is produced in Hokkaido region of Japan, while information on its quality and safety related to foodborne pathogens is limited. To assess the microbiological safety of domestic natural cheese, a total of 126 natural cheese samples produced in Hokkaido were collected from December, 2012, to July, 2013. In addition to standard plate count (SPC) and coliform counts, the prevalence study of three pathogens (Listeria monocytogenes, pathogenic Escherichia coli, and Salmonella spp.) was performed on each sample. Real-time PCR and matrix-assisted laser desorption-ionization time-of-flight mass spectrometer methods were employed for identification of presumptive pathogens. Coliform was detected in 25 samples (19.8%) with a minimum of 25 cfu/g and a maximum of more than 3.0 × 106 cfu/g. Salmonella spp. and L. monocytogenes were not isolated from any of the samples. Only one sample (0.80%) showed positive PCR amplification for ipaH gene suggesting possible contamination of enteroinvasive E. coli or Shigella in this product. Overall results indicate that natural cheeses produced in Hokkaido region were satisfactory microbiological quality according to existing international standards. PMID:24490148

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

PubMed

Nishiyama, Hiroyuki

2015-04-01

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

[The significance of biofilm for the treatment of infections in orthopedic surgery : 2017 Update].

PubMed

Scheuermann-Poley, C; Wagner, C; Hoffmann, J; Moter, A; Willy, C

2017-06-01

The increase in endoprosthetic and osteosynthetic surgical treatment is associated with a simultaneous increase in implant-associated infections (surgical site infections, SSI). Biofilms appear to play a significant role in the diagnosis and treatment of these infections and heavily contaminated wounds. This article aims to provide a current overview of biofilm and its relevance in orthopedic surgery. A computer-assisted literature search of MedLine (PubMed) was performed using key word combinations with "biofilm" (as of March 2017). Biofilm, a polymicrobial organization and life form surrounded by a polysaccharide matrix, refers to an adaptation strategy of bacteria in unfavorable living conditions (e. g. under antibiotic therapy). Biofilms can develop after 6 h in highly contaminated wounds. In acute and chronic infections, biofilms can occur in 30-80 % of the cases. Only planktonic bacteria (high metabolic activity, cultivable) can be detected in standard microbiological cultures, biofilms, however, cannot. Molecular microscopic methods, such as fluorescence in situ hybridization (FISH), enable the detection of bacteria in biofilms. The core concepts of anti-biofilm therapy include the prevention of biofilm and early surgical debridement, followed by the local and/or systemic administration of antibiotics as well as the local application of antiseptics. The development of biofilm should be anticipated in strongly contaminated wounds as well as in acute and chronic infection sites. The best strategy to combat biofilms is to prevent their development. Standard microbiological culture methods do not enable the detection of biofilm. Therefore, the implementation of molecular biological detection methods (z. B. FISH) is important. Further anti-biofilm strategies are being investigated experimentally, but there are no real options for clinical use as of yet.

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

PubMed

Fridlund, Jimmy; Woksepp, Hanna; Schön, Thomas

2016-10-01

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

Utilization of carrageenan, citric acid and cinnamon oil as an edible coating of chicken fillets to prolong its shelf life under refrigeration conditions.

PubMed

Khare, Anshul Kumar; Abraham, Robinson J J; Appa Rao, V; Babu, R Narendra

2016-02-01

The present study was conducted to determine efficacy of edible coating of carrageenan and cinnamon oil to enhance the shelf life of chicken meat stored under refrigeration conditions. Chicken breast was coated with carrageenan and cinnamon oil by three methods of application viz., spraying brushing and dipping. The coated meat was evaluated for drip loss, pH, thiobarbituric acid number (TBA), tyrosine value (TV), extract release volume (ERV), Warner-Bratzler shear force value (WBSFV), instrumental color, microbiological, and sensory qualities as per standard procedures. There was a significant difference observed for physicochemical parameters (pH, TBA, TV, ERV, drip loss and WBSFV) and microbiological analysis between storage periods in all the samples and between the control and treatments throughout the storage period but samples did not differed significantly for hunter color scores. However, there was no significant difference among three methods of application throughout the storage period though dipping had a lower rate of increase. A progressive decline in mean sensory scores was recorded along with the increase in storage time. The carrageenan and cinnamon edible coating was found to be a good alternative to enhance the shelf life of chicken meat under refrigeration conditions. It was also observed from study that dipping method of the application had comparatively higher shelf life than other methods of application.

Threat of drug resistant Staphylococcus aureus to health in Nepal

PubMed Central

2014-01-01

Background Staphylococcus aureus is the most commonly isolated organism from the different clinical samples in hospital. The emergence and dissemination of methicillin resistant Staphylococcus aureus (MRSA) and growing resistance to non-beta-lactam antibiotics is making treatment of infections due to this organism increasingly difficult. Methods This study was conducted to determine the frequency of Staphylococcus aureus isolated from different clinical samples, rates of MRSA and full antibiotic susceptibility profiles. Clinical samples were cultured and Staphylococcus aureus was identified using standard microbiological methods recommended by the American Society for Microbiology (ASM). Methicillin resistance was confirmed using cefoxitin and oxacillin disks. Inducible clindamycin resistance was identified using D-zone test. Results From the processed samples, 306 isolates of Staphylococcus aureus were recovered. All the isolates were susceptible to vancomycin and teicoplanin. Methicillin resistance was observed in 43.1% of isolates while inducible clindamycin resistance in 12.4% of the isolates. Conclusions The results of our study reveals that rates of resistance to commonly prescribed antibiotics in Staphylococcus aureus clinical isolates is high. In particular, rate of methicillin resistance is alarming, prompting concern on the rational use of antibiotics and vigilant laboratory-based surveillance of resistance rates in Nepal. PMID:24655316

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.

Resistance monitoring of human pathogenic bacteria in Germany, SWOT analysis and examples.

PubMed

Witte, Wolfgang

2006-06-01

Determination of antibiotic resistance has two main goals in clinical-microbiological diagnosis. One aspect is preservation of antibacterial chemotherapy. Furthermore, trends in resistance development should be monitored and should serve as an early warning-system for occurrence and spread of new and clinically important antibiotic resistances. Plenty of data on antibiotic resistance is gathered on a routine basis in medical-microbiological diagnosis and often it is stored in electronic databases that could be interlinked. The main reason that the available data is not being used for resistance monitoring in Germany is the widely used methodology of the agar diffusion test. It is the cheapest and by far the most inaccurate method of determining resistance. The test results are not always comparable with tests for all substance groups from national standards (also limited international comparability). Trend analysis of the resistance situation in Germany can therefore only be determined through individual studies. These studies are discussed according to a SWOT analysis (SWOT = Strengths, Weaknesses, Opportunities, Threats).

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

PubMed

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

2018-03-02

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

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

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

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

2004-04-19

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

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.

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 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.

Interaction of on-site and near real time measured turbidity and enzyme activity in stream water.

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Farnleitner, Andreas H.; Zessner, Matthias

2013-04-01

On-site and on-line systems that provide an integrated surveillance of physicochemical and microbiological parameters gain significance in water quality monitoring. Particular relating to diffuse pollution from agricultural areas and use-orientated protection of waters the detection of faecal pollution is a fundamental part. For the near real time and on-site detection of microbiological faecal pollution of water, the beta-D- Glucuronidase (GLUC) enzymatic activity has been suggested as a surrogate parameter. Due to possible short measure intervals of three hours, this method has high potential as a water quality monitoring tool. While cultivation based standard determination takes more than one working day (Cabral 2010) the potential advantage of detecting the GLUC activity is the high temporal measuring resolution. Yet, there is still a big gap of knowledge on the sensitivity and specificity concerning the faecal indication capacity of GLUC in relation to standard assays (Cabral 2010). Interference effects of physicochemical parameters on the enzymatic activity respectively fluorescence have been discussed (Molina-Munoz et al. 2007; Tryland and Fiksdal 1998, Biswal et al. 2003). Results from a monitoring of a rivulet in an agricultural catchment in Lower Austria (HOAL - Hydrological Open Air Laboratory) are presented here. The HOAL offers technical resources that allow measurements at high temporal and spatial resolution and to apply various hydrological methods in one catchment. Two automated enzymatic measuring devices (Coliguard, mbOnline, Austria) and physicochemical in-stream measurements are used, as well as in-stream spectroscopy (spectrolyser, s::can, Austria). Accuracy of both enzymatic measuring devices is compared through diverse hydrological and seasonal conditions. Reference analyses by cultivation based determination were performed. Data from Coliguard devices is combined with physicochemical and spectroscopy data to gain information about the influence of turbidity on rapid GLUC measurements of stream water. During event run off conditions with high sediment load, accuracy of the GLUC determination was assayed. Various on-site set ups were tested to ascertain the use of sample prefiltration. We would like acknowledge financial support from the Austrian Science Funds (FWF) as part of the Vienna Doctoral Programme on Water Resource Systems (DK-plus W1219-N22). References: Cabral, J. P. S. 2010. "Water Microbiology. Bacterial Pathogens and Water." International Journal of Environmental Research and Public Health 7 (10): 3657-3703. Biswal , N. , S. Gupta, N. Ghosh, and A. Pradhan 2003. "Recovery of turbidity free fluorescence from measured fluorescence: An experimental approach. Optics Express 11, (24): 3320. Molina-Munoz, M., J. M. Poyatos, R. Vilchez, E. Hontoria, B. Rodelas, and J. Gonzalez-Lopez. 2007. "Effect of the Concentration of Suspended Solids on the Enzymatic Activities and Biodiversity of a Submerged Membrane Bioreactor for Aerobic Treatment of Domestic Wastewater." Applied Microbiology and Biotechnology 73 (6): 1441-1451. Tryland, I., and L. Fiksdal. 1998. "Enzyme Characteristics of β-d-Galactosidase-and β-d-Glucuronidase-Positive Bacteria and Their Interference in Rapid Methods for Detection of Waterborne Coliforms andEscherichia Coli." Applied and Environmental Microbiology 64 (3): 1018-1023.

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...

A comparison of indexing methods to evaluate quality of soils subjected to different erosion: the role of soil microbiological properties.

NASA Astrophysics Data System (ADS)

Romaniuk, Romina; Lidia, Giuffre; Alejandro, Costantini; Norberto, Bartoloni; Paolo, Nannipieri

2010-05-01

Soil quality assessment is needed to evaluate the soil conditions and sustainability of soil and crop management properties, and thus requires a systematic approach to select and interpret soil properties to be used as indicators. The aim of this work was to evaluate and compare different indexing methods to assess quality of an undisturbed grassland soil (UN), a degraded pasture soil (GL) and a no tilled soil (NT) with four different A horizon depths (25, 23, 19 and 14 cm) reflecting a diverse erosion. Twenty four soil properties were measured from 0 to10 (1) and 10 to 20 cm. (2) and a minimum data set was chosen by multivariate principal component analysis (PCA) considering all measured soil properties together (A), or according to their classification in physical, chemical or microbiological (B) properties. The measured soil properties involved either inexpensive or not laborious standard protocols, to be used in routine laboratory analysis (simple soil quality index - SSQI), or a more laborious, time consuming and expensive protocols to determine microbial diversity and microbial functionality by methyl ester fatty acids (PLFA) and catabolic response profiles (CRP), respectively (complex soil quality index - CSQI). The selected properties were linearly normalized and integrated by the weight additive method to calculate SSQI A, SSQI B, CSQI A and CSQI B indices. Two microbiological soil quality indices (MSQI) were also calculated: the MSQI 1 only considered microbiological properties according to the procedure used for calculating SQI; the MSQI 2 was calculated by considering microbial carbon biomass (MCB), microbial activity (Resp) and functional diversity determined by CPR (E). The soil quality indices were SSQI A = MCB 1 + Particulate Organic Carbon (POC)1 + Mean Weight Diameter (MWD)1; SSQI B = Saturated hydraulic conductivity (K) 1 + Total Organic Carbon (TOC) 1 + MCB 1; CSQI A = MCB 1 + POC 1 + MWD 1; CSQI B = K 1+ TOC 1+ 0.3 * (MCB 1+ i/a +POC 1) + 0,05 * (E + cy/pre), where i/a and cy/pre are the iso/anteiso and cyclopropyl/precursors ratios determined by PLFA; MSQI 1 (0,3 * (MCB 1+ i/a 1 +POC 1) + 0,05 * (E 1+ cy/pre 1) ) and MSQI 2 (MCB 1+Resp 1+ E 1). All the calculated indices differentiated references plots (UN and GL), from those under no tillage (NT) system. Values were similar in NT plots with low erosion levels (NT 25 and 23) but higher than values of plots with high erosion (NT 19 and 14). Soil quality indices constructed by procedure B, (SSQI B and CSQI B) differentiated among the studied plots with the same or higher sensitivity than the other indices and allowed evaluating the impact of soil management practices and erosion on soil physical, chemical and microbiological properties. The lack of indicators representing all soil properties (physical, chemical and biological) in SQI constructed by procedure A could decrease the index sensitivity to changes in management; and the same may happen when physical, chemical and biological properties present different weights into the calculated SQI. The inclusion of CRP and PLFA data in the indices slightly increased or did not increase the index sensitivity (CSQI A and CSQI B). Generally microbiological indices (MSQI 1 and MSQI 2) were highly sensitive to soil erosion. However, we suggest that indices integrating physical, chemical and microbiological properties may give a more complete view of the soil quality than indices only based on measurement of a few microbiological properties.

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

PubMed

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

2015-04-01

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

Evaluation of microbiological, cellular and risk factors associated with subclinical mastitis in female buffaloes

PubMed Central

de Oliveira Moura, Emmanuella; do Nascimento Rangel, Adriano Henrique; de Melo, Maria Celeste Nunes; Borba, Luiz Henrique Fernandes; de Lima Júnior, Dorgival Morais; Novaes, Luciano Patto; Urbano, Stela Antas; de Andrade Neto, Júlio César

2017-01-01

Objective This study aimed to evaluate the microbiological and cellular milk profile for the diagnosis of subclinical mastitis in female buffaloes and to assess risk factors for predisposition of the disease. Methods Analyses were carried out by standard plate count (SPC), identification of species and antibiotic resistance, somatic cell count (SCC), electrical electrical conductivity of milk (ECM), and lactoferrin content in milk. Teat cups were swabbed to evaluate risk factors, observing hyperkeratosis, milking vacuum pressure and cleanliness of the site. Hence, 30 female buffaloes were randomly selected (15 from a group in early lactation and 15 in late lactation). Results The most common bacteria in the microbiological examination were Staphylococcus spp., Streptococcus spp. and Corynebacterium sp. In the antibiotic sensitivity test, 10 (58.82%) of the 17 antibiotics tested were sensitive to all isolates, and resistant bacteria were Streptococcus uberis, Streptococcus dysgalactiae, Streptococcus haemolyticus, and Escherichia coli. It was observed that positive samples in the microbiological examination showed total bacterial count between 9.10×103 to 6.94×106 colony forming units/mL, SCC between 42,000 to 4,320,000 cells/mL and ECM ranging from 1.85 to 7.40 mS/cm. It was also found that the teat cups had high microbial counts indicating poor hygiene, and even faults in the cleanliness of the animals’ waiting room were observed. It is concluded that values of SCC above 537,000 cells/mL and ECM above 3.0 mS/mL are indications of mammary gland infection for this herd; however, the association of these values with a microbiological analysis is necessary to more accurately evaluate the health status of mammary glands with subclinical mastitis. Conclusion Through phenotypic characterization of bacteria involved in the samples, the genera Staphylococcus spp., Streptococcus spp., and Corynebacterimum bovis were the most prevalent in this study. Faults in environment and equipment hygienization are factors that are directly associated with mastitis. PMID:28183165

Surface Dielectric Barrier Discharge Jet for Skin Disinfection

NASA Astrophysics Data System (ADS)

Creyghton, Yves; Meijer, Rogier; Verweij, Paul; van der Zanden, Frank; Leenders, Paul

A consortium consisting of the research institute TNO, the medical ­university and hospital St Radboud and two industrial enterprises is working on a non-thermal plasma treatment method for hand disinfection. The group is seeking for cooperation, in particular in the field of validation methods and potential ­standardization for plasma based disinfection procedures. The present paper describes technical progress in plasma source development together with initial microbiological data. Particular properties of the sheet shaped plasma volume are the possibility of treating large irregular surfaces in a short period of time, effective plasma produced species transfer to the surface together with high controllability of the nature of plasma species by means of temperature conditioning.

[What should be the length and inner diameter of the testing device for microbiological efficacy testing of formaldehyde gas sterilization methods?].

PubMed

Spicher, G; Borchers, U

1984-10-01

The series of tests described in a preceding publication (Spicher and Borchers, 1983) has been continued in a modified way. This time, the dependency of the microbiological test results of a formaldehyde gas sterilization procedure on length and inner diameter of the tubes serving as test pieces was examined. The tubes were 1 or 2 m in length with an inner diameter of 1 or 2 mm. The tests were performed with four different preparations of bioindicators. Spores of Bac. stearothermophilus served as test germs. The preparations differed in the type of suspension used for the preparation of the bioindicators: distilled water, diluted blood (10%), undiluted blood, 10% albumin solution. The spore suspensions had been dried on linen thread. During the test procedure, the bioindicators were located near the sealed end of the tube. After completion of the sterilization procedure, the bioindicators were examined for viable germs. In tubes of identical length, the frequency of indicators carrying viable germs was always higher in those of 1 mm than in those of 2 mm inner diameter. In tubes of identical inner diameter, the frequency of indicators carrying viable germs in those of 2 m length was always higher than in those of 1 m length. This regularity was independent of the type of bioindicators used. The bioindicators for the preparation of which a 10% albumin solution had been employed showed the highest resistance. A somewhat lower resistance was found for the bioindicators prepared with undiluted blood. The bioindicators for which the spores had been suspended in diluted blood proved to have the lowest resistance. If the spores had been suspended in distilled water, the resistance of the bioindicators was a little lower than that of those suspended in undiluted blood, but was higher than that of the dried spores with diluted blood. The test results confirm the effectiveness of the method proposed earlier, i.e. to deposit the bioindicators in special test pieces (e.g. tubes or sounds) for the microbiological testing of formaldehyde gas sterilization procedures. These test pieces must be at least as long and as narrow as the longest and narrowest cavity of the object to be sterilized (tubes, catheters). In order to standardize the microbiological testing of formaldehyde gas sterilization procedures and to guarantee a certain minimum efficiency, the bioindicator as well as the test piece and its size (length and inner diameter) should be standardized.(ABSTRACT TRUNCATED AT 400 WORDS)

[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.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

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

1989-01-01

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

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

PubMed Central

Hsu, M C; Hsu, P W

1992-01-01

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

Utilization of carrageenan, citric acid and cinnamon oil as an edible coating of chicken fillets to prolong its shelf life under refrigeration conditions

PubMed Central

Khare, Anshul Kumar; Abraham, Robinson J. J.; Appa Rao, V.; Babu, R. Narendra

2016-01-01

Aim: The present study was conducted to determine efficacy of edible coating of carrageenan and cinnamon oil to enhance the shelf life of chicken meat stored under refrigeration conditions. Materials and Methods: Chicken breast was coated with carrageenan and cinnamon oil by three methods of application viz., spraying brushing and dipping. The coated meat was evaluated for drip loss, pH, thiobarbituric acid number (TBA), tyrosine value (TV), extract release volume (ERV), Warner-Bratzler shear force value (WBSFV), instrumental color, microbiological, and sensory qualities as per standard procedures. Results: There was a significant difference observed for physicochemical parameters (pH, TBA, TV, ERV, drip loss and WBSFV) and microbiological analysis between storage periods in all the samples and between the control and treatments throughout the storage period but samples did not differed significantly for hunter color scores. However, there was no significant difference among three methods of application throughout the storage period though dipping had a lower rate of increase. A progressive decline in mean sensory scores was recorded along with the increase in storage time. Conclusion: The carrageenan and cinnamon edible coating was found to be a good alternative to enhance the shelf life of chicken meat under refrigeration conditions. It was also observed from study that dipping method of the application had comparatively higher shelf life than other methods of application. PMID:27051203

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

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

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

1985-05-01

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

A waterborne outbreak of multiple diarrhoeagenic Escherichia coli infections associated with drinking water at a school camp.

