Evidence map›Paper›PMID 40781228›Full record

ArticleNature communications2025

Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong.

Xiaoqing Xu, Yunqi Lin, Yu Deng, Lei Liu, Dou Wang, Qinling Tang, Chunxiao Wang, Xi Chen, You Che, Ethan R Wyrsch and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

  1. Whole-genome surveillance supports hazard profiling ofApplied and environmental microbiology · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Xiaoqing XuEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Yunqi LinEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Yu DengEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Lei LiuEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Dou WangEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Qinling TangEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Chunxiao WangEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Xi ChenEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
You CheEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China.
Ethan R WyrschAustralian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia.
Veronica M JarockiAustralian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0003-1249-0994
Steven P DjordjevicAustralian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0001-9301-5372
Tong ZhangEnvironmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Center for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China. zhangt@hku.hk.ORCID http://orcid.org/0000-0003-1148-4322

Funding

Research Grants Council, University Grants Committee (RGC, UGC) 17209823Shenzhen Science and Technology Innovation Commission SGDX20230821091559021
6 · The paper itself

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.

Indexed as

Drug Resistance, BacterialEscherichia coliGenome, BacterialAnimalsAnti-Bacterial AgentsEcosystemEscherichia coli InfectionsGenetic MarkersGenomicsHong KongHumansPhylogenyPlasmidsWater MicrobiologyAnti-Bacterial AgentsGenetic Markers

Identifiers

PMID40781228
PMCPMC12334759

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.