S. Abraham, D. J. Trott, D. Jordan, D. M. Gordon, M. D. Groves et al., Phylogenetic and molecular insights into the evolution of multidrug-resistant porcine enterotoxigenic Escherichia coli in Australia, International Journal of Antimicrobial Agents, vol.44, issue.2, pp.105-116, 2014.
DOI : 10.1016/j.ijantimicag.2014.04.011

J. Achenbach and K. H. Nierhaus, The mechanics of ribosomal translocation, Biochimie, vol.114, pp.80-89, 2015.
DOI : 10.1016/j.biochi.2014.12.003

A. M. Ahmed and T. Shimamoto, Molecular analysis of multidrug resistance in Shiga toxin-producing Escherichia coli O157:H7 isolated from meat and dairy products, International Journal of Food Microbiology, vol.193, pp.68-73, 2015.
DOI : 10.1016/j.ijfoodmicro.2014.10.014

R. P. Ambler, The Structure of <latex>$\beta$</latex>-Lactamases, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.289, issue.1036, pp.321-352, 1980.
DOI : 10.1098/rstb.1980.0049

. Anses-anmv, Suivi des ventes de médicaments vétérinaires contenant des antibiotiques en France 2013. Volumes et estimation de l'exposition des animaux aux antibiotiques, 2014.

F. Ashton, Multilocus Enzyme Electrophoresis ??? Application to the Study of Meningococcal Meningitis and Listeriosis, Canadian Journal of Infectious Diseases, vol.1, issue.4, pp.146-154, 1990.
DOI : 10.1155/1990/960793

S. Barth, S. Duncker, J. Hempe, G. Breves, G. Baljer et al., Nissle 1917 for probiotic use in piglets: evidence for intestinal colonization, Journal of Applied Microbiology, vol.9, issue.5, pp.1697-710, 2009.
DOI : 10.1111/j.1365-2672.2009.04361.x

S. M. Bearson, H. K. Allen, B. L. Bearson, T. Looft, B. W. Brunelle et al., Profiling the gastrointestinal microbiota in response to Salmonella: Low versus high Salmonella shedding in the natural porcine host, Infection, Genetics and Evolution, vol.16, pp.330-370, 2013.
DOI : 10.1016/j.meegid.2013.03.022

A. K. Bej, J. L. Dicesare, L. Haff, and R. M. Atlas, Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uid, Appl Environ Microbiol, vol.57, pp.1013-1020, 1991.

G. S. Bhulibhamon, Transfer of resistance from pig manure to agricultural fields-A field study, RD ASM Conference on AMR in Zoonotic Bacteria and Foodborne Pathogens, p.35, 2012.

M. Bielaszewska, T. Aldick, A. Bauwens, and H. Karch, Hemolysin of enterohemorrhagic Escherichia coli: Structure, transport, biological activity and putative role in virulence, International Journal of Medical Microbiology, vol.304, issue.5-6, pp.521-530, 2014.
DOI : 10.1016/j.ijmm.2014.05.005

M. Bielaszewska, U. Dobrindt, J. Gartner, I. Gallitz, J. Hacker et al., Aspects of genome plasticity in pathogenic Escherichia coli, International Journal of Medical Microbiology, vol.297, issue.7-8, pp.625-664, 2007.
DOI : 10.1016/j.ijmm.2007.03.001

M. Bielaszewska, R. Prager, R. Kock, A. Mellmann, W. Zhang et al., Shiga Toxin Gene Loss and Transfer In Vitro and In Vivo during Enterohemorrhagic Escherichia coli O26 Infection in Humans, Applied and Environmental Microbiology, vol.73, issue.10, pp.3144-50, 2007.
DOI : 10.1128/AEM.02937-06

E. Bok, J. Mazurek, P. Pusz, M. Stosik, and K. Baldy-chudzik, Age as a factor influencing diversity of commensal E. coli microflora in pigs, Pol J Microbiol, vol.62, pp.165-71, 2013.

A. D. Brabban, E. Hite, and T. R. Callaway, Evolution of Foodborne Pathogens via Temperate Bacteriophage-Mediated Gene Transfer, Foodborne Pathogens and Disease, vol.2, issue.4, pp.287-303, 2005.
DOI : 10.1089/fpd.2005.2.287

H. Brugère, F. Auvray, P. Mariani-kurkdjian, A. King, and E. Loukiadis, E. coli producteurs de shigatoxines (STEC) : définitions, virulence et propriétés des souches entérohémorragiques (EHEC) Bulletin épidémiologique, santé animale et alimentation 50, pp.23-31, 2012.

