Prevalence and Molecular Characterization of β-Lactamase and Quinolone Resistance Genes in Imipenem-Non-Susceptible Uropathogenic Escherichia coli (UPEC) Isolates

Abstract

Background: Escherichia coli is the leading cause of urinary tract infections (UTIs), and the increasing prevalence of antimicrobial resistance represents a major public health concern. The dissemination of multidrug-resistant uropathogenic E. coli (UPEC), frequently harboring transferable resistance determinants, poses an urgent clinical challenge.

Methods: This study investigated the prevalence of β-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaCMY, and blaDHA) and plasmid-mediated quinolone resistance genes (qnrA, qnrB, qnrC, qnrD, and qnrS) in 86 imipenem-non-susceptible UPEC isolates using multiplex and single PCR assays. Gene distribution and co-occurrence were examined across E. coli phylogenetic groups, and pairwise associations were evaluated using correlation analysis. Principal component analysis (PCA) was applied to explore global relationships between antibiotic susceptibility profiles, extended-spectrum β-lactamase (ESBL) phenotype, and resistance determinants.

Results: Overall, 74.4% of imipenem-non-susceptible isolates carried at least one β-lactamase gene. blaTEM was the most prevalent (62.8%), followed by blaCMY II (12.8%). blaSHV, blaCTX-M group I, and blaCTX-M group II showed comparable prevalence (10.5% each). The B2 phylogroup showed the greatest diversity of β-lactamase profiles, with phylogroup E representing the second most frequent reservoir. Among quinolone resistance genes, qnrB was the most prevalent (20.9%), followed by qnrD (5.8%), qnrS (4.7%), qnrA (3.5%), and qnrC (1.2%). All qnrC-positive isolates were resistant to all tested quinolones. No statistically significant associations were observed between β-lactamase genes and qnr genes. Significant within-class correlations were detected for blaCTX-M group II-blaCMY II (φ = 0.893, q = 9.33 × 10^-9) and qnrC-qnrA (φ = 0.57, q = 0.374).

Conclusions: A high prevalence of β-lactamase and qnr determinants was observed among imipenem-non-susceptible UPEC, primarily driven by blaTEM and qnrB, frequently detected in B2 isolates. The co-occurrence and correlation of multiple resistance genes highlight the complexity of resistance architectures and underscore the need for ongoing molecular surveillance and strengthened antimicrobial stewardship to limit the dissemination of resistant UPEC.

Keywords: antimicrobial resistance; extended-spectrum β-lactamases (ESBL); phylogroups; plasmid-mediated quinolone resistance (PMQR); public health; urinary tract infection (UTI); uropathogenic Escherichia coli (UPEC); β-lactamase genes.