W. Ahmed, R. Neller, and M. Katouli, Host Species-Specific Metabolic Fingerprint Database for Enterococci and Escherichia coli and Its Application To Identify Sources of Fecal Contamination in Surface Waters, Applied and Environmental Microbiology, vol.71, issue.8, pp.4461-4468, 2005.
DOI : 10.1128/AEM.71.8.4461-4468.2005

L. Armand-lefevre, R. Ruimy, and A. Andremont, Isolates from Healthy Pig Farmers, Human Controls, and Pigs, Emerging Infectious Diseases, vol.11, issue.5, pp.711-714, 2005.
DOI : 10.3201/eid1105.040866
URL : http://doi.org/10.3201/eid1105.040866

M. Bingen-bidois, O. Clermont, S. Bonacorsi, M. Terki, N. Brahimi et al., Phylogenetic Analysis and Prevalence of Urosepsis Strains of Escherichia coli Bearing Pathogenicity Island-Like Domains, Infection and Immunity, vol.70, issue.6, pp.3216-3226, 2002.
DOI : 10.1128/IAI.70.6.3216-3226.2002

O. Clermont, S. Bonacorsi, and E. Bingen, Rapid and Simple Determination of the Escherichia coli Phylogenetic Group, Applied and Environmental Microbiology, vol.66, issue.10, pp.4555-4558, 2000.
DOI : 10.1128/AEM.66.10.4555-4558.2000

F. M. Cohan, Genetic exchange and evolutionary divergence in prokaryotes, Trends in Ecology & Evolution, vol.9, issue.5, pp.175-180, 1994.
DOI : 10.1016/0169-5347(94)90081-7

P. Desjardins, B. Picard, B. Kaltenbock, J. Elion, and E. Denamur, Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism, Journal of Molecular Evolution, vol.18, issue.4, pp.440-448, 1995.
DOI : 10.1007/BF00160315

M. Donnenberg, Escherichia coli virulence mechanisms of versatile pathogen, 2002.

. Denamur, Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations, Microbiology, vol.147, pp.1671-1676, 2001.

. Denamur, A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli, Mol. Biol. Evol, vol.21, pp.1085-1094, 2004.

M. C. Picard, A. Rahimy, E. Andremont, R. Denamur, and . Ruimy, Large-scale population structure of human commensal Escherichia coli isolates, Appl. Environ. Microbiol, vol.70, pp.5698-5700, 2004.

D. M. Gordon, Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination, Microbiology, vol.147, issue.5, pp.1079-1085, 2001.
DOI : 10.1099/00221287-147-5-1079

D. M. Gordon and A. Cowling, The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects, Microbiology, vol.149, issue.12, pp.3575-3586, 2003.
DOI : 10.1099/mic.0.26486-0

P. Goullet and B. Picard, Comparative Esterase Electrophoretic Polymorphism of Escherichia coli Isolates Obtained from Animal and Human Sources, Microbiology, vol.132, issue.7, pp.1843-1851, 1986.
DOI : 10.1099/00221287-132-7-1843

P. G. Hartel, J. D. Summer, J. L. Hill, J. V. Collins, J. A. Entry et al., Geographic Variability of Ribotypes from Animals in Idaho and Georgia, Journal of Environment Quality, vol.31, issue.4, pp.1273-1278, 2002.
DOI : 10.2134/jeq2002.1273

P. G. Hartel, J. D. Summer, and W. I. Segars, Deer diet affects ribotype diversity of Escherichia coli for bacterial source tracking, Water Research, vol.37, issue.13, pp.3263-3268, 2003.
DOI : 10.1016/S0043-1354(03)00170-2

P. J. Herzer, S. Inouye, M. Inouye, and T. S. Whittam, Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli., Journal of Bacteriology, vol.172, issue.11, pp.6175-6181, 1990.
DOI : 10.1128/jb.172.11.6175-6181.1990

J. R. Johnson, P. Goullet, B. Picard, S. L. Moseley, P. L. Roberts et al., Association of carboxylesterase B electrophoretic pattern with presence and expression of urovirulence factor determinants and antimicrobial resistance among strains of Escherichia coli that cause urosepsis, Infect. Immun, vol.59, pp.2311-2315, 1991.

