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Journal of Clinical Microbiology

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https://www.readbyqxmd.com/read/28100602/find-tuberculosis-strain-bank-a-resource-for-researchers-and-developers-working-on-tests-to-detect-mycobacterium-tuberculosis-and-related-drug-resistance
#1
Belay Tessema, Pamela Nabeta, Eloise Valli, Audrey Albertini, Jimena Collantes, Nguyen Huu Lan, Elena Romancenco, Nestani Tukavdze, Claudia M Denkinger, David L Dolinger
BACKGROUND: The spread of multidrug-resistant tuberculosis and extensively drug-resistant TB hampers the global efforts in the fight against tuberculosis. To enhance the development and evaluation of diagnostic tests quickly and efficiently, well characterized strains and samples from drug resistant tuberculosis patients are necessary. In this project, FIND has focused on the collection, characterization and storage of such well-characterized reference materials and to make them available to researchers and developers...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100601/the-use-of-selective-fungal-culture-media-increases-detection-rates-of-fungi-in-the-cystic-fibrosis-respiratory-tract
#2
Gina Hong, Heather B Miller, Sarah Allgood, Richard Lee, Noah Lechtzin, Sean X Zhang
The prevalence of fungi in the respiratory tract of cystic fibrosis (CF) patients has risen. However, fungal surveillance is not routinely performed in most clinical centers in the United States, which may lead to an underestimation of the true prevalence of the problem. We conducted a prospective study comparing fungal detection rates for clinically important fungi (CIF) defined as Aspergillus species, Scedosporium species, Trichosporon species, and Exophiala dermatitidis in CF sputum using standard bacterial culture media and selective-fungal culture media, including Sabouraud dextrose agar with gentamicin (SDA), inhibitory mold agar (IMA), and brain-heart infusion agar (BHI) with chloramphenicol and gentamicin...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100600/suitability-of-the-carbapenem-inactivation-method-cim-to-detect-imp-metallo-%C3%AE-lactamase-producing-enterobacteriaceae
#3
Kyoichi Saito, Ryuichi Nakano, Yuki Suzuki, Akiyo Nakano, Yoshihiko Ogawa, Shinsuke Yonekawa, Shiro Endo, Fumiko Mizuno, Kei Kasahara, Keiichi Mikasa, Mitsuo Kaku, Hisakazu Yano
Carbapenem-resistant Enterobacteriaceae (CRE) have become globally distributed in the past decade, resulting in concern over control of hospital infections and antimicrobial therapies (1. 2).….
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100599/rapid-and-specific-detection-of-the-escherichia-coli-sequence-type-648-complex-stc648-within-phylogroup-f
#4
James R Johnson, Brian D Johnston, David M Gordon
The Escherichia coli sequence type 648 complex (STc648) is an emerging lineage within phylogroup F - formerly included within phylogroup D - that is associated with multidrug resistance. Here, we designed and validated a novel multiplex PCR-based assay for STc648 that took advantage of (i) four distinctive single-nucleotide polymorphisms in icd allele 96 and gyrB allele 87, two of the multi-locus sequence typing alleles that define ST648, and (ii) the typical absence within STc648 of uidA, an E. coli-specific gene encoding β-glucuronidase...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100598/molecular-and-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-characterization-of-clinically-significant-melanized-fungi-in-india
#5
Ashutosh Singh, Pradeep Kumar Singh, Anil Kumar, Jagdish Chander, Geetika Khanna, Pradip Roy, Jacques F Meis, Anuradha Chowdhary
Melanized or black fungi are a heterogeneous group of fungi causing cutaneous to systemic diseases with high mortality. These fungi are rarely reported as agent of human infections primarily due to difficulties in their classical identification. In this study we examined using molecular methods and MALDI-TOF MS the diversity of melanized fungi (MF) isolated from patients in 19 medical centers in India. Overall, during a 4-year period, 718 (5.3%) clinical specimens yielded MF. Of these, 72 (10%) isolates had clinical significance and were identified primarily by sequencing the ITS and LSU regions...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100597/investigation-of-a-candida-guilliermondii-pseudo-outbreak-reveals-a-novel-source-of-laboratory-contamination
