Validation of Whole-Genome Sequencing for Identification and Characterization of Shiga Toxin-Producing Escherichia coli To Produce Standardized Data To Enable Data Sharing

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

(2017) Celine Nadon et al.   Eurosurveillance

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory

(2017) Varvara K. Kozyreva et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial

(2017) Alexander Mellmann et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multiplex polymerase chain reaction for identification of Escherichia coli , Escherichia albertii and Escherichia fergusonii

(2017) Rebecca L. Lindsey et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Antimicrobial resistance in Shiga toxin-producingEscherichia coliserogroups O157 and O26 isolated from human cases of diarrhoeal disease in England, 2015

(2016) Martin Day et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

(2016) Marie A. Chattaway et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) in the United States

(2016) Rebecca L. Lindsey et al.   Frontiers in Microbiology

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks

(2016) Brigida Rusconi et al.   Frontiers in Microbiology

Whole Genome Sequencing for Public Health Surveillance of Shiga Toxin-Producing Escherichia coli Other than Serogroup O157

(2016) Marie A. Chattaway et al.   Frontiers in Microbiology

MOST: a modified MLST typing tool based on short read sequencing

(2016) Rediat Tewolde et al.   PeerJ

Identification ofSalmonellafor public health surveillance using whole genome sequencing

(2016) Philip M. Ashton et al.   PeerJ

Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress

(2015) Claire Jenkins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Whole-Genome Sequencing for National Surveillance of Shiga Toxin–ProducingEscherichia coliO157

(2015) Timothy J. Dallman et al.   CLINICAL INFECTIOUS DISEASES

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

(2015) Katrine G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance

(2015) Anne Holmes et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Insight into Shiga toxin genes encoded byEscherichia coliO157 from whole genome sequencing

(2015) Philip M. Ashton et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Inter-laboratory comparison of multi-locus variable-number tandem repeat analysis (MLVA) for verocytotoxin-producing Escherichia coli O157 to facilitate data sharing

(2014) A. HOLMES et al.   EPIDEMIOLOGY AND INFECTION

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

(2014) T. A. Kohl et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

(2014) K. G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Precise Dissection of an Escherichia coli O157:H7 Outbreak by Single Nucleotide Polymorphism Analysis

(2013) G. Turabelidze et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

(2012) Anthony P. Underwood et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multicenter Evaluation of a Sequence-Based Protocol for Subtyping Shiga Toxins and Standardizing Stx Nomenclature

(2012) F. Scheutz et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genomic anatomy of Escherichia coli O157:H7 outbreaks

(2011) M. Eppinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multistate outbreak of Escherichia coli O157:H7 infections associated with a national fast-food chain, 2006: a study incorporating epidemiological and food source traceback results

(2010) S. V. SODHA et al.   EPIDEMIOLOGY AND INFECTION

Hemolytic Uremic Syndrome and Death in Persons withEscherichia coliO157:H7 Infection, Foodborne Diseases Active Surveillance Network Sites, 2000–2006

(2009) L. Hannah Gould et al.   CLINICAL INFECTIOUS DISEASES

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY