Mao Xuemei, Yin Xiaole, Yang Yu, Gao Fangzhou, Li Shuxian, Shi Xianghui, Deng Yu, Li Liguan, Leung Kenneth M Y, Zhang Tong
Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
School of Environment, South China Normal University, University Town, Guangzhou, China.
Water Res. 2025 Apr 15;274:123102. doi: 10.1016/j.watres.2025.123102. Epub 2025 Jan 5.
Rivers play an important role as reservoirs and sinks for antibiotic resistance genes (ARGs). However, it remains underexplored for the resistome and associated mobilome in river ecosystems, and hosts of riverine ARGs particularly the pathogenic ones are rarely studied. This study for the first time conducted a longitudinal metagenomic analysis to unveil the resistome, mobilome, and microbiome in river water, by collecting samples from 16 rivers in Hong Kong over a three-year period and using both short-read and long-read sequencing. Results revealed that aminoglycoside, bacitracin, β-lactam, macrolide lincosamide-streptogramin, and sulfonamide were the predominant ARG types in the river water samples. Riverine ARGs exhibited high spatial variations in abundance and diversity. Environmental factors such as fecal coliform count, Escherichia coli count, 5-day biochemical oxygen demand (BOD), dissolved oxygen (DO), and total organic carbon (TOC) had a significant correlation to the absolute concentrations of ARGs. Nanopore sequencing was used to reveal the physical genetic linkage of mobile genetic elements (MGEs) with ARGs in river water samples. The results showed that qacEdelta, transposase, integrase, and Tn916 had a high prevalence in ARG-carrying long reads. Host tracking using ARG-carrying reads identified 23 pathogenic bacteria species that harbored ARGs. Some ARGs were shared by different bacterial groups. This study presented a nuanced insight of resistome in river water by a longitudinal metagenomic analysis and deepened our understanding of common and divergent riverine antimicrobial resistant risk across the regional patterns.
河流作为抗生素抗性基因（ARGs）的储存库和汇聚地发挥着重要作用。然而，河流生态系统中的抗性组及相关可移动基因组仍未得到充分研究，河流中ARGs的宿主，尤其是致病宿主，很少被研究。本研究首次进行了纵向宏基因组分析，通过在三年时间里从香港的16条河流采集样本，并使用短读长和长读长测序技术，揭示河流水体中的抗性组、可移动基因组和微生物组。结果显示，氨基糖苷类、杆菌肽、β-内酰胺类、大环内酯-林可酰胺-链阳霉素类和磺胺类是河流水体样本中主要的ARG类型。河流中的ARGs在丰度和多样性上呈现出高度的空间变化。粪便大肠菌群计数、大肠杆菌计数、五日生化需氧量（BOD）、溶解氧（DO）和总有机碳（TOC）等环境因素与ARGs的绝对浓度具有显著相关性。利用纳米孔测序揭示了河流水体样本中移动遗传元件（MGEs）与ARGs的物理遗传联系。结果表明，qacEdelta、转座酶、整合酶和Tn916在携带ARG的长读长中具有较高的流行率。利用携带ARG的读段进行宿主追踪，鉴定出23种携带ARGs的致病细菌物种。一些ARGs由不同细菌群体共享。本研究通过纵向宏基因组分析对河流水体中的抗性组进行了细致入微的洞察，并加深了我们对区域模式中常见和不同的河流抗微生物耐药风险的理解。
