S. Abby, E. Tannier, M. Gouy, and V. Daubin, Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences, vol.4, issue.4, pp.4962-4967, 2012.
DOI : 10.1186/1471-2148-4-18

URL : https://hal.archives-ouvertes.fr/hal-00752055

H. Ochman, J. Lawrence, and E. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.2, issue.6784, pp.299-304, 2000.
DOI : 10.1128/9781555818180.ch15

M. Llosa, F. Gomis-ruth, M. Coll, and F. De-la-cruz, Bacterial conjugation: a two-step mechanism for DNA transport, Molecular Microbiology, vol.174, issue.1, pp.1-8, 2002.
DOI : 10.1046/j.1365-2958.2000.02164.x

X. Bellanger, S. Payot, N. Leblond-bourget, and G. Guédon, Conjugative and mobilizable genomic islands in bacteria: evolution and diversity, FEMS Microbiology Reviews, vol.38, issue.4, pp.720-760, 2014.
DOI : 10.1371/journal.pone.0014016

URL : https://hal.archives-ouvertes.fr/hal-01474898

A. Roberts and P. Mullany, Bacterial integrative mobile genetic elements, Landes Bioscience, 2013.

A. Toussaint and C. Merlin, Mobile Elements as a Combination of Functional Modules, Plasmid, vol.47, issue.1, pp.26-35, 2002.
DOI : 10.1006/plas.2001.1552

V. Burrus, G. Pavlovic, B. Decaris, and G. Guédon, Conjugative transposons: the tip of the iceberg, Molecular Microbiology, vol.67, issue.3, pp.601-610, 2002.
DOI : 10.1128/jb.175.9.2713-2719.1993

URL : https://hal.archives-ouvertes.fr/hal-01659089

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

X. Bellanger, C. Morel, F. Gonot, A. Puymege, B. Decaris et al., Site-specific accretion of an integrative conjugative element together with a related genomic island leads to cis mobilization and gene capture, Molecular Microbiology, vol.21, issue.4, pp.912-925, 2011.
DOI : 10.1111/j.1574-6976.1998.tb00355.x

URL : https://hal.archives-ouvertes.fr/hal-01659267

A. Puymège, S. Bertin, S. Chuzeville, G. Guédon, and S. Payot, Conjugative Transfer and cis-Mobilization of a Genomic Island by an Integrative and Conjugative Element of Streptococcus agalactiae, Journal of Bacteriology, vol.195, issue.6, pp.1142-115102199, 2013.
DOI : 10.1128/JB.02199-12

C. Ambroset, C. Coluzzi, G. Guédon, M. Devignes, V. Loux et al., New insights into the classification and integration specificity of Streptococcus integrative conjugative elements through extensive genome exploration. Front Microbiol 6:1483. https, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01262284

J. Guglielmini, L. Quintais, M. Garcillan-barcia, F. De-la-cruz, and E. Rocha, The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation, PLoS Genetics, vol.22, issue.8, 2011.
DOI : 10.1371/journal.pgen.1002222.s002

URL : https://hal.archives-ouvertes.fr/pasteur-00647077

R. Overbeek, R. Olson, G. Pusch, G. Olsen, J. Davis et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Research, vol.1, issue.D1, pp.206-214
DOI : 10.1046/j.1365-2958.2002.02839.x

T. Carver, M. Berriman, A. Tivey, C. Patel, U. Bohme et al., Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database, Bioinformatics, vol.16, issue.23, pp.2672-2676, 2008.
DOI : 10.1093/bioinformatics/16.10.944

F. Sievers, A. Wilm, D. Dineen, T. Gibson, K. Karplus et al., Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Molecular Systems Biology, vol.7, issue.1, p.539, 2011.
DOI : 10.1093/nar/gkn174

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.87, issue.12, pp.2725-2729, 2013.
DOI : 10.1128/JVI.02478-12

URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.24, issue.8, pp.221-224, 2010.
DOI : 10.1093/molbev/msm092

URL : https://hal.archives-ouvertes.fr/lirmm-00705187

G. Blaiotta, A. Sorrentino, A. Ottombrino, and M. Aponte, Short communication: Technological and genotypic comparison between Streptococcus macedonicus and Streptococcus thermophilus strains coming from the same dairy environment, Journal of Dairy Science, vol.94, issue.12, pp.5871-5877, 2011.
DOI : 10.3168/jds.2011-4630

E. Guédon, C. Delorme, N. Pons, C. Cruaud, V. Loux et al., Complete Genome Sequence of the Commensal Streptococcus salivarius Strain JIM8777, Journal of Bacteriology, vol.193, issue.18, pp.5024-502505390, 2011.
DOI : 10.1128/JB.05390-11

A. Jacob and S. Hobbs, Conjugal transfer of plasmid-borne multiple antibiotic resistance in Streptococcus faecalis var. zymogenes, J Bacteriol, vol.117, pp.360-372, 1974.

D. Takamatsu, M. Osaki, and T. Sekizaki, Thermosensitive Suicide Vectors for Gene Replacement in Streptococcus suis, Plasmid, vol.46, issue.2, pp.140-148, 2001.
DOI : 10.1006/plas.2001.1532

C. Delorme, C. Poyart, S. Ehrlich, and R. P. , Extent of Horizontal Gene Transfer in Evolution of Streptococci of the Salivarius Group, Journal of Bacteriology, vol.189, issue.4, pp.1330-134101058, 2007.
DOI : 10.1128/JB.01058-06

URL : https://hal.archives-ouvertes.fr/hal-01204331

E. V. Koonin, E. Ballesté, and M. Muniesa, Horizontal gene transfer: essentiality and evolvability in 555 prokaryotes, and roles in evolutionary transitions Beyond the canonical strategies of 557 horizontal gene transfer in prokaryotes, Curr Opin Microbiol, vol.38, pp.95-105, 2016.

M. Llosa, F. Gomis-ruth, M. Coll, and C. F. La, Bacterial conjugation: a two-step mechanism for DNA transport, Molecular Microbiology, vol.174, issue.1, pp.1-8, 2002.
DOI : 10.1046/j.1365-2958.2000.02164.x

X. Bellanger, S. Payot, N. Leblond-bourget, and G. Guédon, Conjugative and 561 mobilizable genomic islands in bacteria: evolution and diversity, FEMS Microbiol Rev, vol.562, pp.38720-760, 2014.

C. Johnson and A. Grossman, Integrative and Conjugative Elements (ICEs): What They Do and How They Work, Annual Review of Genetics, vol.49, issue.1, pp.577-601, 2015.
DOI : 10.1146/annurev-genet-112414-055018

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180612/pdf

F. Delavat, R. Miyazaki, N. Carraro, N. Pradervand, and J. Van-der-meer, The hidden life of integrative and conjugative elements, FEMS Microbiology Reviews, vol.8, issue.Pt 4, pp.512-537, 2017.
DOI : 10.1186/1471-2164-8-121

N. Carraro and V. Burrus, Biology of three ICE families: SXT/R391, 2014.

C. Johnson and A. Grossman, ABSTRACT, Journal of Bacteriology, vol.198, issue.8, pp.1241-1250, 2016.
DOI : 10.1128/JB.01044-15

URL : https://hal.archives-ouvertes.fr/hal-01336771

C. Johnson and A. Grossman, Identification of host genes that affect acquisition 572 of an integrative and conjugative element in Bacillus subtilis, Mol Microbiol, vol.93, pp.1284-573, 2014.

G. Guédon, Conjugative transfer of the integrative conjugative elements ICESt1 576 and ICESt3 from Streptococcus thermophilus, J Bacteriol, vol.191, pp.2764-2775, 2009.

N. Carraro, V. Libante, C. Morel, B. Decaris, F. Charron-bourgoin et al., Differential regulation of two closely related integrative and conjugative 579 elements from Streptococcus thermophilus, BMC Microbiol, vol.578, issue.11, p.238, 2011.

