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

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

Application of multilocus variable number tandem repeat analysis to monitor Verocytotoxin-producingEscherichia coliO157 phage type 8 in England and Wales: emergence of a profile associated with a national outbreak

(2013) N. Perry et al.   JOURNAL OF APPLIED MICROBIOLOGY

Phylogenetically Related Argentinean and Australian Escherichia coli O157 Isolates Are Distinguished by Virulence Clades and Alternative Shiga Toxin 1 and 2 Prophages

(2012) Glen E. Mellor et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak

(2012) Matthew W Gilmour et al.   BMC GENOMICS

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

(2012) Marc W Allard et al.   BMC GENOMICS

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

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

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

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

(2012) Xavier Didelot et al.   GENOME BIOLOGY

Large outbreak of verocytotoxin-producing Escherichia coli O157 infection in visitors to a petting farm in South East England, 2009

(2011) C. IHEKWEAZU et al.   EPIDEMIOLOGY AND INFECTION

German Outbreak ofEscherichia coliO104:H4 Associated with Sprouts

(2011) Udo Buchholz et al.   NEW ENGLAND JOURNAL OF MEDICINE

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

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

(2010) Heng Li et al.   BIOINFORMATICS

Escherichia coli O157:H7: Animal Reservoir and Sources of Human Infection

(2010) Witold A. Ferens et al.   Foodborne Pathogens and Disease

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

(2010) A. McKenna et al.   GENOME RESEARCH

Escherichia coli O157

(2010) Hugh Pennington   LANCET

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS