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Journal of Clinical Microbiology

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https://www.readbyqxmd.com/read/28330895/speciation-and-strain-typing-of-staphylococcus-agnetis-and-staphylococcus-hyicus-isolated-from-bovine-milk-using-a-novel-multiplex-pcr-and-pulsed-field-gel-electrophoresis
#1
P R F Adkins, J R Middleton, M J Calcutt, G C Stewart, L K Fox
Staphylococcus hyicus and Staphylococcus agnetis are two coagulase variable staphylococcal species that can be isolated from bovine milk and are difficult to differentiate. The objectives of this study were to characterize isolates of bovine milk origin from a collection that had previously been characterized as coagulase positive S. hyicus based on phenotypic speciation methods and to develop a PCR-based method for differentiating S. hyicus, S. agnetis, and S. aureus. Isolates (n = 62) were selected from a previous study in which milk samples were collected from cows on 15 dairy herds...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330894/targeted-enrichment-for-pathogen-detection-and-characterization-in-three-felid-species
#2
Justin S Lee, Ryan S Mackie, Thomas Harrison, Basir Shariat, Trey Kind, Timo Kehl, Martin Löchelt, Christina Boucher, Sue VandeWoude
Traditional diagnostic assays often lack sensitivity and can be difficult to multiplex across many pathogens. Next-generation sequencing (NGS) can overcome some of these problems but has limited application detecting low-copy-number pathogens in complex samples. Targeted genome capture (TGC) utilizes oligonucleotide probes to enrich specific nucleic acids in heterogeneous extracts and can therefore increase the proportion of NGS reads for low-abundance targets. While prior studies have demonstrated the utility of this technology for detection of novel pathogens in human clinical samples, the capacity and practicality of TGC-NGS in a veterinary diagnostic setting has not yet been evaluated...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330893/analysis-of-mic-and-disk-diffusion-testing-variables-for-gepotidacin-and-comparator-agents-against-select-bacterial-pathogens
#3
L K Koeth, J M DiFranco-Fisher, N E Scangarella-Oman, L A Miller
This study was conducted to determine the effect of testing parameters on the in vitro activity of gepotidacin, a new triazaacenaphthylene antibacterial agent for the treatment of conventional and biothreat pathogens. CLSI methods, and variations of these methods were used to test 10 Staphylococcus aureus, 10 Streptococcus pneumoniae, 10 Haemophilus influenzae, and 5 Escherichia coli by MIC and 30 S. aureus, 15 S. pneumoniae and 15 S. pyogenes by disk diffusion (DD) methods. Levofloxacin and linezolid were tested as comparator agents for MIC and DD methods, respectively...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330892/in-vitro-susceptibility-testing-of-tedizolid-against-nontuberculous-mycobacteria
#4
Barbara A Brown-Elliott, Richard J Wallace
Tedizolid is a new oxazolidinone with improved in vitro and intracellular potency against Mycobacterium tuberculosis, including multidrug resistant strains, and some species of nontuberculous mycobacteria (NTM) compared with linezolid.Using the current Clinical and Laboratory Standards Institute (CLSI) recommended method of broth microdilution, susceptibility testing of 170 isolates of rapidly growing mycobacteria showed equivalent or lower (1- to 8-fold MIC50 and/or MIC90 values) for tedizolid compared to linezolid...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330891/evaluation-of-the-bionexia-legionella-test-including-the-impact-of-incubation-time-extension-for-the-detection-of-legionella-pneumophila-serogroup-1-antigen-in-urine
#5
Paul Badoux, Sjoerd M Euser, Jacob P Bruin, Patrick P G Mulder, Ed P F Yzerman
