Application of microbiological data

The Open Emergency Medicine Journal

Standardized microbiological methods used in clinical analysis are based on traditional microbial enrichment on selective media, possibly followed by characterization of bacteria with molecular methods. These techniques present several difficulties, such as the subjectivity in the interpretation of genetic, biochemical or morphological tests and the possible interference of biological matrices, specially when low levels of contamination are present. In addition, standardized microbiological analyses are characterised by the high cost of the method, both in terms of labor and supplies, and above all, by the long time needed to obtain definitive results (from 3 to 7 days). These reasons have led to the development and refinement of microbiological POCTs which are now available for several microorganisms, even thought no microbiological POCT was up to now developed for the count of total viable bacteria (TVC) in serum, urine or other biological fluids. MBS srl (a spin-off of Roma Tre University, Rome, Italy) has developed and patented an alternative method for selective counting of bacteria, called Micro Biological Survey (MBS) method. The MBS method is based on colorimetric survey performed in mono-use disposable reaction vials in which samples can be inoculated without any preliminary treatment. The analyses can be carried out by untrained personnel and anywhere they are necessary, without the need for any other instrumentation than a thermostated optical reader that can automatically detect the colour change providing the number of bacteria present into the sample. The MBS method measures the catalytic activity of redox enzymes in the main metabolic pathways of bacteria, allowing an unequivocal correlation between the observed enzymatic activity and the number of viable cells present in the samples. The time required for a color change is inversely related to the log of bacterial concentration; like an enzymatic reaction, the greater the number of bacteria, the faster the color change. The objective of this study was the primary validation, in accord with ISO 13843:2003 (Guidance on validation of microbiological methods), of the quantitative Micro Biological Survey (MBS) method for Total Viable Count (TVC). Validation aims to compare the results obtained with an alternative method, in this case the MBS method, with the results obtained with the reference method. To verify the equivalence between the two methods different parameters were analyzed: selectivity, linearity and accuracy. The validation has shown that the MBS method gives similar results and is in agreement with the reference methods. The MBS method could therefore represent a worthy aid in microbiological analysis as POCT device without replacing the analysis carried out with traditional methods which are very precise though often long and complex.

EFSA Journal

The European Food Safety Authority asked the Panel on Biological Hazards (BIOHAZ) to deliver a scientific opinion providing: (i) a review of the approaches used by the BIOHAZ Panel to address requests from risk managers to suggest the establishment of microbiological criteria; (ii) guidance on the required scientific evidence, data and methods/tools necessary for considering the development of microbiological criteria for pathogenic microorganisms and indicator microorganisms; (iii) recommendations on methods/tools to design microbiological criteria and (iv) guidelines for the requirements and tasks of risk assessors, compared to risk managers, in relation to microbiological criteria. This document provides guidance on approaches when: (i) a quantitative microbial risk assessment (QMRA) is available, (ii) prevalence and concentration data are available, but not a QMRA model, and (iii) neither a QMRA nor prevalence and/or concentration data are available. The role of risk assessors should be focused on assessing the impact of different microbiological criteria on public health and on product compliance. It is the task of the risk managers to: (1) formulate unambiguous questions, preferably in consultation with risk assessors, (2) decide on the establishment of a microbiological criterion, or target in primary production sectors, and to formulate the specific intended purpose for using such criteria, (3) consider the uncertainties in impact assessments on public health and on product compliance and (4) decide the point in the food chain where the microbiological criteria are intended to be applied and decide on the actions which should be taken in case of noncompliance. It is the task of the risk assessors to support risk managers to ensure that questions are formulated in a way that a precise answer can be given, if sufficient information is available, and to ensure clear and unambiguous answers, including the assessment of uncertainties, based on available scientific evidence.

