O. Clermont, J. K. Christenson, E. Denamur, and D. M. Gordon, The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups, Environ Microbiol Rep, vol.5, issue.1, pp.58-65, 2013.

S. Lee, J. K. Yu, K. Park, E. J. Oh, S. Y. Kim et al., Phylogenetic groups and virulence factors in pathogenic and commensal strains of Escherichia coli and their association with blaCTX-M, Ann Clin Lab Sci, vol.2010, issue.4, pp.361-367

G. Piatti, A. Mannini, M. Balistreri, and A. M. Schito, Virulence factors in urinary escherichia coli strains: phylogenetic background and quinolone and fluoroquinolone resistance, J Clin Microbiol, vol.46, issue.2, pp.480-487, 2008.

T. Kudinha, J. R. Johnson, S. D. Andrew, F. Kong, P. Anderson et al., Distribution of phylogenetic groups, sequence type ST131, and virulence-associated traits among Escherichia coli isolates from men with pyelonephritis or cystitis and healthy controls, Clin Microbiol Infect, vol.19, issue.4, pp.173-180, 2013.

R. Koczura and A. Kaznowski, The Yersinia high-pathogenicity island and iron-uptake systems in clinical isolates of Escherichia coli, J Med Microbiol, vol.52, issue.8, pp.637-642, 2003.

F. Feldmann, L. J. Sorsa, K. Hildinger, and S. Schubert, The Salmochelin siderophore receptor IroN contributes to invasion of urothelial cells by extraintestinal pathogenic escherichia coli In Vitro, Infect Immun, vol.75, issue.6, pp.3183-3187, 2007.

Q. Gao, X. Wang, H. Xu, Y. Xu, J. Ling et al., Roles of iron acquisition systems in virulence of extraintestinal pathogenic Escherichia coli: salmochelin and aerobactin contribute more to virulence than heme in a chicken infection model, BMC Microbiol, vol.12, issue.1, p.143, 2012.

E. Antão, L. Wieler, and C. Ewers, Adhesive threads of extraintestinal pathogenic Escherichia coli, Gut Pathogens, vol.1, issue.1, pp.1-12, 2009.

J. R. Johnson, P. Delavari, M. Kuskowski, and A. L. Stell, Phylogenetic distribution of extraintestinal virulence-associated traits in Escherichia coli, J Infect Dis, vol.183, issue.1, pp.78-88, 2001.

K. S. Abdallah, Y. Cao, and D. J. Wei, Epidemiologic investigation of extra-intestinal pathogenic E. coli (ExPEC) based on PCR phylogenetic group and fimH single nucleotide polymorphisms (SNPs) in China, Int J Mol Epidemiol Genet, vol.2011, issue.4, pp.339-353

R. E. Besser, S. M. Lett, J. Weber, M. P. Doyle, T. J. Barrett et al., An outbreak of diarrhea and hemolytic uremic syndrome from escherichia coli o157:h7 in fresh-pressed apple cider, JAMA, vol.269, issue.17, pp.2217-2220, 1993.

M. A. Davis, D. C. Gordon, P. I. Tarr, C. A. Bartleson, J. H. Lewis et al., A multistate outbreak of escherichia coli o157:h7-associated bloody diarrhea and hemolytic uremic syndrome from hamburgers: the washington experience, JAMA, vol.1994, issue.17, pp.1349-1353

M. L. Ackers, B. E. Mahon, E. Leahy, B. Goode, T. Damrow et al., An outbreak of Escherichia coli O157:H7 infections associated with leaf lettuce consumption, J Infect Dis, vol.177, issue.6, pp.1588-1593, 1998.

S. Dundas, W. Todd, A. I. Stewart, P. S. Murdoch, A. Chaudhuri et al., The Central Scotland Escherichia coli O157:H7 outbreak: risk factors for the hemolytic uremic syndrome and death among hospitalized patients, Clin Infect Dis, vol.33, issue.7, pp.923-931, 2001.

H. Rohde, J. Qin, Y. Cui, D. Li, N. J. Loman et al., Open-source genomic analysis of shiga-toxin-producing E. coli O104:H4, N Engl J Med, vol.365, issue.8, pp.718-724, 2011.

L. C. Crossman, R. R. Chaudhuri, S. A. Beatson, T. J. Wells, M. Desvaux et al., A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic escherichia coli strain H10407, J Bacteriol, vol.192, issue.21, pp.5822-5831, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02666623

J. R. Johnson and T. A. Russo, Extraintestinal pathogenic Escherichia coli, J Lab Clin Med, vol.139, issue.3, pp.155-162, 2002.

F. L. Nowrouzian, A. E. Wold, and I. Adlerberth, Escherichia coli strains belonging to phylogenetic group B2 have superior capacity to persist in the intestinal microflora of infants, J Infect Dis, vol.191, issue.7, pp.1078-1083, 2005.

M. Diard, L. Garry, M. Selva, T. Mosser, E. Denamur et al., Pathogenicity-Associated Islands in extraintestinal pathogenic Escherichia coli are fitness elements involved in intestinal colonization, J Bacteriol, vol.192, issue.19, pp.4885-4893, 2010.