In this study, we compared the bioNexia (bioMérieux, Marcy-l'Étoile, France), a new immunochromatographic assay for the detection of Legionella pneumophila serogroup 1 in urine, with the BinaxNOW urinary antigen test (Alere, Waltham, Massachusetts, USA). After 15 minutes of incubation (in accordance with the manufactures instructions), the sensitivity and specificity were, respectively, 76.5% and 97.2% for the bioNexia test and 87.1% and 100% for the BinaxNOW test. After a prolonged incubation time of 60 minutes, the sensitivity and specificity increased to, respectively, 89...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330890/direct-detection-of-rifampicin-and-isoniazid-resistance-in-sputum-samples-from-tuberculosis-patients-by-high-resolution-melt-curve-analysis
#6
Divya Anthwal, Rakesh Kumar Gupta, Manpreet Bhalla, Shinjini Bhatnagar, Jaya Sivaswami Tyagi, Sagarika Haldar
Drug-resistant tuberculosis (TB) is a major threat for TB control worldwide. Globally, only 40% of the 340,000 notified TB patients estimated to have multidrug resistant-TB (MDR-TB) were detected in 2015. This study was carried out to evaluate the utility of High Resolution Melt curve analysis (HRM) for the rapid and direct detection of MDR-TB in Mycobacterium tuberculosis (M. tb) in sputum samples. A reference plasmid library was first generated of the most frequently observed mutations in the resistance determining regions of rpoB, katG and inhA promoter and used as positive controls in HRM...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330889/robust-microbiota-based-diagnostics-for-inflammatory-bowel-disease
#7
A Eck, E F J de Groot, T G J de Meij, M Welling, P H M Savelkoul, A E Budding
Strong evidence suggests that gut microbiota is altered in inflammatory bowel disease (IBD), indicating its potential role in non-invasive diagnostics. However, no clinical applications are currently used for routine patient care. The main obstacle to implementing a gut microbiota test for IBD is the lack of standardization, which leads to high inter-laboratory variations. We studied the between-hospital and between-platform batch effects and their effect on predictive accuracy for IBD.Fecal samples from 91 pediatric IBD patients and 58 healthy children were collected...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330888/defining-a-core-genome-multilocus-sequence-typing-scheme-for-the-global-epidemiology-of-vibrio-parahaemolyticus
#8
Narjol Gonzalez-Escalona, Keith A Jolley, Elizabeth Reed, Jaime Martinez-Urtaza
Vibrio parahaemolyticus is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 2008 and a large number of clones have been identified causing severe outbreaks worldwide (ST3), recurrent outbreaks in certain regions (e.g., ST36) or spreading to other regions where they are non-endemic (e.g...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330887/usefulness-of-two-aspergillus-pcr-assays-and-aspergillus-galactomannan-and-%C3%AE-d-glucan-testing-of-bronchoalveolar-lavage-fluid-for-diagnosis-of-chronic-pulmonary-aspergillosis
#9
Naohisa Urabe, Susumu Sakamoto, Go Sano, Junko Suzuki, Akira Hebisawa, Yasuhiko Nakamura, Kazuya Koyama, Yoshikazu Ishii, Kazuhiro Tateda, Sakae Homma
We evaluated the usefulness of an Aspergillus galactomannan (GM) test, a β-D-glucan (βDG) test, and two different Aspergillus polymerase chain reaction (PCR) assays of bronchoalveolar lavage fluid (BALF) samples for diagnosis of chronic pulmonary aspergillosis (CPA). BALF samples from 28 patients with and 120 patients without CPA were collected. We calculated the sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio for each test individually and in combination with other tests...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330886/preclinical-diagnosis-predicting-its-ability-to-improve-control-of-farm-to-farm-foot-and-mouth-disease-transmission-in-cattle
#10
Noel Nelson, David J Paton, Simon Gubbins, Claire Colenutt, Emma Brown, Sophia Hodgson, Jose L Gonzales