C. Delorme, A. Abraham, R. P. Guédon, and E. , Genomics of Streptococcus salivarius, a major human commensal, Infection, Genetics and Evolution, vol.33, pp.381-392, 2015.
DOI : 10.1016/j.meegid.2014.10.001

URL : https://hal.archives-ouvertes.fr/hal-01154007

P. Hols, Complete sequence and comparative genome analysis of the dairy 586 bacterium Streptococcus thermophilus, Nat Biotechnol, vol.22, pp.1554-1558, 2004.

A. Bolotin, C. Delorme, S. Duskoehrlich, E. Guédon, V. Monnet et al., New insights in the molecular biology and physiology of Streptococcus 593 thermophilus revealed by comparative genomics, FEMS Microbiol Rev, vol.29, pp.435-463, 2005.

S. Salivarius-vers-des-réceptrices and S. Salivarius, thermophilus mutées au niveau des molécules de surface ayant démontré une augmentation d'acquisition d'ICESt3, afin d'évaluer si celles-ci pouvaient également provoquer l'augmentation de l'acquisition des ICE de S. salivarius. Par ailleurs, l'impact observé sur le transfert d'ICESt3 lorsque la donatrice est mutée semble indépendant de l'impact de la réceptrice. Dans le but de conforter cette observation, il serait intéressant d

I. Bibliographie-alexander, H. E. Hahn, E. Leidy, and G. , On the specificity of the desoxyribonucleic acid which induces streptomycin resistance in Hemophilus, J Exp Med, vol.104, pp.305-320, 1956.

C. Ambroset, C. Coluzzi, G. Guédon, M. D. Devignes, V. Loux et al., New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration, Frontiers in Microbiology, vol.8, issue.31, 1483.
DOI : 10.1038/nrmicro2382

URL : https://hal.archives-ouvertes.fr/hal-01262284

R. I. Aminov, Horizontal Gene Exchange in Environmental Microbiota, Frontiers in Microbiology, vol.2, p.158, 2011.
DOI : 10.3389/fmicb.2011.00158

D. Arutyunov and L. S. Frost, F conjugation: Back to the beginning, Plasmid, vol.70, issue.1, pp.18-32, 2013.
DOI : 10.1016/j.plasmid.2013.03.010

M. B. Aspiras, R. P. Ellen, and D. G. Cvitkovitch, ComX activity of Streptococcus mutans growing in biofilms, FEMS Microbiol Lett, vol.238, pp.167-174, 2004.

J. M. Auchtung, N. Aleksanyan, A. Bulku, and M. B. Berkmen, Biology of ICE Bs1 , an integrative and conjugative element in Bacillus subtilis, Plasmid, vol.86, pp.14-25, 2016.
DOI : 10.1016/j.plasmid.2016.07.001

G. Aviv, G. Rahav, and O. Gal-mor, Horizontal transfer of the Salmonella enterica serovar Infantis resistance and virulence plasmid pESI to the gut microbiota of warm-blooded hosts, MBio, vol.7, 2016.

J. Azeredo and N. F. Azevedo, Critical review on biofilm methods, Critical Reviews in Microbiology, vol.60, issue.3, pp.313-351, 2017.
DOI : 10.1016/S0079-6107(00)00014-6

URL : https://hal.archives-ouvertes.fr/hal-01548680

M. Balado, M. L. Lemos, and C. R. Osorio, encode restriction-modification systems that confer resistance to bacteriophages, FEMS Microbiology Ecology, vol.5, issue.2, pp.457-467, 2013.
DOI : 10.1371/journal.pgen.1000786

URL : https://academic.oup.com/femsec/article-pdf/83/2/457/19536407/83-2-457.pdf

J. W. Beaber, B. Hochhut, and M. K. Waldor, Genomic and Functional Analyses of SXT, an Integrating Antibiotic Resistance Gene Transfer Element Derived from Vibrio cholerae, Journal of Bacteriology, vol.184, issue.15, pp.4259-4269, 2002.
DOI : 10.1128/JB.184.15.4259-4269.2002

J. W. Beaber, B. Hochhut, and M. K. Waldor, SOS response promotes horizontal dissemination of antibiotic resistance genes, Nature, vol.53, issue.6969, pp.72-74, 2004.
DOI : 10.1073/pnas.120163297

S. Chuzeville, S. Dramsi, J. Y. Madec, M. Haenni, and S. Payot, Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation, Microbial Pathogenesis, vol.88, pp.1-9, 2015.
DOI : 10.1016/j.micpath.2015.07.018

URL : https://hal.archives-ouvertes.fr/hal-01475853

L. Ciric, M. Ellatif, P. Sharma, R. Patel, X. Song et al., Tn916-like elements from human, oral, commensal streptococci possess a variety of antibiotic and antiseptic resistance genes, International Journal of Antimicrobial Agents, vol.39, issue.4, pp.360-361, 2012.
DOI : 10.1016/j.ijantimicag.2011.12.007

D. C. Coleman, D. J. Sullivan, R. J. Russell, J. P. Arbuthnott, B. F. Carey et al., Staphylococcus aureus bacteriophages mediating the simultaneous lysogenic conversion of beta-lysin, staphylokinase and enterotoxin A: molecular mechanism of triple conversion, J Gen Microbiol, vol.135, pp.1679-1697, 1989.

C. Coluzzi, G. Guedon, M. D. Devignes, C. Ambroset, V. Loux et al., A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins, Frontiers in Microbiology, vol.99, issue.539, p.443, 2017.
DOI : 10.1111/mmi.13270

URL : https://hal.archives-ouvertes.fr/hal-01580789

L. C. Cook and G. M. Dunny, The influence of biofilms in the biology of plasmids, Microbiol Spectr, vol.2, 2014.

Y. Cui, T. Xu, X. Qu, T. Hu, X. Jiang et al., New Insights into Various Production Characteristics of Streptococcus thermophilus Strains, International Journal of Molecular Sciences, vol.99, issue.10, 2016.
DOI : 10.1007/s10529-007-9542-z

Y. Cui, X. Jiang, M. Hao, X. Qu, and T. Hu, New advances in exopolysaccharides production of Streptococcus thermophilus, Archives of Microbiology, vol.86, issue.4, pp.799-809, 2017.
DOI : 10.3168/jds.S0022-0302(03)73944-7

R. Ari, The SOS system, Biochimie, vol.67, issue.3-4, pp.343-347, 1985.
DOI : 10.1016/S0300-9084(85)80077-8

D. Elia, M. A. Millar, K. E. Beveridge, T. J. Brown, and E. D. , Wall Teichoic Acid Polymers Are Dispensable for Cell Viability in Bacillus subtilis, Journal of Bacteriology, vol.188, issue.23, pp.8313-8316, 2006.
DOI : 10.1128/JB.01336-06

D. Elia, M. A. Pereira, M. P. Chung, Y. S. Zhao, W. Chau et al., Lesions in Teichoic Acid Biosynthesis in Staphylococcus aureus Lead to a Lethal Gain of Function in the Otherwise Dispensable Pathway, Journal of Bacteriology, vol.188, issue.12, pp.4183-4189, 2006.
DOI : 10.1128/JB.00197-06

S. Das, T. Kanamoto, X. Ge, P. Xu, T. Unoki et al., Contribution of Lipoproteins and Lipoprotein Processing to Endocarditis Virulence in Streptococcus sanguinis, Journal of Bacteriology, vol.191, issue.13, pp.4166-4179, 2009.
DOI : 10.1128/JB.01739-08

B. David, A. Radziejwoski, and F. Toussaint, Natural DNA transformation is functional in Lactococcus lactis ssp. cremoris KW2, & other authors Appl Environ Microbiol, 2017.

J. R. Davies, G. Svensater, and M. C. Herzberg, Identification of novel LPXTGlinked surface proteins from Streptococcus gordonii, Microbiology, vol.155, 1977.