#6
James E Kirby, Westyn Branch-Elliman, Mary T LaSalvia, Lorinda Longhi, Matthew MacKechnie, Grigoriy Urman, Linda M Baldini, Fatima R Muriel, Bernadette Sullivan, David S Yassa, Howard S Gold, Trevor K Wagner, Daniel J Diekema, Sharon B Wright
Candida guilliermondii was isolated from sterile specimens with increasing frequency over a several-month period despite a paucity of clinical evidence suggesting true Candida infections. However, a healthcare-associated outbreak was strongly considered due to growth patterns in the microbiology laboratory more consistent with true infection than environmental contamination. Therefore, an extensive investigation was performed to identify its cause. With the exception of one case, patient clinical courses were not consistent with true invasive fungal infections...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100596/genomic-epidemiology-of-penicillin-non-susceptible-pneumococci-with-non-vaccine-serotypes-causing-invasive-disease-in-the-usa
#7
Cheryl P Andam, Patrick K Mitchell, Alanna Callendrello, Qiuzhi Chang, Jukka Corander, Chrispin Chaguza, Lesley McGee, Bernard W Beall, William P Hanage
Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic resistant strains throughout the 2000s; however, disease caused by resistant non-vaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with 581 isolates from 2012-2013, collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC)...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100595/determinants-of-viral-oncogenes-e6-e7-mrna-over-expression-in-a-population-based-large-sample-of-women-infected-by-high-risk-hpv-types
#8
Paolo Giorgi Rossi, Simonetta Bisanzi, Elena Allia, Alessandra Mongia, Francesca Carozzi, Anna Gillio-Tos, Laura De Marco, Guglielmo Ronco, Daniela Gustinucci, Annarosa Del Mistro, Helena Frayle, Anna Iossa, Giulia Fantacci, Giampaolo Pompei, Elena Cesarini, Simonetta Bulletti, Basilio Passamonti, Martina Rizzi, Maria Gabriella Penon, Alessandra Barca, Maria Benevolo
Cervical cancer screening by HPV-DNA testing with cytology triage is more effective than cytology testing. Compared to cytology, the HPV-DNA test higher sensitivity, that allows better protection with longer intervals, makes it necessary to triage the women with a positive result to compensate its lower specificity.We are conducting a large randomized clinical trial (New Technologies for Cervical Cancer 2, NTCC2) within organized population-based screening programs in Italy using HPV-DNA as primary screening test, to evaluate, by Aptima HPV Assay (Hologic), HPV E6-E7 mRNA as triage test in comparison to cytology...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100594/rapid-aminoglycoside-np-test-for-rapid-detection-of-multiple-aminoglycoside-resistance-in-enterobacteriaceae
#9
Patrice Nordmann, Aurélie Jayol, Jan Dobias, Laurent Poirel
The Rapid Aminoglycoside NP (Nordmann/Poirel) test was developed to rapidly identify multiple aminoglycoside (AG) resistance in Enterobacteriaceae It is based on the detection of the glucose metabolism related to enterobacterial growth in presence of a defined concentration of amikacin plus gentamicin. Formation of acid metabolites was evidenced by a color change (orange to yellow) of the red phenol pH indicator. The Rapid Aminoglycoside NP test was evaluated by using bacterial colonies of 18 AG-resistant isolates producing 16S rRNA methylases, 20 AG-resistant isolates expressing AG-modifying enzymes (acetyl, adenyl and phospho transferases), and 10 isolates susceptible to AG...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077701/a-comparison-of-eleven-phenotypic-assays-for-the-accurate-detection-of-carbapenemase-producing-enterobacteriaceae
#10
Pranita D Tamma, Belita N A Opene, Andrew Gluck, Krizia K Chambers, Karen C Carroll, Patricia J Simner
BACKGROUND: Early identification of carbapenemase-producing Enterobacteriaceae (CPE) is essential to prevent their dissemination within healthcare settings. Our objective was to evaluate the accuracy of 11 phenotypic assays for the detection of CPE. METHODS: Two collections of carbapenem-resistant Enterobacteriaceae (CRE) isolates were evaluated including 191 retrospective isolates (122 CP-CRE and 69 non-CP isolates) as well as 45 prospective clinical isolates (15 CP-CRE and 30 non-CP-CRE) obtained over a 3-month period...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077700/evaluation-of-alere%C3%A2-i-rsv-for-rapid-detection-of-respiratory-syncytial-virus-in-children-hospitalized-with-acute-respiratory-tract-infection
