E. Eu, Summary Report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2014, EFSA J, vol.14, issue.2, p.4380, 2016.

D. Girlich, L. Poirel, A. Carattoli, I. Kempf, M. 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

C. Chauvin, L. Devendec, L. Jouy, E. , L. Cornec et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.57, issue.12, pp.6351-6354, 2013.
DOI : 10.1128/AAC.01460-13
URL : https://hal.archives-ouvertes.fr/hal-01272616

A. Kojima, Y. Ishii, K. Ishihara, H. Esaki, T. Asai et al., Extended-Spectrum-??-Lactamase-Producing Escherichia coli Strains Isolated from Farm Animals from 1999 to 2002: Report from the Japanese Veterinary Antimicrobial Resistance Monitoring Program, Antimicrobial Agents and Chemotherapy, vol.49, issue.8, pp.3533-3540, 1999.
DOI : 10.1128/AAC.49.8.3533-3537.2005

N. Woodford, E. Fagan, and M. 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 : 10.1128/JCM.42.12.5715-5721.2004

A. Bej, J. Dicesare, L. Haff, and R. Atlas, Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uid, Applied Environ Microbiol, vol.57, issue.4, pp.1013-1020, 1991.

O. Clermont, J. Christenson, E. Denamur, and D. 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 : 10.1128/AEM.01262-09

I. Rivera, M. Chowdhury, A. Huq, D. Jacobs, M. Martins et al., Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non-O1 strains, pplied Environ Microbiol, issue.8, pp.612898-904, 1995.

G. Chu, D. Vollrath, and R. Davis, Separation of large DNA molecules by contour-clamped homogeneous electric fields, Science, vol.234, issue.4783, pp.1582-1587, 1986.
DOI : 10.1126/science.3538420

S. Takahashi and Y. Nagano, Rapid procedure for isolation of plasmid DNA and application to epidemiological analysis, J Clinical Microbiol, vol.20, issue.4, pp.608-621, 1984.

B. Barton, G. Harding, and A. Zuccarelli, A General Method for Detecting and Sizing Large Plasmids, Analytical Biochemistry, vol.226, issue.2, pp.235-275, 1995.
DOI : 10.1006/abio.1995.1220

A. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.18, issue.15, pp.2114-2134, 2014.
DOI : 10.1101/gr.074492.107

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://europepmc.org/articles/pmc3322381?pdf=render

R. Chikhi and P. Medvedev, Informed and automated k-mer size selection for genome assembly, Bioinformatics, vol.18, issue.5, pp.31-38, 2014.
DOI : 10.1101/gr.074492.107
URL : https://hal.archives-ouvertes.fr/hal-01477511

B. Chevreux, T. Wetter, and S. Suhai, Genome Sequence Assembly Using Trace Signals and Additional Sequence Information, Proceedings of the German Conference on Bioinformatics (GCB) 99. Presented at the German Conference on Bioinformatics (GCB), pp.45-56, 1999.

J. Mariette, F. Escudie, N. Allias, G. Salin, C. Noirot et al., NG6: Integrated next generation sequencing storage and processing environment, BMC Genomics, vol.13, issue.1, pp.462-22958229, 2012.
DOI : 10.1128/AEM.01541-09
URL : https://hal.archives-ouvertes.fr/inserm-00733481

T. Johnson, S. Johnson, and L. Nolan, Complete DNA Sequence of a ColBM Plasmid from Avian Pathogenic Escherichia coli Suggests that It Evolved from Closely Related ColV Virulence Plasmids, Journal of Bacteriology, vol.188, issue.16, pp.5975-83, 2006.
DOI : 10.1128/JB.00204-06

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

M. Day, I. Rodríguez, A. Van-essen-zandbergen, C. Dierikx, K. Kadlec et al., from humans, animals and food in Germany, the Netherlands and the UK, Journal of Antimicrobial Chemotherapy, vol.71, issue.5, pp.1178-82, 2016.
DOI : 10.1111/j.1469-0691.2011.03497.x

S. Mo, M. Norstrom, J. Slettemeas, A. Lovland, A. Urdahl et al., Emergence of AmpC-producing Escherichia coli in the broiler production chain in a country with a low antimicrobial usage profile, Veterinary Microbiology, vol.171, issue.3-4, pp.3-4315, 2014.
DOI : 10.1016/j.vetmic.2014.02.002

S. 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. Rodríguez, K. Thomas, A. Van-essen, A. Schink, M. Day et al., Chromosomal location of blaCTX-M genes in clinical isolates of Escherichia coli from Germany, The Netherlands and the UK, International Journal of Antimicrobial Agents, vol.43, issue.6, pp.553-560, 2014.
DOI : 10.1016/j.ijantimicag.2014.02.019

M. De-been, V. Lanza, M. De-toro, J. Scharringa, W. Dohmen et al., Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages, PLoS Genetics, vol.22, issue.2529, p.25522320, 2014.
DOI : 10.1371/journal.pgen.1004776.s004

M. De-toro, P. Garcia, I. Rodriguez, B. Rojo-bezares, R. Helmuth et al., Characterisation of plasmids implicated in the mobilisation of extended-spectrum and AmpC ??-lactamase genes in clinical Salmonella enterica isolates and temporal stability of the resistance genotype, International Journal of Antimicrobial Agents, vol.42, issue.2, pp.167-72, 2013.
DOI : 10.1016/j.ijantimicag.2013.04.016

K. Hansen, V. Bortolaia, C. Nielsen, J. Nielsen, K. Schønning et al., ABSTRACT, Applied and Environmental Microbiology, vol.82, issue.15, pp.4705-4719, 2016.
DOI : 10.1128/AEM.00495-16

A. Dheilly, L. Devendec, L. Mourand, G. Bouder, A. Jouy et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.1, pp.189-96, 2012.
DOI : 10.1128/AAC.05617-11

J. Wang, R. Stephan, K. Zurfluh, H. Hachler, and S. Fanning, Characterization of the genetic environment of bla ESBL genes, integrons and toxin-antitoxin systems identified on large transferrable plasmids in multi-drug resistant Escherichia coli, Frontiers Microbiol, vol.5, p.716, 2014.

