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

G. Killgore, A. Thompson, S. Johnson, J. Brazier, and E. Kuijper, Comparison of Seven Techniques for Typing International Epidemic Strains of Clostridium difficile: Restriction Endonuclease Analysis, Pulsed-Field Gel Electrophoresis, PCR-Ribotyping, Multilocus Sequence Typing, Multilocus Variable-Number Tandem-Repeat Analysis, Amplified Fragment Length Polymorphism, and Surface Layer Protein A Gene Sequence Typing, Journal of Clinical Microbiology, vol.46, issue.2, pp.431-437, 2008.
DOI : 10.1128/JCM.01484-07

S. Borgmann, M. Kist, T. Jakobiak, M. Reil, and E. Scholz, Increased number of Clostridium difficile infections and prevalence of Clostridium difficile PCR ribotype 001 in southern Germany, Euro Surveill, vol.13, 2008.

J. Brazier, B. Patel, and A. Pearson, Distribution of Clostridium difficile PCR ribotype 027 in British hospitals, Euro Surveill, vol.12, pp.70426-070422, 2007.

A. Indra, D. Schmid, S. Huhulescu, M. Hell, and R. Gattringer, Characterization of clinical Clostridium difficile isolates by PCR ribotyping and detection of toxin genes in Austria, 2006-2007, Journal of Medical Microbiology, vol.57, issue.6, pp.702-708, 2006.
DOI : 10.1099/jmm.0.47476-0

E. Kuijper, B. Coignard, J. Brazier, C. Suetens, and D. Drudy, Update of Clostridium difficile-associated disease due to PCR ribotype 027 in Europe, Euro Surveill, vol.12, pp.1-2, 2007.

P. Spigaglia, F. Barbanti, A. Dionisi, and P. Mastrantonio, Clostridium difficile Isolates Resistant to Fluoroquinolones in Italy: Emergence of PCR Ribotype 018, Journal of Clinical Microbiology, vol.48, issue.8, pp.2892-2896, 2010.
DOI : 10.1128/JCM.02482-09

A. Goorhuis, D. Bakker, J. Corver, S. Debast, and C. Harmanus, Infection Due to a New Hypervirulent Strain, Polymerase Chain Reaction Ribotype 078, Clinical Infectious Diseases, vol.47, issue.9, pp.1162-1170, 2008.
DOI : 10.1086/592257

A. Cheknis, S. Sambol, D. Davidson, K. Nagaro, and M. Mancini, Distribution of Clostridium difficile strains from a North American, European and Australian trial of treatment for C. difficile infections, Anaerobe, vol.15, pp.2005-2007, 2009.

H. Genth, S. Dreger, J. Huelsenbeck, and I. Just, Clostridium difficile toxins: More than mere inhibitors of Rho proteins, The International Journal of Biochemistry & Cell Biology, vol.40, issue.4, pp.592-597, 2008.
DOI : 10.1016/j.biocel.2007.12.014

I. Just, J. Selzer, V. Eichel-streiber, C. Aktories, and K. , The low molecular mass GTP-binding protein Rho is affected by toxin A from Clostridium difficile., Journal of Clinical Investigation, vol.95, issue.3, pp.1026-1031, 1995.
DOI : 10.1172/JCI117747

I. Just, J. Selzer, M. Wilm, V. Eichel-streiber, C. Mann et al., Glucosylation of Rho proteins by Clostridium difficile toxin B, Nature, vol.375, issue.6531, pp.500-503, 1995.
DOI : 10.1038/375500a0

S. Kuehne, S. Cartman, J. Heap, M. Kelly, and A. Cockayne, 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

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

C. Hennequin, F. Porcheray, A. Waligora-dupriet, A. Collignon, and M. Barc, GroEL (Hsp60) of Clostridium difficile is involved in cell adherence, Microbiology, vol.147, issue.1, pp.87-96, 2001.
DOI : 10.1099/00221287-147-1-87

A. Waligora, C. Hennequin, P. Mullany, P. Bourlioux, and A. Collignon, 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. 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

S. Arora, B. Ritchings, E. Almira, S. Lory, and R. Ramphal, The Pseudomonas aeruginosa flagellar cap protein, FliD, is responsible for mucin adhesion, Infect Immun, vol.66, pp.1000-1007, 1998.

E. Lillehoj, B. Kim, and K. Kim, flagellin as an adhesin for Muc1 mucin, American Journal of Physiology - Lung Cellular and Molecular Physiology, vol.282, issue.4, pp.751-756, 2002.
DOI : 10.1152/ajplung.00383.2001

K. Eaton, S. Suerbaum, C. Josenhans, and S. Krakowka, Colonization of gnotobiotic piglets by Helicobacter pylori deficient in two flagellin genes, Infect Immun, vol.64, pp.2445-2448, 1996.

