S. Cartman, J. Heap, S. Kuehne, A. Cockayne, and N. Minton, The emergence of ???hypervirulence??? in Clostridium difficile, International Journal of Medical Microbiology, vol.300, issue.6, pp.387-395, 2010.
DOI : 10.1016/j.ijmm.2010.04.008

E. Kuijper, B. Coignard, J. Brazier, C. Suetens, D. Drudy et al., Update of Clostridium difficileassociated disease due to PCR ribotype 027 in Europe. Euro surveillance: bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, pp.1-2, 2007.

C. Deneve, C. Janoir, I. Poilane, C. Fantinato, and A. Collignon, New trends in Clostridium difficile virulence and pathogenesis, International Journal of Antimicrobial Agents, vol.33, issue.109, pp.24-28, 2009.
DOI : 10.1016/S0924-8579(09)70012-3

E. Calabi, F. Calabi, A. Phillips, and N. Fairweather, Binding of Clostridium difficile Surface Layer Proteins to Gastrointestinal Tissues, Infection and Immunity, vol.70, issue.10, pp.5770-5778, 2002.
DOI : 10.1128/IAI.70.10.5770-5778.2002

A. Waligora, C. Hennequin, P. Mullany, P. Bourlioux, A. Collignon et al., Characterization of a Cell Surface Protein of Clostridium difficile with Adhesive Properties, Infection and Immunity, vol.69, issue.4, pp.2144-2153, 2001.
DOI : 10.1128/IAI.69.4.2144-2153.2001

A. Barketi-klai, S. Hoys, S. Lambert-bordes, A. Collignon, and I. Kansau, Role of fibronectin-binding protein A in Clostridium difficile intestinal colonization, Journal of Medical Microbiology, vol.60, issue.8, pp.1155-1161, 2011.
DOI : 10.1099/jmm.0.029553-0

L. Tulli, S. Marchi, R. Petracca, H. Shaw, N. Fairweather et al., CbpA: a novel surface exposed adhesin of Clostridium difficile targeting human collagen, Cellular microbiology, vol.15, issue.10, pp.1674-1687, 2013.

A. Kovacs-simon, R. Leuzzi, M. Kasendra, N. Minton, R. Titball et al., Lipoprotein CD0873 is a novel adhesin of Clostridium difficile. The Journal of infectious diseases, pp.274-284, 2014.

A. Tasteyre, M. Barc, A. Collignon, H. Boureau, and T. Karjalainen, Role of FliC and FliD Flagellar Proteins of Clostridium difficile in Adherence and Gut Colonization, Infection and Immunity, vol.69, issue.12, pp.7937-7940, 2001.
DOI : 10.1128/IAI.69.12.7937-7940.2001

V. Cafardi, M. Biagini, M. Martinelli, R. Leuzzi, J. Rubino et al., Identification of a Novel Zinc Metalloprotease through a Global Analysis of Clostridium difficile Extracellular Proteins, PLoS ONE, vol.21, issue.11, p.24303041, 2013.
DOI : 10.1371/journal.pone.0081306.s005

P. Hensbergen, O. Klychnikov, D. Bakker, V. Van-winden, N. Ras et al., A Novel Secreted Metalloprotease (CD2830) from Clostridium difficile Cleaves Specific Proline Sequences in LPXTG Cell Surface Proteins, Molecular & Cellular Proteomics, vol.13, issue.5, pp.1231-1244, 2014.
DOI : 10.1074/mcp.M113.034728

C. Janoir, C. Deneve, 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.3757-3769, 2013.
DOI : 10.1128/IAI.00515-13

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

M. Awad, P. Johanesen, G. Carter, E. Rose, and D. Lyras, virulence factors: Insights into an anaerobic spore-forming pathogen, Gut Microbes, vol.2013, issue.5, pp.579-593, 2014.
DOI : 10.1111/1574-6968.12367

B. Dupuy and A. Sonenshein, toxin genes, Molecular Microbiology, vol.27, issue.1, pp.107-120, 1998.
DOI : 10.1046/j.1365-2958.1998.00663.x

