, Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest

R. M. Houben and P. J. Dodd, The global burden of latent tuberculosis infection: a re-estimation using mathematical modelling, PLoS Med, vol.13, 2016.

P. Supply, M. Marceau, S. Mangenot, D. Roche, C. Rouanet et al., Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis, Nat Genet, vol.45, pp.172-179, 2013.

P. Supply and R. Brosch, Biology and epidemiology of Mycobacterium canettii, Adv Exp Med Biol, vol.1019, pp.27-41, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-02046359

D. Van-soolingen, T. Hoogenboezem, P. E. De-haas, P. W. Hermans, M. A. Koedam et al., A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa, Int J Syst Bacteriol, vol.47, pp.1236-1245, 1997.

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, pp.21-28, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00948497

J. L. Koeck, M. Fabre, F. Simon, M. Daffe, E. Garnotel et al., Clinical characteristics of the smooth tubercle bacilli 'Mycobacterium canettii' infection suggest the existence of an environmental reservoir, Clin Microbiol Infect, vol.17, pp.1013-1019, 2011.

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

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

E. C. Boritsch, W. Frigui, A. Cascioferro, W. Malaga, G. Etienne et al., Experimental clarification of the observed smooth and rough colony morphotypes of tubercle bacilli and integration of these informations into the evolutionary emergence of M, Nat Microbiol, vol.1, p.15019, 2016.

H. Ren, L. G. Dover, S. T. Islam, D. C. Alexander, J. M. Chen et al., Identification of the lipooligosaccharide biosynthetic gene cluster from Mycobacterium marinum, Mol Microbiol, vol.63, pp.1345-1359, 2007.

V. Nataraj, P. C. Pang, S. M. Haslam, N. Veerapen, D. E. Minnikin et al., MKAN27435 is required for the biosynthesis of higher subclasses of lipooligosaccharides in Mycobacterium kansasii, PLoS ONE, vol.10, 2015.

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, pp.3260-3266, 2015.

, Genome-based model of evolution of the tubercle bacilli on the African continent, confirming and refining previous schemes based on genomic deletion analysis

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, pp.1176-1182, 2013.

H. Nebenzahl-guimaraes, S. A. Yimer, C. Holm-hansen, J. De-beer, R. Brosch et al., Genomic characterization of Mycobacterium tuberculosis lineage, vol.7, p.63, 2016.

M. Coscolla, A. Lewin, S. Metzger, K. Maetz-rennsing, S. Calvignacspencer et al., Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee, Emerg Infect Dis, vol.19, pp.969-976, 2013.

K. A. Alexander, C. E. Sanderson, M. H. Larsen, S. Robbe-austerman, M. C. Williams et al., Emerging tuberculosis pathogen hijacks social communication behavior in the group-living banded mongoose (Mungos mungo), MBio, pp.281-297, 2016.

R. Brosch, S. V. Gordon, M. Marmiesse, P. Brodin, C. Buchrieser et al., A new evolutionary scenario for the Mycobacterium tuberculosis complex, Proc Natl Acad Sci U S A, vol.99, pp.3684-3689, 2002.

D. Stucki, D. Brites, L. Jeljeli, M. Coscolla, Q. Liu et al., Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages, Nat Genet, vol.48, pp.1535-1543, 2016.

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.

, Genome based description of one of the most important lineages of M. tuberculosis

M. Merker, C. Blin, S. Mona, N. Duforet-frebourg, S. Lecher et al., 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

, Genome based description of one of the most important lineages of M. tuberculosis

L. S. Ates, A. Dippenaar, R. Ummels, S. R. Piersma, A. D. Van-der-woude et al., Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis, Nat Microbiol, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-02046016

J. Gonzalo-asensio, W. Malaga, A. Pawlik, C. Astarie-dequeker, C. Passemar et al., Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator, Identification of an association between the loss of PE_PGRS secretion and increase of virulence that was also found for the modern Beijing lineage of M. tuberculosis strains, vol.22, pp.11491-11496, 2014.

