K. Edmond, C. Kortsalioudaki, S. Scott, S. Schrag, A. Zaidi et al., Group B streptococcal disease in infants aged younger than 3 months: systematic review and meta-analysis, The Lancet, vol.379, issue.9815, pp.547-556, 2012.
DOI : 10.1016/S0140-6736(11)61651-6

M. Kobayashi, J. Vekemans, C. Baker, A. Ratner, L. Doare et al., Group B Streptococcus vaccine development: present status and future considerations, with emphasis on perspectives for low and middle income countries, F1000Research, vol.5, 1000.
DOI : 10.12688/f1000research.9363.1
URL : https://doi.org/10.12688/f1000research.9363.1

A. Johri, L. Paoletti, P. Glaser, M. Dua, P. Sharma et al., Group B Streptococcus: global incidence and vaccine development, Nature Reviews Microbiology, vol.60, issue.12, pp.932-942, 2006.
DOI : 10.1093/infdis/151.4.672
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742968/pdf

N. Bisharat, N. Jones, D. Marchaim, C. Block, R. Harding et al., Population structure of group B streptococcus from a low-incidence region for invasive neonatal disease, Microbiology, vol.151, issue.6, pp.1875-1881, 2005.
DOI : 10.1099/mic.0.27826-0

J. Bohnsack, A. Whiting, M. Gottschalk, D. Dunn, R. Weiss et al., Population Structure of Invasive and Colonizing Strains of Streptococcus agalactiae from Neonates of Six U.S. Academic Centers from 1995 to 1999, Journal of Clinical Microbiology, vol.46, issue.4, pp.1285-129102105, 2008.
DOI : 10.1128/JCM.02105-07

A. Seale, A. Koech, A. Sheppard, H. Barsosio, J. Langat et al., Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya, Nature Microbiology, vol.38, issue.7, p.16067, 2016.
DOI : 10.1371/journal.pcbi.1004041
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936517/pdf

C. Poyart, H. Réglier-poupet, A. Tazi, A. Billoët, N. Dmytruk et al., Invasive Group B Streptococcal Infections in Infants, France, Emerging Infectious Diseases, vol.14, issue.10, pp.1647-1649, 2008.
DOI : 10.3201/eid1410.080185
URL : https://hal.archives-ouvertes.fr/hal-00307826

T. Mitchell, The pathogenesis of streptococcal infections: from Tooth decay to meningitis, Nature Reviews Microbiology, vol.19, issue.3, pp.219-230, 2003.
DOI : 10.1128/JB.183.19.5709-5717.2001

A. Tazi, O. Disson, S. Bellais, A. Bouaboud, N. Dmytruk et al., The surface protein HvgA mediates group B streptococcus hypervirulence and meningeal tropism in neonates, The Journal of Experimental Medicine, vol.59, issue.11, pp.2313-2322, 2010.
DOI : 10.1111/j.1365-2958.2005.04555.x
URL : http://jem.rupress.org/content/jem/207/11/2313.full.pdf

A. Six, S. Bellais, A. Bouaboud, A. Fouet, C. Gabriel et al., involved in binding to both fibrinogen and plasminogen, Molecular Microbiology, vol.155, issue.6, pp.1209-1222, 2015.
DOI : 10.1099/mic.0.025221-0
URL : https://hal.archives-ouvertes.fr/pasteur-01299767

M. Brochet, E. Couvé, M. Zouine, T. Vallaeys, C. Rusniok et al., Genomic diversity and evolution within the species Streptococcus agalactiae, Microbes and Infection, vol.8, issue.5, pp.1227-1243, 2006.
DOI : 10.1016/j.micinf.2005.11.010
URL : https://hal.archives-ouvertes.fr/hal-00084225

M. Stålhammar-carlemalm, L. Stenberg, and G. Lindahl, Protein rib: a novel group B streptococcal cell surface protein that confers protective immunity and is expressed by most strains causing invasive infections, Journal of Experimental Medicine, vol.177, issue.6, pp.1593-1603, 1993.
DOI : 10.1084/jem.177.6.1593

D. Cunha, V. Davies, M. Douarre, P. Rosinski-chupin, I. Margarit et al., Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline, Nat Commun, vol.5, p.4544, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01299769

A. Flores, J. Galloway-peña, P. Sahasrabhojane, M. Saldaña, H. Yao et al., , an emerging cause of invasive disease in adults, evolves by small genetic changes, Proceedings of the National Academy of Sciences, vol.6, issue.2, pp.6431-6436, 2015.
DOI : 10.1371/journal.ppat.1004088