K. Bush, G. A. Jacoby, and A. A. Medeiros, A functional classification scheme for beta-lactamases and its correlation with molecular structure, Antimicrobial Agents and Chemotherapy, vol.39, issue.6, pp.1211-1244, 1995.
DOI : 10.1128/AAC.39.6.1211

R. Canton, J. M. Gonzalez-alba, and J. C. Galan, CTX-M Enzymes: Origin and Diffusion, Frontiers in Microbiology, vol.3, p.110, 2012.
DOI : 10.3389/fmicb.2012.00110

A. Caprioli, S. Morabito, H. Brugere, and E. Oswald, : emerging issues on virulence and modes of transmission, Veterinary Research, vol.36, issue.3, pp.289-311, 2005.
DOI : 10.1051/vetres:2005002

A. Carattoli, Resistance Plasmid Families in Enterobacteriaceae, Antimicrobial Agents and Chemotherapy, vol.53, issue.6, pp.2227-2265, 2009.
DOI : 10.1128/AAC.01707-08

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687249

A. Carattoli, A. Bertini, L. Villa, V. Falbo, K. L. Hopkins et al., Identification of plasmids by PCR-based replicon typing, Journal of Microbiological Methods, vol.63, issue.3, pp.219-247, 2005.
DOI : 10.1016/j.mimet.2005.03.018

A. Carattoli, E. Zankari, A. Garcia-fernandez, M. Voldby-larsen, O. Lund et al., In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing, Antimicrobial Agents and Chemotherapy, vol.58, issue.7, pp.3895-903, 2014.
DOI : 10.1128/AAC.02412-14

C. Carlos, M. M. Pires, N. C. Stoppe, E. M. Hachich, M. I. Sato et al., Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination, BMC Microbiology, vol.10, issue.1, p.161, 2010.
DOI : 10.1186/1471-2180-10-161

R. R. Chaudhuri and I. R. Henderson, The evolution of the Escherichia coli phylogeny, Infection, Genetics and Evolution, vol.12, issue.2, pp.214-240, 2012.
DOI : 10.1016/j.meegid.2012.01.005

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.4555-4563, 2000.
DOI : 10.1128/AEM.66.10.4555-4558.2000

O. Clermont, J. K. Christenson, E. Denamur, and D. M. Gordon, phylo-typing method revisited: improvement of specificity and detection of new phylo-groups, Environmental Microbiology Reports, vol.1, issue.1, pp.58-65, 2013.
DOI : 10.1111/1758-2229.12019

O. Clermont, M. Lavollay, S. Vimont, C. Deschamps, C. Forestier et al., The CTX-M-15-producing Escherichia coli diffusing clone belongs to a highly virulent B2 phylogenetic subgroup, Journal of Antimicrobial Chemotherapy, vol.61, issue.5, pp.1024-1032, 2008.
DOI : 10.1093/jac/dkn084

O. Clermont, M. Lescat, C. L. O-'brien, D. M. Gordon, O. 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

M. Couturier, F. Bex, P. L. Bergquist, and W. K. Maas, Identification and classification of bacterial plasmids, Microbiol Rev, vol.52, pp.375-95, 1988.

L. Crouzet, L. Rigottier-gois, and P. Serror, Potential use of probiotic and commensal bacteria as non-antibiotic strategies against vancomycin-resistant enterococci, FEMS Microbiology Letters, vol.362, issue.8, p.12, 2015.
DOI : 10.1093/femsle/fnv012

M. A. Croxen and B. B. Finlay, Molecular mechanisms of Escherichia coli pathogenicity, Nat Rev Microbiol, vol.8, pp.26-38, 2010.

D. , A. M. Arena, F. Pallecchi, L. Rossolini, and G. M. , ) CTX-M-type beta-lactamases: a successful story of antibiotic resistance, Int J Med Microbiol, vol.303, pp.305-322, 2013.

