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
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
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
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
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
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
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
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
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
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
A novel toxinotyping scheme and correlation of toxinotypes with serogroups of Clostridium difficile isolates, J Clin Microbiol, vol.36, pp.2240-2247, 1998. ,
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
Genetic characteristics of toxigenic Clostridia and toxin gene evolution, Toxicon, vol.75, pp.63-89, 2013. ,
DOI : 10.1016/j.toxicon.2013.05.003
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
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
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. ,
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
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
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
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
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
MicroScope: a platform for microbial genome annotation and comparative genomics, Database, vol.2009, issue.0, pp.10-1093, 2009. ,
DOI : 10.1093/database/bap021
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular biology and evolution 30, pp.2725-2729, 2013. ,
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
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
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
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
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
Oligohistidine tag mutagenesis of the lambda holin gene, J Bacteriol, vol.180, pp.4199-4211, 1998. ,
Novel molecular type of Clostridium difficile in neonatal pigs, Western Australia, Emerg Infect Dis, vol.19, pp.790-792, 2013. ,
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
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
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
Holins: the protein clocks of bacteriophage infections. Annual review of microbiology 54, pp.799-825, 2000. ,
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission, Genome Biology, vol.13, issue.12, pp.10-1186, 2012. ,
DOI : 10.1080/10635150802422308
Infection Identified on Whole-Genome Sequencing, New England Journal of Medicine, vol.369, issue.13, pp.1195-1205, 2013. ,
DOI : 10.1056/NEJMoa1216064
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
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
Molecular genetics and pathogenesis of Clostridium perfringens, Microbiol Rev, vol.55, pp.621-648, 1991. ,
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
Clinical Clostridium difficile: Clonality and Pathogenicity Locus Diversity, PLoS ONE, vol.11, issue.5, 2011. ,
DOI : 10.1371/journal.pone.0019993.s004
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
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
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
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
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
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
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
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