Food Control, 2020

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2015

10:30 a.m. Plenary Session II: Status of Current Chapters Moderator: Karen McCullough, M.S. Member, USP General Chapters–Microbiology Expert Committee This session will highlight current status of the chapters on Alternative Microbiological Methods in U.S. and European Pharmacopoeias. a. New Draft <1223.1>: Alternate Procedures to Antibiotic Microbial Assays James Akers, Ph.D., Chair, USP General Chapters–Microbiology Expert Committee

Journal of Exposure Science and Environmental Epidemiology, 2016

In the event of an indoor release of an environmentally persistent microbial pathogen such as Bacillus anthracis, the potential for human exposure will be considered when remedial decisions are made. Microbial site characterization and clearance sampling data collected in the field might be used to estimate exposure. However, there are many challenges associated with estimating environmental concentrations of B. anthracis or other spore-forming organisms after such an event before being able to estimate exposure. These challenges include: (1) collecting environmental field samples that are adequate for the intended purpose, (2) conducting laboratory analyses and selecting the reporting format needed for the laboratory data, and (3) analyzing and interpreting the data using appropriate statistical techniques. This paper summarizes some key challenges faced in collecting, analyzing, and interpreting microbial field data from a contaminated site. Although the paper was written with considerations for B. anthracis contamination, it may also be applicable to other bacterial agents. It explores the implications and limitations of using field data for determining environmental concentrations both before and after decontamination. Several findings were of interest. First, to date, the only validated surface/sampling device combinations are swabs and sponge-sticks on stainless steel surfaces, thus limiting availability of quantitative analytical results which could be used for statistical analysis. Second, agreement needs to be reached with the analytical laboratory on the definition of the countable range and on reporting of data below the limit of quantitation. Finally, the distribution of the microbial field data and statistical methods needed for a particular data set could vary depending on these data that were collected, and guidance is needed on appropriate statistical software for handling microbial data. Further, research is needed to develop better methods to estimate human exposure from pathogens using environmental data collected from a field setting.

2021

Identification of unknown microorganisms in a mixed population through various lab techniques.

Cell, 2014

Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Advances depend on carefully executed, controlled, and reproducible studies. Here, we provide a Primer for researchers from diverse disciplines interested in conducting microbiome research. We discuss factors to be considered in the design, execution, and data analysis of microbiome studies. These recommendations should help researchers to enter and contribute to this rapidly developing field.

Journal of AOAC International, 2009

Journal of Clinical Microbiology, 2004

Antimicrobial surveillance may be defined as a systematic collection, analysis, and dissemination of data that may be used to identify resistance trends and assess the need for intervention (2). In 1988 the Centers for Disease Control and Prevention published guidelines for evaluation of surveillance systems for antimicrobial resistance (7), and an American Society for Microbiology task force (1) highlighted the importance of performing antimicrobial surveillance through local, national, and global networks. Unfortunately, the recommendations from this task force were not implemented, in part due to lack of funding (6). To this end, however, international as well as more than 21 national programs designed to capture susceptibility data for most clinically significant organisms (e.g., SENTRY and TSN) and 24 programs that focused on specific organisms (e.g., CARE and TRUST), were identified in 1999 through the World Health Organization Antimicrobial Resistance Information Bank (9). These programs may be government (e.g., ICARE and NNIS,), commercial (e.g., TSN), or industry (e.g., ARMp, MYSTIC, PROTEKT, SENTRY, and TRUST) supported. Additional data may be gleaned from postmarketing surveillance studies by pharmaceutical companies who monitor their new antimicrobial for resistance, e.g., MYSTIC (meropenem), SMART (quinupristin-dalfopristin), and ZAP (linezolid). Since testing methods may vary between laboratories and may potentially bias multilaboratory databases, some programs rely on a central laboratory to generate standardized susceptibility data. Quantitative (MIC) rather than qualitative (susceptible, intermediate, and resistant) data and the use of molecular methods, as employed in the MYSTIC and SENTRY programs, generally offer greater value in identifying resistance trends and providing a genetic basis for observed resistance, respectively. ADVANTAGES OF SURVEILLANCE FOR ANTIMICROBIAL RESISTANCE Appropriately and continuously collected data can be used to develop yearly antibiograms, detect shifts in susceptibility, and serve as a basis for empirical therapy, formulary decisions, and changes in prescribing and infection control practices. Solid data may be used to develop strategies for intervention by a multidisciplinary task force (5). Although regional, na