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Microbiology laboratory quality

Michael A Noble, Robert Rennie
BACKGROUND: Reporting on the presence of antimicrobial resistance is of considerable concern both for individual patient care and for understanding the underlying health status within the community at large. Antimicrobial resistance is solely dependent upon clinical laboratory detection and thus can be impacted upon by the quality and competence of medical laboratories. Proficiency testing or external quality assessment (PT/EQA) is the international standard for the direct measurement of medical laboratory performance on critical testing...
June 15, 2018: Diagnosis
Estelle Baurès, Olivier Blanchard, Fabien Mercier, Emilie Surget, Pierre le Cann, Alexandre Rivier, Jean-Pierre Gangneux, Arnaud Florentin
In addition to being influenced by the environment, the indoor air pollution in hospitals may be associated with specific compounds emitted from various products used, health care activities and building materials. This study has enabled assessment of the chemical and microbiological concentrations of indoor air in two French hospitals. Based on an integrated approach, the methodology defined aims to measure concentrations of a wide range of chemical compounds (>50 volatile and semi-volatile organic compounds), particle concentrations (PM10 and PM2...
June 9, 2018: Science of the Total Environment
R J Gruninger, R J Forster, T A McAllister
Metatranscriptomics can be used to examine both the composition of a microbial community as well as its metabolic activity under a particular set of conditions and complement metagenomic studies. The availability of low-cost, high-throughput next-generation sequencing has led to a rapid increase in the number of metatranscriptomic studies being undertaken. One of the primary difficulties when conducting transcriptomics is the ability to isolate high-quality RNA from samples of interest. The application of metatranscriptomics in rumen microbiology is still relatively novel but there is a significant push toward applying this technology in this field...
2018: Methods in Molecular Biology
Adelumola Oladeinde, Erin Lipp, Chia-Ying Chen, Richard Muirhead, Travis Glenn, Kimberly Cook, Marirosa Molina
In this study, we investigated gene expression changes in three bacterial strains ( Escherichia coli C3000, Escherichia coli O157:H7 B6914, and Enterococcus faecalis ATCC 29212), commonly used as indicators of water quality and as control strains in clinical, food, and water microbiology laboratories. Bacterial transcriptome responses from pure cultures were monitored in microcosms containing water amended with manure-derived dissolved organic matter (DOM), previously exposed to simulated sunlight for 12 h...
2018: Frontiers in Microbiology
Tewodros Tesfa Hailegiyorgis, Wondemagegn Demsiss Sarhie, Hailemariam Mekonnen Workie
Background: Otitis media is inflammation of the middle ear and tympanic membrane, which often occurs after an acute upper respiratory tract infection. It is the most common episode of infection in children and the second most important cause of hearing loss affecting 1.23 billion people, thus ranked fifth global burden of disease with a higher incidence in sub-Saharan Africa. Thus, the aim of this study was to determine the isolation rate of bacterial pathogens from pediatric patients with otitis media...
2018: BMC Ear, Nose, and Throat Disorders
Roberta B Carey, Sanjib Bhattacharyya, Sue C Kehl, Larissa M Matukas, Michael A Pentella, Max Salfinger, Audrey N Schuetz
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...
July 2018: Clinical Microbiology Reviews
Lucas Djelic, Nisha Andany, Jeffrey Craig, Nick Daneman, Andrew Simor, Jerome A Leis
Observational studies suggest that Infectious Diseases (ID) consultation is associated with improved outcomes for patients with Staphylococcus aureus bacteremia (SAB), but few studies have sought to standardize timely ID consultation through automatic notification by the Microbiology laboratory. In this 3-year quasi-experimental evaluation, introduction of this change resulted in increased ID consultation for SAB (70% versus 100%, P < 0.001) and decreased time to consultation (14.5 versus 4 h, P < 0...
July 2018: Diagnostic Microbiology and Infectious Disease
Joost Theo Petra Verhoeven, Marta Canuti, Hannah J Munro, Suzanne C Dufour, Andrew S Lang
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...
April 19, 2018: Canadian Journal of Microbiology
Kathy Raven, Beth Blane, Carol Churcher, Julian Parkhill, Sharon J Peacock
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality...
April 5, 2018: Microbial Genomics
Barbara Albiger, Joana Revez, Katrin Claire Leitmeyer, Marc J Struelens
In an era of global health threats caused by epidemics of infectious diseases and rising multidrug resistance, microbiology laboratories provide essential scientific evidence for risk assessment, prevention, and control. Microbiology has been at the core of European infectious disease surveillance networks for decades. Since 2010, these networks have been coordinated by the European Centre for Disease Prevention and Control (ECDC). Activities delivered in these networks include harmonization of laboratory diagnostic, antimicrobial susceptibility and molecular typing methods, multicentre method validation, technical capacity mapping, training of laboratory staff, and continuing quality assessment of laboratory testing...
2018: Frontiers in Public Health
Sien Ombelet, Jean-Baptiste Ronat, Timothy Walsh, Cedric P Yansouni, Janneke Cox, Erika Vlieghe, Delphine Martiny, Makeda Semret, Olivier Vandenberg, Jan Jacobs
Low-resource settings are disproportionately burdened by infectious diseases and antimicrobial resistance. Good quality clinical bacteriology through a well functioning reference laboratory network is necessary for effective resistance control, but low-resource settings face infrastructural, technical, and behavioural challenges in the implementation of clinical bacteriology. In this Personal View, we explore what constitutes successful implementation of clinical bacteriology in low-resource settings and describe a framework for implementation that is suitable for general referral hospitals in low-income and middle-income countries with a moderate infrastructure...
