K. Mulholland, Onsare 14 , Lupeoletalalelei Isaia 46 , Guy Thwaites 3

J. Crump, S. Luby, and E. Mintz, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge, United Kingdom References 1 The global burden of typhoid fever, Bull World Health Organ. Epub PMID, vol.8210, issue.5, pp.346-53, 2004.

J. Crump and E. Mintz, Global Trends in Typhoid and Paratyphoid Fever, Clinical Infectious Diseases, vol.50, issue.2, pp.241-247, 2010.
DOI : 10.1086/649541

V. Mogasale, B. Maskery, R. Ochiai, J. Lee, V. Mogasale et al., 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.570-80, 2014.
DOI : 10.1016/S2214-109X(14)70301-8

C. Parry, T. Hien, G. Dougan, N. White, and J. Farrar, Typhoid Fever, New England Journal of Medicine, vol.347, issue.22, pp.1770-82, 2002.
DOI : 10.1056/NEJMra020201

G. Enwere, E. Biney, Y. Cheung, S. Zaman, B. Okoko et al., Epidemiologic and Clinical Characteristics of Community-Acquired Invasive Bacterial Infections in Children Aged 2???29 Months in The Gambia, The Pediatric Infectious Disease Journal, vol.25, issue.8, pp.700-705, 2006.
DOI : 10.1097/01.inf.0000226839.30925.a5

J. Berkley, B. Lowe, I. Mwangi, T. Williams, E. Bauni et al., Bacteremia among Children Admitted to a Rural Hospital in Kenya, New England Journal of Medicine, vol.352, issue.1, pp.39-47, 2005.
DOI : 10.1056/NEJMoa040275

J. Isendahl, C. Manjuba, A. Rodrigues, W. Xu, B. Henriques-normark et al., Prevalence of community-acquired bacteraemia in Guinea-Bissau: an observational study, BMC Infectious Diseases, vol.7, issue.Suppl 2, pp.3859-4297428, 2014.
DOI : 10.1371/journal.pone.0051981

O. Arulogun, J. Adeniyi, S. Asa, and C. Adegbenro, Why Actions for Early Treatment of Febrile Illnesses in Children are Delayed by Caregivers, International Quarterly of Community Health Education, vol.87, issue.3, pp.219-250, 2011.
DOI : 10.2190/IQ.32.3.e

S. Obaro, F. Hassan-hanga, E. Olateju, D. Umoru, L. Lawson et al., Salmonella Bacteremia Among Children in Central and Northwest Nigeria, Clin Infect Dis, vol.61, issue.4, p.4596937, 2008.
DOI : 10.1093/cid/civ745

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596937

K. Holt, J. Parkhill, C. Mazzoni, P. Roumagnac, F. Weill et al., High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nature Genetics, vol.149, issue.8, pp.987-93, 2008.
DOI : 10.1186/gb-2004-5-2-r12

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652037

P. Roumagnac, F. Weill, C. Dolecek, S. Baker, S. Brisse et al., Evolutionary History of Salmonella Typhi, Science, vol.314, issue.5803, pp.1301-1305, 2006.
DOI : 10.1126/science.1134933

V. Wong, S. Baker, D. Pickard, J. Parkhill, A. Page et al., 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.632-641, 2015.
DOI : 10.1128/AAC.02412-14

T. Abuja, Available at: http://9ja-land.blogstop.com/2010/05/ abuja-beautiful-capital-city.html. Accessed, Beautiful Capital city, 2011.

S. Obaro, L. Lawson, U. Essen, I. K. Brooks, K. Otuneye et al., Community Acquired Bacteremia in Young Children from Central Nigeria- A Pilot Study, BMC Infectious Diseases, vol.86, issue.Suppl 2, p.3111365, 2011.
DOI : 10.2471/BLT.06.039818

F. Republic and N. Naftcoa, Available at: http://www.unaids.org/sites, Global AIDS Response Country Progress Report, 2014.

