L. Mcfarland, Epidemiology, Risk Factors and Treatments for Antibiotic-Associated Diarrhea, Digestive Diseases, vol.16, issue.5, pp.292-307, 1998.
DOI : 10.1159/000016879

S. Cohen, D. Gerding, S. Johnson, C. Kelly, V. Loo et al., Infection in Adults: 2010 Update by the Society for Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA), Infection Control and Hospital Epidemiology, vol.31, issue.5, pp.431-455, 2010.
DOI : 10.1086/651706

L. Kyne, M. Hamel, R. Polavaram, and C. Kelly, Health Care Costs and Mortality Associated with Nosocomial Diarrhea Due to Clostridium difficile, Clinical Infectious Diseases, vol.34, issue.3, pp.346-353, 2002.
DOI : 10.1086/338260

M. Goudarzi, S. Seyedjavadi, H. Goudarzi, M. Aghdam, E. Nazeri et al., Clostridium difficile infection: epidemiology, pathogenesis, risk factors, and therapeutic options, 2014.

M. Popoff and P. Bouvet, Clostridial toxins, Future Microbiology, vol.274, issue.8, pp.1021-1064, 2009.
DOI : 10.1074/jbc.274.16.11046

URL : https://hal.archives-ouvertes.fr/hal-00105901

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.34, issue.3, pp.5844-5849, 2001.
DOI : 10.1046/j.1365-2958.1999.01586.x

N. Mani, D. Lyras, L. Barroso, P. Howarth, T. Wilkins et al., Environmental Response and Autoregulation of Clostridium difficile TxeR, a Sigma Factor for Toxin Gene Expression, Journal of Bacteriology, vol.184, issue.21, pp.5971-5978, 2002.
DOI : 10.1128/JB.184.21.5971-5978.2002

E. Meouche, I. Peltier, J. Monot, M. Soutourina, O. Pestel-caron et al., 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, p.83748, 2013.
DOI : 10.1371/journal.pone.0083748.s004

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

S. Dineen, S. Mcbride, and A. Sonenshein, Integration of Metabolism and Virulence by Clostridium difficile CodY, Journal of Bacteriology, vol.192, issue.20, pp.5350-536200341, 2010.
DOI : 10.1128/JB.00341-10

S. Dineen, A. Villapakkam, J. Nordman, and A. Sonenshein, Repression of Clostridium difficile toxin gene expression by CodY, Molecular Microbiology, vol.47, issue.1, pp.206-219, 2007.
DOI : 10.1128/AAC.23.5.784

A. Antunes, E. Camiade, M. Monot, E. Courtois, F. Barbut et al., Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile, Nucleic Acids Research, vol.40, issue.21, pp.10701-10718, 2012.
DOI : 10.1093/nar/gks864

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

A. Antunes, I. Martin-verstraete, and B. Dupuy, CcpA-mediated repression of Clostridium difficile toxin gene expression, Molecular Microbiology, vol.44, issue.1, pp.882-899, 2011.
DOI : 10.1099/00222615-44-2-111

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

S. Reddy, A. Girinathan, B. 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

B. Dupuy and A. Sonenshein, toxin genes, Molecular Microbiology, vol.27, issue.1, pp.107-120, 1998.
DOI : 10.1093/clinids/18.2.181

B. Dupuy, N. Mani, S. Katayama, and A. Sonenshein, Transcription activation of a UV-inducible Clostridium perfringens bacteriocin gene by a novel ?? factor, Molecular Microbiology, vol.180, issue.4, pp.1196-1206, 2005.
DOI : 10.1099/0022-1317-50-7-613

J. Heap, S. Kuehne, M. Ehsaan, S. Cartman, C. Cooksley et al., The ClosTron: Mutagenesis in Clostridium refined and streamlined, Journal of Microbiological Methods, vol.80, issue.1, pp.49-55, 2010.
DOI : 10.1016/j.mimet.2009.10.018

L. Saujet, F. Pereira, M. Serrano, O. Soutourina, M. Monot et al., Genome-Wide Analysis of Cell Type-Specific Gene Transcription during Spore Formation in Clostridium difficile, PLoS Genetics, vol.181, issue.10, p.1003756
DOI : 10.1371/journal.pgen.1003756.s016