U. Dobrindt, (Patho-)Genomics of Escherichia coli, International Journal of Medical Microbiology, vol.295, issue.6-7, pp.357-71, 2005.
DOI : 10.1016/j.ijmm.2005.07.009

J. Dolezel, J. Bartos, H. Voglmayr, and J. Greilhuber, Nuclear DNA content and genome size of trout and human, Cytometry A, vol.51, issue.9, pp.127-135, 2003.

E. G. Dudley, C. Abe, J. M. Ghigo, P. Latour-lambert, J. C. Hormazabal et al., An IncI1 Plasmid Contributes to the Adherence of the Atypical Enteroaggregative Escherichia coli Strain C1096 to Cultured Cells and Abiotic Surfaces, Infection and Immunity, vol.74, issue.4, pp.2102-2116, 2006.
DOI : 10.1128/IAI.74.4.2102-2114.2006

P. Duriez and E. Topp, Temporal Dynamics and Impact of Manure Storage on Antibiotic Resistance Patterns and Population Structure of Escherichia coli Isolates from a Commercial Swine Farm, Applied and Environmental Microbiology, vol.73, issue.17, pp.5486-93, 2007.
DOI : 10.1128/AEM.00218-07

J. Ellem, S. R. Partridge, and J. R. Iredell, Efficient Direct Extended-Spectrum ??-Lactamase Detection by Multiplex Real-Time PCR: Accurate Assignment of Phenotype by Use of a Limited Set of Genetic Markers, Journal of Clinical Microbiology, vol.49, issue.8, pp.3074-3081, 2011.
DOI : 10.1128/JCM.02647-10

C. Ewers, M. Grobbel, I. Stamm, P. A. Kopp, I. Diehl et al., Emergence of human pandemic O25:H4-ST131 CTX-M-15 extended-spectrum-??-lactamase-producing Escherichia coli among companion animals, Journal of Antimicrobial Chemotherapy, vol.65, issue.4, pp.651-60, 2010.
DOI : 10.1093/jac/dkq004

F. Who, WHO expert consultation on evaluation of health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria, pp.1-4, 2001.

P. Z. Fekete, E. Brzuszkiewicz, G. Blum-oehler, F. Olasz, M. Szabo et al., DNA sequence analysis of the composite plasmid pTC conferring virulence and antimicrobial resistance for porcine enterotoxigenic Escherichia coli, International Journal of Medical Microbiology, vol.302, issue.1, pp.4-9, 2012.
DOI : 10.1016/j.ijmm.2011.07.003

J. M. Fleckenstein, P. R. Hardwidge, G. P. Munson, D. A. Rasko, H. Sommerfelt et al., Molecular mechanisms of enterotoxigenic Escherichia coli infection, Microbes and Infection, vol.12, issue.2, pp.89-98, 2010.
DOI : 10.1016/j.micinf.2009.10.002

M. A. Fleury, G. Mourand, E. Jouy, F. Touzain, L. Devendec et al., Impact of Ceftiofur Injection on Gut Microbiota and Escherichia coli Resistance in Pigs, Antimicrobial Agents and Chemotherapy, vol.59, issue.9, pp.5171-80, 2015.
DOI : 10.1128/AAC.00177-15

A. C. Fluit and F. J. Schmitz, Resistance integrons and super-integrons, Clinical Microbiology and Infection, vol.10, issue.4, pp.272-88, 2004.
DOI : 10.1111/j.1198-743X.2004.00858.x

URL : http://doi.org/10.1111/j.1198-743x.2004.00858.x

J. P. Furet, O. Firmesse, M. Gourmelon, C. Bridonneau, J. Tap et al., Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR, FEMS Microbiology Ecology, vol.68, issue.3, pp.351-62, 2009.
DOI : 10.1111/j.1574-6941.2009.00671.x

D. Girlich, L. Poirel, A. Carattoli, I. Kempf, M. F. Lartigue et al., Extended-Spectrum ??-Lactamase CTX-M-1 in Escherichia coli Isolates from Healthy Poultry in France, Applied and Environmental Microbiology, vol.73, issue.14, pp.4681-4686, 2007.
DOI : 10.1128/AEM.02491-06

D. M. 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.2484-96, 2008.
DOI : 10.1111/j.1462-2920.2008.01669.x

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.3575-86, 2003.
DOI : 10.1099/mic.0.26486-0

A. Gotz, R. Pukall, E. Smit, E. Tietze, R. Prager et al., Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR, Appl Environ Microbiol, vol.62, pp.2621-2629, 1996.

