M. W. Allard, Y. Luo, E. Strain, and J. Pettengill, On the Evolutionary History, Population Genetics and Diversity among Isolates of Salmonella Enteritidis PFGE Pattern JEGX01.0004, H143380471 Austria 2 ? Human H143380472 Austria 2 ? Human H143380473 Austria 2 ? Human H143380474 Austria 2 ? Human H143360568 France 2. & other authors (2013). On the evolutionary history population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004, p.55254
DOI : 10.1371/journal.pone.0055254.s001

P. Ashton, S. Nair, T. Peters, R. Tewolde, M. Day et al., Revolutionising public health reference microbiology using whole genome sequencing: Salmonella as an exemplar, A. & other authors, 2015.
DOI : 10.1101/033225

K. S. Baker, T. J. Dallman, P. M. Ashton, M. Day, G. Hughes et al., Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study, The Lancet Infectious Diseases, vol.15, issue.8, pp.913-921, 2015.
DOI : 10.1016/S1473-3099(15)00002-X

J. M. Bryant, D. M. Grogono, D. Greaves, J. Foweraker, I. Roddick et al., Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study, The Lancet, vol.381, issue.9877, pp.1551-1560, 2013.
DOI : 10.1016/S0140-6736(13)60632-7

N. J. Croucher, A. J. Page, T. R. Connor, A. J. Delaney, J. A. Keane et al., Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Research, vol.43, issue.3, p.15, 2015.
DOI : 10.1093/nar/gku1196

G. Csardi and T. Nepusz, The igraph software package for complex network research, InterJournal Complex Syst, vol.1695, pp.1-9, 2006.

T. J. Dallman, P. M. Ashton, L. Byrne, N. T. Perry, L. Petrovska et al., Whole genome sequencing for national surveillance of Shiga toxin producing Escherichia coli O157, A. & other authors Clin Infect Dis, vol.3, pp.305-312, 2015.

H. C. Den-bakker, M. W. Allard, D. Bopp, E. W. Brown, J. Fontana et al., Serovar Enteritidis, Emerging Infectious Diseases, vol.20, issue.8, pp.1306-1314, 2014.
DOI : 10.3201/eid2008.131399

X. Deng, P. T. Desai, H. C. Den-bakker, M. Mikoleit, B. Tolar et al., Serotype Enteritidis based on Population Structure of Prevalent Lineages, Emerging Infectious Diseases, vol.20, issue.9, pp.1481-1489, 2014.
DOI : 10.3201/eid2009.131095

S. Dray and A. Dufour, The ade4 package: implementing the duality diagram for ecologists, Journal of Statistical Software, vol.22, pp.1-20, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00434575

A. J. Drummond, M. A. Suchard, D. Xie, and A. Rambaut, Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, vol.29, issue.8, pp.1969-1973, 2012.
DOI : 10.1093/molbev/mss075
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408070

D. W. Eyre, M. L. Cule, D. J. Wilson, D. Griffiths, A. Vaughan et al., Diverse sources of C. difficile infection identified on wholegenome sequencing, Batty, E. M. & other authors N Engl J Med, vol.369, pp.1195-1205, 2013.

K. S. Harker, C. Lane, F. J. Gormley, and G. K. Adak, National outbreaks of Salmonella infection in the UK, 2000???2011, Epidemiology and Infection, vol.16, issue.03, pp.601-607, 2000.
DOI : 10.1017/S0950268810002281

S. R. Harris, E. J. Cartwright, M. E. Török, M. T. Holden, N. M. Brown et al., Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study, The Lancet Infectious Diseases, vol.13, issue.2, pp.130-136, 2013.
DOI : 10.1016/S1473-3099(12)70268-2

J. Hawkey, D. J. Edwards, K. Dimovski, L. Hiley, H. Billman-jacobe et al., Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm, BMC Genomics, vol.14, issue.1, 2013.
DOI : 10.1016/j.mimet.2004.06.014

T. R. Connor, S. R. Harris, and D. Fairley, Emergence and global spread of epidemic healthcare-associated Clostridium difficile, & other authors Nat Genet, vol.45, pp.109-113, 2013.

K. E. Holt, S. Baker, F. X. Weill, E. C. Holmes, A. Kitchen et al., Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe, Nature Genetics, vol.28, issue.9, pp.1056-1059, 2012.
DOI : 10.1186/1471-2164-9-75
URL : https://hal.archives-ouvertes.fr/pasteur-01117702

M. Hugas and P. Beloeil, Controlling Salmonella along the food chain in the European Union - progress over the last ten years, Eurosurveillance, vol.19, issue.19, 2014.
DOI : 10.2807/1560-7917.ES2014.19.19.20804

T. Inns, C. Lane, T. Peters, T. Dallman, C. Chatt 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, J. & other authors Euro Surveill, vol.20, 2014.

C. Jenkins, T. J. Dallman, N. Launders, C. Willis, L. Byrne et al., Public health investigation of two outbreaks of Shiga toxinproducing Escherichia coli O157 associated with consumption of watercress, & other authors Appl, vol.81, pp.3946-3952, 2015.

T. Jombart, F. Balloux, and S. Dray, adephylo: new tools for investigating the phylogenetic signal in biological traits, Bioinformatics, vol.26, issue.15, pp.1907-1909, 2010.
DOI : 10.1093/bioinformatics/btq292
URL : https://hal.archives-ouvertes.fr/hal-00539508

C. R. Lane, S. Lebaigue, O. B. Esan, A. A. Awofisyo, N. L. Adams et al., Salmonella enterica serovar Enteritidis, & other authors Emerg Infect Dis, vol.20, pp.1945-2011, 2014.

P. Legendre and L. F. Legendre, Numerical ecology, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00530195

H. Li and R. Durbin, Fast and accurate long-read alignment with Burrows???Wheeler transform, Bioinformatics, vol.26, issue.5, pp.589-595, 2010.
DOI : 10.1093/bioinformatics/btp698
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828108

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer Res, vol.27, pp.209-220, 1967.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data, Genome Research, vol.20, issue.9, pp.1297-1303, 2010.
DOI : 10.1101/gr.107524.110

E. Poirier, L. Watier, E. Espie, F. X. Weill, D. Valk et al., Evaluation of the impact on human salmonellosis of control measures targeted to Salmonella Enteritidis and Typhimurium in poultry breeding using time-series analysis and intervention models in France, Epidemiology and Infection, vol.28, issue.09, pp.1217-1224, 2008.
DOI : 10.1093/aje/kwf155

J. Quick, P. Ashton, S. Calus, C. Chatt, S. Gossain et al., Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, & other authors Genome Biol Bioinformatics, vol.16, issue.30, pp.1312-1313, 2014.

A. J. Taylor, V. Lappi, W. J. Wolfgang, P. Lapierre, M. J. Palumbo et al., Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection, Journal of Clinical Microbiology, vol.53, issue.10, pp.3334-3340, 2015.
DOI : 10.1128/JCM.01280-15

R. C. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2014.

V. Wuyts, S. Denayer, N. H. Roosens, W. Mattheus, S. Bertrand et al., Whole Genome Sequence Analysis of Salmonella Enteritidis PT4 Outbreaks from a National Reference Laboratory???s Viewpoint, PLoS Currents, vol.7, issue.1, p.248792, 2015.
DOI : 10.1371/currents.outbreaks.aa5372d90826e6cb0136ff66bb7a62fc