W. Geneva, Global tuberculosis report

S. Sharma and A. Mohan, Extrapulmonary tuberculosis, Indian J Med Res, vol.120, issue.4, pp.316-53, 2004.

C. Kang-'ombe, A. Harries, K. Ito, T. Clark, T. Nyirenda et al., Longterm outcome in patients registered with tuberculosis in Zomba, Malawi: mortality at 7 years according to initial HIV status and type of TB, Int J Tuberc Lung Dis, vol.8, issue.7, pp.829-865, 2004.

A. Fanning, Tuberculosis: 6. Extrapulmonary disease, CMAJ, vol.160, issue.11, pp.1597-603, 1999.

U. Handa, I. Mundi, and S. Mohan, Nodal tuberculosis revisited: a review, The Journal of Infection in Developing Countries, vol.6, issue.01, pp.6-12, 2012.
DOI : 10.3855/jidc.2090

M. Clinic, Tuberculosis treatment centre. Mulago Hospital TB clinic patient register, 2012.

K. Brudey, J. Driscoll, L. Rigouts, W. Prodinger, A. Gori et al., Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology, BMC Microbiol, vol.608, p.2303, 2006.

S. Gagneux, Genetic Diversity in Mycobacterium tuberculosis, Curr Top Microbiol Immunol, vol.16, p.16, 2013.
DOI : 10.1007/82_2013_329

J. Kamerbeek, L. Schouls, A. Kolk, M. Van-agterveld, D. Van-soolingen et al., Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology, J Clin Microbiol, vol.35, issue.401, pp.907-921, 1997.

B. Asiimwe, T. Koivula, G. Kallenius, R. Huard, S. Ghebremichael et al., Mycobacterium tuberculosis Uganda genotype is the predominant cause of TB in Kampala, Uganda, Int J Tuberc Lung Dis Off J Int Union Against Tuberc Lung Dis, vol.1229, issue.4, pp.386-9103, 2008.

D. Wamala, B. Asiimwe, E. Kigozi, G. Mboowa, M. Joloba et al., Clinicopathological features of tuberculosis due to Mycobacterium tuberculosis Uganda genotype in patients with tuberculous lymphadenitis: a cross sectional study, BMC Clin Pathol, vol.14, issue.1, pp.1472-6890, 2014.

R. Huard, L. Lazzarini, W. Butler, D. Van-soolingen, and J. Ho, PCR-Based Method To Differentiate the Subspecies of the Mycobacterium tuberculosis Complex on the Basis of Genomic Deletions, Journal of Clinical Microbiology, vol.41, issue.4, pp.1637-50, 2003.
DOI : 10.1128/JCM.41.4.1637-1650.2003

B. Springer, L. Stockman, K. Teschner, G. Roberts, and E. Bottger, Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods, J Clin Microbiol, vol.34, issue.2, pp.296-303, 1996.

C. Turenne, L. Tschetter, J. Wolfe, and A. Kabani, Necessity of Quality-Controlled 16S rRNA Gene Sequence Databases: Identifying Nontuberculous Mycobacterium Species, Journal of Clinical Microbiology, vol.39, issue.10, pp.3637-3685, 2001.
DOI : 10.1128/JCM.39.10.3638-3648.2001

J. Muhumuza, B. Asiimwe, S. Kayes, R. Mugyenyi, C. Whalen et al., Introduction of an in-house PCR for routine identification of M. tuberculosis in a low-income country, Int J Tuberc Lung Dis, vol.10, issue.11, pp.1262-1269, 2006.

J. Dale, D. Brittain, A. Cataldi, D. Cousins, J. Crawford et al., Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature, Int J Tuberc Lung Dis, vol.5, issue.3, pp.216-225, 2001.

