{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T02:14:28Z","timestamp":1774404868696,"version":"3.50.1"},"reference-count":98,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T00:00:00Z","timestamp":1679443200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 <jats:italic>E. coli<\/jats:italic>, 1 <jats:italic>Enterobacter cloacae<\/jats:italic>, 1 <jats:italic>Klebsiella pneumoniae<\/jats:italic>, and 1 <jats:italic>Citrobacter gillenii<\/jats:italic>) isolated from farm effluents in Ireland before (<jats:italic>n<\/jats:italic>\u2009=\u200972) and after (<jats:italic>n<\/jats:italic>\u2009=\u200910) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (<jats:italic>n<\/jats:italic>\u2009=\u200924), identified in <jats:italic>E. coli<\/jats:italic> isolates. Five plasmid replicons were confined to the <jats:italic>Enterobacter cloacae<\/jats:italic> isolate and two were confined to the <jats:italic>Klebsiella pneumoniae<\/jats:italic> isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2023.1118264","type":"journal-article","created":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T05:18:59Z","timestamp":1679462339000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing"],"prefix":"10.3389","volume":"14","author":[{"given":"Deirdre M.","family":"Prendergast","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosemarie","family":"Slowey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine M.","family":"Burgess","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Declan","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dayle","family":"Johnston","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dearbh\u00e1ile","family":"Morris","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00c1ine","family":"O\u2019 Doherty","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Moriarty","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Montserrat","family":"Gutierrez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,3,22]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e02430","DOI":"10.1128\/AEM.02430-17","article-title":"Molecular epidemiology of dairy cattle-associated Escherichia coli carrying Bla (CTX\u2212M) genes in Washington state","volume":"84","author":"Afema","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1093\/jac\/dkr507","article-title":"Prevalence of extended-spectrum cephalosporinase (ESC)-producing Escherichia coli in Danish slaughter pigs and retail meat identified by selective enrichment and association with cephalosporin usage","volume":"67","author":"Agers\u00f8","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1128\/iai.46.3.740-746.1984","article-title":"A plasmid-encoded outer membrane protein, TraT, enhances resistance of Escherichia coli to phagocytosis","volume":"46","author":"Ag\u00fcero","year":"1984","journal-title":"Infect. Immun."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"5882","DOI":"10.1128\/AEM.00141-10","article-title":"Prevalence and persistence of Escherichia coli strains with uropathogenic virulence characteristics in sewage tratment plants","volume":"76","author":"Anastasi","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/s41579-021-00650-4","article-title":"Horizontal gene transfer and adaptive evolution in bacteria","volume":"20","author":"Arnold","year":"2022","journal-title":"Nat. Rev."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1093\/trstmh\/traa041","article-title":"Molecular mechanisms associated with quinolone resistace in Enterobacteriaceae: Review and update","volume":"114","author":"Azargun","year":"2020","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1099\/mgen.0.000192","article-title":"Clermontyping: An easy-to-use and accurate in silico method for Escherichia genus strain phylotyping","volume":"4","author":"Beghain","year":"2018","journal-title":"Microb. Genom."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"415","DOI":"10.3201\/eid1803.111099","article-title":"Chicken as reservoir for human extraintestinal pathogenic Escherichia coli, Canada","volume":"18","author":"Bergeron","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"5400","DOI":"10.1038\/s41467-021-25679-0","article-title":"Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae","volume":"12","author":"Bharatham","year":"2021","journal-title":"Nat. Commun."