Y. Feng, H. Zhang, Z. Wu, S. Wang, M. Cao et al., Streptococcus suis infection: An emerging/reemerging challenge of bacterial infectious diseases? Virulence, vol.5, pp.477-497, 2014.

V. T. Huong, N. Ha, N. T. Huy, P. Horby, H. D. Nghia et al., Epidemiology, clinical manifestations, and outcomes of Streptococcus suis infection in humans, Emerg. Infect. Dis, vol.20, pp.1105-1114, 2014.

T. Eisenberg, C. Hudemann, H. M. Hossain, A. Hewer, K. Tello et al., Characterization of five zoonotic Streptococcus suis strains from Germany, including one isolate from a recent fatal case of streptococcal toxic shock-like syndrome in a hunter, J. Clin. Microbiol, vol.53, pp.3912-3915, 2015.

J. Gomez-torres, A. Nimir, J. Cluett, A. Aggarwal, S. Elsayed et al., Human case of Streptococcus suis disease, Canada. Emerg. Infect. Dis, vol.23, pp.2107-2109, 2017.

G. Goyette-desjardins, J. P. Auger, J. Xu, M. Segura, and M. Gottschalk, Streptococcus suis, an important pig pathogen and emerging zoonotic agent-an update on the worldwide distribution based on serotyping and sequence typing, Emerg. Microbes

A. Kerdsin, R. Hatrongjit, M. Gottschalk, D. Takeuchi, S. Hamada et al., Emergence of Streptococcus suis serotype 9 infection in humans, J. Microbiol. Immunol. Infect, vol.50, pp.545-546, 2017.

, European Centre for Disease Prevention and Control. Surveillance of Antimicrobial Resistance in Europe, Annual Report of the European Antimicrobial Resistance Surveillance Network (EARS-Net, 2017.

, The National Antimicrobial Resistance Monitoring System: NARMS, U.S. Department of Health and Human Services, p.13, 2015.

N. P. Varela, P. Gadbois, C. Thibault, M. Gottschalk, P. Dick et al., Antimicrobial resistance and prudent drug use for Streptococcus suis, Anim. Health. Res. Rev, vol.14, pp.68-77, 2013.

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, Front. Microbiol, vol.6, 1483.
URL : https://hal.archives-ouvertes.fr/hal-01262284

T. B. Athey, S. Teatero, D. Takamatsu, J. Wasserscheid, K. Dewar et al., Population structure and antimicrobial resistance profiles of Streptococcus suis serotype 2 sequence type 25 strains, PLoS ONE, vol.11, 2016.

J. Huang, Y. Liang, D. Guo, K. Shang, L. Ge et al., Comparative genomic analysis of the ICESa2603 family ICEs and spread of erm(B)-and tet(O)-carrying transferable 89K-subtype ICEs in swine and bovine isolates in china, Front. Microbiol, vol.7, p.55, 2016.

J. Huang, J. Ma, K. Shang, X. Hu, Y. Liang et al., Evolution and diversity of the antimicrobial resistance associated mobilome in Streptococcus suis: A probable mobile genetic elements reservoir for other streptococci, Front. Cell. Infect. Microbiol, vol.6, 2016.

K. Huang, Y. Song, Q. Zhang, A. Zhang, and M. Jin, Characterisation of a novel integrative and conjugative element ICESsD9 carrying erm(B) and tet(O) resistance determinants in Streptococcus suis, and the distribution of ICESsD9-like elements in clinical isolates, J. Glob. Antimicrob. Resist, vol.7, pp.13-18, 2016.

C. Palmieri, P. E. Varaldo, and B. Facinelli, Streptococcus suis, an emerging drug-resistant animal and human pathogen, Front. Microbiol, 2011.

Z. Pan, J. Liu, Y. Zhang, S. Chen, J. Ma et al., A novel integrative conjugative element mediates transfer of multi-drug resistance between Streptococcus suis strains of different serotypes, Vet. Microbiol, vol.229, pp.110-116, 2019.

X. Bellanger, S. Payot, N. Leblond-bourget, and G. Guédon, Conjugative and mobilizable genomic islands in bacteria: Evolution and diversity, FEMS Microbiol. Rev, vol.38, pp.720-760, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01474898

E. Grohmann, P. J. Christie, G. Waksman, and S. Backert, Type IV secretion in gram-negative and gram-positive bacteria, Mol. Microbiol, vol.107, pp.455-471, 2018.

