P. M. Ashton, S. Nair, T. M. Peters, J. A. Bale, D. G. Powell et al., Identification of Salmonella for public health surveillance using whole genome sequencing, Jenkins, C. & other authors PeerJ, vol.4, 1752.

A. V. Alekseyenko, Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty, Mol Biol Evol, vol.29, pp.2157-2167, 2012.

G. Baele, W. L. Li, A. J. Drummond, M. A. Suchard, and P. Lemey, Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics, Molecular Biology and Evolution, vol.30, issue.2, pp.239-243, 2013.
DOI : 10.1093/molbev/mss243

A. Bankevich, S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin et al., SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012.
DOI : 10.1089/cmb.2012.0021

M. K. Bhan, R. Bahl, and S. Bhatnagar, Typhoid and paratyphoid fever, The Lancet, vol.366, issue.9487, pp.749-762, 2005.
DOI : 10.1016/S0140-6736(05)67181-4

C. Eucast, Comité de l'Antibiogramme de la Société Française de Microbiologie Recommandations 2014, 2014.

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

A. J. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, 2007.
DOI : 10.1186/1471-2148-7-214
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2247476

M. C. Judd, J. E. Grass, E. D. Mintz, A. Bicknese, and B. E. Mahon, Paratyphi A Infections in Travelers Returning from Cambodia, United States, Emerging Infectious Diseases, vol.21, issue.6, pp.1089-1091, 2015.
DOI : 10.3201/eid2106.150088

A. Karkey, C. N. Thompson, T. Vu-thieu, N. Dongol, S. Le-thi-phuong et al., Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: a matched case control investigation in a highly endemic enteric fever setting Fast gapped-read alignment with Bowtie 2, & other authors PLoS Negl Trop Dis e2391. Langmead, B. & Salzberg, S. L. Nat Methods, vol.7, issue.9, pp.357-359, 2012.

L. Hello, S. Harrois, D. Bouchrif, B. Sontag, L. Elhani et al., Highly drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a microbiological study, The Lancet Infectious Diseases, vol.13, issue.8, pp.672-679, 2013.
DOI : 10.1016/S1473-3099(13)70124-5
URL : https://hal.archives-ouvertes.fr/pasteur-01109890

F. M. Aarestrup, Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica, PLoS One, vol.9, p.87991, 2014.

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

M. Mcclelland, K. E. Sanderson, S. W. Clifton, P. Latreille, S. Porwollik et al., Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid, Nature Genetics, vol.60, issue.12, pp.1268-1274, 2004.
DOI : 10.1128/JB.184.9.2411-2419.2002

A. E. Newton, J. A. Routh, and B. E. Mahon, Infectious diseases related to travel: typhoid & paratyphoid fever, CDC Health Information for International Travel, 2016.

R. L. Ochiai, X. Wang, L. Von-seidlein, J. Yang, Z. A. Bhutta et al., Paratyphi A Rates, Asia, Emerging Infectious Diseases, vol.11, issue.11, pp.1764-1766, 2005.
DOI : 10.3201/eid1111.050168
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367370

E. M. Ribot, M. A. Fair, R. Gautom, D. N. Cameron, S. B. Hunter et al., for PulseNet, Foodborne Pathogens and Disease, vol.3, issue.1, pp.59-67, 2006.
DOI : 10.1089/fpd.2006.3.59

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

P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, and M. Chandler, ISfinder: the reference centre for bacterial insertion sequences, Nucleic Acids Research, vol.34, issue.90001, pp.32-36, 2006.
DOI : 10.1093/nar/gkj014
URL : https://hal.archives-ouvertes.fr/hal-00021179

C. S. Teh, K. H. Chua, and K. L. Thong, Paratyphoid Fever: Splicing the Global Analyses, International Journal of Medical Sciences, vol.11, issue.7, pp.732-741, 2014.
DOI : 10.7150/ijms.7768

M. Tourdjman, L. Hello, S. Gossner, C. Delmas, G. Tubiana et al., Unusual increase in reported cases of paratyphoid A fever among travellers returning from Cambodia, Fruth, A. & other authors, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01109921

E. Vlieghe, T. Phe, D. Smet, B. Veng, C. H. Kham et al., Increase in Salmonella enterica serovar Paratyphi A infections in Phnom Penh, Cambodia, Thai, S. & other authors, 2011.

A. M. Vollaard, S. Ali, H. A. Van-asten, S. Widjaja, L. G. Visser et al., Risk Factors for Typhoid and Paratyphoid Fever in Jakarta, Indonesia, JAMA, vol.291, issue.21, pp.2607-2615, 2004.
DOI : 10.1001/jama.291.21.2607

F. X. Weill, S. Bertrand, F. Guesnier, S. Baucheron, A. Cloeckaert et al., Kentucky in Travelers, Emerging Infectious Diseases, vol.12, issue.10, pp.1611-1612, 2006.
DOI : 10.3201/eid1210.060589

M. Yan, B. Yang, Z. Wang, S. Wang, X. Zhang et al., A large-scale communitybased outbreak of paratyphoid fever caused by hospital-derived transmission in Southern China, & other authors PLoS Negl Trop Dis, vol.9, p.3859, 2015.

&. Achtman and M. , Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever, Proc Natl Acad Sci, vol.111, pp.12199-12204, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01104820