R. , T. Tanaka, and . Rosenberg-;-c-rosenberg, , 2001.

R. Z. Aandahl, J. F. Reyes, S. A. Sisson, and M. M. Tanaka, A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis, PLoS Comput Biol, vol.8, issue.6, p.1002573, 2012.

N. Ahmed, M. Alam, A. Majeed, A. , A. Rahman et al., Genome sequence based, comparative analysis of the fluorescent amplified fragment length polymorphisms (FAFLP) of tubercle bacilli from seals provides molecular evidence for a new species within the Mycobacterium tuberculosis complex, Infect Genet Evol, vol.2, issue.3, pp.193-199, 2003.

E. Aleksic, M. Merker, H. Cox, B. Reiher, Z. Sekawi et al., First molecular epidemiology study of Mycobacterium tuberculosis in Kiribati, PLoS One, vol.8, issue.1, p.55423, 2013.

A. Sa, O. Akkerman, I. Parwati, S. Al-gamdi, Z. Rahim et al., Microevolution of Mycobacterium tuberculosis in a tuberculosis patient, J Clin Microbiol, vol.48, issue.10, pp.3813-3816, 2010.

C. Allix, P. Supply, and M. Fauville-dufaux, Utility of fast mycobacterial interspersed repetitive unit-variable number tandem repeat genotyping in clinical mycobacteriological analysis, Clin Infect Dis, vol.39, issue.6, pp.783-789, 2004.

C. Allix-beguec, M. Fauville-dufaux, and P. Supply, Three-year population-based evaluation of standardized mycobacterial interspersed repetitiveunit-variable-number tandem-repeat typing of Mycobacterium tuberculosis, J Clin Microbiol, vol.46, issue.4, pp.1398-1406, 2008.

C. Allix-beguec, D. Harmsen, T. Weniger, P. Supply, and S. Niemann, Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates, J Clin Microbiol, vol.46, issue.8, 2008.

C. Allix-beguec, P. Supply, M. Wanlin, P. Bifani, and M. Fauvilledufaux, Standardised PCR-based molecular epidemiology of tuberculosis, Eur Respir J, vol.31, issue.5, pp.1077-1084, 2008.

C. Allix-beguec, C. Wahl, M. Hanekom, V. Nikolayevskyy, F. Drobniewski et al., Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandemrepeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates, J Clin Microbiol, vol.52, issue.1, pp.164-172, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01011025

N. Alonso-rodriguez, M. Martinez-lirola, M. L. Sanchez, M. Herranz, T. Penafiel et al., Prospective universal application of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping to characterize Mycobacterium tuberculosis isolates for fast identification of clustered and orphan cases, J Clin Microbiol, vol.47, issue.7, 2009.

R. D. Arbeit, M. Arthur, R. Dunn, C. Kim, R. K. Selander et al., Resolution of recent evolutionary divergence among Escherichia coli from related lineages: the application of pulsed field electrophoresis to molecular epidemiology, J Infect Dis, vol.161, issue.2, pp.230-235, 1990.

A. Arnold, A. A. Witney, S. Vergnano, A. Roche, C. A. Cosgrove et al., XDR-TB transmission in London: case management and contact tracing investigation assisted by early whole genome sequencing, J Infect, 2016.

L. Baker, T. Brown, M. C. Maiden, and F. Drobniewski, Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis, Emerg Infect Dis, vol.10, issue.9, pp.1568-1577, 2004.

M. E. Balcells, P. Garcia, P. Meza, C. Pena, M. Cifuentes et al., A first insight on the population structure of Mycobacterium tuberculosis complex as studied by spoligotyping and MIRUVNTRs in, PLoS One, vol.10, issue.2, p.118007, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01153988

P. F. Barnes and M. D. Cave, Molecular epidemiology of tuberculosis, N Engl J Med, vol.349, issue.12, pp.1149-1156, 2003.

J. H. Bates and D. A. Mitchison, Geographic distribution of bacteriophage types of Mycobacterium tuberculosis, Am Rev Respir Dis, vol.100, issue.2, pp.189-193, 1969.

J. L. De-beer, K. Kremer, C. Kodmon, P. Supply, and D. Van-soolingen, First worldwide proficiency study on variable-number tandem-repeat typing of Mycobacterium tuberculosis complex strains, J Clin Microbiol, vol.50, issue.3, pp.662-669, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00762210

J. L. De-beer, J. Van-ingen, G. De-vries, C. Erkens, M. Sebek et al., Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey, J Clin Microbiol, vol.51, issue.4, pp.1193-1198, 2013.

J. L. De-beer, O. W. Akkerman, A. C. Schurch, A. Mulder, T. S. Van-der-werf et al., Optimization of standard inhouse 24-locus variable-number tandem-repeat typing for Mycobacterium tuberculosis and its direct application to clinical material, J Clin Microbiol, vol.52, issue.5, pp.1338-1342, 2014.

J. L. De-beer, C. Kodmon, J. Van-ingen, P. Supply, and D. Van-soolingen, Second worldwide proficiency study on variable number of tandem repeats typing of Mycobacterium tuberculosis complex, Int J Tuberc Lung Dis, vol.18, issue.5, pp.594-600, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01024982

M. A. Behr, M. A. Wilson, W. P. Gill, H. Salamon, G. K. Schoolnik et al., Comparative genomics of BCG vaccines by whole-genome DNA microarray, Science, vol.284, issue.5419, pp.1520-1523, 1999.

S. Berg, M. C. Garcia-pelayo, B. Muller, E. Hailu, B. Asiimwe et al., African 2, a clonal complex of Mycobacterium bovis epidemiologically important in East Africa, J Bacteriol, vol.193, issue.3, pp.670-678, 2011.

F. Biadglegne, M. Merker, U. Sack, A. C. Rodloff, and S. Niemann, Tuberculous lymphadenitis in Ethiopia predominantly caused by strains belonging to the Delhi/CAS lineage and newly identified Ethiopian clades of the Mycobacterium tuberculosis complex, PLoS One, vol.10, issue.9, p.137865, 2015.

U. Bidovec-stojkovic, M. Zolnir-dovc, and P. Supply, One year nationwide evaluation of 24-locus MIRUVNTR genotyping on Slovenian Mycobacterium tuberculosis isolates, Respir Med, vol.105, issue.1, pp.67-73, 2011.

R. Biek, A. O'hare, D. Wright, T. Mallon, C. Mccormick et al., Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations, PLoS Pathog, vol.8, issue.11, 2012.

P. J. Bifani, B. B. Plikaytis, V. Kapur, K. Stockbauer, X. Pan et al., Origin and interstate spread of a New York City multidrug-resistant Mycobacterium tuberculosis clone family, JAMA, vol.275, issue.6, pp.452-457, 1996.

K. Bjorn-mortensen, B. Soborg, A. Koch, K. Ladefoged, M. Merker et al., Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective populationbased study in, East Greenland. Sci Rep, vol.6, p.33180, 2016.

Y. Blouin, G. Cazajous, C. Dehan, C. Soler, R. Vong et al., Progenitor "Mycobacterium canettii" clone responsible for lymph node tuberculosis epidemic, Emerg Infect Dis, vol.20, issue.1, pp.21-28, 2014.
DOI : 10.3201/eid2001.130652

URL : https://hal.archives-ouvertes.fr/hal-00948497

E. C. Boritsch, P. Supply, N. Honore, T. Seemann, T. P. Stinear et al., A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent, Mol Microbiol, vol.93, issue.5, pp.835-852, 2014.

E. C. Boritsch, W. Frigui, A. Cascioferro, W. Malaga, G. Etienne et al., recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence, Nat Microbiol, vol.1, p.15019, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01265519

E. C. Boritsch, V. Khanna, A. Pawlik, N. Honore, V. H. Navas et al., Key experimental evidence of chromosomal DNA transfer among selected tuberculosiscausing mycobacteria, Proc Natl Acad Sci U S A, vol.113, issue.35, pp.9876-9881, 2016.

K. I. Bos, K. M. Harkins, A. Herbig, M. Coscolla, N. Weber et al., Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis, Nature, vol.514, issue.7523, pp.494-497, 2014.

P. Bradley, N. C. Gordon, T. M. Walker, L. Dunn, S. Heys et al., Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis, Nat Commun, vol.6, p.10063, 2015.

R. Brosch, S. V. Gordon, A. Billault, T. Garnier, K. Eiglmeier et al., Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing, and comparative genomics, Infect Immun, vol.66, issue.5, pp.2221-2229, 1998.

B. , Gen Microbiol, vol.130, issue.4, pp.1019-1021

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.4, issue.11, p.7815, 2009.

I. Comas, J. Chakravartti, P. M. Small, J. Galagan, S. Niemann et al., Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved, Nat Genet, vol.42, issue.6, pp.498-503, 2010.

I. Comas, M. Coscolla, T. Luo, S. Borrell, K. E. Holt et al., Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans, Nat Genet, vol.45, issue.10, pp.1176-1182, 2013.

I. Comas, E. Hailu, T. Kiros, S. Bekele, W. Mekonnen et al., Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in Sub-Saharan Africa, Curr Biol, vol.25, issue.24, pp.3260-3266, 2015.

G. S. Cooke, R. K. Beaton, R. J. Lessells, L. John, S. Ashworth et al., International spread of MDR TB from Tugela Ferry, South Africa. Emerg Infect Dis, vol.17, issue.11, pp.2035-2037, 2011.

E. L. Corbett, C. J. Watt, N. Walker, D. Maher, B. G. Williams et al., The growing burden of tuberculosis: global trends and interactions with the HIV epidemic, Arch Intern Med, vol.163, issue.9, pp.1009-1021, 2003.

M. Coscolla and S. Gagneux, Consequences of genomic diversity in Mycobacterium tuberculosis, Semin Immunol, vol.26, issue.6, pp.431-444, 2014.

M. Coscolla, P. M. Barry, J. E. Oeltmann, H. Koshinsky, T. Shaw et al., Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread, J Infect Dis, vol.212, issue.2, pp.302-310, 2015.

L. S. Cowan, L. Mosher, L. Diem, J. P. Massey, and J. T. Crawford, Variable-number tandem repeat typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 by using mycobacterial interspersed repetitive units, J Clin Microbiol, vol.40, issue.5, pp.1592-1602, 2002.

L. S. Cowan, L. Diem, M. C. Brake, and J. T. Crawford, Transfer of a Mycobacterium tuberculosis genotyping method, Spoligotyping, from a reverse lineblot hybridization, membrane-based assay to the Luminex multianalyte profiling system, J Clin Microbiol, vol.42, issue.1, pp.474-477, 2004.

L. S. Cowan, L. Diem, T. Monson, P. Wand, D. Temporado et al., Evaluation of a twostep approach for large-scale, prospective genotyping of Mycobacterium tuberculosis isolates in the United States, J Clin Microbiol, vol.43, issue.2, 2005.

L. S. Cowan, D. P. Hooks, S. Christianson, M. K. Sharma, D. C. Alexander et al., Evaluation of mycobacterial interspersed repetitive-unit-variablenumber tandem-repeat genotyping as performed in laboratories in Canada, France, and the United States, J Clin Microbiol, vol.50, issue.5, pp.1830-1831, 2012.

H. S. Cox, T. Kubica, D. Doshetov, Y. Kebede, S. Rusch-gerdess et al., The Beijing genotype and drug resistant tuberculosis in the Aral Sea region of Central Asia, Respir Res, vol.6, p.134, 2005.

H. S. Cox, K. Sibilia, S. Feuerriegel, S. Kalon, J. Polonsky et al., Emergence of extensive drug resistance during treatment for multidrug-resistant tuberculosis, N Engl J Med, vol.359, issue.22, pp.2398-2400, 2008.

J. T. Crawford, Applications of molecular methods to epidemiology of tuberculosis, Res Microbiol, vol.144, issue.2, pp.111-116, 1993.

C. Soini, H. Roscanni, G. C. Jaques, M. Villares, M. C. Musser et al., Extensive cross-contamination of specimens with Mycobacterium tuberculosis in a reference laboratory, J Clin Microbiol, vol.37, issue.4, pp.916-919, 1999.

C. L. Daley and C. R. Horsburgh, Editorial commentary: treatment for multidrug-resistant tuberculosis: it's worse than we thought!, Clin Infect Dis, vol.59, issue.8, pp.1064-1065, 2014.

C. Demay, B. Liens, T. Burguiere, V. Hill, D. Couvin et al., SITVITWEB-a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology, Infect Genet Evol, vol.12, issue.4, pp.755-766, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-00691750

K. M. Derbyshire and T. A. Gray, Distributive conjugal transfer: new insights into horizontal gene transfer and genetic exchange in mycobacteria, Microbiol Spectrum, vol.2, issue.1, 2014.

R. Diel, S. Schneider, K. Meywald-walter, C. M. Ruf, S. Ruschgerdes et al., long-term populationbased analysis applying classical and molecular epidemiological techniques, J Clin Microbiol, vol.40, issue.2, pp.532-539, 2002.
DOI : 10.1128/jcm.40.2.532-539.2002

URL : https://jcm.asm.org/content/40/2/532.full.pdf

R. Diel, J. Vandeputte, G. De-vries, J. Stillo, M. Wanlin et al., Costs of tuberculosis disease in the European Union: a systematic analysis and cost calculation, Eur Respir J, vol.43, issue.2, pp.554-565, 2014.

E. L. Doughty, M. J. Sergeant, I. Adetifa, M. Antonio, and M. J. Pallen, Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer, p.585, 2014.

C. Dye and B. G. Williams, The population dynamics and control of tuberculosis, Science, vol.328, issue.5980, pp.856-861, 2010.

V. Eldholm, J. Monteserin, A. Rieux, B. Lopez, B. Sobkowiak et al., Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain, Nat Commun, vol.6, p.7119, 2015.

J. T. Evans, P. M. Hawkey, E. G. Smith, K. A. Boese, R. E. Warren et al., Automated high-throughput mycobacterial interspersed repetitive unit typing of Mycobacterium tuberculosis strains by a combination of PCR and nondenaturing high-performance liquid chromatography, J Clin Microbiol, vol.42, issue.9, pp.4175-4180, 2004.

M. Fabre, J. L. Koeck, L. Fleche, P. Simon, F. Herve et al., High genetic diversity revealed by variable-number tandem repeat genotyping and analysis of hsp65 gene polymorphism in a large collection of "Mycobacterium canettii, J Clin Microbiol, vol.42, issue.7, pp.3248-3255, 2004.
URL : https://hal.archives-ouvertes.fr/hal-01158318

M. Fabre, Y. Hauck, C. Soler, J. L. Koeck, J. Van-ingen et al., Molecular characteristics of "Mycobacterium canettii" the smooth Mycobacterium tuberculosis bacilli, Infect Genet Evol, vol.10, issue.8, pp.1165-1173, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00534312

L. Fenner, B. Malla, B. Ninet, O. Dubuis, D. Stucki et al., Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis, PLoS One, vol.6, issue.9, p.24737, 2011.

I. Filliol, J. R. Driscoll, D. Van-soolingen, B. N. Kreiswirth, K. Kremer et al., Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study, J Clin Microbiol, vol.41, issue.5, pp.1963-1970, 2003.

I. Filliol, A. S. Motiwala, M. Cavatore, W. Qi, M. H. Hazbon et al., Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set, J Bacteriol, vol.188, issue.2, pp.759-772, 2006.

R. D. Fleischmann, D. Alland, J. A. Eisen, L. Carpenter, O. White et al., Wholegenome comparison of Mycobacterium tuberculosis clinical and laboratory strains, J Bacteriol, vol.184, pp.5479-5490, 2002.

N. G. Fomukong, T. H. Tang, S. Al-maamary, W. A. Ibrahim, S. Ramayah et al., Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110, Tuber Lung Dis, vol.75, issue.6, pp.435-440, 1994.

N. Fomukong, M. Beggs, H. El-hajj, G. Templeton, K. Eisenach et al., Differences in the prevalence of IS6110 insertion sites in Mycobacterium tuberculosis strains: low and high copy number of IS6110, Tuber Lung Dis, vol.78, issue.2, pp.109-116, 1997.

C. B. Ford, P. L. Lin, M. R. Chase, R. R. Shah, O. Iartchouk et al., Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection, Nat Genet, vol.43, issue.5, pp.482-486, 2011.

R. Frothingham, Differentiation of strains in Mycobacterium tuberculosis complex by DNA sequence polymorphisms, including rapid identification of M. bovis BCG, J Clin Microbiol, vol.33, issue.4, pp.840-844, 1995.

R. Frothingham, -. Meeker, and W. A. Connell, Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats, Microbiology, vol.144, pp.1189-1196, 1998.

S. Gagneux, K. Deriemer, T. Van, M. Kato-maeda, B. C. Jong et al., Variable host-pathogen compatibility in Mycobacterium tuberculosis, Proc Natl Acad Sci U S A, vol.103, issue.8, pp.2869-2873, 2006.

N. R. Gandhi, P. Nunn, K. Dheda, H. S. Schaaf, M. Zignol et al., Multidrug-resistant and extensively drugresistant tuberculosis: a threat to global control of tuberculosis, Lancet, vol.375, issue.9728, pp.60410-60412, 2010.

D. Garcia-de-viedma, A. Rodriguez, N. Andres, S. , R. Serrano et al., Characterization of clonal complexity in tuberculosis by mycobacterial interspersed repetitive unit-variablenumber tandem repeat typing, J Clin Microbiol, vol.43, issue.11, pp.5660-5664, 2005.

J. L. Gardy, J. C. Johnston, H. Sui, S. J. Cook, V. J. Shah et al., Wholegenome sequencing and social-network analysis of a tuberculosis outbreak, N Engl J Med, vol.364, issue.8, pp.730-739, 2011.

M. Gauthier, F. Bidault, A. Mosnier, N. Bablishvili, N. Tukvadze et al., High-throughput MIRU-VNTR genotyping for Mycobacterium tuberculosis epidemiological studies, J Clin Microbiol, 2014.

H. Getahun, A. Matteelli, R. E. Chaisson, M. Raviglione, M. K. Gomgnimbou et al., Spoligoriftyping," a dual-priming-oligonucleotidebased direct-hybridization assay for tuberculosis control with a multianalyte microbead-based hybridization system, J Clin Microbiol, vol.372, issue.22, pp.3172-3179, 2012.

S. V. Gordon, R. Brosch, A. Billault, T. Garnier, K. Eiglmeier et al., Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays, Mol Microbiol, vol.32, issue.3, pp.643-655, 1999.

A. Grant, C. Arnold, N. Thorne, S. Gharbia, and A. Underwood, Mathematical modelling of Mycobacterium tuberculosis VNTR loci estimates a very slow mutation rate for the repeats, J Mol Evol, vol.66, issue.6, pp.565-574, 2008.

M. M. Gutacker, J. C. Smoot, C. A. Migliaccio, S. M. Ricklefs, S. Hua et al., Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains, Genetics, vol.162, issue.4, pp.1533-1543, 2002.

M. M. Gutacker, B. Mathema, H. Soini, E. Shashkina, B. N. Kreiswirth et al., Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites, J Infect Dis, vol.193, issue.1, pp.121-128, 2006.

M. C. Gutierrez, S. Brisse, R. Brosch, M. Fabre, B. Omais et al., Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis, PLoS Pathog, vol.1, issue.1, p.5, 2005.
URL : https://hal.archives-ouvertes.fr/inserm-00080315

M. C. Gutierrez, N. Ahmed, E. Willery, S. Narayanan, S. E. Hasnain et al., Predominance of ancestral lineages of Mycobacterium tuberculosis in India, Emerg Infect Dis, vol.12, issue.9, pp.1367-1374, 2006.

S. R. Harris, M. E. Torok, E. J. Cartwright, M. A. Quail, S. J. Peacock et al., Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks, Nat Biotechnol, vol.31, issue.7, pp.592-594, 2013.

P. W. Hermans, D. Van-soolingen, E. M. Bik, P. E. De-haas, J. W. Dale et al., Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains, Infect Immun, vol.59, issue.8, pp.2695-2705, 1991.

R. Hershberg, M. Lipatov, P. M. Small, H. Sheffer, S. Niemann et al., High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography, PLoS Biol, vol.6, issue.12, 2008.

A. E. Hirsh, A. G. Tsolaki, K. Deriemer, M. W. Feldman, and P. M. Small, Stable association between strains of Mycobacterium tuberculosis and their human host populations, Proc Natl Acad Sci U S A, vol.101, issue.14, pp.4871-4876, 2004.

S. Homolka, M. Projahn, S. Feuerriegel, T. Ubben, R. Diel et al., High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms, PLoS One, vol.7, issue.7, p.39855, 2012.

T. Iwamoto, S. Yoshida, K. Suzuki, M. Tomita, R. Fujiyama et al., Hypervariable loci that enhance the discriminatory ability of newly proposed 15-loci and 24-loci variablenumber tandem repeat typing method on Mycobacterium tuberculosis strains predominated by the Beijing family, FEMS Microbiol Lett, vol.270, issue.1, pp.67-74, 2007.

K. A. Jolley and M. C. Maiden, BIGSdb: scalable analysis of bacterial genome variation at the population level, BMC Bioinforma, vol.11, p.595, 2010.

S. Junemann, F. J. Sedlazeck, K. Prior, A. Albersmeier, U. John et al., Updating benchtop sequencing performance comparison, Nat Biotechnol, vol.31, issue.4, pp.294-296, 2013.

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.

M. Kato-maeda, C. Ho, B. Passarelli, N. Banaei, J. Grinsdale et al., Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak, PLoS One, vol.8, issue.3, p.58235, 2013.

P. Keim, A. M. Klevytska, L. B. Price, J. M. Schupp, G. Zinser et al., Molecular diversity in Bacillus anthracis, J Appl Microbiol, vol.87, issue.2, pp.215-217, 1999.

K. Kitahara, Studies on the identification of infection source for pulmonary tuberculosis in a family using bacteriophage types as a marker. 2. Studies on the source of infection in family, Kekkaku, vol.48, issue.3, pp.61-69, 1973.

T. A. Kohl, R. Diel, D. Harmsen, J. Rothganger, K. M. Walter et al., Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach, J Clin Microbiol, vol.52, issue.7, pp.2479-2486, 2014.

K. Kremer, D. Van-soolingen, R. Frothingham, W. H. Haas, P. W. Hermans et al., Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility, J Clin Microbiol, vol.37, issue.8, pp.2607-2618, 1999.

K. Kremer, J. R. Glynn, T. Lillebaek, S. Niemann, N. E. Kurepina et al., Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers, J Clin Microbiol, vol.42, issue.9, pp.4040-4049, 2004.

K. Kremer, C. Arnold, A. Cataldi, M. C. Gutierrez, W. H. Haas et al., Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains, 2005.

, J Clin Microbiol, vol.43, issue.11, pp.5628-5638

K. Kremer, B. K. Au, P. C. Yip, R. Skuce, P. Supply et al., Use of variable-number tandem-repeat typing to differentiate Mycobacterium tuberculosis Beijing family isolates from Hong Kong and comparison with IS6110 restriction fragment length polymorphism typing and spoligotyping, J Clin Microbiol, vol.43, issue.1, pp.314-320, 2005.

N. E. Kurepina, S. Sreevatsan, B. B. Plikaytis, P. J. Bifani, N. D. Connell et al., Characterization of the phylogenetic distribution and chromosomal insertion sites of five IS6110 elements in Mycobacterium tuberculosis: non-random integration in the dnaA-dnaN region, Tuber Lung Dis, vol.79, issue.1, pp.31-42, 1998.

E. Lafeuille, N. Veziris, W. Sougakoff, F. Roure, L. Du et al., XDR-tuberculosis in France: community transmission due to non-compliance with isolation precautions, Med Mal Infect, vol.46, issue.1, pp.52-55, 2016.

C. S. Lambregts-van-weezenbeek, M. M. Sebek, P. J. Van-gerven, G. De-vries, S. Verver et al., Tuberculosis contact investigation and DNA fingerprint surveillance in The Netherlands: 6 years' experience with nation-wide cluster feedback and cluster monitoring, Int J Tuberc Lung Dis, vol.7, issue.12, pp.463-470, 2003.

T. Laver, J. Harrison, O. Neill, P. A. Moore, K. Farbos et al., Assessing the performance of the Oxford Nanopore Technologies MinION, Biomol Detect Quantif, vol.3, pp.1-8, 2015.

L. C. Lazzarini, R. C. Huard, N. L. Boechat, H. M. Gomes, M. C. Oelemann et al., Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil, J Clin Microbiol, vol.45, issue.12, pp.3891-3902, 2007.

, , pp.1394-1401

L. Fleche, P. Fabre, M. Denoeud, F. Koeck, J. L. Vergnaud et al., High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing, BMC Microbiol, vol.2, p.37, 2002.
URL : https://hal.archives-ouvertes.fr/hal-01158328

R. S. Lee, N. Radomski, J. F. Proulx, I. Levade, B. J. Shapiro et al., Population genomics of Mycobacterium tuberculosis in the Inuit, Proc Natl Acad Sci U S A, vol.112, issue.44, pp.13609-13614, 2015.

R. S. Lee, N. Radomski, J. F. Proulx, J. Manry, F. Mcintosh et al., Reemergence and amplification of tuberculosis in the Canadian arctic, J Infect Dis, vol.211, issue.12, pp.1905-1914, 2015.

X. Liu, M. M. Gutacker, J. M. Musser, and Y. X. Fu, Evidence for recombination in Mycobacterium tuberculosis, J Bacteriol, vol.188, p.8169, 2006.

N. J. Loman, R. V. Misra, T. J. Dallman, C. Constantinidou, S. E. Gharbia et al., Performance comparison of benchtop high-throughput sequencing platforms, Nat Biotechnol, vol.30, issue.5, pp.434-439, 2012.

H. Lu, F. Giordano, and Z. Ning, Oxford Nanopore MinION sequencing and genome assembly, Genomics Proteomics Bioinformatics, vol.14, issue.5, pp.265-279, 2016.

T. Luo, C. Yang, Y. Pang, Y. Zhao, J. Mei et al., Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China, PLoS One, vol.9, issue.2, p.89726, 2014.

T. Luo, C. Yang, Y. Peng, L. Lu, G. Sun et al., Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis, Tuberculosis (Edinb), vol.94, issue.4, pp.434-440, 2014.

T. Luo, I. Comas, D. Luo, B. Lu, J. Wu et al., Southern east Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese, Proc Natl Acad Sci U S A, vol.112, issue.26, pp.8136-8141, 2015.

S. Maeda, Y. Murase, S. Mitarai, I. Sugawara, and S. Kato, Rapid, simple genotyping method by the variable numbers of tandem repeats (VNTR) for Mycobacterium tuberculosis isolates in Japan-analytical procedure of JATA (12)-VNTR, Kekkaku, vol.83, issue.10, pp.673-678, 2008.

M. Maes, K. Kremer, D. Van-soolingen, H. Takiff, and J. H. De-waard, 24-locus MIRU-VNTR genotyping is a useful tool to study the molecular epidemiology of tuberculosis among Warao Amerindians in Venezuela, Tuberculosis (Edinb), vol.88, issue.5, pp.490-494, 2008.

