Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river
The microbiological safety of urban rivers that flow through cities is crucial to local public health. However, detailed insights into the key characteristics of pathogens in urban rivers remain limited due to the lack of efficient high-throughput analysis tools. In this study, a comprehensive profi...
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Elsevier
2025-04-01
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| Series: | Ecotoxicology and Environmental Safety |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0147651325003999 |
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| author | Ting Zhang Shuqing Zhou Chunyan Cheng Yang Yang Dong Yang Danyang Shi Haibei Li Zhongwei Yang Tianjiao Chen Junwen Li Min Jin |
| author_facet | Ting Zhang Shuqing Zhou Chunyan Cheng Yang Yang Dong Yang Danyang Shi Haibei Li Zhongwei Yang Tianjiao Chen Junwen Li Min Jin |
| author_sort | Ting Zhang |
| collection | DOAJ |
| description | The microbiological safety of urban rivers that flow through cities is crucial to local public health. However, detailed insights into the key characteristics of pathogens in urban rivers remain limited due to the lack of efficient high-throughput analysis tools. In this study, a comprehensive profiling of potential pathogens, antibiotic-resistant pathogens (ARPs), and multidrug-resistant pathogens (MDRPs) in the Hai River, which runs through the central city of Tianjin, was conducted using metagenomic assembled genome (MAG) analysis. Of the 436 recovered MAGs assigned to 430 species, 110 MAGs were identified as potential pathogens due to the presence of virulence factors (VFs), whereas 19 MAGs containing both antibiotic resistance genes (ARGs) and VFs, were classified as potential ARPs, predominantly belonging to the genera Kluyvera, Enterobacter, and Klebsiella. Notably, nine species of MDRPs, including Enterobacter kobei, Klebsiella pneumoniae, Morganella morganii, Kluyvera intermedia, Aeromonas salmonicida, Rahnella aceris, Hafnia paralvei, the unidentified species Sep. D_bin46, and Vibrio cholerae, exhibited resistance to multidrug, beta-lactam, polymyxin, bacitracin, tetracycline, other peptide antibiotics, macrolide-lincosamide-streptogramin, aminoglycoside, and chloramphenicol. The unknown pathogen Sep. D_bin46, classified under Aeromonas, showed resistance to both carbapenems and polymyxins. The strong co-occurrence of ARGs, VFs, and mobile genetic elements suggests a significant risk of ARGs and VFs transfers among MDRPs with last-resort ARGs (r > 0.8; p < 0.05). Interestingly, the sampling location significantly influenced the presence of pathogens, ARPs, and MDRPs carrying last-resort ARGs in the water. Notably, their abundance was lower downstream of the Hai River compared to upstream. This observation suggests that urban environmental sanitation facilities may be more effective in reducing contaminants as the river flows from upstream to downstream. Nevertheless, the presence of pathogens, ARPs, and MDRPs with last-resort ARGs in the water underscores the ongoing microbiological risks associated with urban surface water. |
| format | Article |
| id | doaj-art-183dab2230c64744a0d3b8c5063c2f16 |
| institution | OA Journals |
| issn | 0147-6513 |
| language | English |
| publishDate | 2025-04-01 |
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| series | Ecotoxicology and Environmental Safety |
| spelling | doaj-art-183dab2230c64744a0d3b8c5063c2f162025-08-20T01:54:16ZengElsevierEcotoxicology and Environmental Safety0147-65132025-04-0129411806310.1016/j.ecoenv.2025.118063Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban riverTing Zhang0Shuqing Zhou1Chunyan Cheng2Yang Yang3Dong Yang4Danyang Shi5Haibei Li6Zhongwei Yang7Tianjiao Chen8Junwen Li9Min Jin10Department of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaDepartment of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaCorresponding author.; Department of Environment and Health, Tianjin Key Laboratory of Risk Assessment and Control for Environment & Food Safety, State Key Laboratory of Pathogen and Biosecurity,Tianjin Institute of Environmental & Operational Medicine, Tianjin 300050, ChinaThe microbiological safety of urban rivers that flow through cities is crucial to local public health. However, detailed insights into the key characteristics of pathogens in urban rivers remain limited due to the lack of efficient high-throughput analysis tools. In this study, a comprehensive profiling of potential pathogens, antibiotic-resistant pathogens (ARPs), and multidrug-resistant pathogens (MDRPs) in the Hai River, which runs through the central city of Tianjin, was conducted using metagenomic assembled genome (MAG) analysis. Of the 436 recovered MAGs assigned to 430 species, 110 MAGs were identified as potential pathogens due to the presence of virulence factors (VFs), whereas 19 MAGs containing both antibiotic resistance genes (ARGs) and VFs, were classified as potential ARPs, predominantly belonging to the genera Kluyvera, Enterobacter, and Klebsiella. Notably, nine species of MDRPs, including Enterobacter kobei, Klebsiella pneumoniae, Morganella morganii, Kluyvera intermedia, Aeromonas salmonicida, Rahnella aceris, Hafnia paralvei, the unidentified species Sep. D_bin46, and Vibrio cholerae, exhibited resistance to multidrug, beta-lactam, polymyxin, bacitracin, tetracycline, other peptide antibiotics, macrolide-lincosamide-streptogramin, aminoglycoside, and chloramphenicol. The unknown pathogen Sep. D_bin46, classified under Aeromonas, showed resistance to both carbapenems and polymyxins. The strong co-occurrence of ARGs, VFs, and mobile genetic elements suggests a significant risk of ARGs and VFs transfers among MDRPs with last-resort ARGs (r > 0.8; p < 0.05). Interestingly, the sampling location significantly influenced the presence of pathogens, ARPs, and MDRPs carrying last-resort ARGs in the water. Notably, their abundance was lower downstream of the Hai River compared to upstream. This observation suggests that urban environmental sanitation facilities may be more effective in reducing contaminants as the river flows from upstream to downstream. Nevertheless, the presence of pathogens, ARPs, and MDRPs with last-resort ARGs in the water underscores the ongoing microbiological risks associated with urban surface water.http://www.sciencedirect.com/science/article/pii/S0147651325003999Microbiological safetyUrban riverPathogenAntibiotic-resistant pathogen |
| spellingShingle | Ting Zhang Shuqing Zhou Chunyan Cheng Yang Yang Dong Yang Danyang Shi Haibei Li Zhongwei Yang Tianjiao Chen Junwen Li Min Jin Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river Ecotoxicology and Environmental Safety Microbiological safety Urban river Pathogen Antibiotic-resistant pathogen |
| title | Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river |
| title_full | Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river |
| title_fullStr | Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river |
| title_full_unstemmed | Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river |
| title_short | Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river |
| title_sort | metagenomic assembled genomes profile potential pathogens and antibiotic resistant pathogens in an urban river |
| topic | Microbiological safety Urban river Pathogen Antibiotic-resistant pathogen |
| url | http://www.sciencedirect.com/science/article/pii/S0147651325003999 |
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