Functional resistomes in municipal wastewater treatment plant posing challenges to public health

Wastewater treatment plants (WWTPs) serve as critical control points for managing antimicrobial resistance, yet also function as hotspots for the persistence and dissemination of resistance genes. A novel combinative approach of genome-resolved metagenomics and metatranscriptomics was applied to assess the resistome of a full-scale municipal WWTP across treatment stages and seasons. Our results revealed that while human-associated, potentially pathogenic ARG-harbouring MAGs (ARBMAGs) declined in abundance during treatment, a significant fraction of ARGs remained transcriptionally active, especially efflux and glycopeptide resistance genes such as adeF and van homologues. Environmental and treatment-adapted microbes became dominant as treatment progressed, and plasmids were identified as primary vectors of mobile resistance. Fluoroquinolone resistance genes and other clinically relevant ARGs showed different expression levels across ARBMAG types during the wastewater treatment process. These findings highlight the importance of integrating genomic and transcriptomic data to assess location- and ARBMAG-type-specific resistance and support antibiotic resistance surveillance in engineered environments.

污水处理厂（Wastewater Treatment Plants, WWTPs）是管控抗菌耐药性的关键防控节点，同时也是耐药基因持续存在与传播的热点区域。本研究采用基因组解析宏基因组学与宏转录组学相结合的创新方法，对某大型市政污水处理厂各处理阶段与不同季节下的耐药组进行评估。研究结果显示，尽管在处理过程中，与人类相关的潜在致病性携带抗菌耐药基因（Antimicrobial Resistance Gene, ARG）的宏基因组组装基因组（Metagenome-assembled Genome, MAG，简称为ARBMAGs）丰度有所下降，但仍有相当比例的ARG保持转录活性，尤其是外排泵与糖肽类抗菌药耐药基因，如adeF与van同源基因。随着处理流程推进，环境来源且适应处理环境的微生物逐渐占据主导地位，而质粒被确定为可移动耐药性的主要载体。在污水处理过程中，氟喹诺酮类耐药基因与其他临床相关ARG在不同ARBMAG类型中呈现出不同的表达水平。本研究结果凸显了整合基因组与转录组数据的重要性，以此评估特定位置与特定ARBMAG类型下的耐药性，并为工程化环境中的抗菌耐药性监测提供支撑。