J. Magdalena, P. Supply, and C. Locht, Specific differentiation between Mycobacterium bovis BCG and virulent strains of the Mycobacterium tuberculosis complex, J Clin Microbiol, vol.36, issue.9, pp.2471-2476, 1998.

M. C. Maiden, J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell et al., Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms, Proc Natl Acad Sci U S A, vol.95, issue.6, pp.3140-3145, 1998.

M. C. Maiden, J. Van-rensburg, M. J. Bray, J. E. Earle, S. G. Ford et al., MLST revisited: the gene-by-gene approach to bacterial genomics, Nat Rev Microbiol, vol.11, issue.10, pp.728-736, 2013.

K. S. Makarova, D. H. Haft, R. Barrangou, S. J. Brouns, E. Charpentier et al., Evolution and classification of the CRISPR-Cas systems, Nat Rev Microbiol, vol.9, issue.6, pp.467-477, 2011.

E. Mankiewicz and M. Liivak, Phage types of mycobacterium tuberculosis in cultures isolated from Eskimo patients, Am Rev Respir Dis, vol.111, issue.3, pp.307-312, 1975.

B. J. Marais, The global tuberculosis situation and the inexorable rise of drug-resistant disease, Adv Drug Deliv Rev, 2016.

T. Matsumoto, Y. Koshii, K. Sakane, T. Murakawa, Y. Hirayama et al., A novel approach to automated genotyping of Mycobacterium tuberculosis using a panel of 15 MIRU VNTRs, J Microbiol Methods, vol.93, issue.3, pp.239-241, 2013.

E. Mazars, S. Lesjean, A. L. Banuls, M. Gilbert, V. Vincent et al., High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology, Proc Natl Acad Sci U S A, vol.98, issue.4, pp.1901-1906, 2001.

E. V. Mbugi, B. Z. Katale, E. M. Streicher, J. D. Keyyu, S. L. Kendall et al., Mapping of mycobacterium tuberculosis complex genetic diversity profiles in Tanzania and other African countries, PLoS One, vol.11, issue.5, p.154571, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01652118

R. A. Mcadam, P. W. Hermans, D. Van-soolingen, Z. F. Zainuddin, D. Catty et al., Characterization of a Mycobacterium tuberculosis insertion sequence belonging to the IS3 family, Mol Microbiol, vol.4, issue.9, pp.1607-1613, 1990.

M. Merker, T. A. Kohl, A. Roetzer, L. Truebe, E. Richter et al., Whole genome sequencing reveals complex evolution patterns of multidrugresistant Mycobacterium tuberculosis Beijing strains in patients, PLoS One, vol.8, issue.12, p.82551, 2013.

M. Merker, C. Blin, S. Mona, N. Duforet-frebourg, S. Lecher et al., Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01153552

T. M. Michele, W. A. Cronin, N. M. Graham, D. M. Dwyer, D. S. Pope et al., Transmission of Mycobacterium tuberculosis by a fiberoptic bronchoscope. Identification by DNA fingerprinting, JAMA, vol.278, issue.13, pp.1093-1095, 1997.

M. Miyamoto, D. Motooka, K. Gotoh, T. Imai, K. Yoshitake et al., Performance comparison of second-and third-generation sequencers using a bacterial genome with two chromosomes, BMC Genomics, vol.15, p.699, 2014.

I. Mokrousov, Insights into the origin, emergence, and current spread of a successful Russian clone of Mycobacterium tuberculosis, Clin Microbiol Rev, vol.26, issue.2, pp.342-360, 2013.

I. Mokrousov, O. Narvskaya, A. Vyazovaya, J. Millet, T. Otten et al., Mycobacterium tuberculosis Beijing genotype in Russia: in search of informative variable-number tandemrepeat loci, J Clin Microbiol, vol.46, issue.11, pp.3576-3584, 2008.

I. Mokrousov, A. Vyazovaya, T. Iwamoto, Y. Skiba, I. Pole et al., Latin-American-Mediterranean lineage of Mycobacterium tuberculosis: human traces across pathogen's phylogeography, Mol Phylogenet Evol, vol.99, pp.133-143, 2016.

T. D. Mortimer and C. S. Pepperell, Genomic signatures of distributive conjugal transfer among mycobacteria, Genome Biol Evol, vol.6, issue.9, pp.2489-2500, 2014.

S. Mostowy, D. Cousins, J. Brinkman, A. Aranaz, and M. A. Behr, Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex, J Infect Dis, vol.186, issue.1, pp.74-80, 2002.

B. Muller, M. Hilty, S. Berg, M. C. Garcia-pelayo, J. Dale et al., African 1, an epidemiologically important clonal complex of Mycobacterium bovis dominant in Mali, J Bacteriol, vol.191, issue.6, pp.1951-1960, 2009.

C. A. Nadon, E. Trees, L. K. Ng, M. Nielsen, E. Reimer et al., Development and application of MLVA methods as a tool for inter-laboratory surveillance. Euro surveillance: bulletin Europeen sur les maladies transmissibles, Eur Commun Dis Bull, vol.18, issue.35, p.20565, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01118664

A. Namouchi, X. Didelot, U. Schock, B. Gicquel, and E. P. Rocha, After the bottleneck: genomewide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection, Genome Res, vol.22, issue.4, pp.721-734, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01374954

S. Niemann and P. Supply, Diversity and evolution of Mycobacterium tuberculosis: moving to wholegenome-based approaches, Cold Spring Harb Perspect Med, vol.4, issue.12, p.21188, 2014.

S. Niemann, S. Rusch-gerdes, and E. Richter, IS6110 fingerprinting of drug-resistant Mycobacterium tuberculosis strains isolated in Germany during 1995, J Clin Microbiol, vol.35, issue.12, pp.3015-3020, 1997.

S. Niemann, D. Harmsen, S. Rusch-gerdes, and E. Richter, Differentiation of clinical Mycobacterium tuberculosis complex isolates by gyrB DNA sequence polymorphism analysis, J Clin Microbiol, vol.38, issue.9, pp.3231-3234, 2000.

S. Niemann, S. Rusch-gerdes, E. Richter, H. Thielen, H. Heykes-uden et al., Stability of IS6110 restriction fragment length polymorphism patterns of Mycobacterium tuberculosis strains in actual chains of transmission, J Clin Microbiol, vol.38, issue.7, pp.2563-2567, 2000.

S. Niemann, C. U. Koser, S. Gagneux, C. Plinke, S. Homolka et al., Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints, PLoS One, vol.4, issue.10, p.7407, 2009.

V. Nikolayevskyy, K. Gopaul, Y. Balabanova, T. Brown, I. Fedorin et al., Differentiation of tuberculosis strains in a population with mainly Beijing-family strains, Emerg Infect Dis, vol.12, issue.9, pp.1406-1413, 2006.

V. Nikolayevskyy, A. Trovato, A. Broda, E. Borroni, D. Cirillo et al., MIRU-VNTR genotyping of mycobacterium tuberculosis strains using QIAxcel technology: a multicentre evaluation study, PLoS One, vol.11, issue.3, p.149435, 2016.

C. L. Nogueira, R. I. Prim, S. G. Senna, D. B. Rovaris, R. Maurici et al., First insight into the molecular epidemiology of Mycobacterium tuberculosis in Santa Catarina, southern Brazil, Tuberculosis (Edinb), vol.97, pp.57-64, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01305192

M. C. Oelemann, R. Diel, V. Vatin, W. Haas, S. Rusch-gerdes et al., Assessment of an optimized mycobacterial interspersed repetitiveunit-variable-number tandem-repeat typing system combined with spoligotyping for population-based molecular epidemiology studies of tuberculosis, J Clin Microbiol, vol.45, issue.3, pp.691-697, 2007.

L. J. Pankhurst, D. Ojo, E. C. Votintseva, A. A. Walker, T. M. Cole et al., Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study, Lancet Respir Med, vol.4, issue.1, pp.49-58, 2016.

C. S. Pepperell, A. M. Casto, A. Kitchen, J. M. Granka, O. E. Cornejo et al., The role of selection in shaping diversity of natural M. tuberculosis populations, PLoS Pathog, vol.9, issue.8, p.1003543, 2013.

L. Perez-lago, I. Comas, Y. Navarro, F. Gonzalez-candelas, M. Herranz et al., Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission, J Infect Dis, vol.209, issue.1, pp.98-108, 2014.

S. Poulet and C. St, Characterization of the highly abundant polymorphic GC-rich-repetitive sequence (PGRS) present in Mycobacterium tuberculosis, Arch Microbiol, vol.163, issue.2, pp.87-95, 1995.

H. Pouseele and P. Supply, Accurate whole-genome sequencing-based epidemiological surveillance of mycobacterium tuberculosis, Current and emerging technologies for the diagnosis of microbial infections, vol.45, pp.359-394, 2015.

G. Guilhot, C. Gutierrez, M. C. Varnerot, A. Gicquel, B. Vincent et al., Rapid discrimination of Mycobacterium tuberculosis complex strains by ligationmediated PCR fingerprint analysis, J Clin Microbiol, vol.35, issue.12, pp.3331-3334, 1997.

M. N. Ragheb, C. B. Ford, M. R. Chase, P. L. Lin, J. L. Flynn et al., The mutation rate of mycobactemacaque infection, BMC Genomics, vol.14, p.145, 2013.

J. W. Raleigh and R. Wichelhausen, Exogenous reinfection with Mycobacterium tuberculosis confirmed by phage typing, Am Rev Respir Dis, vol.108, issue.3, pp.639-642, 1973.

N. Reiling, S. Homolka, K. Walter, J. Brandenburg, L. Niwinski et al., Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice, mBio, vol.4, issue.4, 2013.

J. F. Reyes and M. M. Tanaka, Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis, Infect Genet Evol, vol.10, issue.7, pp.1046-1051, 2010.

E. Richter, M. Weizenegger, S. Rusch-gerdes, and S. Niemann, Evaluation of genotype MTBC assay for differentiation of clinical Mycobacterium tuberculosis complex isolates, J Clin Microbiol, vol.41, issue.6, pp.2672-2675, 2003.

A. Roetzer, S. Schuback, R. Diel, F. Gasau, T. Ubben et al., Evaluation of Mycobacterium tuberculosis typing methods in a 4-year study in Schleswig-Holstein, northern Germany, J Clin Microbiol, vol.49, issue.12, pp.4173-4178, 2011.

A. Roetzer, R. Diel, T. A. Kohl, C. Ruckert, U. Nubel et al., Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study, PLoS Med, vol.10, issue.2, p.1001387, 2013.

S. Roisin, C. Gaudin, D. Mendonca, R. Bellon, J. Van-vaerenbergh et al., Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services, Clin Microbiol Infect, vol.22, issue.6, pp.520-526, 2016.

S. Roring, A. Scott, D. Brittain, I. Walker, G. Hewinson et al., Development of variablenumber tandem repeat typing of Mycobacterium bovis: comparison of results with those obtained by using existing exact tandem repeats and spoligotyping, J Clin Microbiol, vol.40, issue.6, pp.2126-2133, 2002.

N. A. Rosenberg, A. G. Tsolaki, and M. M. Tanaka, Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis, Theor Popul Biol, vol.63, issue.4, pp.347-363, 2003.

L. Sandegren, R. Groenheit, T. Koivula, S. Ghebremichael, A. Advani et al., Genomic stability over 9 years of an isoniazid resistant Mycobacterium tuberculosis outbreak strain in Sweden, PLoS One, vol.6, issue.1, p.16647, 2011.

E. Savine, R. M. Warren, G. D. Van-der-spuy, N. Beyers, P. D. Van-helden et al., Stability of variable-number tandem repeats of mycobacterial interspersed repetitive units from 12 loci in serial isolates of Mycobacterium tuberculosis, J Clin Microbiol, vol.40, issue.12, pp.4561-4566, 2002.

A. C. Schurch, K. Kremer, A. Kiers, O. Daviena, M. J. Boeree et al., The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patientto-patient scale, Infect Genet Evol, vol.10, issue.1, pp.108-114, 2010.

I. C. Shamputa, L. Jugheli, N. Sadradze, E. Willery, F. Portaels et al., Mixed infection and clonal representativeness of a single sputum sample in tuberculosis patients from a penitentiary hospital in Georgia, Respir Res, vol.7, p.99, 2006.
URL : https://hal.archives-ouvertes.fr/inserm-00089426

A. Skrahina, H. Hurevich, A. Zalutskaya, E. Sahalchyk, A. Astrauko et al., Multidrug-resistant tuberculosis in Belarus: the size of the problem and associated risk factors, Bull World Health Organ, vol.91, issue.1, pp.36-45, 2013.

R. A. Skuce, T. P. Mccorry, J. F. Mccarroll, S. M. Roring, A. N. Scott et al., Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets, Microbiology, vol.148, pp.519-528, 2002.

P. M. Small, N. B. Mcclenny, S. P. Singh, G. K. Schoolnik, L. S. Tompkins et al., Molecular strain typing of Mycobacterium tuberculosis to confirm cross-contamination in the mycobacteriology laboratory and modification of procedures to minimize occurrence of false-positive cultures, J Clin Microbiol, vol.31, issue.7, pp.1677-1682, 1993.

P. M. Small, R. W. Shafer, P. C. Hopewell, S. P. Singh, M. J. Murphy et al., Exogenous reinfection with multidrug-resistant Mycobacterium tuberculosis in patients with advanced HIV infection, N Engl J Med, vol.328, issue.16, pp.1137-1144, 1993.

P. M. Small, P. C. Hopewell, S. P. Singh, A. Paz, J. Parsonnet et al., The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods, N Engl J Med, vol.330, issue.24, pp.1703-1709, 1994.

P. W. Smit, T. Vasankari, H. Aaltonen, M. Haanpera, N. Casali et al., Enhanced tuberculosis outbreak investigation using whole genome sequencing and IGRA, Eur Respir J, 2014.

N. H. Smith, R. G. Hewinson, K. Kremer, R. Brosch, S. Gordon et al., Collaborative effort for a centralized worldwide tuberculosis relational sequencing data platform, Clin Infect Dis, vol.61, issue.3, pp.141-146, 2009.

W. W. Stead and J. H. Bates, Primary tuberculosis from the Far East. Transmission by a veteran to two civilians, Ann Intern Med, vol.70, issue.4, pp.707-711, 1969.

D. Stucki, M. Ballif, T. Bodmer, M. Coscolla, A. M. Maurer et al., Tracking a tuberculosis outbreak over 21 years: strainspecific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing, J Infect Dis, vol.211, issue.8, pp.1306-1316, 2015.

D. Stucki, M. Ballif, M. Egger, H. Furrer, E. Altpeter et al., Standard genotyping overestimates transmission of mycobacterium tuberculosis among immigrants in a lowincidence country, J Clin Microbiol, vol.54, issue.7, pp.1862-1870, 2016.

D. Stucki, D. Brites, L. Jeljeli, M. Coscolla, Q. Liu et al., Nat Genet, vol.48, issue.12, pp.1535-1543, 2016.

P. N. Suffys, M. E. Ivens-de-araujo, M. L. Rossetti, A. Zahab, E. W. Barroso et al., Usefulness of IS6110-restriction fragment length polymorphism typing of Brazilian strains of Mycobacterium tuberculosis and comparison with an international fingerprint database, Res Microbiol, vol.151, issue.5, pp.343-351, 2000.

P. Supply, J. Magdalena, S. Himpens, and C. Locht, Identification of novel intergenic repetitive units in a mycobacterial two-component system operon, Mol Microbiol, vol.26, issue.5, pp.991-1003, 1997.

P. Supply, E. Mazars, S. Lesjean, V. Vincent, B. Gicquel et al., Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome, Mol Microbiol, vol.36, issue.3, pp.762-771, 2000.

P. Supply, S. Lesjean, E. Savine, K. Kremer, D. Van-soolingen et al., Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units, J Clin Microbiol, vol.39, issue.10, pp.3563-3571, 2001.

P. Supply, R. M. Warren, A. L. Banuls, S. Lesjean, . Van-der et al., Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area, Mol Microbiol, vol.47, issue.2, pp.529-538, 2003.

P. Supply, C. Allix, S. Lesjean, M. Cardoso-oelemann, S. Rusch-gerdes et al., Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis, J Clin Microbiol, vol.44, issue.12, pp.4498-4510, 2006.

, whole genome sequencing, Clin Microbiol Infect

T. M. Walker, M. K. Lalor, A. Broda, S. Ortega, L. Morgan et al., Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 200712, with whole pathogen genome sequences: an observational study, Lancet Respir Med, vol.2, issue.4, pp.285-292, 2014.

W. Wang, B. Mathema, Y. Hu, Q. Zhao, W. Jiang et al., Role of casual contacts in the recent transmission of tuberculosis in settings with high disease burden, Clin Microbiol Infect, vol.20, issue.11, pp.1140-1145, 2014.

R. M. Warren, S. L. Sampson, M. Richardson, . Van-der, G. D. Spuy et al., Mapping of IS6110 flanking regions in clinical isolates of Mycobacterium tuberculosis demonstrates genome plasticity, Mol Microbiol, vol.37, issue.6, pp.1405-1416, 2000.

R. M. Warren, T. C. Victor, E. M. Streicher, M. Richardson, G. D. Van-der-spuy et al., Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis, 2004.

, J Clin Microbiol, vol.42, issue.12, pp.5774-5782

T. Weniger, J. Krawczyk, P. Supply, S. Niemann, and D. Harmsen, MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria, Nucleic Acids Res, vol.38, pp.326-331, 2010.

G. Wiid, I. J. Werely, C. Beyers, N. Donald, P. Van-helden et al., Oligonucleotide (GTG)5 as a marker for Mycobacterium tuberculosis strain identification, J Clin Microbiol, vol.32, issue.5, pp.1318-1321, 1994.

O. M. Williams, T. Abeel, N. Casali, K. Cohen, A. S. Pym et al., Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing, Emerg Infect Dis, vol.21, issue.6, pp.1082-1084, 2015.

T. Wirth, F. Hildebrand, C. Allix-beguec, F. Wolbeling, T. Kubica et al., Origin, spread and demography of the Mycobacterium tuberculosis complex, PLoS Pathog, vol.4, issue.9, p.1000160, 2008.

R. W. Yeh, A. Ponce-de-leon, C. B. Agasino, J. A. Hahn, C. L. Daley et al., Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides, J Clin Microbiol, vol.177, issue.4, pp.4628-4639, 1998.

Y. Zhang and D. Young, Strain variation in the katG region of Mycobacterium tuberculosis, Mol Microbiol, vol.14, issue.2, pp.301-308, 1994.

R. Andries, K. Villellas, C. Coeck, and N. , Acquired resistance of Mycobacterium tuberculosis to bedaquiline, PLoS One, vol.9, p.102135, 2014.

R. Biek, O. G. Pybus, L. -. Smith, J. O. Didelot, and X. , Measurably evolving pathogens in the genomic era, Trends Ecol Evol, vol.30, pp.306-313, 2015.

P. A. Black, M. De-vos, and G. E. Louw, Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates, BMC Genomics, vol.16, p.857, 2015.

G. V. Bloemberg, P. M. Keller, and D. Stucki, Acquired resistance to bedaquiline and delamanid int for tuberculosis, N Engl J Med, vol.373, pp.1986-1988, 2015.

P. Bradley, N. C. Gordon, and T. M. Walker, Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis, Nat Commun, vol.6, p.10063, 2015.

A. C. Brown, J. M. Bryant, and K. Einer-jensen, Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples, J Clin Microbiol, vol.53, pp.2230-2237, 2015.

J. M. Bryant, S. R. Harris, and J. Parkhill, Whole-genome sequencing to establish relapse or reinfection with Mycobacterium tuberculosis: a retrospective observational study, Lancet Respir Med, vol.1, pp.786-792, 2013.

J. M. Bryant, A. C. Schürch, and H. Van-deutekom, Inferring patient to patient transmission of Mycobac, 2013.

I. Moser, W. M. Prodinger, H. Hotzel, R. Greenwald, K. P. Lyashchenko et al., Mycobacterium pinnipedii: transmission from South American sea lion (Otaria byronia) to Bactrian camel (Camelus bactrianus bactrianus) and Malayan tapirs (Tapirus indicus), Vet Microbiol, vol.127, pp.399-406, 2008.

S. Mostowy, D. Cousins, and M. A. Behr, Genomic interrogation of the dassie bacillus reveals it as a unique RD1 mutant within the Mycobacterium tuberculosis complex, J Bacteriol, vol.186, pp.104-109, 2004.

B. Muller, S. Durr, S. Alonso, J. Hattendorf, C. J. Laisse et al., Zoonotic Mycobacterium bovis-induced tuberculosis in humans, Emerg Infect Dis, vol.19, pp.899-908, 2013.

M. Mendoza, M. Juan, L. Menendez, S. Ocampo, A. Mourelo et al., Tuberculosis due to Mycobacterium bovis and Mycobacterium caprae in sheep, Vet J, vol.191, pp.267-269, 2012.

D. Murphy, E. Costello, F. E. Aldwell, S. Lesellier, M. A. Chambers et al., Oral vaccination of badgers (Meles meles) against tuberculosis: comparison of the protection generated by BCG vaccine strains Pasteur and Danish, Vet J, vol.200, pp.362-367, 2014.

S. Niemann, E. Richter, H. Dalugge-tamm, H. Schlesinger, D. Graupner et al., Two cases of Mycobacterium microti derived tuberculosis in HIV-negative immunocompetent patients, Emerg Infect Dis, vol.6, pp.539-542, 2000.

S. Niemann, E. Richter, and S. Rusch-gerdes, Biochemical and genetic evidence for the transfer of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to the species Mycobacterium bovis Karlson and Lessel 1970 (approved lists 1980) as Mycobacterium bovis subsp. caprae comb. nov, Int J Syst Evol Microbiol, vol.52, pp.433-436, 2002.

F. J. Olea-popelka, O. Flynn, E. Costello, G. Mcgrath, J. D. Collins et al., Spatial relationship between Mycobacterium bovis strains in cattle and badgers in four areas in Ireland, vol.71, pp.57-70, 2005.

F. J. Olea-popelka, P. Fitzgerald, P. White, G. Mcgrath, J. D. Collins et al., Targeted badger removal and the subsequent risk of bovine tuberculosis in cattle herds in county Laois, Prev Vet Med, vol.88, pp.178-184, 2009.

J. M. Pang, E. Layre, L. Sweet, A. Sherrid, D. B. Moody et al., The polyketide Pks1 contributes to biofilm formation in Mycobacterium tuberculosis, J Bacteriol, vol.194, pp.715-721, 2012.

A. Parra, P. Fernandez-llario, A. Tato, J. Larrasa, A. Garcia et al., Epidemiology of Mycobacterium bovis infections of pigs and wild boars using a molecular approach, Vet Microbiol, vol.97, pp.123-133, 2003.

S. D. Parsons, J. A. Drewe, G. Van-pittius, N. C. Warren, R. M. Van-helden et al., Novel cause of tuberculosis in meerkats, South Africa. Emerg Infect Dis, vol.19, pp.2004-2007, 2013.

M. Pate, T. Svara, M. Gombac, T. Paller, M. Zolnir-dovc et al., Outbreak of tuberculosis caused by Mycobacterium caprae in a zoological garden, J Vet Med B Infect Dis Vet Public Health, vol.53, pp.387-392, 2006.

J. Perez, R. Garcia, H. Bach, D. Waard, J. H. Jacobs et al., Mycobacterium tuberculosis transporter MmpL7 is a potential substrate for kinase PknD, Biochem Biophys Res Commun, vol.348, pp.6-12, 2006.

M. A. Perez-jacoiste-asin, M. Fernandez-ruiz, F. Lopezmedrano, C. Lumbreras, A. Tejido et al., Bacillus Calmette-Guerin (BCG) infection following intravesical BCG administration as adjunctive therapy for bladder cancer: incidence, risk factors, and outcome in a single-institution series and review of the literature, Medicine (Baltimore), vol.93, pp.236-254, 2014.

M. Pesciaroli, J. Alvarez, M. B. Boniotti, M. Cagiola, D. Marco et al., Tuberculosis in domestic animal species, Res Vet Sci, vol.97, pp.78-85, 2014.

J. Piercy, D. Werling, and T. J. Coffey, Differential responses of bovine macrophages to infection with bovine-specific and non-bovine specific mycobacteria, Tuberculosis (Edinb), vol.87, pp.415-420, 2007.

W. M. Prodinger, A. Eigentler, F. Allerberger, M. Schonbauer, and W. Glawischnig, Infection of red deer, cattle, and humans with Mycobacterium bovis subsp. caprae in western Austria, J Clin Microbiol, vol.40, pp.2270-2272, 2002.

W. M. Prodinger, A. Indra, O. K. Koksalan, Z. Kilicaslan, and E. Richter, Mycobacterium caprae infection in humans, Expert Rev Anti-Infect Ther, vol.12, pp.1501-1513, 2014.

A. S. Pym, P. Brodin, R. Brosch, M. Huerre, and C. St, Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti, Mol Microbiol, vol.46, pp.709-717, 2002.

G. Rehren, S. Walters, P. Fontan, I. Smith, and A. M. Zarraga, Differential gene expression between Mycobacterium bovis and Mycobacterium tuberculosis, Tuberculosis (Edinb), vol.87, pp.347-359, 2007.

E. Rodriguez, L. P. Sanchez, S. Perez, L. Herrera, M. S. Jimenez et al., Human tuberculosis due to Mycobacterium bovis and M. caprae in Spain, vol.13, pp.1536-1541, 2004.

S. Rodriguez, J. Bezos, B. Romero, D. Juan, L. Alvarez et al., Monitoring of Animal, T (2011) Mycobacterium caprae infection in livestock and wildlife, Spain. Emerg Infect Dis, vol.17, pp.532-535

B. Said-salim, S. Mostowy, A. S. Kristof, and M. A. Behr, Mutations in Mycobacterium tuberculosis Rv0444c, the gene encoding anti-SigK, explain high level expression of MPB70 and MPB83 in Mycobacterium bovis, Mol Microbiol, vol.62, pp.1251-1263, 2006.

R. Abdallah, A. M. , G. Van-pittius, N. C. Champion, P. A. Cox et al., Type VII secretion-mycobacteria show the way, Nat Rev Microbiol, vol.5, pp.883-891, 2007.

A. M. Abdallah, N. D. Savage, M. Van-zon, L. Wilson, C. M. Vandenbroucke-grauls et al., The ESX-5 secretion system of Mycobacterium marinum modulates the macrophage response, J Immunol, vol.181, pp.7166-7175, 2008.

A. M. Abdallah, G. A. Hill-cawthorne, T. D. Otto, F. Coll, J. A. Guerra-assuncao et al., Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations, Sci Rep, vol.5, p.15443, 2015.

D. C. Alexander and M. A. Behr, Rv1773 is a transcriptional repressor deleted from BCG-Pasteur, Tuberculosis (Edinb), vol.87, pp.421-425, 2007.

S. M. Arend and D. Van-soolingen, Editor's choice: editorial commentary: low level INH-resistant BCG: a sheep in wolf's clothing?, Clin Infect Dis, vol.52, pp.89-93, 2011.

J. D. Aronson, C. F. Aronson, and H. C. Taylor, A twentyyear appraisal of BCG vaccination in the control of tuberculosis, AMA Arch Intern Med, vol.101, pp.881-893, 1958.