URL : https://hal.archives-ouvertes.fr/pasteur-01370780

K. Fimlaid, J. Bond, K. Schutz, E. Putnam, J. Leung et al., Global Analysis of the Sporulation Pathway of Clostridium difficile, PLoS Genetics, vol.107, issue.8, p.1003660, 2013.
DOI : 10.1371/journal.pgen.1003660.s023

F. Pereira, L. Saujet, A. Tomé, M. Serrano, M. Monot et al., The Spore Differentiation Pathway in the Enteric Pathogen Clostridium difficile, PLoS Genetics, vol.60, issue.1, 2013.
DOI : 10.1371/journal.pgen.1003782.s013

URL : https://hal.archives-ouvertes.fr/pasteur-01370787

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, p.1002727, 2012.
DOI : 10.1371/journal.ppat.1002727.s001

R. Govind, L. Fitzwater, and R. Nichols, ABSTRACT, Journal of Bacteriology, vol.197, issue.15, pp.2600-260900224, 2015.
DOI : 10.1128/JB.00224-15

R. Losick and P. Stragier, Crisscross regulation of cell-type-specific gene expression during development in B. subtilis, Nature, vol.355, issue.6361, pp.601-604, 1992.
DOI : 10.1038/355601a0

U. Bai, I. Mandic-mulec, and I. Smith, SinI modulates the activity of SinR, a developmental switch protein of Bacillus subtilis, by protein-protein interaction., Genes & Development, vol.7, issue.1, pp.139-148, 1993.
DOI : 10.1101/gad.7.1.139

M. Francis, C. Allen, R. Shrestha, and J. Sorg, Bile Acid Recognition by the Clostridium difficile Germinant Receptor, CspC, Is Important for Establishing Infection, PLoS Pathogens, vol.48, issue.5, p.1003356, 2013.
DOI : 10.1371/journal.ppat.1003356.s003

J. Sorg and A. Sonenshein, Inhibiting the Initiation of Clostridium difficile Spore Germination using Analogs of Chenodeoxycholic Acid, a Bile Acid, Journal of Bacteriology, vol.192, issue.19, pp.4983-499000610, 2010.
DOI : 10.1128/JB.00610-10

D. Bhattacharjee, M. Francis, X. Ding, K. Mcallister, R. Shrestha et al., ABSTRACT, Journal of Bacteriology, vol.198, issue.5, pp.777-78600908, 2015.
DOI : 10.1128/JB.00908-15

K. Mackin, G. Carter, P. Howarth, J. Rood, and D. Lyras, Spo0A Differentially Regulates Toxin Production in Evolutionarily Diverse Strains of Clostridium difficile, PLoS ONE, vol.54, issue.11, p.79666, 2013.
DOI : 10.1371/journal.pone.0079666.s002

L. Deakin, C. S. Fagan, R. Dawson, L. Pickard, D. West et al., Gene Is a Persistence and Transmission Factor, Infection and Immunity, vol.80, issue.8, pp.2704-271100147, 2012.
DOI : 10.1128/IAI.00147-12

R. Stabler, M. He, L. Dawson, M. Martin, E. Valiente et al., Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium, Genome Biology, vol.10, issue.9, p.102, 2009.
DOI : 10.1186/gb-2009-10-9-r102

L. Pettit, H. Browne, L. Yu, W. Smits, R. Fagan et al., Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism, BMC Genomics, vol.15, issue.1, p.160, 2014.
DOI : 10.1111/j.1472-765X.1989.tb00278.x

A. Edwards, R. Tamayo, and S. Mcbride, sporulation, motility and toxin production, Molecular Microbiology, vol.41, issue.6, pp.954-971, 2016.
DOI : 10.1093/nar/gkt546

K. Nawrocki, A. Edwards, N. Daou, L. Bouillaut, and S. Mcbride, ABSTRACT, Journal of Bacteriology, vol.198, issue.15, pp.2113-213000220, 2016.
DOI : 10.1128/JB.00220-16