I. Olayemi, A. Ande, A. Ayanwale, A. Mohammed, I. Bello et al., Seasonal Trends in Epidemiological and Entomological Profiles of Malaria Transmission in North Central Nigeria, Pakistan Journal of Biological Sciences, vol.14, issue.4, pp.293-302, 2011.
DOI : 10.3923/pjbs.2011.293.299

P. Harris, R. Taylor, R. Thielke, J. Payne, N. Gonzalez et al., Research electronic data capture (REDCap)???A metadata-driven methodology and workflow process for providing translational research informatics support, Journal of Biomedical Informatics, vol.42, issue.2, pp.377-81, 2009.
DOI : 10.1016/j.jbi.2008.08.010

S. Herrera-leon, J. Mcquiston, M. Usera, P. Fields, J. Garaizar et al., Multiplex PCR for Distinguishing the Most Common Phase-1 Flagellar Antigens of Salmonella spp., Journal of Clinical Microbiology, vol.42, issue.6, pp.2581-2587, 2004.
DOI : 10.1128/JCM.42.6.2581-2586.2004

C. Fitzgerald, M. Collins, S. Van-duyne, M. Mikoleit, T. Brown et al., Multiplex, Bead-Based Suspension Array for Molecular Determination of Common Salmonella Serogroups, Journal of Clinical Microbiology, vol.45, issue.10, pp.3323-3357, 2007.
DOI : 10.1128/JCM.00025-07

N. Croucher, S. Harris, C. Fraser, M. Quail, J. Burton et al., Rapid Pneumococcal Evolution in Response to Clinical Interventions, Science, vol.331, issue.6016, pp.430-434, 2011.
DOI : 10.1126/science.1198545

J. Parkhill, G. Dougan, K. James, N. Thomson, D. Pickard et al., Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18, Nature, vol.413, issue.6858, pp.848-52, 2001.
DOI : 10.1038/35101607

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.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002

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, p.4330336, 2015.
DOI : 10.1093/nar/gku1196

A. Stamatakis and . Raxml-vi-, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-90, 2006.
DOI : 10.1093/bioinformatics/btl446

I. Letunic and P. Bork, Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, vol.23, issue.1, pp.127-135, 2007.
DOI : 10.1093/bioinformatics/btl529

I. Letunic and P. Bork, Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Research, vol.39, issue.suppl, pp.475-483, 2011.
DOI : 10.1093/nar/gkr201

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

URL : http://doi.org/10.1186/s13073-014-0090-6

S. Gupta, B. Padmanabhan, S. Diene, R. Lopez-rojas, M. Kempf et al., ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes, Antimicrobial Agents and Chemotherapy, vol.58, issue.1, pp.212-232, 2014.
DOI : 10.1128/AAC.01310-13

A. Carattoli, E. Zankari, A. Garcia-fernandez, M. Voldby-larsen, O. Lund et al., In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing, Antimicrobial Agents and Chemotherapy, vol.58, issue.7, pp.3895-903, 2014.
DOI : 10.1128/AAC.02412-14

D. Eaves, L. Randall, D. Gray, A. Buckley, M. Woodward et al., Prevalence of Mutations within the Quinolone Resistance-Determining Region of gyrA, gyrB, parC, and parE and Association with Antibiotic Resistance in Quinolone-Resistant Salmonella enterica, Antimicrobial Agents and Chemotherapy, vol.48, issue.10, pp.4012-4015, 2004.
DOI : 10.1128/AAC.48.10.4012-4015.2004

S. Baucheron, E. Chaslus-dancla, A. Cloeckaert, C. Chiu, and P. Butaye, High-Level Resistance to Fluoroquinolones Linked to Mutations in gyrA, parC, and parE in Salmonella enterica Serovar Schwarzengrund Isolates from Humans in Taiwan, Antimicrobial Agents and Chemotherapy, vol.49, issue.2, pp.862-865, 2005.
DOI : 10.1128/AAC.49.2.862-863.2005

D. Hooper, Quinolone Mode of Action - New Aspects???, Drugs, vol.45, issue.Supplement 3, pp.8-14, 1993.
DOI : 10.2165/00003495-199300453-00004

Y. Song, P. Roumagnac, F. Weill, W. J. Dolecek, C. Mazzoni et al., A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A, Journal of Antimicrobial Chemotherapy, vol.65, issue.8, pp.1631-1672, 2010.
DOI : 10.1093/jac/dkq175

URL : https://hal.archives-ouvertes.fr/pasteur-01134205

K. Holt, M. Phan, S. Baker, P. Duy, T. Nga et al., Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid, PLoS Neglected Tropical Diseases, vol.106, issue.7, p.3139670, 2011.
DOI : 10.1371/journal.pntd.0001245.s003

URL : https://hal.archives-ouvertes.fr/pasteur-01121725