B. Coburn, G. Grassl, and B. Finlay, Salmonella, the host and disease: a brief review, Immunology and Cell Biology, vol.67, issue.2, pp.112-118, 2007.
DOI : 10.1038/sj.icb.7100007

A. Patrick and F. Grimont, Antigenic formulae of the Salmonella serovars, WHO Collab Cent Ref Res Salmonella, 2007.

C. Parry, T. Hien, G. Dougan, N. White, and J. Farrar, Typhoid Fever, New England Journal of Medicine, vol.347, issue.22, pp.1770-1782, 2002.
DOI : 10.1056/NEJMra020201

G. Dougan and S. Baker, Serovar Typhi and the Pathogenesis of Typhoid Fever, Annual Review of Microbiology, vol.68, issue.1, pp.317-336, 2014.
DOI : 10.1146/annurev-micro-091313-103739

W. Rabsch, H. Andrews, R. Kingsley, R. Prager, and H. Tschape, Salmonella enterica Serotype Typhimurium and Its Host-Adapted Variants, Infection and Immunity, vol.70, issue.5, pp.2249-2255, 2002.
DOI : 10.1128/IAI.70.5.2249-2255.2002
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC127920

M. Achtman, W. J. Weill, F. Nair, S. Zhou, and Z. , Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica, PLoS Pathogens, vol.59, issue.6, p.22737074, 2012.
DOI : 10.1371/journal.ppat.1002776.s017
URL : https://hal.archives-ouvertes.fr/pasteur-01117433

S. Porwollik, R. Wong, and M. Mcclelland, Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis, Proceedings of the National Academy of Sciences, vol.99, issue.13, pp.8956-8961, 2002.
DOI : 10.1073/pnas.122153699

K. Chan, S. Baker, C. Kim, C. Detweiler, and G. Dougan, Genomic Comparison of Salmonella enterica Serovars and Salmonella bongori by Use of an S. enterica Serovar Typhimurium DNA Microarray, Journal of Bacteriology, vol.185, issue.2, pp.553-563, 2003.
DOI : 10.1128/JB.185.2.553-563.2003

P. Roumagnac, F. Weill, C. Dolecek, S. Baker, and S. Brisse, Evolutionary History of Salmonella Typhi, Science, vol.314, issue.5803, pp.1301-1304, 2006.
DOI : 10.1126/science.1134933

C. Okoro, L. Barquist, T. Connor, S. Harris, and S. Clare, Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa, PLoS Negl Trop Dis, vol.9, p.25803844, 2015.

M. Arnold, C. Papadopoulou, R. Davies, J. Carrique-mas, and S. Evans, Estimation of Salmonella prevalence in UK egg-laying holdings, Preventive Veterinary Medicine, vol.94, issue.3-4, pp.306-309, 2010.
DOI : 10.1016/j.prevetmed.2010.01.004

T. Inns, C. Lane, T. Peters, T. Dallman, and C. Chatt, 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, Euro Surveill, vol.20, 2014.

R. Gajraj, S. Pooransingh, J. Hawker, and B. Olowokure, associated with consumption of iceberg lettuce, International Journal of Environmental Health Research, vol.33, issue.11, pp.150-155, 2012.
DOI : 10.1046/j.1469-0691.2000.00148.x

E. Ponce, A. Khan, C. Cheng, C. Summage-west, and C. Cerniglia, Prevalence and characterization of Salmonella enterica serovar Weltevreden from imported seafood, Food Microbiology, vol.25, issue.1, pp.29-35, 2008.
DOI : 10.1016/j.fm.2007.09.001

E. Galanis, D. Wong, M. Patrick, N. Binsztein, and A. Cieslik, Distribution, 2000???2002, Emerging Infectious Diseases, vol.12, issue.3, pp.381-16704773, 2000.
DOI : 10.3201/eid1205.050854

K. Emberland, S. Ethelberg, M. Kuusi, L. Vold, and L. Jensvoll, Outbreak of Salmonella Weltevreden infections in Norway, Denmark and Finland associated with alfalfa sprouts, Euro Surveill, vol.12, pp.71129-71133, 2007.

