M. Gutierrez, S. Brisse, and R. Brosch, Ancient Origin and Gene Mosaicism of the Progenitor of Mycobacterium tuberculosis, PLoS Pathogens, vol.21, issue.1, pp.55-61, 2005.
DOI : 10.1371/journal.ppat.0010005.st003
URL : https://hal.archives-ouvertes.fr/inserm-00080315

T. Walker, C. Clp, R. Harrell, J. Evans, and G. Kapatai, Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study, The Lancet Infectious Diseases, vol.13, issue.2, pp.137-146, 2013.
DOI : 10.1016/S1473-3099(12)70277-3

S. Gagneux, K. Deriemer, T. Van, M. Kato-maeda, and B. De-jong, Variable host-pathogen compatibility in Mycobacterium tuberculosis, Proc. Natl Acad. Sci. USA 103, pp.2869-2873, 2006.
DOI : 10.1073/pnas.0511240103

S. Sreevatsan, X. Pan, K. Stockbauer, N. Connell, and B. Kreiswirth, 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.9869-9874, 1997.
DOI : 10.1073/pnas.94.18.9869

D. Couvin and N. Rastogi, The establishment of databases on circulating genotypes of Mycobacterium tuberculosis complex and web tools for an effective response to better monitor, understand and control the tuberculosis epidemic worldwide Available: https://pro.anses, EuroReference?Journal of Reference, vol.12, pp.36-48, 2014.

D. García-de-viedma, I. Mokrousov, N. Rastogi, and . Pmid, Innovations in the molecular epidemiology of tuberculosis, Enfermedades Infecciosas y Microbiolog??a Cl??nica, vol.29, issue.11, pp.8-13, 2011.
DOI : 10.1016/S0213-005X(11)70012-X

M. Kato-maeda, E. Kim, L. Flores, L. Jarlsberg, and D. Osmond, Differences among sublineages of the East-Asian lineage of Mycobacterium tuberculosis in genotypic clustering, Int. J. Tuberc. Lung Dis, vol.14, pp.538-544, 2010.

C. Ford, R. Shah, M. Kato-maeda, S. Gagneux, and M. Murray, Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis, Nature Genetics, vol.69, issue.7, pp.784-790, 2013.
DOI : 10.1126/science.1124410

M. Mancilla, A. Martínez, C. Palavecino, G. Rehren, and P. Lucero, Genetic variants of Mycobacterium tuberculosis isolated from patients of the Xth Region of Chile], Rev Chilena Infectol, vol.23, issue.3, pp.220-225, 2006.

P. Meza, M. Balcells, C. Miranda, M. Cifuentes, and A. Wozniak, Presencia del genotipo Beijing entre cepas del complejo Mycobacterium tuberculosis en dos centros de salud de la Regi??n Metropolitana-Chile, Revista chilena de infectolog??a, vol.31, issue.1, pp.21-27, 2014.
DOI : 10.4067/S0716-10182014000100003
URL : https://doaj.org/article/cb4b7861321c4022bab52b688f84ed18

A. Laszlo, M. Rahman, M. Raviglione, and F. Bustreo, Quality assurance programme for drug susceptibility testing of Mycobacterium tuberculosis in the WHO/IUATLD Supranational Laboratory Network: first round of proficiency testing, Int J Tuberc Lung Dis, vol.1, pp.231-238, 1997.

H. Kasai, T. Ezaki, and S. Harayama, Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences, J Clin Microbiol, vol.38, issue.1, pp.301-308, 2000.

J. Kamerbeek, L. Schouls, A. Kolk, M. Van-agterveld, and D. Van-soolingen, Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology, Journal of Clinical Microbiology, vol.35, issue.4, pp.907-914, 1997.