PubMed

Park, Jungsun; Kim, Jin Seok; Kim, Soojin; Shin, Eunkyung; Oh, Kyung-Hwan; Kim, Yonghoon; Kim, Cheon Hyeon; Hwang, Min Ah; Jin, Chan Mun; Na, Kyoungin; Lee, Jin; Cho, Enhi; Kang, Byung-Hak; Kwak, Hyo-Sun; Seong, Won Keun; Kim, Junyoung

2018-01-01

In June 2015, a local public health laboratory was notified that students had developed gastroenteritis symptoms after attending a camp. An outbreak investigation was conducted to determine the extent and cause of the outbreak. A retrospective cohort study was conducted to determine the correlations between the illness and specific exposures at the school camp. All attendees were interviewed with a standard questionnaire that addressed clinical symptoms, food consumption, and environmental exposures. Clinical specimens were cultured using standard microbiological methods for bacterial and viral pathogens. The genetic relationships of all isolates were determined using pulsed-field gel electrophoresis (PFGE). A total 188 patients with symptoms of diarrhoea, abdominal pain, and nausea were identified. The completed questionnaires suggested that the consumption of drinking water was likely to be linked to this outbreak. Using microbiological methods, enterohaemorrhagic Escherichia coli, enteropathogenic E. coli, and enteroaggregative E. coli were isolated, and the isolates from both patient stool and environmental water samples displayed indistinguishable XbaI-PFGE patterns. The water system in the camp used groundwater drawn from a private underground reservoir for cooking and drinking. The environmental investigation revealed some problems with the water supply system, such as the use of inappropriate filters in the water purifier and a defect in the pipeline between the reservoir and the chlorination device. This outbreak points to the importance of drinking water quality management in group facilities where underground water is used and emphasizes the need for periodic sanitation and inspection to prevent possible waterborne outbreaks. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

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.

Experiments with Writing to Teach Microbiology.

ERIC Educational Resources Information Center

Cannon, Robert E.

1990-01-01

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

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

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

PubMed

Burillo, Almudena; Moreno, Antonio; Salas, Carlos

2007-11-01

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

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.

[CONTEMPORARY MOLECULAR-GENETIC METHODS USED FOR ETIOLOGIC DIAGNOSTICS OF SEPSIS].

PubMed

Gavrilov, S N; Skachkova, T S; Shipulina, O Yu; Savochkina, Yu A; Shipulin, G A; Maleev, V V

2016-01-01

Etiologic diagnostics of sepsis is one of the most difficult problems of contemporary medicine due to a wide variety of sepsis causative agents, many of which are components of normal human microflora. Disadvantages of contemporary "golden standard" of microbiologic diagnostics of sepsis etiology by seeding of blood for sterility are duration of cultivation, limitation in detection of non-cultivable forms of microorganisms, significant effect of preliminary empiric antibiotics therapy on results of the analysis. Methods of molecular diagnostics that are being actively developed and integrated during the last decade are deprived of these disadvantages. Main contemporary methods of molecular-biological diagnostics are examined in the review, actualdata on their diagnostic characteristic are provided. Special attention is given to methods of PCR-diagnostics, including novel Russian developments. Methods of nucleic acid hybridization and proteomic analysis are examined in comparative aspect. Evaluation of application and perspectives of development of methods of molecular diagnostics of sepsis is given.

[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.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-08-25

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

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.

Diagnosis of Pulmonary Tuberculosis in HIV-Positive Patients by Microscopic Observation Drug Susceptibility Assay ▿

PubMed Central

Ha, Dang Thi Minh; Lan, Nguyen Thi Ngoc; Kiet, Vo Sy; Wolbers, Marcel; Hang, Hoang Thi Thanh; Day, Jeremy; Hien, Nguyen Quang; Tien, Nguyen Anh; An, Pham Thuy; Anh, Truong Thi; Oanh, Do Thi Tuong; Hoa, Chau Luong; Chau, Nguyen Thi Minh; Hai, Nguyen Ngoc; Binh, Ngo Thanh; Ngoc, Le Hong; Phuong, Doan Thanh; Quyet, Tran Van; Tuyen, Nguyen Thi Bich; Ha, Vo Thi; Nho, Nguyen Thi; Hoa, Dai Viet; Anh, Phan Thi Hoang; Dung, Nguyen Huy; Farrar, Jeremy; Caws, Maxine

2010-01-01

The microscopic observation drug susceptibility assay (MODS) is a novel and promising test for the early diagnosis of tuberculosis (TB). We evaluated the MODS assay for the early diagnosis of TB in HIV-positive patients presenting to Pham Ngoc Thach Hospital for Tuberculosis and Lung Diseases in southern Vietnam. A total of 738 consecutive sputum samples collected from 307 HIV-positive individuals suspected of TB were tested by smear, MODS, and the mycobacteria growth indicator tube method (MGIT). The diagnostic sensitivity and specificity of MODS compared to the microbiological gold standard (either smear or MGIT) were 87 and 93%, respectively. The sensitivities of smear, MODS, and MGIT were 57, 71, and 75%, respectively, against clinical gold standard (MODS versus smear, P < 0.001; MODS versus MGIT, P = 0.03). The clinical gold standard was defined as patients who had a clinical examination and treatment consistent with TB, with or without microbiological confirmation. For the diagnosis of smear-negative patients, the sensitivities of MODS and MGIT were 38 and 45%, respectively (P = 0.08). The median times to detection using MODS and MGIT were 8 and 11 days, respectively, and they were 11 and 17 days, respectively, for smear-negative samples. The original bacterial/fungal contamination rate of MODS was 1.1%, while it was 2.6% for MGIT. The cross-contamination rate of MODS was 4.7%. In conclusion, MODS is a sensitive, specific, and rapid test that is appropriate for the detection of HIV-associated TB; its cost and ease of use make it particularly useful in resource-limited settings. PMID:20926704

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

PubMed

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

2018-03-21

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

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

PubMed Central

Hecer, Canan; Kaynarca, Doruk; Berkan, Şifa

2018-01-01

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

Experimental methods for studying microbial survival in extraterrestrial environments.

PubMed

Olsson-Francis, Karen; Cockell, Charles S

2010-01-01

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

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.

Differences in sheep and goats milk microbiological profile between conventional and organic farming systems in Greece.

PubMed

Malissiova, Eleni; Papadopoulos, Theofilos; Kyriazi, Aikaterini; Mparda, Maria; Sakorafa, Christina; Katsioulis, Antonios; Katsiaflaka, Anna; Kyritsi, Maria; Zdragas, Antonios; Hadjichristodoulou, Christos

2017-05-01

The aim of this study was to examine differences in the microbiological profile and antimicrobial resistance of bacteria isolated from milk from organic and conventional sheep and goat farms. Twenty-five organic and 25 conventional sheep and goat farms in the region of Thessaly, Greece participated in this study. A standardised detailed questionnaire was used to describe farming practices. A total of 50 samples were collected and analysed for total viable count (TVC), total coliform count (TCC) and somatic cell count (SCC), while Staphylococcus aureus and Escherichia coli were isolated using standard methods. Isolates were identified at species level by Api-test and Matrix-Assisted Laser Desorption/Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF MS). Susceptibility to a panel of 20 for E. coli and 16 for S. aureus antimicrobials was determined by the agar dilution method. Pulsed Field Gel Electrophoresis (PFGE) was performed for S. aureus and E. coli isolates to determine predominant clones. Lower counts of TVC, TCC and SCC were identified in milk from the organic farms, possibly due to differences in the hygienic farming practices found on those farms. API-tests and MALDI-TOF MS showed no significant differences in the S. aureus and E. coli isolates. Overall, antimicrobial resistance rates were low, while a statistically higher percentage was estimated among strains originating from conventional farms in comparison with organic farms, possibly due to the restriction of antibiotic use in organic farming. PFGE revealed diversity among S. aureus and E. coli populations in both organic and conventional farms indicating circulation of 2-3 main clones changing slightly during their evolution. Consequently, there is evidence that milk from the organic farms presents a better microbiological profile when compared with milk from conventional farms.

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

USDA-ARS?s Scientific Manuscript database

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

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.

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

PubMed

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

2014-07-01

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

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.

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

PubMed

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

2011-01-01

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

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

USDA-ARS?s Scientific Manuscript database

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

[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.

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.

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.

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.

Principles of Sterilization of Mars Descent Vehicle Elements

NASA Astrophysics Data System (ADS)

Trofimov, Vladislav; Deshevaya, Elena; Khamidullina, N.; Kalashnikov, Viktor

Due to COSPAR severe requirements to permissible microbiological contamination of elements of down-to-Mars S/C as well as complexity of their chemical composition and structure the exposure of such S/C elements to antimicrobial treatment (sterilization) at their integration requires application of a wide set of methods: chemical, ultraviolet, radiation. The report describes the analysis of all the aspects of applicable methods of treatment for cleaning of elements’ surfaces and inner contents from microbiota. The analysis showed that the most important, predictable and controllable method is radiation processing (of the elements which don’t change their properties after effective treatment). The experience of ionizing radiation application for sterilization of products for medicine, etc. shows that, depending on initial microbial contamination of lander elements, the required absorbed dose can be within the range 12 ÷ 35 kGr. The analysis of the effect of irregularity of radiation absorption in complex structure elements to the choice of radiation methodology was made and the algorithm of the choice of effective conditions of radiation treatment and control of sterilization efficiency was suggested. The important phase of establishing of the effective condition of each structure element treatment is experimental verification of real microbiological contamination in terms of S/C integration, contamination maximum decrease using another cleaning procedures (mechanical, chemical, ultraviolet) and determination of radiation resistance of spore microorganisms typical for the shops of space technology manufacturing and assembling. Proceeding from three parameters (irregularity of radiation absorption in a concrete element, its initial microbial contamination and resistance of microorganisms to the effect of radiation) the condition of the packed object sterilization is chosen, the condition that prevents secondary contamination, ensures given reliability of the treatment without final experimental microbiological verification only by simple control of the absorbed dose at critical points. All the process phases (from the choice of treatment conditions to provision of the procedure safety) are strictly regulated by Russian legislation in accordance with international standards.

[Rapid identification of microorganisms by mass spectrometry in a blood culture system. Comparison of two procedures].

PubMed

Cattani, María E; Posse, Tamara; Hermes, Ricardo L; Kaufman, Sara C

2015-01-01

Rapid identification of microorganisms is critical in hospitalized infected patients. Blood culture is currently the gold standard for detecting and identifying microorganisms causing bacteremia or sepsis. The introduction of mass spectrometry by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS) in microbiology laboratories, especially in microorganisms growing in blood culture bottles, provides rapid identification. This study evaluates the performance of the Maldi Sepsityper Biotyper procedure (hereinafter, MS) compared to that of an in-home method (hereinafter, HF). Eight hundred and forty (840) positive blood culture bottles were processed using the HF procedure, 542 of which were also processed using MS. The organisms were identified in 670 (79.76%) and 391 (72.14%) bottles respectively (p = 0,0013). This study demonstrates the effectiveness of both procedures for identifying microorganisms directly from positive blood culture bottles. However, the HF procedure proved to be more effective than MS, especially in the presence of Gram positive organisms. Copyright © 2015 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

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

PubMed

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

2017-08-01

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

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

PubMed

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

2012-01-01

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

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.

Destruction of Bacillus cereus spores in a thick soy bean paste (doenjang) by continuous ohmic heating with five sequential electrodes.

PubMed

Ryang, J H; Kim, N H; Lee, B S; Kim, C T; Rhee, M S

2016-07-01

This study selected spores from Bacillus cereus FSP-2 strain (the isolate from a commercial doenjang processing line) as the test strain which showed significantly higher thermal resistance (P < 0·05) than B. cereus reference strain (ATCC 27348). The spores in doenjang were subjected to ohmic heating (OH) at 95, 105, 115 and 125°C for 30, 60 or 90 s using a five sequential electrode system (electrical field: 26·7 V cm(-1) ; alternating current frequency: 25 kHz). OH at 105°C for 30-90 s reduced the B. cereus spore count in doenjang samples to <4 log CFU g(-1) . Since OH treatment at 115 and 125°C caused a perceivable colour change in the product (>1·5 National Bureau of Standards units), treatment at 105°C for 60 s was selected and applied on a large scale (500 kg of product). Reliable and reproducible destruction of B. cereus spores occurred; the reductions achieved (to < 4 log CFU g(-1) ) met the Korean national standards. Scanning electron microscopy revealed microstructural alterations in the spores (shrinkage and a distorted outer spore coat). OH is an effective method for destroying B. cereus spores to ensure the microbiological quality and safety of a thick, highly viscous sauce. This study shows that an ohmic heating (OH) using a five sequential electrode system can effectively destroy highly heat-resistant Bacillus cereus spores which have been frequently found in a commercial doenjang processing line without perceivable quality change in the product. In addition, it may demonstrate high potential of the unique OH system used in this study that will further contribute to ensure microbiological quality and safety of crude sauces containing high levels of electrolyte other than doenjang as well. © 2016 The Society for Applied Microbiology.

Comparative performance of Thin Layer Agar and Löwenstein-Jensen culture for diagnosis of tuberculosis.

PubMed

Battaglioli, T; Rintiswati, N; Martin, A; Palupi, K R; Bernaerts, G; Dwihardiani, B; Ahmad, R A; Matthys, F; Mahendradhata, Y; Van der Stuyft, P

2013-11-01

Sputum smear microscopy for the diagnosis of tuberculosis (TB) is cheap and simple but its sensitivity is low. Culture on Löwenstein-Jensen (LJ) is more sensitive but it takes a long time to yield results. Thin-Layer Agar (TLA) culture was suggested as an equally sensitive and faster alternative. We evaluated the performance of TLA for diagnosing TB in Jogjakarta, Indonesia. People with suspected TB presenting from July 2010 to July 2011 to two chest clinics of the National TB Control Programme network of Jogjakarta were eligible for inclusion. A sputum sample was sent to the Gadjah Mada University microbiology laboratory for concentration, smearing, Ziehl-Neelsen staining and culture on LJ and TLA. Sensitivity of cultures was evaluated against a composite reference standard (any positive culture). Time to detection of Mycobacteria was recorded. Out of 1414 samples, 164 (12%) were smear positive, 99 (7%) were scanty and 1151 (81%) were negative. On TLA and LJ respectively, 168 (12%) and 149 (11%) samples were positive, 72 (5%) and 32 (2%) were contaminated (κ = 0.64; 95% CI 0.59-0.69, p <0.01). Using the reference standard, 196 (14%) TB cases were identified. The sensitivity of TLA was 0.86 (95% CI 0.80-0.90), significantly higher (p 0.03) than for LJ (0.76; 95% CI 0.69-0.81). The median time to detection in days was significantly shorter (p <0.01) for TLA (12; 95% CI 11-13) than for LJ (44; 95% CI 43-45). TLA is a rapid and sensitive method for the diagnosis of TB. Implementation studies to evaluate the cost-effectiveness and impact of its introduction into programmatic settings are urgently needed. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Diagnosing periprosthetic infection: false-positive intraoperative Gram stains.

PubMed

Oethinger, Margret; Warner, Debra K; Schindler, Susan A; Kobayashi, Hideo; Bauer, Thomas W

2011-04-01

Intraoperative Gram stains have a reported low sensitivity but high specificity when used to help diagnose periprosthetic infections. In early 2008, we recognized an unexpectedly high frequency of apparent false-positive Gram stains from revision arthroplasties. The purpose of this report is to describe the cause of these false-positive test results. We calculated the sensitivity and specificity of all intraoperative Gram stains submitted from revision arthroplasty cases during a 3-month interval using microbiologic cultures of the same samples as the gold standard. Methods of specimen harvesting, handling, transport, distribution, specimen processing including tissue grinding/macerating, Gram staining, and interpretation were studied. After a test modification, results of specimens were prospectively collected for a second 3-month interval, and the sensitivity and specificity of intraoperative Gram stains were calculated. The retrospective review of 269 Gram stains submitted from revision arthroplasties indicated historic sensitivity and specificity values of 23% and 92%, respectively. Systematic analysis of all steps of the procedure identified Gram-stained but nonviable bacteria in commercial broth reagents used as diluents for maceration of periprosthetic membranes before Gram staining and culture. Polymerase chain reaction and sequencing showed mixed bacterial DNA. Evaluation of 390 specimens after initiating standardized Millipore filtering of diluent fluid revealed a reduced number of positive Gram stains, yielding 9% sensitivity and 99% specificity. Clusters of false-positive Gram stains have been reported in other clinical conditions. They are apparently rare related to diagnosing periprosthetic infections but have severe consequences if used to guide treatment. Even occasional false-positive Gram stains should prompt review of laboratory methods. Our observations implicate dead bacteria in microbiologic reagents as potential sources of false-positive Gram stains.

Adenosine Triphosphate Quantification Correlates Poorly with Microbial Contamination of Duodenoscopes.

PubMed

Olafsdottir, Lovisa B; Wright, Sharon B; Smithey, Anne; Heroux, Riley; Hirsch, Elizabeth B; Chen, Alice; Lane, Benjamin; Sawhney, Mandeep S; Snyder, Graham M

2017-06-01

OBJECTIVE The aim of this study was to quantify the correlation between adenosine triphosphate (ATP) measurements and bacterial cultures from duodenoscopes for evaluation of contamination following high-level disinfection. DESIGN Duodenoscopes used for any intended endoscopic retrograde cholangiopancreatography (ERCP) procedure were included. Microbiologic and ATP data were collected concomitantly and in the same manner from ERCP duodenoscopes. SETTING A high-volume endoscopy unit at a tertiary referral acute-care facility. METHODS Duodenoscopes were sampled for ATP and bacterial contamination in a contemporaneous and highly standardized fashion using a "flush-brush-flush" method for the working channel (WC) and a dry flocked swab for the elevator mechanism (EM). Specimens were processed for any aerobic bacterial growth (colony-forming units, CFU). Growth of CFU>0 and ATP relative light unit (RLU)>0 was considered a contaminated result. Frequency of discord between among WC and EM measurements were calculated using 2×2 contingency tables. The Spearman correlation coefficient was used to calculate the relatedness of bacterial contamination and ATP as continuous measurements. RESULTS The Spearman correlation coefficient did not demonstrate significant relatedness between ATP and CFU for either a WC or EM site. Among 390 duodenoscope sampling events, ATP and CFU assessments of contamination were discordant in 82 of 390 WC measurements (21%) and 331 of 390 of EM measurements (84.9%). The EM was frequently and markedly positive by ATP measurement. CONCLUSION ATP measurements correlate poorly with a microbiologic standard assessing duodenoscope contamination, particularly for EM sampling. ATP may reflect biological material other than nonviable aerobic bacteria and may not serve as an adequate marker of bacterial contamination. Infect Control Hosp Epidemiol 2017;38:678-684.

