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.DOI: http://dx.doi.org/10.7554/eLife.13195.001

Antimicrobial usage and resistance in beef production

“…This identified 300 unique AMR genes, and showed that, the diversity of the AMR genes decreased while cattle were in the feedlot, indicative of selective pressure imposed by antimicrobials, consistent with other studies showing diversity reduction following antimicrobial exposure [163]. Examination of post-slaughter samples obtained from belts and tables in the slaughterhouse, meat trimmings, and market-ready samples revealed no AMR genes [186]. The authors concluded that effective practices at slaughter minimized the likelihood of AMR gene being passed through the food chain.…”

“…Noyes et al [186] examined AMR genes of 1,741 beef cattle as they moved longitudinally through the production chain, characterizing feedlot, slaughter, and beef product resistomes via shotgun metagenomics performed on the Illumina HiSeq platform, and assessed against the Resfinder [187], ARG-ANNOT [188], and CARD [185] AMR gene databases. This identified 300 unique AMR genes, and showed that, the diversity of the AMR genes decreased while cattle were in the feedlot, indicative of selective pressure imposed by antimicrobials, consistent with other studies showing diversity reduction following antimicrobial exposure [163].…”

Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems

“…Such problems can be partially resolved by parallel culturing of organisms (from the same source as the metagenomics data), selection of specific phenotypes, and determining the genetic context of specific genes in such isolates. However, the majority of organisms found in environmental systems cannot be cultured under standard laboratory conditions, which poses a problem for linking ARB and ARG metagenomics data within environmental compartments …”

MEGARes: an antimicrobial resistance database for high throughput sequencing

“…More recently, increasing accessibility to high-throughput quantitative PCR, microarrays, and high throughput sequencing (HTS) technologies have enabled identification of hundreds to thousands of AMR determinants in single genome or metagenomic samples (11–13). Metagenomic high-throughput sequencing specifically is currently being explored for expanded use in public health surveillance efforts related to AMR (1,4,9,14–17).…”