S. Teatero, E. Ramoutar, A. Mcgeer, A. Li, R. Melano et al., Clonal Complex 17 Group B Streptococcus strains causing invasive disease in neonates and adults originate from the same genetic pool, Scientific Reports, vol.12, issue.3, 2016.
DOI : 10.1186/1471-2164-12-402

A. Almeida, A. Villain, C. Joubrel, G. Touak, E. Sauvage et al., ABSTRACT, Journal of Bacteriology, vol.197, issue.20, pp.3354-336600429, 2015.
DOI : 10.1128/JB.00429-15

R. Rosini, E. Campisi, D. Chiara, M. Tettelin, H. Rinaudo et al., Genomic Analysis Reveals the Molecular Basis for Capsule Loss in the Group B Streptococcus Population, PLOS ONE, vol.294, issue.2???3, p.125985, 2015.
DOI : 10.1371/journal.pone.0125985.s005

E. Campisi, R. Rosini, W. Ji, S. Guidotti, M. Rojas-lópez et al., Genomic Analysis Reveals Multi-Drug Resistance Clusters in Group B Streptococcus CC17 Hypervirulent Isolates Causing Neonatal Invasive Disease in Southern Mainland China, Frontiers in Microbiology, vol.8, issue.e0120035, p.1265, 2016.
DOI : 10.1038/nrmicro2382
URL : http://journal.frontiersin.org/article/10.3389/fmicb.2016.01265/pdf

S. Bellais, A. Six, A. Fouet, M. Longo, N. Dmytruk et al., Capsular Switching in Group B Streptococcus CC17 Hypervirulent Clone: A Future Challenge for Polysaccharide Vaccine Development, Journal of Infectious Diseases, vol.206, issue.11, pp.1745-1752, 2012.
DOI : 10.1093/infdis/jis605
URL : https://hal.archives-ouvertes.fr/pasteur-01300172

L. Rajagopal, A. Vo, A. Silvestroni, and C. Rubens, Regulation of cytotoxin expression by converging eukaryotic-type and two-component signalling mechanisms in Streptococcus agalactiae, Molecular Microbiology, vol.4, issue.10, pp.941-957, 2006.
DOI : 10.1111/j.1365-2958.1996.tb02483.x

S. Jiang, S. Park, P. Yadav, L. Paoletti, and M. Wessels, Regulation and Function of Pilus Island 1 in Group B Streptococcus, Journal of Bacteriology, vol.194, issue.10, pp.2479-249000202, 2012.
DOI : 10.1128/JB.00202-12

R. Maruvada, N. Prasadarao, and C. Rubens, Acquisition of factor H by a novel surface protein on group B Streptococcus promotes complement degradation, The FASEB Journal, vol.23, issue.11, pp.3967-3977, 2009.
DOI : 10.1096/fj.09-138149

L. Heath, H. Heath, P. Leblanc, S. Smithberg, M. Dufour et al., The streptococcolytic enzyme zoocin A is a penicillin-binding protein, FEMS Microbiology Letters, vol.236, issue.2, pp.205-211, 2004.
DOI : 10.1111/j.1574-6968.2004.tb09648.x

M. Lamy, M. Zouine, J. Fert, M. Vergassola, E. Couve et al., CovS/CovR of group B streptococcus: a two-component global regulatory system involved in virulence, Molecular Microbiology, vol.234, issue.5, pp.1250-1268, 2004.
DOI : 10.1016/S0378-1097(97)00423-0
URL : https://hal.archives-ouvertes.fr/hal-00019892

I. Rosinski-chupin, E. Sauvage, O. Sismeiro, A. Villain, D. Cunha et al., Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae, BMC Genomics, vol.31, issue.1, pp.419-12864, 2015.
DOI : 10.1093/nar/gkg595
URL : https://hal.archives-ouvertes.fr/hal-01169621

B. Spellerberg, S. Martin, C. Brandt, and R. Lütticken, are involved in the production of pigment, FEMS Microbiology Letters, vol.188, issue.2, pp.125-128, 2000.
DOI : 10.1111/j.1574-6968.2000.tb09182.x

