M. S. Edwards and C. J. Baker, Group B streptococcal infections, Infectious Diseases of the Fetus and Newborn Infant, 2005.

K. M. Edmond, 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

T. C. Eickhoff, J. O. Klein, A. K. Daly, D. Ingall, and M. Finland, Neonatal Sepsis and Other Infections Due to Group B Beta-Hemolytic Streptococci, New England Journal of Medicine, vol.271, issue.24, pp.1221-1228, 1964.
DOI : 10.1056/NEJM196412102712401

G. Kexel and S. Schoenbohm, Streptococcus agalactiae als Erreger von S??uglingsmeningitiden, DMW - Deutsche Medizinische Wochenschrift, vol.90, issue.06, pp.258-261, 1965.
DOI : 10.1055/s-0028-1111328

N. Jones, Multilocus Sequence Typing System for Group B Streptococcus, Journal of Clinical Microbiology, vol.41, issue.6, pp.2530-2536, 2003.
DOI : 10.1128/JCM.41.6.2530-2536.2003

A. Tazi, 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

M. Brochet, E. Couve, R. Bercion, J. M. Sire, and P. Glaser, Population Structure of Human Isolates of Streptococcus agalactiae from Dakar and Bangui, Journal of Clinical Microbiology, vol.47, issue.3, pp.800-803, 2009.
DOI : 10.1128/JCM.01103-08

URL : https://hal.archives-ouvertes.fr/pasteur-00584027

M. Nocard and H. Mollereau, Sur unemammite contagieuse des vaches laitieres, Ann. Inst. Pasteur, vol.1, pp.109-126, 1887.

U. B. Sorensen, K. Poulsen, C. Ghezzo, I. Margarit, and M. Kilian, Emergence and Global Dissemination of Host-Specific Streptococcus agalactiae Clones, mBio, vol.1, issue.3, pp.178-188, 2010.
DOI : 10.1128/mBio.00178-10

M. Brochet, Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae, Proc. Natl Acad. Sci. USA 105, pp.15961-15966, 2008.
DOI : 10.1073/pnas.0803654105

URL : https://hal.archives-ouvertes.fr/hal-00352709

G. Lindahl, M. Stalhammar-carlemalm, and T. Areschoug, Surface Proteins of Streptococcus agalactiae and Related Proteins in Other Bacterial Pathogens, Clinical Microbiology Reviews, vol.18, issue.1, pp.102-127, 2005.
DOI : 10.1128/CMR.18.1.102-127.2005

A. J. Drummond, M. A. Suchard, D. Xie, and A. Rambaut, Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, vol.29, issue.8, pp.1969-1973, 2012.
DOI : 10.1093/molbev/mss075

M. He, Emergence and global spread of epidemic healthcare-associated Clostridium difficile, Nature Genetics, vol.377, issue.1, pp.109-113, 2012.
DOI : 10.1093/molbev/msi103

N. J. Croucher, Rapid Pneumococcal Evolution in Response to Clinical Interventions, Science, vol.331, issue.6016, pp.430-434, 2011.
DOI : 10.1126/science.1198545

C. R. Usein, Molecular characterization of adult-colonizing Streptococcus agalactiae from an area-based surveillance study in Romania, European Journal of Clinical Microbiology & Infectious Diseases, vol.17, issue.12, pp.2301-2310, 2012.
DOI : 10.1007/s10096-012-1569-y

S. S. Boswihi, E. E. Udo, and N. Sweih, Serotypes and antibiotic resistance in Group B streptococcus isolated from patients at the Maternity Hospital, Kuwait, Journal of Medical Microbiology, vol.61, issue.1, pp.126-131, 2012.
DOI : 10.1099/jmm.0.035477-0

M. Hraoui, I. Boutiba-ben-boubaker, M. Rachdi, A. Slim, and S. Ben-redjeb, Macrolide and tetracycline resistance in clinical strains of Streptococcus agalactiae isolated in Tunisia, Journal of Medical Microbiology, vol.61, issue.Pt_8, pp.1109-1113, 2012.
DOI : 10.1099/jmm.0.037853-0

M. G. Rato, Antimicrobial resistance and molecular epidemiology of streptococci from bovine mastitis, Veterinary Microbiology, vol.161, issue.3-4, pp.286-294, 2013.
DOI : 10.1016/j.vetmic.2012.07.043

