W. Amanfu, The situation of tuberculosis and tuberculosis control in animals of economic interest, Tuberculosis (Edinb), vol.86, p.16644282, 2006.

O. Cosivi, J. M. Grange, C. J. Daborn, M. C. Raviglione, and T. Fujikura, Zoonotic tuberculosis due to Mycobacterium bovis in developing countries, Emerg Infect Dis, vol.4, p.9452399, 1998.

A. L. Michel, B. Muller, and P. D. Van-helden, Mycobacterium bovis at the animal-human interface: a problem, or not?, Vet Microbiol, vol.140, pp.371-381, 2010.

N. H. Smith, S. V. Gordon, R. De-la-rua-domenech, C. , R. S. Hewinson et al., Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis, Nat Rev Microbiol, vol.4, p.16912712, 2006.

M. V. Palmer, T. C. Thacker, W. R. Waters, C. Gortazar, and L. A. Corner, Mycobacterium bovis: A Model Pathogen at the Interface of Livestock, Wildlife, and Humans, Vet Med Int, p.236205, 2012.

J. Gonzalo-asensio, W. Malaga, A. Pawlik, C. Astarie-dequeker, and C. Passemar, Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator, Proc Natl Acad Sci U S A, vol.111, p.25049399, 2014.

S. Berg and N. H. Smith, Why doesn't bovine tuberculosis transmit between humans?, Trends Microbiol, vol.22, pp.552-553, 2014.

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

P. R. Torgerson and D. J. Torgerson, Public health and bovine tuberculosis: what's all the fuss about?, Trends Microbiol, vol.18, pp.67-72, 2010.

R. Gordejo, F. J. Vermeersch, and J. P. , Towards eradication of bovine tuberculosis in the European Union, Vet Microbiol, vol.112, p.16388921, 2006.

C. Thoen, P. Lobue, and I. De-kantor, The importance of Mycobacterium bovis as a zoonosis, Vet Microbiol, vol.112, p.16387455, 2006.

S. D. Fitzgerald and J. B. Kaneene, Wildlife reservoirs of bovine tuberculosis worldwide: hosts, pathology, surveillance, and control, Vet Pathol, vol.50, pp.488-499, 2013.

N. Le-roex, P. D. Van-helden, A. P. Koets, and E. G. Hoal, Bovine TB in livestock and wildlife: what's in the genes?, Physiol Genomics, vol.45, pp.631-637, 2013.

I. Schiller, W. R. Waters, H. M. Vordermeier, T. Jemmi, and M. Welsh, Bovine tuberculosis in Europe from the perspective of an officially tuberculosis free country: trade, surveillance and diagnostics, Vet Microbiol, vol.151, pp.153-159, 2011.

M. E. Bekara, L. Azizi, J. J. Benet, and B. Durand, Spatial-temporal Variations of Bovine Tuberculosis Incidence in France between, Transbound Emerg Dis, p.25516263, 1965.

. Anonymous, amending the decision 99/ 467/CE establishing the officially tuberculosis-free status of bovine herds of certain member states or regions of member states, Commission Decision C, vol.176, issue.11, p.51, 2000.

A. Aranaz, E. Liebana, A. Mateos, L. Dominguez, and D. Vidal, Spacer oligonucleotide typing of Mycobacterium bovis strains from cattle and other animals: a tool for studying epidemiology of tuberculosis, J Clin Microbiol, vol.34, p.8897175, 1996.

C. Allix, K. Walravens, C. Saegerman, J. Godfroid, and P. Supply, Evaluation of the epidemiological relevance of variable-number tandem-repeat genotyping of Mycobacterium bovis and comparison of the method with IS6110 restriction fragment length polymorphism analysis and spoligotyping, J Clin Microbiol, vol.44, p.16757584, 2006.

R. A. Skuce, S. W. Mcdowell, T. R. Mallon, B. Luke, and E. L. Breadon, Discrimination of isolates of Mycobacterium bovis in Northern Ireland on the basis of variable numbers of tandem repeats (VNTRs), Vet Rec, vol.157, p.16244231, 2005.

P. Supply, C. Allix, S. Lesjean, M. Cardoso-oelemann, and S. Rusch-gerdes, Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis, J Clin Microbiol, vol.44, p.17005759, 2006.

N. Haddad, A. Ostyn, C. Karoui, M. Masselot, and M. F. Thorel, Spoligotype diversity of Mycobacterium bovis strains isolated in France from 1979 to 2000, J Clin Microbiol, vol.39, p.11574583, 2001.

C. Richomme, M. L. Boschiroli, J. Hars, F. Casabianca, and C. Ducrot, Bovine tuberculosis in livestock and wild boar on the Mediterranean island, Corsica. J Wildl Dis, vol.46, p.20688663, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00506068

G. Zanella, B. Durand, J. Hars, F. Moutou, and B. Garin-bastuji, Mycobacterium bovis in wildlife in France, J Wildl Dis, vol.44, p.18263825, 2008.

