title: Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin.
abstract: Although dairy manure is widely applied to land, it is relatively understudied compared to other livestock as a potential source of antibiotic resistance genes (ARGs) to the environment and ultimately to human pathogens. Ceftiofur, the most widely used antibiotic used in U.S. dairy cows, is a 3rd generation cephalosporin, a critically important class of antibiotics to human health. The objective of this study was to evaluate the effect of typical ceftiofur antibiotic treatment on the prevalence of ARGs in the fecal microbiome of dairy cows using a metagenomics approach. β-lactam ARGs were found to be elevated in feces from Holstein cows administered ceftiofur (n = 3) relative to control cows (n = 3). However, total numbers of ARGs across all classes were not measurably affected by ceftiofur treatment, likely because of dominance of unaffected tetracycline ARGs in the metagenomics libraries. Functional analysis via MG-RAST further revealed that ceftiofur treatment resulted in increases in gene sequences associated with "phages, prophages, transposable elements, and plasmids", suggesting that this treatment also enriched the ability to horizontally transfer ARGs. Additional functional shifts were noted with ceftiofur treatment (e.g., increase in genes associated with stress, chemotaxis, and resistance to toxic compounds; decrease in genes associated with metabolism of aromatic compounds and cell division and cell cycle), along with measureable taxonomic shifts (increase in Bacterioidia and decrease in Actinobacteria). This study demonstrates that ceftiofur has a broad, measureable and immediate effect on the cow fecal metagenome. Given the importance of 3rd generation cephalospirins to human medicine, their continued use in dairy cattle should be carefully considered and waste treatment strategies to slow ARG dissemination from dairy cattle manure should be explored.
authors.affiliation: Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Lindsey
authors.initials: L
authors.lastname: Chambers
authors.affiliation: University of Hong Kong, Hong Kong, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Heather
authors.initials: H
authors.lastname: Littier
authors.affiliation: Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Partha
authors.initials: P
authors.lastname: Ray
authors.affiliation: University of Hong Kong, Hong Kong, China.
authors.forename: Tong
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Amy
authors.initials: A
authors.lastname: Pruden
authors.affiliation: Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Strickland
authors.affiliation: Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Katharine
authors.initials: K
authors.lastname: Knowlton
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D002417:Cattle; D002453:Cell Cycle; D002455:Cell Division; D002511:Cephalosporins / Q000627:therapeutic use*; D002633:Chemotaxis; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D004926:Escherichia coli; D005243:Feces; D015723:Gene Library; D005798:Genes, Bacterial; D008372:Manure; D054892:Metagenome; D056186:Metagenomics; D017422:Sequence Analysis, DNA; D047090:beta-Lactams / Q000737:chemistry*
chemical_list: D000900:Anti-Bacterial Agents; D002511:Cephalosporins; D008372:Manure; D047090:beta-Lactams; C053503:ceftiofur