Li Wenxuan, Mao Feijian, Ng Charmaine, Jong Mui Choo, Goh Shin Giek, Charles Francis Rathinam, Ng Oon Tek, Marimuthu Kalisvar, He Yiliang, Gin Karina Yew-Hoong
NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01 T-Lab Building, 117411 Singapore.
Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China.
Environ Int. 2022 May;163:107185. doi: 10.1016/j.envint.2022.107185. Epub 2022 Mar 17.
Sewage-based surveillance is widely employed to understand the occurrence and distribution of antimicrobial resistance (AMR) in urban community. However, there are limited studies which investigated the sewage of different sources within community. The present study used metagenomics to decipher the AMR profiles in five sources: local residence's source, animal source, migrant workers' source, clinical source , and urban wastewater treatment plant influent. A core resistome of ARGs was found across all samples, accounting for 81.4%-93.3% of the abundance of total resistome with only 17.3% diversity, irrespective of the sewage sources. Clinically relevant ARGs were identified in the core resistome across all wastewater sources. This included genes conferring resistance to beta-lactams as biomarkers of hospital sewage. The pet center wastewater showed a high abundance of genes encoding resistance to tetracycline, which is a commonly used veterinary antibiotic. The resistome profile of sewage from the migrant workers' dormitories showed a slight variation to that of the local residential population, suggesting possible differences in the human gut resistome of the foreign/migrant population, with biomarkers of genes encoding resistance to fosfomycin, fosmidomycin, kasugamycin, MLS, and polymyxin. The co-localization of ARGs and plasmid, MGEs and integrative and conjugative elements (ICEs) could explain variations in the core resistome, presumably a result of high antibiotic selection pressure. Further analysis showed a specific host-associated resistance pattern, in which core hosts mediated the core resistome profile. The core BMRGs were also co-localized with MGEs/ICEs and carried by core potential bacterial hosts. Local healthy population carried the lowest ARG load (copy number discharged by each person per day) but contributed the highest ARG burden (copy number discharged by the population). This study elucidates population-based variations of a core resistome, and further provides important insights into source tracking and management of AMR in urban environments.
基于污水的监测被广泛用于了解城市社区中抗菌药物耐药性（AMR）的发生和分布情况。然而，针对社区内不同来源污水进行调查的研究有限。本研究采用宏基因组学方法来解析五种来源污水中的AMR谱：当地居民来源、动物来源、农民工来源、临床来源以及城市污水处理厂进水。在所有样本中均发现了一个ARG核心耐药组，无论污水来源如何，其占总耐药组丰度的81.4% - 93.3%，多样性仅为17.3%。在所有废水来源的核心耐药组中均鉴定出了与临床相关的ARGs。这包括赋予对β-内酰胺类抗生素耐药性的基因，作为医院污水的生物标志物。宠物中心废水显示出高丰度的编码对四环素耐药性的基因，四环素是一种常用的兽用抗生素。农民工宿舍污水的耐药组谱与当地居民的略有不同，这表明外来/流动人群的人类肠道耐药组可能存在差异，其生物标志物为编码对磷霉素、磷胺霉素、春雷霉素、MLS和多粘菌素耐药性的基因。ARGs与质粒、移动遗传元件（MGEs）以及整合和接合元件（ICEs）的共定位可以解释核心耐药组的变化，这可能是高抗生素选择压力的结果。进一步分析显示出一种特定的宿主相关耐药模式，其中核心宿主介导了核心耐药组谱。核心BMRGs也与MGEs/ICEs共定位，并由核心潜在细菌宿主携带。当地健康人群携带的ARG负荷最低（每人每天排放的拷贝数），但贡献的ARG负担最高（该人群排放的拷贝数）。本研究阐明了基于人群的核心耐药组变异情况，并进一步为城市环境中AMR的来源追踪和管理提供了重要见解。