#11
Rebecca Marie Peters, Sarah Valerie Schnee, Julia Tabatabai, Paul Schnitzler, Johannes Pfeil
Alere™ i RSV is a novel rapid test which applies a nicking enzyme amplification reaction to detect respiratory syncytial virus in point-of-care settings. In this study, we evaluated the Alere™ i RSV assay by using frozen nasopharyngeal swab samples that were collected in viral transport medium from children hospitalized with acute respiratory tract infection during winter season 2015/2016. Alere™ i RSV assay test results were compared to Altona® RealStar RSV real-time reverse transcription PCR (RT-PCR)...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077699/antimicrobial-susceptibility-patterns-among-a-large-nationwide-cohort-of-abiotrophia-and-granulicatella-clinical-isolates
#12
Kunatum Prasidthrathsint, Mark A Fisher
Antimicrobial susceptibility patterns from 599 A. defectiva, G. adiacens and G. elegans clinical isolates were determined by broth microdilution. We observed significant differences in susceptibility across species, particularly to penicillin and ceftriaxone, and across geographical regions. A. defectiva was the least susceptible species overall to penicillin. All isolates were susceptible to vancomycin and >90% were susceptible to levofloxacin.
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077698/detection-of-antigenic-variants-of-swine-subtype-h3-influenza-a-viruses-from-clinical-samples
#13
Brigitte E Martin, Andrew S Bowman, Lei Li, Jacqueline M Nolting, David R Smith, Larry A Hanson, Xiu-Feng Wan
A large population of genetically and antigenically diverse influenza A viruses (IAVs) are circulating among the swine population, playing an important role in influenza ecology. Swine IAVs not only cause outbreaks among swine, but they can also be transmitted to humans, causing sporadic infections and even pandemic outbreaks. Antigenic characterization of swine IAVs are key to understanding the natural history of these viruses in swine and to selecting strains for effective vaccines. However, influenza outbreaks generally spread rapidly among swine, and the conventional methods for antigenic characterization require virus propagation, a time-consuming process that can significantly reduce the effectiveness of vaccination programs...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077697/point-counterpoint-what-is-the-optimal-approach-for-detection-of-clostridium-difficile-infection
#14
Ferric C Fang, Christopher R Polage, Mark H Wilcox
In 2010, we published an initial point-counterpoint on laboratory diagnosis of C. difficile infection (CDI). At that time, nucleic acid amplification tests (NAATs) were just becoming commercially available, and the idea of algorithmic approaches to CDI was being explored. Now there are numerous NAATs in the marketplace and based on recent proficiency test surveys, they have become the predominant method used for CDI diagnosis in the United States. At the same time, there is a body of literature that suggests that NAATs lack clinical specificity and thus inflate CDI rates...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077696/a-new-development-in-trypanosoma-cruzi-diagnosis
#15
Herbert B Tanowitz, Louis M Weiss
Chagas disease caused by the parasite, Trypanosoma cruzi is an important cause of morbidity and mortality in endemic areas of Latin America and among infected individuals who have migrated to non-endemic areas of North America and Europe. There are many diagnostic tests that are employed in the serological diagnosis of this infection. In this issue of the J Clin Microbiol 55: XXX-XXX http://dx.doi:10.1128/JCM.01649-16 by Bautista-López et al provide characterization of excretory vesicles (EV) from Vero cells infected with T...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077695/stability-studies-on-dry-swabs-and-wet-mailed-swabs-for-the-detection-of-c-trachomatis-and-n-gonorrhoeae-in-the-aptima-assays
#16
Jeanne Moncada, Carey B Clark, Jeffrey Holden, Edward W Hook, Charlotte A Gaydos, Julius Schachter
