L. Sherwood and M. Gorbach, Antibiotics and Clostridium difficile, The New England Journal of Medicine, vol.341, pp.1690-1691, 1999.

V. Loo, L. Poirier, M. Miller, M. Oughton, and M. Libman, ???Associated Diarrhea with High Morbidity and Mortality, New England Journal of Medicine, vol.353, issue.23, pp.2442-2449, 2005.
DOI : 10.1056/NEJMoa051639

M. Merrigan, A. Venugopal, M. Mallozzi, B. Roxas, and V. Viswanathan, 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

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

S. Janezic and M. Rupnik, Molecular Typing Methods for Clostridium difficile: Pulsed-Field Gel Electrophoresis and PCR Ribotyping, 2010.
DOI : 10.1007/978-1-60327-365-7_4

A. Indra, M. Blaschitz, S. Kernbichler, U. Reischl, and G. Wewalka, Mechanisms behind variation in the Clostridium difficile 16S-23S rRNA intergenic spacer region, Journal of Medical Microbiology, vol.59, issue.11, pp.1317-1323, 2010.
DOI : 10.1099/jmm.0.020792-0

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

V. Forgetta, M. Oughton, P. Marquis, I. Brukner, and R. Blanchette, Fourteen-Genome Comparison Identifies DNA Markers for Severe-Disease-Associated Strains of Clostridium difficile, Journal of Clinical Microbiology, vol.49, issue.6, pp.2230-2238, 2011.
DOI : 10.1128/JCM.00391-11

M. He, F. Miyajima, P. Roberts, L. Ellison, and D. Pickard, Emergence and global spread of epidemic healthcare-associated Clostridium difficile, Nature Genetics, vol.377, issue.1, 2012.
DOI : 10.1093/molbev/msi103

M. He, M. Sebaihia, T. Lawley, R. Stabler, and L. Dawson, Evolutionary dynamics of Clostridium difficile over short and long time scales, Proceedings of the National Academy of Sciences, vol.107, issue.16, pp.7527-7532, 2010.
DOI : 10.1073/pnas.0914322107

C. Knetsch, E. Terveer, C. Lauber, A. Gorbalenya, and C. Harmanus, Comparative analysis of an expanded Clostridium difficile reference strain collection reveals genetic diversity and evolution through six lineages, Infection, Genetics and Evolution, vol.12, issue.7, pp.1577-1585, 2012.
DOI : 10.1016/j.meegid.2012.06.003

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

M. Bauer, D. Notermans, B. Benthem, J. Brazier, and M. Wilcox, Clostridium difficile infection in Europe: a hospital-based survey, The Lancet, vol.377, issue.9759, pp.63-73, 2010.
DOI : 10.1016/S0140-6736(10)61266-4

C. Knetsch, M. Hensgens, C. Harmanus, M. Van-der-bijl, and P. Savelkoul, 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

R. Stabler, L. Dawson, E. Valiente, M. Cairns, and M. Martin, Macro and Micro Diversity of Clostridium difficile Isolates from Diverse Sources and Geographical Locations, PLoS ONE, vol.178, issue.3, p.31559, 2012.
DOI : 10.1371/journal.pone.0031559.s013

F. Barbut and M. Rupnik, Editorial Commentary: 027, 078, and Others: Going Beyond the Numbers (and Away From the Hypervirulence), Clinical Infectious Diseases, vol.55, issue.12, pp.1669-1672, 2012.
DOI : 10.1093/cid/cis790

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

D. 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

S. Altschul, W. Gish, W. Miller, E. Myers, and D. 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

S. Salzberg, A. L. Kasif, S. White, and O. , Microbial gene identification using interpolated Markov models, Nucleic Acids Research, vol.26, issue.2, pp.544-548, 1998.
DOI : 10.1093/nar/26.2.544

A. Delcher, D. Kasif, S. White, O. Salzberg, and S. L. , Improved microbial gene identification with GLIMMER, Nucleic Acids Research, vol.27, issue.23, pp.4636-4641, 1999.
DOI : 10.1093/nar/27.23.4636

A. Delcher, K. Bratke, E. Powers, and S. Salzberg, Identifying bacterial genes and endosymbiont DNA with Glimmer, Bioinformatics, vol.23, issue.6, pp.673-679, 2007.
DOI : 10.1093/bioinformatics/btm009

W. Ludwig, Molecular Phylogeny of Microorganisms: Is rRNA Still a Useful Marker?, 2010.

T. Consortium, Reorganizing the protein space at the Universal Protein Resource (UniProt), Nucleic Acids Research, vol.40, issue.D1, pp.71-75, 2012.
DOI : 10.1093/nar/gkr981

W. Ludwig, O. Strunk, R. Westram, L. Richter, and H. Meier, ARB: a software environment for sequence data, Nucleic Acids Research, vol.32, issue.4, pp.1363-1371, 2004.
DOI : 10.1093/nar/gkh293

M. Rupnik, toxinotypes, FEMS Microbiology Reviews, vol.32, issue.3, pp.541-555, 2008.
DOI : 10.1111/j.1574-6976.2008.00110.x

R. Stabler, D. Gerding, J. Songer, D. Drudy, and J. Brazier, Comparative Phylogenomics of Clostridium difficile Reveals Clade Specificity and Microevolution of Hypervirulent Strains, Journal of Bacteriology, vol.188, issue.20, pp.7297-7305, 2006.
DOI : 10.1128/JB.00664-06

C. Knetsch, T. Lawley, M. Hensgens, J. Corver, and M. Wilcox, Current application and future perspectives of molecular typing methods to study Clostridium difficile infections, 2013.

E. Kuijper, R. Van-den-berg, and J. Brazier, Comparison of Molecular Typig Methods Applied to Clostridium difficile, pp.159-171, 2009.

M. Rupnik, J. Brazier, B. Duerden, M. Grabner, and S. Stubbs, Comparison of toxinotyping and PCR ribotyping of Clostridium difficile strains and description of novel toxinotypes, Microbiology, vol.147, issue.2, pp.439-447, 2001.
DOI : 10.1099/00221287-147-2-439

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. Indra, S. Huhulescu, M. Schneeweis, P. Hasenberger, and S. Kernbichler, Characterization of Clostridium difficile isolates using capillary gel electrophoresis-based PCR ribotyping, Journal of Medical Microbiology, vol.57, issue.11, pp.1377-1382, 2008.
DOI : 10.1099/jmm.0.47714-0