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Background <p>Urinary tract infections (UTIs) caused by Uropathogenic <i>Escherichia coli</i> (UPEC) belonging to global strains such as ST-131 pose a significant health challenge. To understand the evolutionary landscape and molecular mechanisms defining ST-131 UPEC, the complete genome of <i>E. coli</i> NS30 was generated and analyzed.</p> Results <p>The complete genome assembly of <i>E. coli</i> NS30, belonging to high-risk ST-131, C2 subclade, revealed a chromosome and two plasmids. A large conjugative plasmid, pNS30-1, harboured a multi-drug resistance (MDR) cassette within a Tn402-like class 1 integron, which was functionally demonstrated to be transferable. Comparative genomic analysis identified four distinct genomic islands (GIs) that are absent in its closest ST-131 neighbour. Two of these, including a novel pathogenicity island (PAI), were acquired from other <i>E. coli</i> lineages, harbouring Virulence factors (VFs) and efflux pump genes. The remaining two GIs are phage-like elements contributing to genome plasticity.</p> Conclusions <p><i>E. coli</i> NS30 is distinct from the other ST-131 UPEC genomes by the acquisition of novel GIs. The presence of GIs, virulence factors and AMR genes in a conjugative MDR plasmid has driven its evolution into a formidable uropathogen with a high potential to spread resistance and virulence traits.</p>

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Genomic islands and plasmid borne antimicrobial resistance genes drive the evolution of high-risk, ST-131 uropathogenic E. coli NS30

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  • 发表日期：

    2025年11月19日

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  • Arun Sai Kumar Peketi,
  • Valakunja Nagaraja,
  • Eswarappa Pradeep Bulagonda

摘要

Background

Urinary tract infections (UTIs) caused by Uropathogenic Escherichia coli (UPEC) belonging to global strains such as ST-131 pose a significant health challenge. To understand the evolutionary landscape and molecular mechanisms defining ST-131 UPEC, the complete genome of E. coli NS30 was generated and analyzed.

Results

The complete genome assembly of E. coli NS30, belonging to high-risk ST-131, C2 subclade, revealed a chromosome and two plasmids. A large conjugative plasmid, pNS30-1, harboured a multi-drug resistance (MDR) cassette within a Tn402-like class 1 integron, which was functionally demonstrated to be transferable. Comparative genomic analysis identified four distinct genomic islands (GIs) that are absent in its closest ST-131 neighbour. Two of these, including a novel pathogenicity island (PAI), were acquired from other E. coli lineages, harbouring Virulence factors (VFs) and efflux pump genes. The remaining two GIs are phage-like elements contributing to genome plasticity.

Conclusions

E. coli NS30 is distinct from the other ST-131 UPEC genomes by the acquisition of novel GIs. The presence of GIs, virulence factors and AMR genes in a conjugative MDR plasmid has driven its evolution into a formidable uropathogen with a high potential to spread resistance and virulence traits.