J. Davison, Genetic Exchange between Bacteria in the Environment, Plasmid, vol.42, issue.2, pp.73-91, 1999.
DOI : 10.1006/plas.1999.1421

F. De-la-cruz, L. S. Frost, R. J. Meyer, and E. L. Zechner, Conjugative DNA metabolism in Gram-negative bacteria, FEMS Microbiology Reviews, vol.34, issue.1, pp.18-40, 2010.
DOI : 10.3109/10425179109020786

F. Delavat, S. Mitri, S. Pelet, and J. R. Van-der-meer, Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element, Proceedings of the National Academy of Sciences, vol.55, issue.10, pp.3375-3383, 2016.
DOI : 10.1046/j.1462-2920.2001.00218.x

F. Delavat, R. Miyazaki, N. Carraro, N. Pradervand, and J. R. Van-der-meer, The hidden life of integrative and conjugative elements, FEMS Microbiology Reviews, vol.8, issue.Pt 4, pp.512-537, 2017.
DOI : 10.1186/1471-2164-8-121

C. Delorme, C. Poyart, S. D. Ehrlich, and P. Renault, Extent of Horizontal Gene Transfer in Evolution of Streptococci of the Salivarius Group, Journal of Bacteriology, vol.189, issue.4, pp.1330-1341, 2007.
DOI : 10.1128/JB.01058-06

URL : https://hal.archives-ouvertes.fr/hal-01204331

C. Delorme, C. Bartholini, A. Bolotine, S. D. Ehrlich, and P. Renault, Emergence of a Cell Wall Protease in the Streptococcus thermophilus Population, Applied and Environmental Microbiology, vol.76, issue.2, pp.451-460, 2010.
DOI : 10.1128/AEM.01018-09

URL : https://hal.archives-ouvertes.fr/hal-01204329

C. Delorme, A. L. Abraham, P. Renault, and E. Guedon, Genomics of Streptococcus salivarius, a major human commensal, Infection, Genetics and Evolution, vol.33, pp.381-392, 2015.
DOI : 10.1016/j.meegid.2014.10.001

URL : https://hal.archives-ouvertes.fr/hal-01154007

S. Demaneche, E. Kay, F. Gourbiere, and P. Simonet, Natural Transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in Soil, Applied and Environmental Microbiology, vol.67, issue.6, pp.2617-2621, 2001.
DOI : 10.1128/AEM.67.6.2617-2621.2001

E. L. Denham, P. N. Ward, and J. A. Leigh, Lipoprotein Signal Peptides Are Processed by Lsp and Eep of Streptococcus uberis, Journal of Bacteriology, vol.190, issue.13, pp.4641-4647, 2008.
DOI : 10.1128/JB.00287-08

U. Dobrindt, B. Hochhut, U. Hentschel, and J. Hacker, Genomic islands in pathogenic and environmental microorganisms, Nature Reviews Microbiology, vol.37, issue.5, pp.414-424, 2004.
DOI : 10.1006/plas.1997.1280

G. M. Dunny, The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signalling, gene transfer, complexity and evolution, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.172, issue.5, pp.1185-1193, 2007.
DOI : 10.1128/jb.172.5.2633-2641.1990

C. Eng, A. Thibessard, M. Danielsen, T. B. Rasmussen, J. F. Mari et al., In silico prediction of horizontal gene transfer in Streptococcus thermophilus, Archives of Microbiology, vol.6, issue.4, pp.287-297, 2011.
DOI : 10.1186/1471-2105-6-184

URL : https://hal.archives-ouvertes.fr/inria-00569081

F. Fabretti, C. Theilacker, L. Baldassarri, Z. Kaczynski, A. Kropec et al., Alanine Esters of Enterococcal Lipoteichoic Acid Play a Role in Biofilm Formation and Resistance to Antimicrobial Peptides, Infection and Immunity, vol.74, issue.7, pp.4164-4171, 2006.
DOI : 10.1128/IAI.00111-06

I. Fedtke, D. Mader, and T. Kohler, A Staphylococcus aureus ypfP mutant with strongly reduced lipoteichoic acid (LTA) content: LTA governs bacterial surface properties and autolysin activity, Molecular Microbiology, vol.177, issue.4, pp.1078-1091, 2007.
DOI : 10.1038/nm991

L. Fontaine, C. Boutry, M. H. De-frahan, B. Delplace, C. Fremaux et al., A Novel Pheromone Quorum-Sensing System Controls the Development of Natural Competence in Streptococcus thermophilus and Streptococcus salivarius, Journal of Bacteriology, vol.192, issue.5, pp.1444-1454, 2010.
DOI : 10.1128/JB.01251-09

A. E. Franke and D. B. Clewell, Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of "conjugal" transfer in the absence of a conjugative plasmid, J Bacteriol, vol.145, pp.494-502, 1981.

V. J. Freeman, Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae, J Bacteriol, vol.61, pp.675-688, 1951.

M. E. Frischer, J. M. Thurmond, and J. H. Paul, Natural plasmid transformation in a high-frequency-of-transformation marine Vibrio strain, Appl Environ Microbiol, vol.56, pp.3439-3444, 1990.

R. Fronzes, E. Schafer, L. Wang, H. R. Saibil, E. V. Orlova et al., Structure of a Type IV Secretion System Core Complex, Science, vol.306, issue.5698, pp.266-268, 2009.
DOI : 10.1126/science.1102610

J. P. Furste, W. Pansegrau, G. Ziegelin, M. Kroger, and E. Lanka, Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin., Proceedings of the National Academy of Sciences, vol.86, issue.6, pp.1771-1775, 1989.
DOI : 10.1073/pnas.86.6.1771

M. Furushita, H. Akagi, A. Kaneoka, K. Awamura, T. Maeda et al., Structural Variation of Tn10 that Carries tetB Found in Fish Farm Bacteria, Microbes and Environments, vol.26, issue.1, pp.84-87, 2011.
DOI : 10.1264/jsme2.ME10160

E. Y. Furuya and F. D. Lowy, Antimicrobial-resistant bacteria in the community setting, Nature Reviews Microbiology, vol.340, issue.Suppl. A, pp.36-45, 2006.
DOI : 10.1056/NEJM199905203402001

M. Gaillard, N. Pernet, C. Vogne, O. Hagenbuchle, and J. R. Van-der-meer, Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1, Proceedings of the National Academy of Sciences, vol.99, issue.1, pp.7058-7063, 2008.
DOI : 10.1007/BF00696222

C. Garcia-aljaro, E. Balleste, and M. Muniesa, Beyond the canonical strategies of horizontal gene transfer in prokaryotes, Current Opinion in Microbiology, vol.38, pp.95-105, 2017.
DOI : 10.1016/j.mib.2017.04.011

M. P. Garcillan-barcia and F. De-la-cruz, Why is entry exclusion an essential feature of conjugative plasmids?, Plasmid, vol.60, issue.1, pp.1-18, 2008.
DOI : 10.1016/j.plasmid.2008.03.002

G. Garriss, D. Poulin-laprade, and V. Burrus, DNA-Damaging Agents Induce the RecA-Independent Homologous Recombination Functions of Integrating Conjugative Elements of the SXT/R391 Family, Journal of Bacteriology, vol.195, issue.9, 1991.
DOI : 10.1128/JB.02090-12

J. M. Ghigo, Natural conjugative plasmids induce bacterial biofilm development, Nature, vol.143, issue.6845, pp.442-445, 2001.
DOI : 10.1007/978-1-4757-9357-4_7

J. M. Ghigo, Are there biofilm-specific physiological pathways beyond a reasonable doubt?, Research in Microbiology, vol.154, issue.1, pp.1-8, 2003.
DOI : 10.1016/S0923-2508(02)00012-8

N. Goessweiner-mohr, K. Arends, W. Keller, and E. Grohmann, Conjugation in Gram-Positive Bacteria, Microbiol Spectr, vol.2, pp.4-2013, 2014.

