Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk

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

The epidemiology, microbiology and clinical impact of Shiga toxin-producing Escherichia coli in England, 2009–2012

(2015) L. BYRNE et al.   EPIDEMIOLOGY AND INFECTION

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

(2015) Philip M. Ashton et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Epidemiology and microbiology of Shiga toxin-producing Escherichia coli other than serogroup O157 in England, 2009-2013

(2014) L. Byrne et al.   JOURNAL OF MEDICAL MICROBIOLOGY

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

Sale of Raw Milk in Northern Italy: Food Safety Implications and Comparison of Different Analytical Methodologies for Detection of Foodborne Pathogens

(2012) Federica Giacometti et al.   Foodborne Pathogens and Disease

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

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

Shiga toxin-producingEscherichia colifrom raw milk cheese in Egypt: prevalence, molecular characterization and survival to stress conditions

(2012) M. Elhadidy et al.   LETTERS IN APPLIED MICROBIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Heng Li et al.   BIOINFORMATICS

Outbreak ofEscherichia coliO157 Associated with Raw Milk, Connecticut, 2008

(2010) Alice Guh et al.   CLINICAL INFECTIOUS DISEASES

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

(2010) A. McKenna et al.   GENOME RESEARCH

Verocytotoxigenic Escherichia coli O157 in animals on public amenity premises in England and Wales, 1997 to 2007

(2010) G. C. Pritchard et al.   VETERINARY RECORD