{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T23:29:19Z","timestamp":1781652559516,"version":"3.54.5"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2018,1,23]],"date-time":"2018-01-23T00:00:00Z","timestamp":1516665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007546","name":"Agence Nationale de S\u00e9curit\u00e9 Sanitaire de l\u2019Alimentation, de l\u2019Environnement et du Travail","doi-asserted-by":"publisher","award":["in the framework of joint research for the CoVetLab (Club 5) network"],"award-info":[{"award-number":["in the framework of joint research for the CoVetLab (Club 5) network"]}],"id":[{"id":"10.13039\/501100007546","id-type":"DOI","asserted-by":"publisher"}]},{"name":"France G\u00e9nomique National Infrastructure","award":["ANR-10-INBS-09"],"award-info":[{"award-number":["ANR-10-INBS-09"]}]},{"name":"Conseil D\u00e9partemental des C\u00f4tes d'Armor","award":["Not applicable"],"award-info":[{"award-number":["Not applicable"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0188768","type":"journal-article","created":{"date-parts":[[2018,1,23]],"date-time":"2018-01-23T18:24:24Z","timestamp":1516731864000},"page":"e0188768","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers"],"prefix":"10.1371","volume":"13","author":[{"given":"Fabrice","family":"Touzain","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laetitia","family":"Le Devendec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"de Boiss\u00e9son","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandrine","family":"Baron","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Jouy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agn\u00e8s","family":"Perrin-Guyomard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yannick","family":"Blanchard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8912-3044","authenticated-orcid":true,"given":"Isabelle","family":"Kempf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,1,23]]},"reference":[{"key":"ref1","unstructured":"ANSES. R\u00e9sapath\u2014R\u00e9seau d&apos;\u00e9pid\u00e9miosurveillance de l&apos;antibior\u00e9sistance des bact\u00e9ries pathog\u00e8nes animales, bilan 2015, Lyon et Ploufragan-Plouzan\u00e9, France, novembre 2016, rapport, 152p. Maisons-Alfort; 2016. French"},{"issue":"2","key":"ref2","first-page":"4380","article-title":"EU Summary Report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2014","volume":"14","year":"2016","journal-title":"EFSA J"},{"issue":"14","key":"ref3","doi-asserted-by":"crossref","first-page":"4681","DOI":"10.1128\/AEM.02491-06","article-title":"Extended-spectrum beta-lactamase CTX-M-1 in <italic>Escherichia coli<\/italic> isolates from healthy poultry in France","volume":"73","author":"D Girlich","year":"2007","journal-title":"Applied Environ Microbiol"},{"issue":"12","key":"ref4","doi-asserted-by":"crossref","first-page":"6351","DOI":"10.1128\/AAC.01460-13","article-title":"National prevalence of resistance to third-generation cephalosporins in <italic>Escherichia coli<\/italic> isolates from layer flocks in France","volume":"57","author":"C Chauvin","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"ref5","doi-asserted-by":"crossref","first-page":"3533","DOI":"10.1128\/AAC.49.8.3533-3537.2005","article-title":"Extended-spectrum-\u03b2-lactamase-producing <italic>Escherichia coli<\/italic> strains isolated from farm animals from 1999 to 2002: Report from the Japanese veterinary antimicrobial resistance monitoring program","volume":"49","author":"A Kojima","year":"2005","journal-title":"Antimicrobial Agents Chemother"},{"issue":"1","key":"ref6","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1093\/jac\/dki412","article-title":"Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum (beta)-lactamases","volume":"57","author":"N Woodford","year":"2006","journal-title":"J Antimicrobial Chemother"},{"issue":"4","key":"ref7","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1128\/AEM.57.4.1013-1017.1991","article-title":"Detection of <italic>Escherichia coli<\/italic> and <italic>Shigella<\/italic> spp. in water by using the polymerase chain reaction and gene probes for <italic>uid<\/italic>","volume":"57","author":"AK Bej","year":"1991","journal-title":"Applied Environ Microbiol"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The Clermont <italic>Escherichia coli<\/italic> phylo-typing method revisited: improvement of specificity and detection of new phylo-groups","volume":"5","author":"O Clermont","year":"2013","journal-title":"Environ Microbiol Reports"},{"issue":"8","key":"ref9","doi-asserted-by":"crossref","first-page":"2898","DOI":"10.1128\/AEM.61.8.2898-2904.1995","article-title":"Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non- O1 strains","volume":"61","author":"IG Rivera","year":"1995","journal-title":"pplied Environ Microbiol"},{"issue":"4783","key":"ref10","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1126\/science.3538420","article-title":"Separation of large DNA molecules by contour-clamped homogeneous electric fields","volume":"234","author":"G Chu","year":"1986","journal-title":"Sci"},{"issue":"4","key":"ref11","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1128\/JCM.20.4.608-613.1984","article-title":"Rapid procedure for isolation of plasmid DNA and application to epidemiological analysis","volume":"20","author":"S Takahashi","year":"1984","journal-title":"J Clinical Microbiol"},{"key":"ref12","unstructured":"CLSI. Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals, aproved standard-fourth edition. 2013."},{"issue":"2","key":"ref13","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1006\/abio.1995.1220","article-title":"A general method for detecting and sizing large plasmids","volume":"226","author":"BM Barton","year":"1995","journal-title":"Anal Biochem"},{"issue":"15","key":"ref14","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"4","key":"ref15","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nature Methods"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1093\/bioinformatics\/btt310","article-title":"Informed and automated k-mer size selection for genome assembly","volume":"30","author":"R Chikhi","year":"2014","journal-title":"Bioinformatics"},{"key":"ref17","unstructured":"Chevreux B, Wetter T, Suhai S. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information, in: Proceedings of the German Conference on Bioinformatics (GCB) 99. Presented at the German Conference on Bioinformatics (GCB), pp. 45\u201356. 1999."},{"key":"ref18","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1186\/1471-2164-13-462","article-title":"NG6: Integrated next generation sequencing storage and processing environment","volume":"13","author":"J Mariette","year":"2012","journal-title":"BMC Genomics"},{"issue":"16","key":"ref19","doi-asserted-by":"crossref","first-page":"5975","DOI":"10.1128\/JB.00204-06","article-title":"Complete DNA sequence of a ColBM plasmid from avian pathogenic <italic>Escherichia coli<\/italic> suggests that it evolved from closely related ColV virulence plasmids","volume":"188","author":"TJ Johnson","year":"2006","journal-title":"J Bacteriol"},{"issue":"10","key":"ref20","doi-asserted-by":"crossref","first-page":"4555","DOI":"10.1128\/AEM.66.10.4555-4558.2000","article-title":"Rapid and simple determination of the <italic>Escherichia coli<\/italic> phylogenetic group","volume":"66","author":"O Clermont","year":"2000","journal-title":"Applied Environ Microbiol"},{"issue":"5","key":"ref21","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1093\/jac\/dkv485","article-title":"Diversity of STs, plasmids and ESBL genes among <italic>Escherichia coli<\/italic> from humans, animals and food in Germany, the Netherlands and the UK","volume":"71","author":"MJ Day","year":"2016","journal-title":"J Antimicrobial Chemother"},{"issue":"3\u20134","key":"ref22","first-page":"315","article-title":"Emergence of AmpC-producing <italic>Escherichia coli<\/italic> in the broiler production chain in a country with a low antimicrobial usage profile","volume":"171","author":"SS Mo","year":"2014","journal-title":"Veterinary microbiology"},{"issue":"1\u20132","key":"ref23","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.drup.2012.12.001","article-title":"Extended-spectrum cephalosporin-resistant Gram-negative organisms in livestock: an emerging problem for human health?","volume":"16","author":"SN Seiffert","year":"2013","journal-title":"Drug Resist Updat"},{"issue":"6","key":"ref24","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/j.ijantimicag.2014.02.019","article-title":"Chromosomal