M. Rupnik, M. H. Wilcox, and D. N. Gerding, Clostridium difficile infection: new developments in epidemiology and pathogenesis, Nature Reviews Microbiology, vol.36, issue.7, pp.526-536, 2009.
DOI : 10.1016/S0140-6736(97)08062-8

P. N. Wiegand, Clinical and economic burden of Clostridium difficile infection in Europe: a systematic review of healthcare-facility-acquired infection, Journal of Hospital Infection, vol.81, issue.1, pp.1-14, 2012.
DOI : 10.1016/j.jhin.2012.02.004

K. A. Davies, Underdiagnosis of Clostridium difficile across Europe: the European, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), The Lancet Infectious Diseases, vol.14, issue.12, pp.1208-1219, 2014.
DOI : 10.1016/S1473-3099(14)70991-0

N. Mani and B. Dupuy, Regulation of toxin synthesis in Clostridium difficile by an alternative RNA polymerase sigma factor, Proceedings of the National Academy of Sciences, vol.98, issue.10, pp.5844-5849, 2001.
DOI : 10.1073/pnas.101126598

R. Govind and B. Dupuy, Secretion of Clostridium difficile Toxins A and B Requires the Holin-like Protein TcdE, PLoS Pathogens, vol.38, issue.Pt 1, 2012.
DOI : 10.1371/journal.ppat.1002727.s001

S. Matamouros, P. England, and B. Dupuy, Clostridium difficile toxin expression is inhibited by the novel regulator TcdC, Molecular Microbiology, vol.180, issue.Part 7, pp.1274-1288, 2007.
DOI : 10.1111/j.1365-2958.2007.05739.x

V. Braun, T. Hundsberger, P. Leukel, M. Sauerborn, and C. Von-eichel-streiber, Definition of the single integration site of the pathogenicity locus in Clostridium difficile, Gene, vol.181, issue.1-2, pp.29-38, 1996.
DOI : 10.1016/S0378-1119(96)00398-8

K. E. Dingle, Evolutionary History of the Clostridium difficile Pathogenicity Locus, Genome Biology and Evolution, vol.6, issue.1, pp.36-52, 2014.
DOI : 10.1093/gbe/evt204

M. P. Bauer, Clostridium difficile infection in Europe: a hospital-based survey, The Lancet, vol.377, issue.9759, pp.63-73, 2011.
DOI : 10.1016/S0140-6736(10)61266-4

G. P. Carter, Binary Toxin Production in Clostridium difficile Is Regulated by CdtR, a LytTR Family Response Regulator, Journal of Bacteriology, vol.189, issue.20, pp.7290-730100731, 1128.
DOI : 10.1128/JB.00731-07

M. Rupnik, V. Avesani, M. Janc, C. Von-eichel-streiber, and M. Delmee, A novel toxinotyping scheme and correlation of toxinotypes with serogroups of Clostridium difficile isolates, J Clin Microbiol, vol.36, pp.2240-2247, 1998.

M. Rupnik, Revised nomenclature of Clostridium difficile toxins and associated genes, Journal of Medical Microbiology, vol.54, issue.2, pp.113-117, 2005.
DOI : 10.1099/jmm.0.45810-0

M. R. Popoff and P. Bouvet, Genetic characteristics of toxigenic Clostridia and toxin gene evolution, Toxicon, vol.75, pp.63-89, 2013.
DOI : 10.1016/j.toxicon.2013.05.003

R. A. Stabler, Comparative Phylogenomics of Clostridium difficile Reveals Clade Specificity and Microevolution of Hypervirulent Strains, Journal of Bacteriology, vol.188, issue.20, pp.7297-730500664, 1128.
DOI : 10.1128/JB.00664-06

B. Elliott, K. E. Dingle, X. Didelot, D. Crook, and T. Riley, The Complexity and Diversity of the Pathogenicity Locus in Clostridium difficile Clade 5, Genome Biology and Evolution, vol.6, issue.12, pp.10-1093, 2014.
DOI : 10.1093/gbe/evu248

S. Janezic, M. Marin, A. Martin, and M. Rupnik, A new type of toxin A-negative, toxin B-positive Clostridium difficile strain lacking a complete tcdA gene, J Clin Microbiol, pp.10-112802211, 2014.

C. Eckert, Clinical and microbiological features of Clostridium difficile infections in France: The ICD-RAISIN 2009 national survey, M??decine et Maladies Infectieuses, vol.43, issue.2, pp.67-74, 2013.
DOI : 10.1016/j.medmal.2013.01.004

P. Bidet, F. Barbut, V. Lalande, B. Burghoffer, and J. Petit, based on ribosomal RNA gene sequencing, FEMS Microbiology Letters, vol.175, issue.2, pp.261-266, 1999.
DOI : 10.1111/j.1574-6968.1999.tb13629.x

V. Lalande, Infections, Journal of Clinical Microbiology, vol.49, issue.7, pp.2714-2716, 2011.
DOI : 10.1128/JCM.01835-10

URL : https://hal.archives-ouvertes.fr/hal-00597126

H. Kurka, Sequence Similarity of Clostridium difficile Strains by Analysis of Conserved Genes and Genome Content Is Reflected by Their Ribotype Affiliation, PLoS ONE, vol.57, issue.1, p.86535, 2014.
DOI : 10.1371/journal.pone.0086535.s021

URL : https://hal.archives-ouvertes.fr/pasteur-01370765

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

D. Vallenet, MicroScope: a platform for microbial genome annotation and comparative genomics, Database, vol.2009, issue.0, pp.10-1093, 2009.
DOI : 10.1093/database/bap021

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular biology and evolution 30, pp.2725-2729, 2013.

S. S. Dineen, A. C. Villapakkam, J. T. Nordman, and A. L. Sonenshein, Repression of Clostridium difficile toxin gene expression by CodY, Molecular Microbiology, vol.47, issue.1, pp.206-219, 2007.
DOI : 10.1016/S0140-6736(05)67420-X

A. Antunes, Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile, Nucleic Acids Research, vol.40, issue.21, p.864, 2012.
DOI : 10.1093/nar/gks864

URL : https://hal.archives-ouvertes.fr/pasteur-01370790

B. Dupuy and S. Matamouros, Regulation of toxin and bacteriocin synthesis in Clostridium species by a new subgroup of RNA polymerase ??-factors, Research in Microbiology, vol.157, issue.3, pp.201-205, 2006.
DOI : 10.1016/j.resmic.2005.11.004

E. Meouche and I. , Characterization of the SigD Regulon of C. difficile and Its Positive Control of Toxin Production through the Regulation of tcdR, PLoS ONE, vol.4, issue.12, 2013.
DOI : 10.1371/journal.pone.0083748.s004

URL : https://hal.archives-ouvertes.fr/pasteur-01370779

C. Sao-jose, Diversity in the lysis-integration region of oenophage genomes and evidence for multiple tRNA loci, as targets for prophage integration in Oenococcus oeni, Virology, vol.325, issue.1, pp.82-95, 2004.
DOI : 10.1016/j.virol.2004.04.029

D. L. Smith and R. Young, Oligohistidine tag mutagenesis of the lambda holin gene, J Bacteriol, vol.180, pp.4199-4211, 1998.

M. M. Squire, Novel molecular type of Clostridium difficile in neonatal pigs, Western Australia, Emerg Infect Dis, vol.19, pp.790-792, 2013.

B. Elliott, New types of toxin A-negative, toxin B-positive strains among clinical isolates of Clostridium difficile in Australia, Journal of Medical Microbiology, vol.60, issue.8, pp.1108-1111, 2011.
DOI : 10.1099/jmm.0.031062-0

T. Garnier and S. T. Cole, Complete nucleotide sequence and genetic organization of the bacteriocinogenic plasmid, pIP404, from Clostridium perfringens, Plasmid, vol.19, issue.2, pp.134-150, 1988.
DOI : 10.1016/0147-619X(88)90052-2

A. Regamey and D. Karamata, The N-acetylmuramoyl-L-alanine amidase encoded by the Bacillus subtilis 168 prophage SP??, Microbiology, vol.144, issue.4, pp.885-893, 1998.
DOI : 10.1099/00221287-144-4-885

I. N. Wang, D. L. Smith, and R. Young, Holins: the protein clocks of bacteriophage infections. Annual review of microbiology 54, pp.799-825, 2000.

