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

J. A. Crump and E. D. Mintz, Global Trends in Typhoid and Paratyphoid Fever, Clinical Infectious Diseases, vol.50, issue.2, pp.241-246, 2010.
DOI : 10.1086/649541
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798017

V. Mogasale, Burden of typhoid fever in low-income and middle-income countries: a systematic, literature-based update with risk-factor adjustment, The Lancet Global Health, vol.2, issue.10, pp.570-580, 2014.
DOI : 10.1016/S2214-109X(14)70301-8

B. Sen, Phage typing, biotyping & antimicrobial resistance profile of Salmonella enterica serotype Typhi from Kolkata, Indian J. Med. Res, vol.125, pp.685-688, 2007.

S. Kim, Serovar Typhi Isolates in Korea by PFGE, Ribotyping, and Phage Typing, Foodborne Pathogens and Disease, vol.6, issue.6, pp.733-738, 2009.
DOI : 10.1089/fpd.2008.0212

S. Dutta, Antimicrobial Resistance, Virulence Profiles and Molecular Subtypes of Salmonella enterica Serovars Typhi and Paratyphi A Blood Isolates from Kolkata, India during 2009-2013, PLoS ONE, vol.4, issue.7, p.101347, 2009.
DOI : 10.1371/journal.pone.0101347.t006

P. Roumagnac, Evolutionary History of Salmonella Typhi, Science, vol.314, issue.5803, pp.1301-1304, 2006.
DOI : 10.1126/science.1134933

S. Baker, High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia, Journal of Clinical Microbiology, vol.46, issue.5, pp.1741-1746, 2008.
DOI : 10.1128/JCM.02249-07

K. E. Holt, High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nature Genetics, vol.149, issue.8, pp.987-993, 2008.
DOI : 10.1186/gb-2004-5-2-r12

K. E. Holt, Temporal Fluctuation of Multidrug Resistant Salmonella Typhi Haplotypes in the Mekong River Delta Region of Vietnam, PLoS Neglected Tropical Diseases, vol.95, issue.No. 1, p.929, 2011.
DOI : 10.1371/journal.pntd.0000929.s003

K. E. Holt, High-throughput bacterial SNP typing identifies distinct clusters of SalmonellaTyphi causing typhoid in Nepalese children, BMC Infectious Diseases, vol.34, issue.4, p.144, 2010.
DOI : 10.1038/ng1470

S. Baker, Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission, Open Biology, vol.361, issue.4, p.110008, 2011.
DOI : 10.1056/NEJMoa0807521

K. E. Holt, Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid, PLoS Neglected Tropical Diseases, vol.106, issue.7, p.1245, 2011.
DOI : 10.1371/journal.pntd.0001245.s003
URL : https://hal.archives-ouvertes.fr/pasteur-01121725

V. K. Wong, 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

P. Thanh and D. , Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification

M. Baltazar, Serotype Typhi, Gulf of Guinea Region, Africa, Emerging Infectious Diseases, vol.21, issue.4, pp.655-659, 2015.
DOI : 10.3201/eid2104.141355
URL : https://hal.archives-ouvertes.fr/pasteur-01134243

F. Coll, A robust SNP barcode for typing Mycobacterium tuberculosis complex strains, Nature Communications, vol.5, p.4812, 2014.
DOI : 10.1080/10635150802429642

G. Morelli, Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity, Nature Genetics, vol.17, issue.12, pp.1140-1143, 2010.
DOI : 10.1128/JB.01786-08
URL : https://hal.archives-ouvertes.fr/pasteur-00836130

A. Holmes, Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance, Journal of Clinical Microbiology, vol.53, issue.11, pp.3565-3573, 2015.
DOI : 10.1128/JCM.01066-15

J. L. Gardy, Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak, New England Journal of Medicine, vol.364, issue.8, pp.730-739, 2011.
DOI : 10.1056/NEJMoa1003176

J. Corander, P. Marttinen, J. Siren, and J. Tang, Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations, BMC Bioinformatics, vol.9, issue.1, p.539, 2008.
DOI : 10.1186/1471-2105-9-539

D. M. Aanensen, ABSTRACT, mBio, vol.7, issue.3, 2016.
DOI : 10.1128/mBio.00444-16

. Public-health-england, Health Protection Report: Enteric fever surveillance quarterly report (England, Wales and Northern Ireland): first quarter 2015 Infection reports, 2015.

N. J. Croucher, Rapid Pneumococcal Evolution in Response to Clinical Interventions, Science, vol.331, issue.6016, pp.430-434, 2011.
DOI : 10.1126/science.1198545

J. Parkhill, Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18, Nature, vol.413, issue.6858, pp.848-852, 2001.
DOI : 10.1038/35101607

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

E. Paradis, J. Claude, and K. Strimmer, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

J. Corander and J. Tang, Bayesian analysis of population structure based on linked molecular information, Mathematical Biosciences, vol.205, issue.1, pp.19-31, 2007.
DOI : 10.1016/j.mbs.2006.09.015

N. Casali, Evolution and transmission of drug-resistant tuberculosis in a Russian population, Nature Genetics, vol.29, issue.3, pp.279-286, 2014.
DOI : 10.1183/09031936.00061808

P. R. Hunter, Reproducibility and indices of discriminatory power of microbial typing methods, J. Clin. Microbiol, vol.28, pp.1903-1905, 1990.

V. K. , S. B. , K. E. , G. D. Sequencing-data-generation:-a, J. A. et al., Data analysis: V Isolate acquisition and processing and clinical data collection: D, Author contributions Study design Manuscript writing: V.K.W., K.E.H. and G.D. All authors contributed to manuscript editing

V. K. Wong, An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid, Nature Communications, vol.28, pp.12827-12837, 2016.
DOI : 10.1038/ncomms12827
URL : https://hal.archives-ouvertes.fr/pasteur-01422000

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S. Obaro, Anthony M Smith 38 , Christopher M Parry 39,40 , Abhilasha Karkey 41 , Sabina Dongol 41 , Buddha Basnyat 41 , Amit Arjyal 41 , E Kim Mulholland 5,42 , James I Campbell 3,4 , Muriel Dufour 43 , Don Bandaranayake 44 , Take N Toleafoa 45 , Shalini Pravin Singh 46, Eric J Nilles, vol.3435361537, issue.54

L. School, P. Medicine, K. Place, and . Leuven, PO Box 43640-00100 18 Emory Global Health Institute, 1599 Clifton Road, NE 1599-001-1AH Department of Microbiology and Immunology, Belgium; 25 National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo Democratic Republic of the Congo; 27 Microbiology Department, College of Medicine, University of Malawi, Malawi Fiji; 30 Fiji Health Sector Support Program, PO Box 14986, Suva, Fiji; 31 National Institute of Cholera and Enteric Diseases, P-33 CIT Road Republic of Korea Division in the National Health Laboratory Service and Faculty of Health Sciences People's Democratic Republic, Faculty of Veterinary and Agricultural Sciences Division of Infection and Immunity Department of Clinical Sciences, Institute of Tropical Medicine Centre for Enteric Diseases, National Institute for Communicable Diseases New Zealand; 44 National Centre for Biosecurity and Infectious Disease National Influenza Center, World Health Organization, Center for Communicable Disease Control Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, p.1012827, 1038.