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Microbiology laboratory automation

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https://www.readbyqxmd.com/read/27723450/fully-automated-clinical-grade-bone-marrow-processing-a-single-centre-experience
#1
Benedetta Mazzanti, Serena Urbani, Simone Dal Pozzo, Paola Bufano, Lara Ballerini, Alessia Gelli, Irene Sodi, Irene Donnini, Massimo Di Gioia, Stefano Guidi, Julien Camisani, Riccardo Saccardi
BACKGROUND: Clinical grade processing of harvested bone marrow is required in various clinical situations, particularly in the management of ABO mismatching in allogeneic haematopoietic stem cell transplantation (HSCT) and in regenerative medicine. MATERIAL AND METHODS: We report a single-centre experience using a fully automated, clinical grade, closed system (Sepax, Biosafe, Switzerland). From 2003 to 2015, 125 procedures were performed in our laboratory, including buffy-coat production for HSCT (n=58), regenerative medicine in an orthopaedic setting (n=54) and density-gradient separation in a trial for treatment of critical limb ischaemia (n=13)...
September 27, 2016: Blood Transfusion, Trasfusione del Sangue
https://www.readbyqxmd.com/read/27697104/validation-of-the-applied-biosystems-rapidfinder-shiga-toxin-producing-e-coli-stec-detection-workflow
#2
Sharon Matheny, Robert Tebbs, Erin Crowley, David Goins, Angelia Burrell, Patrick Bird, Michelle Swimley, M Joseph Benzinger, Jonathan Flannery, Jonathan Cloke, James Agin, Benjamin Bastin
The Applied Biosystems™ RapidFinder™ STEC Detection Workflow (Thermo Fisher Scientific) is a complete protocol for the rapid qualitative detection of Escherichia coli (E. coli) O157:H7 and the "Big 6" non-O157 Shiga-like toxin-producing E. coli (STEC) serotypes (defined as serogroups: O26, O45, O103, O111, O121, and O145). The RapidFinder STEC Detection Workflow makes use of either the automated preparation of PCR-ready DNA using the Applied Biosystems PrepSEQ™ Nucleic Acid Extraction Kit in conjunction with the Applied Biosystems MagMAX™ Express 96-well magnetic particle processor or the Applied Biosystems PrepSEQ Rapid Spin kit for manual preparation of PCR-ready DNA...
October 1, 2016: Journal of AOAC International
https://www.readbyqxmd.com/read/27683527/interpretation-of-blood-microbiology-results-function-of-the-clinical-microbiologist
#3
Katalin Kristóf, Júlia Pongrácz
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...
April 2016: EJIFCC
https://www.readbyqxmd.com/read/27650515/methicillin-resistant-staphylococcus-aureus-isolates-with-sccmec-type-v-and-spa-types-t437-or-t1081-associated-to-discordant-susceptibility-results-between-oxacillin-and-cefoxitin-central-taiwan
#4
Cheng-Mao Ho, Chien-Yu Lin, Mao-Wang Ho, Hsiao-Chuan Lin, Chao-Jung Chen, Lee-Chung Lin, Jang-Jih Lu
Staphylococcus aureus isolates with discordant susceptibility results between oxacillin and cefoxitin obtained using automated microbiology systems are infrequently observed. From April 2013 to December 2014, 1956 methicillin-resistant S. aureus (MRSA) and 1761 methicillin-susceptible S. aureus isolates were obtained from different patients. Forty isolates (1.1% and 2% in case of S. aureus and MRSA, respectively) with discordant susceptibility results (oxacillin susceptible and cefoxitin resistant) and carrying mecA gene were obtained...
August 28, 2016: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/27630804/emerging-bacterial-infection-identification-and-clinical-significance-of-kocuria-species
#5
REVIEW
Venkataramana Kandi, Padmavali Palange, Ritu Vaish, Adnan Bashir Bhatti, Vinod Kale, Maheshwar Reddy Kandi, Mohan Rao Bhoomagiri
Recently there have been reports of gram-positive cocci which are morphologically similar to both Staphylococci and the Micrococci. These bacteria have been identified as Kocuria species with the help of automated identification system and other molecular methods including 16S rRNA (ribosomal ribonucleic acid) evaluation. Kocuria belongs to the family Micrococcaceae which also includes Staphylococcus species and Micrococcus species. Isolation and clinical significance of these bacteria from human specimens warrant great caution as it does not necessarily confirm infection due to their ubiquitous presence, and as a normal flora of skin and mucous membranes in human and animals...