H. Smith, A. Bossers, F. Harders, G. Wu, N. Woodford et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.59, issue.9, pp.5357-65, 2015.
DOI : 10.1128/AAC.05006-14

S. Dahmen, M. Haenni, and J. Madec, IncI1/ST3 plasmids contribute to the dissemination of the blaCTX-M-1 gene in Escherichia coli from several animal species in France, Journal of Antimicrobial Chemotherapy, vol.17, issue.6, pp.3011-3013, 2012.
DOI : 10.1111/j.1469-0691.2011.03497.x

J. Madec, M. Haenni, V. Métayer, E. Saras, and M. Nicolas-chanoine, IncI1/ST3 Plasmid in Human Escherichia coli Isolates, Antimicrobial Agents and Chemotherapy, vol.59, issue.9, pp.5860-5861, 2015.
DOI : 10.1128/AAC.00819-15

J. Wang, R. Stephan, K. Power, Q. Yan, H. Hächler et al., Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans, Journal of Antimicrobial Chemotherapy, vol.66, issue.10, pp.2658-68, 2014.
DOI : 10.1016/j.plasmid.2011.06.004

T. Kubasova, J. Matiasovicova, I. Rychlik, and H. Juricova, Complete sequence of multidrug resistance p9134 plasmid and its variants including natural recombinant with the virulence plasmid of Salmonella serovar Typhimurium, Plasmid, vol.76, pp.8-14, 2014.
DOI : 10.1016/j.plasmid.2014.08.003

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

M. Anjum, M. Abuoun, L. Devendec, L. Jouy, E. Baron et al., Etude génétique de E. coli de poulets résistants aux céphalosporines, Proceedings of the 10e Congrès de la Société française de Microbiologie, 2014.

S. Baron, E. Jouy, F. Touzain, S. Bougeard, E. Larvor et al., Impact of the administration of a third-generation cephalosporin (3GC) to one-day-old chicks on the persistence of 3GC-resistant Escherichia coli in intestinal flora: An in vivo experiment, Veterinary Microbiology, vol.185, pp.29-33, 2016.
DOI : 10.1016/j.vetmic.2016.01.020

C. Dierikx, J. Van-der-goot, H. Smith, A. Kant, and D. Mevius, Presence of ESBL/AmpC -Producing Escherichia coli in the Broiler Production Pyramid: A Descriptive Study, PLoS ONE, vol.16, issue.11, p.24244401, 2013.
DOI : 10.1371/journal.pone.0079005.s001

S. Seiffert, A. Carattoli, S. Schwendener, A. Collaud, A. Endimiani et al., Plasmids Carrying blaCMY -2/4 in Escherichia coli from Poultry, Poultry Meat, and Humans Belong to a Novel IncK Subgroup Designated IncK2, Frontiers in Microbiology, vol.69, issue.e0154019, 2017.
DOI : 10.1093/jac/dku206

H. Sidjabat, K. Seah, L. Coleman, A. Sartor, P. Derrington et al., Expansive spread of IncI1 plasmids carrying blaCMY-2 amongst Escherichia coli, International Journal of Antimicrobial Agents, vol.44, issue.3, pp.203-211, 2014.
DOI : 10.1016/j.ijantimicag.2014.04.016

L. Zamorano, E. Miro, C. Juan, L. Gomez, G. Bou et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.59, issue.9, pp.5260-5266, 2015.
DOI : 10.1128/AAC.00562-15

C. Verdet, V. Gautier, E. Chachaty, E. Ronco, N. Hidri et al., Genetic Context of Plasmid-Carried blaCMY-2-Like Genes in Enterobacteriaceae, Antimicrobial Agents and Chemotherapy, vol.53, issue.9, pp.4002-4008, 2009.
DOI : 10.1128/AAC.00753-08
URL : https://hal.archives-ouvertes.fr/inserm-00533112

T. Johnson, Y. Wannemuehler, C. Doetkott, S. Johnson, S. Rosenberger et al., Identification of Minimal Predictors of Avian Pathogenic Escherichia coli Virulence for Use as a Rapid Diagnostic Tool, Journal of Clinical Microbiology, vol.46, issue.12, pp.3987-96, 2008.
DOI : 10.1128/JCM.00816-08

T. Johnson, K. Siek, S. Johnson, and L. Nolan, DNA Sequence of a ColV Plasmid and Prevalence of Selected Plasmid-Encoded Virulence Genes among Avian Escherichia coli Strains, Journal of Bacteriology, vol.188, issue.2, pp.745-58, 2006.
DOI : 10.1128/JB.188.2.745-758.2006

X. Wang, H. Hao, Z. Xu, H. Zheng, C. Liu et al., Plasmid-mediated multidrug resistance and virulence in an avian pathogenic Escherichia coli strain isolated in China, Journal of Global Antimicrobial Resistance, vol.2, issue.1, pp.57-65, 2014.
DOI : 10.1016/j.jgar.2013.10.004

M. Mellata, : Infections, Zoonotic Risks, and Antibiotic Resistance Trends, Foodborne Pathogens and Disease, vol.10, issue.11, pp.916-948, 2013.
DOI : 10.1089/fpd.2013.1533
URL : http://europepmc.org/articles/pmc3865812?pdf=render