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Microbiology laboratory automation

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https://www.readbyqxmd.com/read/29314254/manual-versus-automated-streaking-system-in-clinical-microbiology-laboratory-performance-evaluation-of-previ-isola-for-blood-culture-and-body-fluid-samples
#1
Qute Choi, Hyun Jin Kim, Jong Wan Kim, Gye Cheol Kwon, Sun Hoe Koo
BACKGROUND: The process of plate streaking has been automated to improve routine workflow of clinical microbiology laboratories. Although there were many evaluation reports about the inoculation of various body fluid samples, few evaluations have been reported for blood. In this study, we evaluated the performance of automated inoculating system, Previ Isola for various routine clinical samples including blood. METHODS: Blood culture, body fluid, and urine samples were collected...
January 4, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29310696/methods-for-detecting-gemmata-spp-bacteremia-in-the-microbiology-laboratory
#2
Jacques-Robert Christen, Edwin Edmond, Michel Drancourt
OBJECTIVE: Gemmata bacteria are fastidious, Gram-negative and aerobic. The only representatives are Gemmata obscuriglobus and Gemmata massiliana. These Planctomycetes appear to be a part of human digestive tract microbiome, and G. massiliana has been isolated from water. Further specific detection in the blood of two patients with febrile neutropenia suggests that Gemmata bacteremia may remain under-documented. The objective of this study was to develop an effective protocol to document Gemmata spp...
January 8, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29287094/validation-of-a-novel-automatic-deposition-of-bacteria-and-yeasts-on-maldi-target-for-maldi-tof-ms-based-identification-using-maldi-colonyst-robot
#3
Katerina Chudejova, Michal Bohac, Anna Skalova, Veronika Rotova, Costas C Papagiannitsis, Jana Hanzlickova, Tamara Bergerova, Jaroslav Hrabák
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) -based identification of bacteria and fungi significantly changed the diagnostic process in clinical microbiology. We describe here a novel technique for bacterial and yeast deposition on MALDI target using an automated workflow resulting in an increase of the microbes' score of MALDI identification. We also provide a comparison of four different sample preparation methods. In the first step of the study, 100 Gram-negative bacteria, 100 Gram-positive bacteria, 20 anaerobic bacteria and 20 yeasts were spotted on the MALDI target using manual deposition, semi-extraction, wet deposition onto 70% formic acid and by automatic deposition using MALDI Colonyst...
2017: PloS One
https://www.readbyqxmd.com/read/29242391/method-verification-requirements-for-an-advanced-imaging-system-for-microbial-plate-count-enumeration
#4
David Jones, Tony Cundell
Technical Abstract: The Growth Direct™ System that automates the incubation and reading of membrane filtration microbial counts on soybean-casein digest, Sabouraud dextrose and R2A agar differs only from the traditional method in that micro-colonies on the membrane are counted using an advanced imaging system up to 50% earlier in the incubation. Based on the recommendations in USP <1223> Validation of New Microbiological Testing Methods, the system may be implemented in a microbiology laboratory after simple method verification and not a full method validation...
December 14, 2017: PDA Journal of Pharmaceutical Science and Technology
https://www.readbyqxmd.com/read/29237786/commentary-waltzing-around-sacred-cows-on-the-way-to-the-future
#5
Stephen M Brecher
Our mostly manual, agar based clinical microbiology laboratory is slowly but steadily being re-defined by automation and innovation. Ironically, the oldest test, the Gram stain, is still manually read and interpreted by trained personnel. In this proof of concept study Smith et al. (https://doi.org/10.1128/JCM.01521-17) have used computer imaging with a deep convolutional neural network to examine and interpret Gram-stained slides from positive blood culture bottles. In light of the shortage of medical technologists/microbiologists and the need for results of positive blood culture bottles 24/7, this paper paves the way for the next innovations for the clinical microbiology laboratory of the future...
December 13, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29228397/yeast-identification-by-sequencing-biochemical-kits-maldi-tof-ms-and-rep-pcr-dna-fingerprinting
#6
Ying Zhao, Chi-Ching Tsang, Meng Xiao, Jasper F W Chan, Susanna K P Lau, Fanrong Kong, Yingchun Xu, Patrick C Y Woo
No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29203445/rapid-monitoring-of-local-epidemiology-of-vancomycin-resistant-enterococcus-faecium-on-a-department-level-by-reppcr
#7
Frank Froeschen, Mike Gajdiss, Julia Uebele, Alina Meilaender, Achim Hoerauf, Martin Exner, Ernst Molitor, Gabriele Bierbaum, Steffen Engelhart, Isabelle Bekeredjian-Ding
BACKGROUND: The current increase in nosocomial infections caused by vancomycin-resistant enterococci (VRE) warrants improvement of detection methods and hygiene measures. Knowledge of the local epidemiology is important for monitoring compliance of medical personnel with hygiene measures. AIM: We evaluated semi-automated repPCR for rapid molecular typing of VRE. METHODS: Primary VRE isolates were collected over an observation period of one year and retrospectively typed by repPCR...
December 1, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/29187563/automated-interpretation-of-blood-culture-gram-stains-using-a-deep-convolutional-neural-network
#8
Kenneth P Smith, Anthony D Kang, James E Kirby
Microscopic interpretation of stained smears is one of the most operator-dependent and time intensive activities in the clinical microbiology laboratory. Here, we investigated application of an automated image acquisition and convolutional neural network (CNN)-based approach for automated Gram stain classification. Using an automated microscopy platform, uncoverslipped slides were scanned with a 40x dry objective, generating images of sufficient resolution for interpretation. We collected 25,488 images from positive blood culture Gram stains prepared during routine clinical workup...
November 29, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29140977/low-cost-and-open-source-multi-fluorescence-imaging-system-for-teaching-and-research-in-biology-and-bioengineering
#9
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
#10
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-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-improve-turnaround-times-in-the-clinical-microbiology-laboratory-a-retrospective-analysis
#11
Talent Theparee, Sanchita Das, Richard B Thomson
Technological advances have changed the practice of clinical microbiology. We implemented Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and BD Kiestra total laboratory automation (TLA) 4 and 3 years ago, respectively. To assess the impact of these new technologies, we compared turnaround times (TATs) for positive and negative urine cultures before and after implementation. In comparison I, TATs for 61,157 urine cultures were extracted for two periods corresponding to pre-TLA and post-TLA, both using MALDI-TOF MS for organism identification...
January 2018: 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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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 widespread availability of electronic medical records capable of supporting clinician order entry and of clinical decision support tools (CDSTs) has provided expanded opportunities for implementing effective, automated test stewardship protocols. D. Nikolic et al. (J. Clin...
December 2017: Journal of Clinical Microbiology
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