2016: Curēus
https://www.readbyqxmd.com/read/27598407/mass-spectrometry-applications-in-microbiology-beyond-microbe-identification-progress-and-potential
#6
Maurizio Sanguinetti, Brunella Posteraro
INTRODUCTION: Mass spectrometry (MS), particularly MALDI-time of flight (MALDI-TOF), has become a routine tool for microorganism identification in clinical microbiology laboratories in the last five years. The use of MALDI-TOF MS has accelerated laboratory analysis, thus providing accurate species-level information with very short turnaround times. AREAS COVERED: Beyond microbe identification, MALDI-TOF MS offers great opportunities for fast strain typing and detection of antimicrobial susceptibility/resistance in both bacterial and fungal organisms...
September 6, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27560299/automated-high-throughput-identification-and-characterization-of-clinically-important-bacteria-and-fungi-using-rapid-evaporative-ionization-mass-spectrometry
#7
Frances Bolt, Simon J S Cameron, Tamas Karancsi, Daniel Simon, Richard Schaffer, Tony Rickards, Kate Hardiman, Adam Burke, Zsolt Bodai, Alvaro Perdones-Montero, Monica Rebec, Julia Balog, Zoltan Takats
Rapid evaporative ionization mass spectrometry (REIMS) has been shown to quickly and accurately speciate microorganisms based upon their species-specific lipid profile. Previous work by members of this group showed that the use of a hand-held bipolar probe allowed REIMS to analyze microbial cultures directly from culture plates without any prior preparation. However, this method of analysis would likely be unsuitable for a high-throughput clinical microbiology laboratory. Here, we report the creation of a customized platform that enables automated, high-throughput REIMS analysis that requires minimal user input and operation and is suitable for use in clinical microbiology laboratories...
October 4, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27510833/automatic-digital-plate-reading-for-surveillance-cultures
#8
Thomas J Kirn
The automation of specimen processing and culture workup has rapidly emerged in clinical microbiology laboratories throughout the world and more recently in the United States. While many U.S. laboratories have implemented some form of automated specimen processing and some have begun performing digital plate reading, automated colony analysis is just beginning to be utilized clinically. In this issue of the Journal of Clinical Microbiology, M. L. Faron et al. (J Clin Microbiol 54:2470-2475, 2016, http://dx...
October 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27496125/comparison-of-methods-for-the-identification-of-microorganisms-isolated-from-blood-cultures
#9
Aydir Cecília Marinho Monteiro, Carlos Magno Castelo Branco Fortaleza, Adriano Martison Ferreira, Ricardo de Souza Cavalcante, Alessandro Lia Mondelli, Eduardo Bagagli, Maria de Lourdes Ribeiro de Souza da Cunha
BACKGROUND: Bloodstream infections are responsible for thousands of deaths each year. The rapid identification of the microorganisms causing these infections permits correct therapeutic management that will improve the prognosis of the patient. In an attempt to reduce the time spent on this step, microorganism identification devices have been developed, including the VITEK(®) 2 system, which is currently used in routine clinical microbiology laboratories. METHODS: This study evaluated the accuracy of the VITEK(®) 2 system in the identification of 400 microorganisms isolated from blood cultures and compared the results to those obtained with conventional phenotypic and genotypic methods...
August 5, 2016: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/27476484/technical-note-discard-the-specimen-collection-swab-directly-at-point-of-care-to-improve-extensive-automated-processing-in-clinical-microbiology-laboratories
#10
Manuela Avolio, Shamanta Grosso, Graziano Bruschetta, Alessandro Camporese
We compared, in terms of microorganisms recovery, the discard of specimen collection swab, after swirling into its medium, directly at point of care, with its placing into the medium and vortexing on arrival in the laboratory. Our results show that these two procedures are overlapped in terms of bacterial recovery.