C. Janoir, C. Denève, S. Bouttier, F. Barbut, S. Hoys et al., Adaptive Strategies and Pathogenesis of Clostridium difficile from In Vivo Transcriptomics, Infection and Immunity, vol.81, issue.10, pp.3757-376900515, 2013.
DOI : 10.1128/IAI.00515-13

URL : https://hal.archives-ouvertes.fr/pasteur-01370786

K. Pishdadian, K. Fimlaid, and A. Shen, sporulation, Molecular Microbiology, vol.39, issue.Suppl. 3, pp.189-208, 2015.
DOI : 10.1046/j.1365-2958.2001.02331.x

M. Fujita and R. Losick, An investigation into the compartmentalization of the sporulation transcription factor sigmaE in Bacillus subtilis, Molecular Microbiology, vol.43, issue.1, pp.27-38, 2002.
DOI : 10.1128/JB.182.10.2919-2927.2000

R. Jonas, E. Weaver, T. Kenney, C. Moran, J. Haldenwang et al., The Bacillus subtilis spoIIG operon encodes both sigma E and a gene necessary for sigma E activation., Journal of Bacteriology, vol.170, issue.2, pp.507-511, 1988.
DOI : 10.1128/jb.170.2.507-511.1988

T. Labell, J. Trempy, and W. Haldenwang, Sporulation-specific sigma factor sigma 29 of Bacillus subtilis is synthesized from a precursor Clostridium difficile, 1987.

A. Hofmeister, A. Londoño-vallejo, E. Harry, P. Stragier, and R. Losick, Extracellular signal protein triggering the proteolytic activation of a developmental transcription factor in B. subtilis, Cell, vol.83, issue.2, pp.219-2260092, 1995.
DOI : 10.1016/0092-8674(95)90163-9

M. Karow, P. Glaser, and P. Piggot, Identification of a gene, spoIIR, that links the activation of sigma E to the transcriptional activity of sigma F during sporulation in Bacillus subtilis., Proceedings of the National Academy of Sciences, vol.92, issue.6, pp.2012-2016, 1995.
DOI : 10.1073/pnas.92.6.2012

T. Lawley, N. Croucher, L. Yu, C. S. Sebaihia, M. Goulding et al., Proteomic and Genomic Characterization of Highly Infectious Clostridium difficile 630 Spores, Journal of Bacteriology, vol.191, issue.17, pp.5377-538600597, 2009.
DOI : 10.1128/JB.00597-09

P. Strong, K. Fulton, A. A. Foote, S. Twine, S. Logan et al., Identification and Characterization of Glycoproteins on the Spore Surface of Clostridium difficile, Journal of Bacteriology, vol.196, issue.14, pp.2627-263701469, 2014.
DOI : 10.1128/JB.01469-14

J. Barra-carrasco, V. Olguín-araneda, A. Plaza-garrido, C. Miranda-cárdenas, G. Cofré-araneda et al., The Clostridium difficile Exosporium Cysteine (CdeC)-Rich Protein Is Required for Exosporium Morphogenesis and Coat Assembly, Journal of Bacteriology, vol.195, issue.17, pp.3863-387500369, 2013.
DOI : 10.1128/JB.00369-13

M. Donnelly, K. Fimlaid, and A. Shen, ABSTRACT, Journal of Bacteriology, vol.198, issue.11, pp.1694-170700986, 2016.
DOI : 10.1128/JB.00986-15

D. Paredes-sabja, P. Setlow, and M. Sarker, Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved, Trends in Microbiology, vol.19, issue.2, pp.85-94, 2011.
DOI : 10.1016/j.tim.2010.10.004

B. Orsburn, S. Melville, and D. Popham, Factors Contributing to Heat Resistance of Clostridium perfringens Endospores, Applied and Environmental Microbiology, vol.74, issue.11, pp.3328-3335, 2008.
DOI : 10.1128/AEM.02629-07

N. Chen, S. Jiang, D. Klein, and H. Paulus, Organization and nucleotide sequence of the Bacillus subtilis diaminopimelate operon, a cluster of genes encoding the first three enzymes of diaminopimelate synthesis and dipicolinate synthase, J Biol Chem, vol.268, pp.9448-9465, 1993.

