{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T03:40:56Z","timestamp":1790826056615,"version":"4.1.0"},"reference-count":78,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T00:00:00Z","timestamp":1606953600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008648","name":"Krajowy Naukowy Osrodek Wiodacy","doi-asserted-by":"publisher","award":["05-1\/KNOW2\/2015"],"award-info":[{"award-number":["05-1\/KNOW2\/2015"]}],"id":[{"id":"10.13039\/501100008648","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Fonden","doi-asserted-by":"publisher","award":["NNF16OC0021856"],"award-info":[{"award-number":["NNF16OC0021856"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.<\/jats:p>","DOI":"10.1371\/journal.pone.0242987","type":"journal-article","created":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T14:13:22Z","timestamp":1607004802000},"page":"e0242987","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":55,"title":["A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5666-9510","authenticated-orcid":true,"given":"Magdalena","family":"Skar\u017cy\u0144ska","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pimlapas","family":"Leekitcharoenphon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2934-8214","authenticated-orcid":true,"given":"Rene S.","family":"Hendriksen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank M.","family":"Aarestrup","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dariusz","family":"Wasyl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2020,12,3]]},"reference":[{"key":"pone.0242987.ref001","volume-title":"Antimicrobial resistance: global report on surveillance","author":"World Health Organization","year":"2014"},{"key":"pone.0242987.ref002","volume-title":"he bacterial challenge: Time to React. 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Chemother"},{"issue":"3","key":"pone.0242987.ref043","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.ijantimicag.2017.03.013","article-title":"A cfr-like gene cfr(C) conferring linezolid resistance is common in Clostridium difficile","volume":"50","author":"T Candela","year":"2017","journal-title":"Int J Antimicrob Agents"},{"key":"pone.0242987.ref044","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.anaerobe.2018.04.012","article-title":"Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome","volume":"53","author":"S Connelly","year":"2018","journal-title":"Anaerobe"},{"issue":"5","key":"pone.0242987.ref045","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1099\/0022-1317-49-5-427","article-title":"Prevalence of the carbapenemase gene (cfiA) among clinical and normal flora isolates of Bacteroides species in Hungary","volume":"49","author":"J Soki","year":"2000","journal-title":"J Med 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animals, Spain","volume":"72","author":"C Lozano","year":"2016","journal-title":"Microb Ecol"},{"issue":"3","key":"pone.0242987.ref049","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1089\/mdr.2007.759","article-title":"Characterization of vanA-containing Enterococcus faecium isolates carrying Tn5397-like and Tn916\/Tn1545-like transposons in wild boars (Sus Scrofa)","volume":"13","author":"P Poeta","year":"2007","journal-title":"Microb Drug Resist"},{"issue":"1","key":"pone.0242987.ref050","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/S0167-5877(96)01119-1","article-title":"Avoparcin used as a growth promoter is associated with the occurrence of vancomycin-resistant Enterococcus faecium on Danish poultry and pig farms","volume":"31","author":"F Bager","year":"1997","journal-title":"Prev Vet Med"},{"key":"pone.0242987.ref051","first-page":"11","article-title":"Commission Directive 97\/6\/EC of 30 January 1997 amending Council Directive 70\/524\/EEC concerning additives in feedingstuffs","volume":"1997","author":"European Commission","year":"1997","journal-title":"Off J Eur Commun"},{"issue":"7","key":"pone.0242987.ref052","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.1128\/JCM.38.7.2774-2777.2000","article-title":"Characterization of glycopeptide-resistant enterococcus faecium (GRE) from broilers and pigs in Denmark: genetic evidence that persistence of GRE in pig herds is associated with coselection by resistance to macrolides","volume":"38","author":"FM Aarestrup","year":"2000","journal-title":"J Clin Microbiol"},{"key":"pone.0242987.ref053","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1016\/j.envpol.2018.03.052","article-title":"Global review and analysis of erythromycin in the environment: Occurrence, bioaccumulation and antibiotic resistance hazards","volume":"238","author":"BH Schafhauser","year":"2018","journal-title":"Environ Pollut"},{"key":"pone.0242987.ref054","volume-title":"Assessment of the 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The 2010 Scientific Report, 2010. Development of harmonized schemes for monitoring and reporting of rabies in animals in the European Union. Parma: EFSA; 2010 Jul. EFSA Supporting Publication 7(7):Report no. EN-67. 60 p. Contract\/grant no. 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