, Experimental demonstration of the impact of delta-RD9 lineage-specific mutations of the phoP/phoR cluster encoding a major two componant virulence regulator of the tubercle bacilli

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

, Elucidation of the genome sequences of ancient mycobacterial DNA isolated from 1000-year-old mummies in South-America, with genomic similarity to current tubercle bacilli found in pinnipeds

S. B. Walters, E. Dubnau, I. Kolesnikova, F. Laval, M. Daffe et al., The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis, Mol Microbiol, vol.60, pp.312-330, 2006.
DOI : 10.1111/j.1365-2958.2006.05102.x

B. Blasco, J. M. Chen, R. Hartkoorn, C. Sala, S. Uplekar et al., Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein, PLoS Pathog, vol.8, p.1002621, 2012.

S. Raghavan, P. Manzanillo, K. Chan, C. Dovey, and J. Cox, Secreted transcription factor controls Mycobacterium tuberculosis virulence, Nature, vol.454, pp.717-721, 2008.
DOI : 10.1038/nature07219

URL : http://europepmc.org/articles/pmc2862998?pdf=render

B. R. Gordon, Y. Li, L. Wang, A. Sintsova, H. Van-bakel et al., Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis, Proc Natl Acad Sci, vol.107, pp.5154-5159, 2010.

X. Pang, B. Samten, G. Cao, X. Wang, A. R. Tvinnereim et al., MprAB regulates the espA operon in Mycobacterium tuberculosis and modulates ESX-1 function and host cytokine response, J Bacteriol, vol.195, pp.66-75, 2013.

J. A. Macgurn, S. Raghavan, S. A. Stanley, and J. S. Cox, A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis, Mol Microbiol, vol.57, pp.1653-1663, 2005.

S. M. Fortune, A. Jaeger, D. A. Sarracino, M. R. Chase, C. M. Sassetti et al., Mutually dependent secretion of proteins required for mycobacterial virulence, Proc Natl Acad Sci, vol.102, pp.10676-10681, 2005.

Y. Lou, J. Rybniker, C. Sala, and C. St, EspC forms a filamentous structure in the cell envelope of Mycobacterium tuberculosis and impacts ESX-1 secretion, Mol Microbiol, vol.103, pp.26-38, 2017.

, First description of a multimeric structure of one of the key ESX-1associated proteins, and possible identification of a secretion needle for the type VII secretion system

A. O. Whelan, M. Coad, P. J. Cockle, G. Hewinson, M. Vordermeier et al., PLoS ONE, vol.5, p.8527, 2010.

A. R. Allen, One bacillus to rule them all? Investigating broad range host adaptation in Mycobacterium bovis, vol.53, pp.68-76, 2017.

M. A. Behr and S. V. Gordon, Why doesn't Mycobacterium tuberculosis spread in animals, Trends Microbiol, vol.23, pp.1-2, 2015.
DOI : 10.1016/j.tim.2014.11.001

S. Berg and N. H. Smith, Why doesn't bovine tuberculosis transmit between humans?, Trends Microbiol, vol.22, pp.552-553, 2014.
DOI : 10.1016/j.tim.2014.08.007

M. I. Grö-schel, F. Sayes, R. Simeone, L. Majlessi, and R. Brosch, ESX secretion systems: mycobacterial evolution to counter host immunity, Nat Rev Microbiol, vol.14, pp.677-691, 2016.

D. G. Russell, The ins and outs of the Mycobacterium tuberculosis-containing vacuole, vol.18, pp.1065-1069, 2016.

R. Simeone, L. Majlessi, J. Enninga, and R. Brosch, Perspectives on mycobacterial vacuole-to-cytosol translocation: the importance of cytosolic access, Cell Microbiol, vol.18, pp.1070-1077, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01899438

N. Van-der-wel, D. Hava, D. Houben, D. Fluitsma, M. Van-zon et al., M. tuberculosis and M. leprae translocate from the phagolysosome to the cytosol in myeloid cells, vol.129, pp.1287-1298, 2007.