E. Abadia, J. Zhang, V. Ritacco, K. Kremer, and R. Ruimy, The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: Providing guidelines for Quality Assurance when working on membranes, BMC Infectious Diseases, vol.8, issue.11, pp.110-120, 2011.
DOI : 10.3201/eid0811.020125
URL : https://hal.archives-ouvertes.fr/hal-00590430

L. Cowan, L. Mosher, L. Diem, J. Massey, and J. Crawford, Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis Isolates with Low Copy Numbers of IS6110 by Using Mycobacterial Interspersed Repetitive Units, Journal of Clinical Microbiology, vol.40, issue.5, pp.1592-602, 2002.
DOI : 10.1128/JCM.40.5.1592-1602.2002

P. Supply, C. Allix, S. Lesjean, M. Cardoso-oelemann, and S. Rusch-gerdes, Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis, Journal of Clinical Microbiology, vol.44, issue.12, pp.4498-4510, 2006.
DOI : 10.1128/JCM.01392-06

C. Demay, B. Liens, T. Burguière, V. Hill, and D. Couvin, 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.755-766, 2012.
DOI : 10.1016/j.meegid.2012.02.004
URL : https://hal.archives-ouvertes.fr/pasteur-00691750

A. Shabbeer, C. Ozcaglar, B. Yener, and K. Bennett, Web tools for molecular epidemiology of tuberculosis, Infection, Genetics and Evolution, vol.12, issue.4, pp.767-81, 2012.
DOI : 10.1016/j.meegid.2011.08.019

C. Barbosa, L. Lazzarini, A. Elias, J. Leung, and S. Ribeiro, Tuberculosis caused by RD<SUP>Rio</SUP> <I>Mycobacterium tuberculosis</I> is not associated with differential clinical features, The International Journal of Tuberculosis and Lung Disease, vol.16, issue.10, pp.1377-1382, 2012.
DOI : 10.5588/ijtld.11.0709

J. Monteserin, M. Camacho, L. Barrera, J. Palomino, and V. Ritacco, Genotypes of Mycobacterium tuberculosis in patients at risk of drug resistance in Bolivia, Infection, Genetics and Evolution, vol.17, p.23603419, 2013.
DOI : 10.1016/j.meegid.2013.04.010

H. Mardassi, A. Namouchi, R. Haltiti, M. Zarrouk, and B. Mhenni, Tuberculosis due to Resistant Haarlem Strain, Tunisia, Emerging Infectious Diseases, vol.11, issue.6, pp.957-961, 2005.
DOI : 10.3201/eid1106.041365
URL : https://hal.archives-ouvertes.fr/pasteur-00874087

T. Jagielski, E. Augustynowicz-kope?, T. Zozio, N. Rastogi, and Z. Zwolska, Spoligotype-Based Comparative Population Structure Analysis of Multidrug-Resistant and Isoniazid-Monoresistant Mycobacterium tuberculosis Complex Clinical Isolates in Poland, Journal of Clinical Microbiology, vol.48, issue.11, pp.3899-3909, 2010.
DOI : 10.1128/JCM.00572-10
URL : https://hal.archives-ouvertes.fr/pasteur-00691769

T. Realpe, N. Correa, J. Rozo, B. Ferro, and V. Gomez, Population Structure among Mycobacterium tuberculosis Isolates from Pulmonary Tuberculosis Patients in Colombia, PLoS ONE, vol.205, issue.4, p.24747767, 2014.
DOI : 10.1371/journal.pone.0093848.s005
URL : https://hal.archives-ouvertes.fr/pasteur-01011076

K. Brudey, I. Filliol, F. S. Guernier, V. Duval, and P. , Long-Term Population-Based Genotyping Study of Mycobacterium tuberculosis Complex Isolates in the French Departments of the Americas, Journal of Clinical Microbiology, vol.44, issue.1, 2006.
DOI : 10.1128/JCM.44.1.183-191.2006

K. Bos, K. Harkins, A. Herbig, M. Coscolla, and N. Weber, Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis, Nature, vol.7, issue.7523, p.25533962, 2014.
DOI : 10.1038/nature13591

N. Reiling, S. Homolka, and K. Walter, Clade-specific virulence patterns of Mycobacterium tuberculosis, MBio, vol.4, pp.250-263, 2013.