S. Kuehne, S. Cartman, J. Heap, M. Kelly, A. Cockayne et al., The role of toxin A and toxin B in Clostridium difficile infection, Nature, vol.76, issue.7316, pp.711-713, 2010.
DOI : 10.1038/nature09397

D. Lyras, O. Connor, J. Howarth, P. Sambol, S. Carter et al., Toxin B is essential for virulence of Clostridium difficile, Nature, vol.31, issue.7242, pp.1176-1179, 2009.
DOI : 10.1038/nature07822

D. Gerding, S. Johnson, M. Rupnik, and K. Aktories, binary toxin CDT, Gut Microbes, vol.56, issue.1, pp.15-27, 2014.
DOI : 10.1099/jmm.0.031062-0

T. Akerlund, I. Persson, M. Unemo, T. Noren, B. Svenungsson et al., Increased Sporulation Rate of Epidemic Clostridium difficile Type 027/NAP1, Journal of Clinical Microbiology, vol.46, issue.4, pp.1530-1533, 2008.
DOI : 10.1128/JCM.01964-07

M. Merrigan, A. Venugopal, M. Mallozzi, B. Roxas, V. Viswanathan et al., Human Hypervirulent Clostridium difficile Strains Exhibit Increased Sporulation as Well as Robust Toxin Production, Journal of Bacteriology, vol.192, issue.19, pp.4904-4911, 2010.
DOI : 10.1128/JB.00445-10

D. Burns, D. Heeg, S. Cartman, and N. Minton, Reconsidering the Sporulation Characteristics of Hypervirulent Clostridium difficile BI/NAP1/027, PLoS ONE, vol.46, issue.9, p.21949780, 2011.
DOI : 10.1371/journal.pone.0024894.t001

P. Vohra and I. Poxton, Comparison of toxin and spore production in clinically relevant strains of Clostridium difficile, Microbiology, vol.157, issue.5, pp.1343-1353, 2011.
DOI : 10.1099/mic.0.046243-0

M. Warny, J. Pepin, A. Fang, G. Killgore, A. Thompson et al., Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe, The Lancet, vol.366, issue.9491, pp.1079-1084, 2005.
DOI : 10.1016/S0140-6736(05)67420-X

A. Barketi-klai, M. Monot, S. Hoys, S. Lambert-bordes, S. Kuehne et al., The Flagellin FliC of Clostridium difficile Is Responsible for Pleiotropic Gene Regulation during In Vivo Infection, PLoS ONE, vol.6, issue.5, p.24841151
DOI : 10.1371/journal.pone.0096876.s002

URL : https://hal.archives-ouvertes.fr/pasteur-01370758

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.22685398, 2012.
DOI : 10.1371/journal.ppat.1002727.s001

L. Bouillaut, T. Dubois, A. Sonenshein, and B. Dupuy, Integration of metabolism and virulence in Clostridium difficile, Research in Microbiology, vol.166, issue.4, pp.375-383, 2015.
DOI : 10.1016/j.resmic.2014.10.002

A. Shakeri-garakani, A. Brinkkotter, K. Schmid, S. Turgut, and J. Lengeler, The genes and enzymes for the catabolism of galactitol, D-tagatose, and related carbohydrates in Klebsiella oxytoca M5a1 and other enteric bacteria display convergent evolution. Molecular genetics and genomics: MGG, pp.717-728, 2004.

B. Kempf and E. Bremer, Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments, Archives of Microbiology, vol.170, issue.5, pp.319-330, 1998.
DOI : 10.1007/s002030050649

J. Chen, J. Scaria, C. Mao, B. Sobral, S. Zhang et al., Strains, Journal of Proteome Research, vol.12, issue.3, pp.1151-1161, 2013.
DOI : 10.1021/pr3007528

URL : https://hal.archives-ouvertes.fr/ensl-00707881

D. Paredes-sabja, A. Shen, and J. Sorg, Clostridium difficile spore biology: sporulation, germination, and spore structural proteins, Trends in Microbiology, vol.22, issue.7, pp.406-416, 2014.
DOI : 10.1016/j.tim.2014.04.003

