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<p><i>Escherichia coli</i> is a ubiquitous bacterium that acts both as a commensal and a pathogen, serving as a major reservoir of antimicrobial resistance genes (ARGs). The global spread of ARGs, particularly those conferring resistance to last-resort antibiotics such as carbapenems and colistin, poses a serious threat to human and animal health. </p><p>In this study, we analyzed 9,696 publicly available <i>E. coli</i> genomes from human, animal, and unknown-origin metadata, identifying 42,813 acquired ARG occurrences across ten antibiotic classes. Multidrug resistance (ARGs from ≥ 3 classes) was observed in 44.7% of genomes, with aminoglycoside-modifying enzymes, multidrug efflux pumps, and β-lactamases being the most abundant. Clinically important genes, including <i>bla</i><sub>TEM−1B</sub>, <i>bla</i><sub>CTX−M−15</sub>, bla<sub>NDM−5</sub>, and <i>mcr-1.1</i>, were widely prevalent across hosts. Using binary presence/absence profiles, co-occurrence analyses revealed structured resistance gene modules, with strong associations among aminoglycoside, sulfonamide, and trimethoprim genes consistent with integron-associated assemblages. In contrast, major β-lactamase genes and efflux determinants showed weaker and more heterogeneous co-occurrence patterns, suggesting frequent independent acquisition. Geographic and host analyses highlighted significant heterogeneity and extensive ARG sharing between humans and animals. This study provides a global-scale overview of the <i>E. coli</i> resistome across human and animal hosts, offering a reference framework for genomic surveillance and informing strategies to curb the spread of multidrug-resistant lineages.</p>

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Global resistome architecture of Escherichia coli across human and animal hosts: analysis of 9,696 genome

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月9日

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  • Adel Azour,
  • Ghassan M Matar,
  • Melhem Bilen

摘要

Escherichia coli is a ubiquitous bacterium that acts both as a commensal and a pathogen, serving as a major reservoir of antimicrobial resistance genes (ARGs). The global spread of ARGs, particularly those conferring resistance to last-resort antibiotics such as carbapenems and colistin, poses a serious threat to human and animal health.

In this study, we analyzed 9,696 publicly available E. coli genomes from human, animal, and unknown-origin metadata, identifying 42,813 acquired ARG occurrences across ten antibiotic classes. Multidrug resistance (ARGs from ≥ 3 classes) was observed in 44.7% of genomes, with aminoglycoside-modifying enzymes, multidrug efflux pumps, and β-lactamases being the most abundant. Clinically important genes, including blaTEM−1B, blaCTX−M−15, blaNDM−5, and mcr-1.1, were widely prevalent across hosts. Using binary presence/absence profiles, co-occurrence analyses revealed structured resistance gene modules, with strong associations among aminoglycoside, sulfonamide, and trimethoprim genes consistent with integron-associated assemblages. In contrast, major β-lactamase genes and efflux determinants showed weaker and more heterogeneous co-occurrence patterns, suggesting frequent independent acquisition. Geographic and host analyses highlighted significant heterogeneity and extensive ARG sharing between humans and animals. This study provides a global-scale overview of the E. coli resistome across human and animal hosts, offering a reference framework for genomic surveillance and informing strategies to curb the spread of multidrug-resistant lineages.