L. S. Ates, R. Ummels, S. Commandeur, R. Van-de-weerd, M. Sparrius et al., Essential role of the ESX-5 secretion system in outer membrane permeability of pathogenic mycobacteria, PLoS Genet, vol.11, p.1005190, 2015.

A. K. Azad, T. D. Sirakova, N. D. Fernandes, and P. E. Kolattukudy, Gene knockout reveals a novel gene cluster for the synthesis of a class of cell wall lipids unique to pathogenic mycobacteria, J Biol Chem, vol.272, pp.16741-16745, 1997.

G. Bai, M. A. Gazdik, D. D. Schaak, and K. A. Mcdonough, The Mycobacterium bovis BCG cyclic AMP receptorlike protein is a functional DNA binding protein in vitro and in vivo, but its activity differs from that of its M. tuberculosis ortholog, Rv3676, Infect Immun, vol.75, pp.5509-5517, 2007.

M. A. Behr, BCG-different strains, different vaccines?, Lancet Infect Dis, vol.2, pp.86-92, 2002.

M. A. Behr and D. R. Sherman, Mycobacterial virulence and specialized secretion: same story, different ending, Nat Med, vol.13, pp.286-287, 2007.

M. A. Behr and P. M. Small, A historical and molecular phylogeny of BCG strains, Vaccine, vol.17, pp.915-922, 1999.

M. A. Behr, M. A. Wilson, W. P. Gill, H. Salamon, G. K. Schoolnik et al., Comparative genomics of BCG vaccines by whole-genome DNA microarray, Science, vol.284, pp.1520-1523, 1999.

M. A. Behr, B. G. Schroeder, J. N. Brinkman, R. A. Slayden, and C. E. Barry, A point mutation in the mma3 gene is responsible for impaired methoxymycolic acid production in Mycobacterium bovis BCG strains obtained after 1927, J Bacteriol, vol.182, pp.3394-3399, 2000.

A. Belley, D. Alexander, D. Pietrantonio, T. Girard, M. Jones et al., Impact of methoxymycolic acid production by Mycobacterium bovis BCG vaccines, Infect Immun, vol.72, pp.2803-2809, 2004.

T. F. Brewer, Preventing tuberculosis with Bacillus Calmette-Guerin vaccine: a meta-analysis of the literature, Clin Infect Dis, vol.31, issue.3, pp.64-67, 2000.

R. Brosch, S. V. Gordon, C. Buchrieser, A. S. Pym, T. Garnier et al., Comparative genomics uncovers large tandem chromosomal duplications in Mycobacterium bovis BCG Pasteur, Yeast, vol.17, pp.111-123, 2000.

R. Brosch, S. V. Gordon, T. Garnier, K. Eiglmeier, W. Frigui et al., Genome plasticity of BCG and impact on vaccine efficacy, Proc Natl Acad Sci U S A, vol.104, pp.5596-5601, 2007.

L. Bryder, We shall not find salvation in inoculation': BCG vaccination in Scandinavia, Britain and the USA, 1921-1960, Soc Sci Med, vol.49, pp.1157-1167, 1999.

A. Calmette, L'ninfection bacillaire et la tuberculose chez l'homme et chez les animaux Calmette A, Bull Acad Med, vol.91, pp.787-796, 1922.

D. Charlet, S. Mostowy, A. D. Sit, L. Wiker, H. G. Behr et al., Reduced expression of antigenic proteins MPB70 and MPB83 in Mycobacterium bovis BCG strains due to a start codon mutation in sigK, Mol Microbiol, vol.56, pp.1302-1313, 2005.

J. M. Chen, S. T. Islam, H. Ren, and J. Liu, Differential productions of lipid virulence factors among BCG vaccine strains and implications on BCG safety, Vaccine, vol.25, pp.8114-8122, 2007.

J. M. Chen, S. Uplekar, S. V. Gordon, and C. St, A point mutation in cycA partially contributes to the Dcycloserine resistance trait of Mycobacterium bovis BCG vaccine strains, PLoS One, vol.7, p.43467, 2012.

G. A. Colditz, C. S. Berkey, F. Mosteller, T. F. Brewer, M. E. Wilson et al., The efficacy of bacillus Calmette-Guerin vaccination of newborns and infants in the prevention of tuberculosis: meta-analyses of the published literature, Pediatrics, vol.96, pp.29-35, 1995.

M. J. Corbel, U. Fruth, E. Griffiths, and I. Knezevic, Report on a WHO consultation on the characterisation of BCG strains, Vaccine, vol.22, pp.2675-2680, 2003.

G. Dreyer and R. L. Vollum, BC G. Lancet, vol.1, pp.9-15, 1931.

R. J. Dubos and C. H. Pierce, Differential characteristics in vitro and in vivo of several substrains of BCG. IV. Immunizing effectiveness, Am Rev Tuberc, vol.74, pp.699-717, 1956.

N. D. Fernandes, Q. L. Wu, D. Kong, X. Puyang, S. Garg et al., A mycobacterial extracytoplasmic sigma factor involved in survival following heat shock and oxidative stress, J Bacteriol, vol.181, pp.4266-4274, 1999.

P. E. Fine, Variation in protection by BCG: implications of and for heterologous immunity, Lancet, vol.346, pp.1339-1345, 1995.

R. Frothingham, H. G. Hills, and K. H. Wilson, Extensive DNA sequence conservation throughout the Mycobacterium tuberculosis complex, J Clin Microbiol, vol.32, pp.1639-1643, 1994.

T. Garnier, K. Eiglmeier, J. C. Camus, N. Medina, H. Mansoor et al., The complete genome sequence of Mycobacterium bovis, Proc Natl Acad Sci U S A, vol.100, pp.7877-7882, 2003.

M. Gheorghiu, J. Augier, and P. H. Lagrange, Maintenance and control of the French Bcg strain 1173-P2 (primary and secondary seed-lots), Bull Inst Pasteur, vol.81, pp.281-288, 1983.

S. V. Gordon, R. Brosch, A. Billault, T. Garnier, K. Eiglmeier et al., Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays, Mol Microbiol, vol.32, pp.643-655, 1999.

J. M. Grange, J. Gibson, T. W. Osborn, C. H. Collins, and M. D. Yates, What is BCG? Tubercle, vol.64, pp.129-139, 1983.

J. F. Griffin, D. N. Chinn, C. R. Rodgers, and C. G. Mackintosh, Optimal models to evaluate the protective efficacy of tuberculosis vaccines, Tuberculosis (Edinb), vol.81, pp.133-139, 2001.

K. M. Guinn, M. J. Hickey, S. K. Mathur, K. L. Zakel, J. E. Grotzke et al., Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis, Mol Microbiol, vol.51, pp.359-370, 2004.

S. Gupta, A. Sinha, and D. Sarkar, Transcriptional autoregulation by Mycobacterium tuberculosis PhoP involves recognition of novel direct repeat sequences in the regulatory region of the promoter, FEBS Lett, vol.580, pp.5328-5338, 2006.

T. Hsu, S. M. Hingley-wilson, C. B. Chen, M. Dai, A. Z. Morin et al., The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue, Proc Natl Acad Sci U S A, vol.100, pp.12420-12425, 2003.

R. C. Huard, M. Fabre, D. Haas, P. Lazzarini, L. Van-soolingen et al., Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex, J Bacteriol, vol.188, pp.4271-4287, 2006.

D. M. Hunt, J. W. Saldanha, J. F. Brennan, P. Benjamin, M. Strom et al., Single nucleotide polymorphisms that cause structural changes in the cyclic AMP receptor protein References Abudayyeh OO, Science, 2008.

L. R. Antonelli, G. Rothfuchs, A. Goncalves, R. Roffe, E. Cheever et al., Intranasal poly-IC treatment exacerbates tuberculosis in mice through the pulmonary recruitment of a pathogen-permissive monocyte/macrophage population, J Clin Invest, vol.120, issue.5, pp.1674-1682, 2010.

O. T. Avery and M. Heidelberger, Immunological relationships of cell constituents of pneumococcus: second paper, J Exp Med, vol.42, issue.3, pp.367-376, 1925.

A. G. Barbour, Q. Dai, B. I. Restrepo, H. G. Stoenner, and S. A. Frank, Pathogen escape from host immunity by a genome program for antigenic variation, Proc Natl Acad Sci U S A, vol.103, issue.48, pp.18290-18295, 2006.

E. Bautista, T. Chotpitayasunondh, Z. Gao, S. A. Harper, M. Shaw et al., Clinical aspects of pandemic 2009 influenza A (H1N1) virus infection, N Engl J Med, vol.362, issue.18, pp.1708-1719, 2010.

K. Beiter, F. Wartha, B. Albiger, S. Normark, A. Zychlinsky et al., An endonuclease allows Streptococcus pneumoniae to escape from neutrophil extracellular traps, Curr Biol: CB, vol.16, issue.4, pp.401-407, 2006.

M. P. Berry, C. M. Graham, F. W. Mcnab, Z. Xu, S. A. Bloch et al., An interferoninducible neutrophil-driven blood transcriptional signature in human tuberculosis, Nature, vol.466, issue.7309, pp.973-977, 2010.

K. S. Bhat, C. P. Gibbs, O. Barrera, S. G. Morrison, F. Jahnig et al., The opacity proteins of Neisseria gonorrhoeae strain MS11 are encoded by a family of 11 complete genes, Mol Microbiol, vol.5, issue.8, pp.1889-1901, 1991.

R. Blomgran and J. D. Ernst, Lung neutrophils facilitate activation of naive antigen-specific CD4C T cells during Mycobacterium tuberculosis infection, J Immunol, vol.186, issue.12, pp.7110-7119, 2011.

R. Blomgran, L. Desvignes, V. Briken, and J. D. Ernst, Mycobacterium tuberculosis inhibits neutrophil apoptosis, leading to delayed activation of naive CD4 T cells, Cell Host Microbe, vol.11, issue.1, pp.81-90, 2012.

C. I. Bloom, C. M. Graham, M. P. Berry, K. A. Wilkinson, T. Oni et al., Detectable changes in the blood transcriptome are present after two weeks of antituberculosis therapy, PLoS One, vol.7, issue.10, p.46191, 2012.

W. C. Brown, K. A. Brayton, C. M. Styer, and G. H. Palmer, The hypervariable region of Anaplasma marginale major surface protein 2 (MSP2) contains multiple immunodominant CD4C T lymphocyte epitopes that elicit variant-specific proliferative and IFN-gamma responses in MSP2 vaccinates, J Immunol, vol.170, issue.7, pp.3790-3798, 2003.

C. J. Cambier, K. K. Takaki, R. P. Larson, R. E. Hernandez, D. M. Tobin et al., Mycobacteria manipulate macrophage recruitment through coordinated use of membrane lipids, Nature, vol.505, issue.7482, pp.218-222, 2014.

J. A. Caminero, M. J. Pena, M. I. Campos-herrero, J. C. Rodriguez, O. Afonso et al., Exogenous reinfection with tuberculosis on a European island with a moderate incidence of disease, Am J Respir Crit Care Med, vol.163, 2001.

A. Cerwenka and L. L. Lanier, Natural killer cell memory in infection, inflammation and cancer, Nat Rev Immunol, vol.16, issue.2, pp.112-123, 2016.

A. A. Chackerian, J. M. Alt, T. V. Perera, C. C. Dascher, and S. M. Behar, Dissemination of Mycobacterium tuberculosis is influenced by host factors and precedes the initiation of T-cell immunity, Infect Immun, vol.70, issue.8, pp.4501-4509, 2002.

H. M. Chapel, M. Lee, R. Hargreaves, D. H. Pamphilon, and A. G. Prentice, Randomised trial of intravenous immunoglobulin as prophylaxis against infection in plateau-phase multiple myeloma. The UK Group for Immunoglobulin Replacement Therapy in Multiple Myeloma, Lancet, vol.343, issue.8905, pp.1059-1063, 1994.

S. C. Cheng, J. Quintin, R. A. Cramer, K. M. Shepardson, S. Saeed et al., ) mTOR-and HIF-1alpha-mediated aerobic glycolysis as metabolic basis for trained immunity, Science, vol.345, issue.6204, p.1250684, 2014.

A. Claessens, W. L. Hamilton, M. Kekre, T. D. Otto, A. Faizullabhoy et al., Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis, PLoS Genet, vol.10, issue.12, p.1004812, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01989273

I. Cohen, C. Parada, E. Acosta-gio, and C. Espitia, The PGRS domain from PE_PGRS33 of Mycobacterium tuberculosis is target of humoral immune response in mice and humans, Front Immunol, vol.5, p.236, 2014.

S. T. Cole, R. Brosch, J. Parkhill, T. Garnier, C. Churcher et al., Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence, Nature, vol.393, issue.6685, pp.537-544, 1998.

I. Comas, J. Chakravartti, P. M. Small, J. Galagan, S. Niemann et al., Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved, Nat Genet, vol.42, issue.6, pp.498-503, 2010.

G. Cooper, C. Rosenstein, A. Walter, and L. Peizer, The further separation of types among the pneumococci hitherto included in group iv and the development of therapeutic antisera for these types, J Exp Med, vol.55, issue.4, pp.531-554, 1932.

R. Copin, M. Coscolla, S. N. Seiffert, G. Bothamley, J. Sutherland et al., Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition, MBio, vol.5, issue.1, pp.960-00913, 2014.

M. Coscolla, R. Copin, J. Sutherland, F. Gehre, B. De-jong et al., M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens, Cell Host Microbe, vol.18, issue.5, pp.538-548, 2015.

H. Crawford, J. G. Prado, A. Leslie, S. Hue, I. Honeyborne et al., Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703restricted Gag epitope in chronic human immunodeficiency virus type 1 infection, J Virol, vol.81, issue.15, pp.8346-8351, 2007.

H. Crawford, W. Lumm, A. Leslie, M. Schaefer, D. Boeras et al., Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703-positive individuals and their transmission recipients, J Exp Med, vol.206, issue.4, pp.909-921, 2009.

N. J. Croucher, S. R. Harris, C. Fraser, M. A. Quail, J. Burton et al., Rapid pneumococcal evolution in response to clinical interventions, Science, vol.331, issue.6016, pp.430-434, 2011.

J. M. Cuevas, R. Geller, R. Garijo, J. Lopez-aldeguer, and R. Sanjuan, Extremely high mutation rate of HIV-1 in vivo, PLoS Biol, vol.13, issue.9, p.1002251, 2015.

K. W. Deitsch, S. A. Lukehart, and J. R. Stringer, Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens, Nat Rev Microbiol, vol.7, issue.7, pp.493-503, 2009.

G. Delogu and M. J. Brennan, Comparative immune response to PE and PE_PGRS antigens of Mycobacterium tuberculosis, Infect Immun, vol.69, issue.9, pp.5606-5611, 2001.

A. R. Dochez and L. J. Gillespie, A biologic classification of pneumococci by means of immunity reactions, JAMA, vol.61, pp.727-730, 1913.

N. C. Elde and H. S. Malik, The evolutionary conundrum of pathogen mimicry, Nat Rev Microbiol, vol.7, issue.11, pp.787-797, 2009.

A. L. Erickson, Y. Kimura, S. Igarashi, J. Eichelberger, M. Houghton et al., The outcome of hepatitis C virus infection is predicted by escape mutations in epitopes targeted by cytotoxic T lymphocytes, Immunity, vol.15, issue.6, pp.883-895, 2001.

J. D. Ernst, The immunological life cycle of tuberculosis, Nat Rev Immunol, vol.12, issue.8, pp.581-591, 2012.

D. R. Feikin, E. W. Kagucia, J. D. Loo, R. Link-gelles, M. A. Puhan et al., Serotype-specific changes in invasive pneumococcal disease after pneumococcal conjugate vaccine introduction: a pooled analysis of multiple surveillance sites, PLoS Med, vol.10, issue.9, p.1001517, 2013.

Y. Fu and J. E. Galan, A salmonella protein antagonizes Rac-1 and Cdc42 to mediate host-cell recovery after bacterial invasion, Nature, vol.401, issue.6750, pp.293-297, 1999.

P. A. Goepfert, W. Lumm, P. Farmer, P. Matthews, A. Prendergast et al., Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients, J Exp Med, vol.205, issue.5, pp.1009-1017, 2008.

L. A. Grohskopf, L. Z. Sokolow, S. J. Olsen, J. S. Bresee, K. R. Broder et al., Prevention and control of influenza with vaccines: recommendations of the advisory committee on immunization practices, United States, 2015-16 influenza season, MMWR Morb Mortal Wkly Rep, vol.64, issue.30, pp.818-825, 2015.

W. D. Hardt, L. M. Chen, K. E. Schuebel, X. R. Bustelo, and J. E. Galan, S. typhimurium encodes an activator of Rho GTPases that induces membrane ruffling and nuclear responses in host cells, Cell, vol.93, issue.5, pp.815-826, 1998.
URL : https://hal.archives-ouvertes.fr/inserm-00926613

A. M. Hebert, S. Talarico, D. Yang, R. Durmaz, C. F. Marrs et al., DNA polymorphisms in the pepA and PPE18 genes among clinical strains of Mycobacterium tuberculosis: implications for vaccine efficacy, Infect Immun, vol.75, issue.12, pp.5798-5805, 2007.

D. J. Hill, N. J. Griffiths, E. Borodina, and M. Virji, Cellular and molecular biology of Neisseria meningitidis colonization and invasive disease, Clin Sci (Lond), vol.118, issue.9, pp.547-564, 2010.

N. P. Hoe, K. Nakashima, S. Lukomski, D. Grigsby, M. Liu et al., Rapid selection of complement-inhibiting protein variants in group A Streptococcus epidemic waves, Nat Med, vol.5, issue.8, pp.924-929, 1999.

S. W. Hosea, E. J. Brown, M. I. Hamburger, and M. M. Frank, Opsonic requirements for intravascular clearance after splenectomy, N Engl J Med, vol.304, issue.5, pp.245-250, 1981.

P. Hraber, B. Korber, K. Wagh, E. E. Giorgi, T. Bhattacharya et al., Longitudinal antigenic sequences and sites from intra-host evolution (LASSIE) identifies immune-selected HIV variants, Virus, vol.7, issue.10, pp.5443-5475, 2015.

H. E. Hsu, K. A. Shutt, M. R. Moore, B. W. Beall, N. M. Bennett et al., Effect of pneumococcal conjugate vaccine on pneumococcal meningitis, N Engl J Med, vol.360, issue.3, pp.244-256, 2009.

J. D. Interrante, M. B. Haddad, L. Kim, and N. R. Gandhi, Exogenous reinfection as a cause of late recurrent tuberculosis in the United States, Ann Am Thorac Soc, vol.12, issue.11, pp.1619-1626, 2015.

M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J. A. Doudna et al., A programmable dual-RNAguided DNA endonuclease in adaptive bacterial immunity, Science, vol.337, issue.6096, pp.816-821, 2012.

R. A. Kaslow, M. Carrington, R. Apple, L. Park, A. Munoz et al., Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection, Nat Med, vol.2, issue.4, pp.405-411, 1996.

V. Kasprowicz, Y. H. Kang, M. Lucas, J. Schulze-zur-wiesch, T. Kuntzen et al., Hepatitis C virus (HCV) sequence variation induces an HCV-specific T-cell phenotype analogous to spontaneous resolution, J Virol, vol.84, issue.3, pp.1656-1663, 2010.

K. W. Koh, S. E. Soh, and G. T. Seah, Strong antibody responses to Mycobacterium tuberculosis PEPGRS62 protein are associated with latent and active tuberculosis, Infect Immun, vol.77, issue.8, pp.3337-3343, 2009.

B. Korber and S. Gnanakaran, The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility, Curr Opin HIV AIDS, vol.4, issue.5, pp.408-417, 2009.

J. Lannergard, M. C. Gustafsson, J. Waldemarsson, A. Norrbyteglund, M. Stalhammar-carlemalm et al., The Hypervariable region of Streptococcus pyogenes M protein escapes antibody attack by antigenic variation and weak immunogenicity, Cell Host Microbe, vol.10, issue.2, pp.147-157, 2011.

C. N. Larock, S. Dohrmann, J. Todd, R. Corriden, J. Olson et al., Group a streptococcal M1 protein sequesters cathelicidin to evade innate immune killing, Cell Host Microbe, vol.18, issue.4, pp.471-477, 2015.

C. W. Lawrence and T. J. Braciale, Activation, differentiation, and migration of naive virus-specific CD8C T cells during pulmonary influenza virus infection, J Immunol, vol.173, issue.2, pp.1209-1218, 2004.

C. W. Lawrence, R. M. Ream, and T. J. Braciale, Frequency, specificity, and sites of expansion of CD8C T cells during primary pulmonary influenza virus infection, J Immunol, vol.174, issue.9, pp.5332-5340, 2005.

M. B. Lawrenz, R. M. Wooten, and S. J. Norris, Effects of vlsE complementation on the infectivity of Borrelia burgdorferi lacking the linear plasmid lp28-1, Infect Immun, vol.72, issue.11, pp.6577-6585, 2004.

A. Lazaryan, W. Song, E. Lobashevsky, J. Tang, S. Shrestha et al., Human leukocyte antigen class I supertypes and HIV-1 control in African Americans, J Virol, vol.84, issue.5, pp.2610-2617, 2010.

Y. Li, K. Svehla, M. K. Louder, D. Wycuff, S. Phogat et al., Analysis of neutralization specificities in polyclonal sera derived from human immunodeficiency virus type 1-infected individuals, J Virol, vol.83, issue.2, pp.1045-1059, 2009.

F. T. Liang, J. Yan, M. L. Mbow, S. L. Sviat, R. D. Gilmore et al., Borrelia burgdorferi changes its surface antigenic expression in response to host immune responses, Infect Immun, vol.72, issue.10, pp.5759-5767, 2004.

T. Lillebaek, A. Dirksen, I. Baess, B. Strunge, V. O. Thomsen et al., Molecular evidence of endogenous reactivation of Mycobacterium tuberculosis after 33 years of latent infection, J Infect Dis, vol.185, issue.3, pp.401-404, 2002.

J. Maertzdorf, M. Ota, D. Repsilber, H. J. Mollenkopf, J. Weiner et al., Functional correlations of pathogenesis-driven gene expression signatures in tuberculosis, PLoS One, vol.6, issue.10, p.26938, 2011.

K. S. Makarova, Y. I. Wolf, and E. V. Koonin, Comparative genomics of defense systems in archaea and bacteria, Nucleic Acids Res, vol.41, issue.8, pp.4360-4377, 2013.

E. Martinez, J. Allombert, F. Cantet, A. Lakhani, N. Yandrapalli et al., Coxiella burnetii effector CvpB modulates phosphoinositide metabolism for optimal vacuole development, Proc Natl Acad Sci U S A, vol.113, issue.23, pp.3260-3269, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01999389

K. D. Mayer-barber, B. B. Andrade, D. L. Barber, S. Hieny, C. G. Feng et al., Innate and adaptive interferons suppress IL-1alpha and IL-1beta production by distinct pulmonary myeloid subsets during Mycobacterium tuberculosis infection, Immunity, vol.35, issue.6, pp.1023-1034, 2011.

K. D. Mayer-barber, B. B. Andrade, S. D. Oland, E. P. Amaral, D. L. Barber et al., Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk, Nature, vol.511, issue.7507, pp.99-103, 2014.

D. M. Mckinney, S. Southwood, D. Hinz, C. Oseroff, C. S. Arlehamn et al., A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population, Immunogenetics, vol.65, issue.5, pp.357-370, 2013.

J. D. Miller, R. G. Van-der-most, R. S. Akondy, J. T. Glidewell, S. Albott et al., Human effector and memory CD8C T cell responses to smallpox and yellow fever vaccines, Immunity, vol.28, issue.5, pp.710-722, 2008.

D. G. Mordue and L. D. Sibley, Intracellular fate of vacuoles containing Toxoplasma gondii is determined at the time of formation and depends on the mechanism of entry, J Immunol, vol.159, issue.9, pp.4452-4459, 1997.

D. G. Mordue, S. Hakansson, I. Niesman, and L. D. Sibley, Toxoplasma gondii resides in a vacuole that avoids fusion with host cell endocytic and exocytic vesicular trafficking pathways, Exp Parasitol, vol.92, issue.2, pp.87-99, 1999.

L. J. Morrison, L. Marcello, and R. Mcculloch, Antigenic variation in the African trypanosome: molecular mechanisms and phenotypic complexity, Cell Microbiol, vol.11, issue.12, pp.1724-1734, 2009.

K. P. Murphy, C. Weaver, J. M. Musser, A. Amin, and S. Ramaswamy, Negligible genetic diversity of mycobacterium tuberculosis host immune system protein targets: evidence of limited selective pressure, Genetics, vol.155, issue.1, pp.7-16, 2000.

M. G. Netea, L. A. Joosten, E. Latz, K. H. Mills, G. Natoli et al., Trained immunity: a program of innate immune memory in health and disease, Science, vol.352, issue.6284, p.1098, 2016.

H. J. Newton, L. J. Kohler, J. A. Mcdonough, M. Temochediaz, E. Crabill et al., A screen of Coxiella burnetii mutants reveals important roles for Dot/Icm effectors and host autophagy in vacuole biogenesis, PLoS Pathog, vol.10, issue.7, p.1004286, 2014.

U. K. Nivarthi, S. Gras, L. Kjer-nielsen, R. Berry, I. S. Lucet et al., An extensive antigenic footprint underpins immunodominant TCR adaptability against a hypervariable viral determinant, J Immunol, vol.193, issue.11, pp.5402-5413, 2014.

O. 'garra, A. Redford, P. S. Mcnab, F. W. Bloom, C. I. Wilkinson et al., The immune response in tuberculosis, Annu Rev Immunol, vol.31, pp.475-527, 2013.

S. E. Ohmit, J. G. Petrie, R. T. Cross, J. E. Monto, and A. S. , Influenza hemagglutination-inhibition antibody titer as a correlate of vaccine-induced protection, J Infect Dis, vol.204, issue.12, pp.1879-1885, 2011.

T. H. Ottenhoff, R. H. Dass, N. Yang, M. M. Zhang, H. E. Wong et al., Genome-wide expression profiling identifies type 1 interferon response pathways in active tuberculosis, PLoS One, vol.7, issue.9, p.45839, 2012.

R. Pantophlet and D. R. Burton, GP120: target for neutralizing HIV-1 antibodies, Annu Rev Immunol, vol.24, pp.739-769, 2006.

S. Paul, M. B. Dillon, L. Arlehamn, C. S. Huang, H. Davis et al., A population response analysis approach to assign class II HLAepitope restrictions, J Immunol, vol.194, issue.12, pp.6164-6176, 2015.

J. Persson, B. Beall, S. Linse, and G. Lindahl, Extreme sequence divergence but conserved ligand-binding specificity in Streptococcus pyogenes M protein, PLoS Pathog, vol.2, issue.5, p.47, 2006.

W. Peters, H. M. Scott, H. F. Chambers, J. L. Flynn, I. F. Charo et al., Chemokine receptor 2 serves an early and essential role in resistance to Mycobacterium tuberculosis, Proc Natl Acad Sci U S A, vol.98, issue.14, pp.7958-7963, 2001.