F. Nowrouzian, I. Adlerberth, and A. E. Wold, P fimbriae, capsule and aerobactin characterize colonic resident Escherichia coli, Epidemiol Infect, vol.126, issue.1, pp.11-18, 2001.

F. Nowrouzian and A. E. Wold, Adlerberth I: P fimbriae and aerobactin as intestinal colonization factors for Escherichia coli in Pakistani infants, Epidemiol Infect, vol.126, issue.1, pp.19-23, 2001.

A. Iguchi, N. R. Thomson, Y. Ogura, D. Saunders, T. Ooka et al., Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69, J Bacteriol, vol.191, issue.1, pp.347-354, 2009.

S. J. Elliott, L. A. Wainwright, T. K. Mcdaniel, K. G. Jarvis, Y. K. Deng et al., The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69, Mol Microbiol, vol.28, issue.1, pp.1-4, 1998.

M. S. Donnenberg and T. S. Whittam, Pathogenesis and evolution of virulence in enteropathogenic and enterohemorrhagic Escherichia coli, J Clin Investig, vol.107, issue.5, pp.539-548, 2001.

C. Lemaitre, F. Mahjoub-messai, D. Dupont, V. Caro, L. Diancourt et al., A conserved virulence plasmidic region contributes to the virulence of the multiresistant escherichia coli meningitis strain S286 belonging to phylogenetic group C, PLoS ONE, vol.2013, issue.9, p.74423

I. M. Sheldon, A. N. Rycroft, B. Dogan, M. Craven, J. J. Bromfield et al., Specific strains of Escherichia coli are pathogenic for the endometrium of cattle and cause pelvic inflammatory disease in cattle and mice, PLoS ONE, vol.2010, issue.2, p.9192

L. A. Minarini, I. L. Camargo, A. Pitondo-silva, and A. L. Darini, Multilocus sequence typing of uropathogenic ESBL-producing Escherichia coli isolated in a Brazilian community, Curr Microbiol, vol.55, issue.6, pp.524-529, 2007.

G. Wu, M. J. Day, M. T. Mafura, J. Nunez-garcia, J. J. Fenner et al., Comparative analysis of ESBL-positive Escherichia coli isolates from Animals and Humans from the UK, The Netherlands and Germany, PLoS ONE, vol.8, issue.9, p.75392, 2013.

S. Guenther, A. Bethe, A. Fruth, T. Semmler, R. G. Ulrich et al., Frequent combination of antimicrobial multiresistance and extraintestinal pathogenicity in Escherichia coli isolates from urban rats (Rattus norvegicus, PLoS ONE, vol.2012, issue.11, p.50331

T. S. Sankar, G. Neelakanta, V. Sangal, G. Plum, M. Achtman et al., Fate of the H-NS-repressed bgl operon in evolution of Escherichia coli, PLoS Genet, vol.5, issue.3, p.1000405, 2009.

R. R. Simoes, L. Poirel, D. Costa, P. M. Nordmann, and P. , Seagulls and beaches as reservoirs for multidrug-resistant Escherichia coli, Emerg Infect Dis, vol.16, issue.1, pp.110-112, 2010.

X. Qin, F. Hu, S. Wu, X. Ye, D. Zhu et al., Comparison of adhesin genes and antimicrobial susceptibilities between uropathogenic and intestinal commensal Escherichia coli strains, PLoS ONE, vol.2013, issue.4, p.61169

R. J. Goldstone, R. Talbot, H. Schuberth, S. O. Sheldon, I. M. Smith et al., Draft genome sequence of Escherichia coli MS499, isolated from the infected uterus of a postpartum cow with metritis, Genome Announc, vol.2, issue.4, pp.217-231, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02630057

C. Peigne, P. Bidet, F. Mahjoub-messai, C. Plainvert, V. Barbe et al., The plasmid of Escherichia coli strain S88 (O45:K1:H7) that causes neonatal meningitis is closely related to avian pathogenic E. coli plasmids and is associated with high-level bacteremia in a neonatal rat meningitis model, Infect Immun, vol.77, issue.6, pp.2272-2284, 2009.

T. J. Johnson, J. L. Thorsness, C. P. Anderson, A. M. Lynne, S. L. Foley et al., Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica Serovar Kentucky, PLoS ONE, vol.2010, issue.12, p.15524

J. A. Skyberg, T. J. Johnson, J. R. Johnson, C. Clabots, C. M. Logue et al., Acquisition of avian pathogenic Escherichia coli plasmids by a commensal E. coli isolate enhances its abilities to kill chicken embryos, grow in human urine, and colonize the murine kidney, Infect Immun, vol.74, issue.11, pp.6287-6292, 2006.

S. Schubert, B. Picard, S. Gouriou, J. Heesemann, and E. Denamur, Yersinia highpathogenicity island contributes to virulence in Escherichia coli causing extraintestinal infections, Infect Immun, vol.70, issue.9, pp.5335-5337, 2002.

