The utility and public health implications of PCR and whole genome sequencing for the detection and investigation of an outbreak of Shiga toxin-producing Escherichia coli serogroup O26:H11

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Outbreaks of non-O157 Shiga toxin-producing Escherichia coli infection: USA

(2014) R. E. LUNA-GIERKE et al.   EPIDEMIOLOGY AND INFECTION

Prevalences of Shiga Toxin Subtypes and Selected Other Virulence Factors among Shiga-Toxigenic Escherichia coli Strains Isolated from Fresh Produce

(2013) Peter C. H. Feng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enterohemorrhagic Escherichia coli O26:H11/H−: A New Virulent Clone Emerges in Europe

(2013) Martina Bielaszewska et al.   CLINICAL INFECTIOUS DISEASES

Duration of shedding of Verocytotoxin-producing Escherichia coli in children and risk of transmission in childcare facilities in England

(2013) G. DABKE et al.   EPIDEMIOLOGY AND INFECTION

Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK

(2013) J. McDONNELL et al.   EPIDEMIOLOGY AND INFECTION

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Universal extraction method for gastrointestinal pathogens

(2013) F. D. Halstead et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Shiga Toxin-Producing Escherichia coli O157 Is More Likely to Lead to Hospitalization and Death than Non-O157 Serogroups – Except O104

(2013) Karina Preußel et al.   PLoS One

Short read sequence typing (SRST): multi-locus sequence types from short reads

(2012) Michael Inouye et al.   BMC GENOMICS

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

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

Assessment of a real-time PCR for the detection and characterization of verocytotoxigenic Escherichia coli

(2012) C. Jenkins et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Application of the Modular Approach to an In-House Validation Study of Real-Time PCR Methods for the Detection and Serogroup Determination of Verocytotoxigenic Escherichia coli

(2011) Dafni-Maria Kagkli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Epidemic Profile of Shiga-Toxin–ProducingEscherichia coliO104:H4 Outbreak in Germany

(2011) Christina Frank et al.   NEW ENGLAND JOURNAL OF MEDICINE

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Methods for Genotyping Verotoxin-Producing Escherichia coli

(2009) M. Karama et al.   Zoonoses and Public Health