C. Demay, B. Liens, T. Burguière, V. Hill, D. Couvin et al., SITVITWEB ??? A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology, Infection, Genetics and Evolution, vol.12, issue.4, pp.755-66, 2012.
DOI : 10.1016/j.meegid.2012.02.004

URL : https://hal.archives-ouvertes.fr/pasteur-00691750

J. Bazira, B. Asiimwe, M. Joloba, F. Bwanga, and M. Matee, Mycobacterium tuberculosis spoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in South-Western Uganda, BMC Infectious Diseases, vol.37, issue.4, p.81, 2011.
DOI : 10.1128/JCM.39.1.107-110.2001

R. Warren, E. Streicher, S. Sampson, G. Van-der-spuy, M. Richardson et al., Microevolution of the Direct Repeat Region of Mycobacterium tuberculosis: Implications for Interpretation of Spoligotyping Data, Journal of Clinical Microbiology, vol.40, issue.12, pp.4457-65, 2002.
DOI : 10.1128/JCM.40.12.4457-4465.2002

C. Sola, I. Filliol, E. Legrand, I. Mokrousov, and N. Rastogi, Mycobacterium tuberculosis Phylogeny Reconstruction Based on Combined Numerical Analysis with IS1081, IS6110, VNTR, and DR-Based Spoligotyping Suggests the Existence of Two New Phylogeographical Clades, Journal of Molecular Evolution, vol.53, issue.6, pp.680-689, 2001.
DOI : 10.1007/s002390010255

C. Tang, J. Reyes, F. Luciani, A. Francis, and M. Tanaka, spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex, Bioinformatics, vol.24, issue.20, pp.2414-2419, 2008.
DOI : 10.1093/bioinformatics/btn434

J. Reyes, A. Francis, and M. Tanaka, Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes, BMC Bioinformatics, vol.9, issue.1, p.496, 2008.
DOI : 10.1186/1471-2105-9-496

B. Asiimwe, S. Ghebremichael, G. Kallenius, T. Koivula, and M. Joloba, Mycobacterium tuberculosis spoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in peri-urban Kampala, Uganda, BMC Infect Dis, vol.830, p.101, 2008.

T. Ouassa, E. Borroni, G. Loukou, H. Faye-kette, J. Kouakou et al., High Prevalence of Shared International Type 53 among Mycobacterium tuberculosis Complex Strains in Retreated Patients from C??te d???Ivoire, PLoS ONE, vol.7, issue.9, 2012.
DOI : 10.1371/journal.pone.0045363.t003

R. Stavrum and K. Øvreås, High Diversity of Mycobacterium tuberculosis Genotypes in South Africa and Preponderance of Mixed Infections among ST53 Isolates, Journal of Clinical Microbiology, vol.47, issue.6, pp.1848-56, 2009.
DOI : 10.1128/JCM.02167-08

A. Muwonge, S. Malama, T. Johansen, C. Kankya, D. Biffa et al., Molecular Epidemiology, Drug Susceptibility and Economic Aspects of Tuberculosis in Mubende District, Uganda, PLoS ONE, vol.43, issue.3, p.64745, 2013.
DOI : 10.1371/journal.pone.0064745.s001

J. Bazira, M. Matte, B. Asiimwe, and L. Joloba, Genetic diversity of Mycobacterium tuberculosis in Mbarara, South Western Uganda, Afr Health Sci, vol.10, issue.4, pp.306-317, 2010.

E. Wampande, E. Mupere, S. Debanne, B. Asiimwe, M. Nsereko et al., Long-term dominance of Mycobacterium tuberculosisUganda family in peri-urban Kampala-Uganda is not associated with cavitary disease, BMC Infectious Diseases, vol.18, issue.2, p.484, 2013.
DOI : 10.1093/hmg/ddn352

L. Rindi, N. Lari, and C. Garzelli, Large Sequence Polymorphisms of the Euro-American lineage of Mycobacterium tuberculosis: A phylogenetic reconstruction and evidence for convergent evolution in the DR locus, Infection, Genetics and Evolution, vol.12, issue.7, pp.1551-1558, 2012.
DOI : 10.1016/j.meegid.2012.06.008

V. Valcheva, I. Mokrousov, S. Panaiotov, E. Bachiiska, T. Zozio et al., spoligotype ST125_BGR, FEMS Immunology & Medical Microbiology, vol.59, issue.1, pp.90-99, 2010.
DOI : 10.1111/j.1574-695X.2010.00667.x

URL : https://hal.archives-ouvertes.fr/pasteur-00691770

A. Gibson, R. Huard, G. Van-pittius, N. Lazzarini, L. Driscoll et al., Application of Sensitive and Specific Molecular Methods To Uncover Global Dissemination of the Major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis Spoligotype Family, Journal of Clinical Microbiology, vol.46, issue.4, pp.1259-67, 2008.
DOI : 10.1128/JCM.02231-07