M. Haenni, Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis, Applied and Environmental Microbiology, vol.76, issue.24, pp.7957-7965, 2010.
DOI : 10.1128/AEM.00805-10

P. Kalmus, B. Aasmae, A. Karssin, T. Orro, and K. Kask, Udder pathogens and their resistance to antimicrobial agents in dairy cows in Estonia, Acta Veterinaria Scandinavica, vol.53, issue.1, p.4, 2011.
DOI : 10.1186/1751-0147-53-4

B. Dogan, Y. H. Schukken, C. Santisteban, and K. J. Boor, Distribution of Serotypes and Antimicrobial Resistance Genes among Streptococcus agalactiae Isolates from Bovine and Human Hosts, Journal of Clinical Microbiology, vol.43, issue.12, pp.5899-5906, 2005.
DOI : 10.1128/JCM.43.12.5899-5906.2005

F. Baquero, A. P. Tedim, and T. M. Coque, Antibiotic resistance shaping multi-level population biology of bacteria, Frontiers in Microbiology, vol.4, p.15, 2013.
DOI : 10.3389/fmicb.2013.00015

J. R. Verani, L. Mcgee, and S. J. Schrag, Prevention of perinatal group B streptococcal disease?revised guidelines from CDC, 2010, MMWR Recomm. Rep, vol.59, pp.1-36, 2010.

D. Francesco, M. A. Caracciolo, S. Gargiulo, F. Manca, and N. , Phenotypes, genotypes, serotypes and molecular epidemiology of erythromycin-resistant Streptococcus agalactiae in Italy, European Journal of Clinical Microbiology & Infectious Diseases, vol.44, issue.9, pp.1741-1747, 2012.
DOI : 10.1007/s10096-011-1495-4

L. K. Mcdougal, Detection of Tn917-like sequences within a Tn916-like conjugative transposon (Tn3872) in erythromycin-resistant isolates of Streptococcus pneumoniae, Antimicrob. Agents Chemother, vol.42, pp.2312-2318, 1998.

K. M. Puopolo, D. C. Klinzing, M. P. Lin, D. L. Yesucevitz, and M. J. Cieslewicz, A composite transposon associated with erythromycin and clindamycin resistance in group B Streptococcus, Journal of Medical Microbiology, vol.56, issue.7, pp.947-955, 2007.
DOI : 10.1099/jmm.0.47131-0

M. J. Patterson and A. Hafeez, Group B streptococci in human disease, Bacteriol. Rev, vol.40, pp.774-792, 1976.

I. Chopra and M. Roberts, Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance, Microbiology and Molecular Biology Reviews, vol.65, issue.2, pp.232-260, 2001.
DOI : 10.1128/MMBR.65.2.232-260.2001

K. L. Wyres, Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974, BMC Genomics, vol.14, issue.1, p.500, 2013.
DOI : 10.1186/1471-2105-11-119

M. Thaker, P. Spanogiannopoulos, and G. Wright, The tetracycline resistome, Cellular and Molecular Life Sciences, vol.43, issue.3, pp.419-431, 2010.
DOI : 10.1007/s00018-009-0172-6

A. P. Roberts and P. Mullany, -like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance, FEMS Microbiology Reviews, vol.35, issue.5, pp.856-871, 2011.
DOI : 10.1111/j.1574-6976.2011.00283.x

URL : https://hal.archives-ouvertes.fr/halshs-00656179

J. Celli and P. Trieu-cuot, Circularization of Tn916 is required for expression of the transposon-encoded transfer functions: characterization of long tetracycline-inducible transcripts reading through the attachment site, Molecular Microbiology, vol.28, issue.1, pp.103-117, 1998.
DOI : 10.1016/0378-1119(85)90120-9

Y. Hu, Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota, Nature Communications, vol.62, p.2151, 2013.
DOI : 10.1007/s10126-010-9259-1

C. A. Arias and B. Murray, The rise of the Enterococcus: beyond vancomycin resistance, Nature Reviews Microbiology, vol.5, issue.4, pp.266-278, 2012.
DOI : 10.1038/nrmicro2761

J. Davies and D. Davies, Origins and Evolution of Antibiotic Resistance, Microbiology and Molecular Biology Reviews, vol.74, issue.3, pp.417-433, 2010.
DOI : 10.1128/MMBR.00016-10