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

PubMed

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

2010-08-05

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

Microbiology Education in Nursing Practice.

PubMed

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

2017-01-01

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

Microbiology Education in Nursing Practice†

PubMed Central

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

2017-01-01

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

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

USGS Publications Warehouse

Briggs, Kay Marano

2010-01-01

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

Quality assessment of pollution indicators in marine water at critical locations of the Gulf of Mannar Biosphere Reserve, Tuticorin.

PubMed

Rajendran, Viji; Nirmaladevi D, Shrinithivihahshini; Srinivasan, Balakrishnan; Rengaraj, Chithradevi; Mariyaselvam, Sheelamary

2018-01-01

The present study focused on the shoreline environment of urban and industrial areas, and the aim of this study was to assess the coastal water quality in the Gulf of Mannar Biosphere Reserve. Water samples were collected from five different coastal sites during the premonsoon and monsoon seasons. The samples were analyzed following the standard methods. The results showed that the levels of microbiological indicators in the samples highly exceeded the regional and national standard seawater permissible limits, and environmental parameters such as the total suspended solid and dissolved oxygen were affected significantly (p<0.05). To identify frequent pollution indicators, their levels should be estimated to determine possible pollution in coastal ecosystems due to human interventions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Blood thiamine values in captive adult African lions (Panthera leo).

PubMed

Hoover, John P; DiGesualdo, Cynthia L

2005-09-01

Heparinized whole-blood samples from 22 adult African lions (Panthera leo) fed diets considered nutritionally adequate in 10 American Zoo and Aquarium Association member zoos in North America were provided for this study. Blood thiamine values were estimated using a standard microbiological assay method. The mean +/- standard deviation for blood thiamine values was 249.3 +/- 43.5 nmol/L with a range in values from 160 to 350 nmol/L after exclusion of one outlier. There were no differences (P > 0.05) in the mean blood thiamine values of male and female lions, or of lions that were over and under 10 yr of age. This range (160 to 350 nmol/L) is proposed as a reasonable estimate of the expected range in blood thiamine values for captive adult African lions as currently fed in North American zoos.

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

PubMed Central

Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor Faksvaag; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael

2017-01-01

Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution. PMID:28045981

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.

PubMed

Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor Faksvaag; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael; Ambur, Ole Herman

2017-01-01

Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

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.

Rapid bacterial antibiotic susceptibility test based on simple surface-enhanced Raman spectroscopic biomarkers

NASA Astrophysics Data System (ADS)

Liu, Chia-Ying; Han, Yin-Yi; Shih, Po-Han; Lian, Wei-Nan; Wang, Huai-Hsien; Lin, Chi-Hung; Hsueh, Po-Ren; Wang, Juen-Kai; Wang, Yuh-Lin

2016-03-01

Rapid bacterial antibiotic susceptibility test (AST) and minimum inhibitory concentration (MIC) measurement are important to help reduce the widespread misuse of antibiotics and alleviate the growing drug-resistance problem. We discovered that, when a susceptible strain of Staphylococcus aureus or Escherichia coli is exposed to an antibiotic, the intensity of specific biomarkers in its surface-enhanced Raman scattering (SERS) spectra drops evidently in two hours. The discovery has been exploited for rapid AST and MIC determination of methicillin-susceptible S. aureus and wild-type E. coli as well as clinical isolates. The results obtained by this SERS-AST method were consistent with that by the standard incubation-based method, indicating its high potential to supplement or replace existing time-consuming methods and help mitigate the challenge of drug resistance in clinical microbiology.

[Mass spectrometry in the clinical microbiology laboratory].

PubMed

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

2012-12-01

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

Recent advances in diagnostic microbiology.

PubMed

Bravo, Lulette Tricia C; Procop, Gary W

2009-07-01

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

Sampling methods and data generation

USDA-ARS?s Scientific Manuscript database

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

Antimicrobial Testing Methods & Procedures: MB-10-06

EPA Pesticide Factsheets

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

Salmonella enterica isolates from pasture-raised poultry exhibit antimicrobial resistance and class I integrons.

PubMed

Melendez, S N; Hanning, I; Han, J; Nayak, R; Clement, A R; Wooming, A; Hererra, P; Jones, F T; Foley, S L; Ricke, S C

2010-12-01

While considerable foodborne pathogen research has been conducted on conventionally produced broilers and turkeys, few studies have focused on free-range (organic) or pastured poultry. The current surveillance study was designed to isolate, identify and genetically characterize Salmonella from pastured poultry farm environment and from retail samples. In this study, 59 isolates were collected from two pastured poultry farms (n = 164; pens, feed, water and insect traps) and retail carcasses (n = 36) from a local natural foods store and a local processing plant. All isolates were serotyped and analysed phenotypically (antimicrobial resistance profiles) and genotypically (DNA fingerprints, plasmid profiles and integron analysis). Salmonella enterica was detected using standard microbiological methods. Salmonella Kentucky was the most prevalent serotype detected from the sampled sources (53%), followed by Salmonella Enteritidis (24%), Bareilly (10%), Mbandaka (7%), Montevideo (5%) or Newport (2%). All isolates were resistant to sulfisoxazole and novobiocin, and the majority (40/59) possessed class I integrons shown by PCR detection. Each Salmonella serotype elicited a distinct pulsed-field gel electrophoresis fingerprint profile, and unique differences were observed among the serotypes.  The findings of this study show that Salmonella serotypes isolated from pasture-raised poultry exhibit antimicrobial resistance and class I integrons.  This study demonstrates that despite the cessation of antibiotic usage in poultry production, antibiotic resistant Salmonella may still be recovered from the environment and poultry products. © 2010 The Authors. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology.

Methods for microbiological and immunological studies of space flight crews

NASA Technical Reports Server (NTRS)

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

1978-01-01

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

Extreme value theory applied to the definition of bathing water quality discounting limits.

PubMed

Haggarty, R A; Ferguson, C A; Scott, E M; Iroegbu, C; Stidson, R

2010-02-01

The European Community Bathing Water Directive (European Parliament, 2006) set compliance standards for bathing waters across Europe, with minimum standards for microbiological indicators to be attained at all locations by 2015. The Directive allows up to 15% of samples affected by short-term pollution episodes to be disregarded from the figures used to classify bathing waters, provided certain management criteria have been met, including informing the public of short-term water pollution episodes. Therefore, a scientifically justifiable discounting limit is required which could be used as a management tool to determine the samples that should be removed. This paper investigates different methods of obtaining discounting limits, focusing in particular on extreme value methodology applied to data from Scottish bathing waters. Return level based limits derived from threshold models applied at a site-specific level improved the percentage of sites which met at least the minimum required standard. This approach provides a method of obtaining limits which identify the samples that should be removed from compliance calculations, although care has to be taken in terms of the quantity of data which is removed. (c) 2009 Elsevier Ltd. All rights reserved.

Emerging Technologies for the Clinical Microbiology Laboratory

PubMed Central

Buchan, Blake W.

2014-01-01

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

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

PubMed

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

2012-08-01

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

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

PubMed

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

2013-07-01

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

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

PubMed Central

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

2013-01-01

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

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

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

Microbial Load Monitor

NASA Technical Reports Server (NTRS)

Gibson, S. F.; Royer, E. R.

1979-01-01

The Microbial Load Monitor (MLM) is an automated and computerized system for detection and identification of microorganisms. Additionally, the system is designed to enumerate and provide antimicrobic susceptibility profiles for medically significant bacteria. The system is designed to accomplish these tasks in a time of 13 hours or less versus the traditional time of 24 hours for negatives and 72 hours or more for positives usually required for standard microbiological analysis. The MLM concept differs from other methods of microbial detection in that the system is designed to accept raw untreated clinical samples and to selectively identify each group or species that may be present in a polymicrobic sample.

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.

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.

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.

Unique blood culture for diagnosis of bloodstream infections in emergency departments: a prospective multicentre study.

PubMed

Dargère, S; Parienti, J-J; Roupie, E; Gancel, P-E; Wiel, E; Smaiti, N; Loiez, C; Joly, L-M; Lemée, L; Pestel-Caron, M; du Cheyron, D; Verdon, R; Leclercq, R; Cattoir, V

2014-11-01

Detection of microorganisms by blood cultures (BCs) is essential in managing patients with bacteraemia. Rather than the number of punctures, the volume of blood drawn is considered paramount in efficient and reliable detection of microorganisms. We performed a 1-year prospective multicentre study in adult emergency departments of three French university hospitals comparing two methods for BCs: a unique blood culture (UBC) collecting a large volume of blood (40 mL) and the standard method of multiple blood cultures (MBC). The performances of both methods for bacterial contamination and efficient microbial detection were compared, each patient serving as his own control. Amongst the 2314 patients included, three hundred were positive for pathogens (n=245) or contaminants (n=55). Out of the 245 patients, 11 were positive for pathogens by UBC but negative by MBC and seven negative by UBC but positive by MBC (p 0.480). In the subgroup of 137 patients with only two BCs, UBC was superior to MBC (p 0.044). Seven and 17 patients had contaminated BCs by UBC and MBC only, respectively (p 0.062). Considering the sums of pathogens missed and contaminants, UBC significantly outperformed MBC (p 0.045). Considering the complete picture of cost savings, efficient detection of microorganisms and decrease in contaminations, UBC offers an interesting alternative to MBC. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

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.

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

PubMed

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

2010-10-01

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

Use of an automated blood culture system (BD BACTEC™) for diagnosis of prosthetic joint infections: easy and fast.

PubMed

Minassian, Angela M; Newnham, Robert; Kalimeris, Elizabeth; Bejon, Philip; Atkins, Bridget L; Bowler, Ian C J W

2014-05-04

For the diagnosis of prosthetic joint infection (PJI) automated BACTEC™ blood culture bottle methods have comparable sensitivity, specificity and a shorter time to positivity than traditional cooked meat enrichment broth methods. We evaluate the culture incubation period required to maximise sensitivity and specificity of microbiological diagnosis, and the ability of BACTEC™ to detect slow growing Propionibacteria spp. Multiple periprosthetic tissue samples taken by a standardised method from 332 patients undergoing prosthetic joint revision arthroplasty were cultured for 14 days, using a BD BACTEC™ instrumented blood culture system, in a prospective study from 1st January to 31st August 2012. The "gold standard" definition for PJI was the presence of at least one histological criterion, the presence of a sinus tract or purulence around the device. Cases where > =2 samples yielded indistinguishable isolates were considered culture-positive. 1000 BACTEC™ bottle cultures which were negative after 14 days incubation were sub-cultured for Propionibacteria spp. 79 patients fulfilled the definition for PJI, and 66 of these were culture-positive. All but 1 of these 66 culture-positive cases of PJI were detected within 3 days of incubation. Only one additional (clinically-insignificant) Propionibacterium spp. was identified on terminal subculture of 1000 bottles. Prolonged microbiological culture for 2 weeks is unnecessary when using BACTEC™ culture methods. The majority of clinically significant organisms grow within 3 days, and Propionibacteria spp. are identified without the need for terminal subculture. These findings should facilitate earlier decisions on final antimicrobial prescribing.

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...

Evaluation of antimicrobial effect of azadirachtin plant extract (Soluneem (™)) on commonly found root canal pathogenic microorganisms (viz. Enterococcus faecalis) in primary teeth: A microbiological study.

PubMed

Shah, Shanal; Venkataraghavan, Karthik; Choudhary, Prashant; Mohammad, Shameer; Trivedi, Krishna; Shah, Shalin G

2016-01-01

The aim of this study is to evaluate the antimicrobial activity of Soluneem ™ when used as an irrigating solution along with other commonly used irrigating solution sodium hypochlorite (NaOCl) against Enterococcus faecalis. Microorganism used in this study was E. faecalis (Microbial Type Culture Collection 439). Test substance used was Soluneem ™, which was obtained from Vittal Mallya Scientific Research Foundation (VMSRF), Bengaluru. This study was conducted in a microbiology laboratory (Biocare Research India Pvt., Ltd. Laboratory, Ahmedabad, Gujarat) to evaluate the antimicrobial effect of Soluneem ™ (Azadirachtin) on E. faecalis. Antimicrobial activity testing was performed using the macrobroth dilution method according to the Clinical Laboratory Standards Institute guidelines. All determinations were performed thrice. Minimum bactericidal concentration (MBC) was seen as 2.6% for Soluneem ™ while the same was seen at 0.1% for NaOCl. Independent sample t-test was carried out to compare the MBC of Soluneem ™ and NaOCl, which showed that there was no statistically significant difference between them, i.e., 2.6% Soluneem ™ was as effective as 0.1% NaOCl. Soluneem ™ showed antimicrobial activity against E. faecalis at various concentrations. It was also found that the efficacy of Soluneem ™ at 2.6% concentration and above was relatively similar to that of gold standard irrigating solution (NaOCl) on inhibition of E. faecalis.

Determination of teicoplanin concentrations in serum by high-pressure liquid chromatography.

PubMed Central

Joos, B; Lüthy, R

1987-01-01

An isocratic reversed-phase high-pressure liquid chromatographic method for the determination of six components of the teicoplanin complex in biological fluid was developed. By using fluorescence detection after precolumn derivatization with fluorescamine, the assay is specific and highly sensitive, with reproducibility studies yielding coefficients of variation ranging from 1.5 to 8.5% (at 5 to 80 micrograms/ml). Response was linear from 2.5 to 80 micrograms/ml (r = 0.999); the recovery from spiked human serum was 76%. An external quality control was performed to compare this high-pressure liquid chromatographic method (H) with a standard microbiological assay (M); no significant deviation from slope = 1 and intercept = 0 was found by regression analysis (H = 1.03M - 0.45; n = 15). PMID:2957953

Commutability of food microbiology proficiency testing samples.

PubMed

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

2014-03-01

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

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.

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

PubMed Central

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

2017-01-01

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

Cutibacterium acnes molecular typing: time to standardize the method.

PubMed

Dagnelie, M-A; Khammari, A; Dréno, B; Corvec, S

2018-03-12

The Gram-positive, anaerobic/aerotolerant bacterium Cutibacterium acnes is a commensal of healthy human skin; it is subdivided into six main phylogenetic groups or phylotypes: IA1, IA2, IB, IC, II and III. To decipher how far specific subgroups of C. acnes are involved in disease physiopathology, different molecular typing methods have been developed to identify these subgroups: i.e. phylotypes, clonal complexes, and types defined by single-locus sequence typing (SLST). However, as several molecular typing methods have been developed over the last decade, it has become a difficult task to compare the results from one article to another. Based on the scientific literature, the aim of this narrative review is to propose a standardized method to perform molecular typing of C. acnes, according to the degree of resolution needed (phylotypes, clonal complexes, or SLST types). We discuss the existing different typing methods from a critical point of view, emphasizing their advantages and drawbacks, and we identify the most frequently used methods. We propose a consensus algorithm according to the needed phylogeny resolution level. We first propose to use multiplex PCR for phylotype identification, MLST9 for clonal complex determination, and SLST for phylogeny investigation including numerous isolates. There is an obvious need to create a consensus about molecular typing methods for C. acnes. This standardization will facilitate the comparison of results between one article and another, and also the interpretation of clinical data. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)

PubMed Central

Turner, Cameron R.; Miller, Derryl J.; Coyne, Kathryn J.; Corush, Joel

2014-01-01

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species. PMID:25474207

Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.).

PubMed

Turner, Cameron R; Miller, Derryl J; Coyne, Kathryn J; Corush, Joel

2014-01-01

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

Elaboration and validation of the method for the quantification of the emetic toxin of Bacillus cereus as described in EN-ISO 18465 - Microbiology of the food chain - Quantitative determination of emetic toxin (cereulide) using LC-MS/MS.

PubMed

In 't Veld, P H; van der Laak, L F J; van Zon, M; Biesta-Peters, E G

2018-04-12

A method for the quantification of the Bacillus cereus emetic toxin (cereulide) was developed and validated. The method principle is based on LC-MS as this is the most sensitive and specific method for cereulide. Therefore the study design is different from the microbiological methods validated under this mandate. As the method had to be developed a two stage validation study approach was used. The first stage (pre-study) focussed on the method applicability and the experience of the laboratories with the method. Based on the outcome of the pre-study and comments received during voting at CEN and ISO level a final method was agreed to be used for the second stage the (final) validation of the method. In the final (validation) study samples of cooked rice (both artificially contaminated with cereulide or contaminated with B. cereus for production of cereulide in the rice) and 6 other food matrices (fried rice dish, cream pastry with chocolate, hotdog sausage, mini pancakes, vanilla custard and infant formula) were used. All these samples were spiked by the participating laboratories using standard solutions of cereulide supplied by the organising laboratory. The results of the study indicate that the method is fit for purpose. Repeatability values were obtained of 0.6 μg/kg at low level spike (ca. 5 μg/kg) and 7 to 9.6 μg/kg at high level spike (ca. 75 μg/kg). Reproducibility at low spike level ranged from 0.6 to 0.9 μg/kg and from 8.7 to 14.5 μg/kg at high spike level. Recovery from the spiked samples ranged between 96.5% for mini-pancakes to 99.3% for fries rice dish. Copyright © 2018. Published by Elsevier B.V.

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

EPA Science Inventory

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

Measurement of water-soluble B vitamins in infant formula by liquid chromatography/tandem mass spectrometry.

PubMed

Huang, Min; Winters, Doug; Crowley, Richard; Sullivan, Darryl

2009-01-01

A method has been developed for the simultaneous measurement of multiple B vitamins (i.e., B1, B2, B3, B5, and B6) in infant formulas by LC-MSIMS. The vitamins were extracted with acidic solvent, followed by protein precipitation at a pH range of 4.5 to 5.5, and filtered. This simplified procedure eliminates many of the potential sources of laboratory error and facilitates rapid and efficient analysis. As is common in most cases, isotope internal standards were added to account for variations in sample preparation, as well as changes in MS measurement. In this method, isotope-labeled internal standards of B1, B3, B5, and B6 were used. The factors affecting analytical performance were investigated and optimized. In addition, the stability of these vitamins in the extraction solution was investigated. An acidic condition (5 mM HCl) was applied to successfully stabilize B1, which had shown a decrease in signal when other solvents were used. The quantitative extraction and good stability allowed isotope standards to be added to the filtered sample solution, instead of to the extraction solvent. The addition of the isotope to the small portion of the filtered sample solution significantly reduces cost. A comprehensive evaluation of the analysis of the standard reference material and good spike recovery of the vitamins (100 +/- 6%) demonstrates the accuracy of the method. The results for commercially available infant formula samples were also compared with those obtained using the current microbiological method.