J. Gafirita, A. Umubyeyi, and B. Asiimwe, A first insight into the genotypic diversity of Mycobacterium tuberculosis from Rwanda, BMC Clinical Pathology, vol.3, issue.9, pp.1472-6890, 2012.
DOI : 10.1016/S1473-3099(07)70108-1

L. Garedew, A. Mihret, T. Abebe, and G. Ameni, Molecular typing of mycobacteria isolated from extrapulmonary tuberculosis patients at Debre Birhan Referral Hospital, central Ethiopia, Scandinavian Journal of Infectious Diseases, vol.44, issue.7, pp.512-520, 2013.
DOI : 10.3109/00365548.2013.773068

N. Lari, L. Rindi, R. Cristofani, N. Rastogi, E. Tortoli et al., Association of Mycobacterium tuberculosis complex isolates of BOVIS and Central Asian (CAS) genotypic lineages with extrapulmonary disease, Clinical Microbiology and Infection, vol.15, issue.6, pp.538-581, 2009.
DOI : 10.1111/j.1469-0691.2009.02712.x

URL : https://hal.archives-ouvertes.fr/pasteur-00694593

M. Sankar, J. Singh, S. Diana, and S. Singh, Molecular characterization of Mycobacterium tuberculosis isolates from North Indian patients with extrapulmonary tuberculosis, Tuberculosis, vol.93, issue.1, pp.75-83, 2013.
DOI : 10.1016/j.tube.2012.10.005

A. Hirsh, A. Tsolaki, K. Deriemer, M. Feldman, and P. Small, Stable association between strains of Mycobacterium tuberculosis and their human host populations, Proceedings of the National Academy of Sciences, vol.101, issue.14, pp.4871-4877, 2004.
DOI : 10.1073/pnas.0305627101

M. Behr and W. Waters, Is tuberculosis a lymphatic disease with a pulmonary portal?, The Lancet Infectious Diseases, vol.14, issue.3, pp.250-255, 2013.
DOI : 10.1016/S1473-3099(13)70253-6

M. Coscolla and S. Gagneux, Does M. tuberculosis genomic diversity explain disease diversity?, Drug Discovery Today: Disease Mechanisms, vol.7, issue.1, pp.43-59, 2010.
DOI : 10.1016/j.ddmec.2010.09.004

D. Garcia-de-viedma, G. Lorenzo, P. Cardona, N. Rodriguez, S. Gordillo et al., Strains and Their Efficiency for Extrarespiratory Infection, The Journal of Infectious Diseases, vol.192, issue.12, pp.2059-65, 2005.
DOI : 10.1086/498245

M. Caws, G. Thwaites, S. Dunstan, T. Hawn, T. N. Lan et al., The Influence of Host and Bacterial Genotype on the Development of Disseminated Disease with Mycobacterium tuberculosis, PLoS Pathogens, vol.31, issue.3, p.1000034, 2008.
DOI : 10.1371/journal.ppat.1000034.t005

E. Click, P. Moonan, C. Winston, L. Cowan, and J. Oeltmann, Relationship Between Mycobacterium tuberculosis Phylogenetic Lineage and Clinical Site of Tuberculosis, Clinical Infectious Diseases, vol.54, issue.2, pp.211-220, 2012.
DOI : 10.1093/cid/cir788

G. Ameni, K. Tadesse, E. Hailu, Y. Deresse, G. Medhin et al., Transmission of Mycobacterium tuberculosis between Farmers and Cattle in Central Ethiopia, PLoS ONE, vol.6, issue.21, p.76891, 2013.
DOI : 10.1371/journal.pone.0076891.t004

D. Kidane, J. Olobo, A. Habte, Y. Negesse, A. Aseffa et al., Identification of the Causative Organism of Tuberculous Lymphadenitis in Ethiopia by PCR, Journal of Clinical Microbiology, vol.40, issue.11, pp.4230-4234, 2002.
DOI : 10.1128/JCM.40.11.4230-4234.2002

S. Cleaveland, D. Shaw, S. Mfinanga, G. Shirima, R. Kazwala et al., Mycobacterium bovis in rural Tanzania: Risk factors for infection in human and cattle populations, Tuberculosis, vol.87, issue.1, pp.30-43, 2007.
DOI : 10.1016/j.tube.2006.03.001