Foot-and-mouth disease (FMD) can cause large disruptive epidemics in livestock. Current eradication measures rely on the rapid clinical detection and removal of infected herds. Here, we have evaluated the potential for preclinical diagnosis during reactive surveillance to reduce the risk of between farm transmission. We used data from transmission experiments in cattle where both individual animal samples, such as blood, probang, saliva or nasal swabs, and herd level samples, such as air samples, were taken daily during the course of infection...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330885/dientamoeba-fragilis-a-commensal-in-children-in-danish-day-care-centers
#11
Pikka Jokelainen, Betina Hebbelstrup Jensen, Bente Utoft Andreassen, Andreas Munk Petersen, Dennis Röser, Karen A Krogfelt, Henrik V Nielsen, Christen R Stensvold
Dientamoeba fragilis is an intestinal protozoan of debated clinical significance. Here, we present cross-sectional and longitudinal observations on D. fragilis in children aged 0-6 years from a 1-year multi-day-care-center cohort study set in Copenhagen, Denmark. The inclusion period for the cohort was 2009-2012. Stool samples collected from the children were accompanied by questionnaires completed by the parents or guardians of the children. Using real-time PCR, D. fragilis was detected in the first stool sample from 97 (68...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330884/evaluation-of-biom%C3%A3-rieux-s-dissociated-vidas-lyme-igm-ii-lym-and-igg-ii-lyg-as-a-first-tier-diagnostic-assay-for-lyme-disease
#12
Claudia R Molins, Mark J Delorey, Adam Replogle, Christopher Sexton, Martin E Schriefer
The recommended laboratory diagnostic approach for Lyme disease is a standard two-tiered testing (STTT) algorithm where the first-tier is typically an enzyme immunoassay (EIA) that if positive or equivocal is reflexed to Western immunoblotting as the second-tier. bioMérieux manufacturers one of the most commonly used first-tier EIAs in the U.S., the combined IgM/IgG VIDAS (LYT). Recently, bioMérieux launched its dissociated first-tier tests, the VIDAS Lyme IgM II (LYM) and IgG II (LYG) EIAs, which use purified recombinant test antigens and a different algorithm than STTT...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330883/comparative-evaluation-of-sensititre-yeastone%C3%A2-and-clsi-m38-a2-reference-method-for-antifungal-susceptibility-testing-of-aspergillus-spp-against-echinocandins
#13
Maria Siopi, Spyros Pournaras, Joseph Meletiadis
Sensititre YeastOne® (YO) panels were assessed for in vitro susceptibility testing of echinocandins against 39 isolates of A. fumigatus, A. flavus and A. terreus, including two echinocandin-resistant A. fumigatus, using different inocula (10(3), 10(4) and 10(5) cfu/mL), incubation times (16-48h) and endpoints (first blue or purple) and compared with CLSI M38-A2. The best agreement was found with inoculum of 10(4) cfu/mL, incubation time of 20h for A. flavus and 30h for A. fumigatus and A. terreus and reading the first purple well...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28298455/evaluation-of-quantiferon%C3%A2-tb-gold-plus-in-healthcare-workers-in-a-low-incidence-setting
#14
Hee-Won Moon, Rajiv L Gaur, Sara Shu-Hwa Tien, Mary Spangler, Madhukar Pai, Niaz Banaei
Background: Although launched in 2015, little is known about the accuracy of QuantiFERON-TB Gold-Plus (QFT-Plus) for diagnosis of latent M. tuberculosis infection (LTBI). Unlike its predecessor, QFT-Plus utilizes two antigen tubes to elicit an immune response from CD4+ and CD8+ T lymphocytes. We conducted a cross-sectional study in low-risk healthcare workers (HCWs) at a single U.S. center to compare QFT-Plus to QuantiFERON-TB Gold in-tube (QFT).Method: 989 HCWs were tested with both QFT and QFT-Plus. Risk factors for LTBI were obtained from a questionnaire...
