摘要
      联合国环境大会（UNEA-3）已经认识到环境在抗微生物耐药性（AMR）的发展、传播和向人类和动物传播中的重要性。这种认识要求对废水和其他环境水库中的抗微生物耐药性基因（ARG）进行更广泛的监测。为了使ARG监测对监管机构有价值，它必须能够进行来源跟踪和风险评估。充分的监测还需要以相对较低的成本处理大量样本，并需要较低的检测极限来量化风险最高的ARG。然而，目前追踪ARG的方法有各种限制。目前的研究提出了一种多路靶向扩增子测序方法，用于检测环境样本中ARGs的序列变异。为了证明这项技术的应用，分析了从位于加拿大魁北克省圣劳伦斯河440公里断面沿线的16个处理厂的入口收集的废水样本。在检测的ARG中，检测到3至45个核酸序列变体，这表明源自单一样本类型的基因中存在高序列多样性，以及使用传统技术遗漏的信息。使用PLSDB和综合抗生素耐药性数据库（CARD），根据ARG序列变异在病原体中的流动性和检测结果推断其风险。结果表明，单个ARG类内的序列变异对公众健康具有不同的风险。在未来，靶向扩增子测序可能是环境研究中的一种有价值的工具，用于风险评估和AMR源跟踪。
Abstract
The United Nations Environment Assembly (UNEA-3) have recognised the importance of the environment in the development, spread and transmission of antimicrobial resistance (AMR) to humans and animals. Such recognition calls for wider surveillance of antimicrobial resistance genes (ARG) in wastewater and other environmental reservoirs. For ARG surveillance to be valuable to regulators, it must enable source tracking and risk assessment. Adequate surveillance also requires the processing of a large number of samples at a relatively low cost, and a low detection limit to allow quantification of the riskiest ARGs. However, current methods for tracking ARGs have various limitations. The current study presents a multiplexed targeted amplicon sequencing approach for the detection of sequence variants of ARGs in environmental samples. To demonstrate the application of this technique, wastewater samples collected from the inlet to 16 treatment plants located along a 440-km transect of the St-Lawrence river in the province of Quebec (Canada) were analysed. Among the ARGs examined, between 3 and 45 nucleic acid sequence variants were detected demonstrating the high sequence diversity that occurs within genes originating from a single sample type and the information that is missed using traditional techniques. Using the PLSDB and Comprehensive Antibiotic Resistance Database (CARD), the risk of ARG sequence variants was inferred based upon their reported mobility and detection in pathogens. Results suggest that sequence variants within a single ARG class present different risks to public health. In the future, targeted amplicon sequencing could be a valuable tool in environmental studies for both risk assessment purposes and in AMR source tracking.

https://www.biorxiv.org/content/10.1101/2023.03.06.531290v1.abstract