{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T03:30:43Z","timestamp":1773199843398,"version":"3.50.1"},"reference-count":68,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2023,7,8]],"date-time":"2023-07-08T00:00:00Z","timestamp":1688774400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,7,8]],"date-time":"2023-07-08T00:00:00Z","timestamp":1688774400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, I. P.","award":["JPIAMR\/0002\/2016"],"award-info":[{"award-number":["JPIAMR\/0002\/2016"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, I. P.","award":["2020.07562.BD"],"award-info":[{"award-number":["2020.07562.BD"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, I. P.","award":["2020.06540.BD"],"award-info":[{"award-number":["2020.06540.BD"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, I. P.","award":["UIDB\/00276\/2020"],"award-info":[{"award-number":["UIDB\/00276\/2020"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, I. P.","award":["LA\/P\/0059\/2020"],"award-info":[{"award-number":["LA\/P\/0059\/2020"]}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/R000042\/1"],"award-info":[{"award-number":["MR\/R000042\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Eur J Clin Microbiol Infect Dis"],"published-print":{"date-parts":[[2023,8]]},"DOI":"10.1007\/s10096-023-04629-2","type":"journal-article","created":{"date-parts":[[2023,7,7]],"date-time":"2023-07-07T23:22:06Z","timestamp":1688772126000},"page":"1011-1024","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Longitudinal study of ESBL\/AmpC-producing Enterobacterales strains sharing between cohabiting healthy companion animals and humans in Portugal and in the United Kingdom"],"prefix":"10.1007","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4392-5372","authenticated-orcid":false,"given":"Juliana","family":"Menezes","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4601-4566","authenticated-orcid":false,"given":"Si\u00e2n-Marie","family":"Frosini","sequence":"additional","affiliation":[]},{"given":"Adriana","family":"Belas","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9648-6380","authenticated-orcid":false,"given":"C\u00e1tia","family":"Marques","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1983-4120","authenticated-orcid":false,"given":"Joana Moreira","family":"da Silva","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0958-5570","authenticated-orcid":false,"given":"Andreia J.","family":"Amaral","sequence":"additional","affiliation":[]},{"given":"Anette","family":"Loeffler","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0504-6820","authenticated-orcid":false,"given":"Constan\u00e7a","family":"Pomba","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,7,8]]},"reference":[{"key":"4629_CR1","volume-title":"Antimicrobial resistance in the EU\/EEA (EARS-Net) - Annual Epidemiological Report 2021","author":"European Centre for Disease Prevention and Control (ECDC)","year":"2022","unstructured":"European Centre for Disease Prevention and Control (ECDC) (2022) Antimicrobial resistance in the EU\/EEA (EARS-Net) - Annual Epidemiological Report 2021. ECDC, Stockholm"},{"key":"4629_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/femsre\/fuac031","volume":"46","author":"J Geurtsen","year":"2022","unstructured":"Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J (2022) Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol. Rev. 46:1\u201330. https:\/\/doi.org\/10.1093\/femsre\/fuac031","journal-title":"FEMS Microbiol. Rev."},{"key":"4629_CR3","unstructured":"World Health Organization (WHO) (2017) WHO publishes list of bacteria for which new antibiotics are urgently needed. World Health Organization.\u00a0https:\/\/www.who.int\/news\/item\/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed.\u00a0Accessed 14 Apr 2022"},{"key":"4629_CR4","doi-asserted-by":"publisher","first-page":"2222","DOI":"10.3390\/ijms19082222","volume":"19","author":"W Eiamphungporn","year":"2018","unstructured":"Eiamphungporn W, Schaduangrat N, Malik AA, Nantasenamat C (2018) Tackling the antibiotic resistance caused by class a \u03b2-lactamases through the use of \u03b2-lactamase inhibitory protein. Int. J. Mol. Sci. 19:2222. https:\/\/doi.org\/10.3390\/ijms19082222","journal-title":"Int. J. Mol. Sci."