{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T07:05:12Z","timestamp":1790665512226,"version":"4.1.0"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,12,11]],"date-time":"2021-12-11T00:00:00Z","timestamp":1639180800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Research Programme \u2018Antimicrobial Resistance\u2019"},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["40AR40_180179"],"award-info":[{"award-number":["40AR40_180179"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["407240\u2013167121"],"award-info":[{"award-number":["407240\u2013167121"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Eccellenza Fellowship","award":["PCEFP3_181248"],"award-info":[{"award-number":["PCEFP3_181248"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Next-generation sequencing has considerably increased the number of genomes available in the public domain. However, efforts to use these genomes for surveillance of antimicrobial resistance have thus far been limited and geographically heterogeneous. We inferred global resistance trends in Escherichia coli in food animals using genomes from public databases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We retrieved 7632 E. coli genomes from public databases (NCBI, PATRIC and EnteroBase) and screened for antimicrobial resistance genes (ARGs) using ResFinder. Selection bias towards resistance, virulence or specific strains was accounted for by screening BioProject descriptions. Temporal trends for MDR, resistance to antimicrobial classes and ARG prevalence were inferred using generalized linear models for all genomes, including those not subjected to selection bias.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>MDR increased by 1.6 times between 1980 and 2018, as genomes carried, on average, ARGs conferring resistance to 2.65 antimicrobials in swine, 2.22 in poultry and 1.58 in bovines. Highest resistance levels were observed for tetracyclines (42.2%\u201369.1%), penicillins (19.4%\u201347.5%) and streptomycin (28.6%\u201356.6%). Resistance trends were consistent after accounting for selection bias, although lower mean absolute resistance estimates were associated with genomes not subjected to selection bias (difference of 3.16%\u00b13.58% across years, hosts and antimicrobial classes). We observed an increase in extended-spectrum cephalosporin ARG blaCMY-2 and a progressive substitution of tetB by tetA. Estimates of resistance prevalence inferred from genomes in the public domain were in good agreement with reports from systematic phenotypic surveillance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Our analysis illustrates the potential of using the growing volume of genomes in public databases to track AMR trends globally.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkab451","type":"journal-article","created":{"date-parts":[[2021,11,27]],"date-time":"2021-11-27T20:09:15Z","timestamp":1638043755000},"page":"646-655","source":"Crossref","is-referenced-by-count":23,"title":["Increase in antimicrobial resistance in <i>Escherichia coli<\/i> in food animals between 1980 and 2018 assessed using genomes from public databases"],"prefix":"10.1093","volume":"77","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9738-4423","authenticated-orcid":false,"given":"Jo\u00e3o","family":"Pires","sequence":"first","affiliation":[{"name":"Institute for Environmental Decisions, ETH Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1782-8109","authenticated-orcid":false,"given":"Jana S","family":"Huisman","sequence":"additional","affiliation":[{"name":"Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8052-3925","authenticated-orcid":false,"given":"Sebastian","family":"Bonhoeffer","sequence":"additional","affiliation":[{"name":"Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6556-0952","authenticated-orcid":false,"given":"Thomas P","family":"Van Boeckel","sequence":"additional","affiliation":[{"name":"Institute for Environmental Decisions, ETH Zurich, Zurich, Switzerland"},{"name":"Center for Disease Dynamics, Economics & Policy, New Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,12,11]]},"reference":[{"key":"2022022312594068500_dkab451-B1","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/S0140-6736(15)00473-0","article-title":"Understanding the mechanisms and drivers of antimicrobial resistance","volume":"387","author":"Holmes","year":"2016","journal-title":"Lancet"},{"key":"2022022312594068500_dkab451-B2","doi-asserted-by":"crossref","first-page":"20140083","DOI":"10.1098\/rstb.2014.0083","article-title":"Antimicrobial resistance in humans, livestock and the wider environment","volume":"370","author":"Woolhouse","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"2022022312594068500_dkab451-B3","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1073\/pnas.1503141112","article-title":"Global trends in antimicrobial use in food animals","volume":"112","author":"Van Boeckel","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022022312594068500_dkab451-B4","author":"Center for Veterinary Medicine and Food and Drug Administration","year":"2019"},{"key":"2022022312594068500_dkab451-B5","doi-asserted-by":"crossref","first-page":"20140085","DOI":"10.1098\/rstb.2014.0085","article-title":"The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward","volume":"370","author":"Aarestrup","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"2022022312594068500_dkab451-B6","doi-asserted-by":"crossref","first-page":"242","DOI":"10.3389\/fpubh.2019.00242","article-title":"Using genomics to track global antimicrobial resistance","volume":"7","author":"Hendriksen","year":"2019","journal-title":"Front Public Health"},{"key":"2022022312594068500_dkab451-B7","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.envint.2018.04.041","article-title":"Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance","volume":"117","author":"Larsson","year":"2018","journal-title":"Environ Int"},{"key":"2022022312594068500_dkab451-B8","doi-asserted-by":"crossref","first-page":"e51","DOI":"10.1016\/S1473-3099(20)30003-7","article-title":"The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years later","volume":"20","author":"Laxminarayan","year":"2020","journal-title":"Lancet Infect Dis"},{"key":"2022022312594068500_dkab451-B9","author":"NCBI. 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