Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis

A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014

(2015) T Inns et al.   Eurosurveillance

Whole-Genome Sequencing: Opportunities and Challenges for Public Health, Food-borne Outbreak Investigations, and the Global Food Supply

(2015) John R. Dunn   JOURNAL OF INFECTIOUS DISEASES

Tracing Origins of theSalmonellaBareilly Strain Causing a Food-borne Outbreak in the United States

(2015) Maria Hoffmann et al.   JOURNAL OF INFECTIOUS DISEASES

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Controlling Salmonella along the food chain in the European Union - progress over the last ten years

(2014) M Hugas et al.   Eurosurveillance

National outbreaks of Salmonella infection in the UK, 2000–2011

(2013) K. S. HARKER et al.   EPIDEMIOLOGY AND INFECTION

The "Decline and Fall" of Nontyphoidal Salmonella in the United Kingdom

(2012) S. J. O'Brien   CLINICAL INFECTIOUS DISEASES

adephylo: new tools for investigating the phylogenetic signal in biological traits

(2010) Thibaut Jombart et al.   BIOINFORMATICS

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

Sensitivity of environmental sampling methods for detecting Salmonella Enteritidis in commercial laying flocks relative to the within-flock prevalence

(2009) M. E. ARNOLD et al.   EPIDEMIOLOGY AND INFECTION

Persistence and clearance of different Salmonella serovars in buildings housing laying hens

(2008) J. J. CARRIQUE-MAS et al.   EPIDEMIOLOGY AND INFECTION

History, changing scenarios and future strategies to induce moulting in laying hens

(2008) M. YOUSAF et al.   WORLDS POULTRY SCIENCE JOURNAL