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.23950727
DOI : 10.1371/journal.pgen.1003660.s023

F. Pereira, L. Saujet, A. Tome, M. Serrano, M. Monot et al., The Spore Differentiation Pathway in the Enteric Pathogen Clostridium difficile, PLoS Genetics, vol.60, issue.1, p.24098139
DOI : 10.1371/journal.pgen.1003782.s013

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

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, 2009.
DOI : 10.1186/gb-2009-10-9-r102

R. Stabler, E. Valiente, L. Dawson, M. He, J. Parkhill et al., PCR-ribotype 027 strains reveals high genome fluidity including point mutations and inversions, Gut Microbes, vol.9, issue.4, pp.269-276, 2010.
DOI : 10.1093/nar/gkg304

M. Martin, C. S. Goulding, D. Faulds-pain, A. Barquist, L. Browne et al., The agr Locus Regulates Virulence and Colonization Genes in Clostridium difficile 027, Journal of Bacteriology, vol.195, issue.16, pp.3672-3681, 2013.
DOI : 10.1128/JB.00473-13

F. Escartin, S. Skouloubris, U. Liebl, and H. Myllykallio, Flavin-dependent thymidylate synthase X limits chromosomal DNA replication, Proceedings of the National Academy of Sciences, vol.105, issue.29, pp.9948-9952, 2008.
DOI : 10.1073/pnas.0801356105

URL : https://hal.archives-ouvertes.fr/hal-00353456

C. Knetsch, M. Hensgens, C. Harmanus, M. Van-der-bijl, P. Savelkoul et al., Genetic markers for Clostridium difficile lineages linked to hypervirulence, Microbiology, vol.157, issue.11, pp.3113-3123, 2011.
DOI : 10.1099/mic.0.051953-0

S. Baban, S. Kuehne, A. Barketi-klai, S. Cartman, M. Kelly et al., The Role of Flagella in Clostridium difficile Pathogenesis: Comparison between a Non-Epidemic and an Epidemic Strain, PLoS ONE, vol.29, issue.9, p.24086268, 2013.
DOI : 10.1371/journal.pone.0073026.s006

M. Merrigan, A. Venugopal, J. Roxas, F. Anwar, M. Mallozzi et al., Surface-Layer Protein A (SlpA) Is a Major Contributor to Host-Cell Adherence of Clostridium difficile, PLoS ONE, vol.20, issue.9, p.24265687, 2013.
DOI : 10.1371/journal.pone.0078404.s001

J. Scaria, T. Janvilisri, S. Fubini, R. Gleed, S. Mcdonough et al., Clostridium difficile Transcriptome Analysis Using Pig Ligated Loop Model Reveals Modulation of Pathways Not Modulated In Vitro, Journal of Infectious Diseases, vol.203, issue.11, pp.1613-1620, 2011.
DOI : 10.1093/infdis/jir112

S. Kuehne, M. Collery, M. Kelly, S. Cartman, A. Cockayne et al., Importance of toxin A, toxin B, and CDT in virulence of an epidemic Clostridium difficile strain. The Journal of infectious diseases, pp.83-86, 2014.

C. Robinson, J. Auchtung, J. Collins, and R. Britton, Epidemic Clostridium difficile Strains Demonstrate Increased Competitive Fitness Compared to Nonepidemic Isolates, Infection and Immunity, vol.82, issue.7, pp.2815-2825, 2014.
DOI : 10.1128/IAI.01524-14

A. Edwards, K. Nawrocki, and S. Mcbride, Conserved Oligopeptide Permeases Modulate Sporulation Initiation in Clostridium difficile, Infection and Immunity, vol.82, issue.10, pp.4276-4291, 2014.
DOI : 10.1128/IAI.02323-14

F. Diaz-gonzalez, M. Milano, V. Olguin-araneda, J. Pizarro-cerda, P. Castro-cordova et al., Protein composition of the outermost exosporium-like layer of Clostridium difficile 630 spores, Journal of Proteomics, vol.123, p.25849250, 2015.
DOI : 10.1016/j.jprot.2015.03.035