October 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27447173/evaluation-of-the-nanochip%C3%A2-gastrointestinal-panel-gip-test-for-simultaneous-detection-of-parasitic-and-bacterial-enteric-pathogens-in-fecal-specimens
#11
Shifra Ken Dror, Elsa Pavlotzky, Mira Barak
Infectious gastroenteritis is a global health problem associated with high morbidity and mortality rates. Rapid and accurate diagnosis is crucial to allow appropriate and timely treatment. Current laboratory stool testing has a long turnaround time (TAT) and demands highly qualified personnel and multiple techniques. The need for high throughput and the number of possible enteric pathogens compels the implementation of a molecular approach which uses multiplex technology, without compromising performance requirements...
2016: PloS One
https://www.readbyqxmd.com/read/27420106/the-influence-of-corneal-collagen-crosslinking-on-conjunctival-flora
#12
Nihat Polat, Abuzer Gunduz, Ayten Gunduz, Tongabay Cumurcu, Göksel Gunduz
PURPOSE: To investigate the influence of corneal collagen crosslinking (CXL) on conjunctival flora. MATERIALS AND METHODS: Included in this study were 42 patients, all of whom were treated with CXL for progressive keratoconus (KC). Conjunctival swab samples were collected under operating-room conditions immediately before and immediately after the procedure. Samples were quickly immersed in Amies Transport Medium (ATM), transferred to the microbiology laboratory, diluted, and inoculated into three areas each of blood agar, chocolate agar, eosin methylene blue (EMB) agar, and Saboraud-Dextrose agar plates...
July 15, 2016: Current Eye Research
https://www.readbyqxmd.com/read/27391894/the-synthesis-of-l-alanyl-and-%C3%AE-alanyl-derivatives-of-2-aminoacridone-and-their-application-in-the-detection-of-clinically-important-microorganisms
#13
Marie Cellier, Arthur L James, Sylvain Orenga, John D Perry, Graeme Turnbull, Stephen P Stanforth
In clinical microbiology the speed with which pathogenic microorganisms may be detected has a direct impact on patient health. One important strategy used in the laboratory is the growth of cultures in the presence of an enzymatic substrate which, once transformed by the appropriate microbial enzyme, generates a detectable colour or fluorescence output. Such substrates have previously been prepared by our group and others and are available as commercial diagnostic kits, however they all suffer from some degree of diffusion when used in a solid growth medium...
2016: PloS One
https://www.readbyqxmd.com/read/27335151/verification-of-an-automated-digital-dispensing-platform-for-at-will-broth-microdilution-based-antimicrobial-susceptibility-testing
#14
Kenneth P Smith, James E Kirby
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...
September 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27328762/performance-evaluation-of-three-automated-identification-systems-in-detecting-carbapenem-resistant-enterobacteriaceae
#15
Qingwen He, Weiyuan Chen, Liya Huang, Qili Lin, Jingling Zhang, Rui Liu, Bin Li
BACKGROUND: Carbapenem-resistant Enterobacteriaceae (CRE) is prevalent around the world. Rapid and accurate detection of CRE is urgently needed to provide effective treatment. Automated identification systems have been widely used in clinical microbiology laboratories for rapid and high-efficient identification of pathogenic bacteria. However, critical evaluation and comparison are needed to determine the specificity and accuracy of different systems. The aim of this study was to evaluate the performance of three commonly used automated identification systems on the detection of CRE...
June 21, 2016: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/27327771/a-bacterial-analysis-platform-an-integrated-system-for-analysing-bacterial-whole-genome-sequencing-data-for-clinical-diagnostics-and-surveillance
#16
Martin Christen Frølund Thomsen, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Vanessa Jurtz, Mette Voldby Larsen, Henrik Hasman, Frank Møller Aarestrup, Ole Lund
Recent advances in whole genome sequencing have made the technology available for routine use in microbiological laboratories. However, a major obstacle for using this technology is the availability of simple and automatic bioinformatics tools. Based on previously published and already available web-based tools we developed a single pipeline for batch uploading of whole genome sequencing data from multiple bacterial isolates. The pipeline will automatically identify the bacterial species and, if applicable, assemble the genome, identify the multilocus sequence type, plasmids, virulence genes and antimicrobial resistance genes...
