短读和长读宏基因组学揭示了斯里兰卡医院废水中的移动扩展谱β-内酰胺酶（ESBL）和碳青霉烯酶基因

IF 11.4 1区环境科学与生态学 Q1 ENGINEERING, ENVIRONMENTAL

Water Research Pub Date : 2025-05-15 DOI:10.1016/j.watres.2025.123831

Shashika Kumudumali Guruge , Ziming Han , S.H.P. Parakrama Karunaratne , Rohana Chandrajith , Titus Cooray , Chengzhi Hu , Yu Zhang , Min Yang

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引用次数: 0

摘要

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。本研究首次利用Illumina短读测序和Nanopore长读测序技术对斯里兰卡医院和城市污水处理厂的抗生素耐药基因（ARGs）进行宏基因组研究。从斯里兰卡的四个地区收集了接收医院和/或城市污水（生活污水）的三个代表性污水处理厂的样本，作为比较，还收集了未经处理直接排放的废水。医院废水中的ARG丰度（7.22拷贝/细胞）显著高于城市废水（2.33拷贝/细胞），经过处理后分别大幅下降82%和93%。在移动遗传元素上也观察到类似的趋势。医院废水中临床相关延伸谱β-内酰胺酶（ESBL）和碳青霉烯酶基因的流行亚型为blaOXA、blaGES、blaVEB和blaTEM，而blaCTX-M和blaNDM的优势程度较低，这表明ESBL和碳青霉烯酶基因在斯里兰卡可能存在独特的分布模式。利用长读元基因组法预测污泥样品中ARGs的细菌宿主范围和遗传位置（质粒或染色体）。医院污水中病原菌种类多样（假单胞菌、链球菌、沙门氏菌和埃希氏菌），质粒比例较高（39.8%比21.5%）。本研究检测到的移动遗传背景IS6100-sul1-blaOXA-329-blaGES-5-blaGES-5-intI1和ISKpn6-blaKPC-2-ISKpn7-ISPsy42在来自不同国家的肠杆菌科耐药质粒中也很常见。这些数据将有助于扩大全球ARG流行病学清单。此外，研究结果强调，废水处理项目，特别是医疗设施中的废水处理项目，对于减少临床相关的ARG排放到环境中至关重要。使用先进的元组学方法进行进一步监测对于评估潜在的ARG风险和优化控制战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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Short- and long-read metagenomics uncover the mobile extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater in Sri Lanka

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Short- and long-read metagenomics uncover the mobile extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater in Sri Lanka

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_OXA, bla_GES, bla_VEB and bla_TEM, whereas bla_CTX−_M and bla_NDM 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_OXA-329-bla_GES-5-bla_GES-5-intI1 and ISKpn6-bla_KPC-2-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.

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来源期刊

Water Research 环境科学-工程：环境

CiteScore

20.80

自引率

9.40%

发文量

1307

审稿时长

38 days

期刊介绍： Water Research, along with its open access companion journal Water Research X, serves as a platform for publishing original research papers covering various aspects of the science and technology related to the anthropogenic water cycle, water quality, and its management worldwide. The audience targeted by the journal comprises biologists, chemical engineers, chemists, civil engineers, environmental engineers, limnologists, and microbiologists. The scope of the journal include: •Treatment processes for water and wastewaters (municipal, agricultural, industrial, and on-site treatment), including resource recovery and residuals management; •Urban hydrology including sewer systems, stormwater management, and green infrastructure; •Drinking water treatment and distribution; •Potable and non-potable water reuse; •Sanitation, public health, and risk assessment; •Anaerobic digestion, solid and hazardous waste management, including source characterization and the effects and control of leachates and gaseous emissions; •Contaminants (chemical, microbial, anthropogenic particles such as nanoparticles or microplastics) and related water quality sensing, monitoring, fate, and assessment; •Anthropogenic impacts on inland, tidal, coastal and urban waters, focusing on surface and ground waters, and point and non-point sources of pollution; •Environmental restoration, linked to surface water, groundwater and groundwater remediation; •Analysis of the interfaces between sediments and water, and between water and atmosphere, focusing specifically on anthropogenic impacts; •Mathematical modelling, systems analysis, machine learning, and beneficial use of big data related to the anthropogenic water cycle; •Socio-economic, policy, and regulations studies.