location of blaCTX-M genes in clinical isolates of <italic>Escherichia coli<\/italic> from Germany, The Netherlands and the UK","volume":"43","author":"I Rodr\u00edguez","year":"2014","journal-title":"Internat J Antimicrob Agents"},{"issue":"12","key":"ref25","doi-asserted-by":"crossref","first-page":"e1004776","DOI":"10.1371\/journal.pgen.1004776","article-title":"Dissemination of cephalosporin resistance genes between <italic>Escherichia coli<\/italic> strains from farm animals and humans by specific plasmid lineages","volume":"10","author":"M de Been","year":"2014","journal-title":"PLoS Genet"},{"issue":"2","key":"ref26","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.ijantimicag.2013.04.016","article-title":"Characterisation of plasmids implicated in the mobilisation of extended-spectrum and AmpC beta-lactamase genes in clinical <italic>Salmonella<\/italic> enterica isolates and temporal stability of the resistance genotype","volume":"42","author":"M de Toro","year":"2013","journal-title":"Int J Antimicrob Agents"},{"issue":"15","key":"ref27","doi-asserted-by":"crossref","first-page":"4705","DOI":"10.1128\/AEM.00495-16","article-title":"Host-specific patterns of genetic diversity among IncI1-I\u03b3 and IncK plasmids encoding CMY-2 \u03b2 -lactamase in <italic>Escherichia coli<\/italic> isolates from humans, poultry meat, poultry, and dogs in Denmark","volume":"82","author":"KH Hansen","year":"2016","journal-title":"Applied Environ Microbiol"},{"issue":"1","key":"ref28","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1128\/AAC.05617-11","article-title":"Resistance gene transfer during treatments for experimental avian colibacillosis","volume":"56","author":"A Dheilly","year":"2012","journal-title":"Antimicrob Agents Chemother"},{"key":"ref29","first-page":"716","article-title":"Characterization of the genetic environment of bla ESBL genes, integrons and toxin-antitoxin systems identified on large transferrable plasmids in multi-drug resistant <italic>Escherichia coli<\/italic>","volume":"5","author":"J Wang","year":"2014","journal-title":"Frontiers Microbiol"},{"issue":"9","key":"ref30","doi-asserted-by":"crossref","first-page":"5357","DOI":"10.1128\/AAC.05006-14","article-title":"Characterization of Epidemic IncI1-Igamma Plasmids Harboring Ambler Class A and C Genes in <italic>Escherichia coli<\/italic> and <italic>Salmonella<\/italic> enterica from Animals and Humans","volume":"59","author":"H Smith","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"issue":"12","key":"ref31","doi-asserted-by":"crossref","first-page":"3011","DOI":"10.1093\/jac\/dks308","article-title":"IncI1\/ST3 plasmids contribute to the dissemination of the blaCTX-M-1 gene in <italic>Escherichia coli<\/italic> from several animal species in France","volume":"67","author":"S Dahmen","year":"2012","journal-title":"J Antimicrobial Chemother"},{"issue":"9","key":"ref32","doi-asserted-by":"crossref","first-page":"5860","DOI":"10.1128\/AAC.00819-15","article-title":"High prevalence of the animal-associated blaCTX-M-1 IncI1\/ST3 plasmid in human <italic>Escherichia coli<\/italic> isolates","volume":"59","author":"JY Madec","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"issue":"10","key":"ref33","doi-asserted-by":"crossref","first-page":"2658","DOI":"10.1093\/jac\/dku206","article-title":"Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant <italic>Escherichia coli<\/italic> isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans","volume":"69","author":"J Wang","year":"2014","journal-title":"J Antimicrobial Chemother"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.plasmid.2014.08.003","article-title":"Complete sequence of multidrug resistance p9134 plasmid and its variants including natural recombinant with the virulence plasmid of <italic>Salmonella<\/italic> serovar Typhimurium","volume":"76","author":"T Kubasova","year":"2014","journal-title":"Plasmid"},{"key":"ref35","unstructured":"Anses-ANMV. Suivi des ventes de m\u00e9dicaments v\u00e9t\u00e9rinaires contenant des antibiotiques en France en 2013, Volumes et estimation de l\u2019exposition des animaux aux antibiotiques. Maisons-Alfort; 2014. French"},{"key":"ref36","unstructured":"Anjum M, AbuOun M, Le Devendec L, Jouy