S. L. Sheridan, K. Frith, T. L. Snelling, K. Grimwood, P. B. Mcintyre et al., Waning vaccine immunity in teenagers primed with whole cell and acellular pertussis vaccine: recent epidemiology, Expert Review of Vaccines, vol.13, issue.9, pp.1081-1106, 2014.
DOI : 10.1586/14760584.2014.944167

S. L. Sheridan, R. S. Ware, K. Grimwood, and S. B. Lambert, Number and Order of Whole Cell Pertussis Vaccines in Infancy and Disease Protection, JAMA, vol.308, issue.5, pp.454-456, 2012.
DOI : 10.1001/jama.2012.6364

M. Gambhir, T. A. Clark, S. Cauchemez, S. Y. Tartof, D. L. Swerdlow et al., A Change in Vaccine Efficacy and Duration of Protection Explains Recent Rises in Pertussis Incidence in the United States, PLOS Computational Biology, vol.64, issue.4, 2015.
DOI : 10.1371/journal.pcbi.1004138.s001

J. Parkhill, M. Sebaihia, A. Preston, L. D. Murphy, N. Thomson et al., Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica, Nature Genetics, vol.35, issue.1, pp.32-40, 2003.
DOI : 10.1038/ng1227

D. A. Diavatopoulos, C. A. Cummings, L. M. Schouls, M. M. Brinig, D. A. Relman et al., Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica. PLoS Pathog, p.45, 2005.

F. R. Mooi, Bordetella pertussis and vaccination: The persistence of a genetically monomorphic pathogen, Infection, Genetics and Evolution, vol.10, issue.1, pp.36-49, 2010.
DOI : 10.1016/j.meegid.2009.10.007

N. Hegerle, A. S. Paris, D. Brun, G. Dore, E. Njamkepo et al., Evolution of French Bordetella pertussis and Bordetella parapertussis isolates: increase of Bordetellae not expressing pertactin, Clinical Microbiology and Infection, vol.18, issue.9, pp.340-346, 2012.
DOI : 10.1111/j.1469-0691.2012.03925.x

F. R. Mooi, N. A. Van-der-maas, and H. De-melker, Pertussis resurgence: waning immunity and pathogen adaptation ??? two sides of the same coin, Epidemiology and Infection, vol.18, issue.04, pp.685-694, 2014.
DOI : 10.1016/S0264-410X(98)00226-6

I. H. Van-loo, K. J. Heuvelman, A. J. King, and F. Mooi, Multilocus Sequence Typing of Bordetella pertussis Based on Surface Protein Genes, Journal of Clinical Microbiology, vol.40, issue.6, 1994.
DOI : 10.1128/JCM.40.6.1994-2001.2002

V. Chenal-francisque, V. Caro, C. Boursaux-eude, and N. Guiso, Genomic analysis of the adenylate cyclase-hemolysin C-terminal region of Bordetella pertussis, Bordetella parapertussisand Bordetella bronchiseptica, Research in Microbiology, vol.160, issue.5, pp.330-336, 2009.
DOI : 10.1016/j.resmic.2009.03.006

M. J. Bart, M. Van-gent, H. G. Van-der-heide, J. Boekhorst, P. Hermans et al., Comparative genomics of prevaccination and modern Bordetella pertussis strains, BMC Genomics, vol.11, issue.1, pp.10-1186, 2010.
DOI : 10.1186/1471-2164-11-627

M. Van-gent, M. J. Bart, H. G. Van-der-heide, K. J. Heuvelman, and F. Mooi, Small Mutations in Bordetella pertussis Are Associated with Selective Sweeps, PLoS ONE, vol.7, issue.9, 2012.
DOI : 10.1371/journal.pone.0046407.s005

J. Park, Y. Zhang, A. M. Buboltz, X. Zhang, S. C. Schuster et al., Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens, BMC Genomics, vol.13, issue.1, pp.10-1186, 2012.
DOI : 10.1093/molbev/msr121

T. Dalby and N. K. Fry, Global population structure and evolution of Bordetella pertussis and their relationship with vaccination, 1074.

