Whole-genome characterisation of high-risk ST131 and the emerging ST1193 UPEC lineages in Romanian patients with recurrent urinary tract infections.

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 bla CTX-M-15 and bla CTX-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 bla CTX-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.