R. Simeone, A. Bobard, J. Lippmann, W. Bitter, L. Majlessi et al., Phagosomal rupture by Mycobacterium tuberculosis results in toxicity and host cell death, PLoS Pathog, vol.8, p.1002507, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01899479

R. Simeone, F. Sayes, O. Song, M. I. Groschel, P. Brodin et al., Cytosolic access of Mycobacterium tuberculosis: critical impact of phagosomal acidification control and demonstration of occurrence in vivo, Independent confirmation of phagosomal rupture induced by M. tuberculosis by using FRET-based technology in combination with a flowcytometric approach, vol.11, 2015.

L. Majlessi and R. Brosch, Mycobacterium tuberculosis meets the cytosol: the role of cGAS in anti-mycobacterial immunity, Cell Host Microbe, vol.17, pp.733-735, 2015.

A. Kupz, U. Zedler, M. Staber, C. Perdomo, A. Dorhoi et al., ESAT-6-dependent cytosolic pattern recognition drives noncognate tuberculosis control in vivo, J Clin Invest, vol.126, pp.2109-2122, 2016.

K. W. Wong and W. R. Jacobs, Critical role for NLRP3 in necrotic death triggered by Mycobacterium tuberculosis, vol.13, pp.1371-1384, 2011.

M. I. Groschel, F. Sayes, S. J. Shin, W. Frigui, A. Pawlik et al., Recombinant BCG expressing ESX-1 of Mycobacterium marinum combines low virulence with cytosolic immune signaling and improved TB protection, Cell Rep, vol.18, pp.2752-2765, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01503927

N. H. Smith, T. Crawshaw, J. Parry, and R. J. Birtles, Mycobacterium microti: more diverse than previously thought, J Clin Microbiol, vol.47, pp.2551-2559, 2009.

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.

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, 2004.

J. Augenstreich, A. Arbues, R. Simeone, E. Haanappel, A. Wegener et al., ESX-1 and phthiocerol dimycocerosates of Mycobacterium tuberculosis act in concert to cause phagosomal rupture and host cell apoptosis, Cell Microbiol, vol.19, p.12726, 2017.

J. Quigley, V. K. Hughitt, C. A. Velikovsky, R. A. Mariuzza, N. M. El-sayed et al., The cell wall lipid PDIM contributes to phagosomal escape and host cell exit of Mycobacterium tuberculosis, vol.8, 2017.

A. K. Barczak, R. Avraham, S. Singh, S. S. Luo, W. R. Zhang et al., Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence, PLoS Pathog, vol.13, 2017.

L. S. Ates and R. Brosch, Discovery of the type VII ESX-1 secretion needle?, Mol Microbiol, vol.103, pp.7-12, 2017.

D. Wong, H. Bach, J. Sun, Z. Hmama, and Y. Av-gay, Mycobacterium tuberculosis protein tyrosine phosphatase (PtpA) excludes host vacuolar-H+-ATPase to inhibit phagosome acidification, Proc Natl Acad Sci U S A, vol.108, pp.19371-19376, 2011.

C. J. Queval, O. R. Song, J. P. Carralot, J. M. Saliou, A. Bongiovanni et al., Mycobacterium tuberculosis controls phagosomal acidification by targeting CISH-mediated signalling, Cell Rep, vol.20, pp.3188-3198, 2017.

, Description of a new mechanism identified that explains that M. tuberculosis has more than one possibility to inhibit acidification of the M. tuberculosis-containing phagosome

A. V. Grant, A. Sabri, A. Abid, A. Rhorfi, I. Benkirane et al., A genome-wide association study of pulmonary tuberculosis in Morocco, Hum Genet, vol.135, pp.299-307, 2016.

A. Pacis, L. Tailleux, A. M. Morin, J. Lambourne, J. L. Macisaac et al., First comprehensive epigenome and transcriptome analysis of monocyte-derived dendritic cells, corresponding to professional antigen presenting cells at the interface between innate and adaptive immunity, before and after in vitro infection with live pathogenic bacteria, Genome Res, vol.21, pp.496-501, 2015.

, Demonstration of the ability and usefulness to provide transcriptional information from the pathogen and the host cell