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Whole-genome characterisation of high-risk ST131 and the emerging ST1193 UPEC lineages in Romanian patients with recurrent urinary tract infections
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DOI：10.3389/fmicb.2026.1891649.png)
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Abstract
En 中文
Recurrent urinary tract infections (UTIs) are frequently associated with persistent uropathogenic Escherichia coli (UPEC) lineages that combine antimicrobial resistance with virulence traits; contributing to treatment failure. Whole-genome sequencing was performed on 199 UPEC isolates recovered from patients with recurrent or difficult-to-treat UTIs for whom autovaccine therapy was recommended. Assemblies were analysed using AMRFinderPlus; VFDB; MOB-suite; mobile genetic element detection; serotyping; and clonotype assignment tools; MLST; cgMLST and SNP-based phylogenetic analyses. Recurrent urinary tract infections (UTIs) were associated with multiple pandemic UPEC lineages; including ST131; ST69; ST10 and the emerging ST1193. Genomic analyses identified acquired antimicrobial resistance genes in nearly 80% of isolates; including extended-spectrum β-lactamase (ESBL) genes such as blaCTX-M-15 and blaCTX-M-27; alongside chromosomal resistance-associated mutations linked to fluoroquinolone resistance. All ST131 and ST1193 isolates fulfilled the molecular UPEC criteria; while all but one isolate was classified as extraintestinal pathogenic E. coli (ExPEC). MOB-suite plasmid prediction analysis showed that IncF replicons were the most common and frequently associated with ESBL genes. Almost half of the plasmids were predicted to be mobilizable or conjugative; and one third indicated multireplicon structures. Phylogenetic analyses identified the predominant ST131 O25: H4/CH40-30 and O16: H5/CH40-41 lineages; while most ST1193 isolates belonged to the O75: H5/CH14-64 lineage. Mobile genetic element profiling identified lineage-associated insertion sequence repertoires; class 1 integrons and distinct blaCTX-M-associated genetic environments. The results indicate that recurrent UTIs in Romania are largely driven by globally disseminated ExPEC clones that combine ESBL production; fluoroquinolone resistance-associated mutations and virulence-associated traits. The detection of closely related isolates recovered in different collection years is consistent with the circulation of successful UPEC lineages within the studied population.
Keywords:
antibiotic resistance
ESBL
recurrent infections
high-risk clone
UPEC
ST1193 E. coli
ST131 E. coli
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