A. Rabaan, I. Gryllos, J. Tomas, and J. Shaw, Motility and the Polar Flagellum Are Required for Aeromonas caviae Adherence to HEp-2 Cells, Infection and Immunity, vol.69, issue.7, pp.4257-4267, 2001.
DOI : 10.1128/IAI.69.7.4257-4267.2001

E. Mcsweegan and R. Walker, Identification and characterization of two Campylobacter jejuni adhesins for cellular and mucous substrates, Infect Immun, vol.53, pp.141-148, 1986.

C. Dietrich, K. Heuner, B. Brand, J. Hacker, and M. Steinert, Flagellum of Legionella pneumophila Positively Affects the Early Phase of Infection of Eukaryotic Host Cells, Infection and Immunity, vol.69, issue.4, pp.2116-2122, 2001.
DOI : 10.1128/IAI.69.4.2116-2122.2001

C. Grant, M. Konkel, W. Cieplak, J. Tompkins, and L. , Role of flagella in adherence, internalization, and translocation of Campylobacter jejuni in nonpolarized and polarized epithelial cell cultures, Infect Immun, vol.61, pp.1764-1771, 1993.

S. Kirov, M. Castrisios, and J. Shaw, Aeromonas Flagella (Polar and Lateral) Are Enterocyte Adhesins That Contribute to Biofilm Formation on Surfaces, Infection and Immunity, vol.72, issue.4, pp.1939-1945, 2004.
DOI : 10.1128/IAI.72.4.1939-1945.2004

K. Blair, L. Turner, J. Winkelman, H. Berg, and D. Kearns, A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm, Science, vol.320, issue.5883, pp.1636-1638, 2008.
DOI : 10.1126/science.1157877

T. Ethapa, R. Leuzzi, Y. Ng, S. Baban, and R. Adamo, Multiple Factors Modulate Biofilm Formation by the Anaerobic Pathogen Clostridium difficile, J Bacteriol, vol.195, pp.545-555, 2013.

M. Konkel, J. Klena, V. Rivera-amill, M. Monteville, and D. Biswas, Secretion of Virulence Proteins from Campylobacter jejuni Is Dependent on a Functional Flagellar Export Apparatus, Journal of Bacteriology, vol.186, issue.11, pp.3296-3303, 2004.
DOI : 10.1128/JB.186.11.3296-3303.2004

F. Poly, C. Ewing, S. Goon, T. Hickey, and D. Rockabrand, Heterogeneity of a Campylobacter jejuni Protein That Is Secreted through the Flagellar Filament, Infection and Immunity, vol.75, issue.8, pp.3859-3867, 2007.
DOI : 10.1128/IAI.00159-07

Y. Song, J. S. Louie, H. Ng, D. Lau, and R. , FlaC, a protein of Campylobacter jejuni TGH9011 (ATCC43431) secreted through the flagellar apparatus, binds epithelial cells and influences cell invasion, Molecular Microbiology, vol.277, issue.2, pp.541-553, 2004.
DOI : 10.1111/j.1365-2958.2004.04175.x

J. Anderson, T. Smith, and T. Hoover, Sense and sensibility: flagellum-mediated gene regulation, Trends in Microbiology, vol.18, issue.1, pp.30-37, 2010.
DOI : 10.1016/j.tim.2009.11.001

A. Tasteyre, T. Karjalainen, V. Avesani, M. Delmee, and A. Collignon, Molecular Characterization of fliD Gene Encoding Flagellar Cap and Its Expression among Clostridium difficile Isolates from Different Serogroups, Journal of Clinical Microbiology, vol.39, issue.3, pp.1178-1183, 2001.
DOI : 10.1128/JCM.39.3.1178-1183.2001

J. Heap, S. Kuehne, M. Ehsaan, S. Cartman, and C. Cooksley, 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

T. Dingle, G. Mulvey, and G. Armstrong, Mutagenic Analysis of the Clostridium difficile Flagellar Proteins, FliC and FliD, and Their Contribution to Virulence in Hamsters, Infection and Immunity, vol.79, issue.10, pp.4061-4067, 2011.
DOI : 10.1128/IAI.05305-11

R. Stabler, M. He, L. Dawson, M. Martin, and E. Valiente, 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

A. Tasteyre, T. Karjalainen, V. Avesani, M. Delmee, and A. Collignon, Phenotypic and genotypic diversity of the flagellin gene (fliC) among Clostridium difficile isolates from different serogroups, J Clin Microbiol, vol.38, pp.3179-3186, 2000.