. Sadowsky, Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution, Appl. Environ. Microb, vol.70, pp.4478-4485, 2004.

B. Levin, The Evolution and Maintenance of Virulence in Microparasites, Emerging Infectious Diseases, vol.2, issue.2, pp.93-102, 1996.
DOI : 10.3201/eid0202.960203

M. Smith and J. , The Population Genetics of Bacteria, Proceedings of the Royal Society B: Biological Sciences, vol.245, issue.1312, pp.37-41, 1991.
DOI : 10.1098/rspb.1991.0085

I. Mühldorfer and J. Hacker, Genetic aspects of Escherichia coli virulence, Microbial Pathogenesis, vol.16, issue.3, pp.171-181, 1994.
DOI : 10.1006/mpat.1994.1018

E. Nevo, Genetic Diversity in Nature, Evolutionary Biology, vol.23, pp.217-247, 1988.
DOI : 10.1007/978-1-4613-1043-3_6

E. Nevo, Evolution of genome-phenome diversity under environmental stress, Proc. Natl. Acad. Sci. USA, pp.6233-6240, 2001.
DOI : 10.1073/pnas.101109298

B. Picard, J. Garcia, S. Gouriou, P. Duriez, N. Brahimi et al., The link between phylogeny and virulence in Escherichia coli extraintestinal infection, Infect. Immun, vol.67, pp.546-553, 1999.

J. L. Ram, R. P. Ritchie, J. Fang, F. S. Gonzales, and J. P. Selegean, Sequence-Based Source Tracking of Based on Genetic Diversity of ??-Glucuronidase, Journal of Environment Quality, vol.33, issue.3, pp.1024-1032, 2004.
DOI : 10.2134/jeq2004.1024

S. Schubert, B. Picard, S. Gouriou, J. Heesemann, and E. Denamur, Yersinia High-Pathogenicity Island Contributes to Virulence in Escherichia coli Causing Extraintestinal Infections, Infection and Immunity, vol.70, issue.9, pp.5335-5337, 2002.
DOI : 10.1128/IAI.70.9.5335-5337.2002

R. Selander, D. Caugant, and T. Whittnam, Genetic structure and variation in natural populations of Escherichia coli Escherichia coli and Salmonella typhimurium: cellular and molecular biology, pp.1625-1648, 1987.

R. Andremont and . Ruimy, Integron-associated antibiotic resistance and phylogenetic grouping of Escherichia coli isolates from healthy subjects free of recent antibiotic exposure, Antimicrob Agents Chemother, vol.49, pp.3062-3065, 2005.

V. Souza, M. Rocha, A. Valera, and L. E. Eguiarte, Genetic structure of natural populations of Escherichia coli in wild hosts on different continents, Appl. Environ. Microbiol, vol.65, pp.3373-3385, 1999.

M. Tenehaus and F. W. Young, An analysis and synthesis of multiple correspondence analysis, optimal scaling, dual scaling, homogeneity analysis and other methods for quantifying categorical multivariate data, Psychometrika, vol.25, issue.2, pp.91-119, 1985.
DOI : 10.1007/BF02294151

L. Van-valen, Morphological Variation and Width of Ecological Niche, The American Naturalist, vol.99, issue.908, pp.377-389, 1965.
DOI : 10.1086/282379

A. E. Wold, D. A. Caugant, G. Lidin-janson, P. De-man, and C. Svanborg, Resident Colonic Escherichia coli Strains Frequently Display Uropathogenic Characteristics, Journal of Infectious Diseases, vol.165, issue.1, pp.46-52, 1992.
DOI : 10.1093/infdis/165.1.46
URL : http://jid.oxfordjournals.org/cgi/content/short/165/1/46