2016: PloS One
https://www.readbyqxmd.com/read/27281992/streptococcus-anginosus-milleri-group-strains-isolated-in-poland-1996-2012-and-their-antibiotic-resistance-patterns
#17
Katarzyna Obszańska, Izabella Kern-Zdanowicz, Aleksandra Kozińska, Katarzyna Machura, Elzbieta Stefaniuk, Waleria Hryniewicz, Izabela Sitkiewicz
Streptococcus anginosus, Streptococcus intermedius and Streptococcus constellatus form a group of related streptococcal species, namely the Streptococcus Anginosus Group (SAG). The group, previously called "milleri" had been rarely described until 1980/1990 as source of infections. Nowadays SAG bacteria are often described as pathogens causing predominantly purulent infections. The number of infections is highly underestimated, as SAG strains are often classified in the microbiology laboratory as less virulent "viridans streptococci" Epidemiological situation regarding SAG infections in Poland has been unrecognized, therefore we performed a retrospective analysis of strains isolated between 1996 and 2012...
2016: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/27262553/real-time-monitoring-of-beta-d-glucuronidase-activity-in-sediment-laden-streams-a-comparison-of-prototypes
#18
Philipp Stadler, Günter Blöschl, Wolfgang Vogl, Juri Koschelnik, Markus Epp, Maximilian Lackner, Markus Oismüller, Monika Kumpan, Lukas Nemeth, Peter Strauss, Regina Sommer, Gabriela Ryzinska-Paier, Andreas H Farnleitner, Matthias Zessner
Detection of enzymatic activities has been proposed as a rapid surrogate for the culture-based microbiological pollution monitoring of water resources. This paper presents the results of tests on four fully automated prototype instruments for the on-site monitoring of beta-d-glucuronidase (GLUC) activity. The tests were performed on sediment-laden stream water in the Hydrological Open Air Laboratory (HOAL) during the period of March 2014 to March 2015. The dominant source of faecal pollution in the stream was swine manure applied to the fields within the catchment...
September 15, 2016: Water Research
https://www.readbyqxmd.com/read/27247572/evaluation-of-antimicrobial-resistance-in-staphylococcus-aureus-isolates-by-years
#19
Cennet Rağbetli, Mehmet Parlak, Yasemin Bayram, Huseyin Guducuoglu, Nesrin Ceylan
Objective. Recently, community and hospital-acquired infections with Staphylococcus aureus have increased and raised antibiotic resistant isolates. In this study, we aimed to evaluate the antibiotic resistance profile of S. aureus isolates over several years in various clinical specimens from our hospital. Materials and Methods. S. aureus strains from 2009 to 2014 were isolated from various clinical samples at Yuzuncu Yil University, Dursun Odabas Medical Center, Microbiology Laboratory, and their antibiotic susceptibility test results were retrospectively investigated...
2016: Interdisciplinary Perspectives on Infectious Diseases
https://www.readbyqxmd.com/read/27239799/rapid-identification-of-klebsiella-pneumoniae-by-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-and-detection-of-meropenem-resistance-by-flow-cytometric-assay
#20
Abdullah Kilic, Eyup Dogan, Sinem Kaya, Sema Oren, Duran Tok, Nurittin Ardic, Mehmet Baysallar
BACKGROUND: The aim of this study was to develop a rapid detection method of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains both MALDI-TOF MS and flow cytometry (FCM). METHODS: A total of 174 K. pneumoniae strains were included in this study. Molecular characterization of carbapenemase gene was performed by PCR. Bacterial identification was performed by MALDI-TOF-MS. Meropenem susceptibility was tested at the concentrations of breakpoints described by the Clinical and Laboratory Standards Institute (CLSI) guide by FCM...
May 30, 2016: Journal of Clinical Laboratory Analysis
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