A. Prüss, Review of epidemiological studies on health effects from exposure to recreational water, International Journal of Epidemiology, vol.27, issue.1, pp.1-9, 1998.
DOI : 10.1093/ije/27.1.1

H. Kelsey, D. Porter, G. Scott, M. Neet, and D. White, Using geographic information systems and regression analysis to evaluate relationships between land use and fecal coliform bacterial pollution, Journal of Experimental Marine Biology and Ecology, vol.298, issue.2, pp.197-209, 2004.
DOI : 10.1016/S0022-0981(03)00359-9

R. Muirhead, R. Collins, and P. Bremer, Numbers and transported state of Escherichia coli in runoff direct from fresh cowpats under simulated rainfall*, Letters in Applied Microbiology, vol.31, issue.2, pp.83-87, 2006.
DOI : 10.1111/j.1475-2743.2004.tb00332.x

R. Saini, L. Halverson, and J. Lorimor, Rainfall Timing and Frequency Influence on Leaching of RS2G through Soil Following Manure Application, Journal of Environment Quality, vol.32, issue.5, pp.1865-1872, 2003.
DOI : 10.2134/jeq2003.1865

D. Kay, J. Fleisher, R. Salmon, F. Jones, M. Wyer et al., Predicting likelihood of gastroenteritis from sea bathing: results from randomised exposure, The Lancet, vol.344, issue.8927, pp.905-909, 1994.
DOI : 10.1016/S0140-6736(94)92267-5

I. Van-asperen, G. Medema, M. Borgdorff, M. Sprenger, and A. Havelaar, Risk of gastroenteritis among triathletes in relation to faecal pollution of fresh waters, International Journal of Epidemiology, vol.27, issue.2, pp.309-315, 1998.
DOI : 10.1093/ije/27.2.309

A. Wiedenmann, K. Dietz, and P. Krüger, Epidemiological determination of disease risks from bathing, 2004.

R. Berg, The indigenous gastrointestinal microflora, Trends in Microbiology, vol.4, issue.11, pp.430-435, 1996.
DOI : 10.1016/0966-842X(96)10057-3

D. 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

I. Arana, M. Orruno, D. Perez-pascual, C. Seco, A. Muela et al., Inability of Escherichia coli to resuscitate from the viable but nonculturable state, FEMS Microbiology Ecology, vol.62, issue.1, pp.1-11, 2007.
DOI : 10.1111/j.1574-6941.2007.00362.x

M. Habteselassie, M. Bischoff, E. Blume, B. Applegate, B. Reuhs et al., Environmental Controls on the Fate of Escherichia coli in Soil, Water, Air, and Soil Pollution, vol.67, issue.397, pp.143-155, 2008.
DOI : 10.1007/s11270-007-9587-6

Y. Rozen and S. Belkin, Survival of enteric bacteria in seawater: Table 1, FEMS Microbiology Reviews, vol.25, issue.5, pp.513-529, 2001.
DOI : 10.1111/j.1574-6976.2001.tb00589.x

R. Artz and K. Killham, O157:H7 in private drinking water wells: influences of protozoan grazing and elevated copper concentrations, FEMS Microbiology Letters, vol.216, issue.1, pp.117-122, 2002.
DOI : 10.1111/j.1574-6968.2002.tb11424.x

M. Byappanahalli, R. Whitman, D. Shively, M. Sadowsky, and S. Ishii, Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed, Environmental Microbiology, vol.48, issue.3, pp.504-513, 2006.
DOI : 10.1128/AEM.69.8.4714-4719.2003

S. Walk, E. Alm, L. Calhoun, J. Mladonicky, and T. Whittam, Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches, Environmental Microbiology, vol.61, issue.6, pp.2274-2288, 2007.
DOI : 10.1111/j.1365-2958.2006.05172.x

