title: Resistome diversity in cattle and the environment decreases during beef production.
abstract: Antimicrobial resistant determinants (ARDs) can be transmitted from livestock systems through meat products or environmental effluents. The public health risk posed by these two routes is not well understood, particularly in non-pathogenic bacteria. We collected pooled samples from 8 groups of 1741 commercial cattle as they moved through the process of beef production from feedlot entry through slaughter. We recorded antimicrobial drug exposures and interrogated the resistome at points in production when management procedures could potentially influence ARD abundance and/or transmission. Over 300 unique ARDs were identified. Resistome diversity decreased while cattle were in the feedlot, indicating selective pressure. ARDs were not identified in beef products, suggesting that slaughter interventions may reduce the risk of transmission of ARDs to beef consumers. This report highlights the utility and limitations of metagenomics for assessing public health risks regarding antimicrobial resistance, and demonstrates that environmental pathways may represent a greater risk than the food supply.
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Noelle R
authors.identifier: http://orcid.org/0000-0001-6149-1008
authors.initials: NR
authors.lastname: Noyes
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Xiang
authors.initials: X
authors.lastname: Yang
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Lyndsey M
authors.initials: LM
authors.lastname: Linke
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Roberta J
authors.initials: RJ
authors.lastname: Magnuson
authors.affiliation: Department of Computer Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Adam
authors.initials: A
authors.lastname: Dettenwanger
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, Canada.
authors.forename: Shaun
authors.initials: S
authors.lastname: Cook
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Ifigenia
authors.initials: I
authors.lastname: Geornaras
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Dale E
authors.initials: DE
authors.lastname: Woerner
authors.affiliation: Centre for Food-borne, Environmental Zoonotic Infectious Diseases, Public Health Agency of Canada, University of Saskatoon, Saskatoon, Canada.
authors.forename: Sheryl P
authors.initials: SP
authors.lastname: Gow
authors.affiliation: Agriculture and Agri-Food Canada Research Centre, Lethbridge, Canada.
authors.forename: Tim A
authors.initials: TA
authors.lastname: McAllister
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Hua
authors.initials: H
authors.lastname: Yang
authors.affiliation: Department of Computer Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Jaime
authors.initials: J
authors.lastname: Ruiz
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Jones
authors.affiliation: Department of Computer Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Boucher
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Morley
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, United States.
authors.forename: Keith E
authors.initials: KE
authors.lastname: Belk
mesh_terms: D000822:Animal Husbandry / Q000379:methods*; D000818:Animals; D000900:Anti-Bacterial Agents / Q000008:administration & dosage / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects* / Q000302:isolation & purification; D002417:Cattle / Q000254:growth & development / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D004783:Environmental Microbiology; D005243:Feces / Q000382:microbiology*; D008137:Longitudinal Studies
chemical_list: D000900:Anti-Bacterial Agents
keywords: agriculture; antimicrobial resistance; epidemiology; feedlots; global health; infectious disease; microbiology; microbiome; public health; resistome