A. Firon, A. Tazi, D. Cunha, V. Brinster, S. Sauvage et al., The Abi-domain Protein Abx1 Interacts with the CovS Histidine Kinase to Control Virulence Gene Expression in Group B Streptococcus, PLoS Pathogens, vol.18, issue.2, p.1003179, 2013.
DOI : 10.1371/journal.ppat.1003179.s007
URL : https://hal.archives-ouvertes.fr/pasteur-01300159

M. Brochet, C. Rusniok, E. Couvé, S. Dramsi, C. Poyart et al., Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae, Proceedings of the National Academy of Sciences, vol.60, issue.6, pp.15961-15966, 2008.
DOI : 10.1111/j.1365-2958.2006.05190.x
URL : https://hal.archives-ouvertes.fr/hal-00352709

H. Pailhories, R. Quentin, and M. Lartigue, The transcription of the neuD gene is stronger in serotype III group B streptococci strains isolated from cerebrospinal fluid than in strains isolated from vagina, FEMS Microbiol Lett, vol.349, pp.71-75, 2013.

C. Gravekamp, D. Kasper, J. Michel, D. Kling, V. Carey et al., Immunogenicity and protective efficacy of the alpha C protein of group B streptococci are inversely related to the number of repeats, Infect Immun, vol.65, pp.5216-5221, 1997.

L. Madoff, J. Michel, E. Gong, D. Kling, and D. Kasper, Group B streptococci escape host immunity by deletion of tandem repeat elements of the alpha C protein., Proceedings of the National Academy of Sciences, vol.93, issue.9, pp.4131-4136, 1996.
DOI : 10.1073/pnas.93.9.4131

D. Palo, B. Rippa, V. Santi, I. Brettoni, C. Muzzi et al., Adaptive Response of Group B Streptococcus to High Glucose Conditions: New Insights on the CovRS Regulation Network, PLoS ONE, vol.77, issue.4, p.61294, 2013.
DOI : 10.1371/journal.pone.0061294.s005

S. Park, S. Jiang, and M. Wessels, CsrRS and environmental pH regulate group B Streptococcus adherence to human epithelial cells and Almeida et al, 2012.
DOI : 10.1128/iai.00699-12
URL : http://iai.asm.org/content/80/11/3975.full.pdf

P. Sarkar and P. Sumby, strain- and serotype-specific variation, Molecular Microbiology, vol.4, issue.4, pp.576-589, 2017.
DOI : 10.1016/j.chom.2008.07.002
URL : http://onlinelibrary.wiley.com/doi/10.1111/mmi.13584/pdf

M. Inouye, H. Dashnow, L. Raven, M. Schultz, B. Pope et al., SRST2: Rapid genomic surveillance for public health and hospital microbiology labs, Genome Medicine, vol.202, issue.11, p.90, 2014.
DOI : 10.1086/656319
URL : https://genomemedicine.biomedcentral.com/track/pdf/10.1186/s13073-014-0090-6?site=genomemedicine.biomedcentral.com

C. Florindo, J. Gomes, M. Rato, L. Bernardino, B. Spellerberg et al., Molecular epidemiology of group B streptococcal meningitis in children beyond the neonatal period from Angola, Journal of Medical Microbiology, vol.60, issue.9, pp.1276-1280, 2011.
DOI : 10.1099/jmm.0.031674-0

D. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107
URL : http://genome.cshlp.org/content/18/5/821.full.pdf

A. Bankevich, S. Nurk, D. Antipov, 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, issue.5, pp.455-477, 2012.
DOI : 10.1089/cmb.2012.0021
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/pdf

K. Berlin, S. Koren, C. Chin, J. Drake, J. Landolin et al., Assembling large genomes with single-molecule sequencing and locality-sensitive hashing, Nature Biotechnology, vol.45, issue.6, pp.623-630, 2015.
DOI : 10.1186/gb-2004-5-2-r12

C. Chin, D. Alexander, P. Marks, A. Klammer, J. Drake et al., Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data, Nature Methods, vol.472, issue.6, pp.563-569, 2013.
DOI : 10.1016/S0076-6879(10)72001-2

A. Almeida, C. Alves-barroco, E. Sauvage, R. Bexiga, P. Albuquerque et al., reveals genomic signatures of host adaptation, Environmental Microbiology, vol.18, issue.11, pp.4216-4229, 2016.
DOI : 10.1101/gr.074492.107

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, issue.14, pp.2068-2069, 2014.
DOI : 10.1093/bioinformatics/btu153
URL : https://academic.oup.com/bioinformatics/article-pdf/30/14/2068/7250406/btu153.pdf

