Antimicrobial resistant determinants (ARDs) can be transmitted from livestock systems to humans through meat products or environmental effluents. However, the public health risk posed by these two routes is not well understood, particularly in non-pathogenic bacteria. We followed 1,741 commercial beef cattle from feedlot entry until resulting beef products were market-ready. We recorded antimicrobial drug exposures and utilized shotgun metagenomics to interrogate the resistome at critical points in beef production. Over 300 unique ARDs were identified. Resistome diversity decreased while cattle were in the feedlot, indicating selective pressure from antimicrobial drugs. ARDs were not identified in market-ready beef products, suggesting that interventions targeted at pathogens also reduce the risk of ARDs transmission to beef consumers. This report highlights the utility of metagenomics for assessing public health risks regarding antimicrobial resistance, and demonstrates that environmental exposure pathways may represent a more salient risk than the food supply chain.

Noelle R Noyes, Xiang Yang, Lyndsey M. Linke, Roberta J. Magnuson, Adam Dettenwanger, Shaun Cook, Ifigenia Geornaras, Dale R. Woerner , Sheryl P. Gow, Tim A. McAllister, Hua Yang, Jaime Ruiz, Kenneth L. Jones, Christina A. Boucher, Paul S. Morley, Keith E. Belk. 2016. Resistome diversity in cattle and the environment decreases during beef production. To appear in eLife. Accepted 2/2016