J. Peters, E. Fowler, M. Gatton, N. Chen, A. Saul et al., High diversity and rapid changeover of expressed var genes during the acute phase of Plasmodium falciparum infections in human volunteers, Proc Natl Acad Sci U S A, vol.99, issue.16, pp.10689-10694, 2002.

W. Peters, J. G. Cyster, M. Mack, D. Schlondorff, A. J. Wolf et al., CCR2-dependent trafficking of F4/80dim macrophages and CD11cdim/intermediate dendritic cells is crucial for T cell recruitment to lungs infected with Mycobacterium tuberculosis, J Immunol, vol.172, issue.12, pp.7647-7653, 2004.

B. Pichon, S. N. Ladhani, M. P. Slack, A. Segonds-pichon, N. J. Andrews et al., Changes in molecular epidemiology of streptococcus pneumoniae causing meningitis following introduction of pneumococcal conjugate vaccination in England and Wales, J Clin Microbiol, vol.51, issue.3, pp.820-827, 2013.

R. H. Plasterk, M. I. Simon, and A. G. Barbour, Transposition of structural genes to an expression sequence on a linear plasmid causes antigenic variation in the bacterium Borrelia hermsii, Nature, vol.318, issue.6043, pp.257-263, 1985.

D. G. Du-plessis, R. Warren, M. Richardson, J. J. Joubert, and P. D. Van-helden, Demonstration of reinfection and reactivation in HIV-negative autopsied cases of secondary tuberculosis: multilesional genotyping of Mycobacterium tuberculosis utilizing IS 6110 and other repetitive element-based DNA fingerprinting, Tuberculosis (Edinb), vol.81, issue.3, pp.211-220, 2001.

A. J. Potter, C. Trappetti, and J. C. Paton, Streptococcus pneumoniae uses glutathione to defend against oxidative stress and metal ion toxicity, J Bacteriol, vol.194, issue.22, pp.6248-6254, 2012.

A. Poulsen, Some clinical features of tuberculosis. 1. Incubation period, Acta Tuberc Scand, vol.24, issue.3-4, pp.311-346, 1950.

T. Proft, S. L. Moffatt, K. D. Weller, A. Paterson, D. Martin et al., The streptococcal superantigen SMEZ exhibits wide allelic variation, mosaic structure, and significant antigenic variation, J Exp Med, vol.191, issue.10, pp.1765-1776, 2000.

S. A. Ralph, C. Scheidig-benatar, and A. Scherf, Antigenic variation in Plasmodium falciparum is associated with movement of var loci between subnuclear locations, Proc Natl Acad Sci U S A, vol.102, issue.15, pp.5414-5419, 2005.

S. S. Richter, K. P. Heilmann, C. L. Dohrn, F. Riahi, D. J. Diekema et al., Pneumococcal serotypes before and after introduction of conjugate vaccines, United States, Emerg Infect Dis, vol.19, issue.7, pp.1074-1083, 1999.

J. D. Roberts, K. Bebenek, and T. A. Kunkel, The accuracy of reverse transcriptase from HIV-1, Science, vol.242, issue.4882, pp.1171-1173, 1988.

S. Saeed, J. Quintin, H. H. Kerstens, N. A. Rao, A. Aghajanirefah et al., Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity, Science, vol.345, issue.6204, p.1251086, 2014.

M. Samstein, H. A. Schreiber, I. M. Leiner, B. Susac, M. S. Glickman et al., Essential yet limited role for CCR2(C) inflammatory monocytes during Mycobacterium tuberculosis-specific T cell priming, vol.2, p.1086, 2013.

C. M. Sassetti and E. J. Rubin, Genetic requirements for mycobacterial survival during infection, Proc Natl Acad Sci U S A, vol.100, issue.22, pp.12989-12994, 2003.

C. M. Sassetti, D. H. Boyd, and E. J. Rubin, Genes required for mycobacterial growth defined by high density mutagenesis, Mol Microbiol, vol.48, issue.1, pp.77-84, 2003.

E. Segal, P. Hagblom, H. S. Seifert, and M. So, Antigenic variation of gonococcal pilus involves assembly of separated silent gene segments, Proc Natl Acad Sci U S A, vol.83, issue.7, pp.2177-2181, 1986.

D. J. Smith, A. S. Lapedes, J. C. De-jong, T. M. Bestebroer, G. F. Rimmelzwaan et al., Mapping the antigenic and genetic evolution of influenza virus, Science, issue.5682, pp.371-376, 2004.

S. Srivastava and J. D. Ernst, Cell-to-cell transfer of M. tuberculosis antigens optimizes CD4 T cell priming, Cell Host Microbe, vol.15, issue.6, pp.741-752, 2014.

S. Srivastava, P. S. Grace, and J. D. Ernst, Antigen export reduces antigen presentation and limits T cell control of M. tuberculosis, Cell Host Microbe, vol.19, issue.1, pp.44-54, 2016.

H. G. Stoenner, T. Dodd, and C. Larsen, Antigenic variation of Borrelia hermsii, J Exp Med, vol.156, issue.5, pp.1297-1311, 1982.

S. Talarico, M. D. Cave, C. F. Marrs, B. Foxman, L. Zhang et al., Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene among clinical isolates, J Clin Microbiol, vol.43, issue.10, pp.4954-4960, 2005.

S. Talarico, L. Zhang, C. F. Marrs, B. Foxman, M. D. Cave et al., Mycobacterium tuberculosis PE_PGRS16 and PE_PGRS26 genetic polymorphism among clinical isolates, Tuberculosis (Edinb), vol.88, issue.4, pp.283-294, 2008.

B. Thyagarajan and J. D. Bloom, The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin, vol.3, 2014.

T. Tsibane, D. C. Ekiert, J. C. Krause, O. Martinez, J. E. Crowe et al., Influenza human monoclonal antibody 1F1 interacts with three major antigenic sites and residues mediating human receptor specificity in H1N1 viruses, PLoS Pathog, vol.8, issue.12, p.1003067, 2012.

S. Uplekar, B. Heym, V. Friocourt, J. Rougemont, and C. St, Comparative genomics of Esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation, Infect Immun, vol.79, issue.10, pp.4042-4049, 2011.

S. A. Valkenburg, S. Quiñones-parra, S. Gras, N. Komadina, J. Mcvernon et al., Acute emergence and reversion of influenza A virus quasispecies within CD8C T cell antigenic peptides, Nat Commun, vol.4, 2013.

S. A. Valkenburg, T. M. Josephs, E. B. Clemens, E. J. Grant, T. H. Nguyen et al., Molecular basis for universal HLA-A*0201-restricted CD8C T-cell immunity against influenza viruses, Proc Natl Acad Sci U S A, vol.113, issue.16, pp.4440-4445, 2016.

J. L. Virelizier, Host defenses against influenza virus: the role of anti-hemagglutinin antibody, J Immunol, vol.115, issue.2, pp.434-439, 1975.

G. I. Vladimer, D. Weng, S. W. Paquette, S. K. Vanaja, V. A. Rathinam et al., The NLRP12 inflammasome recognizes Yersinia pestis, Immunity, vol.37, issue.1, pp.96-107, 2012.

S. Vuilleumier and S. Bonhoeffer, Contribution of recombination to the evolutionary history of HIV, Curr Opin HIV AIDS, vol.10, issue.2, pp.84-89, 2015.

R. O. Watson, S. L. Bell, D. A. Macduff, J. M. Kimmey, E. J. Diner et al., The cytosolic sensor cGAS detects Mycobacterium tuberculosis DNA to induce type I interferons and activate autophagy, Cell Host Microbe, vol.17, issue.6, pp.811-819, 2015.

K. E. Wiens and J. D. Ernst, The mechanism for type I interferon induction by Mycobacterium tuberculosis is bacterial strain-dependent, PLoS Pathog, vol.12, issue.8, p.1005809, 2016.

A. J. Wolf, B. Linas, G. J. Trevejo-nunez, K. E. Tamura, T. Takatsu et al., Mycobacterium tuberculosis infects dendritic cells with high frequency and impairs their function in vivo, J Immunol, vol.179, issue.4, pp.2509-2519, 2007.

A. J. Wolf, L. Desvignes, B. Linas, N. Banaiee, T. Tamura et al., Initiation of the adaptive immune response to Mycobacterium tuberculosis depends on antigen production in the local lymph node, not the lungs, J Exp Med, vol.205, issue.1, pp.105-115, 2008.

J. Wrammert, K. Smith, J. Miller, W. A. Langley, K. Kokko et al., Rapid cloning of high-affinity human monoclonal antibodies against influenza virus, Nature, vol.453, issue.7195, pp.667-671, 2008.

K. L. Wyres, L. M. Lambertsen, N. J. Croucher, L. Mcgee, V. Gottberg et al., Pneumococcal capsular switching: a historical perspective, J Infect Dis, vol.207, issue.3, pp.439-449, 2013.

W. Xu, M. R. Edwards, D. M. Borek, A. R. Feagins, A. Mittal et al., Ebola virus VP24 targets a unique NLS binding site on karyopherin alpha 5 to selectively compete with nuclear import of phosphorylated STAT1, Cell Host Microbe, vol.16, issue.2, pp.187-200, 2014.

Q. L. Yang and E. C. Gotschlich, Variation of gonococcal lipooligosaccharide structure is due to alterations in poly-G tracts in lgt genes encoding glycosyl transferases, J Exp Med, vol.183, issue.1, pp.323-327, 1996.

R. Abdallah, A. M. Verboom, T. Weerdenburg, E. M. , G. Van-pittius et al., PPE and PE_PGRS proteins of Mycobacterium marinum are transported via the type VII secretion system ESX, 2009.

, Mol Microbiol, vol.73, pp.329-340

S. Adindla and L. Guruprasad, Sequence analysis corresponding to the PPE and PE proteins in Mycobacterium tuberculosis and other genomes, J Biosci, vol.28, pp.169-179, 2003.

A. Ahmed, A. Das, and S. Mukhopadhyay, Immunoregulatory functions and expression patterns of PE/PPE family members: roles in pathogenicity and impact on anti-tuberculosis vaccine and drug design, IUBMB Life, vol.67, pp.414-427, 2015.

Y. Akhter, M. T. Ehebauer, S. Mukhopadhyay, and S. E. Hasnain, The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more, Biochimie, vol.94, pp.110-116, 2012.

L. S. Ates, E. N. Houben, and W. Bitter, Type VII secretion: a highly versatile secretion system, 2016.

K. N. Balaji, G. Goyal, Y. Narayana, M. Srinivas, R. Chaturvedi et al., Apoptosis triggered by Rv1818c, a PE family gene from Mycobacterium tuberculosis is regulated by mitochondrial intermediates in T cells, Microbes Infect, vol.9, pp.271-281, 2007.

K. Bansal, S. R. Elluru, Y. Narayana, R. Chaturvedi, S. A. Patil et al., PE_PGRS antigens of Mycobacterium tuberculosis induce maturation and activation of human dendritic cells, J Immunol, vol.184, pp.3495-3504, 2010.

K. Bansal, A. Y. Sinha, D. S. Ghorpade, S. K. Togarsimalemath, S. A. Patil et al., Src homology 3-interacting domain of Rv1917c of Mycobacterium tuberculosis induces selective maturation of human dendritic cells by regulating PI3K-MAPK-NF-kappaB signaling and drives Th2 immune responses, J Biol Chem, vol.285, pp.36511-36522, 2010.

S. Banu, N. Honore, B. Saint-joanis, D. Philpott, M. C. Prevost et al., Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens?, Mol Microbiol, vol.44, pp.9-19, 2002.

S. Basu, S. K. Pathak, A. Banerjee, S. Pathak, A. Bhattacharyya et al., Execution of macrophage apoptosis by PE_PGRS33 of Mycobacterium tuberculosis is mediated by Toll-like receptor 2-dependent release of tumor necrosis factor-alpha, J Mol Microbiol Biotechnol, vol.282, pp.97-109, 2007.

M. C. Mortier, E. Jongert, P. Mettens, and J. L. Ruelle, Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens, BMC Immunol, vol.16, p.63, 2015.

S. Mukhopadhyay, . Balaji, and . Kn, The PE and PPE proteins of Mycobacterium tuberculosis, Tuberculosis (Edinb), vol.91, pp.441-447, 2011.

S. Nair, P. A. Ramaswamy, S. Ghosh, D. C. Joshi, N. Pathak et al., The PPE18 of Mycobacterium tuberculosis interacts with TLR2 and activates IL-10 induction in macrophage, J Immunol, vol.183, pp.6269-6281, 2009.

A. Namouchi, A. Karboul, M. Fabre, M. C. Gutierrez, and H. Mardassi, Evolution of smooth tubercle Bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection, PLoS One, vol.8, p.64718, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-00859266

I. Palucci, S. Camassa, A. Cascioferro, M. Sali, S. Anoosheh et al., Contributes to Mycobacterium tuberculosis Entry in Macrophages through Interaction with TLR2, PLoS One, vol.11, p.150800, 2016.

M. Parra, N. Cadieux, T. Pickett, V. Dheenadhayalan, and M. J. Brennan, A PE protein expressed by Mycobacterium avium is an effective T-cell immunogen, Infect Immun, vol.74, pp.786-789, 2006.

S. Poulet and C. St, Characterization of the highly abundant polymorphic GC-rich-repetitive sequence (PGRS) present in Mycobacterium tuberculosis, Arch Microbiol, vol.163, pp.87-95, 1995.

B. Pourakbari, S. Mamishi, M. Marjani, M. Rasulinejad, S. Mariotti et al., Novel T-cell assays for the discrimination of active and latent tuberculosis infection: the diagnostic value of PPE family, Mol Diagn Ther, vol.19, pp.309-316, 2015.

A. S. Pym, P. Brodin, R. Brosch, M. Huerre, and C. St, Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti, Mol Microbiol, vol.46, pp.709-717, 2002.

H. Rachman, M. Strong, T. Ulrichs, L. Grode, J. Schuchhardt et al., Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis, Infect Immun, vol.74, pp.1233-1242, 2006.

L. Ramakrishnan, N. A. Federspiel, and S. Falkow, Granuloma-Specific Expression of Mycobacterium Virulence Proteins from the Glycine-Rich PE-PGRS Family, Science, vol.288, pp.1436-1439, 2000.

S. Raman, R. Hazra, C. C. Dascher, and R. N. Husson, Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence, J Bacteriol, vol.186, pp.6605-6616, 2004.

S. G. Reed, R. N. Coler, W. Dalemans, E. V. Tan, D. Cruz et al., Defined tuberculosis vaccine, Mtb72F/AS02A, evidence of protection in cynomolgus monkeys, Proc Natl Acad Sci U S A, vol.106, pp.2301-2306, 2009.

G. Rehren, S. Walters, P. Fontan, I. Smith, and A. M. Zarraga, Differential gene expression between Mycobacterium bovis and Mycobacterium tuberculosis, Tuberculosis (Edinb), vol.87, pp.347-359, 2007.

R. Riley, M. Pellegrini, and D. Eisenberg, Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis, PLoS Comput Biol, vol.4, p.1000174, 2008.

P. Aia, M. Kal, and E. Lavu, The burden of drug-resistant tuberculosis in Papua New Guinea: results of a large population-based survey, PLoS One, vol.11, 2016.

D. Almeida, C. Rodrigues, and T. F. Ashavaid, High incidence of the Beijing genotype among multidrugresistant isolates of Mycobacterium tuberculosis in a tertiary care, Clin Infect Dis, vol.40, pp.881-886, 2005.

O. J. Billington, T. D. Mchugh, and S. H. Gillespie, Physiological cost of rifampin resistance induced in vitro in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.43, pp.1866-1869, 1999.

S. M. Blower and T. Chou, Modeling the emergence of the "hot zones": tuberculosis and the amplification dynamics of drug resistance, Nat Med, vol.10, pp.1111-1116, 2004.

M. W. Borgdorff, New measurable indicator for tuberculosis case detection, Emerg Infect Dis, vol.10, pp.1523-1528, 2004.

J. A. Caminero, Likelihood of generating MDR-TB and XDR-TB under adequate National Tuberculosis Control Programme implementation, Int J Tuberc Lung Dis, vol.12, pp.869-877, 2008.

, Nosocomial transmission of multidrug-resistant tuberculosis among HIV-infected persons-Florida, Centers for Disease Control, vol.40, pp.585-591, 1991.

T. Cohen and M. Murray, Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness, Nat Med, vol.10, pp.1117-1121, 2004.

T. Cohen, C. Colijn, and B. Finklea, Are surveybased estimates of the burden of drug resistant TB too low? Insight from a simulation study, PLoS One, vol.3, 2008.

T. Cohen, B. L. Hedt, and M. Pagano, Estimating the magnitude and direction of bias in tuberculosis drug resistance surveys conducted only in the public sector: a simulation study, BMC Public Health, vol.10, p.355, 2010.

T. Cohen, H. E. Jenkins, and C. Lu, On the spread and control of MDR-TB epidemics: an examination of trends in anti-tuberculosis drug resistance surveillance data, Drug Resist Updat, vol.17, pp.105-123, 2014.

R. Coninx, D. Maher, H. Reyes, and M. Grzemska, Tuberculosis in prisons in countries with high prevalence, BMJ, vol.320, pp.440-442, 2000.

V. G. Coronado, C. M. Beck-sague, and M. D. Hutton, Transmission of multidrug-resistant Mycobacterium tuberculosis among persons with human immunodeficiency virus infection in an urban hospital: epidemiologic and restriction fragment length polymorphism analysis, J Infect Dis, vol.168, pp.1052-1055, 1993.

H. S. Cox, C. Mcdermid, and V. Azevedo, Epidemic levels of drug resistant tuberculosis (MDR and XDRTB) in a high HIV prevalence setting in Khayelitsha, South Africa. PLoS One, vol.5, p.13901, 2010.

J. Crofton and D. A. Mitchison, Streptomycin resistance in pulmonary tuberculosis, BMJ, vol.2, pp.1009-1015, 1948.

A. S. Dean, M. Zignol, and D. Falzon, HIV and multidrug-resistant tuberculosis: overlapping epidemics, Eur Respir J, vol.44, pp.251-254, 2014.

C. Dye and B. G. Williams, Criteria for the control of drug-resistant tuberculosis, Proc Natl Acad Sci U S A, vol.97, pp.8180-8185, 2000.

B. R. Edlin, J. I. Tokars, and M. H. Grieco, An outbreak of multidrug-resistant tuberculosis among hospitalized patients with the acquired immunodeficiency syndrome, N Engl J Med, vol.326, pp.1514-1521, 1992.

T. R. Frieden, T. Sterling, and A. Pablos-mendez, The emergence of drug-resistant tuberculosis in New York City, N Engl J Med, vol.328, pp.521-526, 1993.

T. R. Frieden, L. F. Sherman, and K. L. Maw, A multiinstitutional outbreak of highly drug-resistant tuberculosis: epidemiology and clinical outcomes, JAMA, vol.276, pp.1229-1235, 1996.

S. Gagneux, M. V. Burgos, and K. Deriemer, Impact of bacterial genetics on the transmission of isoniazidresistant Mycobacterium tuberculosis, PLoS Pathog, vol.2, p.61, 2006.

N. R. Gandhi, A. Moll, and A. W. Sturm, Extensively drug-resistant tuberculosis as a cause of death in patients co-infected with tuberculosis and HIV in a rural area of South Africa, Lancet, vol.368, pp.1575-1580, 2006.

N. R. Gandhi, D. Weissman, and P. Moodley, Nosocomial transmission of extensively drug-resistant tuberculosis in a rural hospital in South Africa, J Infect Dis, vol.207, pp.9-17, 2013.

I. Y. Gelmanova, S. Keshavjee, and V. T. Golubchikova, Barriers to successful tuberculosis treatment in Tomsk, Russian Federation: non-adherence, default and the acquisition of multidrug resistance, Bull World Health Organ, vol.85, pp.703-711, 2007.

J. A. Guerra-assunção, A. C. Crampin, and R. , Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area, 2015.

C. Habeenzu, S. Mitarai, and D. Lubasi, Tuberculosis and multidrug resistance in Zambian prisons, Int J Tuberc Lung Dis, vol.11, pp.1216-1220, 2007.

C. L. Heidebrecht, L. J. Podewils, and A. Pym, Assessing loval risk of rifampicin-resistant tuberculosis in KwaZulu-Natal, South Africa using lot quality assurance sampling, PLoS One, vol.11, p.153143, 2016.

H. E. Jenkins, V. Plesca, and A. Ciobanu, Assessing spatial heterogeneity of multidrug-resistant tuberculosis in a high-burden country, Eur Respir J, vol.42, pp.1291-1301, 2013.

H. E. Jenkins, M. Gegia, and J. Furin, Geographical heterogeneity of multidrug-resistant tuberculosis in Georgia, Euro Surveill, vol.19, p.20743, 2009.

H. E. Jenkins, A. W. Tolman, and C. M. Yuen, Incidence of multidrug-resistant tuberculosis disease in children: systematic review and global estimates, Lancet, vol.383, issue.14, pp.60195-60196, 2014.

E. A. Kendall, M. O. Fofana, and D. W. Dowdy, Burden of transmitted multidrug resistance in epidemics of tuberculosis: a transmission modelling analysis, Lancet Respir Med, vol.3, pp.963-972, 2015.

M. E. Kimerling, H. Kluge, and N. Vezhnina, Inadequacy of the current WHO re-treatment regimen in a central Siberian prison: treatment failure and MDRTB, Int J Tuberc Lung Dis, vol.3, pp.451-453, 1999.

M. Klopper, R. M. Warren, and C. Hayes, Emergence and spread of extensively and totally drug-resistant tuberculosis, South Africa. Emerg Infect Dis, vol.19, pp.449-455, 2013.

D. Lukoye, W. Ssengooba, and K. Musisi, Variation and risk factors of drug resistant tuberculosis in Sub-Saharan Africa: a systematic review and meta-analysis, BMC Public Health, vol.15, p.291, 2015.

Y. M. Mesfin, D. Hailemariam, S. Biadglign, and K. T. Kibret, Association between HIV/AIDS and multidrug resistance tuberculosis: a systematic review and meta-analysis, PLoS One, vol.9, p.82235, 2014.

C. K. Mlambo, R. M. Warren, and X. Poswa, Genotypic diversity of extensively drug-resistant tuberculosis (XDR-TB) in South Africa, Int J Tuberc Lung Dis, vol.12, pp.99-104, 2008.

L. Monno, G. Angarano, and S. Carbonara, Emergence of drug-resistant Mycobacterium tuberculosis in HIV-infected patients, Lancet, vol.337, p.852, 1991.

Y. Murase, S. Maeda, and H. Yamada, Clonal expansion of multidrug-resistant and extensively drugresistant tuberculosis, Japan. Emerg Infect Dis, vol.16, pp.948-954, 2010.

E. Nardell and A. Dharmadhikari, Turning off the spigot: reducing drug-resistant tuberculosis transmission in resource-limited settings, Int J Tuberc Lung Dis, vol.14, pp.1233-1243, 2010.

A. Nodieva, I. Jansone, and L. Broka, Recent nosocomial transmission and genotypes of multidrug-resistant Mycobacterium tuberculosis, Int J Tuberc Lung Dis, vol.14, pp.427-433, 2010.

A. Pablos-méndez, M. C. Raviglione, and A. Laszlo, Global surveillance for antituberculosis-drug resistance, 1994-1997. World Health OrganizationInternational Union against Tuberculosis and Lung Disease Working Group on Anti-Tuberculosis Drug Resistance Surveillance, N Engl J Med, vol.338, pp.1641-1649, 1998.

C. N. Paramasivan and P. Venkataraman, Drug resistance in tuberculosis in India, Indian J Med Res, vol.120, pp.377-386, 2004.

J. Perdigao, R. Macedo, and A. Malaquias, Genetic analysis of extensively drug-resistant Mycobacterium tuberculosis strains in Lisbon, Portugal, J Antimicrob Chemother, vol.65, pp.224-227, 2010.

M. Rifat, J. Hall, and C. Oldmeadow, Factors related to previous tuberculosis treatment of patients with multidrug-resistant tuberculosis in Bangladesh, BMJ Open, vol.5, p.8273, 2015.

L. Rigouts, O. Nolasco, and P. De-rijk, Newly developed primers for comprehensive amplification of the rpoB gene and detection of rifampin resistance in Mycobacterium tuberculosis, J Clin Microbiol, vol.45, pp.252-254, 2007.

A. Roetzer, R. Diel, and T. A. Kohl, Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study, PLoS Med, vol.10, p.1001387, 2013.

K. Schnippel, G. Meyer-rath, and L. Long, Diagnosing Xpert MTB/RIF negative TB: impact and cost of alternative algorithms for South Africa, S Afr Med J, vol.103, pp.101-106, 2013.

S. V. Shenoi, A. R. Escombe, and G. Friedland, Transmission of drug-susceptible and drug-resistant tuberculosis and the critical importance of airborne infection control in the era of HIV infection and highly active antiretroviral therapy rollouts, Clin Infect Dis, vol.50, issue.3, 2010.

D. Stuckler, S. Basu, M. Mckee, and L. King, Mass incarceration can explain population increases in TB and multidrug-resistant TB in European and central Asian countries, P Natl Acad Sci, vol.105, pp.13280-13285, 2008.

D. Ulmasova, G. Uzakova, and M. Tillyashayhov, Multidrug-resistant tuberculosis in Uzbekistan: results of a nationwide survey, Euro Surveill, 2010.

M. Uplekar, D. Weil, and K. Lonnroth, HIV and multidrug-resistant tuberculosis: overlapping risk factors, Eur Respir J, vol.385, pp.567-569, 2015.

C. D. Wells, J. P. Cegielski, and L. J. Nelson, HIV infection and multidrug-resistant tuberculosis: the perfect storm, J Infect Dis, vol.196, issue.1, pp.86-107, 2007.

M. B. Murray and M. C. Becerra, Geneva World Health Organization (2014c) Xpert MTB/RIF implementation manual. Technical and operational "howto": practical considerations World Health Organization (2014d) The use of delamanid in the treatment of multidrug-resistant tuberculosis. WHO/HTM/TB2014.23. Geneva World Health Organization (2016) Global tuberculosis report 2015. Geneva World Health Organization WHO End TB Strategy, The use of bedaquiline in the treatment of multidrug-resistant tuberculosis, vol.213, pp.287-294, 2013.

Y. Zhao, S. Xu, and L. Wang, National survey of drug-resistant tuberculosis in China, N Engl J Med, vol.366, pp.2161-2170, 2012.

M. Zignol, C. Sismanidis, and D. Falzon, Multidrug-resistant tuberculosis in children: evidence from global surveillance, Eur Respir J, vol.42, pp.701-707, 2013.

M. Zignol, A. Dean, and D. Falzon, Twenty years of global surveillance of anti-tuberculosis drug resistance: key achievements and findings, remaining challenges, future direction References Alangaden GJ, Antimicrob Agents Chemother, vol.42, issue.5, pp.1295-1297, 1998.

D. Almeida, T. Ioerger, S. Tyagi, S. Y. Li, K. Mdluli et al., Mutations in pepQ confer low-level resistance to bedaquiline and clofazimine in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.60, issue.8, pp.4590-4599, 2016.

