G. J. Fox, M. Orlova, and E. Schurr, Tuberculosis in Newborns: The Lessons of the, Lü beck Disaster, vol.12, p.1005271, 2016.

A. R. Escombe, C. Oeser, R. H. Gilman, M. Navincopa, E. Ticona et al., The Detection of Airborne Transmission of Tuberculosis from HIV-Infected Patients, Using an In Vivo Air Sampling Model, Clin Infect Dis, vol.44, pp.1349-1357, 2007.

R. D. Turner and G. H. Bothamley, Cough and the Transmission of Tuberculosis, J Infect Dis, vol.211, pp.1367-1372, 2015.

A. Osman, D. Bouzid, F. Canaan, S. Drancourt, and M. , Smooth Tubercle Bacilli: Neglected Opportunistic Tropical Pathogens. Front Public Health, vol.3, 2016.

J. T. Evans, E. G. Smith, A. Banerjee, R. M. Smith, J. Dale et al., Cluster of human tuberculosis caused by Mycobacterium bovis: evidence for person-to-person transmission in the UK. The Lancet, vol.369, pp.1270-1276, 2007.

R. Smith, F. Drobniewski, A. Gibson, J. Montague, M. N. Logan et al., Mycobacterium bovis Infection, United Kingdom, Emerg Infect Dis, vol.10, pp.539-541, 2004.

J. M. Grange, Mycobacterium bovis infection in human beings, Tuberculosis, vol.81, pp.71-77, 2001.

M. A. Calmette, The intestinal origin of pulmonary tuberculosis, and the mechanism of tuberculous infection. Reviews. Agriculture and Fisheries Annual Reports of Proceedings under the Diseases of Animal Actes, for the year 1905, 1905.

C. Pierce, R. J. Dubos, and G. Middlebrook, Infection of Mice with Mammalian Tubercle Bacilli Grown in Tween-Albumin Liquid Medium, Journal of Experimental Medicine, vol.86, pp.159-174, 1947.

M. J. Lefford, Diseases in mice and rats, The mycobacteria, pp.947-977, 1984.

F. Bouzid, F. Bré-geon, H. Lepidi, H. D. Donoghue, D. E. Minnikin et al., Ready Experimental Translocation of Mycobacterium canettii Yields Pulmonary Tuberculosis, Infect Immun, vol.85, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01729789

A. Loukil, P. Kirtania, M. Bedotto, and M. Drancourt, FISHing Mycobacterium tuberculosis Complex by Use of a rpoB DNA Probe Bait, Journal of Clinical Microbiology, vol.56, pp.568-586, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01910320

B. Van-coppenraet, E. S. Lindeboom, J. A. Prins, J. M. Peeters, M. F. Claas et al., Realtime PCR assay using fine-needle aspirates and tissue biopsy specimens for rapid diagnosis of mycobacterial lymphadenitis in children, J Clin Microbiol, vol.42, pp.2644-2650, 2004.

S. Ding, M. M. Chi, B. P. Scull, R. Rigby, N. Schwerbrock et al., High-fat diet: bacteria interactions promote intestinal inflammation which precedes and correlates with obesity and insulin resistance in mouse, PLoS ONE, vol.5, p.12191, 2010.

A. Bankevich, S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin et al., SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, pp.455-477, 2012.

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, pp.2068-2069, 2014.

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.25297886, 2014.

F. Coll, R. Mcnerney, M. D. Preston, J. A. Guerra-assunção, A. Warry et al., Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences, Genome Med, vol.7, p.26019726, 2015.

F. Coll, R. Mcnerney, J. A. Guerra-assunção, J. R. Glynn, J. Perdigão et al., A robust SNP barcode for typing Mycobacterium tuberculosis complex strains, Nature Communications, vol.5, p.4812, 2014.

J. Dormans, M. Burger, D. Aguilar, R. Hernandez-pando, K. Kremer et al., Correlation of virulence, lung pathology, bacterial load and delayed type hypersensitivity responses after infection with different Mycobacterium tuberculosis genotypes in a BALB/c mouse model, Clin Exp Immunol, vol.137, pp.460-468, 2004.

B. Jeon, J. Kwak, M. Hahn, S. Eum, Y. J. Kim et al., In vivo characteristics of Korean Beijing Mycobacterium tuberculosis strain K1 in an aerosol challenge model and in the Cornell latent tuberculosis model, Journal of Medical Microbiology, vol.61, p.22820694, 2012.

J. Dibbern, L. Eggers, and B. E. Schneider, Sex differences in the C57BL/6 model of Mycobacterium tuberculosis infection, Sci Rep, vol.7, p.28887521, 2017.

E. Medina and R. J. North, Resistance ranking of some common inbred mouse strains to Mycobacterium tuberculosis and relationship to major histocompatibility complex haplotype and Nramp1 genotype, Immunology, vol.93, pp.270-274, 1998.

P. L. Dunn and R. J. North, Virulence ranking of some Mycobacterium tuberculosis and Mycobacterium bovis strains according to their ability to multiply in the lungs, induce lung pathology, and cause mortality in mice, Infect Immun, vol.63, pp.3428-3437, 1995.

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, pp.4501-4509, 2002.

S. Smaoui, M. A. Mezghanni, B. Hammami, N. Zalila, C. Marouane et al., Tuberculosis lymphadenitis in a southeastern region in Tunisia: Epidemiology, clinical features, diagnosis and treatment, International Journal of Mycobacteriology, vol.4, pp.196-201, 2015.

J. Lagier, G. Dubourg, M. Million, F. Cadoret, M. Bilen et al., Culturing the human microbiota and culturomics, Nat Rev Microbiol, p.29937540, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01910305

K. Winglee, E. Eloe-fadrosh, S. Gupta, H. Guo, C. Fraser et al., Aerosol Mycobacterium tuberculosis Infection Causes Rapid Loss of Diversity in Gut Microbiota, PLOS ONE, vol.9, 2014.

M. Luo, Y. Liu, P. Wu, D. Luo, Q. Sun et al., Alternation of Gut Microbiota in Patients with Pulmonary Tuberculosis, Front Physiol, vol.8, p.822, 2017.

A. El-khéchine, M. Henry, D. Raoult, and M. Drancourt, Detection of Mycobacterium tuberculosis complex organisms in the stools of patients with pulmonary tuberculosis. Microbiology (Reading, Engl), vol.155, pp.2384-2389, 2009.

J. Lagier, P. Hugon, S. Khelaifia, P. Fournier, B. L. Scola et al., The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota, Clinical Microbiology Reviews, vol.28, pp.237-264, 2015.

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.

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.

J. R. Stewart and C. B. Stringer, Human evolution out of Africa: the role of refugia and climate change, Science, vol.335, pp.1317-1321, 2012.

R. Ghodbane, M. Medie, F. Lepidi, H. Nappez, C. Drancourt et al., Long-term survival of tuberculosis complex mycobacteria in soil, Microbiology, vol.160, p.24425768, 2014.