E, Baron S, Perrin-Guyomard A, et al. Etude g\u00e9n\u00e9tique de <italic>E. coli d<\/italic>e poulets r\u00e9sistants aux c\u00e9phalosporines. In: Proceedings of the 10e Congr\u00e8s de la Soci\u00e9t\u00e9 fran\u00e7aise de Microbiologie; Paris 2014. French"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.vetmic.2016.01.020","article-title":"Impact of the administration of a third-generation cephalosporin (3GC) to one-day-old chicks on the persistence of 3GC-resistant <italic>Escherichia coli<\/italic> in intestinal flora: An in vivo experiment","volume":"185","author":"S Baron","year":"2016","journal-title":"Vet Microbiol"},{"issue":"11","key":"ref38","doi-asserted-by":"crossref","first-page":"e79005","DOI":"10.1371\/journal.pone.0079005","article-title":"Presence of ESBL\/AmpC-producing <italic>Escherichia coli<\/italic> in the broiler production pyramid: a descriptive study","volume":"8","author":"CM Dierikx","year":"2013","journal-title":"PloS one"},{"key":"ref39","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2017.00407","article-title":"Plasmids carrying blaCMY -2\/4 in <italic>Escherichia coli<\/italic> from poultry, poultry meat, and humans belong to a novel IncK subgroup designated IncK2","volume":"8","author":"SN Seiffert","year":"2017","journal-title":"Frontiers Microbiol"},{"issue":"3","key":"ref40","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.ijantimicag.2014.04.016","article-title":"Expansive spread of IncI1 plasmids carrying blaCMY-2 amongst <italic>Escherichia coli<\/italic>","volume":"44","author":"HE Sidjabat","year":"2014","journal-title":"Int J Antimicrob Agents"},{"issue":"9","key":"ref41","doi-asserted-by":"crossref","first-page":"5260","DOI":"10.1128\/AAC.00562-15","article-title":"Mobile genetic elements related to the diffusion of plasmid-mediated AmpC beta-lactamases or carbapenemases from Enterobacteriaceae: findings from a multicenter study in Spain","volume":"59","author":"L Zamorano","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"issue":"9","key":"ref42","doi-asserted-by":"crossref","first-page":"4002","DOI":"10.1128\/AAC.00753-08","article-title":"Genetic context of plasmid-carried blaCMY-2-like genes in Enterobacteriaceae","volume":"53","author":"C Verdet","year":"2009","journal-title":"Antimicrob Agents Chemother"},{"issue":"12","key":"ref43","doi-asserted-by":"crossref","first-page":"3987","DOI":"10.1128\/JCM.00816-08","article-title":"Identification of minimal predictors of avian pathogenic <italic>Escherichia coli<\/italic> virulence for use as a rapid diagnostic tool","volume":"46","author":"TJ Johnson","year":"2008","journal-title":"J Clinical Microbiol"},{"issue":"2","key":"ref44","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1128\/JB.188.2.745-758.2006","article-title":"DNA sequence of a ColV plasmid and prevalence of selected plasmid-encoded virulence genes among avian <italic>Escherichia coli<\/italic> strains","volume":"188","author":"TJ Johnson","year":"2006","journal-title":"J Bacteriol"},{"issue":"1","key":"ref45","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.jgar.2013.10.004","article-title":"Plasmid-mediated multidrug resistance and virulence in an avian pathogenic <italic>Escherichia coli<\/italic> strain isolated in China","volume":"2","author":"X Wang","year":"2014","journal-title":"J Global Antimicrobial Resistance"},{"issue":"11","key":"ref46","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1089\/fpd.2013.1533","article-title":"Human and avian extraintestinal pathogenic <italic>Escherichia coli<\/italic>: infections, zoonotic risks, and antibiotic resistance trends","volume":"10","author":"M Mellata","year":"2013","journal-title":"Foodborne Pathog Dis"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0188768","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,26]],"date-time":"2020-10-26T00:54:55Z","timestamp":1603673695000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0188768"}},"subtitle":[],"editor":[{"given":"Patrick","family":"Butaye","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,1,23]]},"references-count":46,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,1,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0188768","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,23]]}}}