F. C. Tenover and R. V. Goering, Methicillin-resistant Staphylococcus aureus strain USA300: origin and epidemiology, Journal of Antimicrobial Chemotherapy, vol.64, issue.3, pp.441-446, 2009.
DOI : 10.1093/jac/dkp241

P. J. Planet, Emergence of the Epidemic Methicillin-Resistant Staphylococcus aureus Strain USA300 Coincides with Horizontal Transfer of the Arginine Catabolic Mobile Element and speG-mediated Adaptations for Survival on Skin, mBio, vol.4, issue.6, pp.889-902, 2013.
DOI : 10.1128/mBio.00889-13

R. J. Willems, Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium, mBio, vol.3, issue.4, pp.151-00112, 2012.
DOI : 10.1128/mBio.00151-12

F. Lebreton, Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains, mBio, vol.4, issue.4, pp.534-547, 2013.
DOI : 10.1128/mBio.00534-13

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

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

H. Tettelin, Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome", Proc. Natl Acad. Sci. USA, pp.13950-13955, 2005.
DOI : 10.1073/pnas.0506758102

P. Glaser, Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease, Molecular Microbiology, vol.181, issue.6, pp.1499-1513, 2002.
DOI : 10.1046/j.1365-2958.2002.03126.x

A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements, Genome Research, vol.14, issue.7, pp.1394-1403, 2004.
DOI : 10.1101/gr.2289704

H. Tettelin, Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae, Proc. Natl Acad. Sci. USA 99, pp.12391-12396, 2002.
DOI : 10.1073/pnas.182380799

R. K. Aziz, The RAST Server: Rapid Annotations using Subsystems Technology, BMC Genomics, vol.9, issue.1, p.75, 2008.
DOI : 10.1186/1471-2164-9-75

D. R. 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

I. Rosinski-chupin, Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage, BMC Genomics, vol.14, issue.1, p.252, 2013.
DOI : 10.1089/mdr.2012.0005

URL : https://hal.archives-ouvertes.fr/pasteur-00818470

P. Lechat, E. Souche, and I. Moszer, SynTView ??? an interactive multi-view genome browser for next-generation comparative microorganism genomics, BMC Bioinformatics, vol.14, issue.1, p.277, 2013.
DOI : 10.1126/science.1182395

URL : https://hal.archives-ouvertes.fr/pasteur-00870285

K. Tamura, MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011.
DOI : 10.1093/molbev/msr121

A. J. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007.
DOI : 10.1186/1471-2148-7-214

G. Baele, Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty, Molecular Biology and Evolution, vol.29, issue.9, pp.2157-2167, 2012.
DOI : 10.1093/molbev/mss084

G. Baele and P. Lemey, Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency, Bioinformatics, vol.29, issue.16, pp.1970-1979, 2013.
DOI : 10.1093/bioinformatics/btt340

A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, p.88, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001

S. L. Luan, Multilocus Sequence Typing of Swedish Invasive Group B Streptococcus Isolates Indicates a Neonatally Associated Genetic Lineage and Capsule Switching, Journal of Clinical Microbiology, vol.43, issue.8, pp.3727-3733, 2005.
DOI : 10.1128/JCM.43.8.3727-3733.2005

S. D. Manning, Multilocus Sequence Types Associated with Neonatal Group B Streptococcal Sepsis and Meningitis in Canada, Journal of Clinical Microbiology, vol.47, issue.4, pp.1143-1148, 2009.
DOI : 10.1128/JCM.01424-08

J. F. Bohnsack, 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.1285-1291, 2008.
DOI : 10.1128/JCM.02105-07

E. Sadowy, B. Matynia, and W. Hryniewicz, Population structure, virulence factors and resistance determinants of invasive, non-invasive and colonizing Streptococcus agalactiae in Poland, Journal of Antimicrobial Chemotherapy, vol.65, issue.9, pp.1907-1914, 2010.
DOI : 10.1093/jac/dkq230

C. A. Huber, F. Mcodimba, V. Pflueger, C. A. Daubenberger, and G. Revathi, Characterization of Invasive and Colonizing Isolates of Streptococcus agalactiae in East African Adults, Journal of Clinical Microbiology, vol.49, issue.10, pp.3652-3655, 2011.
DOI : 10.1128/JCM.01288-11

. Corrigendum, Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline