WGS

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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
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
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

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
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

Bacteriology
Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory
Varvara K. Kozyreva, Chau-Linda Truong, Alexander L. Greninger, John Crandall, Rituparna Mukhopadhyay, Vishnu Chaturvedi
Mycobacteriology and Aerobic Actinomycetes
Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State
Joseph Shea, Tanya A. Halse, Pascal Lapierre, Matthew Shudt, Donna Kohlerschmidt, Patrick Van Roey, Ronald Limberger, Jill Taylor, Vincent Escuyer, Kimberlee A. Musser
Open Access

Clinical Veterinary Microbiology
Multilaboratory Survey To Evaluate Salmonella Prevalence in Diarrheic and Nondiarrheic Dogs and Cats in the United States between 2012 and 2014
Renate Reimschuessel, Michael Grabenstein, Jake Guag, Sarah M. Nemser, Kyunghee Song, Junshan Qiu, Kristin A. Clothier, Barbara A. Byrne, Stanley L. Marks, Kyran Cadmus, Kristy Pabilonia, Susan Sanchez, Sreekumari Rajeev, Steve Ensley, Timothy S. Frana, Albert E. Jergens, Kimberly H. Chappell, Siddhartha Thakur, Beverly Byrum, Jing Cui, Yan Zhang, Matthew M. Erdman, Shelley C. Rankin, Russell Daly, Seema Das, Laura Ruesch, Sara D. Lawhon, Shuping Zhang, Timothy Baszler, Dubraska Diaz-Campos, Faye Hartmann, Ogi Okwumabua

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