Genomic insights into selected multidrug-resistant and ESBL-producing uropathogenic Escherichia coli isolates in central inner Mongolia

Objective The emergence of multidrug-resistant (MDR) and extended-spectrum β-lactamase (ESBL)-producing UPEC has become a global therapeutic challenge. This study aimed to characterize the genomic characteristics, antimicrobial resistance mechanisms, and virulence determinants of selected MDR and ESBL-producing UPEC isolates from central Inner Mongolia. Methods A total of 78 Escherichia coli isolates were collected from patients with urinary tract infections (UTIs) at Baotou Central Hospital between January 2023 and January 2024. Among them, 28 MDR and ESBL-positive isolates were subjected to whole-genome sequencing using the Illumina platform. Bioinformatics analyses were performed to determine phylogroups, sequence types (STs), antimicrobial resistance genes (ARGs), virulence genes, and plasmid replicons. Statistical analysis was conducted using SPSS 26.0. Results The dominant phylogroups were B2 (35.7%) and D (32.1%). The major STs included ST131 (25.0%), ST38 (14.2%), ST69 (10.7%), and ST1193 (10.7%). All isolates harbored blaCTX-M genes and gyrA S83L mutations. A total of 47 ARGs were identified, among which mph(A) (56.6%), aadA5 (50.0%), and sul1 (50.0%) were the most prevalent. Virulence genes fimH, csgA , and traT were widely distributed. Seven strains belonging to ST131 and ST1193 carried a broad repertoire of virulence-associated genes. IncF plasmids were detected in 85.7% of isolates and were strongly associated with MDR gene clusters. Additionally, traT was identified on IncB/O/K/Z plasmids in five isolates. Conclusion Within the MDR and ESBL-producing UPEC subpopulation in this region, high-risk clones ST131 and ST1193 are predominant. The co-occurrence of resistance and virulence genes on common plasmid types (e.g., IncF) suggests a potential for co-dissemination, which may contribute to the spread of these high-risk clones.