V. Vepachedu and P. Setlow, Role of SpoVA Proteins in Release of Dipicolinic Acid during Germination of Bacillus subtilis Spores Triggered by Dodecylamine or Lysozyme, Journal of Bacteriology, vol.189, issue.5, pp.1565-157201613, 2007.
DOI : 10.1128/JB.01613-06

C. Adams, B. Eckenroth, E. Putnam, S. Doublié, and A. Shen, Structural and Functional Analysis of the CspB Protease Required for Clostridium Spore Germination, PLoS Pathogens, vol.16, issue.2, p.1003165, 2013.
DOI : 10.1371/journal.ppat.1003165.s008

D. Burns, J. Heap, and N. Minton, SleC Is Essential for Germination of Clostridium difficile Spores in Nutrient-Rich Medium Supplemented with the Bile Salt Taurocholate, Journal of Bacteriology, vol.192, issue.3, pp.657-66401209, 2010.
DOI : 10.1128/JB.01209-09

D. Gutelius, K. Hokeness, S. Logan, and C. Reid, Functional analysis of SleC from Clostridium difficile: an essential lytic transglycosylase involved in spore germination, Microbiology, vol.160, issue.Pt_1, pp.209-216, 2014.
DOI : 10.1099/mic.0.072454-0

M. Francis, C. Allen, and J. Sorg, ABSTRACT, Journal of Bacteriology, vol.197, issue.14, pp.2276-228302575, 2015.
DOI : 10.1128/JB.02575-14

R. Govind, G. Vediyappan, R. Rolfe, B. Dupuy, and J. Fralick, Bacteriophage-Mediated Toxin Gene Regulation in Clostridium difficile, Journal of Virology, vol.83, issue.23, pp.12037-12045, 2009.
DOI : 10.1128/JVI.01256-09

L. Saujet, M. Monot, B. Dupuy, O. Soutourina, and I. Martin-verstraete, The Key Sigma Factor of Transition Phase, SigH, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile, Journal of Bacteriology, vol.193, issue.13, pp.3186-319600272, 2011.
DOI : 10.1128/JB.00272-11

URL : https://hal.archives-ouvertes.fr/pasteur-01370840

B. Elliott, K. 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, 2014.
DOI : 10.1093/gbe/evu248

S. Lyon, M. Hutton, J. Rood, J. Cheung, and D. Lyras, CdtR Regulates TcdA and TcdB Production in Clostridium difficile, PLOS Pathogens, vol.19, issue.7, 2016.
DOI : 10.1371/journal.ppat.1005758.s004

E. Putnam, A. Nock, T. Lawley, and A. Shen, SpoIVA and SipL Are Clostridium difficile Spore Morphogenetic Proteins, Journal of Bacteriology, vol.195, issue.6, pp.1214-122502181, 2013.
DOI : 10.1128/JB.02181-12

F. Teng, B. Murray, and G. Weinstock, Conjugal Transfer of Plasmid DNA fromEscherichia colito Enterococci: A Method to Make Insertion Mutations, Plasmid, vol.39, issue.3, pp.182-186, 1998.
DOI : 10.1006/plas.1998.1336

A. Criscuolo and S. Brisse, AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics, vol.102, issue.5-6, pp.500-506, 2013.
DOI : 10.1016/j.ygeno.2013.07.011

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.184-195, 2014.
DOI : 10.1089/omi.2013.0119

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

O. Soutourina, M. Monot, P. Boudry, L. Saujet, C. Pichon et al., Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile, PLoS Genetics, vol.39, issue.1, p.1003493
DOI : 10.1371/journal.pgen.1003493.s014

URL : https://hal.archives-ouvertes.fr/pasteur-01370770

H. Hussain, A. Roberts, and P. Mullany, Generation of an erythromycin-sensitive derivative of Clostridium difficile strain 630 (630??erm) and demonstration that the conjugative transposon Tn916??E enters the genome of this strain at multiple sites, Journal of Medical Microbiology, vol.54, issue.2, pp.137-141, 2005.
DOI : 10.1099/jmm.0.45790-0

R. Fagan and N. Fairweather, Has Two Parallel and Essential Sec Secretion Systems, Journal of Biological Chemistry, vol.10, issue.31, pp.27483-27493, 2011.
DOI : 10.1080/01490450303891