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Microbiology laboratory automation

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https://www.readbyqxmd.com/read/29140977/low-cost-and-open-source-multi-fluorescence-imaging-system-for-teaching-and-research-in-biology-and-bioengineering
#1
Isaac Nuñez, Tamara Matute, Roberto Herrera, Juan Keymer, Timothy Marzullo, Timothy Rudge, Fernán Federici
The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates...
2017: PloS One
https://www.readbyqxmd.com/read/29135992/internal-quality-assurance-in-diagnostic-microbiology-a-simple-approach-for-insightful-data
#2
Valentin Scherz, Christian Durussel, Gilbert Greub
Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91...
2017: PloS One
https://www.readbyqxmd.com/read/29118171/total-laboratory-automation-and-maldi-tof-improve-turnaround-times-in-the-clinical-microbiology-laboratory-a-retrospective-analysis
#3
Talent Theparee, Sanchita Das, Richard B Thomson
Technological advances have changed the practice of clinical microbiology. We implemented Bruker MALDI-TOF and BD Kiestra Total Laboratory Automation (TLA) three and four years ago, respectively. To assess the impact of these new technologies, we compared turnaround times (TAT) for positive and negative urine cultures before and after implementation. Comparison I: TATs for 61,157 urine cultures were extracted for two periods corresponding to pre-TLA and post-TLA, both using MALDI-TOF for organism identification...
November 8, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29118168/use-of-accelerate-pheno%C3%A2-system-for-identification-and-antimicrobial-susceptibility-testing-id-ast-of-pathogens-in-positive-blood-cultures-and-impact-on-time-to-results-and-workflow
#4
Angella Charnot-Katsikas, Vera Tesic, Nedra Love, Brandy Hill, Cindy Bethel, Sue Boonlayangoor, Kathleen G Beavis
The Accelerate Pheno™ system uses automated fluorescence in situ hybridization technology with morphokinetic cellular analysis to provide rapid species identification (ID) and antimicrobial susceptibility testing (AST) results for the most commonly identified organisms in bloodstream infections.Objective was to evaluate the accuracy and workflow of bacterial and yeast ID, and bacterial AST using the Accelerate Pheno™ system in the clinical microbiology laboratory.Consecutive fresh blood cultures received in the laboratory were analyzed by the Accelerate Pheno™ system within 0 - 8 h of growth detection...
November 8, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29102604/fluorometric-determination-of-d-lactate-in-biological-fluids
#5
Torben Larsen
OBJECTIVE: D-lactic acid in the mammalian body is mainly of microbiological origin and is often located somewhere along the digestive tract. Surgical, extensive re-sectioning of the small bowel may be one of the risk factors for altered balance in the microbiological environment. Higher levels in the body may lead to D-lactate acidosis and neurotoxicity; consequently, the possibility of diagnosis of this condition is important. Several analytical procedures for D-lactate have been introduced, but it is absolutely mandatory to distinguish this metabolite from the much more abundant and naturally occurring stereoisomer L-lactate...
November 3, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/29090008/automated-flow-cytometry-an-alternative-to-urine-culture-in-a-routine-clinical-microbiology-laboratory
#6
REVIEW
Patricia Mejuto, Mariam Luengo, Julio Díaz-Gigante
The urine culture is the "gold standard" for the diagnosis of urinary tract infections (UTI) but constitutes a significant workload in the routine clinical laboratory. Due to the high percentage of negative results, there is a need for an efficient screening method, with a high negative predictive value (NPV) that could reduce the number of unnecessary culture tests. With the purpose of improving the efficiency of laboratory work, several methods for screening out the culture-negative samples have been developed, but none of them has shown adequate sensitivity (SE) and high NPV...
2017: International Journal of Microbiology
https://www.readbyqxmd.com/read/29062487/challenges-in-the-identification-of-chryseobacterium-indologenes-and-elizabethkingia-meningoseptica-in-cases-of-nosocomial-infections-and-patients-with-cystic-fibrosis
#7
É B de Carvalho Filho, F A L Marson, C E Levy
Rare nonfermenting Gram-negative bacilli, such as Chryseobacterium indologenes and Elizabethkingia meningoseptica, have clinical importance in nosocomial infections and cystic fibrosis (CF), and their identification is a challenge to microbiology laboratories. Thus, the objective of this study was to verify the performance of phenotypic and mass spectrometry (matrix-assisted desorption ionization-time of flight mass spectrometry, MALDI-TOF MS) methods to identify C. indologenes and E. meningoseptica. In this context, the results obtained with phenotypic methods-namely manual biochemical and automated VITEK 2 (bioMérieux, Marcy l'Etoile, France) and Phoenix tests (Becton Dickinson (BD), San Diego, CA, USA)-and by MALDI-TOF MS-namely MALDI-TOF VITEK MS (MALDI-MS; bioMérieux) and MALDI-TOF BioTyper (MALDI-BD; BD)-of 22 isolates (blood cultures of patients with nosocomial infection (n = 15) and from patients with CF (n = 7)), initially identified as C...