X. Guo, D. Li, W. Lu, X. Piao, and X. Chen, Screening of Bacillus strains as potential probiotics and subsequent confirmation of the in vivo effectiveness of Bacillus subtilis MA139 in pigs, Antonie van Leeuwenhoek, vol.28, issue.2, 2006.
DOI : 10.1007/s10482-006-9067-9

C. Gyles and P. Boerlin, Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease, Veterinary Pathology, vol.264, issue.2, pp.328-368, 2014.
DOI : 10.1101/gr.134437.111

J. Hacker and E. Carniel, Ecological fitness, genomic islands and bacterial pathogenicity: A Darwinian view of the evolution of microbes, EMBO reports, vol.2, issue.5, pp.376-81, 2001.
DOI : 10.1093/embo-reports/kve097

J. Hacker, B. Hochhut, B. Middendorf, G. Schneider, C. Buchrieser et al., Pathogenomics of mobile genetic elements of toxigenic bacteria, International Journal of Medical Microbiology, vol.293, issue.7-8, pp.453-61, 2004.
DOI : 10.1078/1438-4221-00290

T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii et al., Complete Genome Sequence of Enterohemorrhagic Eschelichia coli O157:H7 and Genomic Comparison with a Laboratory Strain K-12, DNA Research, vol.8, issue.1, pp.11-22, 2001.
DOI : 10.1093/dnares/8.1.11

S. Herold, H. Karch, and H. Schmidt, Shiga toxin-encoding bacteriophages ??? genomes in motion, International Journal of Medical Microbiology, vol.294, issue.2-3, pp.115-136, 2004.
DOI : 10.1016/j.ijmm.2004.06.023

H. Heuer, H. Schmitt, and K. Smalla, Antibiotic resistance gene spread due to manure application on agricultural fields, Current Opinion in Microbiology, vol.14, issue.3, pp.236-279, 2011.
DOI : 10.1016/j.mib.2011.04.009

N. K. Ho, A. C. Henry, K. Johnson-henry, and P. M. Sherman, O157:H7 Infection, Canadian Journal of Gastroenterology, vol.27, issue.5, pp.281-286, 2013.
DOI : 10.1155/2013/138673

C. L. Hofacre, A. C. Johnson, B. J. Kelly, and R. Froyman, Effect of a Commercial Competitive Exclusion Culture on Reduction of Colonization of an Antibiotic-Resistant Pathogenic Escherichia coli in Day-Old Broiler Chickens, Avian Diseases, vol.46, issue.1, pp.198-202, 2002.
DOI : 10.1637/0005-2086(2002)046[0198:EOACCE]2.0.CO;2

D. B. Holman and M. R. Chenier, Antimicrobial use in swine production and its effect on the swine gut microbiota and antimicrobial resistance, Canadian Journal of Microbiology, vol.61, issue.11, pp.785-98, 2015.
DOI : 10.1139/cjm-2015-0239

R. A. Horton, L. P. Randall, E. L. Snary, H. Cockrem, S. Lotz et al., Fecal Carriage and Shedding Density of CTX-M Extended-Spectrum ??-Lactamase-Producing Escherichia coli in Cattle, Chickens, and Pigs: Implications for Environmental Contamination and Food Production, Applied and Environmental Microbiology, vol.77, issue.11, pp.3715-3724, 2011.
DOI : 10.1128/AEM.02831-10

C. Hou, X. Zeng, F. Yang, H. Liu, and S. Qiao, Study and use of the probiotic Lactobacillus reuteri in pigs: a review, Journal of Animal Science and Biotechnology, vol.123, issue.Suppl 1, p.14, 2015.
DOI : 10.1186/s40104-015-0014-3

Y. Huang, X. F. Shan, H. Deng, Y. J. Huang, X. P. Mu et al., Epidemiology, Antimicrobial Resistance and &beta;-lactamase Genotypic Features of Enteropathogenic <i>Escherichia coli</i> Isolated from Children with Diarrhea in Southern China, Japanese Journal of Infectious Diseases, vol.68, issue.3, pp.239-282, 2015.
DOI : 10.7883/yoken.JJID.2014.120

