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Journal of Clinical Microbiology
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WGS

  • Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of <em>Clostridioides difficile</em>
    Bacteriology
    Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of Clostridioides difficile

    Multilocus sequence typing (MLST) is a low-resolution but rapid genotyping method for Clostridioides difficile. Whole-genome sequencing (WGS) has emerged as the new gold standard for C. difficile typing, but cost and lack of standardization still limit broad utilization. In this study, we evaluated...

    Mini Kamboj, Tracy McMillen, Mustafa Syed, Hoi Yan Chow, Krupa Jani, Anoshe Aslam, Jennifer Brite, Brian Fanelli, Nur A. Hasan, Manoj Dadlani, Lars Westblade, Ahmet Zehir, Matthew Simon, N. Esther Babady
  • Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus
    Clinical Veterinary Microbiology
    Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic concern worldwide. There are currently large data sets available about the ORF5 gene of the virus, with thousands of sequences available, but little data are currently available on the full-length genome of PRRSV. We hypothesized that whole-genome sequencing (WGS) of the PRRSV genome would allow better epidemiological monitoring than ORF5 gene sequencing....

    Christian Lalonde, Chantale Provost, Carl A. Gagnon
  • Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: a Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Outbreak in a Neonatal Intensive Care Unit
    Epidemiology
    Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: a Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing Klebsiella pneumoniae Outbreak in a Neonatal Intensive Care Unit

    The IR Biotyper is a new automated typing system based on Fourier-transform infrared (FT-IR) spectroscopy that gives results within 4 h. We aimed (i) to use the IR Biotyper to retrospectively analyze an outbreak of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) in a neonatal intensive care unit and to compare results to BOX-PCR and whole-...

    Nadya Rakovitsky, Sammy Frenk, Hadas Kon, David Schwartz, Elizabeth Temkin, Ester Solter, Svetlana Paikin, Regev Cohen, Mitchell J. Schwaber, Yehuda Carmeli, Jonathan Lellouche
  • Open Access
    Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance
    Minireview
    Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance

    Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making.

    Ruth E. Timme, Errol Strain, Joseph D. Baugher, Steven Davis, Narjol Gonzalez-Escalona, Maria Sanchez Leon, Marc W. Allard, Eric W. Brown, Sandra Tallent, Hugh Rand
  • Epidemiological Typing of <span class="named-content genus-species" id="named-content-1">Serratia marcescens</span> Isolates by Whole-Genome Multilocus Sequence Typing
    Epidemiology
    Epidemiological Typing of Serratia marcescens Isolates by Whole-Genome Multilocus Sequence Typing

    Serratia marcescens is an opportunistic bacterial pathogen. It is notorious for its increasing antimicrobial resistance and its potential to cause outbreaks of colonization and infections, predominantly in neonatal intensive care units (NICUs).

    John W. A. Rossen, Jill Dombrecht, Diederik Vanfleteren, Katrien De Bruyne, Alex van Belkum, Sigrid Rosema, Mariette Lokate, Erik Bathoorn, Sandra Reuter, Hajo Grundmann, Julia Ertel, Paul G. Higgins, Harald Seifert
  • Prevalence and Characterization of Heterogeneous Variable-Number Tandem-Repeat Clusters Comprising Drug-Susceptible and/or Variable Resistant <span class="named-content genus-species" id="named-content-1">Mycobacterium tuberculosis</span> Complex Isolates in the Netherlands from 2004 to 2016
    Epidemiology
    Prevalence and Characterization of Heterogeneous Variable-Number Tandem-Repeat Clusters Comprising Drug-Susceptible and/or Variable Resistant Mycobacterium tuberculosis Complex Isolates in the Netherlands from 2004 to 2016

    The variable-number tandem-repeat (VNTR) typing method is used to study tuberculosis (TB) transmission. Clustering of Mycobacterium tuberculosis isolates with identical VNTR patterns is assumed to reflect recent transmission.

    Inge Roof, Rana Jajou, Miranda Kamst, Arnout Mulder, Albert de Neeling, Rianne van Hunen, Wim van der Hoek, Dick van Soolingen
  • Commentary
    Setup, Validation, and Quality Control of a Centralized Whole-Genome-Sequencing Laboratory: Lessons Learned

    Routine use of whole-genome analysis for infectious diseases can be used to enlighten various scenarios pertaining to public health, including identification of microbial pathogens, relating individual cases to an outbreak of infectious disease, establishing an association between an outbreak of food poisoning and a specific food vehicle, inferring drug susceptibility, source tracing of contaminants, and study of variations in the...

    Cath Arnold, Kirstin Edwards, Meeta Desai, Steve Platt, Jonathan Green, David Conway
  • Letter to the Editor
    CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli Based on the fumC and fimH Alleles
    Louise Roer, Thor Bech Johannesen, Frank Hansen, Marc Stegger, Veronika Tchesnokova, Evgeni Sokurenko, Natasha Garibay, Rosa Allesøe, Martin C. F. Thomsen, Ole Lund, Henrik Hasman, Anette M. Hammerum
  • Open Access
    Epidemiology
    A Predominant Variable-Number Tandem-Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole-Genome Sequencing
    Rana Jajou, Albert de Neeling, Erik Michael Rasmussen, Anders Norman, Arnout Mulder, Rianne van Hunen, Gerard de Vries, Walid Haddad, Richard Anthony, Troels Lillebaek, Wim van der Hoek, Dick van Soolingen
  • Open Access
    Mycobacteriology and Aerobic Actinomycetes
    Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping
    T. Phuong Quan, Zharain Bawa, Dona Foster, Tim Walker, Carlos del Ojo Elias, Priti Rathod, MMM Informatics Group, Zamin Iqbal, Phelim Bradley, Janet Mowbray, A. Sarah Walker, Derrick W. Crook, David H. Wyllie, Timothy E. A. Peto, E. Grace Smith

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