E. Andre, L. Goeminne, A. Cabibbe, P. Beckert, K. Mukadi et al., Consensus numbering sys, 2016.

, Clin Microbiol Infect, vol.23, issue.16, pp.30393-30400

K. Andries, P. Verhasselt, J. Guillemont, H. W. Göhlmann, J. M. Neefs et al., A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis, Science, vol.307, issue.5707, pp.223-227, 2005.

K. Andries, C. Villellas, N. Coeck, K. Thys, T. Gevers et al., Acquired resistance of Mycobacterium tuberculosis to bedaquiline, PLoS One, vol.9, issue.7, p.102135, 2014.

M. Arentz, B. Sorensen, D. J. Horne, and J. L. Walson, Systematic review of the performance of rapid rifampicin resistance testing for drug-resistant tuberculosis, PLoS One, vol.8, issue.10, p.76533, 2013.

N. Arinaminpathy and D. Dowdy, Understanding the incremental value of novel diagnostic tests for tuberculosis, Nature, vol.528, issue.7580, pp.60-67, 2015.

,

A. Aubry, N. Veziris, E. Cambau, C. Truffot-pernot, V. Jarlier et al., Novel gyrase mutations in quinolone-resistant and-hypersusceptible clinical isolates of Mycobacterium tuberculosis: functional analysis of mutant enzymes, Antimicrob Agents Chemother, vol.50, issue.1, pp.104-112, 2006.

E. Avalos, D. Catanzaro, A. Catanzaro, T. Ganiats, S. Brodine et al., Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates: a systematic review, PLoS One, vol.10, issue.3, p.120470, 2015.

A. Banerjee, E. Dubnau, A. Quemard, V. Balasubramanian, K. S. Um et al., inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis, Science, vol.263, issue.5144, pp.227-230, 1994.

A. Banerjee, M. Sugantino, J. C. Sacchettini, and W. R. Jacobs, The mabA gene from the inhA operon of Mycobacterium tuberculosis encodes a 3-ketoacyl reductase that fails to confer isoniazid resistance, Microbiology, vol.144, pp.2697-2704, 1998.

F. Baquero, Low-level antibacterial resistance: a gateway to clinical resistance, Drug Resist Updat, vol.4, issue.2, pp.93-105, 2001.

P. Beckert, D. Hillemann, T. A. Kohl, J. Kalinowski, E. Richter et al., rplC T460C identified as a dominant mutation in linezolid-resistant Mycobacterium tuberculosis strains, Antimicrob Agents Chemother, vol.56, issue.5, pp.2743-2745, 2012.

Z. L. Berrada, S. G. Lin, T. C. Rodwell, D. Nguyen, G. F. Schecter et al., Rifabutin and rifampin resistance levels and associated rpoB mutations in clinical isolates of Mycobacterium tuberculosis complex, Diagn Microbiol Infect Dis, vol.85, issue.16, pp.30001-30004, 2016.

G. V. Bloemberg, P. M. Keller, D. Stucki, A. Trauner, S. Borrell et al., Acquired resistance to Bedaquiline and Delamanid in therapy for tuberculosis, N Engl J Med, vol.373, issue.20, pp.1986-1988, 2015.
DOI : 10.1056/nejmc1505196

URL : http://www.zora.uzh.ch/id/eprint/116926/1/NEJMc1505196.pdf

H. M. Blumberg, W. J. Burman, R. E. Chaisson, C. L. Daley, S. C. Etkind et al., /Centers for Disease Control and Prevention/Infectious Diseases Society of America: treatment of tuberculosis, Centers for Disease Control and Prevention and the Infectious Diseases Society, vol.167, pp.603-662, 2003.

T. Bodmer, G. Zürcher, P. Imboden, and A. Telenti, Mutation position and type of substitution in the beta-subunit of the RNA polymerase influence in-vitro activity of rifamycins in rifampicin-resistant Mycobacterium tuberculosis, J Antimicrob Chemother, vol.35, issue.2, pp.345-348, 1995.

C. C. Boehme, P. Nabeta, D. Hillemann, M. P. Nicol, S. Shenai et al., Rapid molecular detection of tuberculosis and rifampin resistance, N Engl J Med, vol.363, issue.11, pp.1005-1015, 2010.
DOI : 10.1056/nejmoa0907847

URL : http://europepmc.org/articles/pmc2947799?pdf=render

P. Bradley, N. C. Gordon, T. M. Walker, L. Dunn, S. Heys et al., Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis, Nat Commun, vol.6, p.10063, 2015.
DOI : 10.1038/ncomms10063

URL : https://www.nature.com/articles/ncomms10063.pdf

G. Brandis, M. Wrande, L. Liljas, and D. Hughes, Fitnesscompensatory mutations in rifampicin-resistant RNA polymerase, Mol Microbiol, vol.85, issue.1, pp.142-151, 2012.
DOI : 10.1111/j.1365-2958.2012.08099.x

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2958.2012.08099.x

F. Brossier, D. Guindo, A. Pham, F. Reibel, W. Sougakoff et al., Performance of the New V2.0 of the GenoType MTBDRsl test for the detection of resistance to second-line drugs in multidrug-resistant Mycobacterium tuberculosis complex strains, J Clin Microbiol, vol.54, 2016.

P. J. Campbell, G. P. Morlock, R. D. Sikes, T. L. Dalton, B. Metchock et al., Molecular detection of mutations associated with first-and second-line drug resistance compared with conventional drug susceptibility testing of mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.55, issue.5, pp.2032-2041, 2011.

G. Canetti, S. Froman, J. Grosset, P. Haudoroy, M. Langerová et al., Mycobacteria: laboratory methods for testing drug susceptibility and resistance, Bull WHO, vol.29, pp.565-578, 1963.

G. Canetti, W. Fox, A. Khomenco, H. T. Mahler, N. K. Menon et al., Advances in techniques of testing mycobacterial drug sensitivity, and the use of sensitivity tests in tuberculosis control programmes, Bull WHO, vol.41, pp.21-43, 1969.

M. Caws and F. A. Drobniewski, Molecular techniques in the diagnosis of Mycobacterium tuberculosis and the detection of drug resistance, Ann N Y Acad Sci, vol.953, pp.138-145, 2001.

S. Chakravorty, A. M. Simmonds, H. Parmar, and Y. Cao, The New Xpert MTB/RIF Ultra: Improving Detection of Mycobacterium tuberculosis and Resistance to Rifampin in an Assay Suitable for Point-of-Care Testing, mBio, vol.8, issue.4, pp.812-00817, 2017.

J. Y. Chien, W. Y. Chiu, S. T. Chien, C. J. Chiang, C. Y. Hsueh et al., Mutations in gyrA and gyrB among fluoroquinolone-and multidrug-resistant mycobacterium tuberculosis isolates, Antimicrob Agents Chemother, vol.60, issue.4, pp.2090-2096, 2016.
DOI : 10.1128/aac.01049-15

URL : https://aac.asm.org/content/60/4/2090.full.pdf

K. P. Choi, T. B. Bair, Y. M. Bae, and L. Daniels, Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium Bovis BCG, J Bacteriol, vol.183, issue.24, pp.7058-7066, 2001.

N. Coeck, B. C. Jong, M. Diels, P. De-rijk, E. Ardizzoni et al., Correlation of different phenotypic drug susceptibility testing methods for four fluoroquinolones in mycobacterium tuberculosis, J Antimicrob Chemother, vol.71, issue.5, pp.1233-1240, 2016.

R. J. Coker, Review: multidrug-resistant tuberculosis: public health challenges, Tropical Med Int Health, vol.9, issue.1, pp.25-40, 2004.
DOI : 10.1046/j.1365-3156.2003.01156.x

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-3156.2003.01156.x

F. Coll, R. Mcnerney, M. D. Preston, J. A. Guerra-assunção, A. Warry et al., Rapid determination of antituberculosis drug resistance from whole-genome sequences, Genome Med, vol.7, issue.1, p.51, 2015.

L. A. Collins and S. G. Franzblau, Microplate Alamar blue assay versus BACTEC 460 system for high-throughput screening of compounds against Mycobacterium tuberculosis and Mycobacterium avium, Antimicrob Agents Chemother, vol.41, pp.1004-1009, 1997.

I. Comas, S. Borrell, A. Roetzer, G. Rose, B. Malla et al., Whole-genome sequencing of rifampicin-resistant mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes, Nat Genet, vol.44, pp.106-110, 2011.

P. E. Silva, V. Groll, A. Martin, A. Palomino, and J. C. , Efflux as a mechanism for drug resistance in mycobacterium tuberculosis, FEMS Immunol Med Microbiol, vol.63, issue.1, pp.1-9, 2011.

V. Dartois and C. E. Barry, A medicinal chemists' guide to the unique difficulties of lead optimization for tuberculosis, Bioorg Med Chem Lett, vol.23, issue.17, pp.4741-4750, 2013.

V. Dartois, K. Saito, T. Warrier, and C. Nathan, New evidence for the complexity of the population structure of mycobacterium tuberculosis increases the diagnostic and biologic challenges, Am J Respir Crit Care Med, vol.194, issue.12, pp.1448-1451, 2016.

E. De-rossi, J. A. Aínsa, and G. Riccardi, Role of mycobacterial efflux transporters in drug resistance: an unresolved question, FEMS Microbiol Rev, vol.30, issue.1, pp.36-52, 2006.

M. De-vos, B. Müller, S. Borrell, P. A. Black, P. D. Van-helden et al., Putative compensatory mutations in the rpoC gene of rifampin-resistant mycobacterium tuberculosis are associated with ongoing transmission, Antimicrob Agents Chemother, vol.57, issue.2, pp.827-832, 2013.

C. M. Denkinger, S. G. Schumacher, C. C. Boehme, N. D. Pai, M. Steingart et al., Xpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis: a systematic review and meta-analysis, Eur Respir J, vol.44, issue.2, pp.435-446, 2014.

C. M. Denkinger, D. Dolinger, M. Schito, W. Wells, F. Cobelens et al., Target product profile of a molecular drug-susceptibility test for use in microscopy centers, J Infect Dis, vol.211, issue.2, pp.39-49, 2015.

D. W. Dowdy, R. E. Chaisson, G. Maartens, E. L. Corbett, and S. E. Dorman, Impact of enhanced tuberculosis diagnosis in South Africa: a mathematical model of expanded culture and drug susceptibility testing, Proc Natl Acad Sci U S A, vol.105, issue.32, pp.11293-11298, 2008.

F. Drobniewski, M. Cooke, J. Jordan, N. Casali, T. Mugwagwa et al., Systematic review, meta-analysis and economic modelling of molecular diagnostic tests for antibiotic resistance in tuberculosis, Health Technol Assess, vol.19, issue.34, pp.1-188, 2015.

E. W. Emmart, The tuberculostatic action of streptothricin and streptomycin with special reference to the action of streptomycin on the chorioallantoic membrane of the chick embryo, Public Health Rep, vol.60, pp.1415-1421, 1945.

I. Escribano, J. C. Rodríguez, B. Llorca, E. García-pachon, M. Ruiz et al., Importance of the efflux pump systems in the resistance of Mycobacterium tuberculosis to fluoroquinolones and linezolid, Chemotherapy, vol.53, issue.6, pp.397-401, 2007.

M. R. Farhat, C. D. Mitnick, M. F. Franke, D. Kaur, A. Sloutsky et al., Concordance of Mycobacterium tuberculosis fluoroquinolone resistance testing: implications for treatment, Int J Tuberc Lung Dis, vol.19, issue.3, pp.339-341, 2015.

M. R. Farhat, K. R. Jacobson, M. F. Franke, D. Kaur, A. Sloutsky et al., Gyrase mutations, 2016.

M. R. Farhat, R. Sultana, O. Iartchouk, S. Bozeman, J. Galagan et al., Genetic determinants of drug resistance in mycobacterium tuberculosis and their diagnostic value, Am J Respir Crit Care Med, vol.194, issue.5, pp.621-630, 2016.

S. Feuerriegel, C. U. Köser, D. Baù, S. Rüsch-gerdes, D. K. Summers et al., Impact of Fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824, Antimicrob Agents Chemother, vol.55, issue.12, pp.5718-5722, 2011.

S. Feuerriegel, C. U. Köser, and S. Niemann, Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex, J Antimicrob Chemother, vol.69, issue.5, pp.1205-1210, 2014.

S. Feuerriegel, V. Schleusener, P. Beckert, T. A. Kohl, P. Miotto et al., PhyResSE: a web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from whole-genome sequencing data, J Clin Microbiol, vol.53, issue.6, pp.1908-1914, 2015.

J. P. Flandrois, G. Lina, and O. Dumitrescu, MUBII-TBDB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis, BMC Bioinformatics, vol.15, p.107, 2014.

D. García-de-viedma, Rapid detection of resistance in Mycobacterium tuberculosis: a review discussing molecular approaches, Clin Microbiol Infect, vol.9, issue.5, pp.349-359, 2003.

S. B. Georghiou, M. Magana, R. S. Garfein, D. G. Catanzaro, A. Catanzaro et al., Evaluation of genetic mutations associated with Mycobacterium tuberculosis resistance to amikacin, kanamycin and capreomycin: a systematic review, PLoS One, vol.7, issue.3, p.33275, 2012.

C. A. Gilchrist, S. D. Turner, M. F. Riley, W. A. Petri, and E. L. Hewlett, Whole-genome sequencing in outbreak analysis, Clin Microbiol Rev, vol.28, issue.3, pp.541-563, 2015.

S. H. Gillespie, Evolution of drug resistance in Mycobacterium tuberculosis: clinical and molecular perspective, Antimicrob Agents Chemother, vol.46, issue.2, pp.267-274, 2002.

C. Gilpin, A. Korobitsyn, and K. Weyer, Current tools available for the diagnosis of drug-resistant tuberculosis, Ther Adv Infectious Dis, vol.3, pp.1-7, 2016.

B. P. Goldstein, Resistance to rifampicin: a review, J Antibiot (Tokyo), vol.67, issue.9, pp.625-630, 2014.

B. G. Guernsey and M. R. Alexander, Tuberculosis: review of treatment failure, relapse and drug resistance, Am J Hosp Pharm, vol.35, issue.6, pp.690-698, 1978.

L. Hall, K. P. Jude, S. L. Clark, K. Dionne, R. Merson et al., Evaluation of the Sensititre MycoTB plate for susceptibility testing of the Mycobacterium tuberculosis complex against firstand second-line agents, J Clin Microbiol, vol.50, issue.11, pp.3732-3734, 2012.

A. Harms, E. Maisonneuve, and K. Gerdes, Mechanisms of bacterial persistence during stress and antibiotic exposure, Science, vol.354, issue.6318, p.4268, 2016.

R. C. Hartkoorn, S. Uplekar, and C. St, Crossresistance between clofazimine and bedaquiline through upregulation of MmpL5 in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.58, issue.5, pp.2979-2981, 2014.

L. He, X. Wang, P. Cui, J. J. Chen, J. Zhang et al., ubiA (Rv3806c) encoding DPPR synthase involved in cell wall synthesis is associated with ethambutol resistance in Mycobacterium tuberculosis, Edinb), vol.95, issue.2, pp.149-154, 2015.

D. Hillemann, S. Rüsch-gerdes, and E. Richter, In vitroselected linezolid-resistant Mycobacterium tuberculosis mutants, Antimicrob Agents Chemother, vol.52, issue.2, pp.800-801, 2008.

M. Hoshide, L. Qian, C. Rodrigues, R. Warren, T. Victor et al., Geographical differences associated with single-nucleotide polymorphisms (SNPs) in nine gene targets among resistant clinical isolates of Mycobacterium tuberculosis, J Clin Microbiol, vol.52, issue.5, pp.1322-1329, 2014.

H. J. Huh, B. H. Jeong, K. Jeon, W. J. Koh, C. S. Ki et al., Performance evaluation of the Xpert MTB/RIF assay according to its clinical application, BMC Infect Dis, vol.14, p.589, 2014.

E. Huitric, P. Verhasselt, A. Koul, K. Andries, S. Hoffner et al., Rates and mechanisms of resistance development in Mycobacterium tuberculosis to a novel diarylquinoline, ATP synthase inhibitor. Antimicrob Agents Chemother, vol.54, issue.3, pp.1022-1028, 2010.

B. R. Imperiale, D. Giulio, Á. B. , A. Cataldi, A. Morcillo et al., Evaluation of Mycobacterium tuberculosis cross-resistance to isoniazid, rifampicin and levofloxacin with their respective structural analogs, J Antibiot (Tokyo), vol.67, issue.11, pp.749-754, 2014.

F. B. Jamieson, J. L. Guthrie, A. Neemuchwala, O. Lastovetska, R. G. Melano et al., Profiling of rpoB mutations and MICs for rifampin and rifabutin in Mycobacterium tuberculosis, J Clin Microbiol, vol.52, issue.6, pp.2157-2162, 2014.

G. L. Jiang, X. Chen, Y. Song, Y. Zhao, H. Huang et al., First proficiency testing of second-line antituberculosis drug susceptibility testing in 12 provinces of China, Int J Tuberc Lung Dis, vol.17, issue.11, pp.1491-1494, 2013.

K. W. Jo, S. D. Lee, W. S. Kim, D. S. Kim, and T. S. Shim, Treatment outcomes and moxifloxacin susceptibility in ofloxacin-resistant multidrug-resistant tuberculosis, Int J Tuberc Lung Dis, vol.18, issue.1, pp.39-43, 2014.

S. K. Johansen, C. E. Maus, B. B. Plikaytis, and S. Douthwaite, Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2 0-O-methylations in 16S and23S rRNAs, Mol Cell, vol.23, issue.2, pp.173-182, 2006.

D. Jones, H. J. Metzger, A. Schatz, and S. A. Waksman, Control of gram-negative bacteria in experimental animals by streptomycin, Science, vol.100, pp.103-105, 1944.

K. M. Kam, C. W. Yip, T. L. Cheung, H. S. Tang, O. C. Leung et al., Stepwise decrease in moxifloxacin susceptibility amongst clinical isolates of multidrugresistant Mycobacterium tuberculosis: correlation with ofloxacin susceptibility, Microb Drug Resist, vol.12, issue.1, 2006.

P. Kambli, K. Ajbani, M. Sadani, C. Nikam, A. Shetty et al., Correlating minimum inhibitory concentrations of ofloxacin and moxifloxacin with gyrA mutations using the genotype MTBDRsl assay, Tuberculosis (Edinb), vol.95, issue.2, pp.137-141, 2015.

P. Kambli, K. Ajbani, C. Nikam, M. Sadani, A. Shetty et al., Correlating rrs and eis promoter mutations in clinical isolates of Mycobacterium tuberculosis with phenotypic susceptibility levels to the second-line injectables, Int J Mycobacteriol, vol.5, issue.1, pp.1-6, 2016.

C. L. Kelley, D. A. Rouse, and S. L. Morris, Analysis of ahpC gene mutations in isoniazid-resistant clinical isolates of Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.41, issue.9, pp.2057-2058, 1997.

P. T. Kent and G. P. Kubica, Public health mycobacteriology. A guide for the level III laboratory, pp.159-184, 1985.

S. V. Kik, C. M. Denkinger, M. Casenghi, C. Vadnais, and M. Pai, Tuberculosis diagnostics: which target product profiles should be prioritised?, Eur Respir J, vol.44, issue.2, pp.537-540, 2014.

S. J. Kim, Drug-susceptibility testing in tuberculosis: methods and reliability of results, Eur Respir J, vol.25, issue.3, pp.564-569, 2005.

C. U. Köser, J. M. Bryant, J. Becq, M. E. Török, M. J. Ellington et al., Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis, N Engl J Med, vol.369, issue.3, pp.290-292, 2013.

G. Kronvall, Normalized resistance interpretation as a tool for establishing epidemiological MIC susceptibility breakpoints, J Clin Microbiol, vol.48, issue.12, pp.4445-4452, 2010.

A. S. Lee, A. S. Teo, and S. Y. Wong, Novel mutations in ndh in isoniazid-resistant Mycobacterium tuberculosis isolates, Antimicrob Agents Chemother, vol.45, issue.7, pp.2157-2159, 2001.

N. Lemaitre, W. Sougakoff, C. Truffot-pernot, and V. Jarlier, Characterization of new mutations in pyrazinamide-resistant strains of Mycobacterium tuberculosis and identification of conserved regions important for the catalytic activity of the pyrazinamidase PncA, Antimicrob Agents Chemother, vol.43, issue.7, pp.1761-1763, 1999.

D. I. Ling, A. A. Zwerling, and M. Pai, GenoType MTBDR assays for the diagnosis of multidrug-resistant tuberculosis: a meta-analysis, Eur Respir J, vol.32, issue.5, pp.1165-1174, 2008.

S. Lingaraju, L. Rigouts, A. Gupta, J. Lee, A. N. Umubyeyi et al., , 2016.

, Ethambutol Resistance in Mycobacterium tuberculosis, Antimicrob Agents Chemother

C. K. Lippincott, M. B. Miller, A. Van-rie, D. J. Weber, A. C. Sena et al., The complexities of Xpert ® MTB/RIF interpretation, Int J Tuberc Lung Dis, vol.19, issue.3, pp.273-275, 2015.

G. E. Louw, R. M. Warren, G. Van-pittius, N. C. Mcevoy, C. R. Van-helden et al., A balancing act: efflux/influx in mycobacterial drug resistance, Antimicrob Agents Chemother, vol.53, issue.8, pp.3181-3189, 2009.

B. Madison, B. Robinson-dunn, and G. I. , Multicenter evaluation of ethambutol susceptibility testing of Mycobacterium tuberculosis by agar proportion and radiometric methods, J Clin Microbiol, vol.40, pp.3976-3979, 2002.

G. G. Makafe, Y. Cao, Y. Tan, J. M. Liu, Z. Wang et al., Role of the Cys154Arg substitution in ribosomal protein L3 in Oxazolidinone resistance in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.60, issue.5, pp.3202-3206, 2016.

S. Malik, M. Willby, D. Sikes, O. V. Tsodikov, and J. E. Posey, New insights into fluoroquinolone resistance in Mycobacterium tuberculosis: functional genetic analysis of gyrA and gyrB mutations, PLoS One, vol.7, issue.6, p.39754, 2012.

U. H. Manjunatha, H. Boshoff, C. S. Dowd, L. Zhang, T. J. Albert et al., Identification of a nitroimidazo-oxazinespecific protein involved in PA-824 resistance in Mycobacterium tuberculosis, Proc Natl Acad Sci U S A, vol.103, issue.2, pp.431-436, 2006.

J. L. Martínez, T. M. Coque, and F. Baquero, What is a resistance gene? Ranking risk in resistomes, Nat Rev Microbiol, vol.13, issue.2, pp.116-123, 2015.

H. J. Marttila and H. Soini, Molecular detection of resistance to antituberculous therapy, Clin Lab Med, vol.23, issue.4, pp.823-841, 2003.

M. Matsumoto, H. Hashizume, T. Tomishige, M. Kawasaki, H. Tsubouchi et al., OPC-67683, a nitro-dihydro-imidazooxazole derivative with promising action against tuberculosis in vitro and in mice, PLoS Med, vol.3, issue.11, p.466, 2006.

C. E. Maus, B. B. Plikaytis, and T. M. Shinnick, Molecular analysis of cross-resistance to capreomycin, kanamycin, amikacin, and viomycin in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.49, issue.8, pp.3192-3197, 2005.

P. Miotto, A. M. Cabibbe, S. Feuerriegel, N. Casali, F. Drobniewski et al., Mycobacterium tuberculosis pyrazinamide resistance determinants: a multicenter study, MBio, vol.5, issue.5, pp.1819-1833, 2014.

P. Miotto, D. M. Cirillo, and G. B. Migliori, Drug resistance in Mycobacterium tuberculosis: molecular mechanisms challenging fluoroquinolones and pyrazinamide effectiveness, Chest, vol.147, issue.4, pp.1135-1143, 2015.

D. A. Moore, D. Mendoza, R. H. Gilman, C. A. Evans, H. Delgado et al., Microscopic observation drug susceptibility assay, a rapid, reliable diagnostic test for multidrug-resistant tuberculosis suitable for use in resource-poor settings, J.Clin.Microbiol, vol.42, pp.4432-4437, 2004.

M. Morgan, S. Kalantri, L. Flores, and M. Pai, A commercial line probe assay for the rapid detection of rifampicin resistance in Mycobacterium tuberculosis: a systematic review and meta-analysis, BMC Infect Dis, vol.5, p.62, 2005.

C. Nathan, Fresh approaches to anti-infective therapies, Sci Transl Med, vol.4, issue.140, pp.140-142, 2012.

R. R. Nathavitharana, D. Hillemann, S. G. Schumacher, B. Schlueter, N. Ismail et al., A Multi-Center Non-inferiority Evaluation of Hain GenoType MTBDRplus Version 2 and Nipro NTMCMDRTB lineprobe assays for the diagnosis of Rifampin and Isoniazid Resistance, J Clin Microbiol, 2016.

E. Y. Nosova, A. A. Bukatina, Y. D. Isaeva, M. V. Makarova, K. Y. Galkina et al., Analysis of mutations in the gyrA and gyrB genes and their association with the resistance of Mycobacteriumtuberculosis to levofloxacin, moxifloxacin and gatifloxacin, J Med Microbiol, vol.62, pp.108-113, 2013.

S. Okamoto, A. Tamaru, C. Nakajima, K. Nishimura, Y. Tanaka et al., Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria, 2007.

, Mol Microbiol, vol.63, issue.4, pp.1096-1106

B. Pandey, S. Grover, C. Tyagi, S. Goyal, S. Jamal et al., Molecular principles behind pyrazinamide resistance due to mutations in panD gene in Mycobacterium tuberculosis, Gene, vol.581, issue.1, pp.31-42, 2016.

L. J. Pankhurst, C. Del-ojo-elias, A. A. Votintseva, T. M. Walker, K. Cole et al., Comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study, Clin Microbiol Rev, vol.4, issue.1, pp.314-350, 2011.

R. J. Patel, J. W. Fries, W. F. Piessens, and D. F. Wirth, Sequence analysis and amplification by polymerase chain reaction of a cloned DNA fragment for identification of Mycobacterium tuberculosis, J Clin Microbiol, vol.28, issue.3, pp.513-518, 1990.

C. Piersimoni, A. Mustazzolu, F. Giannoni, S. Bornigia, G. Gherardi et al., Prevention of false resistance results obtained in testing the susceptibility of Mycobacterium tuberculosis to pyrazinamide with the, 2013.

, Bactec MGIT 960 system using a reduced inoculum, J Clin Microbiol, vol.51, issue.1, pp.291-294

N. V. Punina, N. M. Makridakis, M. A. Remnev, and A. F. Topunov, Whole-genome sequencing targets drugresistant bacterial infections, Hum Genomics, vol.9, p.19, 2015.

S. Ramaswamy and J. M. Musser, Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update, Tuber Lung Dis, vol.79, issue.1, pp.3-29, 1998.

S. M. Ramirez-busby and F. Valafar, Systematic review of mutations in pyrazinamidase associated with pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates, Antimicrob Agents Chemother, vol.59, issue.9, pp.5267-5277, 2015.

A. Z. Reeves, P. J. Campbell, R. Sultana, S. Malik, M. Murray et al., Aminoglycoside cross-resistance in Mycobacterium tuberculosis due to mutations in the 5 0 untranslated region of whiB7, Antimicrob Agents Chemother, vol.57, issue.4, pp.1857-1865, 2013.