},{"key":"4629_CR5","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2021.6712","volume-title":"Third joint inter-agency report on integrated analysis of consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals in the EU\/EEA. JIACRA III 2016\u20132018. Stock","author":"European Centre for Disease Prevention and Control (ECDC), European Food Safety Authority (EFSA), European Medicines Agency (EMA)","year":"2021","unstructured":"European Centre for Disease Prevention and Control (ECDC), European Food Safety Authority (EFSA), European Medicines Agency (EMA) (2021) Third joint inter-agency report on integrated analysis of consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals in the EU\/EEA. JIACRA III 2016\u20132018. Stock. ECDC, EFSA, EMA, Parma, Amsterdam. https:\/\/doi.org\/10.2903\/j.efsa.2021.6712"},{"key":"4629_CR6","volume-title":"Critically important antimicrobials for human medicine, 6th revision","author":"World Health Organization (WHO)","year":"2019","unstructured":"World Health Organization (WHO) (2019) Critically important antimicrobials for human medicine, 6th revision. Licence CC BY-NC-SA 3.0 IGO"},{"key":"4629_CR7","volume-title":"Categorisation of antibiotics in the European Union","author":"European Medicines Agency (EMA)","year":"2019","unstructured":"European Medicines Agency (EMA) (2019) Categorisation of antibiotics in the European Union. European Medicines Agency (EMA)"},{"key":"4629_CR8","volume-title":"Antimicrobial resistance surveillance in Europe 2022 \u2013 2020 data","author":"WHO Regional Office for Europe\/European Centre for Disease Prevention and Control","year":"2022","unstructured":"WHO Regional Office for Europe\/European Centre for Disease Prevention and Control (2022) Antimicrobial resistance surveillance in Europe 2022 \u2013 2020 data. Copenhagen"},{"key":"4629_CR9","doi-asserted-by":"publisher","first-page":"2139","DOI":"10.1093\/jac\/dkw145","volume":"71","author":"MJ Day","year":"2016","unstructured":"Day MJ, Doumith M, Abernethy J, Hope R, Reynolds R, Wain J et al (2016) Population structure of Escherichia coli causing bacteraemia in the UK and Ireland between 2001 and 2010. J Antimicrob. Chemother 71:2139\u20132142. https:\/\/doi.org\/10.1093\/jac\/dkw145","journal-title":"J Antimicrob. Chemother"},{"key":"4629_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2019.01260","volume":"10","author":"A Bortolami","year":"2019","unstructured":"Bortolami A, Zendri F, Maciuca EI, Wattret A, Ellis C, Schmidt V et al (2019) Diversity, virulence, and clinical significance of extended-spectrum \u03b2-lactamase- and pAmpC-producing Escherichia coli from companion animals. Front Microbiol 10:1\u201315. https:\/\/doi.org\/10.3389\/fmicb.2019.01260","journal-title":"Front Microbiol"},{"key":"4629_CR11","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1093\/jac\/dky499","volume":"74","author":"C Marques","year":"2019","unstructured":"Marques C, Menezes J, Belas A, Aboim C, Cavaco-Silva P, Trigueiro G et al (2019) Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: Population structure, antimicrobial resistance and virulence genes. J Antimicrob. Chemother 74:594\u2013602. https:\/\/doi.org\/10.1093\/jac\/dky499","journal-title":"J Antimicrob. Chemother"},{"key":"4629_CR12","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1111\/j.1469-0691.2012.03795.x","volume":"18","author":"P Nordmann","year":"2012","unstructured":"Nordmann P, Cornaglia G (2012) Carbapenemase-producing Enterobacteriaceae: A call for action! Clin Microbiol. Infect 18:411\u2013412. https:\/\/doi.org\/10.1111\/j.1469-0691.2012.03795.x","journal-title":"Clin Microbiol. Infect"},{"key":"4629_CR13","doi-asserted-by":"publisher","first-page":"e02298","DOI":"10.1128\/AAC.02298-19","volume":"64","author":"M Brilhante","year":"2020","unstructured":"Brilhante M, Menezes J, Belas A, Feudi C, Schwarz S, Pomba C et al (2020) OXA-181-producing extra-intestinal pathogenic Escherichia coli ST410 isolated from a dog in Portugal. Antimicrob Agents Chemother 64:e02298\u2013e02219. https:\/\/doi.org\/10.1128\/AAC.02298-19","journal-title":"Antimicrob Agents Chemother"},{"key":"4629_CR14","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.1093\/jac\/dkz017","volume":"74","author":"ME