I. Comas, S. Homolka, S. Niemann, and S. Gagneux, Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies, PLoS ONE, vol.18, issue.11, p.7815, 2009.
DOI : 10.1371/journal.pone.0007815.s006

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.4, pp.907-914, 1997.

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 Microbiology, vol.6, issue.1, p.23, 2006.
DOI : 10.1186/1471-2180-6-23

V. Eldholm, M. Matee, S. Mfinanga, M. Heun, and U. Dahle, A first insight into the genetic diversity of Mycobacterium tuberculosis in Dar es Salaam, Tanzania, assessed by spoligotyping, BMC Microbiology, vol.6, issue.1, p.76, 2006.
DOI : 10.1186/1471-2180-6-76

G. Kibiki, B. Mulder, W. Dolmans, J. De-beer, M. Boeree et al., M. tuberculosis genotypic diversity and drug susceptibility pattern in HIV- infected and non-HIV-infected patients in northern Tanzania, BMC Microbiology, vol.7, issue.1, p.51, 2007.
DOI : 10.1186/1471-2180-7-51

P. Easterbrook, A. Gibson, S. Murad, D. Lamprecht, N. Ives et al., High rates of clustering of strains causing tuberculosis in Harare, Zimbabwe: a molecular epidemiological study, J Clin Microbiol, issue.10, pp.424536-4544, 2004.

W. Githui, A. Jordaan, E. Juma, P. Kinyanjui, F. Karimi et al., Identification of MDR-TB Beijing/W and other Mycobacterium tuberculosis genotypes in Nairobi, Kenya. Int J Tuberc Lung Dis, vol.8, issue.3, pp.352-360, 2004.

V. Chihota, L. Apers, S. Mungofa, W. Kasongo, I. Nyoni et al., Predominance of a single genotype of Mycobacterium tuberculosis in regions of Southern Africa, Int J Tuberc Lung Dis, vol.11, issue.3, pp.311-318, 2007.

Z. Helal, M. Ashour, S. Eissa, G. Abd-elatef, T. Zozio et al., Unexpectedly High Proportion of Ancestral Manu Genotype Mycobacterium tuberculosis Strains Cultured from Tuberculosis Patients in Egypt, Journal of Clinical Microbiology, vol.47, issue.9, pp.472794-2801, 2009.
DOI : 10.1128/JCM.00360-09
URL : https://hal.archives-ouvertes.fr/pasteur-00511972

R. Warren, T. Victor, E. Streicher, M. Richardson, N. Beyers et al., Patients with Active Tuberculosis often Have Different Strains in the Same Sputum Specimen, American Journal of Respiratory and Critical Care Medicine, vol.169, issue.5, pp.610-614, 2004.
DOI : 10.1164/rccm.200305-714OC

J. Glynn, J. Whiteley, P. Bifani, K. Kremer, and D. Van-soolingen, : A Systematic Review, Emerging Infectious Diseases, vol.8, issue.8, pp.843-849, 2002.
DOI : 10.3201/eid0805.020002

K. Kremer, J. Glynn, T. Lillebaek, S. Niemann, N. Kurepina et al., Definition of the Beijing/W Lineage of Mycobacterium tuberculosis on the Basis of Genetic Markers, Journal of Clinical Microbiology, vol.42, issue.9, pp.424040-4049, 2004.
DOI : 10.1128/JCM.42.9.4040-4049.2004

D. Cowley, D. Govender, B. February, M. Wolfe, L. Steyn et al., Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town, South Africa, Clin Infect Dis, issue.10, pp.471252-1259, 2008.

K. Middelkoop, L. Bekker, B. Mathema, E. Shashkina, N. Kurepina et al., Molecular epidemiology of Mycobacterium tuberculosis in a South African community with high HIV prevalence, J Infect Dis, issue.8, pp.2001207-1211, 2009.

J. Glynn, A. Crampin, H. Traore, M. Yates, F. Mwaungulu et al., Beijing Genotype, Northern Malawi, Emerging Infectious Diseases, vol.11, issue.1, pp.150-153, 2005.
DOI : 10.3201/eid1101.040869
URL : http://doi.org/10.3201/eid1101.040869

T. Koivula, M. Ekman, T. Leitner, S. Lofdahl, S. Ghebremicahel et al., Genetic characterization of the Guinea-Bissau family of Mycobacterium tuberculosis complex strains, Microbes and Infection, vol.6, issue.3, pp.272-278, 2004.
DOI : 10.1016/j.micinf.2003.12.006

B. Jong, M. Antonio, T. Awine, K. Ogungbemi, Y. De-jong et al., Use of Spoligotyping and Large Sequence Polymorphisms To Study the Population Structure of the Mycobacterium tuberculosis Complex in a Cohort Study of Consecutive Smear-Positive Tuberculosis Cases in The Gambia, Journal of Clinical Microbiology, vol.47, issue.4, pp.994-1001, 2009.
DOI : 10.1128/JCM.01216-08
URL : https://hal.archives-ouvertes.fr/pasteur-00694598

B. Asiimwe, S. Ghebremichael, G. Kallenius, T. Koivula, and M. Joloba, Mycobacterium tuberculosisspoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in peri-urban Kampala, Uganda, BMC Infectious Diseases, vol.11, issue.2, p.101, 2008.
DOI : 10.3201/eid1101.040869

S. Gagneux, K. Deriemer, T. Van, M. Kato-maeda, B. De-jong et al., Variable host-pathogen compatibility in Mycobacterium tuberculosis, Proceedings of the National Academy of Sciences, vol.103, issue.8, pp.2869-2873, 2006.
DOI : 10.1073/pnas.0511240103

S. Sreevatsan, X. Pan, K. Stockbauer, N. Connell, B. Kreiswirth et al., Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination, Proceedings of the National Academy of Sciences, vol.94, issue.18, pp.949869-9874, 1997.
DOI : 10.1073/pnas.94.18.9869

R. Brosch, S. Gordon, M. Marmiesse, P. Brodin, C. Buchrieser et al., A new evolutionary scenario for the Mycobacterium tuberculosis complex, Proc Natl Acad Sci, issue.6, pp.993684-3689, 2002.

H. Soini, X. Pan, A. Amin, E. Graviss, A. Siddiqui et al., Characterization of Mycobacterium tuberculosis isolates from patients in Houston, Texas, by spoligotyping, J Clin Microbiol, vol.38, issue.2, pp.669-676, 2000.

N. Rastogi and C. Sola, Molecular evolution of the Mycobacterium tuberculosis complex. Amedeo Online Textbooks, pp.53-91, 2007.

. Viegas, Cite this article as Molecular diversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in Mozambique BMC Microbiology, p.195, 2010.