L. Rigouts, M. Gumusboga, W. B. De-rijk, E. Nduwamahoro, C. Uwizeye et al., Rifampin resistance missed in automated liquid culture system for Mycobacterium tuberculosis isolates with specific rpoB mutations, J Clin Microbiol, vol.51, issue.8, pp.2641-2645, 2013.

L. Rigouts, N. Coeck, M. Gumusboga, W. B. De-rijk, K. J. Aung et al., Specific gyrA gene mutations predict poor treatment outcome in MDR-TB, 2016.

, J Antimicrob Chemother, vol.71, issue.2, pp.314-323

J. Rueda, T. Realpe, G. I. Mejia, E. Zapata, J. C. Rozo et al., Genotypic analysis of genes associated with independent resistance and cross-resistance toIsoniazid and Ethionamide in Mycobacterium tuberculosis clinical isolates, Antimicrob Agents Chemother, vol.59, issue.12, pp.7805-7810, 2015.

S. B. Rufai, P. Kumar, A. Singh, S. Prajapati, V. Balooni et al., Comparison of Xpert MTB/RIF with line probe assay for detection of rifampin-monoresistant Mycobacterium tuberculosis, J Clin Microbiol, vol.52, issue.6, pp.1846-1852, 2014.

S. Rüsch-gerdes, C. Domehl, G. Nardi, M. R. Gismondo, H. M. Welscher et al., Multicenter evaluation of the mycobacteria growth indicator tube for testing susceptibility of Mycobacterium tuberculosis to first-line drugs, J Clin Microbiol, vol.37, issue.1, pp.45-48, 1999.

H. Safi, S. Lingaraju, A. Amin, S. Kim, M. Jones et al., Evolution of high-level ethambutolresistant tuberculosis through interacting mutations in decaprenylphosphoryl-"-D-arabinose biosynthetic and utilization pathway genes, Nat Genet, vol.45, issue.10, pp.1190-1197, 2013.

E. Sanchez-padilla, M. Merker, P. Beckert, F. Jochims, T. Dlamini et al., Detection of drug-resistant tuberculosis by Xpert MTB/RIF in Swaziland, N Engl J Med, vol.372, issue.12, pp.1181-1182, 2015.

I. Saraav, K. Pandey, R. Misra, S. Singh, M. Sharma et al., Characterization of MymA protein as a flavincontaining monooxygenase and as a target of isoniazid, Chem Biol Drug Des, vol.89, issue.1, pp.152-160, 2017.

E. Schena, L. Nedialkova, E. Borroni, S. Battaglia, A. M. Cabibbe et al., Delamanid susceptibility testing of Mycobacterium tuberculosis using the resazurin microtitre assay and the BACTEC? MGIT? 960 system, J Antimicrob Chemother, vol.71, issue.6, pp.1532-1539, 2016.

M. Schito and D. L. Dolinger, A collaborative approach for "ReSeq-ing" Mycobacterium tuberculosis drug resistance: convergence for drug and diagnostic developers, EBioMedicine, vol.2, issue.10, pp.1262-1265, 2015.

E. Segala, W. Sougakoff, A. Nevejans-chauffour, V. Jarlier, and S. Petrella, New mutations in the mycobacterial ATP synthase: new insights into the binding of the diarylquinoline TMC207 to the ATP synthase C-ring structure, Antimicrob Agents Chemother, vol.56, issue.5, pp.2326-2334, 2012.

M. Seifert, D. Catanzaro, A. Catanzaro, and T. C. Rodwell, Genetic mutations associated with isoniazid resistance in Mycobacterium tuberculosis: a systematic review, PLoS One, vol.10, issue.3, p.119628, 2015.

M. Seifert, S. B. Georghiou, D. Catanzaro, C. Rodrigues, V. Crudu et al., MTBDRplus and MTBDRsl assays: absence of wild-type probe hybridization and implications for detection of drug-resistant tuberculosis, J Clin Microbiol, vol.54, issue.4, pp.912-918, 2016.

P. Singh, A. Jain, P. Dixit, S. Prakash, I. Jaiswal et al., Prevalence of gyrA and B gene mutations in fluoroquinolone-resistant and-sensitive clinical isolates of Mycobacterium tuberculosis and their relationship with MIC of ofloxacin, J Antibiot (Tokyo), vol.68, issue.1, pp.63-66, 2015.

V. Sintchenko, W. K. Chew, P. J. Jelfs, and G. L. Gilbert, Mutations in rpoB gene and rifabutin susceptibility of multidrug-resistant Mycobacterium tuberculosis strains isolated in Australia, Pathology, vol.31, issue.3, pp.257-260, 1999.

R. A. Slayden and C. E. Barry, The genetics and biochemistry of isoniazid resistance in mycobacterium tuberculosis, Microbes Infect, vol.2, issue.6, pp.659-669, 2000.

D. G. Smith and S. A. Waskman, Tuberculostatic and tuberculocidal action of streptomycin, J Bacteriol, vol.54, issue.1, p.67, 1947.

T. Smith, K. A. Wolff, and L. Nguyen, Molecular biology of drug resistance in Mycobacterium tuberculosis, Curr Top Microbiol Immunol, vol.374, pp.53-80, 2013.

A. Somoskovi and M. Salfinger, The race is on to shorten the turnaround time for diagnosis of multidrugresistant tuberculosis, J Clin Microbiol, vol.53, issue.12, pp.3715-3718, 2015.

S. Sreevatsan, X. Pan, K. E. Stockbauer, D. L. Williams, B. N. Kreiswirth et al., Characterization of rpsL and rrs mutations in streptomycin-resistant Mycobacterium tuberculosis isolates from diverse geographic localities, Antimicrob Agents Chemother, vol.40, issue.4, pp.1024-1026, 1996.

S. Sreevatsan, X. Pan, Y. Zhang, V. Deretic, and J. M. Musser, Analysis of the oxyR-ahpC region in isoniazidresistant and-susceptible Mycobacterium tuberculosis complex organisms recovered from diseased humans and animals in diverse localities, Antimicrob Agents Chemother, vol.41, issue.3, pp.600-606, 1997.

A. M. Starks, E. Avilés, D. M. Cirillo, C. M. Denkinger, D. L. Dolinger et al., Collaborative effort for a centralized worldwide tuberculosis relational sequencing data platform, Clin Infect Dis, vol.61, issue.3, pp.141-146, 2015.

A. Steiner, D. Stucki, M. Coscolla, S. Borrell, and S. Gagneux, KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes, BMC Genomics, vol.15, p.881, 2014.

K. R. Steingart, I. Schiller, D. J. Horne, M. Pai, C. C. Boehme et al., Xpert ® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults, Cochrane Database Syst Rev, vol.1, p.9593, 2014.

C. K. Stover, P. Warrener, D. R. Vandevanter, D. R. Sherman, T. M. Arain et al., Small-molecule nitroimidazopyran drug candidate for the treatment of tuberculosis, Nature, vol.405, issue.6789, pp.962-966, 2000.

E. Tagliani, A. M. Cabibbe, P. Miotto, E. Borroni, J. C. Toro et al., Diagnostic performance of the new version (v2.0) of GenoType MTBDRsl assay for detection of resistance to fluoroquinolones and second-line injectable drugs: a multicenter study, J Clin Microbiol, vol.53, issue.9, pp.2961-2969, 2015.

A. Telenti, P. Imboden, F. Marchesi, D. Lowrie, S. Cole et al., Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis, Lancet, vol.341, issue.8846, pp.647-650, 1993.

A. Telenti, W. J. Philipp, S. Sreevatsan, C. Bernasconi, K. E. Stockbauer et al., The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol, Nat Med, vol.3, issue.5, pp.567-570, 1997.

G. Theron, J. Peter, M. Richardson, M. Barnard, S. Donegan et al., The diagnostic accuracy of the GenoType ® MTBDRsl assay for the detection of resistance to second-line anti-tuberculosis drugs, Cochrane Database Syst Rev, vol.10, p.10705, 2014.

G. Torrea, N. Coeck, C. Desmaretz, T. Van-de-parre, T. Van-poucke et al., Bedaquiline susceptibility testing of Mycobacterium tuberculosis in an automated liquid culture system, J Antimicrob Chemother, vol.70, issue.8, pp.2300-2305, 2015.

E. Tortoli, M. Benedetti, A. Fontanelli, and M. T. Simonetti, Evaluation of automated BACTEC MGIT 960 system for testing susceptibility of Mycobacterium tuberculosis to four major antituberculous drugs: comparison with the radiometric BACTEC 460TB method and the agar plate method of proportion, JClinMicrobiol, vol.40, pp.607-610, 2002.

P. W. Uys, R. Warren, P. D. Van-helden, M. Murray, and T. C. Victor, Potential of rapid diagnosis for controlling drug-susceptible and drug-resistant tuberculosis in communities where Mycobacterium tuberculosis infections are highly prevalent, J Clin Microbiol, vol.47, issue.5, pp.1484-1490, 2009.

A. Van-deun, K. J. Aung, A. Hossain, P. De-rijk, M. Gumusboga et al., Disputed rpoB mutations can frequently cause important rifampicin resistance among newtuberculosis patients, Int J Tuberc Lung Dis, vol.19, issue.2, pp.185-190, 2015.

H. R. Van-doorn, E. C. Claas, K. E. Templeton, A. G. Van-der-zanden, A. Te-koppele-vije et al., Detection of a point mutation associated with high-level isoniazid resistance in Mycobacterium tuberculosis by using real-time PCR technology with 3 0-minor groove binder-DNA probes, J Clin Microbiol, vol.41, issue.10, pp.4630-4635, 2003.

C. Vilchèze, T. R. Weisbrod, B. Chen, L. Kremer, M. H. Hazbón et al., Altered NADH/NADC ratio mediates coresistance to isoniazid and ethionamide in mycobacteria, Antimicrob Agents Chemother, vol.49, issue.2, pp.708-720, 2005.

Y. Wakamoto, N. Dhar, R. Chait, K. Schneider, F. Signorinogelo et al., Dynamic persistence of antibiotic-stressed mycobacteria, Science, vol.339, issue.6115, pp.91-95, 2013.

T. Walker, T. Kohl, S. Omar, J. Hedge, D. Ojo et al., Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study, The Lancet Infectious Diseases, vol.15, pp.62-68, 2015.

W. A. Wells, C. C. Boehme, F. G. Cobelens, C. Daniels, D. Dowdy et al., Alignment of new tuberculosis drug regimens and drug susceptibility testing: a framework for action, Lancet Infect Dis, vol.13, issue.5, pp.449-458, 2013.

M. G. Whitfield, H. M. Soeters, R. M. Warren, T. York, S. L. Sampson et al., A global perspective on pyrazinamide resistance: systematic review and meta-analysis, PLoS One, vol.10, issue.7, p.133869, 2015.

M. Willby, R. D. Sikes, S. Malik, B. Metchock, and J. E. Posey, Correlation between GyrA substitutions and ofloxacin, levofloxacin, and moxifloxacin crossresistance in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.59, issue.9, pp.5427-5434, 2015.

D. A. Williamson, I. Basu, J. Bower, J. T. Freeman, G. Henderson et al., An evaluation of the Xpert MTB/RIF assay and detection of false-positive rifampicin resistance in Mycobacterium tuberculosis, 2012.

, Diagn Microbiol Infect Dis, vol.74, issue.2, pp.207-209, 2012.

A. A. Witney, K. A. Gould, A. Arnold, D. Coleman, R. Delgado et al., Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases, J Clin Microbiol, vol.53, issue.5, pp.1473-1483, 2015.

S. Y. Wong, J. S. Lee, H. K. Kwak, L. E. Via, H. I. Boshoff et al., Mutations in gidB confer low-level streptomycin resistance in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.55, issue.6, pp.2515-2522, 2011.

, Anti-tuberculosis drug resistance in the world, World Health Organization, 2004.

, Molecular line probe assays for rapid screening of patients at risk of multidrug resistant tuberculosis (MDR-TB), Expert group report. WHO, Geneva World Health Organization (2012a) Tuberculosis laboratory biosafety manual. WHO, World Health Organization, vol.978, pp.92-96, 2008.

, Summary of outcomes from WHO expert group meeting on drug susceptibility testing. 4th annual GLI meeting 17, World Health Organization, 2012.

, Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB/RIF assay for the: diagnosis of pulmonary and extrapulmonary TB in adults and children, Policy update. WHO, World Health Organization, pp.978-92, 2013.

, Geneva World Health Organization (2016) The use of molecular line probe assays for the detection of resistance to second-line antituberculosis drugs, Policy guidance. WHO, UNITAID (2015) Tuberculosis. Diagnostics technology and market land-scape, vol.978, pp.150963-150966

W. , G. Xu, Y. Jia, H. Huang, H. Sun et al., Mutations found in embCAB, embR, and ubiA genes of ethambutol-sensitive and-resistant Mycobacterium tuberculosis clinical isolates from China, UNITAID (2015) Tuberculosis diagnostics technology and market landscape, vol.2015, p.951706, 2015.

J. Xu, B. Wang, M. Hu, F. Huo, S. Guo et al., Primary clofazimine and bedaquiline resistance among isolates from patients with multidrug-resistant tuberculosis, Antimicrob Agents Chemother, vol.61, issue.6, pp.239-256, 2017.

J. Yang, J. Liu, Y. Bi, J. Cai, Q. Liao et al., , 2015.

R. Alam, M. K. Alhhazmi, A. Decoteau, J. F. Luo, Y. Geyer et al., RecA inhibitors potentiate antibiotic activity and block evolution of antibiotic resistance, Cell Chem Biol, vol.23, issue.3, pp.381-391, 2016.

C. Barreiro, R. Ullan, T. Barros, J. Guenther, B. Kelch et al., A structural role for the PHP domain in E. coli DNA polymerase III, BMC Struct Biol, vol.13, issue.8, 2013.

T. Basta, Y. Boum, J. Briffotaux, H. F. Becker, I. Lamarrejouenne et al., Mechanistic and structural basis for inhibition of thymidylate synthase ThyX, Open Biol, vol.2, p.120120, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00817165

T. Biswas, E. Resto-roldan, S. K. Sawyer, I. Artsimovitch, and O. V. Tsodikov, A novel non-radioactive primase-pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG, Nucleic Acids Res, vol.41, issue.4, p.56, 2013.

E. C. Boritsch, P. Supply, N. Honore, T. Seeman, T. P. Stinear et al., A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent, Mol Microbiol, vol.93, pp.835-852, 2014.

H. I. Boshoff, M. B. Reed, C. E. Barry, and V. Mizrahi, DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis, Cell, vol.113, issue.2, pp.183-193, 2003.

N. C. Brissett, R. S. Pitcher, R. Juarez, A. J. Picher, A. J. Green et al., Structure of a NHEJ polymerase-mediated DNA synaptic complex, Science, vol.318, issue.5849, pp.456-459, 2007.

H. Brotz-oesterhelt, I. Knezevic, S. Bartel, T. Lampe, U. Warnecke-eberz et al., Specific and potent inhibition of NADC-dependent DNA ligase by pyridochromanones, J Biol Chem, vol.278, issue.41, pp.39435-39442, 2003.

J. J. Bull and C. O. Wilke, Lethal mutagenesis of bacteria, Genetics, vol.180, issue.2, pp.1061-1070, 2008.

, Antiobiotic resistance threats in the United States. Centres for Disease Conotrl and Prevention Cohen NR, Cell Host Microbe, vol.13, issue.6, pp.632-642, 2013.

R. Colangeli, V. L. Arcus, R. T. Cursons, R. A. Karalus, N. Coley et al., Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans, PLoS One, vol.9, issue.3, p.91024, 2014.

S. Crotty, C. E. Cameron, and R. Andino, RNA virus error catastrophe: direct molecular test by using ribavirin, Proc Natl Acad Sci U S A, vol.98, issue.12, pp.6895-6900, 2001.

M. J. Culyba, C. Y. Mo, and R. M. Kohli, Targets for combating the evolution of acquired antibiotic resistance, Biochemistry, vol.54, issue.23, pp.3573-3582, 2015.

K. H. Darwin and C. F. Nathan, Role for nucleotide excision repair in virulence of Mycobacterium tuberculosis, Infect Immun, vol.73, issue.8, pp.4581-4587, 2005.

S. S. Dawes, D. F. Warner, L. Tsenova, J. Timm, J. D. Mckinney et al., Ribonucleotide reduction in Mycobacterium tuberculosis: function and expression of genes encoding class Ib and class II ribonucleotide reductases, Infect Immun, vol.71, issue.11, pp.6124-6131, 2003.

D. Vultos, T. Mestre, O. Rauzier, J. Golec, M. Rastogi et al., Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis, PLoS One, vol.3, issue.2, p.1538, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-00364652

J. W. Drake, The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes, 1999.

, Ann N Y Acad Sci, vol.870, pp.100-107

N. K. Dutta, S. Mehra, P. J. Didier, C. J. Roy, L. A. Doyle et al., Genetic requirements for the survival of tubercle bacilli in primates, J Infect Dis, vol.201, issue.11, pp.1743-1752, 2010.

E. Elleingand, C. Gerez, S. Un, M. Knupling, G. Lu et al., Reactivity studies of the tyrosyl radical in ribonucleotide reductase from Mycobacterium tuberculosis and Arabidopsis thaliana-comparison with Escherichia coli and mouse, Eur J Biochem, vol.258, issue.2, pp.485-490, 1998.

M. R. Farhat, B. J. Shapiro, K. J. Kieser, R. Sultana, K. R. Jacobson et al., Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis, Nat Genet, vol.45, issue.10, pp.1183-1189, 2013.

I. J. Fijalkowska, R. M. Schaaper, and P. Jonczyk, DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair, FEMS Microbiol Rev, vol.36, issue.6, pp.1105-1121, 2012.

A. S. Fivian-hughes, J. Houghton, and E. O. Davis, Mycobacterium tuberculosis thymidylate synthase gene thyX is essential and potentially bifunctional, while thyA deletion confers resistance to p-aminosalicylic acid, Microbiol-Sgm, vol.158, pp.1388-1388, 2012.

C. B. Ford, P. L. Lin, M. R. Chase, R. R. Shah, O. Iartchouk et al., Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection, Nat Genet, vol.43, issue.5, pp.482-486, 2011.

C. B. Ford, R. R. Shah, M. K. Maeda, S. Gagneux, M. B. Murray et al., Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis, Nat Genet, vol.45, issue.7, pp.784-790, 2013.

C. Gajadeera, M. J. Willby, K. D. Green, P. Shaul, M. Fridman et al., Antimycobacterial activity of DNA intercalator inhibitors of Mycobacterium tuberculosis primase DnaG, J Antibiot (Tokyo), vol.68, issue.3, pp.153-157, 2015.

J. E. Galagan, Genomic insights into tuberculosis, Nat Rev Genet, vol.15, issue.5, pp.307-320, 2014.

V. Gamulin, H. Cetkovic, and I. Ahel, Identification of a promoter motif regulating the major DNA damage response mechanism of Mycobacterium tuberculosis, FEMS Microbiol Lett, vol.238, issue.1, pp.57-63, 2004.

E. R. Georgieva, A. J. Narvaez, N. Hedin, and A. Graslund, Secondary structure conversions of Mycobacterium tuberculosis ribonucleotide reductase protein R2 under varying pH and temperature conditions, Biophys Chem, vol.137, issue.1, pp.43-48, 2008.

S. Ghosh, S. Samaddar, P. Kirtania, D. Gupta, and S. K. , A DinB ortholog enables mycobacterial growth under dTTP-limiting conditions induced by the expression of a mycobacteriophage-derived ribonucleotide reductase gene, J Bacteriol, vol.198, issue.2, pp.352-362, 2015.

C. Gong, A. Martins, P. Bongiorno, M. Glickman, and S. Shuman, Biochemical and genetic analysis of the four DNA ligases of mycobacteria, J Biol Chem, vol.279, issue.20, pp.20594-20606, 2004.

B. G. Gordhan, S. J. Andersen, D. Meyer, A. R. Mizrahi, and V. , Construction by homologous recombination and phenotypic characterization of a DNA polymerase domain polA mutant of Mycobacterium smegmatis, Gene, vol.178, issue.1-2, pp.125-130, 1996.

A. E. Gorna, R. P. Bowater, and J. Dziadek, DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: varying activities at different stages of infection, Clin Sci (Lond), vol.119, issue.5, pp.187-202, 2010.

S. Gu, W. Li, H. Zhang, J. Fleming, Y. W. Wang et al., The b 2 clamp in the Mycobacterium tuberculosis DNA polymerase III ab 2 e replicase promotes polymerization and reduces exonuclease activity, Sci Rep, vol.6, p.18418, 2016.

M. Hammerstad, A. K. Rohr, N. H. Andersen, A. Graslund, M. Hogbom et al., The class Ib ribonucleotide reductase from Mycobacterium tuberculosis has two active R2F subunits, J Biol Inorg Chem, vol.19, issue.6, pp.893-902, 2014.

R. Hershberg, M. Lipatov, P. M. Small, H. Sheffer, S. Niemann et al., High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography, PLoS Biol, vol.6, issue.12, p.311, 2008.

D. T. Hoagland, J. Liu, R. B. Lee, and R. E. Lee, New agents for the treatment of drug-resistant Mycobacterium tuberculosis, Adv Drug Deliv Rev, vol.102, p.55, 2016.

J. H. Hunter, C. Pang, R. Gujjar, and P. K. Rathod, Kinetics and ligand-binding preferences of Mycobacterium tuberculosis thymidylate synthases, ThyA and ThyX, PLoS One, vol.3, issue.5, p.2237, 2008.

S. Ishino, Y. Nishi, S. Oda, T. Uemori, T. Sagara et al., Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea, Nucleic Acids Res, vol.44, issue.7, pp.2977-2986, 2016.

B. D. Kana, G. L. Abrahams, N. Sung, D. F. Warner, B. G. Gordhan et al., Role of the DinB homologs Rv1537 and Rv3056 in Mycobacterium tuberculosis, J Bacteriol, vol.192, issue.8, pp.2220-2227, 2010.

A. Kling, P. Lukat, D. V. Almeida, A. Bauer, E. Fontaine et al., Targeting DnaN for tuberculosis therapy using novel griselimycins, Science, vol.348, issue.6239, pp.1106-1112, 2015.

M. Korycka-machala, E. Rychta, A. Brzostek, H. R. Sayer, A. Rumijowska-galewicz et al., Evaluation of NAD(C)-dependent DNA ligase of mycobacteria as a potential target for antibiotics, Antimicrob Agents Chemother, vol.51, issue.8, pp.2888-2897, 2007.

A. Kuron, M. Korycka-machala, A. Brzostek, M. Nowosielski, A. Doherty et al., Evaluation of DNA primase DnaG as a potential target for antibiotics, Antimicrob Agents Chemother, vol.58, issue.3, pp.1699-1706, 2014.

J. E. Leclerc, B. Li, W. L. Payne, and T. A. Cebula, High mutation frequencies among Escherichia coli and Salmonella pathogens, Science, vol.274, issue.5290, pp.1208-1211, 1996.

H. Lee, E. Popodi, H. Tang, and P. L. Foster, Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by wholegenome sequencing, Proc Natl Acad Sci U S A, vol.109, issue.41, pp.2774-2783, 2012.

I. R. Lehman, DNA ligase: structure, mechanism, and function, Science, vol.186, issue.4166, pp.790-797, 1974.

T. Lillebaek, A. Dirksen, I. Baess, B. Strunge, V. O. Thomsen et al., Molecular evidence of endogenous reactivation of Mycobacterium tuberculosis after 33 years of latent infection, J Infect Dis, vol.185, issue.3, pp.401-404, 2002.

A. Liu, S. Potsch, A. Davydov, A. L. Barra, H. Rubin et al., The tyrosyl free radical of recombinant ribonucleotide reductase from Mycobacterium tuberculosis is located in a rigid hydrophobic pocket, Biochemistry, vol.37, pp.16369-16377, 1998.

A. M. Liu, A. L. Barra, H. Rubin, G. Z. Lu, and A. Graslund, Heterogeneity of the local electrostatic environment of the tyrosyl radical in Mycobacterium tuberculosis ribonucleotide reductase observed by high-field electron paramagnetic resonance, J Am Chem Soc, vol.122, issue.9, pp.1974-1978, 2000.

L. A. Loeb, J. M. Essigmann, F. Kazazi, J. Zhang, K. D. Rose et al., Lethal mutagenesis of HIV with mutagenic nucleoside analogs, Proc Natl Acad Sci U S A, vol.96, issue.4, pp.1492-1497, 1999.

M. Mcgrath, G. Van-pittius, N. C. Van-helden, P. D. Warren, R. M. Warner et al., Mutation rate and the emergence of drug resistance in Mycobacterium tuberculosis, J Antimicrob Chemother, vol.69, issue.2, pp.292-302, 2014.

R. Miggiano, V. Casazza, S. Garavaglia, M. Ciaramella, G. Perugino et al., Biochemical and structural studies of the Mycobacterium tuberculosis O 6-methylguanine methyltransferase and mutated variants, J Bacteriol, vol.195, issue.12, pp.2728-2736, 2013.

S. D. Mills, A. E. Eakin, E. T. Buurman, J. V. Newman, N. Gao et al., Novel bacterial NADC-dependent DNA ligase inhibitors with broadspectrum activity and antibacterial efficacy in vivo, Antimicrob Agents Chemother, vol.55, issue.3, pp.1088-1096, 2011.

Y. Minato, J. M. Thiede, S. L. Kordus, E. J. Mcklveen, B. J. Turman et al., Mycobacterium tuberculosis folate metabolism and the mechanistic basis for paraaminosalicylic acid susceptibility and resistance, Antimicrob Agents Chemother, vol.59, issue.9, pp.5097-5106, 2015.

V. Mizrahi and S. J. Andersen, DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?, Mol Microbiol, vol.29, issue.6, pp.1331-1339, 1998.

V. Mizrahi and P. Huberts, Deoxy-and dideoxynucleotide discrimination and identification of critical 5 0 nuclease domain residues of the DNA polymerase I from Mycobacterium tuberculosis, Nucleic Acids Res, vol.24, issue.24, pp.4845-4852, 1996.

A. Morrison, A. L. Johnson, L. H. Johnston, and A. Sugino, Pathway correcting DNA replication errors in Saccharomyces cerevisiae, EMBO J, vol.12, issue.4, pp.1467-1473, 1993.

M. B. Mowa, D. F. Warner, G. Kaplan, B. D. Kana, and V. Mizrahi, Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria, J Bacteriol, vol.191, issue.3, pp.985-995, 2009.

M. Nandakumar, G. A. Prosser, L. P. De-carvalho, and K. Rhee, Metabolomics of Mycobacterium tuberculosis, vol.1285, pp.105-115, 2015.

A. Oliver, R. Canton, P. Campo, F. Baquero, and J. Blazquez, High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection, Science, vol.288, issue.5469, pp.1251-1254, 2000.

H. Ordonez and S. Shuman, Mycobacterium smegmatis DinB2 misincorporates deoxyribonucleotides and ribonucleotides during templated synthesis and lesion bypass, Nucleic Acids Res, vol.42, issue.20, pp.12722-12734, 2014.