N. Hegerle and N. Guiso, and pertactin-deficient clinical isolates: lessons for pertussis vaccines, Expert Review of Vaccines, vol.13, issue.9, pp.1135-1146, 2014.
DOI : 10.1586/14760584.2014.932254

V. Bouchez, D. Brun, T. Cantinelli, G. Dore, E. Njamkepo et al., First report and detailed characterization of B. pertussis isolates not expressing pertussis toxin or pertactin, Vaccine, vol.27, issue.43, pp.6034-6041, 2009.
DOI : 10.1016/j.vaccine.2009.07.074

H. Bodilis and N. Guiso, Isolates from Infants, France, Emerging Infectious Diseases, vol.19, issue.3, pp.471-474
DOI : 10.3201/eid1903.121475

N. Hegerle and N. Guiso, Antibody-mediated inhibition of Bordetella pertussis adenylate cyclase-haemolysin-induced macrophage cytotoxicity is influenced by variations in the bacterial population, Microbiology, vol.160, issue.Pt_5, pp.962-969, 2014.
DOI : 10.1099/mic.0.074690-0

W. Smartin, L. Pawloski, M. Williams, K. Weening, C. Debolt et al., Pertactin-Negative Bordetella pertussis Strains: Evidence for a Possible Selective Advantage, Clinical Infectious Diseases, vol.60, issue.2, pp.223-227, 2015.
DOI : 10.1093/cid/ciu788

D. W. Stainer and M. J. Scholte, A Simple Chemically Defined Medium for the Production of Phase I Bordetella pertussis, Journal of General Microbiology, vol.63, issue.2, pp.211-220, 1970.
DOI : 10.1099/00221287-63-2-211

B. Van-de-waterbeemd, M. Streefland, J. Pennings, L. Van-der-pol, C. Beuvery et al., cultivation for vaccine production, Biotechnology and Bioengineering, vol.81, issue.7, pp.900-908, 2009.
DOI : 10.1002/bit.22326

D. C. Rio, M. Ares, . Jr, G. J. Hannon, and T. W. Nilsen, Purification of RNA Using TRIzol (TRI Reagent), Cold Spring Harbor Protocols, vol.2010, issue.6, 2010.
DOI : 10.1101/pdb.prot5439

M. W. Pfaffl, The ongoing evolution of qPCR, Methods, vol.50, issue.4, pp.215-216, 2010.
DOI : 10.1016/j.ymeth.2010.02.005

R. Development and C. Team, R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing, 2012.

V. Caro, V. Bouchez, and N. Guiso, Is the Sequenced Bordetella pertussis Strain Tohama I Representative of the Species?, Journal of Clinical Microbiology, vol.46, issue.6, pp.2125-2128, 2008.
DOI : 10.1128/JCM.02484-07

D. Gouw, D. Diavatopoulos, D. A. Bootsma, H. J. Hermans, P. W. Mooi et al., Pertussis: a matter of immune modulation, FEMS Microbiology Reviews, vol.35, issue.3, pp.441-474, 2011.
DOI : 10.1111/j.1574-6976.2010.00257.x

K. L. Sealey, S. R. Harris, N. K. Fry, L. D. Hurst, A. R. Gorringe et al., Genomic Analysis of Isolates From the United Kingdom 2012 Pertussis Outbreak Reveals That Vaccine Antigen Genes Are Unusually Fast Evolving, Journal of Infectious Diseases, vol.212, issue.2, pp.294-301, 2015.
DOI : 10.1093/infdis/jiu665

M. Van-gent, M. J. Bart, H. G. Van-der-heide, K. J. Heuvelman, T. Kallonen et al., SNP-Based Typing: A Useful Tool to Study Bordetella pertussis Populations, PLoS ONE, vol.78, issue.5, p.20340, 2011.
DOI : 10.1371/journal.pone.0020340.s005

S. Desai and M. St-laurent, Pertactin-negative Bordetella pertussis strains in Canada: Characterization of a dozen isolates based on a survey of 224 samples collected in different parts of the country over the last 20 years, Int. J. Infect. Dis, vol.28, pp.65-69, 2014.

H. O. Hallander, C. H. Wirsing-von-konig, M. Riffelman, and J. Storsaeter, Investigations into the emergence of pertactin-deficient Bordetella pertussis isolates in six European countries, Euro Surveill. Bull. Eur. Mal. Transm. 2014, vol.19, pp.17-27, 1996.

K. E. Bowden, M. M. Williams, P. K. Cassiday, A. Milton, L. Pawloski et al., Molecular Epidemiology of the Pertussis Epidemic in Washington State in 2012, Journal of Clinical Microbiology, vol.52, issue.10, pp.3549-3557, 2014.
DOI : 10.1128/JCM.01189-14

A. J. Schmidtke, K. O. Boney, S. W. Martin, T. H. Skoff, M. L. Tondella et al., Population diversity among Bordetella pertussis isolates, United States, Emerg. Infect. Dis, vol.18, pp.1935-2009, 2012.