Management and control of microbiologically influenced corrosion (MIC) in the oil and gas industry-Overview and a North Sea case study.

PubMed

Skovhus, Torben Lund; Eckert, Richard B; Rodrigues, Edgar

2017-08-20

Microbiologically influenced corrosion (MIC) is the terminology applied where the actions of microorganisms influence the corrosion process. In literature, terms such as microbial corrosion, biocorrosion, microbially influenced/induced corrosion, and biodegradation are often applied. MIC research in the oil and gas industry has seen a revolution over the past decade, with the introduction of molecular microbiological methods: (MMM) as well as new industry standards and procedures of sampling biofilm and corrosion products from the process system. This review aims to capture the most important trends the oil and gas industry has seen regarding MIC research over the past decade. The paper starts out with an overview of where in the process stream MIC occurs - from the oil reservoir to the consumer. Both biotic and abiotic corrosion mechanisms are explained in the context of managing MIC using a structured corrosion management (CM) approach. The corrosion management approach employs the elements of a management system to ensure that essential corrosion control activities are carried out in an effective, sustainable, well-planned and properly executed manner. The 3-phase corrosion management approach covering of both biotic and abiotic internal corrosion mechanisms consists of 1) corrosion assessment, 2) corrosion mitigation and 3) corrosion monitoring. Each of the three phases are described in detail with links to recent field cases, methods, industry standards and sampling protocols. In order to manage the corrosion threat, operators commonly use models to support decision making. The models use qualitative, semi-quantitative or quantitative measures to help assess the rate of degradation caused by MIC. The paper reviews four existing models for MIC Threat Assessment and describe a new model that links the threat of MIC in the oil processing system located on an offshore platform with a Risk Based Inspection (RBI) approach. A recent field case highlights and explains the conflicting historic results obtained through serial dilution of culture media using the most probable number (MPN) method as compared to data obtained from corrosion monitoring and the quantitative polymerase chain reaction (qPCR) method. Results from qPCR application in the field case have changed the way MIC is monitored on the oil production facility in the North Sea. A number of high quality resources have been published as technical conference papers, books, educational videos and peer-reviewed scientific papers, and thus we end the review with an updated list of state-of-the-art resources for anyone desiring to become more familiar with the topic of MIC in the upstream oil and gas sector. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

Okazaki, Mitsuhiro

2012-10-01

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

[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.

Assessing microbiological water quality in drinking water distribution systems with disinfectant residual using flow cytometry.

PubMed

Gillespie, Simon; Lipphaus, Patrick; Green, James; Parsons, Simon; Weir, Paul; Juskowiak, Kes; Jefferson, Bruce; Jarvis, Peter; Nocker, Andreas

2014-11-15

Flow cytometry (FCM) as a diagnostic tool for enumeration and characterization of microorganisms is rapidly gaining popularity and is increasingly applied in the water industry. In this study we applied the method to obtain a better understanding of total and intact cell concentrations in three different drinking water distribution systems (one using chlorine and two using chloramines as secondary disinfectants). Chloramine tended to result in lower proportions of intact cells than chlorine over a wider residual range, in agreement with existing knowledge that chloramine suppresses regrowth more efficiently. For chlorinated systems, free chlorine concentrations above 0.5 mg L(-1) were found to be associated with relatively low proportions of intact cells, whereas lower disinfectant levels could result in substantially higher percentages of intact cells. The threshold for chlorinated systems is in good agreement with guidelines from the World Health Organization. The fact that the vast majority of samples failing the regulatory coliform standard also showed elevated proportions of intact cells suggests that this parameter might be useful for evaluating risk of failure. Another interesting parameter for judging the microbiological status of water, the biological regrowth potential, greatly varied among different finished waters providing potential help for investment decisions. For its measurement, a simple method was introduced that can easily be performed by water utilities with FCM capability. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed

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

1999-09-01

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

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

PubMed

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

2014-12-01

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

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.

Comparison of phenotypic and genotypic methods for detection of diphtheria toxin among isolates of pathogenic corynebacteria.

PubMed

Efstratiou, A; Engler, K H; Dawes, C S; Sesardic, D

1998-11-01

We have compared molecular, immunochemical, and cytotoxic assays for the detection of diphtheria toxin from 55 isolates of Corynebacterium diphtheriae and Corynebacterium ulcerans originally isolated in five different countries. The suitabilities and accuracies of these assays for the laboratory diagnosis of diphtheria were compared and evaluated against the "gold standard" in vivo methods. The in vivo and Vero cell cytotoxicity assays were accurate in their abilities to detect diphtheria toxin but were time-consuming; however, the cytotoxicity assay is a suitable in vitro alternative to the in vivo virulence test. There was complete concordance between all the phenotypic methods. Genotypic tests based upon PCR were rapid; however, PCR must be used with caution because some isolates of C. diphtheriae possessed toxin genes but failed to express a biologically active toxin. Therefore, phenotypic confirmation of toxigenicity for the microbiological diagnosis of diphtheria is recommended.

The ability of selected plant essential oils to enhance the action of recommended antibiotics against pathogenic wound bacteria.

PubMed

Sienkiewicz, Monika; Łysakowska, Monika; Kowalczyk, Edward; Szymańska, Grażyna; Kochan, Ewa; Krukowska, Jolanta; Olszewski, Jurek; Zielińska-Bliźniewska, Hanna

2017-03-01

The aim of this work was to characterize the ability of essential oils to support antibiotics against pathogenic bacteria in wounds. Gram-positive and Gram-negative bacteria obtained from wound infections were identified according to standard microbiological methods. Essential oils were analysed by GC-FID-MS. The susceptibility of bacteria to antibiotics, essential oils and their combination was assessed using the disc-diffusion method. The Minimal Inhibitory Concentration and Minimum Bactericidal Concentration of the essential oils were established by the micro-dilution broth method. Although cinnamon, clove, thyme and lavender essential oils were found to have the greatest antibacterial activity when used alone, the greatest additive and synergistic effects against pathogenic wound bacteria in combination with recommended antibiotics were demonstrated by basil, clary sage and rosemary oils. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

Thermal and enzymatic recovering of proteins from untanned leather waste.

PubMed

Bajza, Z; Vrucek, V

2001-01-01

The laboratory trials of a process to treat untanned leather waste to isolate valuable protein products are presented. In this comparative study, both thermal and enzymatic treatments of leather waste were performed. The enzymatic method utilizes commercially available alkaline protease at moderate temperatures and for short periods of time. The concentration of the enzyme was 500 units per gram of leather waste which makes the method cost-effective. Amino acid composition in the hydrolysate obtained by the enzyme hydrolysis of untanned leather waste is determined. Chemical and physical properties of protein powder products from untanned leather waste were evaluated by spectrophotometric and chromatographic methods and by use of electron microscope. The results of microbiological assays confirm that these products agree to food safety standards. This relatively simple treatment of untanned leather waste may provide a practical and economical solution to the disposal of potentially dangerous waste.

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

PubMed

Shintani, Hideharu

2016-01-01

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

[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.

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.

Microbiological methods for surveillance of carrier status of multiresistant bacteria.

PubMed

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

2017-12-01

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

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

PubMed Central

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

2006-01-01

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

Providing a sound habitat for man in space

NASA Astrophysics Data System (ADS)

Stranger-Johannessen, Maria

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

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

PubMed Central

Bartz, Sabrina; Tondo, Eduardo Cesar

2013-01-01

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

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

PubMed

Bartz, Sabrina; Tondo, Eduardo Cesar

2013-01-01

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

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

PubMed

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

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

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

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

USDA-ARS?s Scientific Manuscript database

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

Introduction of Molecular Methods into a Food Microbiology Curriculum

ERIC Educational Resources Information Center

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

2014-01-01

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

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.

Comparative study of microbiological, chemical and sensory properties of kefirs produced in Estonia, Latvia and Lithuania.

PubMed

Anton, Dea; Raudsepp, Piret; Roasto, Mati; Meremäe, Kadrin; Kuusik, Sirje; Toomik, Peeter; Elias, Priit; Laikoja, Katrin; Kaart, Tanel; Lepiku, Martin; Püssa, Tõnu

2016-02-01

In the current study the microbiological, sensory and chemical properties of 24 kefirs (12 producers) from Estonian, Latvian and Lithuanian retail market were determined using gas chromatography (GC), high performance liquid chromatography (HPLC-MS/MS-Q-TOF and LC-ion trap MS/MS), spectrophotometry and other methods. Antihypertensive, angiotensin-converting enzyme (ACE) inhibiting, antioxidant and antibacterial peptides were found in the kefir samples. According to the results of principal component analysis of 200 most abundant compounds obtained with HPLC-MS/MS-Q-TOF analysis, Estonian kefirs differed from the rest. Kefirs of Latvian and Lithuanian origin showed similarities in several characteristics, probably related to the starter cultures and technological processes. The fatty acids composition of all Baltic kefirs was uniform. The antioxidant capacity of the kefirs varied slightly, whereas intermediate positive correlation (r = 0.32, P < 0.05) was found between antioxidativity and total bacterial count. The lipid oxidation level, estimated as the content of linoleic and oleic acid primary oxidation products, oxylipins, was very low in all studied kefirs. Only one third of analysed kefirs met the requirements of the minimum sum of viable microorganisms, indicated in the Codex Standard for Fermented Milks.

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

Efficacy of accelerated hydrogen peroxide® disinfectant on foot-and-mouth disease virus, swine vesicular disease virus and Senecavirus A.

PubMed

Hole, K; Ahmadpour, F; Krishnan, J; Stansfield, C; Copps, J; Nfon, C

2017-03-01

In a laboratory, disinfectants used to inactivate pathogens on contaminated surfaces and to prevent spread of diseases often have adverse side effects on personnel and the environment. It is, therefore, essential to find safer, fast-acting and yet effective disinfectants. The objective of this study was to evaluate an accelerated hydrogen peroxide ® (AHP ® )-based disinfectant against high consequence foreign animal disease pathogens such as foot-and-mouth disease virus (FMDV) and swine vesicular disease virus (SVDV), as well as Senecavirus A (SVA), which causes similar lesions as FMDV and SVDV. We tested varying dilutions and contact times of AHP against FMDV, SVDV and SVA by the standard US EPA and modified methods. AHP was effective against all three viruses, albeit at a higher concentration and double the manufacturer recommended contact time when testing wet films of SVDV. AHP is an effective disinfectant against FMDV, SVDV and SVA. AHP-based disinfectant can, therefore, be used in high containment laboratories working with FMDV, SVDV and related pathogens. © 2016 The Canadian Food Inspection Agency. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

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.

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.

Microbiological quality of fresh produce obtained from retail stores on the Eastern Shore of Maryland, United States of America.

PubMed

Korir, Robert Cheruiyot; Parveen, Salina; Hashem, Fawzy; Bowers, John

2016-06-01

The aim of this study was to investigate the microbiological quality of six types of fresh produce obtained from three retail stores located on the Eastern Shore of Maryland, USA. A total of 414 samples representing basil, cilantro, lettuce, scallion, spinach, and parsley were analyzed for total aerobic bacteria (APC), total coliforms, Escherichia coli, and three pathogenic bacteria (E. coli O157:H7, Listeria monocytogenes, and Salmonella), using standard methods. Presumptive pathogenic isolates were confirmed using BAX Polymerase Chain Reaction. Total aerobic populations varied widely between samples, while 38.41% were positive for total coliforms and only 10.15% for E. coli. Median abundance (log CFU/g) of total coliforms and E. coli were less than the limit of detection and that of APC ranged from 5.78 to 6.61 over the six produce types. There was a statistically significant difference in prevalence of total coliforms among the retail stores, but not for abundance of APC or prevalence of E. coli. E. coli O157:H7 and L. monocytogenes were detected in one spinach sample each, while one parsley and one cilantro sample were positive for Salmonella. There were no statistically significant differences in microbiological quality among produce types. Although the results of this study provided some indices of sanitary and/or spoilage level, no relationship was observed among the total aerobic bacteria, total coliforms, E. coli, and the presence of pathogenic bacteria in the samples tested. Copyright © 2015 Elsevier Ltd. All rights reserved.

A review of microbiology service learning.

PubMed

Webb, Ginny

2017-02-01

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

Evaluation of the alpha-amylase activity as an indicator of pasteurization efficiency and microbiological quality of liquid whole eggs.

PubMed

Silva, Guilherme Resende da; Menezes, Liliane Denize Miranda; Lanza, Isabela Pereira; Oliveira, Daniela Duarte de; Silva, Carla Aparecida; Klein, Roger Wilker Tavares; Assis, Débora Cristina Sampaio de; Cançado, Silvana de Vasconcelos

2017-09-01

In order to evaluate the efficiency of the pasteurization process in liquid whole eggs, an UV/visible spectrophotometric method was developed and validated for the assessment of alpha-amylase activity. Samples were collected from 30 lots of raw eggs (n = 30) and divided into three groups: one was reserved for analysis of the raw eggs, the second group was pasteurized at 61.1°C for 3.5 minutes (n = 30), and the third group was pasteurized at 64.4°C for 2.5 minutes (n = 30). In addition to assessing alpha-amylase activity, the microbiological quality of the samples was also evaluated by counting total and thermotolerant coliforms, mesophilic aerobic microorganisms, Staphylococcus spp., and Salmonella spp. The validated spectrophotometric method demonstrated linearity, with a coefficient of determination (R2) greater than 0.99, limits of detection (LOD) and quantification (LOQ) of 0.48 mg kg-1 and 1.16 mg kg-1, respectively, and acceptable precision and accuracy with relative standard deviation (RSD) values of less than 10% and recovery rates between 98.81% and 105.40%. The results for alpha-amylase activity in the raw egg samples showed high enzyme activity due to near-complete hydrolysis of the starch, while in the eggs pasteurized at 61.1°C, partial inactivation of the enzyme was observed. In the samples of whole eggs pasteurized at 64.4°C, starch hydrolysis did not occur due to enzyme inactivation. The results of the microbiological analyses showed a decrease (P < 0.0001) in the counts for all the studied microorganisms and in the frequency of Salmonella spp. in the pasteurized egg samples according to the two binomials under investigation, compared to the raw egg samples, which showed high rates of contamination (P < 0.0001). After pasteurization, only one sample (3.33%) was positive for Salmonella spp., indicating failure in the pasteurization process, which was confirmed by the alpha-amylase test. It was concluded that the validated methodology for testing alpha-amylase activity is adequate for assessing the efficiency of the pasteurization process, and that the time-temperature binomial used in this study is suitable to produce pasteurized eggs with high microbiological quality. © 2017 Poultry Science Association Inc.

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.

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.

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

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.

Microbial sensor for drug susceptibility testing of Mycobacterium tuberculosis.

PubMed

Zhang, Z-T; Wang, D-B; Li, C-Y; Deng, J-Y; Zhang, J-B; Bi, L-J; Zhang, X-E

2018-01-01

Drug susceptibility testing (DST) of clinical isolates of Mycobacterium tuberculosis is critical in treating tuberculosis. We demonstrate the possibility of using a microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The sensor is made of an oxygen electrode with M. tuberculosis cells attached to its surface. This sensor monitors the residual oxygen consumption of M. tuberculosis cells after treatment with anti-TB drugs with glycerine as a carbon source. In principle, after drug pretreatment for 4-5 days, the response differences between the sensors made of drug-sensitive isolates are distinguishable from the sensors made of drug-resistant isolates. The susceptibility of the M. tuberculosis H37Ra strain, its mutants and 35 clinical isolates to six common anti-TB drugs: rifampicin, isoniazid, streptomycin, ethambutol, levofloxacin and para-aminosalicylic acid were tested using the proposed method. The results agreed well with the gold standard method (LJ) and were determined in significantly less time. The whole procedure takes approximately 11 days and therefore has the potential to inform clinical decisions. To our knowledge, this is the first study that demonstrates the possible application of a dissolved oxygen electrode-based microbial sensor in M. tuberculosis drug resistance testing. This study used the microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The overall detection result of the microbial sensor agreed well with that of the conventional LJ proportion method and takes less time than the existing phenotypic methods. In future studies, we will build an O 2 electrode array microbial sensor reactor to enable a high-throughput drug resistance analysis. © 2017 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

Comparison of viable plate count, turbidity measurement and real-time PCR for quantification of Porphyromonas gingivalis.

PubMed

Clais, S; Boulet, G; Van Kerckhoven, M; Lanckacker, E; Delputte, P; Maes, L; Cos, P

2015-01-01

The viable plate count (VPC) is considered as the reference method for bacterial enumeration in periodontal microbiology but shows some important limitations for anaerobic bacteria. As anaerobes such as Porphyromonas gingivalis are difficult to culture, VPC becomes time-consuming and less sensitive. Hence, efficient normalization of experimental data to bacterial cell count requires alternative rapid and reliable quantification methods. This study compared the performance of VPC with that of turbidity measurement and real-time PCR (qPCR) in an experimental context using highly concentrated bacterial suspensions. Our TaqMan-based qPCR assay for P. gingivalis 16S rRNA proved to be sensitive and specific. Turbidity measurements offer a fast method to assess P. gingivalis growth, but suffer from high variability and a limited dynamic range. VPC was very time-consuming and less repeatable than qPCR. Our study concludes that qPCR provides the most rapid and precise approach for P. gingivalis quantification. Although our data were gathered in a specific research context, we believe that our conclusions on the inferior performance of VPC and turbidity measurements in comparison to qPCR can be extended to other research and clinical settings and even to other difficult-to-culture micro-organisms. Various clinical and research settings require fast and reliable quantification of bacterial suspensions. The viable plate count method (VPC) is generally seen as 'the gold standard' for bacterial enumeration. However, VPC-based quantification of anaerobes such as Porphyromonas gingivalis is time-consuming due to their stringent growth requirements and shows poor repeatability. Comparison of VPC, turbidity measurement and TaqMan-based qPCR demonstrated that qPCR possesses important advantages regarding speed, accuracy and repeatability. © 2014 The Society for Applied Microbiology.

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.

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

PubMed

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

2018-06-01

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

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

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

1977-01-01

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

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines.

PubMed

David, Sophia; Mentasti, Massimo; Tewolde, Rediat; Aslett, Martin; Harris, Simon R; Afshar, Baharak; Underwood, Anthony; Fry, Norman K; Parkhill, Julian; Harrison, Timothy G

2016-08-01

Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current "gold standard" typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n = 106) from the standard "typing panel," previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ∼50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila. Copyright © 2016 David et al.

Prospective Evaluation of a Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System in a Hospital Clinical Microbiology Laboratory for Identification of Bacteria and Yeasts: a Bench-by-Bench Study for Assessing the Impact on Time to Identification and Cost-Effectiveness

PubMed Central

Tan, K. E.; Ellis, B. C.; Lee, R.; Stamper, P. D.; Zhang, S. X.

