Lane, CR, et al.
Salmonella enterica serovar Enteritidis, England and Wales, 1945–2011. Emerging Infectious Diseases
2014; 20: 1097–104.
O'Brien, SJ. The ‘decline and fall’ of nontyphoidal Salmonella in the United Kingdom. Clinical Infectious Diseases
2013; 56: 705–710.
Hugas, M, Beloeil, P. Controlling Salmonella along the food chain in the European Union – progress over the last ten years. Eurosurveillance
2014; 19: 20804.
EFSA and ECDC (European Food Safety Authority and European Centre for Disease Prevention and Control). The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2013. EFSA Journal
2015; 13: 3991.
Inns, T, et al.
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. Eurosurveillance
2015; 20: 21098.
Janmohamed, K, et al.
National outbreak of Salmonella Enteritidis phage type 14b in England, September to December 2009: case-control study. Eurosurveillance
Harker, KS, et al.
National outbreaks of Salmonella infection in the UK, 2000–2011. Epidemiology and Infection
2014; 142: 601–607.
Ashton, PM, et al.
Identification and typing of Salmonella for public health surveillance using whole genome sequencing. PeerJ
2015; 4: e1752.
Ashton, PM, et al. Revolutionising public health reference microbiology using whole genome sequencing: Salmonella as an exemplar. bioRxiv preprint 2015. doi:http://dx.doi.org/10.1101/033225.
Li, H, Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics
2010; 26: 589–595.
McKenna, A, et al.
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research
2010; 20: 1297–1303.
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics
2014; 30: 1312–1313.
Ward, LR, De Sa, JDH, Rowe, B. A phage-typing scheme for Salmonella Enteritidis. Epidemiology and Infection
1987; 99: 291–294.
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Csardi, G, Nepusz, T. The igraph software package for complex network research. InterJournal Complex Systems
Jombart, T, Dray, S. adephylo: exploratory analyses for the phylogenetic comparative method. Bioinformatics
2010; 26: 1907–1909.
Dray, S, Dufour, AB. The ade4 package: implementing the duality diagram for ecologists. Journal of Statistical Software
2007; 22: 1–20.
den Bakker, HC, et al.
Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar Enteritidis. Emerging Infectious Diseases
2014; 20: 1306–1314.
Leekitcharoenphon, P, et al.
Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS ONE
2014; 9: e87991.
Hoffmann, M, et al.
Tracing origins of the Salmonella Bareilly strain causing a food-borne outbreak in the United States. Journal of Infectious Diseases
2016; 213: 502–508.
Zheng, J, et al.
Enhanced subtyping scheme for Salmonella Enteritidis. Emerging Infectious Diseases
2007; 13: 1932–1935.
Boxrud, D, et al.
Comparison of multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and phage typing for subtype analysis of Salmonella enterica serotype Enteritidis. Journal of Clinical Microbiology
2007; 45: 536–543.
Yousaf, M, Chaudhry, A. History, changing scenarios and future strategies to induce moulting in laying hens. World's Poultry Science Journal
2008; 64: 65–75.
Carrique-Mas, JJ, et al.
Persistence and clearance of different Salmonella serovars in buildings housing laying hens. Epidemiology and Infection
2009; 137: 837–846.
Arnold, ME, Carrique-Mas, JJ, Davies, RH. Sensitivity of environmental sampling methods for detecting Salmonella Enteritidis in commercial laying flocks relative to the within-flock prevalence. Epidemiology and Infection
2010; 138; 330–339.
Davies, RH, Wales, AD. Developments in Salmonella control in eggs. In: Sofos, J, ed. Advances in Microbial Food Safety. Oxford, UK: Woodhead Publishing, 2015, pp. 281–311.
Dunn, JR. Whole-genome sequencing: opportunities and challenges for public health, food-borne outbreak investigations, and the global food supply. Journal of Infectious Diseases
2016; 213: 499–501.
Dallman, T, Inns, T, Jombart, T, et al.
Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network. Microbial Genomics. Published online 26 May 2016. doi:10.1099/mgen.0.000070.