A. J. King, G. Berbers, H. F. Van-oirschot, P. Hoogerhout, K. Knipping et al., Role of the polymorphic region 1 of the Bordetella pertussis protein pertactin in immunity, Microbiology, vol.147, issue.11, pp.2885-2895, 2001.
DOI : 10.1099/00221287-147-11-2885

A. J. King, S. Van-der-lee, A. Mohangoo, M. Van-gent, A. Van-der-ark et al., Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains, PLoS ONE, vol.9, issue.6, p.66150, 2013.
DOI : 10.1371/journal.pone.0066150.s003

F. Mooi, Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally, PLoS ONE, vol.2014, issue.9, p.84523

F. R. Mooi, I. H. Van-loo, M. Van-gent, Q. He, M. J. Bart et al., Strains with Increased Toxin Production Associated with Pertussis Resurgence, Emerging Infectious Diseases, vol.15, issue.8, pp.1206-1213, 2009.
DOI : 10.3201/eid1508.081511

I. Bibova, K. Skopova, J. Masin, O. Cerny, D. Hot et al., The RNA Chaperone Hfq Is Required for Virulence of Bordetella pertussis, Infection and Immunity, vol.81, issue.11, pp.4081-4090, 2013.
DOI : 10.1128/IAI.00345-13

I. Bibova, D. Hot, K. Keidel, F. Amman, S. Slupek et al., reveals requirement of RNA chaperone Hfq for Type III secretion system functionality, RNA Biology, vol.34, issue.2, pp.175-185, 2015.
DOI : 10.1093/nar/29.9.e45

D. Hot, S. Slupek, B. Wulbrecht, A. Hondt, C. Hubans et al., Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element, BMC Genomics, vol.173, issue.1, pp.10-1186, 2011.
DOI : 10.1186/1471-2164-12-207

E. Leininger, C. A. Ewanowich, A. Bhargava, M. S. Peppler, J. G. Kenimer et al., Comparative roles of the Arg-Gly-Asp sequence present in the Bordetella pertussis adhesins pertactin and filamentous hemagglutinin, Infect. Immun, vol.60, pp.2380-2385, 1992.

C. S. Inatsuka, Q. Xu, I. Vujkovic-cvijin, S. Wong, S. Stibitz et al., Pertactin is required for Bordetella species to resist neutrophil-mediated clearance. Infection and immunity, pp.2901-2909, 2010.

P. Stefanelli, C. Fazio, G. Fedele, F. Spensieri, C. M. Ausiello et al., A natural pertactin deficient strain of Bordetella pertussis shows improved entry in human monocyte-derived dendritic cells, New Microbiol, vol.32, pp.159-166, 2009.

L. Bassinet, P. Gueirard, B. Maitre, B. Housset, P. Gounon et al., Role of Adhesins and Toxins in Invasion of Human Tracheal Epithelial Cells by Bordetella pertussis, Infection and Immunity, vol.68, issue.4, pp.1934-1941, 2000.
DOI : 10.1128/IAI.68.4.1934-1941.2000

Y. Lamberti, J. Gorgojo, C. Massillo, and M. E. Rodriguez, entry into respiratory epithelial cells and intracellular survival, Pathogens and Disease, vol.69, issue.3, pp.194-204, 2013.
DOI : 10.1111/2049-632X.12072

T. J. Merkel and S. A. Halperin, Nonhuman Primate and Human Challenge Models of Pertussis, Journal of Infectious Diseases, vol.209, issue.suppl 1, pp.20-23, 2014.
DOI : 10.1093/infdis/jit493

P. J. Ross, C. E. Sutton, S. Higgins, A. C. Allen, K. Walsh et al., Relative Contribution of Th1 and Th17 Cells in Adaptive Immunity to Bordetella pertussis: Towards the Rational Design of an Improved Acellular Pertussis Vaccine, PLoS Pathogens, vol.171, issue.4, p.1003264
DOI : 10.1371/journal.ppat.1003264.s008

C. Boursaux-eude, S. Thiberge, G. Carletti, and N. Guiso, Intranasal murine model of Bordetella pertussis infection: II. Sequence variation and protection induced by a tricomponent acellular vaccine1Financial support for the present study was provided by the Institut Pasteur Fondation and SmithKline Beecham Biologicals. All animal studies were conducted in accordance with the French and Belgian national legislative guidelines for animal experimentation.1, Vaccine, vol.17, issue.20-21, pp.2651-2660, 1999.
DOI : 10.1016/S0264-410X(99)00038-9

P. Denoel, F. Godfroid, N. Guiso, H. Hallander, and J. Poolman, Comparison of acellular pertussis vaccines-induced immunity against infection due to Bordetella pertussis variant isolates in a mouse model, Vaccine, vol.23, issue.46-47, pp.5333-5341, 2005.
DOI : 10.1016/j.vaccine.2005.06.021