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https://www.readbyqxmd.com/read/27990823/abrf-proteome-informatics-research-group-iprg-2015-study-detection-of-differentially-abundant-proteins-in-label-free-quantitative-lc-ms-ms-experiments
#1
Meena Choi, Zeynep F Eren-Dogu, Christopher Colangelo, John Cottrell, Michael R Hoopmann, Eugene A Kapp, Sangtae Kim, Henry Lam, Thomas A Neubert, Magnus Palmblad, Brett S Phinney, Susan T Weintraub, Brendan MacLean, Olga Vitek
Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments requires a series of computational steps that identify and quantify LC-MS features. It also requires statistical analyses that distinguish systematic changes in abundance between conditions from artifacts of biological and technical variation. The 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results...
January 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/27987046/matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms-for-rapid-identification-of-micro-organisms-in-the-routine-clinical-microbiology-laboratory
#2
C Wattal, J K Oberoi, N Goel, R Raveendran, S Khanna
The study evaluates the utility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) Vitek MS for identification of microorganisms in the routine clinical microbiology laboratory. From May 2013 to April 2014, microbial isolates recovered from various clinical samples were identified by Vitek MS. In case of failure to identify by Vitek MS, the isolate was identified using the Vitek 2 system (bioMerieux, France) and serotyping wherever applicable or otherwise by nucleic acid-mediated methods...
December 16, 2016: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/27955639/control-of-carbapenem-resistant-acinetobacter-baumannii-outbreak-in-an-intensive-care-unit-of-a-teaching-hospital-in-southern-italy
#3
Aida Bianco, Angela Quirino, Mariavalentina Giordano, Vito Marano, Claudia Rizzo, Maria Carla Liberto, Alfredo Focà, Maria Pavia
BACKGROUND: Acinetobacter baumannii is an opportunistic pathogen that has become a major cause of concern, since it is a frequent cause of healthcare-associated infections (HAIs). The aim of the study was to describe the occurrence, the management and the control of an outbreak that occurred in an intensive care unit (ICU) of a teaching hospital in Southern Italy caused by multiple strains of extensively drug-resistant A. baumannii (XDRAB). METHODS: Case-patient was defined as a patient with an healthcare-associated infection caused by an XDRAB isolate identified in a clinically significant culture...
December 12, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27934842/infections-related-to-granulicatella-adiacens-report-of-two-cases-and-review-of-literature
#4
S Macin, A Ç İnkaya, Ö Tuncer, S Ünal, Y Akyön
Infections due to nutritionally variant streptococci are diagnosed rarely due to difficulties encountered during identification and isolation. Mortality rate in these infections is high therefore appropriate supplemented media and reliable detection systems should be implemented to isolate these fastidious organisms. Here, we describe two cases of Granulicatella adiacens infections. All microbiologic identifications were made with MALDI-TOF Vitek MS (BioMerieux, France), and the results confirmed by 16S ribotyping...
October 2016: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27847376/relative-prevalence-and-antimicrobial-susceptibility-of-clinical-isolates-of-elizabethkingia-species-based-on-16s-rrna-gene-sequencing
#5
Mi-Soon Han, Hyunsoo Kim, Yangsoon Lee, Myungsook Kim, Nam Su Ku, Jun Yong Choi, Dongeun Yong, Seok Hoon Jeong, Kyungwon Lee, Yunsop Chong
Some of the previously reported clinical isolates of Elizabethkingia meningoseptica may be later named species of Elizabethkingia We determined the accuracy of species identification (with two matrix-assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS] systems and the Vitek 2 GN card), relative prevalence of three Elizabethkingia spp. in clinical specimens, and antimicrobial susceptibility of the species identified by 16S rRNA gene sequencing. Specimens for culture were collected from patients in a university hospital in Seoul, South Korea, between 2009 and 2015...
