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27 January 2017 Genomic approaches to characterizing and reducing antimicrobial resistance in beef cattle production systems
Cassidy Klima, Andrew Cameron, Muhammad Afzal Javed, Trevor Alexander, Rahat Zaheer, Krysty Munns, Tim A. McAllister
Author Affiliations +
Abstract

Antimicrobial resistance (AMR) is a global health threat, and a standstill in the discovery and design of new antibiotics has been linked to the growing number of human deaths attributed to AMR infections. Intensive beef production utilizes antimicrobials to promote health and growth efficiency. To understand the magnitude and risk of AMR in beef production, it is important to assess the prevalence and diversity of antimicrobial resistant genes (ARGs) within microbial populations. Antimicrobial resistant bacteria are traditionally identified by isolation and growth in the presence of selective antibiotics. Whole-genome, metagenomic, and RNA sequencing provide new avenues to detect and identify novel ARGs in both culturable and unculturable bacterial communities. Some of these approaches place ARGs within the context of mobile genetic elements, gauging their likelihood of transfer across genomes. Genomics can also mitigate AMR, contributing to rational drug design or the development of alternatives to antimicrobials such as vaccines and probiotics. RNA-seq-based transcriptomics and Tn-seq may provide new ways to examine mechanisms that promote or prevent AMR. Finally, clustered regularly interspaced short palindromic repeats (CRISPR) – Cas gene editing could directly reduce AMR by killing AMR-resistant bacteria without harming beneficial bacteria. Together, these technologies may provide new opportunities to identify, quantify, and mitigate AMR while developing alternatives to antimicrobials for beef production.

© Her Majesty the Queen in right of Canada 2017. Permission for reuse (free in most cases) can be obtained from RightsLink.
Cassidy Klima, Andrew Cameron, Muhammad Afzal Javed, Trevor Alexander, Rahat Zaheer, Krysty Munns, and Tim A. McAllister "Genomic approaches to characterizing and reducing antimicrobial resistance in beef cattle production systems," Canadian Journal of Animal Science 97(3), 347-364, (27 January 2017). https://doi.org/10.1139/cjas-2016-0208
Received: 8 November 2016; Accepted: 18 January 2017; Published: 27 January 2017
JOURNAL ARTICLE
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KEYWORDS
antimicrobial resistance
beef
bœufs
bouvillons
cattle
CRISPR–Cas
genomics
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