2012-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been found to be an accurate, rapid, and inexpensive method for the identification of bacteria and yeasts. Previous evaluations have compared the accuracy, time to identification, and costs of the MALDI-TOF MS method against standard identification systems or commercial panels. In this prospective study, we compared a protocol incorporating MALDI-TOF MS (MALDI protocol) with the current standard identification protocols (standard protocol) to determine the performance in actual practice using a specimen-based, bench-by-bench approach. The potential impact on time to identification (TTI) and costs had MALDI-TOF MS been the first-line identification method was quantitated. The MALDI protocol includes supplementary tests, notably for Streptococcus pneumoniae and Shigella, and indications for repeat MALDI-TOF MS attempts, often not measured in previous studies. A total of 952 isolates (824 bacterial isolates and 128 yeast isolates) recovered from 2,214 specimens were assessed using the MALDI protocol. Compared with standard protocols, the MALDI protocol provided identifications 1.45 days earlier on average (P < 0.001). In our laboratory, we anticipate that the incorporation of the MALDI protocol can reduce reagent and labor costs of identification by $102,424 or 56.9% within 12 months. The model included the fixed annual costs of the MALDI-TOF MS, such as the cost of protein standards and instrument maintenance, and the annual prevalence of organisms encountered in our laboratory. This comprehensive cost analysis model can be generalized to other moderate- to high-volume laboratories. PMID:22855510

Prospective evaluation of a matrix-assisted laser desorption ionization-time of flight mass spectrometry system in a hospital clinical microbiology laboratory for identification of bacteria and yeasts: a bench-by-bench study for assessing the impact on time to identification and cost-effectiveness.

PubMed

Tan, K E; Ellis, B C; Lee, R; Stamper, P D; Zhang, S X; Carroll, K C

2012-10-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been found to be an accurate, rapid, and inexpensive method for the identification of bacteria and yeasts. Previous evaluations have compared the accuracy, time to identification, and costs of the MALDI-TOF MS method against standard identification systems or commercial panels. In this prospective study, we compared a protocol incorporating MALDI-TOF MS (MALDI protocol) with the current standard identification protocols (standard protocol) to determine the performance in actual practice using a specimen-based, bench-by-bench approach. The potential impact on time to identification (TTI) and costs had MALDI-TOF MS been the first-line identification method was quantitated. The MALDI protocol includes supplementary tests, notably for Streptococcus pneumoniae and Shigella, and indications for repeat MALDI-TOF MS attempts, often not measured in previous studies. A total of 952 isolates (824 bacterial isolates and 128 yeast isolates) recovered from 2,214 specimens were assessed using the MALDI protocol. Compared with standard protocols, the MALDI protocol provided identifications 1.45 days earlier on average (P < 0.001). In our laboratory, we anticipate that the incorporation of the MALDI protocol can reduce reagent and labor costs of identification by $102,424 or 56.9% within 12 months. The model included the fixed annual costs of the MALDI-TOF MS, such as the cost of protein standards and instrument maintenance, and the annual prevalence of organisms encountered in our laboratory. This comprehensive cost analysis model can be generalized to other moderate- to high-volume laboratories.

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

PubMed

Wilrich, Cordula; Wilrich, Peter-Theodor

2009-01-01

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

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

USDA-ARS?s Scientific Manuscript database

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

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

PubMed

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

2010-11-01

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

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

PubMed

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

2018-01-01

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

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

PubMed Central

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

2018-01-01

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

Microbiological contamination with moulds in work environment in libraries and archive storage facilities.

PubMed

Zielinska-Jankiewicz, Katarzyna; Kozajda, Anna; Piotrowska, Malgorzata; Szadkowska-Stanczyk, Irena

2008-01-01

Microbiological contamination with fungi, including moulds, can pose a significant health hazard to those working in archives or museums. The species involved include Aspergillus, Penicillium, Geotrichum, Alternaria, Cladosporium, Mucor, Rhizopus, Trichoderma, Fusarium which are associated mostly with allergic response of different types. The aim of the study was to analyse, both in quantitative and qualitative terms, workplace air samples collected in a library and archive storage facilities. Occupational exposure and the related health hazard from microbiological contamination with moulds were assessed in three archive storage buildings and one library. Air samples (total 60) were collected via impact method before work and at hourly intervals during work performance. Surface samples from the artifacts were collected by pressing a counting (RODAC) plate filled with malt extract agar against the surface of the artifacts. The air sample and surface sample analyses yielded 36 different mould species, classified into 19 genera, of which Cladosporium and Penicillium were the most prevalent. Twelve species were regarded as potentially pathogenic for humans: 8 had allergic and 11 toxic properties, the latter including Aspergillus fumigatus. Quantitative analysis revealed air microbiological contamination with moulds at the level ranging from 1.8 x 10(2)-2.3 x 10(3) cfu/m(3). In surface samples from library and archive artifacts, 11 fungal species were distinguished; the number of species per artifact varying from 1-6 and colony count ranging from 4 x 10(1) to 8-10(1) cfu/100 cm(2). Higher contamination levels were found only for Cladosporium cladosporioides (1.48 x 10(3) cfu/100 cm(2)) and Paecillomyces varioti (1.2 x 10(2) cfu/100 cm(2)). At the workposts examined, although no clearly visible signs of mould contamination could be found, the study revealed abundant micromycetes, with the predominant species of Cladosporium and Penicillium. The detected species included also potentially pathogenic microorganisms which can cause allergic and toxic effects, such as Aspergillus fumigatus, that could be hazardous to workers' health. For some species, the concentration levels exceeded the values considered the proposed hygienic standards for total microscopical fungi in occupational settings. The findings of the study point to unsatisfactory hygienic conditions at the worksites examined, resulting in microbiological contamination with moulds, as well as the necessity for prompt remedial activities on the part of the employers.

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.

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

PubMed

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

2005-04-01

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

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.

Evaluation of a New System, VITEK 2, for Identification and Antimicrobial Susceptibility Testing of Enterococci

PubMed Central

Garcia-Garrote, Fernando; Cercenado, Emilia; Bouza, Emilio

2000-01-01

We evaluated the new automated VITEK 2 system (bioMérieux) for the identification and antimicrobial susceptibility testing of enterococci. The results obtained with the VITEK 2 system were compared to those obtained by reference methods: standard identification by the scheme of Facklam and Sahm [R. R. Facklam and D. F. Sahm, p. 308–314, in P. R. Murray et al., ed., Manual of Clinical Microbiology, 6th ed., 1995] and with the API 20 STREP system and, for antimicrobial susceptibility testing, broth microdilution and agar dilution methods by the procedures of the National Committee for Clinical Laboratory Standards. The presence of vanA and vanB genes was determined by PCR. A total of 150 clinical isolates were studied, corresponding to 60 Enterococcus faecalis, 55 Enterococcus faecium, 26 Enterococcus gallinarum, 5 Enterococcus avium, 2 Enterococcus durans, and 2 Enterococcus raffinosus isolates. Among those isolates, 131 (87%) were correctly identified to the species level with the VITEK 2 system. Approximately half of the misidentifications were for E. faecium with low-level resistance to vancomycin, identified as E. gallinarum or E. casseliflavus; however, a motility test solved the discrepancies and increased the agreement to 94%. Among the strains studied, 66% were vancomycin resistant (57 VanA, 16 VanB, and 26 VanC strains), 23% were ampicillin resistant (MICs, ≥16 μg/ml), 31% were high-level gentamicin resistant, and 45% were high-level streptomycin resistant. Percentages of agreement for susceptibility and resistance to ampicillin, vancomycin, and teicoplanin and for high-level gentamicin resistance and high-level streptomycin resistance were 93, 95, 97, 97, and 96%, respectively. The accuracy of identification and antimicrobial susceptibility testing of enterococci with the VITEK 2 system, together with the significant reduction in handling time, will have a positive impact on the work flow of the clinical microbiology laboratory. PMID:10834961

Comparison of Diagnostic Accuracy of Periprosthetic Tissue Culture in Blood Culture Bottles to That of Prosthesis Sonication Fluid Culture for Diagnosis of Prosthetic Joint Infection (PJI) by Use of Bayesian Latent Class Modeling and IDSA PJI Criteria for Classification.

PubMed

Yan, Qun; Karau, Melissa J; Greenwood-Quaintance, Kerryl E; Mandrekar, Jayawant N; Osmon, Douglas R; Abdel, Matthew P; Patel, Robin

2018-06-01

We have previously demonstrated that culturing periprosthetic tissue in blood culture bottles (BCBs) improves sensitivity compared to conventional agar and broth culture methods for diagnosis of prosthetic joint infection (PJI). We have also shown that prosthesis sonication culture improves sensitivity compared to periprosthetic tissue culture using conventional agar and broth methods. The purpose of this study was to compare the diagnostic accuracy of tissue culture in BCBs (subsequently referred to as tissue culture) to prosthesis sonication culture (subsequently referred to as sonicate fluid culture). We studied 229 subjects who underwent arthroplasty revision or resection surgery between March 2016 and October 2017 at Mayo Clinic in Rochester, Minnesota. Using the Infectious Diseases Society of America (IDSA) PJI diagnostic criteria (omitting culture criteria) as the gold standard, the sensitivity of tissue culture was similar to that of the sonicate fluid culture (66.4% versus 73.1%, P = 0.07) but was significantly lower than that of the two tests combined (66.4% versus 76.9%, P < 0.001). Using Bayesian latent class modeling, which assumes no gold standard for PJI diagnosis, the sensitivity of tissue culture was slightly lower than that of sonicate fluid culture (86.3% versus 88.7%) and much lower than that of the two tests combined (86.3% versus 99.1%). In conclusion, tissue culture in BCBs reached sensitivity similar to that of prosthesis sonicate fluid culture for diagnosis of PJI, but the two tests combined had the highest sensitivity without compromising specificity. The combination of tissue culture in BCBs and sonicate fluid culture is recommended to achieve the highest level of microbiological diagnosis of PJI. Copyright © 2018 American Society for Microbiology.

Low sensitivity of fecal toxin A/B enzyme immunoassay for diagnosis of Clostridium difficile infection in immunocompromised patients.

PubMed

Erb, S; Frei, R; Strandén, A M; Dangel, M; Tschudin-Sutter, S; Widmer, A F

2015-11-01

The optimal approach in laboratory diagnosis of Clostridium difficile infection (CDI) is still not well defined. Toxigenic culture (TC) or alternatively fecal toxin assay by cell cytotoxicity neutralization assay are considered to be the reference standard, but these methods are time-consuming and labor intensive. In many medical centers, diagnosis of CDI is therefore still based on fecal toxin A/B enzyme immunoassay (EIA) directly from stool alone, balancing cost and speed against limited diagnostic sensitivity. The aim of the study was to assess in which patient population the additional workload of TC is justified. All consecutive stool specimens submitted for diagnosis of suspected CDI between 2004 and 2011 at a tertiary-care center were examined by toxin EIA and TC. Clinical data of patients with established diagnosis of CDI were collected in a standardized case-report form. From 12,481 stool specimens submitted to the microbiologic laboratory, 480 (3.8%) fulfilled CDI criteria; 274 (57.1%) were diagnosed by toxin EIA; and an additional 206 (42.9%) were diagnosed by TC when toxin EIA was negative. Independent predictors for negative toxin EIA but positive TC were high-dose corticosteroids (odds ratio (OR) 2.97, 95% confidence interval (CI) 1.50-5.90, p 0.002), leukocytopenia <1000/μL (OR 2.52, 95% CI 1.22-5.23, p 0.013) and nonsevere CDI (OR 2.21, 95% CI 1.39-3.50, p 0.001). There was no difference in outcomes such as in-hospital mortality and recurrence between both groups. In conclusion, negative toxin EIA does not rule out CDI in immunocompromised patients in the setting of relevant clinical symptoms. Methods with improved sensitivity such as TC or PCR should be used, particularly in this patient population. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

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

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

PubMed

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

2014-09-21

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

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

ERIC Educational Resources Information Center

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

2009-01-01

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

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

ERIC Educational Resources Information Center

Uggioni, Paula Lazzarin; Salay, Elisabette

2013-01-01

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

Future of diagnostic microbiology.

PubMed

Khardori, N

2014-01-01

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

Misidentification of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals in Tripoli, Libya

PubMed Central

Ahmed, Mohamed O.; Abuzweda, Abdulbaset R.; Alghazali, Mohamed H.; Elramalli, Asma K.; Amri, Samira G.; Aghila, Ezzeddin Sh.; Abouzeed, Yousef M.

2010-01-01

Background Methicillin-resistant Staphylococcus aureus (MRSA) is a nosocomial (hospital-acquired) pathogen of exceptional concern. It is responsible for life-threatening infections in both the hospital and the community. Aims To determine the frequency of MRSA misidentification in hospitals in Tripoli, Libya using current testing methods. Methods One hundred and seventy S. aureus isolates previously identified as MRSA were obtained from three hospitals in Tripoli. All isolates were reidentified by culturing on mannitol salt agar, API 20 Staph System and retested for resistance to methicillin using the cefoxitin disk diffusion susceptibility test and PBP2a. D-tests and vancomycin E-tests (Van-E-tests) were also performed for vancomycin-resistant isolates. Results Of the 170 isolates examined, 86 (51%) were confirmed as MRSA (i.e. 49% were misidentified as MRSA). Fifteen (17%) of the confirmed MRSA strains exhibited inducible clindamycin resistance. Of the 86 confirmed MRSA isolates, 13 (15%) were resistant to mupirocin, 53 (62%) were resistant to ciprofloxacin, 41 (48%) were resistant to trimethoprim-sulfamethoxazole, and none were resistant to linezolid. Although disc-diffusion testing indicated that 23 (27%) of the isolates were resistant to vancomycin, none of the isolates were vancomycin-resistant by Van-E-test. Conclusions Misidentification of nosocomial S. aureus as MRSA is a serious problem in Libyan hospitals. There is an urgent need for the proper training of microbiology laboratory technicians in standard antimicrobial susceptibility procedures and the implementation of quality control programs in microbiology laboratories of Libyan hospitals. PMID:21483574

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.

What's growing on General Practitioner's stethoscope?

PubMed

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

2016-01-01

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

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.

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

PubMed

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

2014-12-02

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

A new method for evaluation of compatibility of contact lenses and lens cases with contact lens disinfecting solutions.

PubMed

Mowrey-McKee, Mary; Borazjani, Roya; Collins, Gary; Cook, James; Norton, Susan

2012-01-01

The purpose of this article is to describe new methodology, antimicrobial efficacy endpoint methodology to determine compatibility of contact lens solutions, lens cases and hydrogel lenses for disinfection (AEEMC), to evaluate the effect of a contact lens and a lens case on disinfection efficacy, and to present the ring test used to justify the use of the method in multiple laboratories. A prototype solution containing chlorhexidine as the disinfecting agent and four representative lens types (group I and IV hydrogels and two silicone hydrogels) were used in these ring tests. Five laboratories participated in the chemical and microbiologic analyses. The residual chlorhexidine in lens cases containing the contact lenses was determined using high-performance liquid chromatography; uptake by the lenses was then determined by extrapolation. For the microbiologic part of the study, a contact lens was placed in the well of the lens case, inoculated at 10 to 10 cfu (colony forming units) per lens with microorganisms in 10% organic soil. The microorganisms, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Candida albicans, and Fusarium solani, were prepared as in International Organization for Standardization (ISO) 14729. After a 3- to 10-min exposure time, the prototype solution was dispensed into each well. Aliquots of the inoculated solutions were removed at 4 and 24 hrs and 7 and 30 days and cultured in neutralizing media for determination of survivors; lenses were also cultured for survivors. Chemical uptake data confirmed the differences observed in kill of the challenge organisms according to lens type. It was observed that the culturing of the solution provided adequate data to show the effect of a lens on disinfection efficacy of a lens care product. The findings of the ring test indicated that the separate culturing of the contact lenses is not necessary for routine assessment. The methodology in the November 12, 2008, draft standard (AEEMC), meets the stated objective of demonstrating the effect of a contact lens on the disinfection efficacy of a simulated lens care product. This method, used in combination with the methodology in ISO 14729, should provide for a more robust evaluation of applicable contact lens care disinfecting products.

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.

Sampling and Data Analysis for Environmental Microbiology

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

Murray, Christopher J.

2001-06-01

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

Whole genome sequencing in clinical and public health microbiology

PubMed Central

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

2015-01-01

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

Whole genome sequencing in clinical and public health microbiology.

PubMed

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

2015-04-01

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

Verification of an Automated, Digital Dispensing Platform for At-Will Broth Microdilution-Based Antimicrobial Susceptibility Testing.

PubMed

Smith, Kenneth P; Kirby, James E

2016-09-01

With rapid emergence of multidrug-resistant bacteria, there is often a need to perform susceptibility testing for less commonly used or newer antimicrobial agents. Such testing can often be performed only by using labor-intensive, manual dilution methods and lies outside the capacity of most clinical labs, necessitating reference laboratory testing and thereby delaying the availability of susceptibility data. To address the compelling clinical need for microbiology laboratories to perform such testing in-house, we explored a novel, automated, at-will broth microdilution-based susceptibility testing platform. Specifically, we used the modified inkjet printer technology in the HP D300 digital dispensing system to dispense, directly from stock solutions into a 384-well plate, the 2-fold serial dilution series required for broth microdilution testing. This technology was combined with automated absorbance readings and data analysis to determine MICs. Performance was verified by testing members of the Enterobacteriaceae for susceptibility to ampicillin, cefazolin, ciprofloxacin, colistin, gentamicin, meropenem, and tetracycline in comparison to the results obtained with a broth microdilution reference standard. In precision studies, essential and categorical agreement levels were 96.8% and 98.3%, respectively. Furthermore, significantly fewer D300-based measurements were outside ±1 dilution from the modal MIC, suggesting enhanced reproducibility. In accuracy studies performed using a panel of 80 curated clinical isolates, rates of essential and categorical agreement and very major, major, and minor errors were 94%, 96.6%, 0%, 0%, and 3.4%, respectively. Based on these promising initial results, it is anticipated that the D300-based methodology will enable hospital-based clinical microbiology laboratories to perform at-will broth microdilution testing of antimicrobials and to address a critical testing gap. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Economic and Microbiologic Evaluation of Single-Dose Vial Extension for Hazardous Drugs

PubMed Central

Rowe, Erinn C.; Savage, Scott W.; Rutala, William A.; Weber, David J.; Gergen-Teague, Maria; Eckel, Stephen F.