E. Brzuszkiewicz, H. Brüggemann, H. Liesegang, M. Emmerth, T. Ölschläger et al., How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains, Proc Natl Acad Sci, vol.103, issue.34, pp.12879-12884, 2006.

A. Lügering, I. Benz, S. Knochenhauer, M. Ruffing, and M. A. Schmidt, The Pix pilus adhesin of the uropathogenic Escherichia coli strain X2194 (O2 : K? : H6) is related to Pap pili but exhibits a truncated regulatory region, Microbiology, vol.149, issue.6, pp.1387-1397, 2003.

T. A. Russo, S. Wenderoth, U. B. Carlino, J. M. Merrick, and A. J. Lesse, Identification, Genomic Organization, and Analysis of the Group III Capsular Polysaccharide Genes kpsD, kpsM, kpsT, and kpsE from an Extraintestinal Isolate of Escherichia coli (CP9, O4/K54/H5), J Bacteriol, vol.180, issue.2, pp.338-349, 1998.

C. Whitfield and I. S. Roberts, Structure, assembly and regulation of expression of capsules in Escherichia coli, Mol Microbiol, vol.31, issue.5, pp.1307-1319, 1999.

T. Rojas, R. P. Maluta, L. P. Parizzi, L. V. Koenigkan, J. Yang et al., Genome sequences of avian pathogenic escherichia coli strains isolated from Brazilian commercial poultry, Genome Announc, vol.2013, issue.2, pp.110-123

I. Connell, A. W. Klemm, P. Schembri, M. M?rild, S. Svanborg et al., Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract, Proc Natl Acad Sci, vol.93, issue.18, pp.9827-9832, 1996.

F. Hommais, S. Gouriou, C. Amorin, H. Bui, M. C. Rahimy et al., The FimH A27V Mutation Is Pathoadaptive for Urovirulence in Escherichia coli B2 Phylogenetic Group Isolates, Infect Immun, vol.71, issue.6, pp.3619-3622, 2003.

M. Sabri, M. Caza, J. Proulx, M. H. Lymberopoulos, A. Brée et al., Contribution of the SitABCD, MntH, and FeoB metal transporters to the virulence of avian pathogenic Escherichia coli O78 strain ?7122, Infect Immun, vol.76, issue.2, pp.601-611, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-00720797

M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler et al., Gene Ontology: tool for the unification of biology, Nat Genet, vol.25, issue.1, pp.25-29, 2000.

N. Y. Yu, J. R. Wagner, M. R. Laird, M. G. Rey, S. Lo et al., PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes, Bioinformatics, vol.2010, issue.13, pp.1608-1615

T. J. Johnson and L. K. Nolan, Pathogenomics of the virulence plasmids of Escherichia coli, Microbiol Mol Biol Rev, vol.73, issue.4, pp.750-774, 2009.

S. Schubert, A. Rakin, and J. Heesemann, The Yersinia high-pathogenicity island (HPI): evolutionary and functional aspects, Int J Med Microbiol, vol.294, issue.2-3, pp.83-94, 2004.

C. Laing, C. Buchanan, E. Taboada, Y. Zhang, A. Kropinski et al., Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions, BMC Bioinformatics, vol.11, issue.1, p.461, 2010.

R. C. Bicalho, V. S. Machado, M. Bicalho, R. O. Gilbert, A. Teixeira et al., Molecular and epidemiological characterization of bovine intrauterine Escherichia coli, J Dairy Sci, vol.93, issue.12, pp.5818-5830, 2010.

D. Hyatt, G. Chen, P. Locascio, M. Land, F. Larimer et al., Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, issue.1, p.119, 2010.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, issue.3, pp.403-410, 1990.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, issue.5, pp.1792-1797, 2004.

S. Guindon, J. F. Dufayard, W. Hordijk, V. Lefort, and O. Gascuel, PhyML: fast and accurate phylogeny reconstruction by maximum likelihood, Infect Genet Evol, vol.9, issue.3, pp.384-385, 2009.

R. G. Fitzjohn, Diversitree: comparative phylogenetic analyses of diversification in R, Methods Ecol Evol, vol.2012, issue.6, pp.1084-1092

E. Paradis, J. Claude, and K. Strimmer, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
URL : https://hal.archives-ouvertes.fr/ird-01887318

S. Dray and A. Dufour, The ade4 package: implementing the duality diagram for ecologists, J Stat Softw, vol.22, issue.4, pp.1-20, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00434575

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., Genome Project Data Processing S: the sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.

R. , A Language and Environment for Statistical Computing, 2013.

E. Dimmer, R. Huntley, Y. Alam-faruque, T. Sawford, C. O'donovan et al., The UniProt-GO annotation database in 2011, Nucleic Acids Res, vol.40, pp.565-570, 2012.

A. Conesa, S. Gotz, J. M. Garcia-gomez, J. Terol, M. Talon et al., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, issue.18, pp.3674-3676, 2005.

S. Falcon and R. Gentleman, Using GOstats to test gene lists for GO term association, Bioinformatics, vol.23, issue.2, pp.257-258, 2007.

. Goldstone, Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity, BMC Genomics, vol.15, p.1075, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02635289