V. Wong, S. Baker, D. Pickard, J. Parkhill, and A. Page, Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events, Nature Genetics, vol.47, issue.6, pp.632-639, 2015.
DOI : 10.1128/AAC.02412-14

C. Okoro, R. Kingsley, T. Connor, S. Harris, and C. Parry, Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa, Nature Genetics, vol.4, issue.11, pp.1215-1221, 2012.
DOI : 10.1093/bioinformatics/btn529

V. Deekshit, K. Ballamoole, P. Rai, . Madhushankara, and I. Karunasagar, serovar Weltevreden Isolated from Seafood, Journal of Genomics, vol.3, pp.57-58, 2015.
DOI : 10.7150/jgen.11253
URL : http://doi.org/10.7150/jgen.11253

K. Brankatschk, J. Blom, A. Goesmann, T. Smits, and B. Duffy, Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars, International Journal of Food Microbiology, vol.155, issue.3, pp.247-256, 2012.
DOI : 10.1016/j.ijfoodmicro.2012.01.024

D. Wood and S. Salzberg, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biology, vol.15, issue.3, p.24580807, 2014.
DOI : 10.1186/1471-2105-12-385
URL : http://doi.org/10.1186/gb-2014-15-3-r46

H. Li, B. Handsaker, A. Wysoker, T. Fennell, and J. Ruan, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

D. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, 2008.
DOI : 10.1101/gr.074492.107
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801

M. Boetzer, C. Henkel, H. Jansen, D. Butler, and W. Pirovano, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, vol.27, issue.4, pp.578-579, 2011.
DOI : 10.1093/bioinformatics/btq683
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/27/4/578

M. Boetzer and W. Pirovano, Toward almost closed genomes with GapFiller, Genome Biology, vol.13, issue.6, p.22731987, 2012.
DOI : 10.1186/gb-2009-10-10-r103
URL : http://doi.org/10.1186/gb-2012-13-6-r56

D. Sommer, A. Delcher, S. Salzberg, and M. Pop, Minimus: a fast, lightweight genome assembler, BMC Bioinformatics, vol.8, issue.1, pp.64-17324286, 2007.
DOI : 10.1186/1471-2105-8-64
URL : http://doi.org/10.1186/1471-2105-8-64

M. Hunt, T. Kikuchi, M. Sanders, C. Newbold, and M. Berriman, REAPR: a universal tool for genome assembly evaluation, Genome Biology, vol.14, issue.5, p.23710727, 2013.
DOI : 10.1101/gr.092759.109
URL : http://doi.org/10.1186/gb-2013-14-5-r47

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, issue.14, pp.2068-2069, 2014.
DOI : 10.1093/bioinformatics/btu153

N. Croucher, A. Page, T. Connor, A. Delaney, and J. Keane, Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Research, vol.43, issue.3, p.25414349, 2015.
DOI : 10.1093/nar/gku1196

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014.
DOI : 10.1093/bioinformatics/btu033

H. Ashkenazy, O. Penn, A. Doron-faigenboim, O. Cohen, and G. Cannarozzi, FastML: a web server for probabilistic reconstruction of ancestral sequences, Nucleic Acids Research, vol.40, issue.W1, pp.580-584, 2012.
DOI : 10.1093/nar/gks498

L. Cheng, T. Connor, J. Siren, D. Aanensen, and J. Corander, Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software, Molecular Biology and Evolution, vol.30, issue.5, pp.1224-1228, 2013.
DOI : 10.1093/molbev/mst028

W. Mclaren, B. Pritchard, D. Rios, Y. Chen, and P. Flicek, Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor, Bioinformatics, vol.26, issue.16, pp.2069-2070, 2010.
DOI : 10.1093/bioinformatics/btq330

H. Harris, S. Mather, and A. , ARIBA: Antibiotic Resistance Identification By Assembly.: https://github, 2015.

W. Li and A. Godzik, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, issue.13, pp.1658-1659, 2006.
DOI : 10.1093/bioinformatics/btl158

S. Kurtz, A. Phillippy, A. Delcher, M. Smoot, and M. Shumway, Versatile and open software for comparing large genomes, Genome Biology, vol.5, issue.2, pp.12-14759262, 2004.
DOI : 10.1186/gb-2004-5-2-r12

A. Page, C. Cummins, M. Hunt, V. Wong, and S. Reuter, Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, 2015.
DOI : 10.1101/019315
URL : http://hdl.handle.net/10023/7563

A. Enright, S. Van-dongen, and C. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research, vol.30, issue.7, pp.1575-1584, 2002.
DOI : 10.1093/nar/30.7.1575

A. Loytynoja, Phylogeny-aware alignment with PRANK, Methods Mol Biol, vol.1079, pp.155-170, 2014.
DOI : 10.1007/978-1-62703-646-7_10

J. Yu, R. Rossi, C. Hale, D. Goulding, and G. Dougan, Interaction of Enteric Bacterial Pathogens with Murine Embryonic Stem Cells, Infection and Immunity, vol.77, issue.2, pp.585-597, 2009.
DOI : 10.1128/IAI.01003-08