M. Winfield and E. Groisman, Role of Nonhost Environments in the Lifestyles of Salmonella and Escherichia coli, Applied and Environmental Microbiology, vol.69, issue.7, pp.3687-3694, 2003.
DOI : 10.1128/AEM.69.7.3687-3694.2003

S. Ishii, W. Ksoll, R. Hicks, and M. Sadowsky, Presence and Growth of Naturalized Escherichia coli in Temperate Soils from Lake Superior Watersheds, Applied and Environmental Microbiology, vol.72, issue.1, pp.612-621, 2006.
DOI : 10.1128/AEM.72.1.612-621.2006

M. Power, J. Littlefield-wyer, D. Gordon, D. Veal, and M. Slade, Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes, Environmental Microbiology, vol.15, issue.5, pp.631-640, 2005.
DOI : 10.1046/j.1365-2958.1999.01276.x

A. Farnleitner, N. Kreuzinger, G. Kavka, S. Grillenberger, J. Rath et al., Simultaneous Detection and Differentiation of Escherichia coli Populations from Environmental Freshwaters by Means of Sequence Variations in a Fragment of the beta -D-Glucuronidase Gene, Applied and Environmental Microbiology, vol.66, issue.4, pp.1340-1346, 2000.
DOI : 10.1128/AEM.66.4.1340-1346.2000

J. Ram, R. Ritchie, J. Fang, F. Gonzales, and J. 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

P. Dombek, L. Johnson, S. Zimmerley, and M. Sadowsky, Use of Repetitive DNA Sequences and the PCR To Differentiate Escherichia coli Isolates from Human and Animal Sources, Applied and Environmental Microbiology, vol.66, issue.6, pp.2572-2577, 2000.
DOI : 10.1128/AEM.66.6.2572-2577.2000

L. Johnson, M. Brown, E. Carruthers, J. Ferguson, P. Dombek et al., Sample Size, Library Composition, and Genotypic Diversity among Natural Populations of Escherichia coli from Different Animals Influence Accuracy of Determining Sources of Fecal Pollution, Applied and Environmental Microbiology, vol.70, issue.8, pp.4478-4485, 2004.
DOI : 10.1128/AEM.70.8.4478-4485.2004

C. Carson, B. Shear, and M. Ellersieck, Identification of Fecal Escherichia coli from Humans and Animals by Ribotyping, Applied and Environmental Microbiology, vol.67, issue.4, pp.1503-1507, 2001.
DOI : 10.1128/AEM.67.4.1503-1507.2001

V. Harwood, J. Whitlock, and V. Withington, Classification of Antibiotic Resistance Patterns of Indicator Bacteria by Discriminant Analysis: Use in Predicting the Source of Fecal Contamination in Subtropical Waters, Applied and Environmental Microbiology, vol.66, issue.9, pp.3698-3704, 2000.
DOI : 10.1128/AEM.66.9.3698-3704.2000

A. Vantarakis, D. Venieri, G. Komninou, and M. Papapetropoulou, Differentiation of faecal Escherichia coli from humans and animals by multiple antibiotic resistance analysis, Letters in Applied Microbiology, vol.65, issue.1, pp.71-77, 2006.
DOI : 10.1016/S0924-8579(00)00145-X

D. Gordon, O. Clermont, H. Tolley, and E. Denamur, Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method, Environmental Microbiology, vol.60, issue.10, pp.2484-2496, 2008.
DOI : 10.1111/j.1462-2920.2008.01669.x

P. Herzer, S. Inouye, M. Inouye, and T. 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

T. Wirth, D. Falush, R. Lan, F. Colles, P. Mensa et al., Sex and virulence in Escherichia coli: an evolutionary perspective, Molecular Microbiology, vol.179, issue.5, pp.1136-1151, 2006.
DOI : 10.1111/j.1365-2958.2005.04985.x

URL : https://hal.archives-ouvertes.fr/hal-00174910

O. Tenaillon, D. Skurnik, B. Picard, and E. Denamur, The population genetics of commensal Escherichia coli, Nature Reviews Microbiology, vol.75, issue.3, pp.207-217, 2010.
DOI : 10.1038/nrmicro2298

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.

