, WHO. Global tuberculosis report, 2019.

R. Brosch, A new evolutionary scenario for the Mycobacterium tuberculosis complex, Proc. Natl Acad. Sci. USA, vol.99, pp.3684-3689, 2002.

P. Supply, Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis, Nat. Genet, vol.45, pp.172-179, 2013.

E. C. Boritsch, pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence, Nat. Microbiol, vol.1, p.15019, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01265519

I. Comas, Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans, Nat. Genet, vol.45, pp.1176-1182, 2013.

M. Orgeur and R. Brosch, Evolution of virulence in the Mycobacterium tuberculosis complex, Curr. Opin. Microbiol, vol.41, pp.68-75, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-02046172

L. S. Ates, Unexpected genomic and phenotypic diversity of Mycobacterium africanum lineage 5 affects drug resistance, protein secretion, and immunogenicity, Genome Biol. Evol, vol.10, pp.1858-1874, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01884644

J. Gonzalo-asensio, Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator, Proc. Natl Acad. Sci. USA, vol.111, pp.11491-11496, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02325922

D. Brites, A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex. Front Microbiol, vol.9, p.2820, 2018.

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, pp.537-544, 2009.

S. Gagneux and P. M. Small, Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development, Lancet Infect. Dis, vol.7, pp.328-337, 2007.

M. Merker, Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage, Nat. Genet, vol.47, pp.242-249, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01153552

D. Stucki, Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages, Nat. Genet, vol.48, pp.1535-1543, 2016.

K. Kremer, 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, pp.2607-2618, 1999.

D. Couvin, A. David, T. Zozio, and N. Rastogi, Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database, Infect. Genet. Evol, vol.72, pp.31-43, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01986923

R. Firdessa, Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg. Infect. Dis, vol.19, pp.460-463, 2013.

Y. Blouin, Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade, PLoS ONE, vol.7, p.52841, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00772379

H. Nebenzahl-guimaraes, Genomic characterization of Mycobacterium tuberculosis lineage 7 and a proposed name, Aethiops vetus". Microb. Genomics, vol.2, p.63, 2016.

F. Coll, A robust SNP barcode for typing Mycobacterium tuberculosis complex strains, Nat. Commun, vol.5, p.4812, 2014.

P. Palittapongarnpim, Evidence for host-bacterial co-evolution via genome sequence analysis of 480 Thai Mycobacterium tuberculosis lineage 1 isolates, Sci. Rep, vol.8, p.11597, 2018.

G. Thwaites, Relationship between Mycobacterium tuberculosis genotype and the clinical phenotype of pulmonary and meningeal tuberculosis, J. Clin. Microbiol, vol.46, pp.1363-1368, 2008.

B. Varghese, Impact of Mycobacterium tuberculosis complex lineages as a determinant of disease phenotypes from an immigrant rich moderate tuberculosis burden country, Respir. Res, vol.19, p.259, 2018.

D. Portevin, S. Gagneux, I. Comas, and D. Young, Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages, PLoS Pathog, vol.7, p.1001307, 2011.

N. Reiling, Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice, MBio, vol.4, pp.250-263, 2013.

S. Homolka, S. Niemann, D. G. Russell, and K. H. Rohde, Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival, PLoS Pathog, vol.6, p.1000988, 2010.

A. Romagnoli, Clinical isolates of the modern Mycobacterium tuberculosis lineage 4 evade host defense in human macrophages through eluding IL-1beta-induced autophagy, Cell Death Dis, vol.9, p.624, 2018.

R. Szekely and S. T. Cole, Mechanistic insight into mycobacterial MmpL protein function, Mol. Microbiol, vol.99, pp.831-834, 2016.

P. Domenech, M. B. Reed, and C. E. Barry, Contribution of the Mycobacterium tuberculosis MmpL protein family to virulence and drug resistance, Infect. Immun, vol.73, pp.3492-3501, 2005.

G. Melly and G. E. Purdy, MmpL proteins in physiology and pathogenesis of M. tuberculosis. Microorganisms. 7, 2019.

S. V. Gordon, Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays, Molec Microbiol, vol.32, pp.643-656, 1999.

D. A. Mitchison, J. B. Selkon, and J. Lloyd, Virulence in the guinea-pig, susceptibility to hydrogen peroxide, and catalase activity of isoniazid-sensitive tubercle bacilli from South Indian and British patients, J. Pathol. Bacteriol, vol.86, pp.377-386, 1963.

M. C. Gutierrez, Predominance of ancestral lineages of Mycobacterium tuberculosis in India, Emerg. Infect. Dis, vol.12, pp.1367-1374, 2006.

P. R. Gangadharam, M. L. Cohn, C. L. Davis, and G. Middlebrook, Infectivity and pathogenicity of Indian and British strains of tubercle bacilli studied by aerogenic infection of guinea pigs, Am. Rev. Respir. Dis, vol.87, pp.200-205, 1963.