Y. J. Goh, C. Goin, S. O-'flaherty, E. Altermann, and R. Hutkins, Specialized adaptation of a lactic acid bacterium to the milk environment: the comparative genomics of Streptococcus thermophilus LMD-9, Microbial Cell Factories, vol.10, issue.Suppl 1, p.22, 2011.
DOI : 10.1128/AEM.01984-08

F. X. Gomis-ruth, M. Sola, F. De-la-cruz, and M. Coll, Coupling Factors in Macromolecular Type-IV Secretion Machineries, Current Pharmaceutical Design, vol.10, issue.13, pp.1551-1565, 2004.
DOI : 10.2174/1381612043384817

F. Griffith, The Significance of Pneumococcal Types, Journal of Hygiene, vol.27, issue.02, pp.113-159, 1928.
DOI : 10.1017/S0022172400031879

A. Grundling and O. Schneewind, Synthesis of glycerol phosphate lipoteichoic acid in Staphylococcus aureus, Proceedings of the National Academy of Sciences, vol.305, issue.5936, pp.8478-8483, 2007.
DOI : 10.1038/305709a0

J. Guglielmini, F. De-la-cruz, and E. P. Rocha, Evolution of Conjugation and Type IV Secretion Systems, Molecular Biology and Evolution, vol.27, issue.1, pp.315-331, 2013.
DOI : 10.1046/j.1365-2958.1998.00724.x

URL : https://hal.archives-ouvertes.fr/pasteur-01374951

S. B. Guttenplan, K. M. Blair, and D. B. Kearns, The EpsE Flagellar Clutch Is Bifunctional and Synergizes with EPS Biosynthesis to Promote Bacillus subtilis Biofilm Formation, PLoS Genetics, vol.17, issue.12, 2010.
DOI : 10.1371/journal.pgen.1001243.s008

M. Haenni, E. Saras, S. Bertin, P. Leblond, J. Y. Madec et al., 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

URL : https://hal.archives-ouvertes.fr/hal-01637787

D. B. Haniford and M. J. Ellis, Transposons Tn10 and Tn5, Microbiology Spectrum, vol.3, issue.1, pp.3-5, 2015.
DOI : 10.1128/microbiolspec.MDNA3-0002-2014

URL : http://www.asmscience.org/deliver/fulltext/microbiolspec/3/1/MDNA3-0002-2014.pdf?itemId=/content/journal/microbiolspec/10.1128/microbiolspec.MDNA3-0002-2014&mimeType=pdf&isFastTrackArticle=

C. J. Harmer and R. M. Hall, The A to Z of A/C plasmids, Plasmid, vol.80, pp.63-82, 2015.
DOI : 10.1016/j.plasmid.2015.04.003

T. L. Haskett, J. J. Terpolilli, A. Bekuma, G. W. O-'hara, J. T. Sullivan et al., Assembly and transfer of tripartite integrative and conjugative genetic elements, Proceedings of the National Academy of Sciences, vol.169, issue.6, pp.12268-12273, 2016.
DOI : 10.1016/0378-1119(93)90611-6

M. Hausner and S. Wuertz, High rates of conjugation in bacterial biofilms as determined by quantitative in situ analysis, Appl Environ Microbiol, vol.65, pp.3710-3713, 1999.

L. Haustenne, G. Bastin, P. Hols, and L. Fontaine, Modeling of the ComRS Signaling Pathway Reveals the Limiting Factors Controlling Competence in Streptococcus thermophilus, Frontiers in Microbiology, vol.9, 1413.
DOI : 10.1371/journal.pone.0099394

D. Hinerfeld and G. Churchward, Specific Binding of Integrase to the Origin of Transfer (oriT) of the Conjugative Transposon Tn916, Journal of Bacteriology, vol.183, issue.9, pp.2947-2951, 2001.
DOI : 10.1128/JB.183.9.2947-2951.2001

D. Hinerfeld and G. Churchward, Xis protein of the conjugative transposon Tn916 plays dual opposing roles in transposon excision, Molecular Microbiology, vol.82, issue.6, pp.1459-1467, 2001.
DOI : 10.1073/pnas.82.4.1040

M. T. Holden, H. Hauser, and M. Sanders, Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis, PLoS ONE, vol.4, issue.7, p.6072, 2009.
DOI : 10.1371/journal.pone.0006072.s003

L. M. Holland, B. Conlon, and J. P. Gara, Mutation of tagO reveals an essential role for wall teichoic acids in Staphylococcus epidermidis biofilm development, Microbiology, vol.157, issue.2, pp.408-418, 2011.
DOI : 10.1099/mic.0.042234-0

P. Hols, F. Hancy, and L. Fontaine, New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics, FEMS Microbiol Rev, vol.29, pp.435-463, 2005.

T. P. Hong, M. Q. Carter, P. Struffi, S. Casonato, Y. Hao et al., Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa, BMC Microbiology, vol.205, issue.2, p.31, 2017.
DOI : 10.1016/0014-5793(86)80905-X

R. D. Hotchkiss, TRANSFER OF PENICILLIN RESISTANCE IN PNEUMOCOCCI BY THE DESOXYRIBONUCLEATE DERIVED FROM RESISTANT CULTURES, Cold Spring Harbor Symposia on Quantitative Biology, vol.16, issue.0, pp.457-461, 1951.
DOI : 10.1101/SQB.1951.016.01.032

S. L. Hyder and M. M. Streitfeld, Transfer of Erythromycin Resistance from Clinically Isolated Lysogenic Strains of Streptococcus pyogenes via Their Endogenous Phage, Journal of Infectious Diseases, vol.138, issue.3, pp.281-286, 1978.
DOI : 10.1093/infdis/138.3.281

S. A. Jackson, R. E. Mckenzie, R. D. Fagerlund, S. N. Kieper, P. C. Fineran et al., CRISPR-Cas: Adapting to change, Science, vol.1, issue.6333, 2017.
DOI : 10.1126/science.aag0511

C. Janion, Inducible SOS Response System of DNA Repair and Mutagenesis in Escherichia coli, International Journal of Biological Sciences, vol.4, pp.338-344, 2008.
DOI : 10.7150/ijbs.4.338

L. Jarup and A. Akesson, Current status of cadmium as an environmental health problem, Toxicology and Applied Pharmacology, vol.238, issue.3, pp.201-208, 2009.
DOI : 10.1016/j.taap.2009.04.020

S. S. Jean and P. R. Hsueh, Antimicrobial Drug Resistance in Taiwan, Journal of the Formosan Medical Association, vol.110, issue.1, pp.4-13, 2011.
DOI : 10.1016/S0929-6646(11)60002-8

O. Johnsborg, V. Eldholm, and L. S. Havarstein, Natural genetic transformation: prevalence, mechanisms and function, Research in Microbiology, vol.158, issue.10, pp.767-778, 2007.
DOI : 10.1016/j.resmic.2007.09.004

C. M. Johnson and A. D. Grossman, Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis, Mol Microbiol, vol.93, pp.1284-1301, 2014.

C. M. Johnson and A. D. Grossman, Integrative and Conjugative Elements (ICEs): What They Do and How They Work, Annual Review of Genetics, vol.49, issue.1, pp.577-601, 2015.
DOI : 10.1146/annurev-genet-112414-055018

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180612/pdf

C. M. Johnson and A. D. Grossman, ABSTRACT, Journal of Bacteriology, vol.198, issue.8, pp.1241-1249, 2016.
DOI : 10.1128/JB.01044-15

URL : https://hal.archives-ouvertes.fr/hal-01336771

C. Johnston, B. Martin, G. Fichant, P. Polard, and J. P. Claverys, Bacterial transformation: distribution, shared mechanisms and divergent control, Nature Reviews Microbiology, vol.16, issue.3, pp.181-196, 2014.
DOI : 10.1093/oxfordjournals.molbev.a026201

URL : https://hal.archives-ouvertes.fr/hal-01117850

M. Juhas, D. W. Crook, I. D. Dimopoulou, G. Lunter, R. M. Harding et al., Novel Type IV Secretion System Involved in Propagation of Genomic Islands, Journal of Bacteriology, vol.189, issue.3, pp.761-771, 2007.
DOI : 10.1128/JB.01327-06

G. Kaci, D. Goudercourt, and V. Dennin, ABSTRACT, Applied and Environmental Microbiology, vol.80, issue.3, pp.928-934, 2014.
DOI : 10.1128/AEM.03133-13

URL : https://hal.archives-ouvertes.fr/lirmm-00857793

E. Kilelee, A. Pokorny, M. R. Yeaman, and A. S. Bayer, Lysyl-Phosphatidylglycerol Attenuates Membrane Perturbation Rather than Surface Association of the Cationic Antimicrobial Peptide 6W-RP-1 in a Model Membrane System: Implications for Daptomycin Resistance, Antimicrobial Agents and Chemotherapy, vol.54, issue.10, pp.4476-4479, 2010.
DOI : 10.1128/AAC.00191-10