A. Payne, M. L. Boschiroli, E. Gueneau, J. L. Moyen, and T. Rambaud, Bovine tuberculosis in "Eurasian" badgers (Meles meles) in France, European Journal of Wildlife Diseases, vol.59, pp.331-339, 2013.

, OIE, editor. Manual of diagnostic tests and vaccines for terrestrial animals (mammals, birds and bees, p.16642778, 2012.

S. Henault, C. Karoui, and M. L. Boschiroli, A PCR-based method for tuberculosis detection in wildlife, Dev Biol (Basel), vol.126, p.17058488, 2006.

J. Kamerbeek, L. Schouls, A. Kolk, M. Van-agterveld, and D. Van-soolingen, Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology, J Clin Microbiol, vol.35, p.9157152, 1997.

J. Zhang, E. Abadia, G. Refregier, S. Tafaj, and M. L. Boschiroli, Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay, J Med Microbiol, vol.59, pp.285-294, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00527223

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, p.9611793, 1998.

S. Roring, A. Scott, D. Brittain, I. Walker, and G. Hewinson, Development of variable-number 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, p.12037076, 2002.

M. B. Boniotti, M. Goria, D. Loda, A. Garrone, and A. Benedetto, Molecular typing of Mycobacterium bovis strains isolated in Italy from 2000 to 2006 and evaluation of variable-number tandem repeats for geographically optimized genotyping, J Clin Microbiol, vol.47, pp.636-644, 2009.

P. R. Hunter and M. A. Gaston, Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity, J Clin Microbiol, vol.26, p.3069867, 1988.

L. Dommergues, S. Rautureau, E. Petit, and B. Dufour, Network of contacts between cattle herds in a French area affected by bovine tuberculosis in 2010, Transbound Emerg Dis, vol.59, pp.292-302, 2012.

M. F. Humblet, M. L. Boschiroli, and C. Saegerman, Classification of worldwide bovine tuberculosis risk factors in cattle: a stratified approach, Vet Res, vol.40, p.50, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00903100

N. H. Smith, The global distribution and phylogeography of Mycobacterium bovis clonal complexes, Infect Genet Evol, vol.12, pp.857-865, 2012.

S. Rodriguez, B. Romero, J. Bezos, L. De-juan, and J. Alvarez, High spoligotype diversity within a Mycobacterium bovis population: clues to understanding the demography of the pathogen in Europe, Vet Microbiol, vol.141, pp.89-95, 2010.

S. Rodriguez-campos, N. H. Smith, M. B. Boniotti, and A. Aranaz, Overview and phylogeny of Mycobacterium tuberculosis complex organisms: Implications for diagnostics and legislation of bovine tuberculosis, Res Vet Sci, p.25577545, 2014.

S. Rodriguez-campos, Y. Navarro, B. Romero, L. De-juan, and J. Bezos, Splitting of a prevalent Mycobacterium bovis spoligotype by variable-number tandem-repeat typing reveals high heterogeneity in an evolving clonal group, J Clin Microbiol, vol.51, pp.3658-3665, 2013.

C. Richomme, M. Boadella, A. Courcoul, B. Durand, and A. Drapeau, Exposure of wild boar to Mycobacterium tuberculosis complex in France since 2000 is consistent with the distribution of bovine tuberculosis outbreaks in cattle, PLoS One, vol.8, p.77842, 2013.

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

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

N. H. Smith, S. Berg, J. Dale, A. Allen, and S. Rodriguez, European 1: a globally important clonal complex of Mycobacterium bovis, Infect Genet Evol, vol.11, p.21571099, 2011.

S. Rodriguez-campos, A. C. Schurch, J. Dale, A. J. Lohan, and M. V. Cunha, European 2-a clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula, Infect Genet Evol, vol.12, p.21945286, 2012.

R. Biek, A. O'hare, D. Wright, T. Mallon, and C. Mccormick, Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations, PLoS Pathog, vol.8, p.1003008, 2012.

T. A. Kohl, R. Diel, D. Harmsen, J. Rothganger, and K. M. Walter, Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach, J Clin Microbiol, vol.52, pp.2479-2486, 2014.
DOI : 10.1128/jcm.00567-14

URL : https://jcm.asm.org/content/52/7/2479.full.pdf

D. Joshi, N. B. Harris, R. Waters, T. Thacker, and B. Mathema, Single nucleotide polymorphisms in the Mycobacterium bovis genome resolve phylogenetic relationships, J Clin Microbiol, vol.50, p.22993186, 2012.
DOI : 10.1128/jcm.01499-12

URL : https://jcm.asm.org/content/50/12/3853.full.pdf

D. M. Wright, A. R. Allen, T. R. Mallon, S. W. Mcdowell, and S. C. Bishop, Field-isolated genotypes of Mycobacterium bovis vary in virulence and influence case pathology but do not affect outbreak size, PLoS One, vol.8, p.24086351, 2013.