March 5, 2018: Lancet Infectious Diseases
Aslı Turan, Sibel Soycan Önenç
Objective: This study was carried out to determine the effects of cumin essential oil on the silage fermentation, aerobic stability and in vitro digestibility of alfalfa silages. Methods: Alfalfa was harvested at early bloom (5 th cutting) stage in October and wilted for about 3 hours. The research was carried out at three groups which were the control group where no additive control was done (CON), cumin essential oil (CMN3) with 300 mg/kg and CMN5 with 500 mg/kg cumin essential oil addition...
March 2, 2018: Asian-Australasian Journal of Animal Sciences
Silvia Forni, Giulio Toccafondi, Bruno Viaggi, Maddalena Grazzini, Sara D'Arienzo, Fabrizio Gemmi, Andrea Vannucci, Giorgio Tulli
Antimicrobial resistance is a global threat caused by the rapid spread of multiresistant microorganisms. Antimicrobial stewardship (AS) is a coordinated intervention designed to improve the appropriate use of antimicrobials by promoting the selection of the optimal drug regimen, dose, duration of therapy and route of administration. AS programs have proved effective in reducing antimicrobial resistance, inappropriate antimicrobial use and in improving patient outcomes. Recently developed rapid diagnostic technologies in microbiology (RDTM) allows a faster and etiological diagnosis of infection and a reduction in the use of unnecessary empirical therapies...
February 2018: Recenti Progressi in Medicina
Olivier Vandenberg, Zisis Kozlakidis, Jacques Schrenzel, Marc Jean Struelens, Judith Breuer
Many new innovative diagnostic approaches have been made available during the last 10 years with major impact on patient care and public health surveillance. In parallel, to enhance the cost-effectiveness of the clinical microbiology laboratories (CMLs), European laboratory professionals have streamlined their organization leading to amalgamation of activities and restructuring of their professional relationships with clinicians and public health specialists. Through this consolidation process, an operational model has emerged that combines large centralized clinical laboratories performing most tests on one high-throughput analytical platform connected to several distal laboratories dealing locally with urgent analyses at near point of care...
2018: Frontiers in Medicine
Rossana Rosa, Bruno Zavala, Natalie Cain, Shweta Anjan, Laura Aragon, Lilian M Abbo
Antimicrobial stewardship programs can optimize the management of Staphylococcus aureus bacteremia by integrating information technology and microbiology laboratory resources. This study describes our experience implementing an intervention consisting of real-time feedback and the use of an electronic order set for the management of S. aureus bacteremia. Infect Control Hosp Epidemiol 2018;39:346-349.
March 2018: Infection Control and Hospital Epidemiology
Antony Croxatto, Raphaël Marcelpoil, Cédrick Orny, Didier Morel, Guy Prod'hom, Gilbert Greub
BACKGROUND: Automation in microbiology laboratories impacts management, workflow, productivity and quality. Further improvements will be driven by the development of intelligent image analysis allowing automated detection of microbial growth, release of sterile samples, identification and quantification of bacterial colonies and reading of AST disk diffusion assays. We investigated the potential benefit of intelligent imaging analysis by developing algorithms allowing automated detection, semi-quantification and identification of bacterial colonies...
December 2017: Biomedical Journal
Daleniece Higgins, Chandan Pal, Irshad M Sulaiman, Chunrong Jia, Tyler Zerwekh, Scot E Dowd, Pratik Banerjee
With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA...
March 2018: Food Research International
Mattia Savardi, Alessandro Ferrari, Alberto Signoroni
BACKGROUND AND OBJECTIVE: The recent introduction of Full Laboratory Automation systems in clinical microbiology opens to the availability of streams of high definition images representing bacteria culturing plates. This creates new opportunities to support diagnostic decisions through image analysis and interpretation solutions, with an expected high impact on the efficiency of the laboratory workflow and related quality implications. Starting from images acquired under different illumination settings (top-light and back-light), the objective of this work is to design and evaluate a method for the detection and classification of diagnostically relevant hemolysis effects associated with specific bacteria growing on blood agar plates...
March 2018: Computer Methods and Programs in Biomedicine
M Isabel Sánchez-Romero, Juan Manuel García-Lechuz Moya, Juan José González López, Nieves Orta Mira
The interpretation and the accuracy of the microbiological results still depend to a great extent on the quality of the samples and their processing within the Microbiology laboratory. The type of specimen, the appropriate time to obtain the sample, the way of sampling, the storage and transport are critical points in the diagnostic process. The availability of new laboratory techniques for unusual pathogens, makes necessary the review and update of all the steps involved in the processing of the samples. Nowadays, the laboratory automation and the availability of rapid techniques allow the precision and turn-around time necessary to help the clinicians in the decision making...
February 6, 2018: Enfermedades Infecciosas y Microbiología Clínica
Natalie Wilhelm, Anya Kaufmann, Elizabeth Blanton, Daniele Lantagne
Household water treatment with chlorine can improve the microbiological quality of household water and reduce diarrheal disease. We conducted laboratory and field studies to inform chlorine dosage recommendations. In the laboratory, reactors of varying turbidity (10-300 NTU) and total organic carbon (0-25 mg/L addition) were created, spiked with Escherichia coli, and dosed with 3.75 mg/L sodium hypochlorite. All reactors had >4 log reduction of E. coli 24 hours after chlorine addition. In the field, we tested 158 sources in 22 countries for chlorine demand...
February 2018: Journal of Water and Health
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