T. Kloesges, O. Popa, W. Martin, and T. Dagan, Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths, Molecular Biology and Evolution, vol.16, issue.9, pp.1057-1074, 2011.
DOI : 10.1101/gr.5322306

E. V. Koonin, Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions, F1000Research, vol.5, 2016.
DOI : 10.12688/f1000research.8737.1

M. Kuroda, T. Ohta, and I. Uchiyama, Whole genome sequencing of meticillin-resistant Staphylococcus aureus, The Lancet, vol.357, issue.9264, pp.1225-1240, 2001.
DOI : 10.1016/S0140-6736(00)04403-2

T. Kyndt, D. Quispe, H. Zhai, R. Jarret, M. Ghislain et al., T-DNAs with expressed genes: An example of a naturally transgenic food crop, Proceedings of the National Academy of Sciences, vol.12, issue.1, pp.5844-5849, 2015.
DOI : 10.1093/molbev/msr121

L. Lalioui, E. Pellegrini, and S. Dramsi, The SrtA Sortase of Streptococcus agalactiae Is Required for Cell Wall Anchoring of Proteins Containing the LPXTG Motif, for Adhesion to Epithelial Cells, and for Colonization of the Mouse Intestine, Infection and Immunity, vol.73, issue.6, pp.3342-3350, 2005.
DOI : 10.1128/IAI.73.6.3342-3350.2005

URL : https://hal.archives-ouvertes.fr/hal-00019655

A. S. Lang, O. Zhaxybayeva, and J. T. Beatty, Gene transfer agents: phage-like elements of genetic exchange, Nature Reviews Microbiology, vol.24, issue.7, pp.472-482, 2012.
DOI : 10.1093/molbev/msm088

J. Lang and D. Faure, Functions and regulation of quorum-sensing in Agrobacterium tumefaciens, Frontiers in Plant Science, vol.5, p.14, 2014.
DOI : 10.3389/fpls.2014.00014

J. J. Laurila, P. A. Kostamovaara, and S. Alahuhta, Streptococcus salivarius Meningitis after Spinal Anesthesia, Anesthesiology, vol.89, issue.6, pp.1579-1580, 1998.
DOI : 10.1097/00000542-199812000-00041

M. Lautner, E. Schunder, V. Herrmann, and K. Heuner, Regulation, Integrase-Dependent Excision, and Horizontal Transfer of Genomic Islands in Legionella pneumophila, Journal of Bacteriology, vol.195, issue.7, pp.1583-1597, 2013.
DOI : 10.1128/JB.01739-12

J. G. Lawrence and H. Ochman, Molecular archaeology of the Escherichia coli genome, Proceedings of the National Academy of Sciences, vol.2, issue.5, pp.9413-9417, 1998.
DOI : 10.3201/eid0204.960403

C. A. Lee, J. M. Auchtung, R. E. Monson, and A. D. Grossman, Identification and characterization of int (integrase), xis (excisionase) and chromosomal attachment sites of the integrative and conjugative element ICEBs1 of Bacillus subtilis, Molecular Microbiology, vol.59, issue.0, pp.1356-1369, 2007.
DOI : 10.1093/nar/30.4.866

D. E. Lewis, G. N. Gussin, and S. Adhya, New Insights into the Phage Genetic Switch: Effects of Bacteriophage Lambda Operator Mutations on DNA Looping and Regulation of P R , P L , and P RM, Journal of Molecular Biology, vol.428, issue.22, pp.4438-4456, 2016.
DOI : 10.1016/j.jmb.2016.08.027

Y. H. Li, N. Tang, M. B. Aspiras, P. C. Lau, J. H. Lee et al., A Quorum-Sensing Signaling System Essential for Genetic Competence in Streptococcus mutans Is Involved in Biofilm Formation, Journal of Bacteriology, vol.184, issue.10, pp.2699-2708, 2002.
DOI : 10.1128/JB.184.10.2699-2708.2002

S. Liao, M. I. Klein, and K. Heim, Streptococcus mutans Extracellular DNA Is Upregulated during Growth in Biofilms, Actively Released via Membrane Vesicles, and Influenced by Components of the Protein Secretion Machinery, P. & other authors, pp.2355-2366, 2014.
DOI : 10.1128/JB.01493-14

J. K. Lodge, K. Weston-hafer, and D. E. Berg, Transposon Tn5 target specificity: preference for insertion at G/C pairs, Genetics, vol.120, pp.645-650, 1988.

M. Lopez-perez, N. Ramon-marco, and F. Rodriguez-valera, Networking in microbes: conjugative elements and plasmids in the genus Alteromonas, BMC Genomics, vol.28, issue.10, p.36, 2017.
DOI : 10.1093/molbev/msr121

M. J. Lopez-sanchez, E. Sauvage, V. Da-cunha, D. Clermont, R. Hariniaina et al., controls the diversity of its mobilome, Molecular Microbiology, vol.18, issue.6, pp.1057-1071, 2012.
DOI : 10.1101/gr.074492.107

R. Manganelli, L. Romano, S. Ricci, M. Zazzi, and G. Pozzi, Dosage of Tn916 Circular Intermediates in Enterococcus faecalis, Plasmid, vol.34, issue.1, pp.48-57, 1995.
DOI : 10.1006/plas.1995.1032

J. Marrero and M. K. Waldor, Interactions between Inner Membrane Proteins in Donor and Recipient Cells Limit Conjugal DNA Transfer, Developmental Cell, vol.8, issue.6, pp.963-970, 2005.
DOI : 10.1016/j.devcel.2005.05.004

J. Marrero and M. K. Waldor, The SXT/R391 Family of Integrative Conjugative Elements Is Composed of Two Exclusion Groups, Journal of Bacteriology, vol.189, issue.8, pp.3302-3305, 2007.
DOI : 10.1128/JB.01902-06

L. Mashburn-warren, R. J. Mclean, and M. Whiteley, Gram-negative outer membrane vesicles: beyond the cell surface, Geobiology, vol.180, issue.8, pp.214-219, 2008.
DOI : 10.1128/AEM.66.10.4414-4420.2000

H. Masuda and M. Inouye, Toxins of Prokaryotic Toxin-Antitoxin Systems with Sequence-Specific Endoribonuclease Activity, Toxins, vol.6, issue.4, 2017.
DOI : 10.1074/jbc.M110.163105

C. A. Mccullen and A. N. Binns, and Plant Cell Interactions and Activities Required for Interkingdom Macromolecular Transfer, Annual Review of Cell and Developmental Biology, vol.22, issue.1, pp.101-127, 2006.
DOI : 10.1146/annurev.cellbio.22.011105.102022

W. M. Mcshan and S. V. Nguyen, The Bacteriophages of Streptococcus pyogenes Basic Biology to Clinical Manifestations, Streptococcus pyogenes, 2016.