The Aptima Combo2 (AC2) and Aptima CT (ACT) (Hologic Inc., San Diego, CA) are nucleic acid amplified tests (NAATs) that detect Chlamydia trachomatis (CT). AC2 also detects Neisseria gonorrhoeae (NG). Storage and temperature conditions may impact the utility of NAATs in some settings and screening programs. We evaluated specimen stability for use beyond the Aptima package insert temperature and duration of storage specifications (between 2° to 30°C, 60 days) in two studies: 1) dry CT seeded swabs were used with ACT after storage at 4°C, 23°C or 36°C for up to 84 days and 2) swabs seeded with CT and NG then placed in transport media were tested with AC2, after mailing via the U...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077694/laboratory-testing-of-donors-and-stool-for-fecal-microbiota-transplantation-for-recurrent-c-difficile-infection
#17
Michael H Woodworth, Emma M Neish, Nancy S Miller, Tanvi Dhere, Eileen M Burd, Cynthia Carpentieri, Kaitlin L Sitchenko, Colleen S Kraft
Fecal microbiota transplantation is an efficacious and inexpensive therapy for recurrent Clostridium difficile, yet its safety is thought to depend on appropriate fecal donor screening. FDA guidance for regulation of this procedure is in flux but screening and manufacture of fecal material from asymptomatic donors presents many challenges to clinical laboratories. This minireview summarizes FDA regulatory changes, principles of donor selection and recommended laboratory screening for fecal microbiota transplantation...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28053219/a-unique-capsule-locus-in-the-newly-designated-actinobacillus-pleuropneumoniae-serovar-16-and-development-of-a-diagnostic-pcr
#18
Janine T Bossé, Yanwen Li, Rita Sárközi, Marcelo Gottschalk, Øystein Angen, Katerina Nedbalcova, Andrew N Rycroft, László Fodor, Paul R Langford
Actinobacillus pleuropneumoniae causes pleuropneumonia, an economically significant, lung disease of pigs. Recently, isolates of A. pleuropneumoniae that were serologically distinct from the previously characterized 15 serovars were described, and a proposal put forward that they comprised a new serovar 16. Here we used whole genome sequencing of the proposed serovar 16 reference strain A-85/14 to confirm presence of a unique capsular polysaccharide biosynthetic locus. For molecular diagnostics, primers were designed from the capsule locus of A-85/14 and a PCR formulated that differentiated serovar 16 isolates from all 15 known serovars, and other common respiratory pathogenic/commensal bacteria of pigs...
January 4, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28053218/singleton-st382-an-emerging-clonal-group-of-listeria-monocytogenes-associated-with-three-multistate-outbreaks-linked-to-contaminated-stone-fruit-caramel-apples-and-leafy-green-salad
#19
Yi Chen, Yan Luo, James Pettengill, Ruth Timme, David Melka, Matthew Doyle, Alikeh Jackson, Mickey Parish, Thomas S Hammack, Marc Allard, Eric W Brown, Errol A Strain
Three multistate outbreaks between 2014 and 2016, involving case patients in and outside the United States, were linked to stone fruit, caramel apples and packaged leafy green salad contaminated with Listeria monocytogenes singleton ST382. Isolates from these outbreaks and other ST382 isolates not associated with these outbreaks were analyzed by whole genome sequencing (WGS) analysis. The primary difference among these three ST382 outbreak strains were single nucleotide polymorphisms (SNPs). WGS analysis using these SNPs differentiated ST382 from a clonal complex 1 outbreak strain co-contaminating the caramel apples...
January 4, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28053217/high-interlaboratory-reproducibility-and-accuracy-of-next-generation-sequencing-based-bacterial-genotyping-in-a-ring-trial
#20
Alexander Mellmann, Paal Skytt Andersen, Stefan Bletz, Alexander W Friedrich, Thomas A Kohl, Berit Lilje, Stefan Niemann, Karola Prior, John W Rossen, Dag Harmsen
Today, next-generation whole genome sequencing (WGS) technology is increasingly used to determine the genetic relationship of bacteria on a nearly whole genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring-trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing.The participating laboratories sequenced 20 blind-coded Staphylococcus aureus DNA samples using the 250 bp paired-end chemistry for library preparation in a single sequencing run on an Illumina Miseq sequencer...
January 4, 2017: Journal of Clinical Microbiology
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