P. Duriez, O. Clermont, S. Bonacorsi, E. Bingen, A. Chaventre et al., Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations, Microbiology, vol.147, issue.6, pp.1671-1676, 2001.
DOI : 10.1099/00221287-147-6-1671

P. Escobar-paramo, K. Grenet, L. Menac-'h, A. Rode, L. Salgado et al., Large-Scale Population Structure of Human Commensal Escherichia coli Isolates, Applied and Environmental Microbiology, vol.70, issue.9, pp.5698-5700, 2004.
DOI : 10.1128/AEM.70.9.5698-5700.2004

D. Skurnik, D. Bonnet, C. Bernede-bauduin, R. Michel, C. Guette et al., with changing environments, Environmental Microbiology, vol.60, issue.8, pp.2132-2137, 2008.
DOI : 10.1111/j.1462-2920.2008.01636.x

O. Clermont, M. Lescat, O. Brien, C. Gordon, D. Tenaillon et al., Evidence for a human-specific Escherichia coli clone, Environmental Microbiology, vol.65, issue.4, pp.1000-1006, 2008.
DOI : 10.1111/j.1365-2958.2006.05172.x

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

P. Escobar-paramo, L. Menac-'h, L. Gall, T. Amorin, C. Gouriou et al., Identification of forces shaping the commensal Escherichia coli genetic structure by comparing animal and human isolates, Environmental Microbiology, vol.165, issue.11, pp.1975-1984, 2006.
DOI : 10.1086/282379

URL : https://hal.archives-ouvertes.fr/hal-00554799

S. Walk, J. Mladonicky, J. Middleton, A. Heidt, J. Cunningham et al., Influence of Antibiotic Selection on Genetic Composition of Escherichia coli Populations from Conventional and Organic Dairy Farms, Applied and Environmental Microbiology, vol.73, issue.19, pp.5982-5989, 2007.
DOI : 10.1128/AEM.00709-07

L. Dussart-baptista, N. Massei, J. Dupont, and T. Jouenne, Transfer of bacteria-contaminated particles in a karst aquifer: evolution of contaminated materials from a sinkhole to a spring, Journal of Hydrology, vol.284, issue.1-4, pp.285-295, 2003.
DOI : 10.1016/j.jhydrol.2003.08.007

D. Skurnik, R. Ruimy, A. Andremont, C. Amorin, P. Rouquet et al., Effect of human vicinity on antimicrobial resistance and integrons in animal faecal Escherichia coli, Journal of Antimicrobial Chemotherapy, vol.57, issue.6, pp.1215-1219, 2006.
DOI : 10.1093/jac/dkl122

S. Walk, E. Alm, D. Gordon, J. Ram, G. Toranzos et al., Cryptic Lineages of the Genus Escherichia, Applied and Environmental Microbiology, vol.75, issue.20, pp.6534-6544, 2009.
DOI : 10.1128/AEM.01262-09

G. Reischer, J. Haider, R. Sommer, H. Stadler, K. Keiblinger et al., Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics, Environmental Microbiology, vol.73, issue.10, pp.2598-2608, 2008.
DOI : 10.1111/j.1462-2920.2008.01682.x

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

O. Clermont, J. Johnson, M. Menard, and E. Denamur, Determination of Escherichia coli O types by allele-specific polymerase chain reaction: application to the O types involved in human septicemia, Diagnostic Microbiology and Infectious Disease, vol.57, issue.2, pp.129-136, 2007.
DOI : 10.1016/j.diagmicrobio.2006.08.007

. Comité, Antibiogramme de la Société Française de Microbiologie: Communiqué du comité de l'antibiogramme de la société française de microbiologie, pp.2-13, 2001.