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Xiao Z, Qin Y, Han L, Liu Y, Wang Z, Huang Y, Ma Y, Zou Y. Effects of wastewater treatment plant effluent on microbial risks of pathogens and their antibiotic resistance in the receiving river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123461. [PMID: 38286261 DOI: 10.1016/j.envpol.2024.123461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
The increase in effluent discharge from wastewater treatment plants (WWTPs) into urban rivers has raised concerns about the potential effects on pathogen risks. This study utilized metagenomic sequencing combined with flow cytometry to analyze pathogen concentrations and antibiotic resistance in a typical effluent-receiving river. Quantitative microbial risk assessment (QMRA) was employed to assess the microbial risks of pathogens. The results indicated obvious spatial-temporal differences (i.e., summer vs. winter and effluent vs. river) in microbial composition. Microcystis emerged as a crucial species contributing to these variations. Pathogen concentrations were found to be higher in the river than in the effluent, with the winter exhibiting higher concentrations compared to the summer. The effluent discharge slightly increased the pathogen concentrations in the river in summer but dramatically reduced them in winter. The combined effects of cyanobacterial bloom and high temperature were considered key factors suppressing pathogen concentrations in summer. Moreover, the prevalence of antibiotic resistance of pathogens in the river was inferior to that in the effluent, with higher levels in winter than in summer. Three high-concentration pathogens (Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were selected for QMRA. The results showed that the risks of pathogens exceeded the recommended threshold value. Escherichia coli posed the highest risks. And the fishing scenario posed significantly higher risks than the walking scenario. Importantly, the effluent discharge helped reduce the microbial risks in the receiving river in winter. The study contributes to the management and decision-making regarding microbial risks in the effluent-receiving river.
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Affiliation(s)
- Zijian Xiao
- The National Key Laboratory of Water Disaster Prevention, Yangtze Institute for Conservation and Development, Hohai University, Nanjing, 210098, PR China; Dayu College, Hohai University, Nanjing, 210098, PR China
| | - Yuanyuan Qin
- Dayu College, Hohai University, Nanjing, 210098, PR China
| | - Li Han
- Dayu College, Hohai University, Nanjing, 210098, PR China
| | - Yifan Liu
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Ziyi Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yanping Huang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yujing Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yina Zou
- The National Key Laboratory of Water Disaster Prevention, Yangtze Institute for Conservation and Development, Hohai University, Nanjing, 210098, PR China.
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Feng T, Wu S, Zhou H, Fang Z. MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model. Gigascience 2024; 13:giae047. [PMID: 39101782 PMCID: PMC11299106 DOI: 10.1093/gigascience/giae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/31/2024] [Accepted: 06/24/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Mobilization typing (MOB) is a classification scheme for plasmid genomes based on their relaxase gene. The host ranges of plasmids of different MOB categories are diverse, and MOB is crucial for investigating plasmid mobilization, especially the transmission of resistance genes and virulence factors. However, MOB typing of plasmid metagenomic data is challenging due to the highly fragmented characteristics of metagenomic contigs. RESULTS We developed MOBFinder, an 11-class classifier, for categorizing plasmid fragments into 10 MOB types and a nonmobilizable category. We first performed MOB typing to classify complete plasmid genomes according to relaxase information and then constructed an artificial benchmark dataset of plasmid metagenomic fragments (PMFs) from those complete plasmid genomes whose MOB types are well annotated. Next, based on natural language models, we used word vectors to characterize the PMFs. Several random forest classification models were trained and integrated to predict fragments of different lengths. Evaluating the tool using the benchmark dataset, we found that MOBFinder outperforms previous tools such as MOBscan and MOB-suite, with an overall accuracy approximately 59% higher than that of MOB-suite. Moreover, the balanced accuracy, harmonic mean, and F1-score reached up to 99% for some MOB types. When applied to a cohort of patients with type 2 diabetes (T2D), MOBFinder offered insights suggesting that the MOBF type plasmid, which is widely present in Escherichia and Klebsiella, and the MOBQ type plasmid might accelerate antibiotic resistance transmission in patients with T2D. CONCLUSIONS To the best of our knowledge, MOBFinder is the first tool for MOB typing of PMFs. The tool is freely available at https://github.com/FengTaoSMU/MOBFinder.
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Affiliation(s)
- Tao Feng
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Shufang Wu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Zhencheng Fang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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Fu S, Zhang Y, Wang R, Qiu Z, Song W, Yang Q, Shen L. A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118737. [PMID: 37657296 DOI: 10.1016/j.jenvman.2023.118737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 09/03/2023]
Abstract
Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.
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Affiliation(s)
- Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 116023, China.
| | - Yixiang Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences. Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China
| | - Rui Wang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 116023, China
| | - Zhiguang Qiu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Weizhi Song
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong, China
| | - Qian Yang
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China.
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Priyadarsini M, Kushwaha J, Pandey KP, Rani J, Dhoble AS. Application of flow cytometry for rapid, high-throughput, multiparametric analysis of environmental microbiomes. J Microbiol Methods 2023; 214:106841. [PMID: 37832922 DOI: 10.1016/j.mimet.2023.106841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
Quantification of the abundance and understanding of the dynamics of the microbial communities is essential to establish a basis for microbiome characterization. The conventional techniques used for the quantification of microbes are complicated and time-consuming. With scientific advancement, many techniques evolved and came into account. Among them, flow cytometry is a robust, high-throughput technique through which microbial dynamics, morphology, microbial distribution, physiological characteristics, and many more attributes can be studied in a high-throughput manner with comparatively less time and resources. Flow cytometry, when combined with other omics-based methods, offers a rapid and efficient platform to analyze and understand the composition of microbiome at the cellular level. The microbial diversity observed through flow cytometry will not be equivalent to that obtained by sequencing methods, but this integrated approach holds great potential for high throughput characterization of microbiomes. Flow cytometry is regarded as an established characterization tool in haematology, oncology, immunology, and medical microbiology research; however, its application in environmental microbiology is yet to be explored. This comprehensive review aims to delve into the diverse environmental applications of flow cytometry across various domains, including but not limited to bioremediation, landfills, anaerobic digestion, industrial bioprocesses, water quality regulation, and soil quality regulation. By conducting an in-depth analysis, this article seeks to shed light on the potential benefits and challenges associated with the utilization of flow cytometry in addressing environmental concerns.
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Affiliation(s)
- Madhumita Priyadarsini
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Jeetesh Kushwaha
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Kailash Pati Pandey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Jyoti Rani
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Abhishek S Dhoble
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
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