N. Krishnan, Mycobacterium tuberculosis lineage influences innate immune response and virulence and is associated with distinct cell envelope lipid profiles, PLoS ONE, vol.6, p.23870, 2011.

J. C. Van-kessel and G. F. Hatfull, Recombineering in Mycobacterium tuberculosis, Nat. Methods, vol.4, pp.147-152, 2007.

F. C. Bange, F. M. Collins, and W. R. Jacobs, Survival of mice infected with Mycobacterium smegmatis containing large DNA fragments from Mycobacterium tuberculosis, Tuber. Lung Dis, vol.79, pp.171-180, 1999.

I. Kramnik, W. F. Dietrich, P. Demant, and B. R. Bloom, Genetic control of resistance to experimental infection with virulent Mycobacterium tuberculosis, Proc. Natl Acad. Sci. USA, vol.97, pp.8560-8565, 2000.

J. Harper, Mouse model of necrotic tuberculosis granulomas develops hypoxic lesions, J. Infect. Dis, vol.205, pp.595-602, 2012.

B. Carow, Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma, Nat. Commun, vol.10, p.1823, 2019.

S. Verma, Transmission phenotype of Mycobacterium tuberculosis strains is mechanistically linked to induction of distinct pulmonary pathology, PLoS Pathog, vol.15, p.1007613, 2019.

R. Bailo, A. Bhatt, and J. A. Ainsa, Lipid transport in Mycobacterium tuberculosis and its implications in virulence and drug development, Biochem Pharmacol, vol.96, pp.159-167, 2015.

G. Larrouy-maumus and G. Puzo, Mycobacterial envelope lipids fingerprint from direct MALDI-TOF MS analysis of intact bacilli, Tuberculosis (Edinb.), vol.95, pp.75-85, 2015.

R. Bansal-mutalik and H. Nikaido, Mycobacterial outer membrane is a lipid bilayer and the inner membrane is unusually rich in diacyl phosphatidylinositol dimannosides, Proc. Natl Acad. Sci. USA, vol.111, pp.4958-4963, 2014.

E. Layre, Deciphering sulfoglycolipids of Mycobacterium tuberculosis, J. Lipid Res, vol.52, pp.1098-1110, 2011.

O. Mestre, High throughput phenotypic selection of Mycobacterium tuberculosis mutants with impaired resistance to reactive oxygen species identifies genes important for intracellular growth, PLoS ONE, vol.8, p.53486, 2013.

L. G. Wayne and C. D. Sohaskey, Nonreplicating persistence of Mycobacterium tuberculosis, Annu Rev. Microbiol, vol.55, pp.139-163, 2001.

I. Filliol, 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, pp.1963-1970, 2003.

S. Banu, Genotypic analysis of Mycobacterium tuberculosis in Bangladesh and Prevalence of the Beijing Strain, J. Clin. Microbiol, vol.42, pp.674-682, 2004.

Q. Liu, China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis, Nat. Ecol. Evol, vol.2, pp.1982-1992, 2018.

O. Pasechnik, Major genotype families and epidemic clones of Mycobacterium tuberculosis in Omsk region, Tuberculosis (Edinb.), vol.108, pp.163-168, 2018.

Y. Shah, Genetic diversity of Mycobacterium tuberculosis Central Asian Strain isolates from Nepal and comparison with neighboring countries, Trans. R. Soc. Trop. Med Hyg, vol.113, pp.203-211, 2019.

F. Vaziri, Genetic diversity of multi-and extensively drug-resistant Mycobacterium tuberculosis Isolates in the capital of Iran, revealed by wholegenome sequencing, J. Clin. Microbiol, vol.57, pp.1477-1495, 2019.

I. Comas, Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in Sub-Saharan Africa, Curr. Biol, vol.25, pp.3260-3266, 2015.

B. C. De-jong, M. Antonio, and S. Gagneux, Mycobacterium africanum-review of an important cause of human tuberculosis in West Africa, PLoS Negl. Trop. Dis, vol.4, p.744, 2010.

A. L. Bhatia, The virulence in the guinea-pig of tubercle bacilli isolated before treatment from South Indian patients with pulmonary tuberculosis. 2. Comparison with virulence of tubercle bacilli from British patients, Bull. World Health Organ, vol.25, pp.313-322, 1961.

S. Clark, Y. Hall, and A. Williams, Animal models of tuberculosis: Guinea pigs. Cold Spring Harb, Perspect. Med, vol.5, p.18572, 2014.

O. C. Turner, R. J. Basaraba, and I. M. Orme, Immunopathogenesis of pulmonary granulomas in the guinea pig after infection with Mycobacterium tuberculosis, Infect. Immun, vol.71, pp.864-871, 2003.

L. E. Via, Tuberculous granulomas are hypoxic in guinea pigs, rabbits, and nonhuman primates, Infect. Immun, vol.76, pp.2333-2340, 2008.