X. Didelot, Microevolutionary analysis of Clostridium difficile genomes to investigate transmission, Genome Biology, vol.13, issue.12, pp.10-1186, 2012.
DOI : 10.1080/10635150802422308

D. W. Eyre, Infection Identified on Whole-Genome Sequencing, New England Journal of Medicine, vol.369, issue.13, pp.1195-1205, 2013.
DOI : 10.1056/NEJMoa1216064

P. J. Bouvet and M. R. Popoff, Genetic Relatedness of Clostridium difficile Isolates from Various Origins Determined by Triple-Locus Sequence Analysis Based on Toxin Regulatory Genes tcdC, tcdR, and cdtR, Journal of Clinical Microbiology, vol.46, issue.11, pp.3703-3713, 2008.
DOI : 10.1128/JCM.00866-08

G. P. Carter, TcsL Is an Essential Virulence Factor in Clostridium sordellii ATCC 9714, Infection and Immunity, vol.79, issue.3, pp.1025-103200968, 2011.
DOI : 10.1128/IAI.00968-10

J. I. Rood and S. T. Cole, Molecular genetics and pathogenesis of Clostridium perfringens, Microbiol Rev, vol.55, pp.621-648, 1991.

T. Anthony, G. S. Chellappa, T. Rajesh, and P. Gunasekaran, Functional analysis of a putative holin-like peptide-coding gene in the genome of Bacillus licheniformis AnBa9, Archives of Microbiology, vol.187, issue.1, pp.51-56, 2010.
DOI : 10.1007/s00203-009-0530-7

K. E. Dingle, Clinical Clostridium difficile: Clonality and Pathogenicity Locus Diversity, PLoS ONE, vol.11, issue.5, 2011.
DOI : 10.1371/journal.pone.0019993.s004

M. Monot, Reannotation of the genome sequence of Clostridium difficile strain 630, Journal of Medical Microbiology, vol.60, issue.8, pp.1193-1199, 2011.
DOI : 10.1099/jmm.0.030452-0

URL : https://hal.archives-ouvertes.fr/pasteur-01370838

M. S. Brouwer, Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers, Nature Communications, vol.153, pp.10-1038, 2013.
DOI : 10.1038/ncomms3601

URL : http://doi.org/10.1038/ncomms3601

S. Reddy, A. R. Girinathan, B. P. Zapotocny, R. Govind, and R. , Identification and Characterization of Clostridium sordellii Toxin Gene Regulator, Journal of Bacteriology, vol.195, issue.18, pp.4246-425400711, 2013.
DOI : 10.1128/JB.00711-13

E. C. Couchman, Clostridium sordellii genome analysis reveals plasmid localized toxin genes encoded within pathogenicity loci, BMC Genomics, vol.61, issue.5, pp.10-1186, 2015.
DOI : 10.1186/s12864-015-1613-2

M. Brudno, LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA, Genome Research, vol.13, issue.4, pp.721-731926603, 2003.
DOI : 10.1101/gr.926603

C. Mayor, VISTA : visualizing global DNA sequence alignments of arbitrary length, Bioinformatics, vol.16, issue.11, pp.1046-1047, 2000.
DOI : 10.1093/bioinformatics/16.11.1046

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

M. Monot, M. Orgeur, E. Camiade, C. Brehier, and B. Dupuy, COV2HTML: A Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists, OMICS: A Journal of Integrative Biology, vol.18, issue.3, pp.184-1950119, 2014.
DOI : 10.1089/omi.2013.0119

URL : https://hal.archives-ouvertes.fr/pasteur-01370754