{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T02:27:39Z","timestamp":1781058459242,"version":"3.54.1"},"reference-count":37,"publisher":"American Society for Microbiology","issue":"13","license":[{"start":{"date-parts":[[2018,6,18]],"date-time":"2018-06-18T00:00:00Z","timestamp":1529280000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,7,1]],"date-time":"2018-07-01T00:00:00Z","timestamp":1530403200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100005825","name":"USDA | National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2010-51110-21083"],"award-info":[{"award-number":["2010-51110-21083"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"USDA | National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2008-35201-04682"],"award-info":[{"award-number":["2008-35201-04682"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"USDA | National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2008-35210-30235"],"award-info":[{"award-number":["2008-35210-30235"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"USDA | National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2015-68003-23048"],"award-info":[{"award-number":["2015-68003-23048"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2018,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Treatment of food-producing animals with antimicrobial drugs (AMD) is controversial because of concerns regarding promotion of antimicrobial resistance (AMR). To investigate this concern, resistance genes in metagenomic bovine fecal samples during a clinical trial were analyzed to assess the impacts of treatment on beef feedlot cattle resistomes. Four groups of cattle were exposed, using a 2-by-2 factorial design, to different regimens of antimicrobial treatment. Injections of ceftiofur crystalline-free acid (a third-generation cephalosporin) were used to treat all cattle in treatment pens or only a single animal, and either chlortetracycline was included in the feed of all cattle in a pen or the feed was untreated. On days 0 and 26, respectively, pre- and posttrial fecal samples were collected, and resistance genes were characterized using shotgun metagenomics. Treatment with ceftiofur was not associated with changes to \u03b2-lactam resistance genes. However, cattle fed chlortetracycline had a significant increase in relative abundance of tetracycline resistance genes. There was also an increase of an AMR class not administered during the study, which is a possible indicator of coselection of resistance genes. Samples analyzed in this study had previously been evaluated by culture characterization (\n            <jats:named-content content-type=\"genus-species\">Escherichia coli<\/jats:named-content>\n            and\n            <jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>\n            ) and quantitative PCR (qPCR) of metagenomic fecal DNA, which allowed comparison of results with this study. In the majority of samples, genes that were selectively enriched through culture and qPCR were not identified through shotgun metagenomic sequencing in this study, suggesting that changes previously documented did not reflect changes affecting the majority of bacterial genetic elements found in the predominant fecal resistome.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            Despite significant concerns about public health implications of AMR in relation to use of AMD in food animals, there are many unknowns about the long- and short-term impact of common uses of AMD for treatment, control, and prevention of disease. Additionally, questions commonly arise regarding how to best measure and quantify AMR genes in relation to public health risks and how to determine which genes are most important. These data provide an introductory view of the utility of using shotgun metagenomic sequencing data as an outcome for clinical trials evaluating the impact of using AMD in food animals.\n          <\/jats:p>","DOI":"10.1128\/aem.00610-18","type":"journal-article","created":{"date-parts":[[2018,5,1]],"date-time":"2018-05-01T10:03:04Z","timestamp":1525168984000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":37,"title":["Effects of Ceftiofur and Chlortetracycline on the Resistomes of Feedlot Cattle"],"prefix":"10.1128","volume":"84","author":[{"given":"Margaret D.","family":"Weinroth","sequence":"first","affiliation":[{"name":"Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. Morgan","family":"Scott","sequence":"additional","affiliation":[{"name":"Department of Veterinary Pathobiology, Texas A&amp;M University, College Station, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Norby","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy H.","family":"Loneragan","sequence":"additional","affiliation":[{"name":"Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6149-1008","authenticated-orcid":false,"given":"Noelle R.","family":"Noyes","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Rovira","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Investigacion Agropecuaria, Treinta y Tres, Uruguay"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrique","family":"Doster","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of California\u2014Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dale R.","family":"Woerner","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul S.","family":"Morley","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keith E.","family":"Belk","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","volume-title":"Global action plan on antimicrobial resistance","author":"World Health Organization","year":"2015","unstructured":"World Health Organization. 2015. 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