S. K. Jacobi, A. J. Moeser, A. T. Blikslager, J. M. Rhoads, B. A. Corl et al., Acute effects of rotavirus and malnutrition on intestinal barrier function in neonatal piglets, World Journal of Gastroenterology, vol.19, issue.31, pp.5094-102, 2013.
DOI : 10.3748/wjg.v19.i31.5094

B. Jaurin and T. Grundstrom, ampC cephalosporinase of Escherichia coli K-12 has a different evolutionary origin from that of beta-lactamases of the penicillinase type., Proceedings of the National Academy of Sciences, vol.78, issue.8, pp.4897-901, 1981.
DOI : 10.1073/pnas.78.8.4897

C. Jehl and G. Weber, De l???antibiogramme ?? la prescription, Antibiotiques, vol.8, issue.2, 2004.
DOI : 10.1016/S1294-5501(06)77691-9

J. R. Johnson, O. Clermont, B. Johnston, C. Clabots, V. Tchesnokova et al., Rapid and Specific Detection, Molecular Epidemiology, and Experimental Virulence of the O16 Subgroup within Escherichia coli Sequence Type 131, Journal of Clinical Microbiology, vol.52, issue.5, pp.1358-65, 2014.
DOI : 10.1128/JCM.03502-13

T. J. Johnson, E. M. Bielak, D. Fortini, L. H. Hansen, H. Hasman et al., Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae, Plasmid, vol.68, issue.1, pp.43-50, 2012.
DOI : 10.1016/j.plasmid.2012.03.001

M. Juhas, Horizontal gene transfer in human pathogens, Critical Reviews in Microbiology, vol.54, issue.1, pp.101-109, 2015.
DOI : 10.1128/JB.00480-08

B. G. Kelly, A. Vespermann, and D. J. Bolton, The role of horizontal gene transfer in the evolution of selected foodborne bacterial pathogens, Food and Chemical Toxicology, vol.47, issue.5, pp.951-68, 2009.
DOI : 10.1016/j.fct.2008.02.006

I. J. Kempf, E. Granier, S. Bruneau, and M. , L'antibiorésistance des bactéries isolées chez le porc (première partie) Le nouveau praicien vétérinaire, élevages et snaté, pp.189-194, 2014.

M. Kenny, H. Smidt, E. Mengheri, and B. Miller, Probiotics ??? do they have a role in the pig industry?, animal, vol.137, issue.03, pp.462-70, 2011.
DOI : 10.1017/S175173111000193X

C. D. Kohler and U. Dobrindt, What defines extraintestinal pathogenic Escherichia coli?, International Journal of Medical Microbiology, vol.301, issue.8, pp.642-649, 2011.
DOI : 10.1016/j.ijmm.2011.09.006

J. K. Lallès and H. Rothkötter, Bases physiologiques, microbiologiques et immunitaires des troubles digestifs du sevrage chez lz porcelet: données récentes dans le contexte de la suppression des antibiotiques additifs alimentaires, Journées Recherche Porcine, pp.139-50, 2004.

M. Lescat, O. Clermont, P. L. Woerther, J. Glodt, S. Dion et al., strains in Guiana reveal a high genetic diversity with host-dependant population structure, Environmental Microbiology Reports, vol.202, issue.1, pp.49-57, 2013.
DOI : 10.1111/j.1758-2229.2012.00374.x

M. Macvanin and S. Adhya, Architectural organization in E. coli nucleoid, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1819, issue.7, pp.830-835, 2012.
DOI : 10.1016/j.bbagrm.2012.02.012

J. Mainil, Escherichia coli virulence factors, Veterinary Immunology and Immunopathology, vol.152, issue.1-2, pp.2-12, 2013.
DOI : 10.1016/j.vetimm.2012.09.032

L. Melin, S. Mattsson, M. Katouli, and P. Wallgren, Development of Post-weaning Diarrhoea in Piglets. Relation to Presence of Escherichia coli Strains and Rotavirus, Journal of Veterinary Medicine Series B, vol.45, issue.1, pp.12-22, 2004.
DOI : 10.1016/0165-2427(94)90075-2

