Introduction
The global dissemination of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Escherichia coli sequence type 131 (ST131), particularly clade C, represents a major public health concern. However, the clade-specific genomic features underlying the long-term persistence and international spread of this lineage remain incompletely understood.
Methods
We performed whole-genome sequencing and comparative genomic analyses of 121 clinical E. coli isolates, including 83 ST131 and 38 non-ST131 strains, collected from 24 healthcare-associated facilities in Japan between 2001 and 2018. Plasmid replicon types, antimicrobial resistance genes, virulence factors, quinolone resistance–determining region (QRDR) mutations, and chromosomal structural variations were analyzed across ST131 clades.
Results
ST131 isolates, particularly clade C, showed a significantly higher prevalence of IncF plasmid replicons, QRDR mutations, and uropathogenic virulence genes such as iha, papA, kpsM, and usp compared with non-ST131 isolates. In contrast, dfrA family genes were less frequent in clade C, suggesting potential retained susceptibility to trimethoprim–sulfamethoxazole. Phylogenetic analysis demonstrated long-term persistence of clade C subclades (C1-nM27, C1-M27, and C2) in Japan. A clade-specific chromosomal region, M27PP1, encoding an ATP-binding protein with a conserved AAA + ATPase domain within a clade-specific genomic island, was identified exclusively in C1-M27 isolates.
Conclusions
Our findings highlight distinct clade-specific genomic characteristics of ST131 clade C in Japan, particularly in C1-M27. While the biological function of M27PP1 remains to be experimentally determined, its lineage-restricted distribution suggests a potential role in the long-term persistence and dissemination of this subclade. Continued genomic surveillance is essential for understanding and controlling high-risk E. coli lineages.
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