2012-01-01

Purpose: The update of US Pharmacopeia Chapter <797> in 2008 included guidelines stating that single-dose vials (SDVs) opened and maintained in an International Organization for Standardization Class 5 environment can be used for up to 6 hours after initial puncture. A study was conducted to evaluate the cost of discarding vials after 6 hours and to further test sterility of vials beyond this time point, subsequently defined as the beyond-use date (BUD). Methods: Financial determination of SDV waste included 2 months of retrospective review of all doses prescribed. Additionally, actual waste log data were collected. Active and control vials (prepared using sterilized trypticase soy broth) were recovered, instead of discarded, at the defined 6-hour BUD. Results: The institution-specific waste of 19 selected SDV medications discarded at 6 hours was calculated at $766,000 annually, and tracking waste logs for these same medications was recorded at $770,000 annually. Microbiologic testing of vial extension beyond 6 hours showed that 11 (1.86%) of 592 samples had one colony-forming unit on one of two plates. Positive plates were negative at subsequent time points, and all positives were single isolates most likely introduced during the plating process. Conclusion: The cost of discarding vials at 6 hours was significant for hazardous medications in a large academic medical center. On the basis of microbiologic data, vial BUD extension demonstrated a contamination frequency of 1.86%, which likely represented exogenous contamination; vial BUD extension for the tested drugs showed no growth at subsequent time points and could provide an annual cost savings of more than $600,000. PMID:23180998

Point-of-Care Autofluorescence Imaging for Real-Time Sampling and Treatment Guidance of Bioburden in Chronic Wounds: First-in-Human Results

PubMed Central

DaCosta, Ralph S.; Kulbatski, Iris; Lindvere-Teene, Liis; Starr, Danielle; Blackmore, Kristina; Silver, Jason I.; Opoku, Julie; Wu, Yichao Charlie; Medeiros, Philip J.; Xu, Wei; Xu, Lizhen; Wilson, Brian C.; Rosen, Cheryl; Linden, Ron

2015-01-01

Background Traditionally, chronic wound infection is diagnosed by visual inspection under white light and microbiological sampling, which are subjective and suboptimal, respectively, thereby delaying diagnosis and treatment. To address this, we developed a novel handheld, fluorescence imaging device (PRODIGI) that enables non-contact, real-time, high-resolution visualization and differentiation of key pathogenic bacteria through their endogenous autofluorescence, as well as connective tissues in wounds. Methods and Findings This was a two-part Phase I, single center, non-randomized trial of chronic wound patients (male and female, ≥18 years; UHN REB #09-0015-A for part 1; UHN REB #12-5003 for part 2; clinicaltrials.gov Identifier: NCT01378728 for part 1 and NCT01651845 for part 2). Part 1 (28 patients; 54% diabetic foot ulcers, 46% non-diabetic wounds) established the feasibility of autofluorescence imaging to accurately guide wound sampling, validated against blinded, gold standard swab-based microbiology. Part 2 (12 patients; 83.3% diabetic foot ulcers, 16.7% non-diabetic wounds) established the feasibility of autofluorescence imaging to guide wound treatment and quantitatively assess treatment response. We showed that PRODIGI can be used to guide and improve microbiological sampling and debridement of wounds in situ, enabling diagnosis, treatment guidance and response assessment in patients with chronic wounds. PRODIGI is safe, easy to use and integrates into the clinical workflow. Clinically significant bacterial burden can be detected in seconds, quantitatively tracked over days-to-months and their biodistribution mapped within the wound bed, periphery, and other remote areas. Conclusions PRODIGI represents a technological advancement in wound sampling and treatment guidance for clinical wound care at the point-of-care. Trial Registration ClinicalTrials.gov NCT01651845; ClinicalTrials.gov NCT01378728 PMID:25790480

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

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

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

PubMed

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

2018-04-19

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

Efficiency tests of samplers for microbiological aerosols, a review

NASA Technical Reports Server (NTRS)

Henningson, E.; Faengmark, I.

1984-01-01

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

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

PubMed

Endimiani, Andrea; Jacobs, Michael R

2016-06-01

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

Microbiological assay of the Marshall Space Flight Center neutral buoyancy simulator

NASA Technical Reports Server (NTRS)

Beyerle, F. J.

1973-01-01

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

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

ERIC Educational Resources Information Center

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

2005-01-01

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

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

PubMed

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

2016-01-01

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

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...

European validation of Real-Time PCR method for detection of Salmonella spp. in pork meat.

PubMed

Delibato, Elisabetta; Rodriguez-Lazaro, David; Gianfranceschi, Monica; De Cesare, Alessandra; Comin, Damiano; Gattuso, Antonietta; Hernandez, Marta; Sonnessa, Michele; Pasquali, Frédérique; Sreter-Lancz, Zuzsanna; Saiz-Abajo, María-José; Pérez-De-Juan, Javier; Butrón, Javier; Prukner-Radovcic, Estella; Horvatek Tomic, Danijela; Johannessen, Gro S; Jakočiūnė, Džiuginta; Olsen, John E; Chemaly, Marianne; Le Gall, Francoise; González-García, Patricia; Lettini, Antonia Anna; Lukac, Maja; Quesne, Segolénè; Zampieron, Claudia; De Santis, Paola; Lovari, Sarah; Bertasi, Barbara; Pavoni, Enrico; Proroga, Yolande T R; Capuano, Federico; Manfreda, Gerardo; De Medici, Dario

2014-08-01

The classical microbiological method for detection of Salmonella spp. requires more than five days for final confirmation, and consequently there is a need for an alternative methodology for detection of this pathogen particularly in those food categories with a short shelf-life. This study presents an international (at European level) ISO 16140-based validation study of a non-proprietary Real-Time PCR-based method that can generate final results the day following sample analysis. It is based on an ISO compatible enrichment coupled to an easy and inexpensive DNA extraction and a consolidated Real-Time PCR assay. Thirteen laboratories from seven European Countries participated to this trial, and pork meat was selected as food model. The limit of detection observed was down to 10 CFU per 25 g of sample, showing excellent concordance and accordance values between samples and laboratories (100%). In addition, excellent values were obtained for relative accuracy, specificity and sensitivity (100%) when the results obtained for the Real-Time PCR-based methods were compared to those of the ISO 6579:2002 standard method. The results of this international trial demonstrate that the evaluated Real-Time PCR-based method represents an excellent alternative to the ISO standard. In fact, it shows an equal and solid performance as well as it reduces dramatically the extent of the analytical process, and can be easily implemented routinely by the Competent Authorities and Food Industry laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.

[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.

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.

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

PubMed

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

2015-10-01

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

[Analysis on 2011 quality control results on aerobic plate count of microbiology laboratories in China].

PubMed

Han, Haihong; Li, Ning; Li, Yepeng; Fu, Ping; Yu, Dongmin; Li Zhigang; Du, Chunming; Guo, Yunchang

2015-01-01

To test the aerobic plate count examining capability of microbiology laboratories, to ensure the accuracy and comparability of quantitative bacteria examination results, and to improve the quality of monitoring. The 4 different concentration aerobic plate count piece samples were prepared and noted as I, II, III and IV. After homogeneity and stability tests, the samples were delivered to monitoring institutions. The results of I, II, III samples were logarithmic transformed, and evaluated with Z-score method using the robust average and standard deviation. The results of IV samples were evaluated as "satisfactory" when reported as < 10 CFU/piece or as "not satisfactory" otherwise. Pearson χ2 test was used to analyze the ratio results. 309 monitoring institutions, which was 99.04% of the total number, reported their results. 271 institutions reported a satisfactory result, and the satisfactory rate was 87.70%. There was no statistical difference in satisfactory rates of I, II and III samples which were 81.52%, 88.30% and 91.40% respectively. The satisfactory rate of IV samples was 93.33%. There was no statistical difference in satisfactory rates between provincial and municipal CDC. The quality control program has provided scientific data that the aerobic plate count capability of the laboratories meets the requirements of monitoring tasks.

Fungal epidemiology and diversity in cystic fibrosis patients over a 5-year period in a national reference center.

PubMed

Ziesing, S; Suerbaum, S; Sedlacek, L

2016-11-01

The knowledge on prevalence rates of yeasts and moulds in patients with cystic fibrosis (CF) in Germany is scarce. The aim of this report is to give an overview of the diversity and epidemiology of fungal species in CF patients. Over a 5-year period, all fungal isolates cultured from microbiological specimen from CF patients were recorded. Beside standard bacteriological culture media two fungal media were used for cultivation. Species were identified by microscopy, biochemical profiling, MALDI-TOF analysis or DNA sequencing methods. In sum, 25,975 clinical samples from CF patients were analyzed. About 75% of CF patients were colonized by yeasts, mainly Candida albicans (38%) and Candida dubliniensis (12%). In 35% of the patients Aspergillus spp. (Aspergillus fumigatus: 29%) were detected, followed by Exophiala dermatitidis and Scedosporium/Lomentospora complex isolates (4% each). Data for other fungal species are shown. Over a 5-year period, the epidemiology of fungal species detected in CF patients was relatively constant. Clinical microbiology laboratories should carefully monitor samples from CF patients for newly occurring fungal pathogens. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2010-12-01

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

Microbiological effectiveness and cost of boiling to disinfect drinking water in rural Vietnam.

PubMed

Clasen, Thomas F; Thao, Do Hoang; Boisson, Sophie; Shipin, Oleg

2008-06-15

Despite certain shortcomings, boiling is still the most common means of treating water in the home and the benchmark against which alternative household-based disinfection and filtration methods must be measured. We assessed the microbiological effectiveness and cost of boiling among a vulnerable population relying on unimproved water sources and commonly practicing boiling as a means of disinfecting water. In a 12 week study among 50 households from a rural community in Vietnam, boiling was associated with a 97% reduction in geometric mean thermotolerant coliforms (TTCs) (p < 0.001). Despite high levels of faecal contamination in source water, 37% of stored water samples from self-reported boilers met the WHO standard for safe drinking water (0 TTC/100 mL), and 38.3% fell within the low risk category (1--10 TTC/100 mL). Nevertheless, 60.5% of stored drinking water samples were positive for TTC, with 22.2% falling into the medium risk category (11--100 TTC/100 mL). The estimated cost of wood used to boil water was US$ 0.272 per month for wood collectors and US$ 1.68 per month for wood purchasers, representing approximately 0.48% to 1.04%, respectively, of the average monthly income of participating households.

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

PubMed

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

2003-11-01

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

Production Methods in Industrial Microbiology.

ERIC Educational Resources Information Center

Gaden, Elmer L., Jr.

1981-01-01

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

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

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

Payne, W.J.

1996-12-31

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

Usefulness of real-time PCR as a complementary tool to the monitoring of Legionella spp. and Legionella pneumophila by culture in industrial cooling systems.

PubMed

Touron-Bodilis, A; Pougnard, C; Frenkiel-Lebossé, H; Hallier-Soulier, S

2011-08-01

This study was designed to evaluate the usefulness of quantification by real-time PCR as a management tool to monitor concentrations of Legionella spp. and Legionella pneumophila in industrial cooling systems and its ability to anticipate culture trends by the French standard method (AFNOR T90-431). Quantifications of Legionella bacteria were achieved by both methods on samples from nine cooling systems with different water qualities. Proportion of positive samples for L. pneumophila quantified by PCR was clearly lower in deionized or river waters submitted to a biocide treatment than in raw river waters, while positive samples for Legionella spp. were quantified for almost all the samples. For some samples containing PCR inhibitors, high quantification limits (up to 4·80 × 10(5) GU l(-1) ) did not allow us to quantify L. pneumophila, when they were quantified by culture. Finally, the monitoring of concentrations of L. pneumophila by both methods showed similar trends for 57-100% of the samples. These results suggest that, if some methodological steps designed to reduce inhibitory problems and thus decrease the quantification limits, could be developed to quantify Legionella in complex waters, the real-time PCR could be a valuable complementary tool to monitor the evolution of L. pneumophila concentrations. This study shows the possibility of using real-time PCR to monitor L. pneumophila proliferations in cooling systems and the importance to adapt nucleic acid extraction and purification protocols to raw waters. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology. No claim to French Government works.

Microbiological Characteristic and Nutrition Quality of Goat Milk Kefir Based on Vitamin D3 Fortification Time

NASA Astrophysics Data System (ADS)

Fauziyyah, F.; Panunggal, B.; Afifah, D. N.; Rustanti, N.; Anjani, G.

2018-02-01

Goat milk kefir fortified with vitamin D3 is expected to benefit individual with insulin resistance. Different vitamin D3 fortification time allegedly effect microbiological characteristic and nutrition quality of goat milk kefir due to its microbial growth curve, thus this study aimed to analyze those parameters. This study was an experimental research. This study contains five treatments (vitamin D3 fortification at 0, 6, 12, 18, or 24 hours of fermentation) and a group of control. Total lactic acid bacteria, vitamin D3, protein level, fat contain, crude fiber, viscosity, and pH was analyzed by Total Plate Count, spectrophotometry, Bradford method, Babcock method, gravimetric analysis, Ostwald method, and pH meter respectively. Time of vitamin D3 fortification significantly effect vitamin D3 content (p=0,021), fat content (p=0,001), crude fiber (p=0,0001), viscosity (p=0,010), and total lactic acid bacteria (p=0,048). The highest vitamin D3 content was found on the group fortified at 6 hours of fermentation. All treatment groups has lower fat content and crude fiber content than control group. Total LAB in all group meet the Codex standard (≥ 107 CFU/ml). Control group and fortification group at 24 hours of fermentation have higher viscosity than other groups. There was no significant difference found in goat milk kefir protein level (p=0,262) and pH (p=0,056) despite the difference of fortification time. Vitamin D3 fortification time effect vitamin D3 content, fat content, crude fiber, viscosity, and total lactic acid bacteria of goat milk kefir, but did not effect protein content and pH of goat milk kefir.

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.

Diagnostic trends in Clostridium difficile detection in Finnish microbiology laboratories.

PubMed

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

2009-12-01

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

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.

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

PubMed

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

2016-12-01

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

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

PubMed

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

2008-01-01

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

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.

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.

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.

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

PubMed

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

2017-04-17

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

Comparison of suction above cuff and standard endotracheal tubes in neurological patients for the incidence of ventilator-associated pneumonia and in-hospital outcome: A randomized controlled pilot study

PubMed Central

Jena, Sritam; Kamath, Sriganesh; Masapu, Dheeraj; Veenakumari, H. B.; Ramesh, Venkatapura J.; Bhadrinarayan, Varadarajan; Ravikumar, R.

2016-01-01

Background: Ventilator-associated pneumonia (VAP) is a common complication with endotracheal intubation. The occurrence of VAP results in significant mortality and morbidity. Earlier studies have shown reduction in the incidence of VAP with subglottic secretion drainage. The incidence of VAP in neurologically injured patients is higher and can impact the neurological outcome. This study aimed to compare the incidence of VAP with standard endotracheal tube (SETT) and suction above cuff endotracheal tube (SACETT) in neurologically ill patients and its impact on clinical outcome. Methods: Fifty-four patients with neurological illnesses aged ≥18 years and requiring intubation and/or ventilation and anticipated to remain on ETT for ≥48 h were randomized to receive either SETT or SACETT. All the VAP preventive measures were similar between two groups except for the difference in type of tube. Results: The data of 50 patients were analyzed. The incidence of clinical VAP was 20% in SETT group and 12% in SACETT group; (P = 0.70). The incidence of microbiological VAP was higher in the SETT group (52%) as compared to SACETT group (44%) but not statistically significant; (P = 0.78). There was no difference between the two groups for measured outcomes such as duration of intubation, mechanical ventilation, and Intensive Care Unit stay. Conclusions: In this pilot study in neurological population, a there was no significant difference in incidence of clinical and microbiological VAP was seen between SETT and SACETT, when other strategies for VAP prevention were similar. Other outcomes were similar with use of either tube for intubation. PMID:27275073

Validation of a Rapid Bacteria Endospore Enumeration System for Planetary Protection Application

NASA Astrophysics Data System (ADS)

Chen, Fei; Kern, Roger; Kazarians, Gayane; Venkateswaran, Kasthuri

NASA monitors spacecraft surfaces to assure that the presence of bacterial endospores meets strict criteria at launch, to minimize the risk of inadvertent contamination of the surface of Mars. Currently, the only approved method for enumerating the spores is a culture based assay that requires three days to produce results. In order to meet the demanding schedules of spacecraft assembly, a more rapid spore detection assay is being considered as an alternate method to the NASA standard culture-based assay. The Millipore Rapid Microbiology Detection System (RMDS) has been used successfully for rapid bioburden enumeration in the pharmaceutical and food industries. The RMDS is rapid and simple, shows high sensitivity (to 1 colony forming unit [CFU]/sample), and correlates well with traditional culture-based methods. It combines membrane filtration, adenosine triphosphate (ATP) bioluminescence chemistry, and image analysis based on photon detection with a Charge Coupled Device (CCD) camera. In this study, we have optimized the assay conditions and evaluated the use of the RMDS as a rapid spore detection tool for NASA applications. In order to select for spores, the samples were subjected to a heat shock step before proceeding with the RMDS incubation protocol. Seven species of Bacillus (nine strains) that have been repeatedly isolated from clean room environments were assayed. All strains were detected by the RMDS in 5 hours and these assay times were repeatedly demonstrated along with low image background noise. Validation experiments to compare the Rapid Sore Assay (RSA) and NASA standard assay (NSA) were also performed. The evaluation criteria were modeled after the FDA Guideline of Process Validation, and Analytical Test Methods. This body of research demonstrates that the Rapid Spore Assay (RSA) is quick, and of equivalent sensitivity to the NASA standard assay, potentially reducing the assay time for bacterial endospores from over 72 hours to less than 8 hours. Accordingly, JPL has produced a report recommending that NASA adopt the RSA method as a suitable alternative to the NASA standard assay.

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

PubMed

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

2015-12-01

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

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

PubMed

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

2016-02-25

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

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.

Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

2015-04-01

On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC bacteria. Therefore the applicability of on-site enzymatic activity determination as a direct surrogate or proxy parameter for microbiological standard assays and quantification of fecal indicator bacteria (FIB) concentration could not be approved and further research in this field is necessary. Presently we conclude that rapid on-site detection of enzymatic activity is applicable for surface water monitoring and that it constitutes a complementary on-site monitoring parameter with high potential. Selection of the type of measured enzymatic activities has to be done on a catchment-specific basis and further work is needed to learn more about its detailed information characteristics in different habitats. The accomplishment of this method detecting continuous data of enzymatic activity in high temporal resolution caused by a target bacterial member is on the way of becoming a powerful tool for water quality monitoring, health related water quality- and early warning requirements.

Evaluation of growth based rapid microbiological methods for sterility testing of vaccines and other biological products.

