F. Kauffmann, Die bakteriologie der Salmonella-gruppe, E Munksgaard, 1941.

F. Kauffmann, Zur Differentialdiagnose und Pathogenit??t von Salmonella java und Salmonella paratyphi B, Zeitschrift f??r Hygiene und Infektionskrankheiten, vol.36, issue.6, pp.546-550, 1955.
DOI : 10.1007/BF02156850

L. Minor and L. , Typing ofSalmonella species, European Journal of Clinical Microbiology & Infectious Diseases, vol.128, issue.2, pp.214-218, 1988.
DOI : 10.1007/BF01963091

B. Malorny, C. Bunge, and H. R. , Discrimination of d-Tartrate-Fermenting and -Nonfermenting Salmonella enterica subsp. enterica Isolates by Genotypic and Phenotypic Methods, Journal of Clinical Microbiology, vol.41, issue.9, pp.4292-4297, 2003.
DOI : 10.1128/JCM.41.9.4292-4297.2003

E. Ezquerra, A. Burnens, C. Jones, and J. Stanley, Genotypic typing and phylogenetic analysis of Salmonella paratyphi B and S. Java with IS200, Journal of General Microbiology, vol.139, issue.10, pp.2409-2414, 1993.
DOI : 10.1099/00221287-139-10-2409

M. Achtman, W. J. Weill, F. Nair, S. Zhou, Z. Sangal et al., Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica, PLoS Pathogens, vol.59, issue.6, 2012.
DOI : 10.1371/journal.ppat.1002776.s017

URL : https://hal.archives-ouvertes.fr/pasteur-01117433

L. Fabre, J. Zhang, G. Guigon, L. Hello, S. Guibert et al., CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections, PLoS ONE, vol.59, issue.5, p.36995, 2012.
DOI : 10.1371/journal.pone.0036995.s011

URL : https://hal.archives-ouvertes.fr/hal-00762219

V. Sangal, H. Harbottle, C. Mazzoni, R. Helmuth, B. Guerra et al., Evolution and Population Structure of Salmonella enterica Serovar Newport, Journal of Bacteriology, vol.192, issue.24, pp.6465-6476, 2010.
DOI : 10.1128/JB.00969-10

URL : https://hal.archives-ouvertes.fr/pasteur-01133818

S. Francis, R. J. Rattenbury, K. Powell, D. Rogers, W. Ward et al., SUMMARY, Epidemiology and Infection, vol.10, issue.03, pp.445-448, 1989.
DOI : 10.1136/bmj.287.6402.1366

B. Doublet, K. Praud, T. Nguyen-ho-bao, M. Argudín, S. Bertrand et al., Extended-spectrum beta-lactamase-and Characterizing Invasive and Noninvasive S. enterica serotype Paratyphi B Strains, 2014.

C. Gaulin, C. Vincent, A. L. Ismail, and J. , Outbreak of Salmonella paratyphi B linked to aquariums in the province of Quebec, Can Commun Dis Rep, vol.28, pp.89-93, 2000.

J. Stratton, L. Stefaniw, K. Grimsrud, D. Werker, A. Ellis et al., Outbreak of Salmonella paratyphi B var java due to contaminated alfalfa sprouts in Alberta, British Columbia and Saskatchewan, Can Commun Dis Rep, vol.27, pp.133-137, 2001.

D. Centers, . Control, and . Prevention, Multistate outbreak of human Salmonella infections associated with exposure to turtles? United States, MMWR Morb Mortal Wkly Rep, vol.57, pp.69-72, 2007.

M. Kendall, S. Crim, K. Fullerton, P. Han, A. Cronquist et al., Travel-associated enteric infections diagnosed after return to the United States, Foodborne Diseases Active Surveillance Network (FoodNet, Clin Infect Dis, vol.54, pp.2004-2009, 2012.
DOI : 10.1093/cid/cis052

URL : http://cid.oxfordjournals.org/cgi/content/short/54/suppl_5/S480

M. Gobin, N. Launders, C. Lane, G. Kafatos, and B. Adak, National outbreak of Salmonella Java phage type 3b variant 9 infection using parallel case-control and case-case study designs, Euro Surveill, vol.16, 2010.

R. Davies, R. Deuchande, L. Larki, R. Collins, and R. Irvine, Multidrug resistant salmonella Java found in British broiler flocks, Vet Rec, vol.172, pp.617-618, 2013.
DOI : 10.1136/vr.f3664

F. Weill, L. Fabre, B. Grandry, P. Grimont, and I. Casin, Multiple-Antibiotic Resistance in Salmonella enterica Serotype Paratyphi B Isolates Collected in France between 2000 and 2003 Is Due Mainly to Strains Harboring Salmonella Genomic Islands 1, 1-B, and 1-C, Antimicrobial Agents and Chemotherapy, vol.49, issue.7, pp.2793-2801, 2005.
DOI : 10.1128/AAC.49.7.2793-2801.2005

A. Miko, K. Pries, A. Schroeter, and H. R. , Multiple-Drug Resistance in D-Tartrate-Positive Salmonella enterica Serovar Paratyphi B Isolates from Poultry Is Mediated by Class 2 Integrons Inserted into the Bacterial Chromosome, Antimicrobial Agents and Chemotherapy, vol.47, issue.11, pp.3640-3643, 2003.
DOI : 10.1128/AAC.47.11.3640-3643.2003

F. Brenner, R. Villar, F. Angulo, R. Tauxe, and B. Swaminathan, Salmonella nomenclature, J Clin Microbiol, vol.38, pp.2465-2467, 2000.