D. Meunier, E. Jouy, C. Lazizzera, M. Kobisch, and J. Y. Madec, CTX-M-1- and CTX-M-15-type ??-lactamases in clinical Escherichia coli isolates recovered from food-producing animals in France, International Journal of Antimicrobial Agents, vol.28, issue.5, pp.402-409, 2006.
DOI : 10.1016/j.ijantimicag.2006.08.016

URL : https://hal.archives-ouvertes.fr/hal-00420302

C. Milani, C. Ferrario, F. Turroni, S. Duranti, M. Mangifesta et al., The human gut microbiota and its interactive connections to diet, Journal of Human Nutrition and Dietetics, vol.473, issue.Suppl 1, 2016.
DOI : 10.1111/jhn.12371

M. De and L. Foret, Décret n° 2016-317 du 16 mars 2016 relatif à la prescription et à la délivrance des médicaments utilisés en médecine vétérinaire contenant une ou plusieurs substances antibiotiques d'importance critique, 2016.

A. Moodley and L. Guardabassi, Transmission of IncN Plasmids Carrying blaCTX-M-1 between Commensal Escherichia coli in Pigs and Farm Workers, Antimicrobial Agents and Chemotherapy, vol.53, issue.4, pp.1709-1720, 2009.
DOI : 10.1128/AAC.01014-08

M. I. Morosini, A. Valverde, M. Garcia-castillo, P. Nordmann, and R. Canton, Persistent isolation of Salmonella Concord harbouring CTX-M-15, SHV-12 and QnrA1 in an asymptomatic adopted Ethiopian child in Spain also colonized with CTX-M-14- and QnrB-producing Enterobacteriaceae, Journal of Antimicrobial Chemotherapy, vol.65, issue.7, pp.1545-1551, 2010.
DOI : 10.1093/jac/dkq168

J. P. Nataro and J. B. Kaper, Diarrheagenic Escherichia coli, Clin Microbiol Rev, vol.11, pp.142-201, 1998.

K. Nordstrom, Plasmid R1???Replication and its control, Plasmid, vol.55, issue.1, pp.1-26, 2006.
DOI : 10.1016/j.plasmid.2005.07.002

L. Nuotio, C. Schneitz, and O. Nilsson, Effect of competitive exclusion in reducing the occurrence of Escherichia coli producing extended-spectrum ??-lactamases in the ceca of broiler chicks, Poultry Science, vol.92, issue.1, pp.250-254, 2013.
DOI : 10.3382/ps.2012-02575

S. Ochi, T. Shimizu, K. Ohtani, Y. Ichinose, H. Arimitsu et al., Nucleotide sequence analysis of the enterotoxigenic Escherichia coli Ent plasmid, DNA Research, vol.16, issue.5, pp.299-309, 2009.
DOI : 10.1093/dnares/dsp015

H. Ochman and R. K. Selander, Standard reference strains of Escherichia coli from natural populations, J Bacteriol, vol.157, pp.690-693, 1984.

M. Ouellette, L. Bissonnette, and P. H. Roy, Precise insertion of antibiotic resistance determinants into Tn21-like transposons: nucleotide sequence of the OXA-1 beta-lactamase gene., Proceedings of the National Academy of Sciences, vol.84, issue.21, pp.7378-82, 1987.
DOI : 10.1073/pnas.84.21.7378

G. V. Peirano and J. Pitout, Characteristics of infections caused by extended-spectrum blactamase (ESBL)-producing Escherichia coli from community hospitals in South Africa In: Forty-ninth Interscience Conference on Antimicrobial Agents and Chemotherapy, 2010.

A. Perrin, M. Bruneau, P. Houee, C. Poirier, I. Kempf et al., 11 years of monitoring on third-generation-cephalosporins resistance in commensal Escherichia coli from food animals in France, proceedings Antimicrobial resistance in animals and environment, 2011.

Y. Pfeifer, A. Cullik, and W. Witte, Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens, International Journal of Medical Microbiology, vol.300, issue.6, pp.371-380, 2010.
DOI : 10.1016/j.ijmm.2010.04.005

A. Philipon, Les bêta-lactamases à spectre élargi ou étendu(BLSE). Immuno-analyse et biologie spécialisée, pp.287-296, 2013.

M. Pietsch, C. Eller, C. Wendt, M. Holfelder, L. Falgenhauer et al., Molecular characterisation of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates from hospital and ambulatory patients in Germany, Vet Microbiol, 2015.