M. T. Holden, H. Hauser, M. Sanders, T. H. Ngo, I. Cherevach et al., Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis, PLoS ONE, vol.4, p.6072, 2009.

H. Zheng, P. Du, X. Qiu, A. Kerdsin, D. Roy et al., Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada, Vet. Res, vol.49, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01679402

V. Burrus, G. Pavlovic, B. Decaris, and G. Guédon, The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration, Plasmid, vol.48, pp.77-97, 2002.
URL : https://hal.archives-ouvertes.fr/hal-01659496

C. Coluzzi, G. Guédon, 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, vol.8, p.443, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01580789

G. Guédon, V. Libante, C. Coluzzi, S. Payot, and N. Leblond-bourget, The obscure world of integrative and mobilizable elements, highly widespread elements that pirate bacterial conjugative systems, Genes, vol.8, p.337, 2017.

F. Wasels, M. Monot, P. Spigaglia, F. Barbanti, L. Ma et al., Inter-and intraspecies transfer of a Clostridium difficile conjugative transposon conferring resistance to MLS B, Microb. Drug Resist, vol.20, pp.555-560, 2014.

L. Lai, J. Dai, H. Tang, S. Zhang, C. Wu et al., Streptococcus suis serotype 9 strain GZ0565 contains a type VII secretion system putative substrate EsxA that contributes to bacterial virulence and a vanZ-like gene that confers resistance to teicoplanin and dalbavancin in Streptococcus agalactiae, Vet. Microbiol, vol.205, pp.26-33, 2017.

E. K. Bjorkeng, E. Hjerde, T. Pedersen, A. Sundsfjord, and K. Hegstad, ICESluvan, a 94-kilobase mosaic integrative conjugative element conferring interspecies transfer of VanB-type glycopeptide resistance, a novel bacitracin resistance locus, and a toxin-antitoxin stabilization system, J. Bacteriol, vol.195, pp.5381-5390, 2013.

P. J. Warburton, R. M. Palmer, M. A. Munson, and W. G. Wade, Demonstration of in vivo transfer of doxycycline resistance mediated by a novel transposon, J. Antimicrob. Chemother, vol.60, pp.973-980, 2007.

G. Lebel, K. Vaillancourt, M. Frenette, M. Gottschalk, and D. Grenier, Suicin 90-1330 from a nonvirulent strain of Streptococcus suis: A nisin-related lantibiotic active on gram-positive swine pathogens, Appl. Environ. Microbiol, vol.80, pp.5484-5492, 2014.

K. Vaillancourt, G. Lebel, M. Frenette, N. Fittipaldi, M. Gottschalk et al., Purification and characterization of suicin 65, a novel class I type B lantibiotic produced by Streptococcus suis, PLoS ONE, vol.10, 2015.

K. Vaillancourt, G. Lebel, M. Frenette, M. Gottschalk, and D. Grenier, Suicin 3908, a new lantibiotic produced by a strain of Streptococcus suis serotype 2 isolated from a healthy carrier pig, PLoS ONE, vol.10, 2015.

T. B. Athey, K. Vaillancourt, M. Frenette, N. Fittipaldi, M. Gottschalk et al., Distribution of suicin gene clusters in Streptococcus suis serotype 2 belonging to sequence types 25 and 28, BioMed Res. Int, 2016.

M. Li, X. Shen, J. Yan, H. Han, B. Zheng et al., GI-type T4SS-mediated horizontal transfer of the 89K pathogenicity island in epidemic Streptococcus suis serotype 2, Mol. Microbiol, vol.79, pp.1670-1683, 2011.

M. Brochet, E. Couve, P. Glaser, G. Guédon, and S. Payot, Integrative conjugative elements and related elements are major contributors to the genome diversity of Streptococcus agalactiae, J. Bacteriol, vol.190, pp.6913-6917, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01637762

A. Puymège, S. Bertin, G. Guédon, and S. Payot, Analysis of Streptococcus agalactiae pan-genome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNA(Lys CTT) gene, Mol. Genet. Genom, vol.290, pp.1727-1740, 2015.

K. Huang, Q. Zhang, Y. Song, Z. Zhang, A. Zhang et al., Characterization of spectinomycin resistance in Streptococcus suis leads to two novel insights into drug resistance formation and dissemination mechanism, Antimicrob. Agents Chemother, vol.60, pp.6390-6392, 2016.

R. Guérillot, V. Da-cunha, E. Sauvage, C. Bouchier, and P. Glaser, Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading, J. Bacteriol, 1979.