November 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/29062009/comparison-of-four-automated-microbiology-systems-with-16s-rrna-gene-sequencing-for-identification-of-chryseobacterium-and-elizabethkingia-species
#8
Jiun-Nong Lin, Chung-Hsu Lai, Chih-Hui Yang, Yi-Han Huang, Hsiu-Fang Lin, Hsi-Hsun Lin
Chryseobacterium and Elizabethkingia species have recently emerged as causative agents in life-threatening infections in humans. We aimed to evaluate the rates at which four common microbial identification systems identify Chryseobacterium and Elizabethkingia species in clinical microbiology laboratories. Based on the results of 16S rRNA gene sequencing, a total of 114 consecutive bacteremic isolates, including 36 (31.6%) C. indologenes, 35 (30.7%) E. anophelis, 22 (19.3%) C. gleum, 13 (11.4%) E. meningoseptica, and other species, were included in this study...
October 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29046409/using-treponemal-assay-signal-strength-cut-off-ratios-to-predict-syphilis-infection
#9
Claire C Bristow, Jeffrey D Klausner
Syphilis screening using the reverse algorithm, a treponemal test for screening followed by a non-treponemal test if reactive, is increasingly being used. This algorithm has several advantages including use of an automated screening test, saving on laboratory time and costs as well as detection of very early syphilis infection. However, under this algorithm, in situations where the treponemal result is positive and the non-treponemal result is non-reactive a second treponemal test must be performed, which may actually lead to inefficiencies in the laboratory...
October 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29046166/evaluation-of-mericon-e-coli-o157-screen-plus-and-mericon-e-coli-stec-o-type-pathogen-detection-assays-in-select-foods-collaborative-study-first-action-2017-05
#10
Patrick Bird, M Joseph Benzinger, Benjamin Bastin, Erin Crowley, James Agin, David Goins, Marcia Armstrong
QIAGEN mericon Escherichia coli O157 Screen Plus and mericon E. coliShiga toxin-producing E. coli (STEC) O-Type Pathogen Detection Assays use Real-Time PCR technology for the rapid, accurate detection of E. coli O157 and the “big six” (O26, O45, O103, O111, O121, O145) (non-O157 STEC) in select food types. Using a paired study design, the assays were compared with the U.S. Department of Agriculture, Food Safety Inspection Service Microbiology Laboratory Guidebook Chapter 5.09 reference method for the detection of E...
October 18, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28961857/comparative-evaluation-of-vitek%C3%A2-2-and-three-commercial-gradient-strip-assays-for-daptomycin-susceptibility-testing-of-staphylococcus-aureus
#11
Robert E Weber, Franziska Layer, Ingo Klare, Guido Werner, Birgit Strommenger
Objectives: MRSA remains a major cause of severe nosocomial infections and the increased use of vancomycin and daptomycin for MRSA treatment over the last decade has led to the isolation of MRSA strains with decreased daptomycin susceptibility. In addition, a growing number of MSSA isolates with reduced susceptibility to daptomycin have been described lately. Surveillance of the emergence of such a daptomycin-non-susceptible MSSA population requires prompt and reliable daptomycin susceptibility testing...
November 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28954899/optimizing-test-utilization-in-the-clinical-microbiology-laboratory-tools-and-opportunities
#12
Bobbi S Pritt
Optimal laboratory test utilization is important for providing high quality clinical care and efficiently using limited health care resources. While microbiologists have long been advocates for appropriate laboratory test utilization, the wide-spread availability of electronic medical records capable of supporting clinician order entry and clinical decision support tools (CDSTs) have provided expanded opportunities for implementing effective, automated test stewardship protocols. In this issue of the Journal of Clinical Microbiology, D...
September 27, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28950760/xpert-flu-as-a-rapid-diagnostic-test-for-respiratory-tract-viral-infection-evaluation-and-implementation-as-a-24-7-service
#13
Sofie Haglund, Maysae Quttineh, Annette Nilsson Bowers, Andreas Matussek, Anna J Henningsson
A rapid and reliable influenza method is important to meet diagnostic needs. Here, the performance of the cartridge-based Xpert Flu assay was evaluated in comparison with an in-house real-time PCR method. Analysis was then decentralized from the clinical microbiology laboratory located at County Hospital Ryhov, Jönköping, Sweden, to the clinical chemistry laboratories present at the three hospitals in Region Jönköping County, allowing a 24/7 service. In total, 189 clinical samples were included in 2014-2015...
September 26, 2017: Infectious Diseases
https://www.readbyqxmd.com/read/28929961/-national-antimicrobial-resistance-surveillance-system-namrss-external-quality-assessment-studies-2011-2016
#14
Serap Süzük Yıldız, Hüsniye Şimşek, Nilay Çöplü, Zeynep Gülay
Establishment of sustainable and evidence-based surveillance systems are recommended for prevention of microbial resistance by the World Health Organization (WHO). As a necessity of these surveillance systems, participants are recommended to implement an external quality assessment (EQA) program. In this scope, National Antimicrobial Resistance Surveillance System (NARSS) has been established within the Public Health Institute of Turkey (PHIT) in our country since 2011. In the scope of this surveillance, NARSS EQA program has been implemented in a cycle per year and four isolates were sent to participants per cycle every year since 2011...