L. Poirel, R. A. Bonnin, and P. Nordmann, Genetic support and diversity of acquired extended-spectrum ??-lactamases in Gram-negative rods, Infection, Genetics and Evolution, vol.12, issue.5, pp.883-93, 2012.
DOI : 10.1016/j.meegid.2012.02.008

A. Ravi, E. Avershina, J. Ludvigsen, T. M. L-'abee-lund, and K. Rudi, Integrons in the Intestinal Microbiota as Reservoirs for Transmission of Antibiotic Resistance Genes, Pathogens, vol.3, issue.2, pp.238-286, 2014.
DOI : 10.3390/pathogens3020238

R. S. Reis and F. Horn, Enteropathogenic Escherichia coli, Samonella, Shigella and Yersinia: cellular aspects of host-bacteria interactions in enteric diseases, Gut Pathogens, vol.2, issue.1, 2010.
DOI : 10.1186/1757-4749-2-8

E. M. Ribot, M. A. Fair, R. Gautom, D. N. Cameron, S. B. Hunter et al., for PulseNet, Foodborne Pathogens and Disease, vol.3, issue.1, pp.59-67, 2006.
DOI : 10.1089/fpd.2006.3.59

C. M. Robinson, J. F. Sinclair, M. J. Smith, and A. D. O-'brien, Shiga toxin of enterohemorrhagic Escherichia coli type O157:H7 promotes intestinal colonization, Proceedings of the National Academy of Sciences, vol.103, issue.25, pp.9667-72, 2006.
DOI : 10.1073/pnas.0602359103

C. Rodrigues, E. Machado, L. Peixe, and A. Novais, IncI1/ST3 and IncN/ST1 plasmids drive the spread of blaTEM-52 and blaCTX-M-1/-32 in diverse Escherichia coli clones from different piggeries, Journal of Antimicrobial Chemotherapy, vol.68, pp.2245-2253, 2013.
DOI : 10.1093/jac/dkt187

B. A. Rogers, H. E. Sidjabat, and D. L. Paterson, Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain, Journal of Antimicrobial Chemotherapy, vol.66, issue.1, pp.1-14, 2011.
DOI : 10.1093/jac/dkq415

URL : http://jac.oxfordjournals.org/cgi/content/short/66/1/1

P. Sanders, A. Bousquet-melou, C. Chauvin, and P. Toutain, Utilisation des antibiotiques en élevage et enjeux de santé publique, INRA Prod.Anim, vol.24, issue.2, pp.199-204, 2011.

H. Schmidt, M. Bielaszewska, and H. Karch, Transduction of enteric Escherichia coli isolates with a derivative of Shiga toxin 2-encoding bacteriophage phi3538 isolated from Escherichia coli O157:H7, Appl Environ Microbiol, vol.65, pp.3855-61, 1999.

S. N. Seiffert, M. Hilty, V. Perreten, and A. Endimiani, Extended-spectrum cephalosporin-resistant gram-negative organisms in livestock: An emerging problem for human health?, Drug Resistance Updates, vol.16, issue.1-2, pp.22-45, 2013.
DOI : 10.1016/j.drup.2012.12.001

I. Sekirov, S. L. Russell, L. C. Antunes, and B. B. Finlay, Gut Microbiota in Health and Disease, Physiological Reviews, vol.90, issue.3, pp.859-904, 2010.
DOI : 10.1152/physrev.00045.2009

A. L. Servin, Pathogenesis of Human Diffusely Adhering Escherichia coli Expressing Afa/Dr Adhesins (Afa/Dr DAEC): Current Insights and Future Challenges, Clinical Microbiology Reviews, vol.27, issue.4, pp.823-69, 2014.
DOI : 10.1128/CMR.00036-14

D. Smajs, J. Bures, J. Smarda, E. Chaloupkova, J. Kvetina et al., Experimental Administration of the Probiotic Escherichia coli Strain Nissle 1917 Results in Decreased Diversity of E. coli Strains in Pigs, Current Microbiology, vol.51, issue.3, pp.205-215, 2012.
DOI : 10.1007/s00284-011-0051-x

