Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong
Abstract Antibiotic-resistant Escherichia coli (E. coli) is a major contributor to the global burden of antimicrobial resistance (AMR). While the One Health concept emphasizes the connection of human, animal, and environmental health, genome-resolved and quantitatively integrated analyses of microbi...
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62455-w |
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| author | Xiaoqing Xu Yunqi Lin Yu Deng Lei Liu Dou Wang Qinling Tang Chunxiao Wang Xi Chen You Che Ethan R. Wyrsch Veronica M. Jarocki Steven P. Djordjevic Tong Zhang |
| author_facet | Xiaoqing Xu Yunqi Lin Yu Deng Lei Liu Dou Wang Qinling Tang Chunxiao Wang Xi Chen You Che Ethan R. Wyrsch Veronica M. Jarocki Steven P. Djordjevic Tong Zhang |
| author_sort | Xiaoqing Xu |
| collection | DOAJ |
| description | Abstract Antibiotic-resistant Escherichia coli (E. coli) is a major contributor to the global burden of antimicrobial resistance (AMR). While the One Health concept emphasizes the connection of human, animal, and environmental health, genome-resolved and quantitatively integrated analyses of microbial exchange across ecological compartments remain limited. Here we show that E. coli populations from urban aquatic ecosystems in Hong Kong, representing human, animal, and environmental sources, exhibit close genetic relatedness. Using Nanopore long-read sequencing, we generated near-complete genomes for 1016 E. coli isolates collected over one year. These isolates encompassed all main phylogroups, 223 sequence types, 141 antibiotic resistance gene subtypes, and 2647 circular plasmids. 142 clonal strain-sharing events were detected between human-associated and environmental water samples. Additionally, 195 plasmids were shared across all three source-attributed sectors. Conjugation assays confirmed that several plasmids were functionally transmissible across ecological boundaries. To quantify these patterns, we established a genomic framework integrating sequence type similarity, genetic relatedness, and clonal sharing to assess ecological connectivity. Our results indicate that ecological connectivity may facilitate AMR dissemination, highlighting the importance of integrated strategies to monitor and manage resistance risks across sectors within the One Health framework. |
| format | Article |
| id | doaj-art-b229c2d3e7a74bcfabd426f122bc2bc6 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-b229c2d3e7a74bcfabd426f122bc2bc62025-08-20T03:43:10ZengNature PortfolioNature Communications2041-17232025-08-0116111610.1038/s41467-025-62455-wEcological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong KongXiaoqing Xu0Yunqi Lin1Yu Deng2Lei Liu3Dou Wang4Qinling Tang5Chunxiao Wang6Xi Chen7You Che8Ethan R. Wyrsch9Veronica M. Jarocki10Steven P. Djordjevic11Tong Zhang12Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongAustralian Institute for Microbiology and Infection, University of Technology SydneyAustralian Institute for Microbiology and Infection, University of Technology SydneyAustralian Institute for Microbiology and Infection, University of Technology SydneyEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong KongAbstract Antibiotic-resistant Escherichia coli (E. coli) is a major contributor to the global burden of antimicrobial resistance (AMR). While the One Health concept emphasizes the connection of human, animal, and environmental health, genome-resolved and quantitatively integrated analyses of microbial exchange across ecological compartments remain limited. Here we show that E. coli populations from urban aquatic ecosystems in Hong Kong, representing human, animal, and environmental sources, exhibit close genetic relatedness. Using Nanopore long-read sequencing, we generated near-complete genomes for 1016 E. coli isolates collected over one year. These isolates encompassed all main phylogroups, 223 sequence types, 141 antibiotic resistance gene subtypes, and 2647 circular plasmids. 142 clonal strain-sharing events were detected between human-associated and environmental water samples. Additionally, 195 plasmids were shared across all three source-attributed sectors. Conjugation assays confirmed that several plasmids were functionally transmissible across ecological boundaries. To quantify these patterns, we established a genomic framework integrating sequence type similarity, genetic relatedness, and clonal sharing to assess ecological connectivity. Our results indicate that ecological connectivity may facilitate AMR dissemination, highlighting the importance of integrated strategies to monitor and manage resistance risks across sectors within the One Health framework.https://doi.org/10.1038/s41467-025-62455-w |
| spellingShingle | Xiaoqing Xu Yunqi Lin Yu Deng Lei Liu Dou Wang Qinling Tang Chunxiao Wang Xi Chen You Che Ethan R. Wyrsch Veronica M. Jarocki Steven P. Djordjevic Tong Zhang Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong Nature Communications |
| title | Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong |
| title_full | Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong |
| title_fullStr | Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong |
| title_full_unstemmed | Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong |
| title_short | Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong |
| title_sort | ecological connectivity of genomic markers of antimicrobial resistance in escherichia coli in hong kong |
| url | https://doi.org/10.1038/s41467-025-62455-w |
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