V. Ritacco, B. Lopez, P. Cafrune, L. Ferrazoli, and P. Suffys, Mycobacterium tuberculosis strains of the Beijing genotype are rarely observed in tuberculosis patients in South America, Mem??rias do Instituto Oswaldo Cruz, vol.103, issue.5, pp.489-92, 2008.
DOI : 10.1590/S0074-02762008000500014

L. Aristimuño, R. Armengol, A. Cebollada, M. España, and A. Guilarte, Molecular characterisation of Mycobacterium tuberculosis isolates in the First National Survey of Anti-tuberculosis Drug Resistance from Venezuela, BMC Microbiology, vol.6, issue.1, pp.90-17032442, 2006.
DOI : 10.1186/1471-2180-6-90

N. Candia, B. Lopez, T. Zozio, M. Carrivale, and C. Diaz, First insight into Mycobacterium tuberculosis genetic diversity in Paraguay, BMC Microbiology, vol.7, issue.1, pp.75-17686181, 2007.
DOI : 10.1186/1471-2180-7-75

E. Abadia, M. Sequera, D. Ortega, M. Mendez, and A. Escalona, Mycobacterium tuberculosis ecology in Venezuela: epidemiologic correlates of common spoligotypes and a large clonal cluster defined by MIRU-VNTR-24, BMC Infectious Diseases, vol.46, issue.8, pp.122-132, 2009.
DOI : 10.1128/JCM.00540-08

N. Morcillo, D. Giulio, B. Chirico, C. Kuriger, A. Dolmann et al., First description of Mycobacterium tuberculosis Beijing genotype in Argentina, Rev. Argent. Microbiol, vol.37, pp.92-95, 2005.

T. Iwamoto, L. Grandjean, K. Arikawa, N. Nakanishi, and L. Caviedes, Genetic Diversity and Transmission Characteristics of Beijing Family Strains of Mycobacterium tuberculosis in Peru, PLoS ONE, vol.7, issue.11, p.23185395, 2012.
DOI : 10.1371/journal.pone.0049651.s005

J. Millet, E. Streit, M. Berchel, A. Bomer, and F. Schuster, A Systematic Follow-Up of Mycobacterium tuberculosis Drug-Resistance and Associated Genotypic Lineages in the French Departments of the Americas over a Seventeen-Year Period BioMed Research International, Article ID, vol.2014689852, issue.14, 2014.

L. Filliol, J. Driscoll, D. Van-soolingen, B. Kreiswirth, and K. Kremer, Snapshot of Moving and Expanding Clones of Mycobacterium tuberculosis and Their Global Distribution Assessed by Spoligotyping in an International Study, Journal of Clinical Microbiology, vol.41, issue.5, pp.1963-1971, 2003.
DOI : 10.1128/JCM.41.5.1963-1970.2003

C. Garzelli and L. Rindi, Molecular epidemiological approaches to study the epidemiology of tuberculosis in low-incidence settings receiving immigrants, Infection, Genetics and Evolution, vol.12, issue.4, pp.610-628, 2012.
DOI : 10.1016/j.meegid.2011.10.015

E. Van-der-eijk, E. Van-de-vosse, J. Vandenbroucke, and J. Van-dissel, Heredity versus Environment in Tuberculosis in Twins, American Journal of Respiratory and Critical Care Medicine, vol.176, issue.12, pp.1281-1288, 2007.
DOI : 10.1164/rccm.200703-435OC

S. Gagneux and P. Small, Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development, The Lancet Infectious Diseases, vol.7, issue.5, pp.328-337, 2007.
DOI : 10.1016/S1473-3099(07)70108-1

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, 2009.
DOI : 10.1371/journal.pone.0007815.s006

V. Ritacco, B. López, M. Ambroggi, D. Palmero, and B. Salvadores, HIV Infection and Geographically Bound Transmission of Drug-Resistant Tuberculosis, Argentina, Emerging Infectious Diseases, vol.18, issue.11, pp.1802-1810, 2012.
DOI : 10.3201/eid1811.120126

V. Ritacco, M. Iglesias, L. Ferrazoli, J. Monteserin, D. Costa et al., Conspicuous multidrug-resistant Mycobacterium tuberculosis cluster strains do not trespass country borders in Latin America and Spain, Infection, Genetics and Evolution, vol.12, issue.4, pp.711-717, 2012.
DOI : 10.1016/j.meegid.2011.06.006

T. Larger, 1371/journal.pone.0118007.s001 S2 Fig. Larger TIF image available online at: http://journals.plos.org/plosone/article/asset?unique&id=info:doi/10.1371/journal.pone.0118007.s002 Supporting Information S3 Fig Geographic distribution of lineages in Latin American and neighboring countries. Note that the map file was downloaded under Creative Commons License using the link: http://en.wikipedia.org/wiki/Latin_America and was manually modified for representative purposes only. Larger TIF image available online at