M. B. Miller and B. L. Bassler, Quorum Sensing in Bacteria, Annual Review of Microbiology, vol.55, issue.1, pp.165-199, 2001.
DOI : 10.1146/annurev.micro.55.1.165

R. V. Miller, Bacterial Gene Swapping in Nature, Scientific American, vol.278, issue.1, pp.66-71, 1998.
DOI : 10.1038/scientificamerican0198-66

R. V. Miller, Environmental bacteriophage-host interactions: factors contribution to natural transduction, Antonie van Leeuwenhoek, vol.79, issue.2, pp.141-147, 2001.
DOI : 10.1023/A:1010278628468

Z. Minic, C. Marie, C. Delorme, J. M. Faurie, G. Mercier et al., Control of EpsE, the Phosphoglycosyltransferase Initiating Exopolysaccharide Synthesis in Streptococcus thermophilus, by EpsD Tyrosine Kinase, Journal of Bacteriology, vol.189, issue.4, pp.1351-1357, 2007.
DOI : 10.1128/JB.01122-06

URL : https://hal.archives-ouvertes.fr/hal-00294436

M. Minoia, M. Gaillard, F. Reinhard, M. Stojanov, V. Sentchilo et al., Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas, Proceedings of the National Academy of Sciences, vol.39, issue.5, pp.20792-20797, 2008.
DOI : 10.1111/j.1365-2958.2001.02313.x

R. Miyazaki and J. R. Van-der-meer, A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13, Molecular Microbiology, vol.5, issue.3, pp.743-758, 2011.
DOI : 10.1371/journal.pgen.1000786

S. R. Modi, H. H. Lee, C. S. Spina, and J. J. Collins, Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome, Nature, vol.108, issue.7457, pp.219-222, 2013.
DOI : 10.1073/pnas.1102938108

S. Molin and T. Tolker-nielsen, Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure, Current Opinion in Biotechnology, vol.14, issue.3, pp.255-261, 2003.
DOI : 10.1016/S0958-1669(03)00036-3

D. Morisato and N. Kleckner, Tn10 transposition and circle formation in vitro, Cell, vol.51, issue.1, pp.101-111, 1987.
DOI : 10.1016/0092-8674(87)90014-6

I. Mruk and I. Kobayashi, To be or not to be: regulation of restriction???modification systems and other toxin???antitoxin systems, Nucleic Acids Research, vol.189, issue.1, pp.70-86, 2014.
DOI : 10.1128/JB.00958-07

J. A. Mulder and G. Venema, Isolation and partial characterization of Bacillus subtilis mutants impaired in DNA entry, J Bacteriol, vol.150, pp.260-268, 1982.

S. Musovic, G. Oregaard, N. Kroer, and S. J. Sorensen, Cultivation-Independent Examination of Horizontal Transfer and Host Range of an IncP-1 Plasmid among Gram-Positive and Gram-Negative Bacteria Indigenous to the Barley Rhizosphere, Applied and Environmental Microbiology, vol.72, issue.10, pp.6687-6692, 2006.
DOI : 10.1128/AEM.00013-06

M. T. Nguyen and F. Gotz, SUMMARY, Microbiology and Molecular Biology Reviews, vol.80, issue.3, pp.891-903, 2016.
DOI : 10.1128/MMBR.00028-16

URL : https://hal.archives-ouvertes.fr/jpa-00229903

A. H. Nobbs, R. M. Vajna, J. R. Johnson, Y. Zhang, S. L. Erlandsen et al., Consequences of a sortase A mutation in Streptococcus gordonii, Microbiology, vol.153, issue.12, pp.4088-4097, 2007.
DOI : 10.1099/mic.0.2007/007252-0

A. Norman, L. H. Hansen, and S. J. Sorensen, Conjugative plasmids: vessels of the communal gene pool, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.304, issue.5667, pp.2275-2289, 2009.
DOI : 10.1126/science.1093857

T. M. Norman, N. D. Lord, J. Paulsson, and R. Losick, Stochastic Switching of Cell Fate in Microbes, Annual Review of Microbiology, vol.69, issue.1, pp.381-403, 2015.
DOI : 10.1146/annurev-micro-091213-112852

R. P. Novick and G. Ram, The Floating (Pathogenicity) Island: A Genomic Dessert, Trends in Genetics, vol.32, issue.2, pp.114-126, 2016.
DOI : 10.1016/j.tig.2015.11.005

H. Ogawa and T. Ogawa, Regulation in repressor inactivation by RecA protein, Advances in Biophysics, vol.26, pp.33-49, 1990.
DOI : 10.1016/0065-227X(90)90006-F

T. Ogura and S. Hiraga, Mini-F plasmid genes that couple host cell division to plasmid proliferation., Proceedings of the National Academy of Sciences, vol.80, issue.15, pp.4784-4788, 1983.
DOI : 10.1073/pnas.80.15.4784

Y. Oku, K. Kurokawa, M. Matsuo, S. Yamada, B. L. Lee et al., Pleiotropic Roles of Polyglycerolphosphate Synthase of Lipoteichoic Acid in Growth of Staphylococcus aureus Cells, Journal of Bacteriology, vol.191, issue.1, pp.141-151, 2009.
DOI : 10.1128/JB.01221-08

P. H. Oliveira, M. Touchon, and E. P. Rocha, The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Research, vol.10, issue.Pt 6, pp.10618-10631, 2014.
DOI : 10.1073/pnas.1012579108

URL : https://hal.archives-ouvertes.fr/pasteur-01374960

P. H. Oliveira, M. Touchon, and E. P. Rocha, Regulation of genetic flux between bacteria by restriction???modification systems, Proceedings of the National Academy of Sciences, vol.6, issue.5, pp.5658-5663, 2016.
DOI : 10.1534/genetics.106.063305

URL : https://hal.archives-ouvertes.fr/pasteur-01374969

U. Pachekrepapol, J. A. Lucey, Y. Gong, R. Naran, and P. Azadi, Characterization of the chemical structures and physical properties of exopolysaccharides produced by various Streptococcus thermophilus strains, Journal of Dairy Science, vol.100, issue.5, pp.3424-3435, 2017.
DOI : 10.3168/jds.2016-12125

D. Perry and H. K. Kuramitsu, Genetic transformation of Streptococcus mutans, Infect Immun, vol.32, pp.1295-1297, 1981.

J. L. Pinyon and R. M. Hall, Evolution of IncP-1?? Plasmids by Acquisition of Antibiotic and Mercuric Ion Resistance Transposons, Microbial Drug Resistance, vol.17, issue.3, pp.339-343, 2011.
DOI : 10.1089/mdr.2010.0196

C. Possoz, J. Gagnat, G. Sezonov, M. Guerineau, and J. L. Pernodet, Conjugal immunity of Streptomyces strains carrying the integrative element pSAM2 is due to the pif gene (pSAM2 immunity factor), Molecular Microbiology, vol.9, issue.57, pp.1385-1393, 2003.
DOI : 10.1128/jb.173.14.4454-4463.1991

D. Poulin-laprade and V. Burrus, ABSTRACT, Journal of Bacteriology, vol.197, issue.24, pp.3822-3833, 2015.
DOI : 10.1128/JB.00638-15

D. Poulin-laprade, N. Carraro, and V. Burrus, The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids, Frontiers in Microbiology, vol.53, issue.837, 2015.
DOI : 10.1128/AAC.00774-09

N. Pradervand, F. Delavat, S. Sulser, R. Miyazaki, and J. R. Van-der-meer, The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICEclc Controls both a Putative Efflux System and Initiation of ICE Transfer, Journal of Bacteriology, vol.196, issue.22, pp.3971-3979, 2014.
DOI : 10.1128/JB.02129-14

A. Puymege, S. Bertin, S. Chuzeville, G. Guedon, and S. Payot, Conjugative Transfer and cis-Mobilization of a Genomic Island by an Integrative and Conjugative Element of Streptococcus agalactiae, Journal of Bacteriology, vol.195, issue.6, pp.1142-1151, 2013.
DOI : 10.1128/JB.02199-12

URL : https://hal.archives-ouvertes.fr/hal-01474816

M. Radman-livaja, C. Shaw, M. Azaro, T. Biswas, T. Ellenberger et al., Arm Sequences Contribute to the Architecture and Catalytic Function of a ?? Integrase-Holliday Junction Complex, Molecular Cell, vol.11, issue.3, pp.783-794, 2003.
DOI : 10.1016/S1097-2765(03)00111-4

M. Radman-livaja, T. Biswas, D. Mierke, and A. Landy, Architecture of recombination intermediates visualized by in-gel FRET of ?? integrase-Holliday junction-arm DNA complexes, Proceedings of the National Academy of Sciences, vol.289, issue.4, pp.3913-3920, 2005.
DOI : 10.1006/jmbi.1999.2771

U. L. Rajbhandary and D. Soll, Aminoacyl-tRNAs, the bacterial cell envelope, and antibiotics, Proceedings of the National Academy of Sciences, vol.231, issue.1, pp.5285-5286, 2008.
DOI : 10.1016/S0378-1097(03)00921-2

J. P. Ramsay and C. W. Ronson, Silencing quorum sensing and ICE mobility through antiactivation and ribosomal frameshifting, Mobile Genetic Elements, vol.104, issue.6, pp.103-108, 2015.
DOI : 10.1038/463288a

URL : http://europepmc.org/articles/pmc4755241?pdf=render

J. P. Ramsay, S. M. Kwong, and R. Murphy, An updated view of plasmid conjugation and mobilization in Staphylococcus, J. & other authors Mob Genet Elements, vol.6, 2016.