Reynolds","year":"2019","unstructured":"Reynolds ME, Phan HTT, George S, Hubbard ATM, Stoesser N, Maciuca IE et al (2019) Occurrence and characterization of Escherichia coli ST410 co-harbouring blaNDM-5, blaCMY-42 and blaTEM-190 in a dog from the UK. J Antimicrob Chemother 74:1207\u20131211. https:\/\/doi.org\/10.1093\/jac\/dkz017","journal-title":"J Antimicrob Chemother"},{"key":"4629_CR15","doi-asserted-by":"publisher","first-page":"1700497","DOI":"10.2807\/1560-7917.ES.2018.23.27.1700497","volume":"23","author":"T Gr\u00f6nthal","year":"2018","unstructured":"Gr\u00f6nthal T, \u00d6sterblad M, Eklund M, Jalava J, Nyk\u00e4senoja S, Pekkanen K et al (2018) Sharing more than friendship \u2013 transmission of NDM-5 ST167 and CTX-M-9 ST69 Escherichia coli between dogs and humans in a family, Finland, 2015. Euro Surveill 23:1700497. https:\/\/doi.org\/10.2807\/1560-7917.ES.2018.23.27.1700497","journal-title":"Euro Surveill"},{"key":"4629_CR16","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1093\/jac\/dkw481","volume":"72","author":"C Pomba","year":"2017","unstructured":"Pomba C, Rantala M, Greko C, Baptiste KE, Catry B, van Duijkeren E et al (2017) Public health risk of antimicrobial resistance transfer from companion animals. J Antimicrob Chemother 72:957\u2013968. https:\/\/doi.org\/10.1093\/jac\/dkw481","journal-title":"J Antimicrob Chemother"},{"key":"4629_CR17","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/j.bjm.2015.11.005","volume":"47","author":"AC Carvalho","year":"2016","unstructured":"Carvalho AC, Barbosa AV, Arais LR, Ribeiro PF, Carneiro VC, Cerqueira AMF (2016) Resistance patterns, ESBL genes, and genetic relatedness of Escherichia coli from dogs and owners. Brazilian J Microbiol 47:150\u2013158. https:\/\/doi.org\/10.1016\/j.bjm.2015.11.005","journal-title":"Brazilian J Microbiol"},{"key":"4629_CR18","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1093\/jac\/dkz462","volume":"75","author":"G Van Den Bunt","year":"2020","unstructured":"Van Den Bunt G, Fluit AC, Spaninks MP, Timmerman AJ, Geurts Y, Kant A et al (2020) 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. J Antimicrob Chemother 75:342\u2013350. https:\/\/doi.org\/10.1093\/jac\/dkz462","journal-title":"J Antimicrob Chemother"},{"key":"4629_CR19","doi-asserted-by":"publisher","first-page":"1242","DOI":"10.3390\/antibiotics11091242","volume":"11","author":"AP Cozma","year":"2022","unstructured":"Cozma AP, Rimbu CM, Zendri F, Maciuca IE, Timofte D (2022) Clonal Dissemination of Extended-Spectrum Cephalosporin-Resistant Enterobacterales between Dogs and Humans in Households and Animal Shelters of Romania. Antibiotics 11:1242. https:\/\/doi.org\/10.3390\/antibiotics11091242","journal-title":"Antibiotics"},{"key":"4629_CR20","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1093\/jac\/49.1.77","volume":"49","author":"C F\u00e9ria","year":"2002","unstructured":"F\u00e9ria C, Ferreira E, Correia JD, Gon\u00e7alves J, Cani\u00e7a M (2002) Patterns and mechanisms of resistance to \u03b2-lactams and \u03b2-lactamase inhibitors in uropathogenic Escherichia coli isolated from dogs in Portugal. J Antimicrob Chemother 49:77\u201385. https:\/\/doi.org\/10.1093\/jac\/49.1.77","journal-title":"J Antimicrob Chemother"},{"key":"4629_CR21","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1093\/ajcp\/107.3.368","volume":"107","author":"SM Salisbury","year":"1997","unstructured":"Salisbury SM, Sabatini LM, Spiegel CA (1997) Identification of methicillin-resistant staphylococci by multiplex polymerase chain reaction assay. Am J Clin Pathol 107:368\u2013373. https:\/\/doi.org\/10.1093\/ajcp\/107.3.368","journal-title":"Am J Clin Pathol"},{"key":"4629_CR22","doi-asserted-by":"publisher","first-page":"3108","DOI":"10.1128\/JCM.01468-12","volume":"50","author":"M Doumith","year":"2012","unstructured":"Doumith M, Day MJ, Hope R, Wain J, Woodford N (2012) Improved multiplex PCR strategy for rapid assignment of the four major Escherichia coli phylogenetic groups. J Clin Microbiol 50:3108\u20133110. https:\/\/doi.org\/10.1128\/JCM.01468-12","journal-title":"J Clin Microbiol"},{"key":"4629_CR23","doi-asserted-by":"publisher","first-page":"6823","DOI":"10.1093\/nar\/19.24.6823","volume":"19","author":"J Versalovic","year":"1991","unstructured":"Versalovic J, Koeuth T, Lupski R (1991) Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes. Nucleic Acids Res 19:6823\u20136831. https:\/\/doi.org\/10.1093\/nar\/19.24.6823","journal-title":"Nucleic Acids Res"},{"key":"4629_CR24","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1111\/j.1365-2958.2006.05172.x","volume":"60","author":"T Wirth","year":"2006","unstructured":"Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH et al (2006) Sex and virulence in Escherichia coli: An evolutionary perspective. Mol Microbiol 60:1136\u20131151. https:\/\/doi.org\/10.1111\/j.1365-2958.2006.05172.x","journal-title":"Mol Microbiol"},{"key":"4629_CR25","doi-asserted-by":"publisher","first-page":"4178","DOI":"10.1128\/JCM.43.8.4178-4182.2005","volume":"43","author":"L Diancourt","year":"2005","unstructured":"Diancourt L, Passet V, Verhoef J, Grimont PAD, Brisse S (2005) Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates. J Clin Microbiol 43:4178\u20134182. https:\/\/doi.org\/10.1128\/JCM.43.8.4178-4182.2005","journal-title":"J Clin Microbiol"},{"issue":"10","key":"4629_CR26","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1186\/1471-2105-10-152","volume":"18","author":"AP Francisco","year":"2009","unstructured":"Francisco AP, Bugalho M, Ramirez M, Carri\u00e7o JA (2009) Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics 18(10):152. https:\/\/doi.org\/10.1186\/1471-2105-10-152","journal-title":"BMC Bioinformatics"},{"key":"4629_CR27","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1093\/jac\/dki398","volume":"57","author":"C Eckert","year":"2006","unstructured":"Eckert C, Gautier V, Arlet G (2006) DNA sequence analysis of the genetic environment of various blaCTX-M genes. J Antimicrob Chemother 57:14\u201323. https:\/\/doi.org\/10.1093\/jac\/dki398","journal-title":"J Antimicrob Chemother"},{"key":"4629_CR28","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/j.diagmicrobio.2006.03.005","volume":"56","author":"C Pomba","year":"2006","unstructured":"Pomba C, Mendon\u00e7a N, Costa M, Louro D, Baptista B, Ferreira M et al (2006) Improved multiplex PCR method for the rapid detection of \u03b2-lactamase genes in Escherichia coli of animal origin. Diagn Microbiol Infect Dis 56:103\u2013106. https:\/\/doi.org\/10.1016\/j.diagmicrobio.2006.03.005","journal-title":"Diagn Microbiol Infect Dis"},{"key":"4629_CR29","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.diagmicrobio.2010.12.002","volume":"70","author":"L Poirel","year":"2011","unstructured":"Poirel L, Walsh TR, Cuvillier V, Nordmann P (2011) Multiplex PCR for detection of acquired carbapenemase genes. Diagn Microbiol Infect Dis 70:119\u2013123. https:\/\/doi.org\/10.1016\/j.diagmicrobio.2010.12.002","journal-title":"Diagn Microbiol Infect Dis"},{"key":"4629_CR30","unstructured":"European Committee on Antimicrobial Susceptibility Testing (EUCAST) (2023) Breakpoint tables for interpretation of MICs and zone diameters European Committee on Antimicrobial susceptibility testing breakpoint tables for interpretation of MICs and zone diameters Version 13.0 http:\/\/www.eucast.org. Accessed 31 Jan 2023"},{"key":"4629_CR31","volume-title":"Performance Standards for Antimicrobial Susceptibility Testing","author":"Clinical and Laboratory Standards Institute (CLSI)","year":"2020","unstructured":"Clinical and Laboratory Standards Institute (CLSI) (2020) Performance Standards for Antimicrobial Susceptibility Testing, 30th edn. Clinical and Laboratory Standards Institute, Wayne, Pennsylvania","edition":"30"},{"key":"4629_CR32","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","volume":"18","author":"A Magiorakos","year":"2012","unstructured":"Magiorakos A, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG et al (2012) Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 18:268\u2013281. https:\/\/doi.org\/10.1111\/j.1469-0691.2011.03570.x","journal-title":"Clin Microbiol Infect"},{"key":"4629_CR33","unstructured":"Andrews S (2010) A quality control tool for high throughput sequence data. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc. Accessed 10 Jan 2021"},{"key":"4629_CR34","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","volume":"27","author":"R Schmieder","year":"2011","unstructured":"Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863\u2013864. https:\/\/doi.org\/10.1093\/bioinformatics\/btr026","journal-title":"Bioinformatics"},{"key":"4629_CR35","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS et al (2012) SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455\u2013477. https:\/\/doi.org\/10.1089\/cmb.2012.0021","journal-title":"J Comput Biol"},{"key":"4629_CR36","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S et al (2014) Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. https:\/\/doi.org\/10.1371\/journal.pone.0112963","journal-title":"PLoS One"},{"key":"4629_CR37","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30:2068\u20132069. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153","journal-title":"Bioinformatics"},{"key":"4629_CR38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0524-x","volume":"15","author":"TJ Treangen","year":"2014","unstructured":"Treangen TJ, Ondov BD, Koren S, Phillippy AM (2014) The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15:1\u201315. https:\/\/doi.org\/10.1186\/s13059-014-0524-x","journal-title":"Genome Biol"},{"key":"4629_CR39","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD et al (2015) Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 43:e15. https:\/\/doi.org\/10.1093\/nar\/gku1196","journal-title":"Nucleic Acids Res"},{"key":"4629_CR40","doi-asserted-by":"publisher","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","volume":"35","author":"AM Kozlov","year":"2019","unstructured":"Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A (2019) RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453\u20134455. https:\/\/doi.org\/10.1093\/bioinformatics\/btz305","journal-title":"Bioinformatics"},{"key":"4629_CR41","unstructured":"Seemann T, Kl\u00f6tzl F, Page AJ (2021) snp-dists. https:\/\/github.com\/tseemann\/snp-dists. Accessed 20 Jan 2022"},{"key":"4629_CR42","doi-asserted-by":"publisher","first-page":"e000093","DOI":"10.1099\/mgen.0.000093","volume":"2","author":"S Argim\u00f3n","year":"2016","unstructured":"Argim\u00f3n S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C et al (2016) Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb genomics 2:e000093. https:\/\/doi.org\/10.1099\/mgen.0.000093","journal-title":"Microb genomics"},{"key":"4629_CR43","unstructured":"Technical University of Denmark (DTU) (2011) Center for genomic epidemiology. http:\/\/www.genomicepidemiology.org"},{"key":"4629_CR44","doi-asserted-by":"publisher","first-page":"2161","DOI":"10.1128\/AAC.47.7.2161-2168.2003","volume":"47","author":"JR Johnson","year":"2003","unstructured":"Johnson JR, Murray AC, Gajewski A, Sullivan M, Snippes P, Kuskowski MA et al (2003) Isolation and molecular characterization of nalidixic acid-resistant extraintestinal pathogenic Escherichia coli from retail chicken products. Antimicrob Agents Chemother 47:2161\u20132168. https:\/\/doi.org\/10.1128\/AAC.47.7.2161-2168.2003","journal-title":"Antimicrob Agents Chemother"},{"key":"4629_CR45","doi-asserted-by":"publisher","first-page":"4115","DOI":"10.1128\/IAI.00752-12","volume":"80","author":"RR Spurbeck","year":"2012","unstructured":"Spurbeck RR, Dinh PC, Walk ST, Stapleton AE, Hooton TM, Nolan LK et al (2012) Escherichia coli isolates that carry vat, fyua, chua, and yfcv efficiently colonize the urinary tract. Infect Immun 80:4115\u20134122. https:\/\/doi.org\/10.1128\/IAI.00752-12","journal-title":"Infect Immun"},{"issue":"55","key":"4629_CR46","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1093\/cid\/cis502","volume":"1","author":"AR Manges","year":"2012","unstructured":"Manges AR, Johnson JR (2012) Food-Borne Origins of Escherichia coli Causing Extraintestinal Infections. Clin Infect Dis 1(55):712\u2013719. https:\/\/doi.org\/10.1093\/cid\/cis502","journal-title":"Clin Infect Dis"},{"key":"4629_CR47","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1128\/CMR.00116-14","volume":"28","author":"AJ Mathers","year":"2015","unstructured":"Mathers AJ, Peirano G, Pitout JDD (2015) The role of epidemic resistance plasmids and international high- risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 28:565\u2013591. https:\/\/doi.org\/10.1128\/CMR.00116-14","journal-title":"Clin Microbiol Rev"},{"key":"4629_CR48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12917-016-0840-3","volume":"12","author":"C Marques","year":"2016","unstructured":"Marques C, Gama LT, Belas A, Bergstr\u00f6m K, Beurlet S, Briend-Marchal A et al (2016) European multicenter study on antimicrobial resistance in bacteria isolated from companion animal urinary tract infections. BMC Vet Res 12:1\u201317. https:\/\/doi.org\/10.1186\/s12917-016-0840-3","journal-title":"BMC Vet Res"},{"key":"4629_CR49","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.prevetmed.2015.01.013","volume":"119","author":"VM Schmidt","year":"2015","unstructured":"Schmidt VM, Pinchbeck GL, Nuttall T, McEwan N, Dawson S, Williams NJ (2015) Antimicrobial resistance risk factors and characterisation of faecal E. coli isolated from healthy Labrador retrievers in the United Kingdom. Prev Vet Med 119:31\u201340. https:\/\/doi.org\/10.1016\/j.prevetmed.2015.01.013","journal-title":"Prev Vet Med"},{"key":"4629_CR50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/antibiotics10081013","volume":"10","author":"I Carvalho","year":"2021","unstructured":"Carvalho I, Cunha R, Martins C, Mart\u00ednez-\u00c1lvarez S, Chenouf NS, Pimenta P et al (2021) Antimicrobial resistance genes and diversity of clones among faecal ESBL-producing Escherichia coli isolated from healthy and sick dogs living in Portugal. Antibiotics 10:1\u201315. https:\/\/doi.org\/10.3390\/antibiotics10081013","journal-title":"Antibiotics"},{"key":"4629_CR51","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.tvjl.2014.12.026","volume":"203","author":"RC Rocha-Gracia","year":"2015","unstructured":"Rocha-Gracia RC, Cort\u00e9s-Cort\u00e9s G, Lozano-Zarain P, Bello F, Mart\u00ednez-Laguna Y, Torres C (2015) Faecal Escherichia coli isolates from healthy dogs harbour CTX-M-15 and CMY-2 \u03b2-lactamases. Vet J 203:315\u2013319. https:\/\/doi.org\/10.1016\/j.tvjl.2014.12.026","journal-title":"Vet J"},{"key":"4629_CR52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0206252","volume":"13","author":"T Boehmer","year":"2018","unstructured":"Boehmer T, Vogler AJ, Thomas A, Sauer S, Hergenroether M, Straubinger RK et al (2018) Phenotypic characterization and whole genome analysis of extended-spectrum betalactamase-producing bacteria isolated from dogs in Germany. PLoS One 13:1\u201317. https:\/\/doi.org\/10.1371\/journal.pone.0206252","journal-title":"PLoS One"},{"key":"4629_CR53","doi-asserted-by":"publisher","first-page":"510","DOI":"10.3390\/antibiotics10050510","volume":"10","author":"JA Benavides","year":"2021","unstructured":"Benavides JA, Salgado-Caxito M, Opazo-Capurro A, Mu\u00f1oz PG, Pi\u00f1eiro A, Medina MO et al (2021) ESBL-producing Escherichia coli carrying CTX-M genes circulating among livestock, dogs, and wild mammals in small-scale farms of central Chile. Antibiotics 10:510. https:\/\/doi.org\/10.3390\/antibiotics10050510","journal-title":"Antibiotics"},{"key":"4629_CR54","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1016\/j.jgar.2020.07.004","volume":"22","author":"C Fournier","year":"2020","unstructured":"Fournier C, Aires de Sousa M, Fuster Escriva B, Sales L, Nordmann P, Poirel L (2020) Epidemiology of extended-spectrum \u03b2-lactamase-producing Enterobacteriaceae among healthcare students, at the Portuguese Red Cross Health School of Lisbon. Portugal J Glob Antimicrob Resist 22:733\u2013737. https:\/\/doi.org\/10.1016\/j.jgar.2020.07.004","journal-title":"Portugal J Glob Antimicrob Resist"},{"key":"4629_CR55","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1093\/cid\/ciw283","volume":"63","author":"S Karanika","year":"2016","unstructured":"Karanika S, Karantanos T, Arvanitis M, Grigoras C, Mylonakis E (2016) Fecal Colonization with Extended-spectrum Beta-lactamase-Producing Enterobacteriaceae and Risk Factors among Healthy Individuals: A Systematic Review and Metaanalysis. Clin Infect Dis 63:310\u2013318. https:\/\/doi.org\/10.1093\/cid\/ciw283","journal-title":"Clin Infect Dis"},{"key":"4629_CR56","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1089\/mdr.2019.0205","volume":"00","author":"I Carvalho","year":"2020","unstructured":"Carvalho I, Alonso CA, Silva V, Pimenta P, Cunha R, Martins C et al (2020) Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolated from Healthy and Sick Dogs in Portugal. Microb Drug Resist 00:1\u20137. https:\/\/doi.org\/10.1089\/mdr.2019.0205","journal-title":"Microb Drug Resist"},{"key":"4629_CR57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13756-021-01012-8","volume":"10","author":"AP Meijs","year":"2021","unstructured":"Meijs AP, Gijsbers EF, Hengeveld PD, Dierikx CM, de Greeff SC, van Duijkeren E (2021) ESBL\/pAmpC-producing Escherichia coli and Klebsiella pneumoniae carriage among veterinary healthcare workers in the Netherlands. Antimicrob Resist Infect Control 10:1\u201312. https:\/\/doi.org\/10.1186\/s13756-021-01012-8","journal-title":"Antimicrob Resist Infect Control"},{"key":"4629_CR58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-016-1655-3","volume":"16","author":"AS Ouedraogo","year":"2016","unstructured":"Ouedraogo AS, Sanou M, Kissou A, Sanou S, Solar\u00e9 H, Kabor\u00e9 F et al (2016) High prevalence of extended-spectrum \u00df-lactamase producing enterobacteriaceae among clinical isolates in Burkina Faso. BMC Infect Dis 16:1\u20139. https:\/\/doi.org\/10.1186\/s12879-016-1655-3","journal-title":"BMC Infect Dis"},{"key":"4629_CR59","doi-asserted-by":"publisher","first-page":"100236","DOI":"10.1016\/j.onehlt.2021.100236","volume":"12","author":"M Salgado-Caxito","year":"2021","unstructured":"Salgado-Caxito M, Benavides JA, Adell AD, Paes AC, Moreno-Switt AI (2021) Global prevalence and molecular characterization of extended-spectrum \u03b2-lactamase producing-Escherichia coli in dogs and cats \u2013 A scoping review and meta-analysis. One Heal 12:100236. https:\/\/doi.org\/10.1016\/j.onehlt.2021.100236","journal-title":"One Heal"},{"key":"4629_CR60","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1093\/jac\/dkx401","volume":"73","author":"C Marques","year":"2018","unstructured":"Marques C, Belas A, Franco A, Aboim C, Gama LT, Pomba C (2018) Increase in antimicrobial resistance and emergence of major international high-risk clonal lineages in dogs and cats with urinary tract infection: 16 year retrospective study. J Antimicrob Chemother 73:377\u2013384. https:\/\/doi.org\/10.1093\/jac\/dkx401","journal-title":"J Antimicrob Chemother"},{"key":"4629_CR61","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1016\/S1473-3099(16)30527-8","volume":"17","author":"Y Wang","year":"2017","unstructured":"Wang Y, Tian GB, Zhang R, Shen Y, Tyrrell JM, Huang X et al (2017) Prevalence, risk factors, outcomes, and molecular epidemiology of mcr-1-positive Enterobacteriaceae in patients and healthy adults from China: an epidemiological and clinical study. Lancet Infect Dis 17:390\u2013399. https:\/\/doi.org\/10.1016\/S1473-3099(16)30527-8","journal-title":"Lancet Infect Dis"},{"key":"4629_CR62","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1128\/JCM.01319-06","volume":"45","author":"S Tofteland","year":"2007","unstructured":"Tofteland S, Haldorsen B, Dahl KH, Simonsen GS, Steinbakk M, Walsh TR et al (2007) Effects of phenotype and genotype on methods for detection of extended-spectrum-\u03b2-lactamase-producing clinical isolates of Escherichia coli and Klebsiella pneumoniae in Norway. J Clin Microbiol 45:199\u2013205. https:\/\/doi.org\/10.1128\/JCM.01319-06","journal-title":"J Clin Microbiol"},{"key":"4629_CR63","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2019.01994","volume":"10","author":"P Zhang","year":"2019","unstructured":"Zhang P, Wang J, Wang X, Bai X, Ma J, Dang R et al (2019) Characterization of five Escherichia coli isolates co-expressing ESBL and MCR-1 resistance mechanisms from different origins in China. Front Microbiol 10:1\u20139. https:\/\/doi.org\/10.3389\/fmicb.2019.01994","journal-title":"Front Microbiol"},{"key":"4629_CR64","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/antibiotics9080468","volume":"9","author":"F Abreu-Salinas","year":"2020","unstructured":"Abreu-Salinas F, D\u00edaz-Jim\u00e9nez D, Garc\u00eda-Meni\u00f1o I, Lumbreras P, L\u00f3pez-Beceiro AM, Fidalgo LE et al (2020) High prevalence and diversity of cephalosporin-resistant enterobacteriaceae including extraintestinal pathogenic E. coli cc648 lineage in rural and urban dogs in Northwest Spain. Antibiotics 9:1\u201312. https:\/\/doi.org\/10.3390\/antibiotics9080468","journal-title":"Antibiotics"},{"key":"4629_CR65","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-019-0569-1","volume":"2","author":"Y Feng","year":"2019","unstructured":"Feng Y, Liu L, Lin J, Ma K, Long H, Wei L et al (2019) Key evolutionary events in the emergence of a globally disseminated, carbapenem resistant clone in the Escherichia coli ST410 lineage. Commun Biol 2:1\u201313. https:\/\/doi.org\/10.1038\/s42003-019-0569-1","journal-title":"Commun Biol"},{"key":"4629_CR66","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/msphere.00337-18","volume":"3","author":"L Roer","year":"2018","unstructured":"Roer L, Overballe-Petersen S, Hansen F, Sch\u00f8nning K, Wang M, R\u00f8der BL et al (2018) Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones. mSphere 3:1\u201314. https:\/\/doi.org\/10.1128\/msphere.00337-18","journal-title":"mSphere"},{"key":"4629_CR67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/femsec\/fiv155","volume":"92","author":"K Schaufler","year":"2016","unstructured":"Schaufler K, Semmler T, Wieler LH, W\u00f6hrmann M, Baddam R, Ahmed N et al (2016) Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410-another successful pandemic clone? FEMS Microbiol Ecol 92:1\u20139. https:\/\/doi.org\/10.1093\/femsec\/fiv155","journal-title":"FEMS Microbiol Ecol"},{"key":"4629_CR68","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/AAC.01118-20","volume":"65","author":"K Nesporova","year":"2020","unstructured":"Nesporova K, Wyrsch ER, Valcek A, Bitar I, Chaw K, Harris P et al (2020) Escherichia coli Sequence Type 457 is an Emerging Extended- Spectrum-\u03b2-Lactam-Resistant Lineage with Reservoirs in Wildlife and Food-Producing Animals. Antimicrob Agents Chemother 65:1\u201318. https:\/\/doi.org\/10.1128\/AAC.01118-20","journal-title":"Antimicrob Agents Chemother"}],"container-title":["European Journal of Clinical Microbiology &amp; Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10096-023-04629-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10096-023-04629-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10096-023-04629-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T11:38:47Z","timestamp":1758973127000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10096-023-04629-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,8]]},"references-count":68,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2023,8]]}},"alternative-id":["4629"],"URL":"https:\/\/doi.org\/10.1007\/s10096-023-04629-2","relation":{},"ISSN":["0934-9723","1435-4373"],"issn-type":[{"value":"0934-9723","type":"print"},{"value":"1435-4373","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,8]]},"assertion":[{"value":"15 February 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 June 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 July 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 September 2025","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Update","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The original online version of this article was revised: The Funder name and Funder ID were incorrectly given. These data have been corrected.","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The study was conducted in accordance with the European Union Directive 2010\/63\/EU on the protection of animals used for scientific purposes and the Declaration of Helsinki. Ethical approval for collection of samples and data from humans, dogs and cats was obtained from Faculty of Veterinary Medicine, University of Lisbon Ethics Committee for Research and Education (CEBEA 027\/2018), and Royal Veterinary College Ethics and Welfare Committee (URN 2017 1750-3).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"Written informed consent was obtained prior to enrolment from each human participant included in the study for themselves and their companion animals.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to participate"}},{"value":"Informed consent was obtained from all individual participants included in the study, for themselves and their companion animals.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}