PubMed

Parveen, Seema; Kaur, Simleen; David, Selwyn A Wilson; Kenney, James L; McCormick, William M; Gupta, Rajesh K

2011-10-19

Most biological products, including vaccines, administered by the parenteral route are required to be tested for sterility at the final container and also at various stages during manufacture. The sterility testing method described in the Code of Federal Regulations (21 CFR 610.12) and the United States Pharmacopoeia (USP, Chapter <71>) is based on the observation of turbidity in liquid culture media due to growth of potential contaminants. We evaluated rapid microbiological methods (RMM) based on detection of growth 1) by adenosine triphosphate (ATP) bioluminescence technology (Rapid Milliflex(®) Detection System [RMDS]), and 2) by CO(2) monitoring technologies (BacT/Alert and the BACTEC systems), as alternate sterility methods. Microorganisms representing Gram negative, Gram positive, aerobic, anaerobic, spore forming, slow growing bacteria, yeast, and fungi were prepared in aliquots of Fluid A or a biological matrix (including inactivated influenza vaccines) to contain approximately 0.1, 1, 10 and 100 colony forming units (CFU) in an inoculum of 10 ml. These preparations were inoculated to the specific media required for the various methods: 1) fluid thioglycollate medium (FTM) and tryptic soy broth (TSB) of the compendial sterility method (both membrane filtration and direct inoculation); 2) tryptic soy agar (TSA), Sabouraud dextrose agar (SDA) and Schaedler blood agar (SBA) of the RMDS; 3) iAST and iNST media of the BacT/Alert system and 4) Standard 10 Aerobic/F and Standard Anaerobic/F media of the BACTEC system. RMDS was significantly more sensitive in detecting various microorganisms at 0.1CFU than the compendial methods (p<0.05), whereas the compendial membrane filtration method was significantly more sensitive than the BACTEC and BacT/Alert methods (p<0.05). RMDS detected all microorganisms significantly faster than the compendial method (p<0.05). BacT/Alert and BACTEC methods detected most microorganisms significantly faster than the compendial method (p<0.05), but took almost the same time to detect the slow growing microorganism P. acnes, compared to the compendial method. RMDS using SBA detected all test microorganisms in the presence of a matrix containing preservative 0.01% thimerosal, whereas the BacT/Alert and BACTEC systems did not consistently detect all the test microorganisms in the presence of 0.01% thimerosal. RMDS was compatible with inactivated influenza vaccines and aluminum phosphate or aluminum hydroxide adjuvants at up to 8 mg/ml without any interference in bioluminescence. RMDS was shown to be acceptable as an alternate sterility method taking 5 days as compared to the 14 days required of the compendial method. Isolation of microorganisms from the RMDS was accomplished by re-incubation of membranes with fresh SBA medium and microbial identification was confirmed using the MicroSEQ Identification System. BacT/Alert and BACTEC systems may be applicable as alternate methods to the compendial direct inoculation sterility method for products that do not contain preservatives or anti-microbial agents. Published by Elsevier Ltd.

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

PubMed

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

2018-04-01

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

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

PubMed

Butler-Wu, Susan M; Abbott, April N

2017-08-01

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

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.

Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

PubMed

Halliday, C L; Kidd, S E; Sorrell, T C; Chen, S C-A

2015-04-01

Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

Recent advances in the microbiological diagnosis of bloodstream infections.

PubMed

Florio, Walter; Morici, Paola; Ghelardi, Emilia; Barnini, Simona; Lupetti, Antonella

2018-05-01

Rapid identification (ID) and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections (BSIs) are essential for the prompt administration of an effective antimicrobial therapy, which can result in clinical and financial benefits. Immediately after blood sampling, empirical antimicrobial therapy, chosen on clinical and epidemiological data, is administered. When ID and AST results are available, the clinician decides whether to continue or streamline the antimicrobial therapy, based on the results of the in vitro antimicrobial susceptibility profile of the pathogen. The aim of the present study is to review and discuss the experimental data, advantages, and drawbacks of recently developed technological advances of culture-based and molecular methods for the diagnosis of BSI (including mass spectrometry, magnetic resonance, PCR-based methods, direct inoculation methods, and peptide nucleic acid fluorescence in situ hybridization), the understanding of which could provide new perspectives to improve and fasten the diagnosis and treatment of septic patients. Although blood culture remains the gold standard to diagnose BSIs, newly developed methods can significantly shorten the turnaround time of reliable microbial ID and AST, thus substantially improving the diagnostic yield.

MALDI-TOF identification of Gram-negative bacteria directly from blood culture bottles containing charcoal: Sepsityper® kits versus centrifugation-filtration method.

PubMed

Riederer, Kathleen; Cruz, Kristian; Shemes, Stephen; Szpunar, Susan; Fishbain, Joel T

2015-06-01

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry has dramatically altered the way microbiology laboratories identify clinical isolates. Direct blood culture (BC) detection may be hampered, however, by the presence of charcoal in BC bottles currently in clinical use. This study evaluates an in-house process for extraction and MALDI-TOF identification of Gram-negative bacteria directly from BC bottles containing charcoal. Three hundred BC aliquots were extracted by a centrifugation-filtration method developed in our research laboratory with the first 96 samples processed in parallel using Sepsityper® kits. Controls were colonies from solid media with standard phenotypic and MALDI-TOF identification. The identification of Gram-negative bacteria was successful more often via the in-house method compared to Sepsityper® kits (94.7% versus 78.1%, P≤0.0001). Our in-house centrifugation-filtration method was further validated for isolation and identification of Gram-negative bacteria (95%; n=300) directly from BC bottles containing charcoal. Copyright © 2015 Elsevier Inc. All rights reserved.

A biochemical protocol for the isolation and identification of current species of Vibrio in seafood.

PubMed

Ottaviani, D; Masini, L; Bacchiocchi, S

2003-01-01

We report a biochemical method for the isolation and identification of the current species of vibrios using just one operative protocol. The method involves an enrichment phase with incubation at 30 degrees C for 8-24 h in alkaline peptone water and an isolation phase on thiosulphate-citrate-salt sucrose agar plates incubating at 30 degrees C for 24 h. Four biochemical tests and Alsina's scheme were performed for genus and species identification, respectively. All biochemical tests were optimized as regards conditions of temperature, time of incubation and media composition. The whole standardized protocol was always able to give a correct identification when applied to 25 reference strains of Vibrio and 134 field isolates. The data demonstrated that the assay method allows an efficient recovery, isolation and identification of current species of Vibrio in seafood obtaining results within 2-7 days. This method based on biochemical tests could be applicable even in basic microbiology laboratories, and can be used simultaneously to isolate and discriminate all clinically relevant species of Vibrio.

A simple method of DNA isolation from jute (Corchorus olitorius) seed suitable for PCR-based detection of the pathogen Macrophomina phaseolina (Tassi) Goid.

PubMed

Biswas, C; Dey, P; Satpathy, S; Sarkar, S K; Bera, A; Mahapatra, B S

2013-02-01

A simple method was developed for isolating DNA from jute seed, which contains high amounts of mucilage and secondary metabolites, and a PCR protocol was standardized for detecting the seedborne pathogen Macrophomina phaseolina. The cetyl trimethyl ammonium bromide method was modified with increased salt concentration and a simple sodium acetate treatment to extract genomic as well as fungal DNA directly from infected jute seed. The Miniprep was evaluated along with five other methods of DNA isolation in terms of yield and quality of DNA and number of PCR positive samples. The Miniprep consistently recovered high amounts of DNA with good spectral qualities at A260/A280. The DNA isolated from jute seed was found suitable for PCR amplification. Macrophomina phaseolina could be detected by PCR from artificially inoculated as well as naturally infected jute seeds. The limit of PCR-based detection of M. phaseolina in jute seed was determined to be 0·62 × 10(-7) CFU g(-1) seed. © 2012 The Society for Applied Microbiology.

Comparative In Vitro Efficacy of Doripenem and Imipenem Against Multi-Drug Resistant Pseudomonas aeruginosa.

PubMed

Wali, Nadia; Mirza, Irfan Ali

2016-04-01

To compare the in vitro efficacy of doripenem and imipenem against multi-drug resistant (MDR) Pseudomonas aeruginosa from various clinical specimens. Descriptive cross-sectional study. Department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, from November 2012 to November 2013. MDR Pseudomonas aeruginosa isolates from various clinical samples were included in the study. Susceptibility of Pseudomonas aeruginosa against doripenem and imipenem was performed by E-test strip and agar dilution methods. The results were interpreted as recommended by Clinical Laboratory Standard Institute (CLSI) guidelines. The maximum number of Pseudomonas aeruginosa were isolated from pure pus and pus swabs. In vitro efficacy of doripenem was found to be more effective as compared to imipenem against MDR Pseudomonas aeruginosa with both E-test strip and agar dilution methods. Overall, p-values of 0.014 and 0.037 were observed when susceptibility patterns of doripenem and imipenem were evaluated with E-test strip and agar dilution methods. In vitro efficacy of doripenem was found to be better against MDR Pseudomonas aeruginosaas compared to imipenem when tested by both E-test and agar dilution methods.

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.

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.

The Diagnostic Value of Urine Lipoarabinomannan (LAM) Antigen in Childhood Tuberculosis

PubMed Central

Nursiloningrum, Erlin; Arthamin, Maimun Zulhaidah; Olivianto, Ery; Chandrakusuma, Mas Slamet

2017-01-01

Introduction Diagnosis of Tuberculosis (TB) in children is difficult because the clinical presentation is not specific, the chest X-ray interpretation has low accuracy and sputum sample is difficult to obtain. Antigen detection test such as rapid urine LAM is a non-invasive alternative for diagnosing TB . Lipoarabinomannan (LAM) is the main component of M.tuberculosis cell wall. Aim To determine the diagnostic value of urinary LAM antigen for diagnosis of childhood TB. Materials and Methods In the present cross-sectional study, subjects were included using consecutive sampling method. All the children aged 0-14 years Suspected of pulmonary or extra pulmonary TB suffering from cough more than two weeks, fever without clear aetiology, loss of body weight or poor weight gain, fatigue, malaise, chronic lymph node enlargement, spine angulation, joint swelling and had history of contact with positive sputum smear adult TB patient were enrolled in the study. Pulmonary and extra pulmonary diagnosis was based on clinical presentation, Tuberculin Skin Test (TST), chest X-ray, Acid Fast Bacillus (AFB) staining and or sputum culture. Urinary LAM level was measured by using Enzyme-Linked Immunosorbent Assay (ELISA). Cut off value and Area Under the Curve (AUC) were determined using ROC statistical analysis (SPSS 21.0). Sensitivity and specificity was measured from 2x2 cross table. Results Out of 61 subjects suspected as TB, 49 (80.3%) were eventually diagnosed with TB. Of those diagnosed with TB, 21 (42.9%) were microbiologically confirmed cases either by sputum microscopy (34.7%) or culture (8.2%), whereas 28 subjects were unconfirmed cases (57.1%). The urinary LAM level was higher in subjects with TB (1.80+1.02) mg/l compared to non-TB group (0.46+0.3) mg/l; p<0.001(independent t-test). Urine LAM had 83% sensitivity and 85% specificity with cut off value 0.98 mg/l using microbiological and clinical confirmation as standard reference and 33% sensitivity and 60% specificity with cut off value 1.69 mg/l using microbiological confirmation only. Conclusion Urinary LAM has good diagnostic value for childhood TB diagnosis. PMID:28511392

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.

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

PubMed

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

2002-01-01

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

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

PubMed

Lech, Tomasz

2016-05-01

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

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.

Preparation and stability of extemporaneous oral liquid formulations of oseltamivir using commercially available capsules.

PubMed

Winiarski, Aleksander P; Infeld, Martin H; Tscherne, Ronald; Bachynsky, Maria; Rucki, Richard; Nagano-Mate, Kathy

2007-01-01

To develop a simple, standardized method for the extemporaneous compounding of an oral liquid form of oseltamivir from commercially available Tamiflu 75 mg capsules (Roche Pharmaceuticals) and to determine the stability of oseltamivir in this preparation. Chemical and microbial stability study. Laboratory. None. Extemporaneous oral liquid formulations of oseltamivir (15 mg/mL) were prepared in Cherry Syrup (Humco) and Ora-Sweet SF (Paddock Laboratories) using methods consistent with current compounding practice in a pharmacy setting. Preparations were stored in amber glass and amber polyethyleneterephthalate bottles at 5 degrees C +/- 2 degrees C (41 degrees F +/- 4 degrees F) and 25 degrees C +/- 2 degrees C (77 degrees F +/- 4 degrees F) at 60% +/- 5% relative humidity (RH) for 35 days and 30 degrees C +/- 2 degrees C (86 degrees F +/- 4 degrees F) at 65% +/- 5% RH for 13 days. Samples were monitored for appearance, pH, assay, degradation products, and microbiologic stability. The Cherry Syrup preparation, in either bottle type, was stable for up to 35 days under refrigeration (5 degrees C) and up to 5 days at room temperature (25 degrees C). It was not stable when stored at 30 degrees C for 5 days. The Ora-Sweet SF preparation was stable for up to 35 days at 5 degrees C or 25 degrees C and for up to 13 days at 30 degrees C in either bottle type. Both preparations maintained microbiologic stability for 35 days. Both preparations are stable under the described conditions and may provide an option in situations where the marketed suspension is unavailable.

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.

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

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...

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

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

PubMed

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

2018-05-01

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

Do English NHS Microbiology laboratories offer adequate services for the diagnosis of UTI in children? Healthcare Quality Improvement Partnership (HQIP) Audit of Standard Operational Procedures.

PubMed

McNulty, Cliodna A M; Verlander, Neville Q; Moore, Philippa C L; Larcombe, James; Dudley, Jan; Banerjee, Jaydip; Jadresic, Lyda

2015-09-01

The National Institute of Care Excellence (NICE) 2007 guidance CG54, on urinary tract infection (UTI) in children, states that clinicians should use urgent microscopy and culture as the preferred method for diagnosing UTI in the hospital setting for severe illness in children under 3 years old and from the GP setting in children under 3 years old with intermediate risk of severe illness. NICE also recommends that all 'infants and children with atypical UTI (including non-Escherichia coli infections) should have renal imaging after a first infection'. We surveyed all microbiology laboratories in England with Clinical Pathology Accreditation to determine standard operating procedures (SOPs) for urgent microscopy, culture and reporting of children's urine and to ascertain whether the SOPs facilitate compliance with NICE guidance. We undertook a computer search in six microbiology laboratories in south-west England to determine urine submissions and urine reports in children under 3 years. Seventy-three per cent of laboratories (110/150) participated. Enterobacteriaceae that were not E. coli were reported only as coliforms (rather than non-E. coli coliforms) by 61% (67/110) of laboratories. Eighty-eight per cent of laboratories (97/110) provided urgent microscopy for hospital and 54% for general practice (GP) paediatric urines; 61% of laboratories (confidence interval 52-70%) cultured 1 μl volume of urine, which equates to one colony if the bacterial load is 106 c.f.u. l(-1). Only 22% (24/110) of laboratories reported non-E. coli coliforms and provided urgent microscopy for both hospital and GP childhood urines; only three laboratories also cultured a 5 μl volume of urine. Only one of six laboratories in our submission audit had a significant increase in urine submissions and urines reported from children less than 3 years old between the predicted pre-2007 level in the absence of guidance and the 2008 level following publication of the NICE guidance. Less than a quarter of laboratories were providing a service that would allow clinicians to fully comply with the first line recommendations in the 2007 NICE UTI in children guidance. Laboratory urine submission report figures suggest that the guidance has not led to an increase in diagnosis of UTI in children under 3 years old.

Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens

PubMed Central

Kostić, Tanja; Sessitsch, Angela

2011-01-01

Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples. PMID:27605332

Infectious Disease Transmission during Organ and Tissue Transplantation

PubMed Central

Kuehnert, Matthew J.; Fishman, Jay A.

2012-01-01

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

[The significance of low-frequency magnetotherapy for local treatment of burns. An experimental comparative approach (author's transl)].

PubMed

Sauer, H D; Rudy, D

1980-02-01

Under standardized experimental conditions 3rd degree burns were produced on the neck of 241 Wistar-rats. The process of wound-healing was documented by means of planimetric, histologic and microbiologic methods. In comparison to an untreated control-group the effectiveness of low-frequency magnetotherapy (system magnetodyn 5 by W. Krauss) as well as coagulation of necrosis according to Grob and autologous skin-transplantation were studied. The results obtained indicate that only early debridement of necrosis and subsequent autologous skin-grafting guarantees sufficient acceleration of wound healing. The low-frequency magnetotherapy according to Krauss showed no effect of therapeutic value. With the coagulation of necrosis, as described by Grob, a germfree status under the necrosis was obtained for nearly 2 weeks.

Safe household water treatment and storage using ceramic drip filters: a randomised controlled trial in Bolivia.

PubMed

Clasen, T; Brown, J; Suntura, O; Collin, S

2004-01-01

A randomised controlled field trial was conducted to evaluate the effectiveness of ceramic drip filters to improve the microbiological quality of drinking water in a low-income community in rural Bolivia. In four rounds of water sampling over five months, 100% of the samples were free of thermotolerant (faecal) coliforms (TTC) compared to an arithmetic mean TTC count of 1517, 406, 167 and 245 among control households which continued to use their customary sources of drinking water. The filter systems produced water that consistently met WHO drinking-water standards despite levels of turbidity that presented a challenge to other low-cost POU treatment methods. The filter systems also demonstrated an ability to maintain the high quality of the treated water against subsequent re-contamination in the home.

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

PubMed

Yilmaz, I; Demirci, M

2010-06-01

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

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

NASA Astrophysics Data System (ADS)

Baumgarten, Kristyne A.

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

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.

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.

[Analysis of the results of the SEIMC External Quality Control Program for HIV-1 and HCV viral loads. Year 2008].

PubMed

Mira, Nieves Orta; Serrano, María del Remedio Guna; Martínez, José Carlos Latorre; Ovies, María Rosario; Pérez, José L; Cardona, Concepción Gimeno

2010-01-01

Human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) viral load determinations are among the most relevant markers for the follow up of patients infected with these viruses. External quality control tools are crucial to ensure the accuracy of results obtained by microbiology laboratories. This article summarized the results obtained from the 2008 SEIMC External Quality Control Program for HIV-1 and HCV viral loads. In the HIV-1 program, a total of five standards were sent. One standard consisted in seronegative human plasma, while the remaining four contained plasma from 3 different viremic patients, in the range of 2-5 log(10) copies/mL; two of these standards were identical aiming to determine repeatability. The specificity was complete for all commercial methods, and no false positive results were reported by the participants. A significant proportion of the laboratories (24% 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 (D < 0.5 log(10) copias/mL). The HCV program consisted of two standards with different viral load contents. Most of the participants (88,7%) obtained results within the accepted range (mean +/- 1.96 SD log(10) UI/mL). Post-analytical errors due to mistranscription of the results were detected for HCV, but not for the HIV-1 program. Data from this analysis reinforce the utility of proficiency programmes to ensure the quality of the results obtained by a particular laboratory, as well as the importance of the post-analytical phase on the overall quality. Due to the remarkable interlaboratory variability, it is advisable to use the same method and the same laboratory for patient follow up. 2010 Elsevier España S.L. All rights reserved.

AOAC Official MethodSM Matrix Extension Validation Study of Assurance GDSTM for the Detection of Salmonella in Selected Spices.

PubMed

Feldsine, Philip; Kaur, Mandeep; Shah, Khyati; Immerman, Amy; Jucker, Markus; Lienau, Andrew

2015-01-01

Assurance GDSTM for Salmonella Tq has been validated according to the AOAC INTERNATIONAL Methods Committee Guidelines for Validation of Microbiological Methods for Food and Environmental Surfaces for the detection of selected foods and environmental surfaces (Official Method of AnalysisSM 2009.03, Performance Tested MethodSM No. 050602). The method also completed AFNOR validation (following the ISO 16140 standard) compared to the reference method EN ISO 6579. For AFNOR, GDS was given a scope covering all human food, animal feed stuff, and environmental surfaces (Certificate No. TRA02/12-01/09). Results showed that Assurance GDS for Salmonella (GDS) has high sensitivity and is equivalent to the reference culture methods for the detection of motile and non-motile Salmonella. As part of the aforementioned validations, inclusivity and exclusivity studies, stability, and ruggedness studies were also conducted. Assurance GDS has 100% inclusivity and exclusivity among the 100 Salmonella serovars and 35 non-Salmonella organisms analyzed. To add to the scope of the Assurance GDS for Salmonella method, a matrix extension study was conducted, following the AOAC guidelines, to validate the application of the method for selected spices, specifically curry powder, cumin powder, and chili powder, for the detection of Salmonella.