A. Page, C. Cummins, M. Hunt, V. Wong, S. Reuter et al., Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, vol.31, issue.22, pp.3691-3693, 2015.
DOI : 10.1093/bioinformatics/btv421
URL : https://academic.oup.com/bioinformatics/article-pdf/31/22/3691/17122651/btv421.pdf

J. Sahl, J. Caporaso, D. Rasko, and P. Keim, The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes, PeerJ, vol.28, issue.3, 2014.
DOI : 10.7717/peerj.332/supp-4

E. Zankari, H. Hasman, S. Cosentino, M. Vestergaard, S. Rasmussen et al., Identification of acquired antimicrobial resistance genes, Journal of Antimicrobial Chemotherapy, vol.67, issue.11, pp.2640-2644, 2012.
DOI : 10.1093/jac/dks261
URL : https://academic.oup.com/jac/article-pdf/67/11/2640/2085909/dks261.pdf

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009.
DOI : 10.1093/bioinformatics/btp324
URL : https://academic.oup.com/bioinformatics/article-pdf/25/14/1754/605544/btp324.pdf

W. Huang, L. Li, J. Myers, and G. Marth, ART: a next-generation sequencing read simulator, Bioinformatics, vol.28, issue.4, pp.593-594, 2012.
DOI : 10.1093/bioinformatics/btr708
URL : https://academic.oup.com/bioinformatics/article-pdf/28/4/593/16911715/btr708.pdf

O. Brynildsrud, L. Snipen, and J. Bohlin, CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data, Bioinformatics, vol.31, issue.11, pp.1708-1715, 2015.
DOI : 10.1093/bioinformatics/btv070

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data, Genome Research, vol.20, issue.9, pp.1297-1303, 2010.
DOI : 10.1101/gr.107524.110

M. Depristo, E. Banks, R. Poplin, K. Garimella, J. Maguire et al., A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nature Genetics, vol.8, issue.5, pp.491-498, 2011.
DOI : 10.1126/science.1177074

G. Van-der-auwera, M. Carneiro, C. Hartl, R. Poplin, G. Del-angel et al., From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline, Curr Protoc Bioinformatics, vol.29, 2013.
DOI : 10.1093/nar/29.1.308

T. Treangen, B. Ondov, S. Koren, and A. Phillippy, The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes, Genome Biology, vol.15, issue.11, p.524, 2014.
DOI : 10.1038/msb4100049

N. Croucher, A. Page, T. Connor, A. Delaney, J. Keane et al., Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Research, vol.43, issue.3, p.15, 2015.
DOI : 10.1093/nar/gku1196

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014.
DOI : 10.1093/bioinformatics/btu033

R. Bouckaert, J. Heled, D. Kühnert, T. Vaughan, C. Wu et al., BEAST 2: A Software Platform for Bayesian Evolutionary Analysis, PLoS Computational Biology, vol.30, issue.94, 2014.
DOI : 10.1371/journal.pcbi.1003537.s006
URL : http://doi.org/10.1371/journal.pcbi.1003537

J. Bollback, SIMMAP: stochastic character mapping of discrete traits on phylogenies, BMC Bioinformatics, vol.7, issue.1, p.88, 1471.
DOI : 10.1186/1471-2105-7-88

L. Revell, phytools: an R package for phylogenetic comparative biology (and other things), Methods in Ecology and Evolution, vol.62, issue.2, pp.217-223, 2012.
DOI : 10.1111/j.1558-5646.2008.00519.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00169.x/pdf

P. Cingolani, A. Platts, L. Wang, M. Coon, N. Tung et al., A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff, Fly, vol.8, issue.2, pp.80-92, 2012.
DOI : 10.1101/gr.4086505

J. Hedge and D. Wilson, Practical Approaches for Detecting Selection in Microbial Genomes, PLOS Computational Biology, vol.40, issue.1, 2016.
DOI : 10.1371/journal.pcbi.1004739.s002
URL : http://doi.org/10.1371/journal.pcbi.1004739

J. Huerta-cepas, D. Szklarczyk, K. Forslund, H. Cook, D. Heller et al., eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Research, vol.44, issue.D1, pp.286-293
DOI : 10.1093/nar/gkv1248

P. Danecek, A. Auton, G. Abecasis, C. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, pp.2156-2158
DOI : 10.1093/bioinformatics/btr330
URL : https://academic.oup.com/bioinformatics/article-pdf/27/15/2156/1125001/btr330.pdf