Guruge Shashika Kumudumali, Han Ziming, Karunaratne S H P Parakrama, Chandrajith Rohana, Cooray Titus, Hu Chengzhi, Zhang Yu, Yang Min
Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, 100049, Beijing, PR China.
National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China.
Water Res. 2025 Sep 1;283:123831. doi: 10.1016/j.watres.2025.123831. Epub 2025 May 15.
The antibiotic resistance issue in low- and middle-income countries has drawn global concern. This study presents the first metagenomic investigation of antibiotic resistance genes (ARGs) in hospital and municipal wastewater treatment plants (WWTPs) in Sri Lanka, using Illumina short-read and Nanopore long-read sequencing. Samples from three representative WWTPs receiving hospital and/or municipal wastewater (domestic generated) were collected from four districts in Sri Lanka, and as a comparison, wastewater directly discharged without treatment was also taken. ARG abundance was significantly higher in hospital wastewater (7.22 copies/cell) than in municipal wastewater (2.33 copies/cell), and greatly decreased by 82 % and 93 % after treatment processes, respectively. Similar trends were observed for mobile genetic elements. The prevalent subtypes of clinically relevant extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater were bla, bla, bla and bla, whereas bla and bla were less dominant, which indicated the potential unique distribution pattern of ESBL and carbapenemase genes in Sri Lanka. Using long-read metagenomics, bacterial host range and genetic locations (plasmid or chromosome) of ARGs in sludge samples were predicted. Diverse pathogenic host taxa (Pseudomonas, Streptococcus, Salmonella and Escherichia) and a higher plasmid proportion were identified in the hospital WWTP (39.8 % vs. 21.5 % in the municipal WWTP). Detected mobile genetic contexts in this study, IS6100-sul1-bla-bla-bla-intI1 and ISKpn6-bla-ISKpn7-ISPsy42, were also common in antibiotic-resistant plasmids in Enterobacteriaceae from different countries. These data will serve to expand the inventory of global ARG epidemiology. Also, the finding emphasizes that the wastewater treatment projects, especially in healthcare facilities, are vital for reducing clinically relevant ARG discharge to the environment. Further monitoring using advanced meta-omics approaches is crucial to assess potential ARG risks and optimize control strategies for improving human and ecosystem health in Sri Lanka.
低收入和中等收入国家的抗生素耐药性问题已引起全球关注。本研究采用Illumina短读长测序和Nanopore长读长测序技术，首次对斯里兰卡医院和城市污水处理厂（WWTPs）中的抗生素耐药基因（ARGs）进行了宏基因组学调查。从斯里兰卡四个地区的三个接收医院和/或城市污水（生活污水）的代表性污水处理厂采集样本，并作为对照，同时采集未经处理直接排放的污水。医院污水中的ARG丰度（7.22拷贝/细胞）显著高于城市污水（2.33拷贝/细胞），经过处理后分别大幅下降了82%和93%。移动遗传元件也呈现出类似趋势。医院污水中临床相关的超广谱β-内酰胺酶（ESBL）和碳青霉烯酶基因的流行亚型为bla、bla、bla和bla，而bla和bla的优势较小，这表明ESBL和碳青霉烯酶基因在斯里兰卡可能具有独特的分布模式。利用长读长宏基因组学预测了污泥样本中ARGs的细菌宿主范围和基因位置（质粒或染色体）。在医院污水处理厂中鉴定出了多种致病宿主分类群（假单胞菌属、链球菌属、沙门氏菌属和大肠杆菌属），且质粒比例更高（医院污水处理厂为39.8%，城市污水处理厂为21.5%）。本研究中检测到的移动遗传背景IS6100-sul1-bla-bla-bla-intI1和ISKpn6-bla-ISKpn7-ISPsy42在来自不同国家的肠杆菌科抗生素耐药质粒中也很常见。这些数据将有助于扩充全球ARG流行病学清单。此外，该研究结果强调，污水处理项目，尤其是医疗设施中的污水处理项目，对于减少临床相关ARG向环境中的排放至关重要。采用先进的元组学方法进行进一步监测对于评估潜在的ARG风险以及优化控制策略以改善斯里兰卡的人类和生态系统健康至关重要。
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