Transformation From a Conventional Clinical Microbiology Laboratory to Full Automation.

PubMed

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

2017-12-22

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

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

PubMed Central

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

2008-01-01

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

Microbiological sampling of returned Surveyor 3 electrical cabling

NASA Technical Reports Server (NTRS)

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

1972-01-01

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

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

DTIC Science & Technology

2007-01-01

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

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

PubMed

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

2006-12-01

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

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.

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

NASA Technical Reports Server (NTRS)

Pyle, Barry H.; Mcfeters, Gordon A.

1992-01-01

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

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

PubMed

Cabello, Felipe C

2008-02-01

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

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

PubMed Central

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

2013-01-01

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

[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.

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

PubMed

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

1980-01-01

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

Stability of extemporaneously prepared preservative-free prochlorperazine nasal spray.

PubMed

Yellepeddi, Venkata K

2018-01-01

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

Prevalence and distribution of Legionella spp in potable water systems in Germany, risk factors associated with contamination, and effectiveness of thermal disinfection.

PubMed

Kruse, Eva-Brigitta; Wehner, Arno; Wisplinghoff, Hilmar

2016-04-01

Worldwide, Legionella spp are a common cause of community-acquired pneumonia. Potable water systems are a main reservoir; however, exposure in the community is unknown. Water samples from 718 buildings in Germany were collected. Possible risk factors were prospectively recorded. All samples were tested for Legionella spp using cultural microbiologic methods. Samples were assigned to 1 of 5 levels of contamination. Statistical analysis was performed to determine the influence of risk factors for contamination and, in a subgroup of buildings, for unsuccessful thermal disinfection. In total, 4,482 water samples from 718 different water supply systems were analyzed. In 233 buildings (32.7%), Legionella spp were identified, 148 (63.5%) of which had a medium or higher level of contamination. The most common species was Legionella pneumophila (94%). Contamination was strongly associated with temperature in the circulation, but not with the size of the building, time of the year, or transport time to the laboratory. Thermal disinfection was successful in fewer than half of the buildings. There is relevant exposure to Legionella spp in the community. Water systems are not always up to current technical standards. Although microbiological risk assessment remains a challenge, there is a case for monitoring for Legionella spp outside of hospitals. Copyright © 2016 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Evaluation of the microbiological quality of conventional and organic leafy greens at the time of purchase from retail markets in Alexandria, Egypt.

PubMed

Khalil, Rowaida; Gomaa, Mohamed

2014-01-01

This is a pioneer study in Egypt that provides some assessment of the microbiological quality of conventional and organic leafy green vegetables that constitute an essential component of the Egyptians' daily diet. A total of 380 samples of unpackaged whole conventional and 84 packaged whole organic leafy greens were collected from retail markets in Alexandria, and analyzed for total aerobic mesophilic count (AMC) and total E. coli count (ECC) using the standard spread plate method. Mean AMC values for organic samples were statistically less (p < 0.05) than those of the corresponding conventional samples. Conventional radish and organic parsley samples had the highest AMC of 7.17 and 7.68 log CFU/g respectively, while conventional green cabbage and organic basil had the lowest AMC of 3.63 and 3.23 log CFU/g respectively. The presence of E. coli in 100% of the studied leafy greens was indicative of potential fecal contamination, in view of open and unhygienic environmental and unsanitary handling conditions, as leafy green items are available for sale by street-vendors. Unsatisfactory AMC and ECC levels encountered in the studied samples, warrant future investigations to determine the potential prevalence of foodborne pathogens, and to identify sources of dominating microorganisms, which could make a contribution to the field of food safety

Ice Recrystallization Inhibiting Polymers Enable Glycerol-Free Cryopreservation of Micro-organisms.

PubMed

Hasan, Muhammad; Fayter, Alice E R; Gibson, Matthew I

2018-06-22

All modern molecular biology and microbiology is underpinned not only by the tools to handle and manipulate microorganisms, but also those to store, bank and transport them. Glycerol is the current gold-standard cryoprotectant but it is intrinsically toxic to most micro-organisms: only a fraction of cells survive freezing and the presence of glycerol can impact down-stream applications and assays. Extremophile organisms survive repeated freeze/thaw cycles by producing antifreeze proteins which are potent ice recrystallization inhibitors. Here we introduce a new concept for the storage/transport of micro-organisms by using ice recrystallization inhibiting poly(vinyl alcohol) in tandem with poly(ethylene glycol). This cryopreserving formulation is shown to result in a 4-fold increase in E. coli yield post-thaw, compared to glycerol, utilizing lower concentrations, with successful cryopreservation at just 1.1 weight percent of additive. The mechanism of protection is demonstrated to be linked to inhibiting ice recrystallization (by comparison to a recombinant antifreeze protein) but also to the significantly lower toxicity of the polymers compared to glycerol. Optimized formulations are presented and shown to be broadly applicable to the cryopreservation of a panel of Gram negative, Gram positive and Mycobacteria strains. This represents a step-change in how micro-organisms will be stored by the design of new macromolecular ice growth inhibitors; it should enable a transition from traditional solvent-based to macromolecular microbiology storage methods.

Microbial contamination of nonsterile pharmaceuticals in public hospital settings

PubMed Central

Mugoyela, Veronica; Mwambete, Kennedy D

2010-01-01

Purpose Contamination of pharmaceuticals with microorganisms irrespective whether they are harmful or nonpathogenic can bring about changes in physicochemical characteristics of the medicines. Although sterility is not a requirement in official compendia for nonsterile pharmaceuticals, bioburdens need to be within acceptable limits. Therefore, this study investigated microbial contamination of 10 nonsterile pharmaceuticals frequently delivered to outpatients by identifying and quantifying microbial contaminants and susceptibility pattern testing on the microbes isolated. Methods The study was carried out at Amana Municipal Hospital in Dar es Salaam, Tanzania. The protocol for the study involved structured selection of representative tablets, syrups, and capsules from the hospital’s outpatient pharmacy. Constitutive microorganisms were elaborated and enumerated using standard microbiologic procedures. Results Results showed that 50% of all tested products were heavily contaminated, and the predominant contaminants comprised Klebsiella, Bacillus, and Candida species. Furthermore, the results showed that the isolated Bacillus and Klebsiella species were resistant to Augmentin ® and cloxacillin. The differences in means for cfu/mL and zones of inhibition among the microorganisms isolated were considered significant at P < 0.05. Conclusion The nonsterile pharmaceuticals were presumably microbiologically contaminated due to poor handling during dispensing, repackaging, and/or nonadherence to good manufacturing practice. Therefore, training and educating the dispensers, as well as patients, on the proper handling and use of medicines cannot be overemphasized, because these are key aspects in controlling cross-contamination of medicines. PMID:20957135

Bacterial water quality and network hydraulic characteristics: a field study of a small, looped water distribution system using culture-independent molecular methods.

PubMed

Sekar, R; Deines, P; Machell, J; Osborn, A M; Biggs, C A; Boxall, J B

2012-06-01

To determine the spatial and temporal variability in the abundance, structure and composition of planktonic bacterial assemblages sampled from a small, looped water distribution system and to interpret results with respect to hydraulic conditions. Water samples were collected from five sampling points, twice a day at 06:00 h and 09:00 h on a Monday (following low weekend demand) and a Wednesday (higher midweek demand). All samples were fully compliant with current regulated parameter standards. This study did not show obvious changes in bacterial abundance (DAPI count) or community structure Denaturing gradient gel electrophoresis analysis with respect to sample site and hence to water age; however, the study did show temporal variability with respect to both sampling day and sample times. Data suggests that variations in the bacterial assemblages may be associated with the local system hydraulics: the bacterial composition and numbers, over short durations, are governed by the interaction of the bulk water and the biofilm influenced by the hydraulic conditions. This study demonstrates general stability in bacterial abundance, community structure and composition within the system studied. Trends and patterns supporting the transfer of idealized understanding to the real world were evident. Ultimately, such work will help to safeguard potable water quality, fundamental to public health. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Microbial water quality risks to public health: potable water assessment for a flood-affected town in northern Pakistan.

PubMed

Baig, Shams Ali A; Xu, Xinhua; Khan, Rashid

2012-01-01

In mid-July 2010 flash flooding in Pakistan destroyed the basic water, environmental sanitation and livelihood infrastructures in 82 districts. Two months later, the local press of Swat (northern Pakistan) reported that several residents of Marghazar town became ill and were hospitalized after drinking contaminated water. A non-governmental organization (Oxfam GB) team took action to determine the causes of this incident and analyzed the community drinking water supply. Standard methods were used to analyze six physio-chemical and four microbiological water quality parameters at five selected sampling locations in the water supply system. The samples from sites numbers (SN)02, 03, 04 and 05 were found to be microbiologically unfit for drinking due to the presence of Escherichia coli, Shigella, Salmonella and Staphylococcus aureus (range 18-96 ± 14 cfu/100 mL). However, the pH, conductivity, total dissolved solid, total hardness as calcium carbonate and nitrate as NO3(-2) of all the samples were within WHO permissible limits. Higher turbidities were recorded at SN04 and 05 of 6 ± 0.23 and 9 ± 1.23, respectively. Quantitative results revealed the presence of pathogenic organisms and water quality risk factors due to the damaged water and environmental sanitation infrastructure. Continued water quality monitoring, the application of household based disinfectants, and healthy domestic hygiene practices are highly recommended in similar circumstances.

Rapid Diagnosis of Bloodstream Infections with PCR Followed by Mass Spectrometry

PubMed Central

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

2013-01-01

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

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...

Design of a water quality monitoring network for the Limpopo River Basin in Mozambique

NASA Astrophysics Data System (ADS)

Chilundo, M.; Kelderman, P.; O´keeffe, J. H.

The measurement of chemical, physical and biological parameters is important for the characterization of streams health. Thus, cost-effective and targeted water quality (WQ) monitoring programmes are required for proper assessment, restoration and protection of such systems. This research proposes a WQ monitoring network for the Limpopo River Basin (LRB) in Mozambique located in Southern Africa, a region prone to severe droughts. In this Basin both anthropogenic and natural driven processes, exacerbated by the increased water demand by the four riparian countries (Botswana, South Africa, Zimbabwe and Mozambique) are responsible for the degradation of surface waters, impairing their downstream use, either for aquatic ecosystem, drinking, industrial or irrigation. Hence, physico-chemical, biological and microbiological characteristics at 23 sites within the basin were studied in November 2006 and January 2007. The physico-chemical and microbiological samples were analyzed according to American Public Health Association (APHA) standard methods, while the biological monitoring working party method (BMWP) was used for biological assessment. The assessment of the final WQ condition at sampled points was done taking into account appropriate indexes, the Mozambican standards for receiving waters and the WHO guidelines for drinking WQ. The assessed data indicated that sites located at proximities to the border with upstream countries were contaminated with heavy metals. The Elephants subcatchment was found with a relatively better WQ, whereas the Changane subcatchment together with the effluent point discharges in the basin were found polluted as indicated by the low dissolved oxygen and high total dissolved solids, electric conductivity, total hardness, sodium adsorption ratio and low benthic macroinvertebrates taxa. Significant differences ( p < 0.05) were found for some parameters when the concentrations recorded in November and January were tested, therefore, indicating possible need for monthly monitoring of WQ. From this study it was concluded that a systematic WQ monitoring network composed of 16 stations would fit the conditions of the LRB. Ambient, earl warning, operational and effluents are the main monitoring types recommended. Additional research at a Basin scale was also recommended to identify the major sources of pollution, their transport and impacts to the downstream ecosystem.

Characterization and multicentric validation of a common standard for Toxoplasma gondii detection using nucleic acid amplification assays.

PubMed

Varlet-Marie, Emmanuelle; Sterkers, Yvon; Brenier-Pinchart, Marie-Pierre; Cassaing, Sophie; Dalle, Frédéric; Delhaes, Laurence; Filisetti, Denis; Pelloux, Hervé; Touafek, Fériel; Yera, Hélène; Bastien, Patrick

2014-11-01

The molecular diagnosis of toxoplasmosis essentially relies upon laboratory-developed methods and suffers from lack of standardization, hence the large diversity of performances between laboratories. Moreover, quantifications of parasitic loads differ among centers, a fact which prevents the possible prediction of the severity of this disease as a function of parasitic loads. The objectives of this multicentric study performed in eight proficient laboratories of the Molecular Biology Pole of the French National Reference Center for Toxoplasmosis (NRC-T) were (i) to assess the suitability of a lyophilized preparation of Toxoplasma gondii as a common standard for use in this PCR-based molecular diagnosis and (ii) to make this standard available to the community. High-quality written procedures were used for the production and qualification of this standard. Three independent batches of this standard, containing concentrations ranging from 10(4) to 0.01 T. gondii genome equivalents per PCR, were first assessed: the linear dynamic range was ≥ 6 log, the intra-assay coefficients of variation (CV) from a sample containing 10 T. gondii organisms per PCR were 0.3% to 0.42%, and the interassay CV over a 2-week period was 0.76% to 1.47%. A further assessment in eight diagnostic centers showed that the standard is stable, robust, and reliable. These lyophilized standards can easily be produced at a larger scale when needed and can be made widely available at the national level. To our knowledge, this is the first quality control assessment of a common standard which is usable both for self-evaluation in laboratories and for accurate quantification of parasitic loads in T. gondii prenatal infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Intersecting Virtual Patients and Microbiology: Fostering a culture of learning.

PubMed

McCarthy, David; O'Gorman, Ciaran; Gormley, Gerard

2015-10-01

The use and integration of Technology Enhanced Learning (TEL) resources in medical education has attracted considerable commentary and support. "Virtual Patients" are one such resource. Whilst evidence exists supporting the benefits of these resources, there has not been specific consideration of their implications for teaching microbiology; nor attention paid to both the internal and external factors that influence learner engagement with virtual patients. The principle aims of this study are to identify factors that explicitly and implicitly influence the student's interaction with a microbiology virtual patient resource and how these interactions reflect upon the use of the resource. A mixed method quantitative (online questionnaire; n=161) and qualitative (student focus groups; N=11) study was undertaken amongst third year medical students enrolled at Queen's University Belfast in the academic year 2012-2013. The results supported prior evidence that virtual patients are a useful learning tool (mean score of 5.09 out of 7) that helped them to integrate microbiology principles with clinical experiences. How students used the virtual patients and the depth of the subsequent benefits was dependent upon their perception of the importance of the resource. This was influenced by a number of factors including how the resources were presented and positioned within the curriculum, whether they were formally examined or timetabled and the importance attributed by peers who had already completed the examinations. Integration of virtual patients into the microbiology curriculum is widely endorsed and may even be considered superior to other methods of teaching. How students use these resources is dependent upon a positive perception of their importance. Educators should be aware of the factors that shape this perception when integrating TEL resources into curricula.

Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

PubMed Central

Kell, Douglas; Potgieter, Marnie; Pretorius, Etheresia

2015-01-01

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically ‘nonculturable’ on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as ‘persisters’. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one’s bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit. PMID:26629334

A pan-European ring trial to validate an International Standard for detection of Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus in seafoods.

PubMed

Hartnell, R E; Stockley, L; Keay, W; Rosec, J-P; Hervio-Heath, D; Van den Berg, H; Leoni, F; Ottaviani, D; Henigman, U; Denayer, S; Serbruyns, B; Georgsson, F; Krumova-Valcheva, G; Gyurova, E; Blanco, C; Copin, S; Strauch, E; Wieczorek, K; Lopatek, M; Britova, A; Hardouin, G; Lombard, B; In't Veld, P; Leclercq, A; Baker-Austin, C

2018-02-10

Globally, vibrios represent an important and well-established group of bacterial foodborne pathogens. The European Commission (EC) mandated the Comite de European Normalisation (CEN) to undertake work to provide validation data for 15 methods in microbiology to support EC legislation. As part of this mandated work programme, merging of ISO/TS 21872-1:2007, which specifies a horizontal method for the detection of V. parahaemolyticus and V. cholerae, and ISO/TS 21872-2:2007, a similar horizontal method for the detection of potentially pathogenic vibrios other than V. cholerae and V. parahaemolyticus was proposed. Both parts of ISO/TS 21872 utilized classical culture-based isolation techniques coupled with biochemical confirmation steps. The work also considered simplification of the biochemical confirmation steps. In addition, because of advances in molecular based methods for identification of human pathogenic Vibrio spp. classical and real-time PCR options were also included within the scope of the validation. These considerations formed the basis of a multi-laboratory validation study with the aim of improving the precision of this ISO technical specification and providing a single ISO standard method to enable detection of these important foodborne Vibrio spp.. To achieve this aim, an international validation study involving 13 laboratories from 9 countries in Europe was conducted in 2013. The results of this validation have enabled integration of the two existing technical specifications targeting the detection of the major foodborne Vibrio spp., simplification of the suite of recommended biochemical identification tests and the introduction of molecular procedures that provide both species level identification and discrimination of putatively pathogenic strains of V. parahaemolyticus by the determination of the presence of theromostable direct and direct related haemolysins. The method performance characteristics generated in this have been included in revised international standard, ISO 21872:2017, published in July 2017. Copyright © 2018. Published by Elsevier B.V.

Microbiological quality of take-away cooked rice and chicken sandwiches: effectiveness of food hygiene training of the management.

PubMed

Little, C L; Barnes, J; Mitchell, R T

2002-12-01

During August 2001 a microbiological study of ready-to-eat cooked rice from take-aways and of chicken sandwiches made on the premises from sandwich bars was undertaken. The intention was to identify risk factors in the production, storage and handling of cooked rice and sandwiches, and to establish their effect on microbiological quality. Examination of cooked rice revealed that the majority of samples (87%; 442 of 508) were of satisfactory/acceptable microbiological quality; 50 (10%) were unsatisfactory, and 16 (3%) were of unacceptable quality due to Bacillus cereus and/or other Bacillus spp in excess of 10(5) cfu/g. The microbiological quality of cooked rice was associated with cuisine type (p < 0.00001), rice type (p < 0.01), cooking (p < 0.01), serving methods (p < 0.00001), and management food hygiene training (p < 0.01). Examination of chicken sandwiches found that most (75%; 335 of 449) were of satisfactory/acceptable microbiological quality and 114 (25%) were unsatisfactory. Acceptable microbiological quality of sandwiches was associated with sandwich bars that had hazard analysis in place (p < 0.05). Smaller businesses, as indicated by Local Authority Inspectors' Consumer at Risk scores, were more likely to have samples classified as unsatisfactory or unacceptable compared to larger businesses (p < 0.001). The majority (90%) of premises had hand-washing facilities accessible and available for use, although only over half (55%) were correctly used as judged by the sampling officer. Where the manager of the premises had received some form of food hygiene training, food safety procedures such as the hazard analysis system were more likely to be in place (p < 0.0001).

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

NASA Technical Reports Server (NTRS)

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