S. Issenhuth-jeanjean, P. Roggentin, M. Mikoleit, M. Guibourdenche, E. De-pinna et al., Supplement 2008???2010 (no. 48) to the White???Kauffmann???Le Minor scheme, Research in Microbiology, vol.165, issue.7, pp.526-530, 2008.
DOI : 10.1016/j.resmic.2014.07.004

URL : https://hal.archives-ouvertes.fr/pasteur-01104894

M. Pallen and B. Wren, Bacterial pathogenomics, Nature, vol.10, issue.7164, pp.835-842, 2007.
DOI : 10.1038/nature06248

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.459.6471

S. Fu, S. Octavia, M. Tanaka, V. Sintchenko, and R. Lan, Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing, Journal of Clinical Microbiology, vol.53, issue.8, pp.2530-253803407, 2015.
DOI : 10.1128/JCM.03407-14

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

L. Cheng, T. Connor, J. Sirén, 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

N. Thomson, D. Clayton, D. Windhorst, G. Vernikos, S. Davidson et al., Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways, Genome Research, vol.18, issue.10, pp.1624-1637, 2008.
DOI : 10.1101/gr.077404.108

F. Kauffmann, ON THE TRANSDUCTION OF SEROLOGICAL PROPERTIES IN THE SALMONELLA GROUP, Acta Pathologica Microbiologica Scandinavica, vol.64, issue.Suppl. IX, pp.409-420, 1953.
DOI : 10.1111/j.1699-0463.1953.tb01537.x

A. Trombert, L. Berrocal, J. Fuentes, and G. Mora, S. Typhimurium sseJ gene decreases the S. Typhi cytotoxicity toward cultured epithelial cells, BMC Microbiology, vol.10, issue.1, p.312, 2010.
DOI : 10.1186/1471-2180-10-312

URL : https://hal.archives-ouvertes.fr/hal-00303478

K. Geddes, M. Worley, G. Niemann, and F. Heffron, Identification of New Secreted Effectors in Salmonella enterica Serovar Typhimurium, Infection and Immunity, vol.73, issue.10, pp.6260-6271, 2005.
DOI : 10.1128/IAI.73.10.6260-6271.2005

R. Prager, W. Rabsch, W. Streckel, W. Voigt, E. Tietze et al., Molecular Properties of Salmonella enterica Serotype Paratyphi B Distinguish between Its Systemic and Its Enteric Pathovars, Journal of Clinical Microbiology, vol.41, issue.9, pp.4270-4278, 2003.
DOI : 10.1128/JCM.41.9.4270-4278.2003

S. Reuter, T. Connor, L. Barquist, D. Walker, T. Feltwell et al., Parallel independent evolution of pathogenicity within the genus Yersinia, Proceedings of the National Academy of Sciences, vol.111, issue.18, pp.6768-6773, 2014.
DOI : 10.1073/pnas.1317161111

E. Barrett and M. Clark, Tetrathionate reduction and production of hydrogen sulfide from thiosulfate, Microbiol Res, vol.51, pp.192-205, 1987.

S. Winter, P. Thiennimitr, M. Winter, B. Butler, D. Huseby et al., Gut inflammation provides a respiratory electron acceptor for Salmonella, Nature, vol.2, issue.7314, pp.426-429, 2010.
DOI : 10.1038/nature09415

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946174

A. Drummond, M. 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

Z. Zhou, A. Mccann, F. Weill, C. Blin, S. Nair et al., Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever, Proceedings of the National Academy of Sciences, vol.111, issue.33, pp.12199-12204, 2014.
DOI : 10.1073/pnas.1411012111

URL : https://hal.archives-ouvertes.fr/pasteur-01104820

C. Okoro, R. Kingsley, T. Connor, S. Harris, C. Parry et al., 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

A. Toboldt, E. Tietze, R. Helmuth, E. Junker, A. Fruth et al., Population Structure of Salmonella enterica Serovar 4,[5],12:b:- Strains and Likely Sources of Human Infection, Applied and Environmental Microbiology, vol.79, issue.17, pp.5121-512901735, 2013.
DOI : 10.1128/AEM.01735-13

M. Quail, M. Smith, P. Coupland, T. Otto, S. Harris et al., A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers, BMC Genomics, vol.13, issue.1, p.341, 2012.
DOI : 10.1186/1471-2164-13-341

D. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801

T. Otto, M. Sanders, M. Berriman, and C. Newbold, Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology, Bioinformatics, vol.26, issue.14, pp.1704-1707, 2010.
DOI : 10.1093/bioinformatics/btq269

J. Sahl, J. Caporaso, D. Rasko, and P. Keim, The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes, PeerJ, vol.28, issue.3, 2014.
DOI : 10.7717/peerj.332/supp-4

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

URL : http://doi.org/10.1093/nar/gkh340

S. Guindon, F. Delsuc, J. Dufayard, and O. Gascuel, Estimating Maximum Likelihood Phylogenies with PhyML, Methods Mol Biol, vol.537, pp.113-137978, 2009.
DOI : 10.1007/978-1-59745-251-9_6

URL : https://hal.archives-ouvertes.fr/lirmm-00511830

M. Inouye, H. Dashnow, L. Raven, M. Schultz, B. Pope et al., SRST2: Rapid genomic surveillance for public health and hospital microbiology labs, Genome Medicine, vol.202, issue.11, p.90, 2014.
DOI : 10.1186/s13073-014-0090-6

T. Connor, N. Loman, S. Thompson, A. Smith, J. Southgate et al., CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community, p.7064451, 2016.