E. Giovanetti, A. Brenciani, E. Tiberi, A. Bacciaglia, and P. E. Varaldo, ICESp2905, the erm(TR)-tet(O) element of Streptococcus pyogenes, is formed by two independent integrative and conjugative elements, Antimicrob. Agents Chemother, vol.56, pp.591-594, 2012.

Y. Sun, I. A. Veseli, K. Vaillancourt, M. Frenette, D. Grenier et al., The bacteriocin from the prophylactic candidate Streptococcus suis 90-1330 is widely distributed across S. suis isolates and appears encoded in an integrative and conjugative element, PLoS ONE, vol.14, 2019.

P. D. Cotter, R. P. Ross, and C. Hill, Bacteriocins-A viable alternative to antibiotics?, Nat. Rev. Microbiol, vol.11, pp.95-105, 2013.

T. B. Athey, J. P. Auger, S. Teatero, A. Dumesnil, D. Takamatsu et al., Complex population structure and virulence differences among serotype 2 Streptococcus suis strains belonging to sequence type 28, PLoS ONE, vol.10, 2015.

E. Guédon, C. Delorme, N. Pons, C. Cruaud, V. Loux et al., Complete genome sequence of the commensal Streptococcus salivarius strain JIM8777, J. Bacteriol, vol.193, pp.5024-5025, 2011.

N. Dahmane, V. Libante, F. Charron-bourgoin, E. Guédon, G. Guédon et al., Diversity of integrative and conjugative elements of Streptococcus salivarius and their intra-and interspecies transfer, Appl. Environ. Microbiol, vol.83, pp.337-354, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01543490

X. Bellanger, A. P. Roberts, C. Morel, F. Choulet, G. Pavlovic et al., Conjugative transfer of the integrative conjugative elements ICESt1 and ICESt3 from Streptococcus thermophilus, J. Bacteriol, vol.191, pp.2764-2775, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01659303

C. Delorme, C. Bartholini, M. Luraschi, N. Pons, V. Loux et al., Complete genome sequence of the pigmented Streptococcus thermophilus strain JIM8232, J. Bacteriol, vol.193, pp.5581-5582, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000180

T. B. Athey, S. Teatero, S. Lacouture, D. Takamatsu, M. Gottschalk et al., Determining Streptococcus suis serotype from short-read whole-genome sequencing data, BMC Microbiol, vol.16, 2016.

A. Tritt, J. A. Eisen, M. T. Facciotti, and A. E. Darling, An integrated pipeline for de novo assembly of microbial genomes, PLoS ONE, vol.7, 2012.

T. Seemann, Prokka: Rapid prokaryotic genome annotation, Bioinformatics, vol.30, pp.2068-2069, 2014.

S. K. Gupta, B. R. Padmanabhan, S. M. Diene, R. Lopez-rojas, M. Kempf et al., Arg-annot, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes, Antimicrob. Agents Chemother, vol.58, pp.212-220, 2014.

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.24, pp.2672-2676, 2008.

M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne et al., Circos: An information aesthetic for comparative genomics, Genome. Res, vol.19, pp.1639-1645, 2009.

S. J. King, J. A. Leigh, P. J. Heath, I. Luque, C. Tarradas et al., Development of a multilocus sequence typing scheme for the pig pathogen Streptococcus suis: Identification of virulent clones and potential capsular serotype exchange, J. Clin. Microbiol, vol.40, pp.3671-3680, 2002.

S. Kumar, G. Stecher, K. Tamura, and . Mega7, Molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol. Biol. Evol, vol.33, pp.1870-1874, 2016.

K. Tamura and M. Nei, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol, vol.10, pp.512-526, 1993.

N. Carraro, V. Libante, C. Morel, F. Charron-bourgoin, P. Leblond et al., Plasmid-like replication of a minimal streptococcal integrative and conjugative element, Microbiology, vol.162, pp.622-632, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01476043

N. Dahmane, E. Robert, J. Deschamps, T. Meylheuc, C. Delorme et al., Impact of cell surface molecules on conjugative transfer of the integrative and conjugative element ICESt3 of Streptococcus thermophilus, Appl. Environ. Microbiol, vol.84, pp.2109-02117, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01678088

L. Fontaine, C. Boutry, E. Guédon, A. Guillot, M. Ibrahim et al., Quorum-sensing regulation of the production of Blp bacteriocins in Streptococcus thermophilus, J. Bacteriol, vol.189, pp.7195-7205, 2007.