C. Thompson, M. Phan, N. Hoang, P. Van-minh, and N. Vinh, A Prospective Multi-Center Observational Study of Children Hospitalized with Diarrhea in Ho Chi Minh City, Vietnam, American Journal of Tropical Medicine and Hygiene, vol.92, issue.5, pp.1045-1052, 2015.
DOI : 10.4269/ajtmh.14-0655

P. Leekitcharoenphon, O. Lukjancenko, C. Friis, F. Aarestrup, and D. Ussery, Genomic variation in Salmonella enterica core genes for epidemiological typing, BMC Genomics, vol.13, issue.1, p.22409488, 2012.
DOI : 10.1186/1471-2164-13-88

J. Han, A. Lynne, D. David, H. Tang, and J. Xu, DNA Sequence Analysis of Plasmids from Multidrug Resistant Salmonella enterica Serotype Heidelberg Isolates, PLoS ONE, vol.6, issue.12, p.23251446, 2012.
DOI : 10.1371/journal.pone.0051160.t001

M. Gilmour, N. Thomson, M. Sanders, J. Parkhill, and D. Taylor, The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics, Plasmid, vol.52, issue.3, pp.182-202, 2004.
DOI : 10.1016/j.plasmid.2004.06.006

E. Sumrall, E. Gallo, A. Aboderin, A. Lamikanra, and I. Okeke, Dissemination of the Transmissible Quinolone-Resistance Gene qnrS1 by IncX Plasmids in Nigeria, PLoS ONE, vol.194, issue.10, p.25340787, 2014.
DOI : 10.1371/journal.pone.0110279.t005

F. Cooke, D. Brown, M. Fookes, D. Pickard, and A. Ivens, Characterization of the Genomes of a Diverse Collection of Salmonella enterica Serovar Typhimurium Definitive Phage Type 104, Journal of Bacteriology, vol.190, issue.24, pp.8155-8162, 2008.
DOI : 10.1128/JB.00636-08

N. Thomson, S. Baker, D. Pickard, M. Fookes, and M. Anjum, The Role of Prophage-like Elements in the Diversity of Salmonella enterica Serovars, Journal of Molecular Biology, vol.339, issue.2, pp.279-300, 2004.
DOI : 10.1016/j.jmb.2004.03.058

L. Bullas, A. Mostaghimi, J. Arensdorf, P. Rajadas, and A. Zuccarelli, Salmonella phage PSP3, another member of the P2-like phage group, Virology, vol.185, issue.2, pp.414-1566584, 1992.
DOI : 10.1016/0042-6822(91)90573-T

A. Bishop, D. House, T. Perkins, S. Baker, and R. Kingsley, Interaction of Salmonella enterica serovar Typhi with cultured epithelial cells: roles of surface structures in adhesion and invasion, Microbiology, vol.154, issue.7, pp.1914-1926, 2008.
DOI : 10.1099/mic.0.2008/016998-0

O. Callaghan, D. Maskell, D. Liew, F. Easmon, C. Dougan et al., Characterization of aromatic-and purine-dependent Salmonella typhimurium: attention, persistence, and ability to induce protective immunity in BALB/c mice, Infect Immun, vol.56, pp.419-423, 1988.

M. Barthel, S. Hapfelmeier, L. Quintanilla-martinez, M. Kremer, and M. Rohde, Pretreatment of Mice with Streptomycin Provides a Salmonella enterica Serovar Typhimurium Colitis Model That Allows Analysis of Both Pathogen and Host, Infection and Immunity, vol.71, issue.5, pp.2839-2858, 2003.
DOI : 10.1128/IAI.71.5.2839-2858.2003

R. Kingsley, C. Msefula, N. Thomson, S. Kariuki, and K. Holt, Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype, Genome Research, vol.19, issue.12, 2009.
DOI : 10.1101/gr.091017.109

B. Antony, M. Dias, A. Shetty, and B. Rekha, serotype weltevreden in Mangalore, Indian Journal of Medical Microbiology, vol.27, issue.3, p.257, 2009.
DOI : 10.4103/0255-0857.53211
URL : http://doi.org/10.4103/0255-0857.53211

K. Holt, S. Baker, S. Dongol, B. Basnyat, and N. Adhikari, High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children, BMC Infect Dis, vol.10, p.20509974, 2010.

S. Baker, K. Holt, A. Clements, A. Karkey, and A. Arjyal, Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission, Open Biology, vol.361, issue.4, p.22645647, 2011.
DOI : 10.1056/NEJMoa0807521