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Objectives <p>This study aimed to characterize the population structure, recombination landscapes and diversification patterns of global <i>tet</i>(X)-positive <i>Escherichia coli</i>.</p> Methods <p>We conducted phylogenomic, recombination and diversifying selection analyses on 1721 global <i>tet</i>(X)-positive <i>E. coli</i> genomes.</p> Results <p>These isolates were primarily distributed in China (72.7%) and most carried <i>tet</i>(X4) variant (97.5%), with phylogroups A (61.4%) and B1 (26.8%) as the most prevalent. Significant positive correlations were observed in <i>tet</i>(X4) with IncHI1A/IncHI1B plasmid and IS<i>Vsa3</i>, <i>bla</i><sub>CTX−M−65</sub> with IncI and <i>bla</i><sub>OXA−181</sub> with IncX3. Phylogenetic analysis identified cluster 17 (30.6%) and cluster 7 (17.7%) as the most prevalent lineages, among which some isolates co-harboring <i>tet</i>(X) with <i>bla</i><sub>CTX−M</sub>, <i>bla</i><sub>NDM</sub>, and <i>bla</i><sub>OXA</sub> exhibited high genetic similarity (&lt; 20 SNPs) across different countries, demonstrating potential clonal transmission. High-recombination regions (HRRs) were enriched in metabolic pathways, two-component systems, and biofilm formation, while Cluster 17 uniquely harbored aromatic compound degradation. Lineage-specific mutation patterns in HRRs included transporters and amino acid-related enzymes in cluster 17 and two-component systems in cluster 7. Genes under diversifying selection in non-recombinant regions mainly enriched in flagellar assembly and bacterial motility, alongside cluster-specific enrichment of motility functions and transporters in cluster 17 and cellular signaling in cluster 7, reflecting virulence, host interaction and immune evasion. Prophage-encoded genes were predominantly categorized as defense mechanisms, signal transduction, stress responses and metabolic functions that enhance bacterial fitness in fluctuating environments.</p> Conclusions <p>The adaptive evolution of <i>tet</i>(X)-positive <i>E. coli</i> is cooperatively driven by horizontal gene transfer, clonal expansion and diversifying selection, underscoring an urgent need for global genomic surveillance.</p>

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Recombination and diversifying selection drive the adaptive evolution of tet(X)-Positive Escherichia coli

  • 期刊论文

  • 发表日期：

    2026年7月17日

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  • Kaikai He,
  • Shuhang Zhang,
  • Jie Xing,
  • Yi Ma

摘要

Objectives

This study aimed to characterize the population structure, recombination landscapes and diversification patterns of global tet(X)-positive Escherichia coli.

Methods

We conducted phylogenomic, recombination and diversifying selection analyses on 1721 global tet(X)-positive E. coli genomes.

Results

These isolates were primarily distributed in China (72.7%) and most carried tet(X4) variant (97.5%), with phylogroups A (61.4%) and B1 (26.8%) as the most prevalent. Significant positive correlations were observed in tet(X4) with IncHI1A/IncHI1B plasmid and ISVsa3, blaCTX−M−65 with IncI and blaOXA−181 with IncX3. Phylogenetic analysis identified cluster 17 (30.6%) and cluster 7 (17.7%) as the most prevalent lineages, among which some isolates co-harboring tet(X) with blaCTX−M, blaNDM, and blaOXA exhibited high genetic similarity (< 20 SNPs) across different countries, demonstrating potential clonal transmission. High-recombination regions (HRRs) were enriched in metabolic pathways, two-component systems, and biofilm formation, while Cluster 17 uniquely harbored aromatic compound degradation. Lineage-specific mutation patterns in HRRs included transporters and amino acid-related enzymes in cluster 17 and two-component systems in cluster 7. Genes under diversifying selection in non-recombinant regions mainly enriched in flagellar assembly and bacterial motility, alongside cluster-specific enrichment of motility functions and transporters in cluster 17 and cellular signaling in cluster 7, reflecting virulence, host interaction and immune evasion. Prophage-encoded genes were predominantly categorized as defense mechanisms, signal transduction, stress responses and metabolic functions that enhance bacterial fitness in fluctuating environments.

Conclusions

The adaptive evolution of tet(X)-positive E. coli is cooperatively driven by horizontal gene transfer, clonal expansion and diversifying selection, underscoring an urgent need for global genomic surveillance.