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"e0206252","DOI":"10.1371\/journal.pone.0206252","article-title":"Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany","volume":"13","author":"Boehmer","year":"2018","journal-title":"PLoS One"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13620-022-00214-9","article-title":"Antimicrobial resistance in Escherichia coli isolated from on-farm and conventional hatching broiler farms in Ireland","volume":"75","author":"Byrne","year":"2022","journal-title":"Ir. Vet. J."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"110","DOI":"10.3389\/fmicb.2012.00110","article-title":"CTX-M enzymes: Origin and diffusion","volume":"3","author":"Canton","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"984","DOI":"10.1111\/jam.12591","article-title":"Detection of carbapenem resistance genes and cephalosporin, and quinolone resistance genes along with oqxAB gene in Escherichia coli in hospital wastewater: A matter of concern","volume":"117","author":"Chandran","year":"2014","journal-title":"J. Appl. Microbiol."},{"key":"ref14","first-page":"43","article-title":"Molecular mechanisms of fluoroquinolone and expanded-spectrum cephalosporin resistance in Vibrio parahaemolyticus: Abridged secondary publication","volume":"26","author":"Chen","year":"2020","journal-title":"Hong Kong Med. J."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"3107","DOI":"10.1111\/1462-2920.14713","article-title":"Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential","volume":"21","author":"Clermont","year":"2019","journal-title":"Environ. Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"960748","DOI":"10.3389\/fmicb.2022.960748","article-title":"Prevalence and distribution of extended-spectrum \u03b2-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments","volume":"13","author":"Collis","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/j.vetmic.2019.02.031","article-title":"Diversity of CTX-M-positive Escherichia coli recovered from animals in Canada","volume":"231","author":"Cormier","year":"2019","journal-title":"Vet. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1016\/j.jinf.2015.09.009","article-title":"Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones","volume":"71","author":"Dale","year":"2015","journal-title":"J. Infect."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"e03206","DOI":"10.1016\/j.heliyon.2020.e03206","article-title":"Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production \u2013 a threat around the world","volume":"6","author":"Dantas Palmeira","year":"2020","journal-title":"Heliyon"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1178","DOI":"10.1093\/jac\/dkv485","article-title":"Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK","volume":"71","author":"Day","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"5090","DOI":"10.3390\/ijms21145090","article-title":"Molecular mechanisms, epidemiology, and clinical importance of \u03b2-lactam resistance in Enterobacteriaceae","volume":"21","author":"De Angelis","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"2635","DOI":"10.3382\/ps\/pev256","article-title":"Virulence gene content in Escherichia coli isolates from poultry flocks with clinical signs of colibacillosis in Brazil","volume":"94","author":"De Carli","year":"2015","journal-title":"Poult. Sci."},{"key":"ref23","unstructured":"2017"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"705230","DOI":"10.3389\/fmicb.2021.705230","article-title":"Emergence of IncHI2 plasmids with mobilized colistin resistance (mcr)-9 gene in ESBL-producing, multidrug-resistant Salmonella Typhimurium and its monophasic variant ST34 from food-producing animals in Italy","volume":"12","author":"Diaconu","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"2122","DOI":"10.1128\/JCM.02365-09","article-title":"Cyclomodulins in Urosepsis strains of Escherichia Coli","volume":"48","author":"Dubois","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"e06651","DOI":"10.2903\/j.efsa.2021.6651","article-title":"Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain","volume":"19","author":"Koutsoumanis","year":"2021","journal-title":"EFSA J."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"105","DOI":"10.2903\/j.efsa.2020.5967","article-title":"Scientific opinion on the pathogenicity assessment of Shiga toxin-producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC","volume":"18","author":"Koutsoumanis","year":"2020","journal-title":"EFSA J."