March 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28298454/in-vitro-activity-of-imipenem-against-carbapenemase-positive-enterobacteriaceae-smart-global-surveillance-program-2008-2014
#15
James A Karlowsky, Sibylle H Lob, Krystyna M Kazmierczak, Robert E Badal, Katherine Young, Mary R Motyl, Daniel F Sahm
The Study for Monitoring Antimicrobial Resistance Trends (SMART) global surveillance program collected 103,960 isolates of Enterobacteriaceae from 2008 to 2014. From this isolate collection all ertapenem-non-susceptible isolates (MIC, ≥1 μg/ml; n = 3,428) and 9,371 isolates of Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, and Proteus mirabilis with an ertapenem-susceptible extended-spectrum β-lactamase (ESBL)-positive phenotype were assessed for the presence of common carbapenemase genes using the Check-MDR CT101 microarray (Check-Points, Wageningen, the Netherlands) and published multiplex PCR assays...
March 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28298453/detection-of-mecc-positive-staphylococcus-aureus-what-to-expect-from-immunological-tests-targeting-pbp2a
#16
Céline Dupieux, Coralie Bouchiat, Anders Rhod Larsen, Bruno Pichon, Mark Holmes, Christopher Teale, Giles Edwards, Robert Hill, Jean-Winoc Decousser, Sophie Trouillet-Assant, Andreas Petersen, Robert Skov, Angela Kearns, Frédéric Laurent
Rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is pivotal for the control of their dissemination and for accurate management of infected patients.….
March 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28298452/applications-of-digital-pcr-for-clinical-microbiology
#17
Jane Kuypers, Keith R Jerome
Digital PCR (dPCR) is an important new tool for use in the clinical microbiology laboratory. Its advantages over quantitative PCR (qPCR), including absolute quantification without a standard curve, improved precision, improved accuracy in the presence of inhibitors, and more accurate quantitation when amplification efficiency is low, make dPCR the assay of choice for several specimen testing applications. This mini-review will discuss the advantages and disadvantages of dPCR compared to qPCR, its applications in clinical microbiology and the considerations for implementation of the method in a clinical laboratory...
March 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28298451/evaluation-of-the-new-fecalswab%C3%A2-to-maintain-stability-of-stool-samples-submitted-for-molecular-tests
#18
Suzane Silbert, Alicia Gostnell, Carly Kubasek, Raymond Widen
Gastrointestinal disease accounts for significant morbidity and mortality worldwide and may be caused by a variety of agents including bacterial, viral and parasitic pathogens (1, 2, 3).….
March 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28298450/cost-effectiveness-study-of-criteria-to-screen-herpes-simplex-pcr-tests-from-cerebrospinal-fluid
#19
Ronald G Hauser, Sheldon M Campbell, Cynthia A Brandt, Shiyi Wang
Background: The absence of markers of inflammation in the cerebrospinal fluid (CSF) commonly predict the absence of herpes simplex virus (HSV) central nervous system (CNS) infection. Consequently, multiple authors have proposed and validated criteria to defer HSV PCR tests from CSF in immune competent hosts with normal CSF white cells and protein (≤5 cells/mm(3), ≤50 mg/dL, respectively). Immune competence equates to age ≥2 years without HIV or transplant. Adoption of the criteria may erroneously exclude HSV infected persons from a necessary diagnostic test, or alternatively, reduce the costs associated with HSV tests with minimal to no effect on patient care...
March 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28298449/real-time-sequencing-of-mycobacterium-tuberculosis-are-we-there-yet
#20
Robyn S Lee, Madhukar Pai
Whole genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, the real-time, clinical utility has been low, in part due to the requirement for culture. In Votintseva et al (J Clin Microbiol https://doi.org/10.1128/JCM.02483-16), authors present a new method for extracting Mycobacterium tuberculosis DNA directly from smear-positive respiratory samples, generating drug resistance predictions and phylogenetic trees in 44 hours using the Illumina MiSeq. Authors also illustrate the potential for < 24 hour turnaround time from DNA extraction to clinically-relevant results, with Illumina MiniSeq and Oxford Nanopore Technologies' MinION...
March 15, 2017: Journal of Clinical Microbiology
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