S. Baban, S. Kuehne, A. Barketi-klai, S. Cartman, and M. Kelly, The Role of Flagella in Clostridium difficile Pathogenesis: Comparison between a Non-Epidemic and an Epidemic Strain, PLoS ONE, vol.29, issue.9, p.73026, 2013.
DOI : 10.1371/journal.pone.0073026.s006

A. Aubry, G. Hussack, W. Chen, R. Kuolee, and S. Twine, Modulation of Toxin Production by the Flagellar Regulon in Clostridium difficile, Infection and Immunity, vol.80, issue.10, pp.3521-3532, 2012.
DOI : 10.1128/IAI.00224-12

S. Twine, C. Reid, A. A. Mcmullin, D. Fulton, and K. , Motility and Flagellar Glycosylation in Clostridium difficile, Journal of Bacteriology, vol.191, issue.22, pp.7050-7062, 2009.
DOI : 10.1128/JB.00861-09

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

F. Chevance and K. Hughes, Coordinating assembly of a bacterial macromolecular machine, Nature Reviews Microbiology, vol.213, issue.6, pp.455-465, 2008.
DOI : 10.1038/nrmicro1887

F. Detmers, F. Lanfermeijer, and B. Poolman, Peptides and ATP binding cassette peptide transporters, Research in Microbiology, vol.152, issue.3-4, pp.245-258, 2001.
DOI : 10.1016/S0923-2508(01)01196-2

B. Lazazzera, The intracellular function of extracellular signaling peptides, Peptides, vol.22, issue.10, pp.1519-1527, 2001.
DOI : 10.1016/S0196-9781(01)00488-0

K. Hu, M. Saier, and J. , Phylogeny of phosphoryl transfer proteins of the phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system, Research in Microbiology, vol.153, issue.7, pp.405-415, 2002.
DOI : 10.1016/S0923-2508(02)01339-6

S. Poncet, E. Milohanic, A. Maze, N. Abdallah, J. Ake et al., Correlations between Carbon Metabolism and Virulence in Bacteria, Contrib Microbiol, vol.16, pp.88-102, 2009.
DOI : 10.1159/000219374

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

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 : 10.1111/j.1365-2958.2010.07495.x

A. Antunes, E. Camiade, M. Monot, E. Courtois, and F. Barbut, 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

W. Konings, Microbial transport: Adaptations to natural environments, Antonie van Leeuwenhoek, vol.18, issue.4, pp.325-342, 2006.
DOI : 10.1007/s10482-006-9089-3

K. Stephenson and R. Lewis, Molecular insights into the initiation of sporulation in Gram-positive bacteria: new technologies for an old phenomenon, FEMS Microbiology Reviews, vol.29, issue.2, pp.281-301, 2005.
DOI : 10.1016/j.fmrre.2004.10.003

P. Permpoonpattana, E. Tolls, R. Nadem, S. Tan, and A. Brisson, Surface Layers of Clostridium difficile Endospores, Journal of Bacteriology, vol.193, issue.23, pp.6461-6470, 2011.
DOI : 10.1128/JB.05182-11

R. Stabler, E. Valiente, L. Dawson, M. He, and J. Parkhill, 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

C. Janoir, C. Deneve, S. Bouttier, F. Barbut, and S. Hoys, 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

V. Molle, M. Fujita, S. Jensen, P. Eichenberger, and J. Gonzalez-pastor, The Spo0A regulon of Bacillus subtilis, Molecular Microbiology, vol.10, issue.5, pp.1683-1701, 2003.
DOI : 10.1046/j.1365-2958.2003.03818.x

URL : https://hal.archives-ouvertes.fr/hal-00314423

S. Kuehne, M. Collery, M. Kelly, S. Cartman, and A. Cockayne, Importance of Toxin A, Toxin B, and CDT in Virulence of an Epidemic Clostridium difficile Strain, Journal of Infectious Diseases, vol.209, issue.1, pp.83-86, 2014.
DOI : 10.1093/infdis/jit426

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.1, pp.24-28, 2009.
DOI : 10.1016/S0924-8579(09)70012-3

A. Kovacs-simon, R. Titball, and S. Michell, Lipoproteins of Bacterial Pathogens, Infection and Immunity, vol.79, issue.2, pp.548-561, 2011.
DOI : 10.1128/IAI.00682-10

A. Boetzkes, K. Felkel, J. Zeiser, N. Jochim, and I. Just, Secretome analysis of Clostridium difficile strains, Archives of Microbiology, vol.44, issue.10, pp.675-687, 2012.
DOI : 10.1007/s00203-012-0802-5