H. Ordonez, M. L. Uson, and S. Shuman, Characterization of three mycobacterial DinB (DNA polymerase IV) paralogs highlights DinB2 as naturally adept at ribonucleotide incorporation, Nucleic Acids Res, vol.42, issue.17, pp.11056-11070, 2014.

R. E. Painter, G. C. Adam, M. Arocho, E. Dinunzio, R. G. Donald et al., Elucidation of DnaE as the antibacterial target of the natural product, Nargenicin. Chem Biol, vol.22, issue.10, pp.1362-1373, 2015.

S. D. Podos, J. A. Thanassi, and M. J. Pucci, Mechanistic assessment of DNA ligase as an antibacterial target in Staphylococcus aureus, Antimicrob Agents Chemother, vol.56, issue.8, pp.4095-4102, 2012.

L. Rand, J. Hinds, B. Springer, P. Sander, R. S. Buxton et al., The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA, Mol Microbiol, vol.50, issue.3, pp.1031-1042, 2003.

A. Robinson, R. J. Causer, and N. E. Dixon, Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target, Curr Drug Targets, vol.13, issue.3, pp.352-372, 2012.

J. M. Rock, U. F. Lang, M. R. Chase, C. B. Ford, E. R. Gerrick et al., DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader, Nat Genet, vol.47, issue.6, pp.677-681, 2015.

A. Sandgren, M. Strong, P. Muthukrishnan, B. K. Weiner, G. M. Church et al., Tuberculosis drug resistance mutation database, PLoS Med, vol.6, issue.2, p.2, 2009.
DOI : 10.1371/journal.pmed.1000002

URL : https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1000002&type=printable

C. M. Sassetti and E. J. Rubin, Genetic requirements for mycobacterial survival during infection, Proc Natl Acad Sci U S A, vol.100, issue.22, pp.12989-12994, 2003.
DOI : 10.1073/pnas.2134250100

URL : http://www.pnas.org/content/100/22/12989.full.pdf

J. W. Schroeder, J. R. Randall, L. A. Matthews, and L. A. Simmons, Ribonucleotides in bacterial DNA, Crit Rev Biochem Mol Biol, vol.50, issue.3, pp.181-193, 2015.
DOI : 10.3109/10409238.2014.981647

URL : http://europepmc.org/articles/pmc4428996?pdf=render

W. R. Shadrick, J. Ndjomou, R. Kolli, S. Mukherjee, A. M. Hanson et al., Discovering new medicines targeting helicases: challenges and recent progress, J Biomol Screen, vol.18, issue.7, pp.761-781, 2013.
DOI : 10.1177/1087057113482586

URL : http://journals.sagepub.com/doi/pdf/10.1177/1087057113482586

A. Sharma and D. T. Nair, MsDpo4-a DinB Homolog from Mycobacterium smegmatis-is an error-prone DNA polymerase that can promote G:T and T:G mismatches, J Nucleic Acids, vol.2012, p.285481, 2012.
DOI : 10.1155/2012/285481

URL : http://downloads.hindawi.com/journals/jna/2012/285481.pdf

L. A. Simmons, J. J. Foti, S. E. Cohen, and G. C. Walker, The SOS regulatory network, EcoSal Plus, vol.3, issue.1, 2008.
DOI : 10.1128/ecosalplus.5.4.3

URL : http://europepmc.org/articles/pmc4196698?pdf=render

V. Singh, M. Brecik, R. Mukherjee, J. C. Evans, Z. Svetlikova et al., The complex mechanism of, 2015.

K. L. Smollett, K. M. Smith, C. Kahramanoglou, K. B. Arnvig, R. S. Buxton et al., Global analysis of the regulon of the transcriptional repressor LexA, a key component of SOS response in Mycobacterium tuberculosis, J Biol Chem, vol.287, issue.26, pp.22004-22014, 2012.

S. K. Srivastava, D. Dube, N. Tewari, N. Dwivedi, R. P. Tripathi et al., Mycobacterium tuberculosis NADC-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I, Nucleic Acids Res, vol.33, issue.22, pp.7090-7101, 2005.
DOI : 10.1093/nar/gki1006

URL : https://academic.oup.com/nar/article-pdf/33/22/7090/4155828/gki1006.pdf

S. K. Srivastava, R. P. Tripathi, and R. Ramachandran, NADC-dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors, J Biol Chem, vol.280, issue.34, pp.30273-30281, 2005.
DOI : 10.1074/jbc.m503780200

URL : http://www.jbc.org/content/280/34/30273.full.pdf

G. Sun, T. Luo, C. Yang, X. Dong, J. Li et al., Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients, J Infect Dis, vol.206, issue.11, pp.1724-1733, 2012.

K. Timinskas, M. Balvociute, A. Timinskas, and C. Venclovas, Comprehensive analysis of DNA polymerase III alpha subunits and their homologs in bacterial genomes, Nucleic Acids Res, vol.42, issue.3, pp.1393-1413, 2014.

M. Uppsten, J. Davis, H. Rubin, and U. Uhlin, Crystal structure of the biologically active form of class 1b ribonucleotide reductase small subunit from Mycobacterium tuberculosis, FEBS Lett, vol.569, issue.1-3, pp.117-122, 2004.

Y. Wang, Y. Huang, C. Xue, Y. He, and Z. G. He, ClpR protein-like regulator specifically recognizes RecA protein-independent promoter motif and broadly regulates expression of DNA damage-inducible genes in mycobacteria, J Biol Chem, vol.286, issue.36, pp.31159-31167, 2011.

D. F. Warner, G. Etienne, X. M. Wang, L. G. Matsoso, S. S. Dawes et al., A derivative of Mycobacterium smegmatis mc 2 155 that lacks the duplicated chromosomal region, Tuberculosis, vol.86, issue.6, pp.438-444, 2006.

D. F. Warner, D. E. Ndwandwe, G. L. Abrahams, B. D. Kana, E. E. Machowski et al., Essential roles for imuA 0-and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis, Proc Natl Acad Sci U S A, vol.107, issue.29, pp.13093-13098, 2010.

D. F. Warner, T. Tonjum, and V. Mizrahi, DNA metabolism in mycobacterial pathogenesis, Curr Top Microbiol, vol.374, pp.27-51, 2014.
DOI : 10.1007/82_2013_328

D. F. Warner, A. Koch, and V. Mizrahi, Diversity and disease pathogenesis in Mycobacterium tuberculosis, Trends Microbiol, vol.23, issue.1, pp.14-21, 2015.
DOI : 10.1016/j.tim.2014.10.005

J. Werngren and S. E. Hoffner, Drug-susceptible Mycobacterium tuberculosis Beijing genotype does not develop mutation-conferred resistance to rifampin at an elevated rate, J Clin Microbiol, vol.41, issue.4, pp.1520-1524, 2003.
DOI : 10.1128/jcm.41.4.1520-1524.2003

URL : https://jcm.asm.org/content/41/4/1520.full.pdf

F. Yang, G. Lu, and H. Rubin, Isolation of ribonucleotide reductase from Mycobacterium tuberculosis and cloning, expression, and purification of the large subunit, J Bacteriol, vol.176, issue.21, pp.6738-6743, 1994.

F. Yang, S. C. Curran, L. S. Li, D. Avarbock, J. D. Graf et al., Characterization of two genes encoding the Mycobacterium tuberculosis ribonucleotide reductase small subunit, J Bacteriol, vol.179, issue.20, pp.6408-6415, 1997.

H. Zhu, J. Nandakumar, J. Aniukwu, L. K. Wang, M. S. Glickman et al., Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D, Proc Natl Acad Sci U S A, vol.103, issue.6, pp.1711-1716, 2006.

H. Zhu, H. Bhattarai, H. G. Yan, S. Shuman, and M. S. Glickman, Characterization of Mycobacterium smegmatis PolD2 and PolD1 as RNA/DNA polymerases homologous to the POL domain of bacterial DNA ligase D, Biochemistry, vol.51, issue.51, pp.10147-10158, 2012.

D. References-agashe, N. C. Martinez-gomez, D. A. Drummond, and C. J. Marx, Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme, Mol Biol Evol, vol.30, pp.549-560, 2013.

P. As, Effect of Katg mutations on the virulence of mycobacterium tuberculosis and the implication for transmission in humans, Infect Immun, vol.70, pp.4955-4960, 2002.

L. Baker, T. Brown, M. C. Maiden, and F. Drobniewski, Silent nucleotide polymorphisms and a phylogeny for mycobacterium tuberculosis, Emerg Infect Dis, vol.10, pp.1568-1577, 2004.

G. P. Bisson, C. Mehaffy, C. Broeckling, J. Prenni, D. Rifat et al., Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampin-resistant, rpoB mutant Mycobacterium tuberculosis, J Bacteriol, vol.194, pp.6441-6452, 2012.

G. V. Bloemberg, P. M. Keller, D. Stucki, A. Trauner, S. Borrell et al., Acquired resistance to bedaquiline and delamanid in therapy for tuberculosis, N Engl J Med, vol.373, pp.1986-1988, 2015.

S. M. Blower and T. Chou, Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance, Nat Med, vol.10, pp.1111-1116, 2004.

S. Bonhoeffer, M. Lipsitch, and B. R. Levin, Evaluating treatment protocols to prevent antibiotic resistance, Proc Natl Acad Sci U S A, vol.94, pp.12106-12111, 1997.

S. Borrell and S. Gagneux, Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis, 2009.

, Int J Tuberc Lung Dis, vol.13, pp.1456-1466

S. Borrell, Y. Teo, F. Giardina, E. M. Streicher, M. Klopper et al., Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis, Evol Med Public Health, pp.65-74, 2013.

K. I. Bos, K. M. Harkins, A. Herbig, M. Coscollà, N. Weber et al., Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis, Nature, vol.514, pp.494-497, 2014.

G. Brandis and D. Hughes, Genetic characterization of compensatory evolution in strains carrying rpoB Ser531Leu, the rifampicin resistance mutation most frequently found in clinical isolates, J Antimicrob Chemother, vol.68, pp.2493-2497, 2013.

G. Brandis, M. Wrande, L. Liljas, and D. Hughes, Fitnesscompensatory mutations in rifampicin-resistant RNA polymerase, Mol Microbiol, vol.85, pp.142-151, 2012.

E. A. Campbell, N. Korzheva, A. Mustaev, K. Murakami, S. Nair et al., Structural mechanism for rifampicin inhibition of bacterial RNA polymerase, Cell, vol.104, pp.901-912, 2001.

N. Casali, V. Nikolayevskyy, Y. Balabanova, S. R. Harris, O. Ignatyeva et al., Evolution and transmission of drug resistant tuberculosis in a Russian population, Nat Genet, vol.46, p.279, 2014.

T. Cohen, H. E. Jenkins, C. Lu, M. Mclaughlin, K. Floyd et al., On the spread and control of MDR-TB epidemics: an examination of trends in antituberculosis drug resistance surveillance data, Drug Resist Updat, vol.17, pp.105-123, 2014.

K. A. Cohen, T. Abeel, A. M. Mcguire, C. A. Desjardins, V. Munsamy et al., Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZuluNatal, PLoS Med, vol.12, p.1001880, 2015.

I. Comas, J. Chakravartti, P. M. Small, J. Galagan, S. Niemann et al., Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved, Nat Genet, vol.42, pp.498-503, 2010.

I. Comas, S. Borrell, A. Roetzer, G. Rose, B. Malla et al., Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes, Nat Genet, vol.44, pp.106-110, 2012.

M. Coscolla and S. Gagneux, Consequences of genomic diversity in Mycobacterium tuberculosis, Semin Immunol, vol.26, pp.431-444, 2014.

M. Da, Tubercle bacilli resistant to isoniazid: virulence and response to treatment with isoniazid in guinea-pigs, Br Med J, vol.1, pp.128-130, 1954.

A. Dalal, A. Pawaskar, M. Das, R. Desai, P. Prabhudesai et al.,

P. Saranchuk, C. Rodrigues, and P. Isaakidis, Resistance patterns among multidrug-resistant tuberculosis patients in greater metropolitan Mumbai: trends over time, PLoS One, vol.10, p.116798, 2015.

T. Dalton, P. Cegielski, S. Akksilp, L. Asencios, C. Caoili et al., Prevalence of and risk factors for resistance to second-line drugs, Lancet, vol.380, pp.1406-1417, 2012.

D. Jong, B. C. Hill, P. C. Aiken, A. Awine, T. Antonio et al., Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia, J Infect Dis, vol.198, pp.1037-1043, 2008.

D. Knegt, G. J. Bruning, O. Marian, T. , D. Jong et al., Rifampicininduced transcriptome response in rifampicin-resistant Mycobacterium tuberculosis, De Steenwinkel JEM, vol.93, pp.96-101, 2013.

M. De-vos, B. Muller, S. Borrell, P. A. Black, P. D. Van-helden et al., Putative compensatory mutations in the rpoC gene of rifampin-resistant Mycobacterium tuberculosis are associated with ongoing transmission, Antimicrob Agents Chemother, vol.57, pp.827-832, 2013.

A. S. Dean, M. Zignol, D. Falzon, H. Getahun, and K. Floyd, HIV and multidrug-resistant tuberculosis: overlapping epidemics, Eur Respir J, vol.44, pp.251-254, 2014.

E. Denamur and I. Matic, Evolution of mutation rates in bacteria, Mol Microbiol, vol.60, pp.820-827, 2006.

I. Du-preez and D. T. Loots, Altered fatty acid metabolism due to rifampicin-resistance conferring mutations in the rpoB gene of Mycobacterium tuberculosis: mapping the potential of pharmacometabolomics for global health and personalized medicine, Omics: J Integr Biol, vol.16, pp.596-603, 2012.

V. Eldholm, J. Monteserin, A. Rieux, B. Lopez, B. Sobkowiak et al., Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain, Nat Commun, vol.6, 2015.

A. R. Escombe, D. A. Moore, R. H. Gilman, W. Pan, M. Navincopa et al., The infectiousness of tuberculosis patients coinfected with HIV, PLoS Med, vol.5, p.188, 2008.

M. R. Farhat, B. J. Shapiro, K. J. Kieser, R. Sultana, K. R. Jacobson et al., Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis, Nat Genet, vol.45, pp.1183-1189, 2013.

L. Fenner, M. Egger, T. Bodmer, E. Altpeter, M. Zwahlen et al., Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.56, pp.3047-3053, 2012.

S. Feuerriegel, C. U. Koser, and S. Niemann, Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex, J Antimicrob Chemother, vol.69, pp.1205-1210, 2014.

C. B. Ford, R. R. Shah, M. K. Maeda, S. Gagneux, M. B. Murray et al., Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis, Nat Genet, vol.45, pp.784-790, 2013.

S. Gagneux, C. D. Long, P. M. Small, T. Van, G. K. Schoolnik et al., The competitive cost of antibiotic resistance in Mycobacterium tuberculosis, Science, vol.312, pp.1944-1946, 2006.

L. Grandjean, R. H. Gilman, L. Martin, E. Soto, B. Castro et al., Transmission of multidrug-resistant and drug-susceptible tuberculosis within households: a prospective cohort study, PLoS Med, vol.12, p.1001843, 2015.

S. Gygli, S. Borrell, A. Trauner, and S. Gagneux, FEMS Microbiol Rev, vol.41, issue.3, pp.354-373, 2017.

R. C. Hartkoorn, S. Uplekar, and C. St, Crossresistance between clofazimine and bedaquiline through upregulation of MmpL5 in Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.58, pp.2979-2981, 2014.

H. L. Haver, A. Chua, P. Ghode, S. B. Lakshminarayana, A. Singhal et al., Mutations in genes for the F420 biosynthetic pathway and a nitroreductase enzyme are the primary resistance determinants in spontaneous in vitro-selected PA-824resistant mutants of Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.59, pp.5316-5323, 2015.

S. Homolka, E. Post, B. Oberhauser, A. G. George, L. Westman et al., High genetic diversity among Mycobacterium tuberculosis complex strains from Sierra Leone, BMC Microbiol, vol.8, p.1, 2008.

Y. Hu, B. Mathema, Q. Zhao, X. Rzheng, D. Li et al., Comparison of the sociodemographic and clinical features of pulmonary TB patients infected with sub-lineages within the W-Beijing and non-Beijing Mycobacterium tuberculosis, Tuberc (Edinb), vol.97, pp.18-25, 2016.

S. Borrell and A. Trauner,

G. M. Knight, C. Colijn, S. Shrestha, M. Fofana, F. Cobelens et al., The distribution of fitness costs of resistance-conferring mutations is a key determinant for the future burden of drugresistant tuberculosis: a model-based analysis, Clin Infect Dis, vol.61, issue.3, pp.147-154, 2015.

A. Koch, V. Mizrahi, and D. F. Warner, The impact of drug resistance on Mycobacterium tuberculosis physiology: what can we learn from rifampicin? Emerg Microbes Infect, vol.3, p.17, 2014.

S. Kryazhimskiy, D. P. Rice, E. R. Jerison, and M. M. Desai, Global epistasis makes adaptation predictable despite sequence-level stochasticity, Science, vol.344, pp.1519-1522, 2014.

M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne et al., Circos: an information aesthetic for comparative genomics, 2009.

, Genome Res, vol.19, pp.1639-1645

N. Lahiri, R. R. Shah, E. Layre, D. Young, C. Ford et al., Rifampin resistance mutations are associated with broad chemical remodeling of mycobacterium tuberculosis, J Biol Chem, vol.291, pp.14248-14256, 2016.

F. Lanzas, P. C. Karakousis, J. C. Sacchettini, and T. R. Ioerger, Multidrug-resistant tuberculosis in panama is driven by clonal expansion of a multidrug-resistant Mycobacterium tuberculosis strain related to the KZN extensively drug-resistant M. tuberculosis strain from South Africa, J Clin Microbiol, vol.51, pp.3277-3285, 2013.

T. Luo, I. Comas, D. Luo, B. Lu, J. Wu et al., Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese, Proc Natl Acad Sci U S A, vol.112, pp.8136-8141, 2015.

S. Magnet and J. S. Blanchard, Molecular insights into aminoglycoside action and resistance, Chem Rev, vol.105, pp.477-498, 2005.

D. H. Mariam, Y. Mengistu, S. E. Hoffner, and D. I. Andersson, Effect of rpoB mutations conferring rifampin resistance on fitness of Mycobacterium tuberculosis, Antimicrob Agents Chemother, vol.48, pp.1289-1294, 2004.

U. Mechold, K. Potrykus, H. Murphy, K. S. Murakami, and M. Cashel, Differential regulation by ppGpp versus pppGpp in Escherichia coli, Nucleic Acids Res, vol.41, pp.6175-6189, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01427537

M. Merker, T. A. Kohl, A. Roetzer, L. Truebe, E. Richter et al., Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients, PLoS One, vol.8, p.82551, 2013.

M. Merker, C. Blin, S. Mona, N. Duforet-frebourg, S. Lecher et al., Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage, vol.47, pp.242-249, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01153552

S. Moreno-gamez, A. L. Hill, D. I. Rosenbloom, D. A. Petrov, M. A. Nowak et al., Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance, Proc Natl Acad Sci U S A, vol.112, pp.2874-2883, 2015.

B. Muller, S. Borrell, G. Rose, and S. Gagneux, The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis, Trends Genet, vol.29, pp.160-169, 2013.

B. Muller, V. N. Chihota, M. Pillay, M. Klopper, E. M. Streicher et al., Programmatically selected multidrug-resistant strains drive the emergence of extensively drug-resistant tuberculosis in South Africa, PLoS One, vol.8, p.70919, 2013.

S. S. Munsiff, B. Nivin, G. Sacajiu, B. Mathema, P. Bifani et al., Persistence of a highly resistant strain of tuberculosis in New York City during 19901999, J Infect Dis, vol.188, pp.356-363, 2003.

. Ochi-k, Y. Tanaka, and S. Tojo, Activating the expression of bacterial cryptic genes by rpoB mutations in RNA polymerase or by rare earth elements, J Ind Microbiol Biotechnol, vol.41, pp.403-414, 2014.

D. C. Perlman, Y. Segal, S. Rosenkranz, P. M. Rainey, R. P. Remmel et al., The clinical pharmacokinetics of rifampin and ethambutol in HIV-infected persons with tuberculosis, Clin Infect Dis, vol.41, pp.1638-1647, 2005.

J. Piton, S. Petrella, M. Delarue, G. André-leroux, V. Jarlier et al., Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase, PLoS One, vol.5, p.12245, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01126607

Q. Qi, G. M. Preston, and R. C. Maclean, Linking systemwide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa, MBio, vol.5, pp.1562-01514, 2014.

M. G. Reynolds, Compensatory evolution in rifampin-resistant Escherichia coli, Genetics, vol.156, pp.1471-1481, 2000.

J. Reynolds and S. K. Heysell, Understanding pharmacokinetics to improve tuberculosis treatment outcome, Expert Opin Drug Metab Toxicol, vol.10, pp.813-823, 2014.
DOI : 10.1517/17425255.2014.895813

URL : http://europepmc.org/articles/pmc4112565?pdf=render

J. M. Rock, U. F. Lang, M. R. Chase, C. B. Ford, E. R. Gerrick et al., DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader, Nat Genet, vol.47, pp.677-681, 2015.

A. Sandgren, M. Strong, P. Muthukrishnan, B. K. Weiner, G. M. Church et al., Tuberculosis drug resistance mutation database, PLoS Med, vol.6, p.2, 2009.
DOI : 10.1371/journal.pmed.1000002

URL : https://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1000002&type=printable

A. Skrahina, H. Hurevich, A. Zalutskaya, E. Sahalchyk, A. Astrauko et al., , 2013.

, Multidrug-resistant tuberculosis in Belarus: the size of the problem and associated risk factors, Bull World Health Organ, vol.91, pp.36-45

T. Song, Y. Park, I. C. Shamputa, S. Seo, S. Y. Lee et al., Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the beta' subunit of RNA polymerase, Mol Microbiol, vol.91, pp.1106-1119, 2014.

F. S. Spies, A. W. Ribeiro, D. F. Ramos, M. O. Ribeiro, A. Martin et al., Streptomycin resistance and lineage-specific polymorphisms in Mycobacterium tuberculosis gidB gene, J Clin Microbiol, vol.49, pp.2625-2630, 2011.
DOI : 10.1128/jcm.00168-11

URL : https://jcm.asm.org/content/49/7/2625.full.pdf

B. Traore, B. Diarra, B. Dembele, A. M. Somboro, A. S. Hammond et al., Molecular strain typing of Mycobacterium tuberculosis complex in Bamako, Mali, Int J Tuberc Lung Dis, vol.16, pp.911-916, 2012.

A. Trauner, S. Borrell, K. Reither, and S. Gagneux, Evolution of drug resistance in tuberculosis: recent progress and implications for diagnosis and therapy, Drugs, vol.74, pp.1063-1072, 2014.

H. R. Van-doorn, D. Haas, P. E. Kremer, K. Vandenbrouckegrauls, C. M. Borgdorff et al., Public health impact of isoniazid-resistant Mycobacterium tuberculosis strains with a mutation at aminoacid position 315 of katG: a decade of experience in The Netherlands, Clin Microbiol Infect, vol.12, pp.769-775, 2006.

T. Vogwill, M. Kojadinovic, V. Furió, and R. C. Maclean, Testing the role of genetic background in parallel evolution using the comparative experimental evolution of antibiotic resistance, Mol Biol Evol. msu262, vol.31, issue.12, pp.3314-3323, 2014.

T. Vogwill, M. Kojadinovic, R. Maclean, G. Who, C. D. Wells et al., Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species of Pseudomonas, Global tuberculosis report, vol.283, pp.86-107, 1830.
URL : https://hal.archives-ouvertes.fr/hal-01444160

K. Winglee, A. M. Mcguire, M. Maiga, T. Abeel, T. Shea et al., Whole genome sequencing of mycobacterium africanum strains from Mali Provides insights into the mechanisms of geographic restriction, PLoS Negl Trop Dis, vol.10, p.4332, 2016.

C. Yang, T. Luo, G. Sun, K. Qiao, G. Sun et al., Mycobacterium tuberculosis Beijing strains favor transmission but not drug resistance in China, Clin Infect Dis, vol.55, pp.1179-1187, 2012.

C. Yang, X. Shen, Y. Peng, R. Lan, Y. Zhao et al., Transmission of Mycobacterium tuberculosis in China: a population-based molecular epidemiologic study, Clin Infect Dis, vol.61, pp.219-227, 2015.

L. Yuan, L. Mi, Y. Li, H. Zhang, F. Zheng et al., Genotypic characteristics of Mycobacterium tuberculosis circulating in Xinjiang, China. Infect Dis (Lond), vol.48, pp.108-115, 2016.

Y. Zhang and W. W. Yew, Mechanisms of drug resistance in Mycobacterium tuberculosis: update 2015, Int J Tuberc Lung Dis, vol.19, pp.1276-1289, 2015.

H. Zhang, D. Li, L. Zhao, J. Fleming, N. Lin et al., Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance, Nat Genet, vol.45, pp.1255-1260, 2013.

M. Zignol, W. Van-gemert, D. Falzon, C. Sismanidis, P. Glaziou et al., Surveillance of anti-tuberculosis drug resistance in the world: an updated analysis, Bull World Health Organ, vol.90, pp.111-119, 2007.

M. Zignol, A. S. Dean, N. Alikhanova, S. Andres, A. M. Cabibbe et al., Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project, Lancet Infect Dis References Aandahl RZ, vol.8, issue.6, p.1002573, 2012.

R. Z. Aandahl, T. Stadler, S. A. Sisson, and M. M. Tanaka, Exact vs. approximate computation: reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters, Genetics, vol.196, issue.4, pp.1227-1230, 2014.

D. Alland, G. Kalkut, A. Moss, R. Mcadam, J. Hahn et al., Transmission of tuberculosis in New York City. An analysis by DNA fingerprinting and conventional epidemiologic methods, N Engl J Med, vol.330, issue.24, pp.1710-1716, 1994.

R. M. Anderson and R. M. May, Population biology of infectious diseases: Part I, Nature, vol.280, pp.361-367, 1979.

J. R. Andrews, S. Basu, D. W. Dowdy, and M. B. Murray, The epidemiological advantage of preferential targeting of tuberculosis control at the poor, Int J Tuberc Lung Dis, vol.19, issue.4, pp.375-380, 2015.

A. Aranaz, B. Romero, N. Montero, J. Alvarez, J. Bezos et al., Spoligotyping profile change caused by deletion of a direct variable repeat in a Mycobacterium tuberculosis isogenic laboratory strain, J Clin Microbiol, vol.42, issue.11, pp.5388-5391, 2004.

S. Basu and A. P. Galvani, The evolution of tuberculosis virulence, Bull Math Biol, vol.71, issue.5, pp.1073-1088, 2009.

N. Becker, R. Bellamy, N. Beyers, K. P. Mcadam, C. Ruwende et al., Genetic susceptibility to tuberculosis in Africans: a genomewide scan, Modeling to inform infectious disease control. Chapman & Hall/CRC biostatistics series, vol.97, pp.8005-8009, 2000.

S. M. Blower and J. L. Gerberding, Understanding, predicting and controlling the emergence of drug-resistant tuberculosis: a theoretical framework, J Mol Med (Berl), vol.76, issue.9, pp.624-636, 1998.