J. P. Ramsay and N. Firth, Diverse mobilization strategies facilitate transfer of non-conjugative mobile genetic elements, Current Opinion in Microbiology, vol.38, pp.1-9, 2017.
DOI : 10.1016/j.mib.2017.03.003

D. A. Rasko, M. J. Rosovitz, and G. S. Myers, The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates, Journal of Bacteriology, vol.190, issue.20, pp.6881-6893, 2008.
DOI : 10.1128/JB.00619-08

P. J. Rauch and W. M. De-vos, Characterization of the novel nisin-sucrose conjugative transposon Tn5276 and its insertion in Lactococcus lactis., Journal of Bacteriology, vol.174, issue.4, pp.1280-1287, 1992.
DOI : 10.1128/jb.174.4.1280-1287.1992

R. Ravatn, S. Studer, A. J. Zehnder, and J. R. Van-der-meer, Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of Pseudomonas sp. Strain B13, J Bacteriol, vol.180, pp.5505-5514, 1998.

S. Ravindran, Barbara McClintock and the discovery of jumping genes, Proceedings of the National Academy of Sciences, vol.35, issue.1, pp.20198-20199, 2012.
DOI : 10.1016/0092-8674(83)90226-X

B. H. Rehm, Bacterial polymers: biosynthesis, modifications and applications, Nature Reviews Microbiology, vol.37, issue.8, pp.578-592, 2010.
DOI : 10.1007/BF00178173

N. T. Reichmann and A. Grundling, Location, synthesis and function of glycolipids and polyglycerolphosphate lipoteichoic acid in Gram-positive bacteria of the phylum Firmicutes, FEMS Microbiology Letters, vol.15, issue.2, pp.97-105, 2011.
DOI : 10.1016/j.chembiol.2008.02.005

F. Reinhard, R. Miyazaki, N. Pradervand, and J. R. Van-der-meer, Cell Differentiation to ???Mating Bodies??? Induced by an Integrating and Conjugative Element in Free-Living Bacteria, Current Biology, vol.23, issue.3, pp.255-259, 2013.
DOI : 10.1016/j.cub.2012.12.025

F. Reinhard and J. R. Van-der-meer, Life History Analysis of Integrative and Conjugative Element Activation in Growing Microcolonies of Pseudomonas, Journal of Bacteriology, vol.196, issue.7, pp.1425-1434, 2014.
DOI : 10.1128/JB.01333-13

S. Roberfroid, J. Vanderleyden, and H. Steenackers, Gene expression variability in clonal populations: Causes and consequences, Critical Reviews in Microbiology, vol.179, issue.6, pp.969-984, 2016.
DOI : 10.1126/science.1229164

A. P. Roberts, M. Chandler, and P. Courvalin, Revised nomenclature for transposable genetic elements, Plasmid, vol.60, issue.3, pp.167-173, 2008.
DOI : 10.1016/j.plasmid.2008.08.001

URL : https://hal.archives-ouvertes.fr/hal-00356030

A. P. Roberts and P. Mullany, A modular master on the move: the Tn916 family of mobile genetic elements, Trends in Microbiology, vol.17, issue.6, pp.251-258, 2009.
DOI : 10.1016/j.tim.2009.03.002

R. E. Ruhfel, N. J. Robillard, and C. B. Thorne, Interspecies transduction of plasmids among Bacillus anthracis, B. cereus, and B. thuringiensis, J Bacteriol, vol.157, pp.708-711, 1984.

A. Ruzin, J. Lindsay, and R. P. Novick, Molecular genetics of SaPI1 - a mobile pathogenicity island in Staphylococcus aureus, Molecular Microbiology, vol.85, issue.2, pp.365-377, 2001.
DOI : 10.1016/0022-2836(74)90312-X

G. P. Salmond and P. C. Fineran, A century of the phage: past, present and future, Nature Reviews Microbiology, vol.494, issue.12, pp.777-786, 2015.
DOI : 10.1038/nature11927

B. Sanchez, P. Bressollier, and M. C. Urdaci, Exported proteins in probiotic bacteria: adhesion to intestinal surfaces, host immunomodulation and molecular cross-talking with the host, FEMS Immunology & Medical Microbiology, vol.7, issue.1, pp.1-17, 2008.
DOI : 10.1111/j.1574-695X.2008.00454.x

URL : https://hal.archives-ouvertes.fr/hal-00687081

Y. Sato-'o, K. Omoe, H. K. Ono, A. Nakane, and D. L. Hu, pathogenicity islands, Microbiology and Immunology, vol.187, issue.13, pp.91-99, 2013.
DOI : 10.1128/JB.187.15.5301-5309.2005

J. Schade and C. Weidenmaier, Cell wall glycopolymers of Firmicutes and their role as nonprotein adhesins, FEBS Letters, vol.282, issue.21, pp.3758-3771, 2016.
DOI : 10.1074/jbc.M703330200

O. Schneewind and D. Missiakas, Sec-secretion and sortase-mediated anchoring of proteins in Gram-positive bacteria, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1843, issue.8, pp.1687-1697, 2014.
DOI : 10.1016/j.bbamcr.2013.11.009

C. Schwechheimer and M. J. Kuehn, Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions, Nature Reviews Microbiology, vol.8, issue.10, pp.605-619, 2015.
DOI : 10.1021/nn405724x

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5308417/pdf

K. Selle, T. R. Klaenhammer, and R. Barrangou, CRISPR-based screening of genomic island excision events in bacteria, Proceedings of the National Academy of Sciences, vol.62, issue.3, pp.8076-8081, 2015.
DOI : 10.1128/AEM.02502-08

V. Sentchilo, K. Czechowska, N. Pradervand, M. Minoia, R. Miyazaki et al., sp. strain B13, Molecular Microbiology, vol.212, issue.5, pp.1293-1306, 2009.
DOI : 10.1128/AAC.39.2.500

H. M. Seth-smith, M. C. Fookes, and C. K. Okoro, Structure, Diversity, and Mobility of the Salmonella Pathogenicity Island 7 Family of Integrative and Conjugative Elements within Enterobacteriaceae, Journal of Bacteriology, vol.194, issue.6, pp.1494-1504, 2012.
DOI : 10.1128/JB.06403-11

&. Beall and B. W. , Streptococcus salivarius meningitis case strain traced to oral flora of anesthesiologist, J Clin Microbiol, vol.48, pp.2589-2591, 2010.

N. B. Shoemaker, R. D. Barber, and A. A. Salyers, Cloning and characterization of a Bacteroides conjugal tetracycline-erythromycin resistance element by using a shuttle cosmid vector., Journal of Bacteriology, vol.171, issue.3, pp.1294-1302, 1989.
DOI : 10.1128/jb.171.3.1294-1302.1989

S. D. Siegel, J. Liu, and H. Ton-that, Biogenesis of the Gram-positive bacterial cell envelope, Current Opinion in Microbiology, vol.34, pp.31-37, 2016.
DOI : 10.1016/j.mib.2016.07.015

S. D. Siegel, M. E. Reardon, and H. Ton-that, Anchoring of LPXTG-Like Proteins to the Gram-Positive Cell Wall Envelope, Curr Top Microbiol Immunol, vol.12, issue.1, pp.159-175, 2017.
DOI : 10.1016/j.str.2003.11.021

P. Siguier, E. Gourbeyre, and M. Chandler, Bacterial insertion sequences: their genomic impact and diversity, FEMS Microbiology Reviews, vol.6, issue.5, pp.865-891, 2014.
DOI : 10.1111/j.1365-2958.1990.tb00613.x