C. Dong, L. Major, V. Srikannathasan, J. Errey, and M. Giraud, RmlC, a C3??? and C5??? Carbohydrate Epimerase, Appears to Operate via an Intermediate with an Unusual Twist Boat Conformation, Journal of Molecular Biology, vol.365, issue.1, pp.146-159, 2007.
DOI : 10.1016/j.jmb.2006.09.063

Y. Tsukioka, Y. Yamashita, T. Oho, Y. Nakano, and T. Koga, Biological function of the dTDP-rhamnose synthesis pathway in Streptococcus mutans., Journal of Bacteriology, vol.179, issue.4, pp.1126-1134, 1997.
DOI : 10.1128/jb.179.4.1126-1134.1997

Y. Yamashita, K. Tomihisa, Y. Nakano, Y. Shimazaki, and T. Oho, Recombination between gtfB and gtfC is required for survival of a dTDPrhamnose synthesis-deficient mutant of Streptococcus mutans in the presence of sucrose, Infect Immun, vol.67, pp.3693-3697, 1999.

A. Strom and I. Kaasen, Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression, Molecular Microbiology, vol.217, issue.2, pp.205-210, 1993.
DOI : 10.1016/0923-2508(91)90094-Q

L. Dawson, E. Donahue, S. Cartman, R. Barton, and J. Bundy, The analysis of para-cresol production and tolerance in Clostridium difficile 027 and 012 strains, BMC Microbiology, vol.11, issue.1, p.86, 2011.
DOI : 10.1046/j.1365-2958.2002.03134.x

L. Dawson, R. Stabler, and B. Wren, Assessing the role of p-cresol tolerance in Clostridium difficile, Journal of Medical Microbiology, vol.57, issue.6, pp.745-749, 2008.
DOI : 10.1099/jmm.0.47744-0

T. Selmer and P. Andrei, Clostridium difficile, European Journal of Biochemistry, vol.55, issue.Suppl. C, pp.1363-1372, 2001.
DOI : 10.1046/j.1432-1327.2001.02001.x

M. Sebaihia, B. Wren, P. Mullany, N. Fairweather, and N. Minton, The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome, Nature Genetics, vol.21, issue.7, pp.779-786, 2006.
DOI : 10.1038/ng1830

M. Martin, C. S. Goulding, D. Faulds-pain, A. Barquist, and L. , 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

C. Litwin and S. Calderwood, Role of iron in regulation of virulence genes., Clinical Microbiology Reviews, vol.6, issue.2, pp.137-149, 1993.
DOI : 10.1128/CMR.6.2.137

M. Johnson, M. Sengupta, J. Purves, E. Tarrant, and P. Williams, Fur is required for the activation of virulence gene expression through the induction of the sae regulatory system in Staphylococcus aureus, International Journal of Medical Microbiology, vol.301, issue.1, pp.44-52, 2011.
DOI : 10.1016/j.ijmm.2010.05.003

P. Hoskisson and S. Rigali, Chapter 1 Variation in Form and Function, Adv Appl Microbiol, vol.69, pp.1-22, 2009.
DOI : 10.1016/S0065-2164(09)69001-8

S. Baban, S. Kuehne, A. Barketi-klai, K. Hardie, and I. Kansau, The Role of Flagella in Clostridium difficile Pathogenesis: Comparison between a Non-Epidemic and an Epidemic Strain, PLoS ONE, vol.29, issue.9, 2013.
DOI : 10.1371/journal.pone.0073026.s006

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, 2011.
DOI : 10.1099/jmm.0.029553-0

J. Rouillard, M. Zuker, and E. Gulari, OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach, Nucleic Acids Research, vol.31, issue.12, pp.3057-3062, 2003.
DOI : 10.1093/nar/gkg426

R. Breitling, A. Amtmann, and P. Herzyk, Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments, BMC Bioinformatics, vol.5, issue.1, p.34, 2004.
DOI : 10.1186/1471-2105-5-34

G. Smyth and T. Speed, Normalization of cDNA microarray data, Methods, vol.31, issue.4, pp.265-273, 2003.
DOI : 10.1016/S1046-2023(03)00155-5

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Stat Soc Ser B, vol.57, pp.289-300, 1995.

J. Hellemans, G. Mortier, D. Paepe, A. Speleman, F. Vandesompele et al., qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data, Genome Biology, vol.8, issue.2, p.19, 2007.
DOI : 10.1186/gb-2007-8-2-r19

K. Livak and T. Schmittgen, Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2???????CT Method, Methods, vol.25, issue.4, pp.402-408, 2001.
DOI : 10.1006/meth.2001.1262

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.24894, 2011.
DOI : 10.1371/journal.pone.0024894.t001