T. B. Stanton and S. B. Humphrey, Persistence of Antibiotic Resistance: Evaluation of a Probiotic Approach Using Antibiotic-Sensitive Megasphaera elsdenii Strains To Prevent Colonization of Swine by Antibiotic-Resistant Strains, Applied and Environmental Microbiology, vol.77, issue.20, pp.7158-66, 2011.
DOI : 10.1128/AEM.00647-11

R. Stenutz, A. Weintraub, and G. Widmalm, O-polysaccharide antigens, FEMS Microbiology Reviews, vol.30, issue.3, pp.382-403, 2006.
DOI : 10.1111/j.1574-6976.2006.00016.x

G. W. Tannock, I. S. Tiong, P. Priest, K. Munro, C. Taylor et al., Testing probiotic strain Escherichia coli Nissle 1917 (Mutaflor) for its ability to reduce carriage of multidrug-resistant E. coli by elderly residents in long-term care facilities, Journal of Medical Microbiology, vol.60, issue.3, pp.366-70, 2011.
DOI : 10.1099/jmm.0.025874-0

D. Timofte, I. E. Maciuca, K. Kemmett, A. Wattret, and N. J. Williams, Detection of the humanpandemic Escherichia coli B2-O25b-ST131 in UK dogs, Vet Rec, vol.174, p.352, 2014.

A. Typas, M. Banzhaf, C. A. Gross, and W. Vollmer, From the regulation of peptidoglycan synthesis to bacterial growth and morphology, Nature Reviews Microbiology, vol.185, pp.123-159, 2012.
DOI : 10.1038/nrmicro2677

A. Ud-din and S. Wahid, Relationship among Shigella spp. and enteroinvasive Escherichia coli (EIEC) and their differentiation, Brazilian Journal of Microbiology, vol.45, issue.4, pp.1131-1139, 2014.
DOI : 10.1590/S1517-83822014000400002

L. Villa, A. Garcia-fernandez, D. Fortini, and A. Carattoli, Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants, Journal of Antimicrobial Chemotherapy, vol.65, issue.12, pp.2518-2547, 2010.
DOI : 10.1093/jac/dkq347

S. Vimont, A. Boyd, A. Bleibtreu, M. Bens, J. M. Goujon et al., The CTX-M-15-Producing Escherichia coli Clone O25b: H4-ST131 Has High Intestine Colonization and Urinary Tract Infection Abilities, PLoS ONE, vol.7, issue.9, p.46547, 2012.
DOI : 10.1371/journal.pone.0046547.t001

X. M. Wang, H. X. Jiang, X. P. Liao, J. H. Liu, W. J. Zhang et al., ??? isolates from diseased pigs, FEMS Microbiology Letters, vol.306, issue.1, pp.15-21, 2010.
DOI : 10.1111/j.1574-6968.2010.01917.x

L. H. Wieler, T. K. Mcdaniel, T. S. Whittam, and J. B. Kaper, Insertion site of the locus of enterocyte effacement in enteropathogenic and enterohemorrhagic Escherichia coli differs in relation to the clonal phylogeny of the strains, FEMS Microbiology Letters, vol.156, issue.1, pp.49-53, 1997.
DOI : 10.1111/j.1574-6968.1997.tb12704.x

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.1136-51, 2006.
DOI : 10.1111/j.1365-2958.2005.04985.x

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

N. Woodford, E. J. Fagan, and M. J. Ellington, Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum ??-lactamases, Journal of Antimicrobial Chemotherapy, vol.57, issue.1, pp.154-159, 2006.
DOI : 10.1093/jac/dki412

P. Xia, Y. Zou, Y. Wang, Y. Song, W. Liu et al., Receptor for the F4 fimbriae of enterotoxigenic Escherichia coli (ETEC), Applied Microbiology and Biotechnology, vol.44, issue.6, pp.4953-4962, 2015.
DOI : 10.1007/s00253-015-6643-9

Z. Yu and M. Morrison, Improved extraction of PCR-quality community DNA from digesta and fecal samples, Biotechniques, vol.36, pp.808-820, 2004.

S. Zhao, D. G. White, B. Ge, S. Ayers, S. Friedman et al., Identification and Characterization of Integron-Mediated Antibiotic Resistance among Shiga Toxin-Producing Escherichia coli Isolates, Applied and Environmental Microbiology, vol.67, issue.4, pp.1558-64, 2001.
DOI : 10.1128/AEM.67.4.1558-1564.2001