S. M. Blower, A. R. Mclean, T. C. Porco, P. M. Small, P. C. Hopewell et al., The intrinsic transmission dynamics of tuberculosis epidemics, Nature Med, vol.1, pp.815-821, 1995.

S. M. Blower, P. M. Small, and P. C. Hopewell, Control strategies for tuberculosis epidemics: new models for old problems, Science, vol.273, pp.497-500, 1996.

C. C. Boehme, P. Nabeta, D. Hillemann, M. P. Nicol, S. Shenai et al., Rapid molecular detection of tuberculosis and rifampin resistance, N Engl J Med, vol.363, issue.11, pp.1005-1015, 2010.

M. W. Borgdorff, S. Van-den-hof, N. Kalisvaart, K. Kremer, and D. Van-soolingen, Influence of sampling on clustering and associations with risk factors in the molecular epidemiology of tuberculosis, Am J Epidemiol, vol.174, issue.2, pp.243-251, 2011.

S. Borrell and S. Gagneux, Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis, Clin Microbiol Infect, vol.17, issue.6, 2011.

K. I. Bos, K. M. Harkins, A. Herbig, M. Coscolla, N. Weber et al., Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis, Nature, vol.514, issue.7523, pp.494-497, 2014.

R. Bouckaert, J. Heled, D. Kuhnert, T. Vaughan, C. H. Wu et al., BEAST 2: a software platform for Bayesian evolutionary analysis, PLoS Comput Biol, vol.10, issue.4, p.1003537, 2014.

E. Brooks-pollock, M. C. Becerra, E. Goldstein, T. Cohen, and M. B. Murray, Epidemiologic inference from the distribution of tuberculosis cases in house, J Infect Dis, vol.203, issue.11, pp.1582-1589, 2011.

K. Brudey, J. R. Driscoll, L. Rigouts, W. M. 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.6, issue.1, p.23, 2006.

N. Casali, V. Nikolayevskyy, Y. Balabanova, S. R. Harris, O. Ignatyeva et al., Evolution and transmission of drug-resistant tuberculosis in a Russian population, 2014.

, Nat Genet, vol.46, issue.3, pp.279-286

M. D. Cave, K. D. Eisenach, P. F. Mcdermott, J. H. Bates, and J. T. Crawford, IS 6110: conservation of sequence in the Mycobacterium tuberculosis complex and its utilization in DNA fingerprinting, Mol Cell Probes, vol.5, issue.1, pp.73-80, 1991.

S. T. Chang, J. J. Linderman, and D. E. Kirschner, Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages, Proc Natl Acad Sci U S A, vol.102, issue.12, pp.4530-4535, 2005.

L. Chindelevitch, C. Colijn, P. Moodley, D. Wilson, and T. Cohen, ClassTR: classifying withinhost heterogeneity based on tandem repeats with application to Mycobacterium tuberculosis infections, PLoS Comput Biol, vol.12, issue.2, p.1004475, 2016.

R. H. Chisholm and M. M. Tanaka, The emergence of latent infection in the early evolution of Mycobacterium tuberculosis, Proc Biol Sci, vol.283, 1831.

R. H. Chisholm, J. M. Trauer, D. Curnoe, and M. M. Tanaka, Controlled fire use in early humans might have triggered the evolutionary emergence of tuberculosis, Proc Natl Acad Sci U S A, vol.113, issue.32, pp.9051-9056, 2016.

T. Cohen and M. Murray, Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness, Nat Med, vol.10, issue.10, pp.1117-1121, 2004.

T. Cohen, M. Lipsitch, R. P. Walensky, and M. Murray, Beneficial and perverse effects of isoniazid preventive therapy for latent tuberculosis infection in HIV-tuberculosis coinfected populations, Proc Natl Acad Sci U S A, vol.103, issue.18, pp.7042-7047, 2006.

T. Cohen, P. D. Van-helden, D. Wilson, C. Colijn, M. M. Mclaughlin et al., Mixed-strain Mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control, Clin Microbiol Rev, vol.25, issue.4, pp.708-719, 2012.

R. Colangeli, V. L. Arcus, R. T. Cursons, R. A. Karalus, N. Coley et al., Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans, PLoS One, vol.9, issue.3, p.91024, 2014.

C. Colijn, T. Cohen, and M. Murray, Latent coinfection and the maintenance of strain diversity, Bull Math Biol, vol.71, issue.1, pp.247-263, 2009.

C. Colijn, T. Cohen, A. Ganesh, and M. Murray, Spontaneous emergence of multiple drug resistance in tuberculosis before and during therapy, PLoS One, vol.6, issue.3, p.18327, 2011.

I. Comas and S. Gagneux, A role for systems epidemiology in tuberculosis research, Trends Microbiol, vol.19, issue.10, pp.492-500, 2011.

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.4, issue.11, p.7815, 2009.

I. Comas, M. Coscolla, T. Luo, S. Borrell, K. E. Holt et al., Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans, Nat Genet, vol.45, issue.10, pp.1176-1182, 2013.

M. Coscolla and S. Gagneux, Consequences of genomic diversity in Mycobacterium tuberculosis, Semin Immunol, vol.26, issue.6, pp.431-444, 2014.

A. S. De-boer, M. W. Borgdorff, P. E. De-haas, N. J. Nagelkerke, J. D. Van-embden et al., Analysis of rate of change of IS6110 RFLP patterns of Mycobacterium tuberculosis based on serial patient isolates, J Infect Dis, vol.180, issue.4, pp.1238-1244, 1999.

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, Infect Genet Evol, vol.12, issue.4, pp.755-766, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-00691750

D. Rienzo, A. Peterson, A. C. Garza, J. C. Valdes, A. M. Slatkin et al., Mutational processes of simple-sequence repeat loci in human populations, Proc Natl Acad Sci U S A, vol.91, issue.8, pp.3166-3170, 1994.

X. Didelot, J. Gardy, and C. Colijn, Bayesian inference of infectious disease transmission from whole-genome sequence data, Mol Biol Evol, vol.31, issue.7, pp.1869-1879, 2014.

, /molbev/msu121

X. Didelot, C. Fraser, J. Gardy, and C. Colijn, Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks, Mol Biol Evol, vol.34, issue.4, pp.997-1007, 2017.

O. Diekmann, J. ;. Heesterbeek, C. Wiley, O. Diekmann, J. Heesterbeek et al., On the definition and the computation of the basic reproduction ratio R 0 in models for infectious diseases in heterogeneous populations, J Math Biol, vol.28, issue.4, 1990.

K. Dietz, The estimation of the basic reproduction number for infectious diseases, Stat Methods Med Res, vol.2, issue.1, pp.23-41, 1993.

D. W. Dowdy, C. Dye, and T. Cohen, Data needs for evidence-based decisions: a tuberculosis modeler's 'wish list', Int J Tuberc Lung Dis, vol.17, issue.7, pp.866-877, 2013.

D. W. Dowdy, R. Houben, T. Cohen, M. Pai, F. Cobelens et al., Impact and cost-effectiveness of current and future tuberculosis diagnostics: the contribution of modelling, Int J Tuberc Lung Dis, vol.18, issue.9, pp.1012-1018, 2014.

A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, Relaxed phylogenetics and dating with confidence, PLoS Biol, vol.4, issue.5, p.88, 2006.

A. J. Drummond, M. A. Suchard, D. Xie, and A. Rambaut, Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, vol.29, issue.8, pp.1969-1973, 2012.

C. Dye and M. A. Espinal, Will tuberculosis become resistant to all antibiotics?, Proc R Soc Lond B Biol Sci, vol.268, pp.45-52, 1462.

C. Dye and B. G. Williams, Criteria for the control of drug-resistant tuberculosis, Proc Natl Acad Sci U S A, vol.97, issue.14, pp.8180-8185, 2000.

C. Dye and B. G. Williams, Slow elimination of multidrug-resistant tuberculosis, Sci Transl Med, vol.1, issue.3, pp.3-8, 2009.

C. Dye and B. G. Williams, The population dynamics and control of tuberculosis, Science, vol.328, issue.5980, pp.856-861, 2010.

C. Dye, G. P. Garnett, K. Sleeman, and B. G. Williams, Prospects for worldwide tuberculosis control under the WHO DOTS strategy, The Lancet, vol.352, issue.9144, pp.3199-3206, 1998.

W. J. Ewens, The sampling theory of selectively neutral alleles, Theor Popul Biol, vol.3, issue.1, pp.87-112, 1972.

W. J. Ewens, Cases in which parsimony or compatibility methods will be positively misleading, Mathematical population genetics 1: theoretical introduction, vol.27, pp.401-410, 1978.

J. Felsenstein, Evolutionary trees from DNA sequences: a maximum likelihood approach, J Mol Evol, vol.17, issue.6, pp.368-376, 1981.

J. Felsenstein, A. S. Motiwala, M. Cavatore, W. Qi, M. H. Hazbon et al., Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set, J Bacteriol, vol.2, issue.2, pp.759-772, 2004.

P. E. Fine and E. Vynnycky, The effect of heterologous immunity upon the apparent efficacy of (e.g. bcg) vaccines, Vaccine, vol.16, issue.20, pp.1923-1928, 1998.

C. B. Ford, P. L. Lin, M. R. Chase, R. R. Shah, O. Iartchouk et al., Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection, 2011.

, Nat Genet, vol.43, issue.5, pp.482-486

C. B. Ford, R. R. Shah, M. K. Maeda, S. Gagneux, M. B. Murray et al., Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis, Nat Genet, vol.45, issue.7, pp.784-790, 2013.

S. Gagneux, Host-pathogen coevolution in human tuberculosis, Philos Trans R Soc B, vol.367, pp.850-859, 1590.

S. Gagneux and P. M. Small, Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development, Lancet Infect Dis, vol.7, issue.5, pp.70108-70109, 2007.

S. Gagneux, C. D. Long, P. M. Small, T. Van, G. K. Schoolnik et al., The competitive cost of antibiotic resistance in Mycobacterium tuberculosis, Science, vol.312, issue.5782, pp.1944-1946, 2006.

J. E. Galagan, Genomic insights into tuberculosis, Nat Rev Genet, vol.15, issue.5, pp.307-320, 2014.

D. Gammack, C. R. Doering, and D. E. Kirschner, Macrophage response to Mycobacterium tuberculosis infection, J Math Biol, vol.48, issue.2, pp.218-242, 2004.

J. L. Gardy, J. C. Johnston, H. Sui, S. J. Cook, V. J. Shah et al., Whole-genome sequencing and social-network analysis of a tuberculosis outbreak, N Engl J Med, vol.364, issue.8, pp.730-739, 2011.

J. R. Glynn, J. Bauer, A. S. De-boer, M. W. Borgdorff, P. E. Fine et al., Interpreting DNA fingerprint clusters of Mycobacterium tuberculosis. European Concerted Action on Molecular Epidemiology and Control of Tuberculosis, Int J Tuberc Lung Dis, vol.3, issue.12, pp.1055-1060, 1999.

J. R. Glynn, E. Vynnycky, and P. E. Fine, Influence of sampling on estimates of clustering and recent transmission of Mycobacterium tuberculosis derived from DNA fingerprinting techniques, Am J Epidemiol, vol.149, issue.4, pp.366-371, 1999.

M. Gomes, A. O. Franco, M. C. Gomes, and G. F. Medley, The reinfection threshold promotes variability in tuberculosis epidemiology and vaccine efficacy, Proc Biol Sci, vol.271, pp.617-623, 1539.

A. Grant, C. Arnold, N. Thorne, S. Gharbia, and A. Underwood, Mathematical modelling of Mycobacterium tuberculosis VNTR loci estimates a very slow mutation rate for the repeats, J Mol Evol, vol.66, issue.6, pp.565-574, 2008.

B. T. Grenfell, O. G. Pybus, J. R. Gog, J. Wood, J. M. Daly et al., Unifying the epidemiological and evolutionary dynamics of pathogens, Science, vol.303, issue.5656, pp.327-332, 2004.

M. Hasegawa, H. Kishino, and Y. Ta, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, J Mol Evol, vol.22, issue.2, pp.160-174, 1985.

H. A. Hatherell, C. Colijn, H. R. Stagg, C. Jackson, J. R. Winter et al., Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review, BMC Med, vol.14, p.21, 2016.

R. Hershberg, M. Lipatov, P. M. Small, H. Sheffer, S. Niemann et al., High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography, PLoS Biol, vol.6, issue.12, p.311, 2008.

S. Ho, M. J. Phillips, A. Cooper, and A. J. Drummond, Time dependency of molecular rate estimates and systematic overestimation of recent divergence times, Mol Biol Evol, vol.22, issue.7, pp.1561-1568, 2005.

, /molbev/msi145

V. N. Houk, Spread of tuberculosis via recirculated air in a naval vessel: the Byrd study, Ann N Y Acad Sci, vol.353, pp.10-24, 1980.

B. C. De-jong, P. C. Hill, A. Aiken, T. Awine, M. Antonio et al., Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia, J Infect Dis, vol.198, issue.7, pp.1037-1043, 2008.

T. Jukes and C. Cantor, Evolution of protein molecules, Munro HN (ed) Mammalian protein metabolism, vol.3, pp.21-132, 1969.

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.

M. J. Keeling, P. Rohani, E. A. Kendall, M. O. Fofana, and D. W. Dowdy, Burden of transmitted multidrug resistance in epidemics of tuberculosis: a transmission modelling analysis, Lancet Respir Med, vol.3, issue.12, pp.963-972, 2008.

W. O. Kermack and A. G. Mckendrick, Contributions to the mathematical theory of epidemics, Proc R Soc Ser, vol.115, pp.700-721, 1927.

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J Mol Evol, vol.16, issue.2, pp.111-120, 1980.

G. M. Knight, C. Colijn, S. Shrestha, M. Fofana, F. Cobelens et al., The distribution of fitness costs of resistance-conferring mutations is a key determinant for the future burden of drug-resistant tuberculosis: a model-based analysis, Clin Infect Dis, vol.61, issue.3, pp.147-154, 2015.

D. Kühnert, T. Stadler, T. G. Vaughan, and A. J. Drummond, Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model, J R Soc Interface, vol.11, issue.94, p.20131106, 2014.

D. Kühnert, T. Stadler, T. G. Vaughan, and A. J. Drummond, Phylodynamics with migration: a computational framework to quantify population structure from genomic data, Mol Biol Evol, 2016.

T. Lillebaek, A. Norman, E. M. Rasmussen, R. L. Marvig, D. B. Folkvardsen et al., Substantial molecular evolution and mutation rates in prolonged latent Mycobacterium tuberculosis infection in humans, Int J Med Microbiol, 2016.

J. J. Linderman and D. E. Kirschner, Computational models of lung diseases Lipsitch M, Levin BR (1997) The within-host population dynamics of antibacterial chemotherapy: conditions for the evolution of resistance, Drug Discov Today Dis Models, vol.15, pp.112-127, 2015.

X. Liu, M. M. Gutacker, J. M. Musser, and Y. X. Fu, Evidence for recombination in Mycobacterium tuberculosis, J Bacteriol, vol.188, issue.23, pp.8169-8177, 2006.

F. Luciani, A. R. Francis, and M. M. Tanaka, Interpreting genotype cluster sizes of Mycobacterium tuberculosis isolates typed with IS6110 and spoligotyping, Infect Genet Evol, vol.8, issue.2, pp.182-190, 2008.

F. Luciani, S. A. Sisson, H. Jiang, A. R. Francis, and M. M. Tanaka, The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis, Proc Natl Acad Sci U S A, vol.106, issue.34, pp.14711-14715, 2009.

S. Marino, H. P. Gideon, C. Gong, S. Mankad, J. T. Mccrone et al., Computational and empirical studies predict Mycobacterium tuberculosis-specific T cells as a biomarker for infection outcome, PLoS Comput Biol, vol.12, issue.4, p.1004804, 2016.

B. Mathema, N. E. Kurepina, P. J. Bifani, and B. N. Kreiswirth, Molecular epidemiology of tuberculosis: current insights, Clin Microbiol Rev, vol.19, issue.4, pp.658-685, 2006.

/. Cmr, , pp.61-66

N. A. Menzies, T. Cohen, H. H. Lin, M. Murray, and J. A. Salomon, Population health impact and cost-effectiveness of tuberculosis diagnosis with Xpert MTB/RIF: a dynamic simulation and economic evaluation, PLoS Med, vol.9, issue.11, 2012.

H. L. Mills, T. Cohen, and C. Colijn, Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis, Sci Transl Med, vol.5, issue.180, 2013.

M. Murray, Determinants of cluster distribution in the molecular epidemiology of tuberculosis, Proc Natl Acad Sci U S A, vol.99, issue.3, pp.1538-1543, 2002.

M. Murray, Sampling bias in the molecular epidemiology of tuberculosis, Emerg Infect Dis, vol.8, issue.4, pp.363-369, 2002.

M. Murray and D. Alland, Methodological problems in the molecular epidemiology of tuberculosis, Am J Epidemiol, vol.155, issue.6, pp.565-571, 2002.

O. Neill, M. B. Mortimer, T. D. Pepperell, and C. S. , Diversity of Mycobacterium tuberculosis across evolutionary scales, PLoS Pathog, vol.11, issue.11, 2015.

A. C. Outhred, N. Holmes, R. Sadsad, E. Martinez, P. Jelfs et al., Identifying likely transmission pathways within a 10-Year community outbreak of tuberculosis by high-depth whole genome sequencing, PLoS One, vol.11, issue.3, p.150550, 2016.

C. Ozcaglar, A. Shabbeer, S. Vandenberg, B. Yener, and K. P. Bennett, Sublineage structure analysis of Mycobacterium tuberculosis complex strains using multiple-biomarker tensors, BMC Genomics, vol.12, issue.2, p.1, 2011.

C. Ozcaglar, A. Shabbeer, S. L. Vandenberg, B. Yener, and K. P. Bennett, Epidemiological models of Mycobacterium tuberculosis complex infections, Math Biosci, vol.236, issue.2, pp.77-96, 2012.

L. J. Pankhurst, D. O. Elias, C. Votintseva, A. A. Walker, T. M. Cole et al., Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study, Lancet Respir Med, vol.4, issue.1, pp.49-58, 2016.

G. Plazzotta, T. Cohen, and C. Colijn, Magnitude and sources of bias in the detection of mixed strain M. tuberculosis infection, J Theor Biol, vol.368, pp.67-73, 2015.

O. G. Pybus, A. J. Drummond, T. Nakano, B. H. Robertson, and A. Rambaut, The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach, Mol Biol Evol, vol.20, issue.3, pp.381-387, 2003.

M. N. Ragheb, C. B. Ford, M. R. Chase, P. L. Lin, J. L. Flynn et al., The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosis from cynomolgus macaque infection, BMC Genomics, vol.14, p.145, 2013.

M. X. Rangaka, S. C. Cavalcante, B. J. Marais, S. Thim, N. A. Martinson et al., Controlling the seedbeds of tuberculosis: diagnosis and treatment of tuberculosis infection, Lancet, vol.386, pp.2344-2353, 2015.

J. F. Reyes and M. M. Tanaka, Mutation rates of spoligotypes and variable numbers of tandem repeat loci in Mycobacterium tuberculosis, Infect Genet Evol, vol.10, issue.7, 2010.

J. F. Reyes, A. R. Francis, and M. M. Tanaka, Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes, BMC Bioinformatics, vol.9, p.496, 2008.

J. F. Reyes, C. Chan, and M. M. Tanaka, Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis, Infect Genet Evol, vol.12, issue.4, pp.811-818, 2012.

N. A. Rosenberg, A. G. Tsolaki, and M. M. Tanaka, Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis, Theor Popul Biol, vol.63, issue.4, pp.347-363, 2003.

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, issue.4, pp.406-425, 1987.

R. Sergeev, C. Colijn, and T. Cohen, Models to understand the population-level impact of mixed strain M. tuberculosis infections, J Theor Biol, vol.280, issue.1, pp.88-100, 2011.

A. Shabbeer, L. S. Cowan, C. Ozcaglar, N. Rastogi, S. L. Vandenberg et al., TB-Lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex, Infect Genet Evol, vol.12, issue.4, pp.789-797, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-00691749

A. Shabbeer, C. Ozcaglar, B. Yener, and K. P. Bennett, Web tools for molecular epidemiology of tuberculosis, Infect Genet Evol, vol.12, issue.4, pp.767-781, 2012.

S. Shrestha, G. M. Knight, M. Fofana, T. Cohen, R. G. White et al., Drivers and trajectories of resistance to new first-line drug regimens for tuberculosis, Open Forum Infect Dis, vol.1, issue.2, p.73, 2014.

P. M. Small, P. C. Hopewell, S. P. Singh, A. Paz, J. Parsonnet et al., The epidemiology of tuberculosis in San Francisco: a population-based study using conventional and molecular methods, N Engl J Med, vol.330, pp.1703-1709, 1994.

N. H. Smith, R. G. Hewinson, K. Kremer, R. Brosch, and S. V. Gordon, Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis, Nat Rev Microbiol, vol.7, issue.7, pp.537-544, 2009.

T. Stadler, Inferring epidemiological parameters on the basis of allele frequencies, Genetics, vol.188, issue.3, pp.663-672, 2011.

T. Stadler and S. Bonhoeffer, Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods, Philos Trans R Soc B: Biolog Sci, vol.368, p.20120198, 1614.

T. Stadler, R. D. Kouyos, V. Von-wyl, S. Yerly, J. Böni et al., Estimating the basic reproductive number from viral sequence data, Mol Biol Evol, vol.29, pp.347-357, 2012.

T. Stadler, D. Kuhnert, S. Bonhoeffer, and A. J. Drummond, Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV), Proc Natl Acad Sci U S A, vol.110, issue.1, pp.228-233, 2013.

M. Steel, Consistency of bayesian inference of resolved phylogenetic trees, J Theor Biol, vol.336, pp.246-249, 2013.

P. Supply, C. Allix, S. Lesjean, M. Cardoso-oelemann, S. Rüsch-gerdes et al., Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis, J Clin Microbiol, vol.44, issue.12, pp.4498-4510, 2006.

K. Tamura and M. Nei, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol Biol Evol, vol.10, issue.3, pp.512-526, 1993.

M. M. Tanaka and A. R. Francis, Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information, Infect Genet Evol, vol.5, issue.1, pp.35-43, 2005.

M. M. Tanaka, N. A. Rosenberg, and P. M. Small, The control of copy number of IS6110 in Mycobacterium tuberculosis, Mol Biol Evol, vol.21, issue.12, pp.2195-2201, 2004.

, /molbev/msh234

M. M. Tanaka, A. R. Francis, F. Luciani, and S. A. Sisson, Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data, Genetics, vol.173, issue.3, pp.1511-1520, 2006.

S. Tavaré, Some probabilistic and statistical problems in the analysis of DNA sequences, Lect Math Life Sci, vol.17, pp.57-86, 1986.

T. H. To, M. Jung, S. Lycett, and O. Gascuel, Fast Dating Using Least-Squares Criteria and Algorithms, Syst Biol, vol.65, issue.1, pp.82-97, 2016.
URL : https://hal.archives-ouvertes.fr/lirmm-01348367

J. M. Trauer, J. T. Denholm, and E. S. Mcbryde, Construction of a mathematical model for tuberculosis transmission in highly endemic regions of the Asia-Pacific, J Theor Biol, vol.358, pp.74-84, 2014.

A. J. Vogler, C. Keys, Y. Nemoto, R. E. Colman, Z. Jay et al., Effect of repeat copy number on variablenumber tandem repeat mutations in Escherichia coli O157:H7, J Bacteriol, vol.188, issue.12, pp.4253-4263, 2006.

E. M. Volz, Complex population dynamics and the coalescent under neutrality, Genetics, vol.190, issue.1, pp.187-201, 2012.

E. M. Volz, K. Pond, S. L. Ward, M. J. , L. Brown et al., Phylodynamics of infectious disease epidemics, Genetics, vol.183, issue.4, 2009.

E. Vynnycky and P. Fine, The natural history of tuberculosis: the implications of age-dependent risks of disease and the role of reinfection, Epidemiol Infect, vol.119, issue.2, pp.183-201, 1997.

H. Waaler, A. Geser, and S. Andersen, The use of mathematical models in the study of the epidemiology of tuberculosis, Am J Public Health Nat Health, vol.52, issue.6, pp.1002-1013, 1962.

J. Wakeley, . Roberts, . Co, . Greenwood-village, T. M. Walker et al., Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study, Lancet Infect Dis, vol.13, issue.2, pp.137-146, 2009.

R. M. Warren, G. D. Van-der-spuy, M. Richardson, N. Beyers, M. W. Borgdorff et al., Calculation of the stability of the IS6110 banding pattern in patients with persistent Mycobacterium tuberculosis disease, J Clin Microbiol, vol.40, issue.5, pp.1705-1708, 2002.

R. M. Warren, T. C. Victor, E. M. Streicher, M. Richardson, N. Beyers et al., Patients with active tuberculosis often have different strains in the same sputum specimen, Am J Respir Crit Care Med, vol.169, issue.5, pp.610-614, 2004.

T. Weniger, J. Krawczyk, P. Supply, D. Harmsen, and S. Niemann, Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: now and next, Infect Genet Evol, vol.12, issue.4, pp.748-754, 2012.

, World Health Organization Wigginton JE, Kirschner D (2001) A model to predict cell-mediated immune regulatory mechanisms during human infection with Mycobacterium tuberculosis, J Immunol, vol.166, issue.3, pp.1951-1967, 2016.

T. Wirth, F. Hildebrand, C. Allix-béguec, F. Wölbeling, T. Kubica et al., Origin, spread and demography of the Mycobacterium tuberculosis complex, PLoS Pathog, vol.4, issue.9, p.1000160, 2008.

Z. Yang, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods, J Mol Evol, vol.39, issue.3, pp.306-314, 1994.

Z. Yang, Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods, Syst Biol, vol.43, issue.3, pp.329-342, 1994.

Z. Yang, Among-site rate variation and its impact on phylogenetic analyses, Trends Ecol Evol, vol.11, issue.9, pp.367-372, 1996.

Z. Yang, Does Mycobacterium tuberculosis have plasmids?, Oxford Zainuddin Z, Dale J, vol.71, pp.43-49, 1990.

N. Zheng, C. C. Whalen, and A. Handel, Modeling the potential impact of host population survival on the evolution of M. tuberculosis latency, PLoS One, vol.9, issue.8, p.105721, 2014.

E. Zuckerkandl and L. Pauling, Evolutionary divergence and convergence in proteins, Evol Genes Proteins, vol.97, pp.97-166, 1965.

A. Zwerling, G. B. Gomez, J. Pennington, F. Cobelens, A. Vassall et al., A simplified costeffectiveness model to guide decision-making for shortened anti-tuberculosis treatment regimens, Int J Tuberc Lung Dis, vol.20, issue.2, pp.257-260, 2016.

S. Sequence, , p.59

, Serine/threonine protein kinases (STPKs), p.147

, Shotgun sequencing, p.81

K. Sigma-factor, , p.163

, Single DNA dye-based multicapillary systems, 51 Single molecule, real-time (SMRT) sequencing, p.58

, Single nucleotide polymorphism (SNP), vol.136, pp.161-162

, Smooth tuberculosis bacilli (STB), vol.2, p.96