January 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27802877/routine-identification-of-nocardia-species-by-maldi-tof-mass-spectrometry
#6
Victoria Girard, Sandrine Mailler, Sophie Polsinelli, Delphine Jacob, Marie Christine Saccomani, Beatrice Celliere, Valerie Monnin, Alex van Belkum, Ferry Hagen, Jacques F Meis, Géraldine Durand
We here show adequate species identification for bacterial isolates of the genus Nocardia spp. through VITEK mass spectrometry. Application of a specific sample preparation method in combination with a robust matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) database leads to 94% accurate identification to the species level on a set of 164 isolates. The possibility to identify Nocardia spp. using MALDI-TOF MS will be available in the next release of VITEK MS update (IVD Version 3...
January 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/27796646/streptococcus-bovis-new-taxonomy-does-subspecies-distinction-matter
#7
E Ben-Chetrit, Y Wiener-Well, L Kashat, A M Yinnon, M V Assous
Bacteremia with Streptococcus bovis/equinus complex strains is associated with hepatobiliary disease, colorectal lesions (CL), and infective endocarditis (IE). This study addressed the clinical significance of subspecies distinction of previously designated S. bovis blood culture isolates according to the updated nomenclature. During 2002-2013, all blood culture isolates previously designated as S. bovis were recultured and identified using 16S rRNA gene sequencing and MALDI-TOF (Bruker BioTyper and Vitek MS, bioMérieux)...
October 28, 2016: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/27771394/bacteroides-pyogenes-causing-serious-human-wound-infection-from-animal-bites
#8
Jillian S Y Lau, Tony M Korman, Alex Yeung, Richard Streitberg, Michelle J Francis, Maryza Graham
Bacteroides pyogenes is part of the normal oral flora of domestic animals. There is one previous report of human infection, with B. pyogenes bacteremia following a cat bite (Madsen 2011). We report seven severe human infections where B. pyogenes was identified by Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDTI-TOF MS), but not by VITEK MS and was misidentified by VITEK ANC card.
December 2016: Anaerobe
https://www.readbyqxmd.com/read/27750157/nosocomial-outbreak-of-extended-spectrum-%C3%AE-lactamase-producing-enterobacter-ludwigii-co-harbouring-ctx-m-8-shv-12-and-tem-15-in-a-neonatal-intensive-care-unit-in-venezuela
#9
Ana Flores-Carrero, Indira Labrador, Alberto Paniz-Mondolfi, David R Peaper, Dana Towle, María Araque
Enterobacter spp. have emerged as an important group of pathogens linked to outbreaks in neonatal intensive care units (NICUs), usually involving strains expressing extended-spectrum β-lactamases (ESBLs). The aim of this study was to describe the first nosocomial bloodstream infection outbreak caused by Enterobacter ludwigii co-harbouring CTX-M-8, SHV-12 and TEM-15 in a NICU in a Venezuelan hospital. Initial bacterial identification was achieved by VITEK(®)2 system and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (VITEK(®) MS) and was subsequently confirmed by nucleotide sequencing of the 16S rDNA gene and hsp60 genotyping...
December 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/27720207/identification-antimicrobial-resistance-and-molecular-characterization-of-the-human-emerging-pathogen-streptococcus-gallolyticus-subsp-pasteurianus
#10
Giovanni Gherardi, Claudio Palmieri, Emanuela Marini, Arianna Pompilio, Valentina Crocetta, Giovanni Di Bonaventura, Roberta Creti, Bruna Facinelli
This study aimed to retrospectively identify 22Streptococcus bovis clinical strains based on the new taxonomy, as well as to investigate their antibiotic-resistance and clonality. Strains were identified by Phoenix100 system, 16S rRNA sequencing, and two MALDI-TOF MS platforms (Bruker Biotyper, Vitek MS). Antibiotic resistance was determined both phenotypically and genotypically, and clonality was assessed by PFGE. Most of strains (63.6%) were isolated from urine, and diabetes was the most common underlying disease (31...
December 2016: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/27713213/identification-of-uncommon-candida-species-using-commercial-identification-systems
#11
Tae-Hyoung Kim, Oh Joo Kweon, Hye Ryoun Kim, Mi-Kyung Lee
Recently, several studies have revealed that commercial microbial identification systems do not accurately identify the uncommon causative species of candidiasis, including Candida famata, Meyerozyma guilliermondii, and C. auris. We investigated the accuracy of species-level identification in a collection of clinical isolates previously identified as C. famata (N = 38), C. lusitaniae (N = 1 2), and M. guilliermondii (N = 5) by the Vitek 2 system. All 55 isolates were re-analyzed by the Phoenix system (Becton Dickinson Diagnostics), two matrix-assisted laser desorption ionization-time of flight mass spectrometry analyzers (a Vitek MS and a Bruker Biotyper), and by sequencing of internal transcribed spacer (ITS) regions or 26S rRNA gene D1/D2 domains...