J. E. Galagan, The Mycobacterium tuberculosis regulatory network and hypoxia, Nature, vol.499, pp.178-183, 2013.

M. I. Voskuil, Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program, J. Exp. Med, vol.198, pp.705-713, 2003.

F. Tekaia, Analysis of the proteome of Mycobacterium tuberculosis in silico, Tube. Lung Dis, vol.79, pp.329-342, 1999.

C. Varela, MmpL genes are associated with mycolic acid metabolism in mycobacteria and corynebacteria, Chem. Biol, vol.19, pp.498-506, 2012.

S. A. Pacheco, F. F. Hsu, K. M. Powers, and G. E. Purdy, MmpL11 protein transports mycolic acid-containing lipids to the mycobacterial cell wall and contributes to biofilm formation in Mycobacterium smegmatis, J. Biol. Chem, vol.288, pp.24213-24222, 2013.

A. E. Grzegorzewicz, Inhibition of mycolic acid transport across the Mycobacterium tuberculosis plasma membrane, Nat. Chem. Biol, vol.8, pp.334-341, 2012.

K. Tahlan, SQ109 targets MmpL3, a membrane transporter of trehalose monomycolate involved in mycolic acid donation to the cell wall core of Mycobacterium tuberculosis, Antimicrob. Agents Chemother, vol.56, pp.1797-1809, 2012.

L. R. Camacho, D. Ensergueix, E. Perez, B. Gicquel, and C. Guilhot, Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis, Mol. Microbiol, vol.34, pp.257-267, 1999.

J. S. Cox, B. Chen, M. Mcneil, and W. R. Jacobs, Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice, Nature, vol.402, pp.79-83, 1999.

S. E. Converse, MmpL8 is required for sulfolipid-1 biosynthesis and Mycobacterium tuberculosis virulence, Proc. Natl Acad. Sci. USA, vol.100, pp.6121-6126, 2003.

J. C. Seeliger, Elucidation and chemical modulation of sulfolipid-1 biosynthesis in Mycobacterium tuberculosis, J. Biol. Chem, vol.287, pp.7990-8000, 2012.

M. Daffe, D. C. Crick, and M. Jackson, Genetics of capsular polysaccharides and cell envelope (Glyco)lipids. Microbiol Spectr, vol.2, pp.2-0021, 2014.

G. Sapriel and R. Brosch, Shared pathogenomic patterns characterize a new phylotype, revealing transition towards host-adaptation long before speciation of Mycobacterium tuberculosis, Genome Biol. Evol, vol.11, pp.2420-2438, 2019.

T. P. Stinear, Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

, Genome Res, vol.18, pp.729-741, 2008.

J. Wang, Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii, Genome Biol. Evol, vol.7, pp.856-870, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01352692

S. Watanabe, Fumarate reductase activity maintains an energized membrane in anaerobic Mycobacterium tuberculosis, PLoS Pathog, vol.7, p.1002287, 2011.

J. C. Betts, Signature gene expression profiles discriminate between isoniazid-, thiolactomycin-, and triclosan-treated Mycobacterium tuberculosis, Antimicrob. Agents Chemother, vol.47, pp.2903-2913, 2003.

P. Arumugam, D. Shankaran, A. Bothra, S. Gandotra, and V. Rao, The MmpS6-MmpL6 operon is an oxidative stress response system providing selective advantage to Mycobacterium tuberculosis in stress, J. Infect. Dis, vol.219, pp.459-469, 2019.

S. Nambi, The Oxidative Stress Network of Mycobacterium tuberculosis Reveals Coordination between Radical Detoxification Systems, Cell Host Microbe, vol.17, pp.829-837, 2015.

K. I. Bos, Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis, Nature, vol.514, pp.494-497, 2014.

G. M. Taylor, D. B. Young, and S. A. Mays, Genotypic analysis of the earliest known prehistoric case of tuberculosis in Britain, J. Clin. Microbiol, vol.43, pp.2236-2240, 2005.

G. L. Kay, Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe, Nat. Commun, vol.6, p.6717, 2015.

L. Chevalier and F. , Revisiting the role of phospholipases C in the virulence of Mycobacterium tuberculosis, Sci. Rep, vol.5, p.16918, 2015.

S. T. Cole, Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence, Nature, vol.393, pp.537-544, 1998.

S. Batzoglou, ARACHNE: a whole-genome shotgun assembler, Genome Res, vol.12, pp.177-189, 2002.

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-829, 2008.

D. Vallenet, MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes, Nucleic Acids Res, vol.45, pp.517-528, 2017.

R. Manganelli, Role of the extracytoplasmic-function sigma factor sigma (H) in Mycobacterium tuberculosis global gene expression, Mol. Microbiol, vol.45, pp.365-374, 2002.

M. Di-luca, The ESX-5 associated eccB-eccC locus is essential for Mycobacterium tuberculosis viability, PLoS One, vol.7, p.52059, 2012.