摘要
       抗菌素耐药性（AMR）是一种全球性的健康威胁，而新型抗生素的发现和设计停滞与因AMR感染导致人类死亡人数增加有关。集约化牛肉生产利用抗菌素来促进健康和生长效率。为了解AMR在牛肉生产中的规模和风险，评估微生物种群中抗性基因（ARG）的流行率和多样性非常重要。传统上通过在选择性抗生素存在下分离和生长来鉴定抗菌素耐药性细菌。全基因组，宏基因组和RNA测序为在检测和鉴定可培养和不可培养的细菌群落中新型ARG提供了新的途径。其中一些方法将ARG置于移动遗传因子的背景下，衡量它们跨基因组转移的可能性。基因组学也可以减轻AMR，促进合理的药物设计或开发抗菌药物替代品，如疫苗和益生菌。基于RNA-seq的转录组学和Tn-seq可提供新方法来检查促进或预防AMR的机制。最后，定期聚集间隔短回文重复序列（CRISPR） - 卡斯基因编辑可以通过杀死抗AMR的细菌直接减少AMR而不伤害有益细菌。总之，这些技术可能为识别，量化和减轻AMR提供新的机会，同时开发用于牛肉生产的抗菌剂替代品。

       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.

http://www.bioone.org/doi/abs/10.1139/cjas-2016-0208