December 28, 2016: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27682129/evaluation-of-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-for-identification-of-mycobacterium-abscessus-subspecies-according-to-whole-genome-sequencing
#12
Liulin Luo, Weijia Liu, Bing Li, Mengling Li, Dongdong Huang, Linjie Jing, Huiping Chen, Jinghui Yang, Jun Yue, Fang Wang, Haiqing Chu, Zhemin Zhang
This study was undertaken to evaluate the utility of matrix-assisted laser desorption ionization-time of flight mass spectrometry with the Vitek MS Plus system for identifying Mycobacterium abscessus subspecies in order to facilitate more rapid and appropriate therapy. A total of 175 clinical M. abscessus strains were identified by whole-genome sequencing analysis: 139 Mycobacterium abscessus subsp. abscessus and 36 Mycobacterium abscessus subsp. massiliense The research-use-only (RUO) Saramis Knowledge Base database v...
December 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27620383/maldi-tof-ms-versus-vitek-%C3%A2-2-comparison-of-systems-for-the-identification-of-microorganisms-responsible-for-bacteremia
#13
Filomena Febbraro, Donatella Maria Rodio, Gianluca Puggioni, Guido Antonelli, Valeria Pietropaolo, Maria Trancassini
We evaluated the reliability and accuracy of the combined use of MALDI-TOF MS and classical ID VITEK2 to identify monomicrobial infection in blood culture bottles. In total, 70 consecutive positive blood cultures were included in this study. Positive blood culture bottles were subjected to Gram staining and subcultured on solid media. Isolates grown from such culture media were used for classical ID using VITEK2 system. In parallel, an aliquot was subjected to a lysing-centrifugation method and used for the identification with the MALDI-TOF system...
December 2016: Current Microbiology
https://www.readbyqxmd.com/read/27617008/using-matrix-assisted-laser-desorption-ionization-time-of-flight-maldi-tof-complemented-with-selected-16s-rrna-and-gyrb-genes-sequencing-to-practically-identify-clinical-important-viridans-group-streptococci-vgs
#14
Menglan Zhou, Qiwen Yang, Timothy Kudinha, Li Zhang, Meng Xiao, Fanrong Kong, Yupei Zhao, Ying-Chun Xu
There are challenges in viridans group streptococci (VGS) identification especially for the mitis group. Few studies have investigated the performance of MALDI-TOF MS system in VGS identification. Using 16S rRNA gene and gyrB gene sequencing as a gold standard, the performance of two MALDI-TOF MS instruments in the identification of 181 VGS clinical isolates was studied. The Bruker Biotyper and Vitek MS IVD systems correctly identified 88.4% and 98.9% of the 181 isolates, respectively. The Vitek MS RUO system was the least reliable, only correctly identifying 38...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27598775/low-enteric-colonization-with-multidrug-resistant-pathogens-in-soldiers-returning-from-deployments-experience-from-the-years-2007-2015
#15
Hagen Frickmann, Dorothea Wiemer, Claudia Frey, Ralf Matthias Hagen, Rebecca Hinz, Andreas Podbielski, Thomas Köller, Philipp Warnke
This assessment describes the enteric colonization of German soldiers 8-12 weeks after returning from mostly but not exclusively subtropical or tropical deployment sites with third-generation cephalosporin-resistant Enterobacteriaceae, vancomycin-resistant enterococci (VRE), and methicillin-resistant Staphylococcus aureus (MRSA). Between 2007 and 2015, 828 stool samples from returning soldiers were enriched in nonselective broth and incubated on selective agars for Enterobacteriaceae expressing extended-spectrum beta-lactamases (ESBL), VRE and MRSA...