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"528","DOI":"10.4161\/viru.2.6.18189","article-title":"Characteristics of Escherichia coli causing persistence or relapse of urinary tract infections: Phylogenetic groups, virulence factors and biofilm formation","volume":"2","author":"Ejrn\u00e6s","year":"2011","journal-title":"Virulence"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"626774","DOI":"10.3389\/fmicb.2021.626774","article-title":"Genomic diversity and virulence potential of ESBL- and AmpC\u03b2-lactamase-producing Escherichia coli strains from healthy food animals across Europe","volume":"12","author":"Ewers","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"172813","DOI":"10.1016\/j.ejphar.2019.172813","article-title":"Antimicrobial pharmaceuticals in the aquatic environment - occurrence and environmental implications","volume":"866","author":"Felis","year":"2020","journal-title":"Eur. J. Pharmacol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1016\/j.scitotenv.2010.12.011","article-title":"Differential patterns of antimicrobial reistance in population subsets of Escherichia coli isolated from waste- and surface waters","volume":"409","author":"Figueira","year":"2011","journal-title":"Sci. Total Environ."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/j.ijid.2014.03.1393","article-title":"Detection of virulence genes in Escherichia coli isolated from patients with cystitis and pyelonephritis","volume":"29","author":"Firoozeh","year":"2014","journal-title":"Int. J. Inf. Secur."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"e0144802","DOI":"10.1371\/journal.pone.0144802","article-title":"Emergence of a clonal lineage of multidrug-resistant ESBL-producing salmonella Infantis transmitted from broilers and broiler meat to humans in Italy between 2011 and 2014","volume":"10","author":"Franco","year":"2015","journal-title":"PLoS One"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e0125621","DOI":"10.1128\/spectrum.01256-21","article-title":"WHO critical priority Escherichia coli as one health challenge for a post-pandemic scenario: Genomic surveillance and analysis of current trends in Brazil","volume":"10","author":"Fuga","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref35","unstructured":"2021"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1111\/nyas.14036","article-title":"Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems","volume":"1441","author":"Graham","year":"2019","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"239","DOI":"10.2217\/fmb-2016-0145","article-title":"Recurrent urinary tract infections in women: Risk factors, etiology, pathogenesis and prophylaxis","volume":"12","author":"Guglietta","year":"2017","journal-title":"Future Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.idc.2013.10.002","article-title":"Management of urinary tract infections from multidrug-resistant organisms","volume":"28","author":"Gupta","year":"2014","journal-title":"Infect. Dis. Clin. N. Am."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"790184","DOI":"10.3389\/fcimb.2022.790184","article-title":"Phylogenetic group distribution of uropathogenic Escherichia coli and related antimicrobial resistance pattern: A meta-analysis and systematic review","volume":"12","author":"Halaji","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"2047","DOI":"10.1093\/jac\/dks148","article-title":"Characterization of CTX-M-14- and CTX-M-15-producing Escherichia coli of porcine origin","volume":"67","author":"Hammerum","year":"2012","journal-title":"JAC"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"101468","DOI":"10.1016\/j.genrep.2021.101468","article-title":"Detection of fimH, kpsMTII, hlyA, and traT genes in Escherichia coli isolated from Iraqi patients with cystitis","volume":"26","author":"Hasan","year":"2022","journal-title":"Gene Rep."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/femspd\/ftv006","article-title":"Role of uropathogenic Escherichia coli outer membrane protein T in pathogenesis of urinary tract infection","volume":"73","author":"He","year":"2015","journal-title":"Pathog. Dis."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1093\/jac\/dkz035","article-title":"Dynamics of faecal shedding of ESBL- or AmpC-producing Escherichia coli on dairy farms","volume":"74","author":"Hordijk","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"105040","DOI":"10.1016\/j.micpath.2021.105040","article-title":"Genetic basis of molecular mechanisms in \u03b2-lactam resistant gram-negative bacteria","volume":"158","author":"Hussain","year":"2021","journal-title":"Microb. Pathog."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"2318","DOI":"10.3389\/fmicb.2017.02318","article-title":"CTX-M-15-Producing E. coli isolates from food products in Germany are mainly associated with an IncF-type plasmid and belong to two predominant Clonal E. coli lineages","volume":"8","author":"Irrgang","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1128\/AAC.47.2.559-562.2003","article-title":"Prevalence of plasmid-mediated quinolone resistance","volume":"47","author":"Jacoby","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1178","DOI":"10.1128\/AAC.50.4.1178-1182.2006","article-title":"qnrB, another plasmid-mediated gene for quinolone resistance","volume":"50","author":"Jacoby","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.rvsc.2015.07.014","article-title":"Impact of medicated feed along with clay mineral supplementation on Escherichia coli resistance to antimicrobial agents in pigs after weaning in field conditions","volume":"102","author":"Jahanbakhsh","year":"2015","journal-title":"Res. Vet. Sci."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"105909","DOI":"10.1016\/j.ijantimicag.2020.105909","article-title":"Resistance to third-generation cephalosporins in Escherichia coli in the French community: The times they are a-changin\u2019?","volume":"55","author":"Jeanvoine","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1093\/jac\/dkn063","article-title":"Plasmid-mediated quinolone resistance determinants qnr and aac(6\u2032)-Ib-cr in extended-spectrum \u03b2-lactamase-producing Escherichia coli and Klebsiella pneumoniae in China","volume":"61","author":"Jiang","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1016\/j.ijmm.2005.07.005","article-title":"Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli","volume":"295","author":"Johnson","year":"2005","journal-title":"Int. J. Med. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"2360","DOI":"10.1128\/AEM.02634-07","article-title":"Evolution of the iss gene in Escherichia coli","volume":"74","author":"Johnson","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1308","DOI":"10.3390\/microorganisms9061308","article-title":"Phenotypic and genotypic properties of fluoroquinolone-resistant, qnr-carrying Escherichia coli isolated from the German food chain in 2017","volume":"9","author":"Juraschek","year":"2021","journal-title":"Microorganisms"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"12","DOI":"10.3389\/fmicb.2021.653595","article-title":"Emergence and clonal spread of CTX-M-65-producing Escherichia coli from retail meat in Portugal","volume":"12","author":"Le\u00e3o","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1007\/s00284-018-1444-x","article-title":"Tellurite resistance in Shiga toxin-producing Escherichia coli","volume":"75","author":"Lewis","year":"2018","journal-title":"Curr. Microbiol."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"633","DOI":"10.3389\/fmicb.2019.00633","article-title":"The role of plasmids in the multiple antibiotic resistance transfer in ESBLs-producing Escherichia coli isolated from wastewater treatment plants","volume":"10","author":"Li","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"ftz014","DOI":"10.1093\/femspd\/ftz014","article-title":"Phenotypic characterization and virulence-related properties of Escherichia albertii strains isolated from children with diarrhea in Brazil","volume":"77","author":"Lima","year":"2019","journal-title":"Path Dis."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1016\/j.vetmic.2014.02.015","article-title":"Enterobacter cloacae with a novel variant of ACT AmpC beta-lactamase originating from glaucous gull (Larus hyperboreus) in Svalbard","volume":"171","author":"Literak","year":"2014","journal-title":"Vet. Microbiol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1093\/jac\/dki239","article-title":"CTX-M: Changing the face of ESBLs in the UK","volume":"56","author":"Livermore","year":"2005","journal-title":"J Antimicrob"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"283","DOI":"10.3389\/fmicb.2017.00283","article-title":"Comparative analysis of phylogenetic assignment of human and avian ExPEC and fecal commensal Escherichia coli using the (previous and revised) Clermont phylogenetic typing methods and its impact on avian pathogenic Escherichia coli (APEC) classification","volume":"8","author":"Logue","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"e01269-20","DOI":"10.1128\/JCM.01269-20","article-title":"In silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of whole-genome sequencing data","volume":"58","author":"Malberg Tetzschner","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1093\/cid\/cis502","article-title":"Food-borne origins of Escherichia coli causing Extraintestinal infections","volume":"55","author":"Manges","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s13620-020-00165-z","article-title":"Current antimicrobial use in farm animals in the Republic of Ireland","volume":"73","author":"Martin","year":"2020","journal-title":"Ir. Vet. J."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"654125","DOI":"10.3389\/fvets.2021.654125","article-title":"Prevalence of antimicrobial resistance and characteristics of Escherichia coli isolates from fecal and manure pit samples on dairy farms in the province of Qu\u00e9bec, Canada","volume":"8","author":"Mass\u00e9","year":"2021","journal-title":"Front. Vet. Sci."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"e1002266","DOI":"10.1371\/journal.pbio.1002266","article-title":"Nonmedical uses of antibiotics: Time to restrict their use?","volume":"13","author":"Meek","year":"2015","journal-title":"PLoS Biol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1590\/S1517-83822012000400010","article-title":"Mutations in the quinolone resistance-determining regions of gyrA and parC in Enterobacteriaceae isolates from Brazil","volume":"43","author":"Minarini","year":"2012","journal-title":"Braz. J. Microbiol."},{"key":"ref68","first-page":"306","article-title":"Detection of AmpC-\u03b2-lactamases producing isolates among carbapenem resistant P. aeruginosa isolated from burn patient","volume":"6","author":"Mirsalehian","year":"2014","journal-title":"Iran J. Microbiol."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1007\/s10482-011-9555-4","article-title":"Phylogenetic groups, virulence genes and quinolone resistance of integron-bearing Escherichia coli strains isolated from a wastewater treatment plant","volume":"99","author":"Mokracka","year":"2011","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"e16217","DOI":"10.5812\/jjm.16217","article-title":"Prevalence of quinolone resistance genes among extended-Spectrum B-lactamase-producing Escherichia coli in Mashhad, Iran","volume":"8","author":"Mood","year":"2015","journal-title":"Jundishapur J. Microbiol."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"16173","DOI":"10.1038\/nmicrobiol.2016.173","article-title":"The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland","volume":"1","author":"Moradigaravand","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"475","DOI":"10.3390\/pathogens10040475","article-title":"Hybrid atypical Enteropathogenic and Extraintestinal Escherichia coli (aEPEC\/ExPEC) BA1250 strain: A draft genome","volume":"10","author":"Munhoz","year":"2021","journal-title":"Pathogens"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"e11025-24","DOI":"10.7717\/peerj.11025","article-title":"Characterizing avian pathogenic Escherichia coli (APEC) from colibacillosis cases","volume":"9","author":"Newman","year":"2021","journal-title":"Peer J"},{"key":"ref74","doi-asserted-by":"publisher","first-page":"681175","DOI":"10.3389\/fmicb.2021.681175","article-title":"Diversity of the tellurite resistance gene operon in Escherichia coli","volume":"12","author":"Nguyen","year":"2021","journal-title":"Front. 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J."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1186\/s12879-021-06036-4","article-title":"Virulence genes and phylogenetic groups of uropathogenic Escherichia coli isolates from patients with urinary tract infection and uninfected control subjects: A case-control study","volume":"21","author":"Rezatofighi","year":"2021","journal-title":"BMC Infect."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"5340","DOI":"10.1128\/AAC.00589-15","article-title":"Characterization of IncI1 sequence type 71 epidemic plasmid lineage responsible for the recent dissemination of CTX-M-65 extended-spectrum \u03b2-lactamase in the Bolivian Chaco region","volume":"59","author":"Riccobono","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1186\/s13756-019-0548-9","article-title":"Extended-spectrum \u03b2-lactamase, plasmid-mediated AmpC \u03b2-lactamase, fluoroquinolone resistance, and decreased susceptibility to carbapenems in Enterobacteriaceae: Fecal carriage rates and associated risk factors in the community of northern Cyprus","volume":"8","author":"Ruh","year":"2019","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref84","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1093\/jac\/36.4.737","article-title":"High frequency of mutations at codon 83 of the gyrA gene of quinolone-resistant clinical isolates of Escherichia coli","volume":"36","author":"Ruiz","year":"1995","journal-title":"J. Antimicrob. 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