URL : https://hal.archives-ouvertes.fr/hal-01117881

T. J. Silhavy, D. Kahne, and S. Walker, The Bacterial Cell Envelope, Cold Spring Harbor Perspectives in Biology, vol.2, issue.5, p.414, 2010.
DOI : 10.1101/cshperspect.a000414

I. Sitkiewicz, N. M. Green, N. Guo, L. Mereghetti, and J. M. Musser, Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2) encoding secreted proteins, BMC Microbiology, vol.11, issue.1, 2011.
DOI : 10.1016/j.micpath.2009.09.006

M. C. Smith and H. M. Thorpe, Diversity in the serine recombinases, Molecular Microbiology, vol.82, issue.2, pp.299-307, 2002.
DOI : 10.1016/0092-8674(95)90307-0

T. B. Stanton, Prophage-like gene transfer agents???Novel mechanisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira, and Rhodobacter species, Anaerobe, vol.13, issue.2, pp.43-49, 2007.
DOI : 10.1016/j.anaerobe.2007.03.004

I. C. Sutcliffe and D. J. Harrington, Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes, Microbiology, vol.148, issue.7, pp.2065-2077, 2002.
DOI : 10.1099/00221287-148-7-2065

L. Terradot and G. Waksman, Architecture of the Helicobacter???pylori Cag-type IV secretion system, FEBS Journal, vol.388, issue.8, pp.1213-1222, 2011.
DOI : 10.1038/41483

C. M. Thomas and K. M. Nielsen, Mechanisms of and Barriers to, Horizontal Gene Transfer between Bacteria, Nature Reviews Microbiology, vol.22, issue.9, pp.711-721, 2005.
DOI : 10.1111/j.1574-6976.1998.tb00362.x

J. Thomas, C. A. Lee, and A. D. Grossman, A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element, PLoS Genetics, vol.48, issue.1, 2013.
DOI : 10.1371/journal.pgen.1003198.t004

M. R. Tock and D. T. Dryden, The biology of restriction and anti-restriction, Current Opinion in Microbiology, vol.8, issue.4, pp.466-472, 2005.
DOI : 10.1016/j.mib.2005.06.003

S. L. Turner, M. J. Bailey, A. K. Lilley, and C. M. Thomas, Ecological and molecular maintenance strategies of mobile genetic elements, FEMS Microbiology Ecology, vol.73, issue.2, pp.177-185, 2002.
DOI : 10.1128/jb.174.23.7533-7541.1992

C. Ubeda, P. Barry, J. R. Penades, and R. P. Novick, A pathogenicity island replicon in Staphylococcus aureus replicates as an unstable plasmid, Proceedings of the National Academy of Sciences, vol.31, issue.23, pp.14182-14188, 2007.
DOI : 10.1093/nar/gkg895

K. Ubukata, M. Konno, and R. Fujii, Transduction of drug resistance to tetracycline, chloramphenicol, macrolides, lincomycin and clindamycin with phages induced from Streptococcus pyogenes., The Journal of Antibiotics, vol.28, issue.9, pp.681-688, 1975.
DOI : 10.7164/antibiotics.28.681

S. J. Unterholzner, B. Poppenberger, and W. Rozhon, Toxin???antitoxin systems, Mobile Genetic Elements, vol.63, issue.5, 2013.
DOI : 10.1371/journal.pone.0032320

J. D. Van-elsas and M. J. Bailey, The ecology of transfer of mobile genetic elements, FEMS Microbiology Ecology, vol.56, issue.2, pp.187-197, 2002.
DOI : 10.1099/00221287-146-10-2409

M. Vergara-irigaray, T. Maira-litran, N. Merino, G. B. Pier, J. R. Penades et al., Wall teichoic acids are dispensable for anchoring the PNAG exopolysaccharide to the Staphylococcus aureus cell surface, Microbiology, vol.154, issue.3, pp.865-877, 2008.
DOI : 10.1099/mic.0.2007/013292-0

W. Vollmer and S. J. Seligman, Architecture of peptidoglycan: more data and more models, Trends in Microbiology, vol.18, issue.2, pp.59-66, 2010.
DOI : 10.1016/j.tim.2009.12.004

A. Wagner, R. J. Whitaker, D. J. Krause, J. H. Heilers, M. Van-wolferen et al., Mechanisms of gene flow in archaea, Nature Reviews Microbiology, vol.12, issue.8, pp.492-501, 2017.
DOI : 10.1038/nrmicro3199

P. L. Wagner, J. Livny, M. N. Neely, D. W. Acheson, D. I. Friedman et al., Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli, Molecular Microbiology, vol.97, issue.4, pp.957-970, 2002.
DOI : 10.1073/pnas.100127597

M. K. Waldor and J. J. Mekalanos, Lysogenic Conversion by a Filamentous Phage Encoding Cholera Toxin, Science, vol.170, issue.2, 1910.
DOI : 10.1093/infdis/170.2.278

H. Wang, M. C. Smith, and P. Mullany, The Conjugative Transposon Tn5397 Has a Strong Preference for Integration into Its Clostridium difficile Target Site, Journal of Bacteriology, vol.188, issue.13, pp.4871-4878, 2006.
DOI : 10.1128/JB.00210-06

Y. Wang, Spatial distribution of high copy number plasmids in bacteria, Plasmid, vol.91, pp.2-8, 2017.
DOI : 10.1016/j.plasmid.2017.02.005

C. M. Waters, H. Hirt, J. K. Mccormick, P. M. Schlievert, C. L. Wells et al., An amino-terminal domain of Enterococcus faecalis aggregation substance is required for aggregation, bacterial internalization by epithelial cells and binding to lipoteichoic acid, Molecular Microbiology, vol.28, issue.4, pp.1159-1171, 2004.
DOI : 10.1111/j.1574-695X.1999.tb01371.x

A. D. Welman and I. S. Maddox, Exopolysaccharides from lactic acid bacteria: perspectives and challenges, Trends in Biotechnology, vol.21, issue.6, pp.269-274, 2003.
DOI : 10.1016/S0167-7799(03)00107-0

V. Winstel, C. Liang, and P. Sanchez-carballo, Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens, Nature Communications, vol.16, 2013.
DOI : 10.1007/BF01639729

URL : http://www.nature.com/articles/ncomms3345.pdf

M. M. Wood and J. F. Gardner, The Integration and Excision of CTnDOT, Microbiology Spectrum, vol.3, issue.2, pp.3-0020, 2015.
DOI : 10.1128/microbiolspec.MDNA3-0020-2014

M. E. Wormann, R. M. Corrigan, P. J. Simpson, S. J. Matthews, and A. Grundling, Enzymatic activities and functional interdependencies of Bacillus subtilis lipoteichoic acid synthesis enzymes, Molecular Microbiology, vol.1, issue.3, pp.566-583, 2011.
DOI : 10.1002/1615-9861(200104)1:4<480::AID-PROT480>3.0.CO;2-O

R. A. Wozniak, D. E. Fouts, M. Spagnoletti, M. M. Colombo, D. Ceccarelli et al., Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs, PLoS Genetics, vol.40, issue.12, 2009.
DOI : 10.1371/journal.pgen.1000786.s002

R. A. Wozniak and M. K. Waldor, A Toxin???Antitoxin System Promotes the Maintenance of an Integrative Conjugative Element, PLoS Genetics, vol.53, issue.1, 2009.
DOI : 10.1371/journal.pgen.1000439.t004

R. A. Wozniak and M. K. Waldor, Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nature Reviews Microbiology, vol.5, issue.8, pp.552-563, 2010.
DOI : 10.1128/jb.173.22.7136-7141.1991

L. D. Wright, C. M. Johnson, and A. D. Grossman, Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis, PLOS Genetics, vol.171, issue.10, 2015.
DOI : 10.1371/journal.pgen.1005556.t002

L. D. Wright and A. D. Grossman, ABSTRACT, Journal of Bacteriology, vol.198, issue.24, pp.3355-3366, 2016.
DOI : 10.1128/JB.00639-16

E. R. Wyrsch, R. Chowdhury, P. Chapman, T. A. Charles, I. G. Hammond et al., Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis, Frontiers in Microbiology, vol.117, issue.38, p.843, 2016.
DOI : 10.1016/j.vetmic.2006.06.017