摘要
      抗微生物耐药性（AMR）是一个日益严重的公共健康威胁。加强对环境水库中AMR基因指标的监测，应能在全球范围内更全面地了解这一问题，就像污水中的严重急性呼吸系统综合征冠状病毒2型监测一样。然而，“最佳”监测方法尚不明确。一些科学工作强调监测已知的抗微生物耐药性基因（ARGs）的丰度；其他人则强调要监测可能出现的新ARG。这项研究的目的是检查在环境工程和农业系统中研究AMR的高引用论文使用了哪些方法，从而深入了解当前和未来监测ARG的方法趋势。我们搜索了最近（2018-2020年）在五个环境矩阵中记录AMR的文献：废水、地表水、饮用水、雨水和牲畜粪便。我们选择了这些矩阵中被引用率最高的论文（来自17篇[稀疏空间（1/6-em）]809个初始结果的89篇论文），并将其分类为使用靶向方法（如qPCR）、非靶向方法或两者兼有。超过80%的论文采用了有针对性的方法。只有33%的人采用了非靶向方法，靶向与非靶向的方法的使用因环境矩阵而异。我们认为，改善环境水库的AMR监测需要评估风险，而不同的监测方法意味着不同的风险评估目标。有针对性的方法适用于量化已知威胁，特别是在可能直接暴露于人类的环境矩阵中（如饮用水）。然而，需要采用非靶向方法进行长期研究，以了解新威胁（即新的ARG）出现的频率。
Abstract
Antimicrobial resistance (AMR) is a growing public health threat. Improved surveillance of AMR's genetic indicators in environmental reservoirs should lead to a more comprehensive understanding of the problem at a global scale, as with SARS-CoV-2 monitoring in sewage. However, the “best” monitoring approach is unclear. Some scientific works have emphasized monitoring for the abundance of already-known antimicrobial resistance genes (ARGs); others have emphasized monitoring for the potential of new ARGs to arise. The goal of this study was to examine which methods were employed by highly-cited papers studying AMR in environmental engineering and agricultural systems, thus providing insight into current and future methodological trends for monitoring ARGs. We searched recent (2018–2020) literature documenting AMR in five environmental matrices: wastewater, surface water, drinking water, stormwater, and livestock manure. We selected the most highly-cited papers across these matrices (89 papers from 17[thin space (1/6-em)]809 initial results) and categorized them as using targeted methods (e.g., qPCR), non-targeted methods (e.g., shotgun metagenomics), or both. More than 80% of papers employed targeted methods. Only 33% employed non-targeted methods, and the use of targeted versus non-targeted methods varied by environmental matrix. We posit that improving AMR surveillance in environmental reservoirs requires assessing risk, and that different monitoring approaches imply different objectives for risk assessment. Targeted methods are appropriate for quantifying known threats, particularly in environmental matrices where direct human exposure is likely (e.g., drinking water). However, long-term studies employing non-targeted methods are needed to provide an understanding of how frequently new threats (i.e., novel ARGs) arise.

https://pubs.rsc.org/en/content/articlehtml/2022/ew/d2ew00087c