2016: PloS One
https://www.readbyqxmd.com/read/27575729/methicillin-resistant-staphylococcus-aureus-in-the-environment-of-public-transport-data-from-the-metropolitan-network-in-lyon-france
#16
Alexandre Gaymard, Maxime Pichon, Michaël Degaud, Jason Tasse, Céline Dupieux, Frédéric Laurent
Methicillin-resistant Staphylococcus aureus (MRSA) is involved in community-acquired and nosocomial diseases. The means of MRSA transmission and dissemination in the community remain uncertain. Studies have shown that public transport systems could be a source of MRSA and may serve as a potential source for community-acquired MRSA infections. This study aimed to investigate MRSA contamination on Lyon's metropolitan network (Métro) in France. Hand-touched surfaces were sampled with sterile swabs (Transystem(®)) during a 1-day transversal study by collecting 50 samples in seven hub stations and two trains for each of the four Métro lines...
October 2016: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/27558618/optimal-turnaround-time-for-direct-identification-of-microorganisms-by-mass-spectrometry-in-blood-culture
#17
Adrien Randazzo, Marc Simon, Pierre Goffinet, Jean-François Classen, Nicolas Hougardy, Pascal Pierre, Philippe Kinzinger, Etienne Mauel, Jean-Sébastien Goffinet
INTRODUCTION: During the past few years, several studies describing direct identification of bacteria from blood culture using mass spectrometry have been published. These methods cannot, however, be easily integrated into a common laboratory workflow because of the high hands-on time they require. In this paper, we propose a new method of identification with a short hands-on time and a turnaround time shorter than 15min. MATERIALS AND METHODS: Positive blood bottles were homogenised and 600μL of blood were transferred to an Eppendorf tube where 600μL of lysis buffer were added...
November 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27535688/identification-and-antifungal-susceptibility-profiles-of-candida-haemulonii-species-complex-clinical-isolates-from-a-multicenter-study-in-china
#18
Xin Hou, Meng Xiao, Sharon C-A Chen, He Wang, Jing-Wei Cheng, Xin-Xin Chen, Zhi-Peng Xu, Xin Fan, Fanrong Kong, Ying-Chun Xu
Candida haemulonii complex (Candida haemulonii, Candida haemulonii var. vulnera, and Candida duobushaemulonii) consists of emerging pathogens. Thirty-one isolates from 14 hospitals in China were studied for their species classification and antifungal susceptibilities. Performances of molecular (i.e., ribosomal DNA [rDNA] internal transcribed spacer [ITS] sequencing, D1/D2 sequencing, and ITS sequencer-based capillary gel electrophoresis [SCGE]) and phenotypic identification methods in species identification were compared...
November 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27525402/-a-sepsis-case-caused-by-a-rare-opportunistic-pathogen-bacillus-pumilus
#19
Barış Ata Borsa, Mehmet Ersoy Aldağ, Birsen Tunalı, Uğur Dinç, Zeynep Güngördü Dalar, Veli Cengiz Özalp
The high prevalence of Bacillus species in nature and the detection of these bacteria as contaminant in cultures may lead diagnostic dilemma, however they should still be considered as a pathogen particularly in case of repeated positive cultures from patients with risk factors. Bacillus pumilus is a bacteria, though rarely, been reported as the causative agent of various infections such as sepsis, endocarditis, skin infections and food poisoning in human. In this report, a sepsis case in an immunocompetent patient caused by B...
July 2016: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/27520338/a-new-rapid-method-for-direct-antimicrobial-susceptibility-testing-of-bacteria-from-positive-blood-cultures
#20
Simona Barnini, Veronica Brucculeri, Paola Morici, Emilia Ghelardi, Walter Florio, Antonella Lupetti
BACKGROUND: Rapid identification and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections can lead to prompt appropriate antimicrobial therapy. To shorten species identification, in this study bacteria were recovered from monomicrobial blood cultures by serum separator tubes and spotted onto the target plate for direct MALDI-TOF MS identification. Proper antibiotics were selected for direct AST based on species identification. In order to obtain rapid AST results, bacteria were recovered from positive blood cultures by two different protocols: by serum separator tubes (further referred to as PR1), or after a short-term subculture in liquid medium (further referred to as PR2)...
2016: BMC Microbiology
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