July 2017: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/28892765/the-performance-of-luminex-aries-%C3%A2-flu-a-b-rsv-and-cepheid-xpert-%C3%A2-flu-rsv-xc-for-the-detection-of-influenza-a-influenza-b-and-respiratory-syncytial-virus-in-prospective-patient-samples
#15
Phillip McMullen, Sue Boonlayangoor, Angella Charnot-Katsikas, Kathleen G Beavis, Vera Tesic
BACKGROUND: The demand for rapid, accurate viral testing has increased the number of assays available for the detection of viral pathogens. One of the newest FDA cleared platforms is the Luminex ARIES(®) Flu A/B & RSV, which is a fully automated, real-time PCR-based assay used for detection of influenza A, influenza B, and respiratory syncytial virus (RSV). OBJECTIVES: We sought to compare the performance of Luminex ARIES(®) Flu A/B & RSV assay to the Cepheid Xpert(®) Flu/RSV XC assay for rapid Flu and RSV testing...
September 5, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28885919/diagnostics-in-a-forward-deployed-setting
#16
Brett Swierczewski, Mark Simons
Current diagnostic methods for enteric pathogens include conventional/traditional microbiology, microscopy, enzyme immunoassay, automated identification platforms, and molecular methods. The choice of diagnostic test in the forward deployed military setting often depends on turnaround time, potential etiologic agents, costs, and laboratory capabilities. The military operational environment presents many challenges that impact the practicality and performance of even robust diagnostic platforms. With recent developments in diagnostic platforms and availability of high-performance multiplex molecular methods to pair with traditional culture and antibiotic susceptibility tests, there are more opportunities to gather information on the etiologic causes and clinical impacts of traveler's diarrhea, both in civilians and in deployed military populations...
September 2017: Military Medicine
https://www.readbyqxmd.com/read/28869004/performance-assessment-of-urine-flow-cytometry-ufc-to-screen-urines-to-reflex-to-culture-in-immunocompetent-and-immunosuppressed-hosts
#17
Aleksandra Stefanovic, Diane Roscoe, Romali Ranasinghe, Titus Wong, Elizabeth Bryce, Charlene Porter, Adelina Lim, Jennifer Grant, Karen Ng, Morris Pudek
PURPOSE: Urine flow cytometry (UFC) is an automated method to quantify bacterial and white blood cell (WBC) counts. We aimed to determine whether a threshold for these parameters can be set to use UFC as a sensitive screen to predict which urine samples will subsequently grow in culture. METHODOLOGY: Urines submitted to our microbiology laboratory at a tertiary care centre from 22 July 2015-17 February 2016 underwent UFC (Sysmex UF-1000i) analysis, regular urinalysis and urine culture...
September 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28844384/implementation-and-evaluation-of-an-automated-surveillance-system-to-detect-hospital-outbreak
#18
Anna Stachel, Gabriela Pinto, John Stelling, Yi Fulmer, Bo Shopsin, Kenneth Inglima, Michael Phillips
BACKGROUND: The timely identification of a cluster is a critical requirement for infection prevention and control (IPC) departments because these events may represent transmission of pathogens within the health care setting. Given the issues with manual review of hospital infections, a surveillance system to detect clusters in health care settings must use automated data capture, validated statistical methods, and include all significant pathogens, antimicrobial susceptibility patterns, patient care locations, and health care teams...
August 22, 2017: American Journal of Infection Control
https://www.readbyqxmd.com/read/28840987/multicenter-evaluation-of-an-image-analysis-device-apas-comparison-between-digital-image-and-traditional-plate-reading-using-urine-cultures
#19
John Glasson, Rhys Hill, Michael Summerford, Dianne Olden, Fotula Papadopoulos, Stephen Young, Steven Giglio
BACKGROUND: The application of image analysis technologies for the interpretation of microbiological cultures is evolving rapidly. The primary aim of this study was to establish whether the image analysis system named Automated Plate Assessment System (APAS; LBT Innovations Ltd., Australia) could be applied to screen urine cultures. A secondary aim was to evaluate differences between traditional plate reading (TPR) and the reading of cultures from images, or digital plate reading (DPR)...
November 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28837780/development-of-mast-a-microscopy-based-antimicrobial-susceptibility-testing-platform
#20
Kenneth P Smith, David L Richmond, Thea Brennan-Krohn, Hunter L Elliott, James E Kirby
Antibiotic resistance is compromising our ability to treat bacterial infections. Clinical microbiology laboratories guide appropriate treatment through antimicrobial susceptibility testing (AST) of patient bacterial isolates. However, increasingly, pathogens are developing resistance to a broad range of antimicrobials, requiring AST of alternative agents for which no commercially available testing methods are available. Therefore, there exists a significant AST testing gap in which current methodologies cannot adequately address the need for rapid results in the face of unpredictable susceptibility profiles...
August 1, 2017: SLAS Technology
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