S. A. Halperin, J. A. Bettinger, B. Greenwood, L. H. Harrison, J. Jelfs et al., The changing and dynamic epidemiology of meningococcal disease, Vaccine, vol.30, issue.2, pp.26-36, 2012.

, World Health Organization. Meningococcal disease control in countries of the African meningitis belt, Wkly Epidemiol Rec, vol.90, pp.123-154, 2014.

D. A. Caugant and P. Nicolas, Molecular surveillance of meningococcal meningitis in Africa, Vaccine, vol.25, issue.1, pp.8-11, 2007.

D. A. Caugant, P. A. Kristiansen, X. Wang, L. W. Mayer, M. K. Taha et al., Molecular characterization of invasive meningococcal isolates from countries in the African meningitis belt before introduction of a serogroup A conjugate vaccine, PLoS ONE, vol.7, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-02085540

M. Consortium, The diversity of meningococcal carriage across the African meningitis belt and the impact of vaccination with a group A meningococcal conjugate vaccine, J Infect Dis, vol.212, pp.1298-307, 2015.

C. L. Trotter and B. M. Greenwood, Meningococcal carriage in the African meningitis belt, Lancet Infect Dis, vol.7, pp.797-803, 2007.

C. V. Broome, M. A. Rugh, A. A. Yada, L. Giat, H. Giat et al., Epidemic group C meningococcal meningitis in Upper Volta, Bull World Health Organ, vol.61, pp.325-355, 1979.

A. Funk, K. Uadiale, C. Kamau, D. A. Caugant, U. Ango et al., Sequential outbreaks due to a new strain of Neisseria meningitidis serogroup C in northern Nigeria, PLoS Curr, vol.6, pp.2013-2027, 2014.

F. Sidikou, M. Zaneidou, I. Alkassoum, S. Schwartz, B. Issaka et al., Emergence of epidemic serogroup C Neisseria meningitidis, Niger-2015: analysis of national surveillance data, Lancet Infect Dis
URL : https://hal.archives-ouvertes.fr/pasteur-01357718

F. Denis, J. L. Rey, A. Amadou, P. Saliou, M. Prince-david et al., Emergence of meningococcal meningitis caused by W 135 subgroup in Africa, Lancet, vol.320, pp.91533-91534, 1982.

A. Kwara, R. A. Adegbola, P. T. Corrah, M. Weber, M. Achtman et al., Meningitis caused by a serogroup W135 clone of the ET-37 complex of Neisseria meningitidis in West Africa

, Trop Med Int Health, vol.3, pp.742-748, 1998.

M. K. Taha, I. Parent-du-chatelet, M. Schlumberger, I. Sanou, S. Djibo et al., Neisseria meningitidis serogroups W135 and A were equally prevalent among meningitis cases occurring at the end of the 2001 epidemics in Burkina Faso and Niger, J Clin Microbiol, vol.40, pp.1083-1087, 2002.

B. Koumaré, R. Ouedraogo-traore, I. Sanou, A. A. Yada, I. Sow et al., The first large epidemic of meningococcal disease caused by serogroup W135, Vaccine, vol.25, issue.1, pp.37-41, 2002.

J. M. Collard, B. Issaka, M. Zaneidou, S. Hugonnet, P. Nicolas et al., Epidemiological changes in meningococcal meningitis in Niger from 2008 to 2011 and the impact of vaccination, BMC Infect Dis, vol.13, p.576, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-00917555

J. R. Macneil, I. Medah, D. Koussoube, R. T. Novak, A. C. Cohn et al., Neisseria meningitidis serogroup W, Emerg Infect Dis, vol.20, pp.394-403, 2012.

J. Lucidarme, D. M. Hill, H. B. Bratcher, S. J. Gray, M. Du-plessis et al., Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage, J Infect, vol.71, pp.544-52, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-02013265

M. M. Mustapha, J. W. Marsh, M. G. Krauland, J. O. Fernandez, A. De-lemos et al., Genomic epidemiology of hypervirulent serogroup W, ST-11 Neisseria meningitidis, EBioMedicine, vol.10, p.26629539, 2015.
DOI : 10.1016/j.ebiom.2015.09.007

URL : https://doi.org/10.1016/j.ebiom.2015.09.007

, Wyeth Pharmaceuticals. Trumenba: prescribing information, 2014.

, Novartis Vaccines and Diagnostics. Bexsero: highlights of prescribing information, 2015.

D. Thomas, J. Hatcher, C. P. Satterfield, D. A. Theodore, M. J. Bach et al., sodC-based real-time PCR for detection of Neisseria meningitidis, PLoS ONE, vol.6, 2011.

C. Chin, D. H. Alexander, P. Marks, A. A. Klammer, J. Drake et al., finished microbial genome assemblies from long-read SMRT sequencing data, Nat Methods, vol.10, pp.563-572, 2013.

B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, 2009.

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

S. Bambini, D. Chiara, M. Muzzi, A. Mora, M. Lucidarme et al., Neisseria adhesin A variation and revised nomenclature scheme, Clin Vaccine Immunol, vol.21, pp.966-71, 2014.

S. N. Gardner and B. G. Hall, When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes