{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T14:15:47Z","timestamp":1788790547887,"version":"build-2803163510"},"reference-count":82,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T00:00:00Z","timestamp":1725840000000},"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":"Introduction<\/jats:title>Raw-meat diets (RMD) for dogs, comprising unprocessed or non-heat-treated animal material, are increasingly popular. However, RMDs have been demonstrated to be contaminated with antimicrobial resistant (AMR) bacteria, and there is concern that such diets may pose a zoonotic disease risk. Additionally, dogs fed RMD may shed more AMR- fecal bacteria compared to those fed conventional cooked diets. Data from the UK remain limited; the present study investigated the presence of AMR-Escherichia coli<\/jats:italic> in the feces of RMD and non-RMD (NRMD)-fed dogs in the UK, the E. coli<\/jats:italic> AMR gene complement, and the lifestyle risk factors associated with AMR- E. coli<\/jats:italic> carriage.<\/jats:p><\/jats:sec>Methods<\/jats:title>Fecal samples from UK-owned dogs (N<\/jats:italic> = 193 RMD, N<\/jats:italic> = 239 NRMD) and questionnaires discussing lifestyle factors, were obtained between October 2020-August 2021. Samples underwent culture and antimicrobial susceptibility testing to determine the presence of AMR-E. coli<\/jats:italic>. Whole genome sequencing determined AMR gene carriage. Risk factors for the presence of AMR-E. coli<\/jats:italic> were determined by multivariable modeling.<\/jats:p><\/jats:sec>Results<\/jats:title>RMD dogs carried significantly more fecal AMR E. coli<\/jats:italic> (p<\/jats:italic> &lt; 0.001), including third-generation cephalosporin resistant, extended-spectrum beta-lactamase (ESBL) producing, and multidrug resistant isolates and multivariable modeling confirmed raw-meat diets to be a significant risk factor. The bla<\/jats:italic>CTX\u2013M\u201315<\/jats:sub> gene was the most frequently identified bla<\/jats:italic>ESBL<\/jats:sub> gene. The bla<\/jats:italic>CTX\u2013M\u201355<\/jats:sub> and bla<\/jats:italic>SHV\u201366<\/jats:sub> genes were also prevalent and were only found in RMD dogs. The mobile colistin resistance gene, mcr-4<\/jats:italic> was identified in one ESBL-producing E. coli<\/jats:italic> isolate from a NRMD-fed dog.<\/jats:p><\/jats:sec>Conclusion<\/jats:title>This study has shown that dogs fed RMD in the UK are significantly more likely to shed E. coli<\/jats:italic> which is resistant to highest priority critically important antibiotics, and multidrug resistant E. coli<\/jats:italic>, than dogs fed NRMD. Additionally, AMR-E. coli<\/jats:italic> isolates from RMD-fed dogs harbor multiple, diverse, and novel AMR genes. Therefore, provision of RMD to dogs could pose an important potential threat to human and animal health, especially given the close nature of the relationship many owners share with their pets. Awareness of these findings should be shared with pet owners, veterinary and medical professionals, pet food manufacturers and public health to mitigate potential risks.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2024.1460143","type":"journal-article","created":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T04:43:16Z","timestamp":1725856996000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Raw meat diets are a major risk factor for carriage of third-generation cephalosporin-resistant and multidrug-resistant E. coli by dogs in the UK"],"prefix":"10.3389","volume":"15","author":[{"given":"Genever","family":"Morgan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gina","family":"Pinchbeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Haldenby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola","family":"Williams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,9,9]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database.","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1093\/jac\/dkx024","article-title":"Analysis of blaSHV-12-carrying Escherichia coli clones and plasmids from human, animal and food sources.","volume":"72","author":"Alonso","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"B3","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 treatment plants.","volume":"76","author":"Anastasi","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0187239","article-title":"Raw pet food as a risk factor for shedding of extended-spectrum beta-lactamase-producing Enterobacteriaceae in household cats.","volume":"12","author":"Baede","year":"2017","journal-title":"PLoS One"},{"key":"B5","doi-asserted-by":"publisher","first-page":"3117","DOI":"10.1128\/AAC.04576-14","article-title":"Longitudinal study of extended-spectrum-\u03b2-lactamase- and AmpC-producing Enterobacteriaceae in household dogs.","volume":"59","author":"Baede","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"B6","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01260","article-title":"Diversity, virulence, and clinical significance of extended-spectrum \u03b2-lactamase- and pAmpC-producing Escherichia coli from companion animals.","volume":"10","author":"Bortolami","year":"2019","journal-title":"Front. Microbiol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics10081013","article-title":"Antimicrobial resistance genes and diversity of clones among faecal ESBL-producing Escherichia coli isolated from healthy and sick dogs living in portugal.","volume":"10","author":"Carvalho","year":"2021","journal-title":"Antibiotics (Basel)"},{"key":"B10","year":"2020","journal-title":"CLSI M100-ED29: 2021 Performance standards for antimicrobial susceptibility testing"},{"key":"B11","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":"B12","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11091242","article-title":"Clonal dissemination of extended-spectrum cephalosporin-resistant enterobacterales between dogs and humans in households and animal shelters of Romania.","volume":"11","author":"Cozma","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"B13","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/j.vetmic.2011.03.015","article-title":"Selection of CMY-2 producing Escherichia coli in the faecal flora of dogs treated with cephalexin.","volume":"151","author":"Damborg","year":"2011","journal-title":"Vet. Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1111\/jsap.13000","article-title":"Raw diets for dogs and cats: A review, with particular reference to microbiological hazards.","volume":"60","author":"Davies","year":"2019","journal-title":"J. Small Anim. Pract."},{"key":"B15","doi-asserted-by":"publisher","first-page":"i57","DOI":"10.1093\/jac\/dkt027","article-title":"Molecular epidemiology of extended-spectrum \u03b2- lactamase-, AmpC \u03b2-lactamase- and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolated from Canadian hospitals over a 5 year period: CANWARD 2007-11.","volume":"68","author":"Denisuik","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"B16","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1080\/21642850.2019.1577738","article-title":"Understanding the relationship between pet owners and their companion animals as a key context for antimicrobial resistance-related behaviours: An interpretative phenomenological analysis.","volume":"7","author":"Dickson","year":"2019","journal-title":"Health Psychol. Behav. Med."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/ani11123543","article-title":"A cross-sectional study of knowledge on ownership, zoonoses and practices among pet owners in Northern Portugal.","volume":"11","author":"do Vale","year":"2021","journal-title":"Animals (Basel)"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1136\/vr.105828","article-title":"An observational study of pet feeding practices and how these have changed between 2008 and 2018.","volume":"186","author":"Dodd","year":"2020","journal-title":"Vet. Rec."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2019.00279","article-title":"Prevalence of beta-lactam and quinolone\/fluoroquinolone resistance in Enterobacteriaceae from dogs in france and spain-characterization of ESBL\/PAMPC isolates, genes, and conjugative plasmids.","volume":"6","author":"Dupouy","year":"2019","journal-title":"Front. Vet. Sci."},{"key":"B20","year":"2022","journal-title":"Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022."},{"key":"B21","first-page":"69","article-title":"The risk of Salmonellae shedding by dogs fed Salmonella-contaminated commercial raw food diets.","volume":"48","author":"Finley","year":"2007","journal-title":"Can. Vet. J."},{"key":"B22","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.2460\/javma.243.11.1549","article-title":"Current knowledge about the risks and benefits of raw meat-based diets for dogs and cats.","volume":"243","author":"Freeman","year":"2013","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"B23","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1016\/j.ajic.2012.11.013","article-title":"Extended-spectrum \u03b2-lactamase-producing Enterobacteriaceae in healthy companion animals living in nursing homes and in the community.","volume":"41","author":"Gandolfi-Decristophoris","year":"2013","journal-title":"Am. J. Infect. Control"},{"key":"B24","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1017\/S0950268810000798","article-title":"Risk factors for multidrug-resistant Escherichia coli rectal colonization of dogs on admission to a veterinary hospital.","volume":"139","author":"Gibson","year":"2011","journal-title":"Epidemiol. Infect."},{"key":"B25","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1111\/jsap.13488","article-title":"UK dogs eating raw meat diets have higher risk of Salmonella and antimicrobial-resistant Escherichia coli faecal carriage.","volume":"63","author":"Groat","year":"2022","journal-title":"J. Small Anim. Pract."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2018.23.27.1700497","article-title":"Sharing more than friendship - transmission of NDM-5 ST167 and CTX-M-9 ST69 Escherichia coli between dogs and humans in a family, Finland, 2015.","volume":"23","author":"Gr\u00f6nthal","year":"2018","journal-title":"Euro Surveill."},{"key":"B27","doi-asserted-by":"publisher","first-page":"2754","DOI":"10.1093\/jac\/dkac268","article-title":"Enterobacterales high-risk clones and plasmids spreading blaESBL\/AmpC and blaOXA-48 genes within and between hospitalized dogs and their environment.","volume":"77","author":"Haenni","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"B28","doi-asserted-by":"publisher","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 Escherichia coli isolates from humans, poultry meat, poultry, and dogs in Denmark.","volume":"82","author":"Hansen","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"5976","DOI":"10.1128\/AAC.04920-14","article-title":"Residues distal to the active site contribute to enhanced catalytic activity of variant and hybrid \u03b2-lactamases derived from CTX-M-14 and CTX-M-15.","volume":"59","author":"He","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"B30","author":"Isgren","year":"2020","journal-title":"The emerging problem of antimicrobial resistance in horses: Investigating faecal carriage and environmental contamination with resistant Escherichia coli"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofw129","article-title":"Household clustering of Escherichia coli sequence type 131 clinical and fecal isolates according to whole genome sequence analysis.","volume":"3","author":"Johnson","year":"2016","journal-title":"Open Forum Infect. Dis."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268821001072","article-title":"A cluster of Shiga Toxin-producing Escherichia coli O157:H7 highlights raw pet food as an emerging potential source of infection in humans.","volume":"149","author":"Kaindama","year":"2020","journal-title":"Epidemiol. Infect."},{"key":"B33","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2.","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"B34","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1111\/j.1863-2378.2008.01145.x","article-title":"Evaluation of the risks of shedding Salmonellae and other potential pathogens by therapy dogs fed raw diets in Ontario and Alberta.","volume":"55","author":"Lefebvre","year":"2008","journal-title":"Zoonoses Public Health"},{"key":"B35","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.prevetmed.2014.09.008","article-title":"Prevalence of antimicrobial resistance in enteric Escherichia coli from domestic pets and assessment of associated risk markers using a generalized linear mixed model.","volume":"117","author":"Leite-Martins","year":"2014","journal-title":"Prev. Vet. Med."},{"key":"B36","doi-asserted-by":"publisher","first-page":"959","DOI":"10.2460\/ajvr.76.11.959","article-title":"Risk factors for carriage of antimicrobial-resistant Salmonella spp and Escherichia coli in pet dogs from volunteer households in Ontario, Canada, in 2005 and 2006.","volume":"76","author":"Leonard","year":"2015","journal-title":"Am. J. Vet. Res."},{"key":"B37","doi-asserted-by":"publisher","first-page":"e002693","DOI":"10.1128\/mBio.02693-18","article-title":"One health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock.","volume":"10","author":"Ludden","year":"2019","journal-title":"mBio"},{"key":"B38","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/jac\/dkx489","article-title":"Emergence of blaCTX-M-55 associated with fosA, rmtB and mcr gene variants in Escherichia coli from various animal species in France.","volume":"73","author":"Lupo","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"B39","doi-asserted-by":"publisher","first-page":"2824","DOI":"10.1128\/AAC.02155-12","article-title":"\u2018Genetic characterization of inci2 plasmids carrying blaCTX-M-55 spreading in both pets and food animals in China Luchao\u2019.","volume":"57","author":"Lv","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"B40","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance.","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-15539-7","article-title":"Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction.","volume":"7","author":"Matamoros","year":"2017","journal-title":"Sci. Rep."},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1301841","article-title":"An investigation of the presence and antimicrobial susceptibility of Enterobacteriaceae in raw and cooked kibble diets for dogs in the United Kingdom.","volume":"14","author":"Morgan","year":"2024","journal-title":"Front. Microbiol."},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1016\/j.prevetmed.2022.105741","article-title":"Dog\u2019s Dinner: Factors affecting food choice and feeding practices for UK dog owners feeding raw meat-based or conventional cooked diets.","volume":"208","author":"Morgan","year":"2022","journal-title":"Prev. Vet. Med."},{"key":"B44","doi-asserted-by":"publisher","first-page":"1524","DOI":"10.2460\/javma.228.10.1524","article-title":"Evaluation of the association between feeding raw meat and Salmonella enterica infections at a Greyhound breeding facility.","volume":"228","author":"Morley","year":"2006","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1016\/j.onehlt.2022.100370","article-title":"Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding.","volume":"14","author":"Mounsey","year":"2022","journal-title":"One Health"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1186\/s12917-022-03298-1","article-title":"Risk of sharing resistant bacteria and\/or resistance elements between dogs and their owners.","volume":"18","author":"Naziri","year":"2022","journal-title":"BMC Vet. Res."},{"key":"B47","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3402\/iee.v5.28758","article-title":"Hygiene quality and presence of ESBL-producing Escherichia coli in raw food diets for dogs.","volume":"5","author":"Nilsson","year":"2015","journal-title":"Infect. Ecol. Epidemiol."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1098\/rsos.191170","article-title":"Raw meat-based diets for companion animals: A potential source of transmission of pathogenic and antimicrobial-resistant Enterobacteriaceae.","volume":"6","author":"N\u00fcesch-Inderbinen","year":"2019","journal-title":"R. Soc. Open Sci."},{"key":"B50","year":"2022","journal-title":"PDSA animal wellbeing PAW report 2022: The essential insight into the wellbeing of UK pets, PDSA animal wellbeing report."},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11040534","article-title":"Fecal shedding of multidrug resistant Escherichia coli isolates in dogs fed with raw meat-based diets in Brazil.","volume":"11","author":"Ramos","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"B52","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1093\/jac\/dkq396","article-title":"Prevalence of Escherichia coli carrying extended-spectrum \u03b2-lactamases (CTX-M and TEM-52) from broiler chickens and turkeys in Great Britain between 2006 and 2009.","volume":"66","author":"Randall","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"B53","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1089\/mdr.2020.0146","article-title":"Multidrug-resistant CTX-M and CMY-2 producing Escherichia coli isolated from healthy household dogs from the great Metropolitan Area, Costa Rica.","volume":"26","author":"Rodr\u00edguez-Gonz\u00e1lez","year":"2020","journal-title":"Microb. Drug Resist."},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1136\/vetreco-2018-000307","article-title":"Prevalence of faecal carriage of extended-spectrum \u03b2-lactamase (ESBL)-producing Escherichia coli in veterinary hospital staff and students.","volume":"6","author":"Royden","year":"2019","journal-title":"Vet. Rec. Open"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1136\/vr.105644","article-title":"Presence of pathogenic bacteria in faeces from dogs fed raw meat-based diets or dry kibble.","volume":"187","author":"Runesv\u00e4rd","year":"2020","journal-title":"Vet. Rec."},{"key":"B56","doi-asserted-by":"publisher","first-page":"3305","DOI":"10.1093\/jac\/dky352","article-title":"Routine antibiotic therapy in dogs increases the detection of antimicrobial-resistant faecal Escherichia coli.","volume":"73","author":"Schmidt","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"B57","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.prevetmed.2015.01.013","article-title":"Antimicrobial resistance risk factors and characterisation of faecal E. coli isolated from healthy Labrador retrievers in the United Kingdom.","volume":"119","author":"Schmidt","year":"2015","journal-title":"Prev. Vet. Med."},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics10020171","article-title":"Transmission chains of extended-spectrum beta-lactamase-producing Enterobacteriaceae at the companion animal veterinary clinic-household interface.","volume":"10","author":"Schmitt","year":"2021","journal-title":"Antibiotics (Basel)"},{"key":"B59","doi-asserted-by":"publisher","first-page":"2399","DOI":"10.1093\/jac\/dkac208","article-title":"Molecular ecology and risk factors for third-generation cephalosporin-resistant Escherichia coli carriage by dogs living in urban and nearby rural settings.","volume":"77","author":"Sealey","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"B60","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B61","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1038\/nmeth.2066","article-title":"Metagenomic microbial community profiling using unique clade-specific marker genes.","volume":"9","author":"Segata","year":"2012","journal-title":"Nat. Methods"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000592","article-title":"Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster.","volume":"7","author":"Shibu","year":"2021","journal-title":"Microb. Genom."},{"key":"B63","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1099\/jmm.0.46598-0","article-title":"Emergence and spread of two distinct clonal groups of multidrug-resistant Escherichia coli in a veterinary teaching hospital in Australia.","volume":"55","author":"Sidjabat","year":"2006","journal-title":"J. Med. Microbiol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs.","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.700698","article-title":"Temporal, spatial, and genomic analyses of Enterobacteriaceae clinical antimicrobial resistance in companion animals reveals phenotypes and genotypes of one health concern.","volume":"12","author":"Singleton","year":"2021","journal-title":"Front. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"1475","DOI":"10.1111\/j.1469-0691.2010.03127.x","article-title":"High prevalence of bla(CTX-M) extended-spectrum \u03b2-lactamase genes in Escherichia coli isolates from pets and emergence of CTX-M-64 in China.","volume":"16","author":"Sun","year":"2010","journal-title":"Clin. Microbiol. Infect."},{"key":"B67","doi-asserted-by":"publisher","first-page":"2705","DOI":"10.1128\/AAC.05598-11","article-title":"Molecular characterization of extended-spectrum-\u03b2-lactamase-producing and plasmid-mediated AmpC \u03b2-lactamase-producing Escherichia coli isolated from stray dogs in South Korea.","volume":"56","author":"Tamang","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"B68","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1089\/mdr.2016.0036","article-title":"Veterinary hospital dissemination of CTX-M-15 extended-spectrum beta-lactamase-producing Escherichia coli ST410 in the United Kingdom.","volume":"22","author":"Timofte","year":"2016","journal-title":"Microb. Drug Resist."},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline.","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol."},{"key":"B70","doi-asserted-by":"publisher","first-page":"e1613","DOI":"10.1128\/AEM.01613-20","article-title":"Carriage of extended-spectrum-beta-lactamase- and AmpC beta-lactamase-producing Escherichia coli strains from humans and pets in the same households.","volume":"86","author":"Toombs-Ruane","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"B71","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1111\/jsap.12525","article-title":"Antimicrobial-resistant Escherichia coli in hospitalised companion animals and their hospital environment.","volume":"57","author":"Tuerena","year":"2016","journal-title":"J. Small Anim. Pract."},{"key":"B72","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1093\/jac\/dkz462","article-title":"Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household.","volume":"75","author":"van den Bunt","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"B73","year":"2021","journal-title":"Supplementary material (UK-VARSS 2020). Veterinary antibiotic resistance and sales surveillance report (UK-VARSS 2020)."},{"key":"B74","year":"2022","journal-title":"UK - veterinary antibiotic resistance and sales surveillance report: 2021. Supplementary material 3 \u2013 resistance data\u2019, Veterinary antibiotic resistance and sales surveillance report (UK-VARSS 2021)."},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0231275","article-title":"Fecal shedding of Salmonella spp., Clostridium perfringens, and Clostridioides difficile in dogs fed raw meat-based diets in Brazil and their owners\u2019 motivation.","volume":"15","author":"Viegas","year":"2020","journal-title":"PLoS One"},{"key":"B76","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.jgar.2021.02.023","article-title":"Colistin-resistance mcr genes in Klebsiella pneumoniae from companion animals.","volume":"25","author":"Wang","year":"2021","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"B77","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.vetmic.2016.11.017","article-title":"Carriage of antimicrobial resistant Escherichia coli in dogs: Prevalence, associated risk factors and molecular characteristics.","volume":"199","author":"Wedley","year":"2017","journal-title":"Vet. Microbiol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1136\/vr.162.14.436","article-title":"Dog-human and dog-dog interactions of 260 dog-owning households in a community in Cheshire.","volume":"162","author":"Westgarth","year":"2008","journal-title":"Vet. Rec."},{"key":"B79","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1093\/jac\/dkm474","article-title":"Successful, multiresistant bacterial clones.","volume":"61","author":"Woodford","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"B80","doi-asserted-by":"publisher","first-page":"736","DOI":"10.1111\/j.1574-6976.2011.00268.x","article-title":"Multiresistant Gram-negative bacteria: The role of high-risk clones in the dissemination of antibiotic resistance.","volume":"35","author":"Woodford","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"B81","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-014-0659-0","article-title":"Nationwide high prevalence of CTX-M and an increase of CTX-M-55 in Escherichia coli isolated from patients with community-onset infections in Chinese county hospitals.","volume":"14","author":"Zhang","year":"2014","journal-title":"BMC Infect. Dis."},{"key":"B82","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2018.00062","article-title":"High prevalence of extended-spectrum \u03b2-lactamase producing Enterobacteriaceae among clinical isolates from cats and dogs admitted to a veterinary hospital in Switzerland.","volume":"5","author":"Zogg","year":"2018","journal-title":"Front. Vet. Sci."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1460143\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T04:43:22Z","timestamp":1725857002000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1460143\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,9]]},"references-count":82,"alternative-id":["10.3389\/fmicb.2024.1460143"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1460143","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,9]]},"article-number":"1460143"}}