Co-occurrence of Quinolone Resistance (Qnr) Genes and ESBL (CTX-M) in Uropathogenic Klebsiella pneumoniae and Escherichia coli from Patients in Onitsha, Nigeria

Abstract

Escherichia coli and Klebsiella pneumoniae are leading uropathogens, with rising resistance to fluoroquinolones and β-lactams posing major treatment challenges. The co-occurrence of plasmid-mediated quinolone resistance (PMQR) genes and extended-spectrum β-lactamase (ESBL) determinants further complicates therapy. A cross-sectional study was conducted on urine specimens collected from patients with suspected urinary tract infections (UTIs) in Onitsha, Nigeria. Isolates were identified by standard microbiological and biochemical procedures. Antibiotic susceptibility study was assessed using the Kirby–Bauer disk diffusion method and interpreted according to CLSI guidelines. Phenotypic ESBL detection was performed by the double-disk synergy test, while PCR was employed to detect qnrA, qnrB, and CTX-M genes. Among 297 urine samples, 158 (53.2%) yielded significant bacterial growth, predominantly K. pneumoniae (51.9%) and E. coli (48.1%). High resistance rates were observed to β-lactams and fluoroquinolones, with over 60% of isolates resistant to cefotaxime and ciprofloxacin. Phenotypic ESBL production was absent, but PCR revealed CTX-M in 6.6% and qnrA/qnrB in 36.7% of isolates. The high prevalence of multidrug resistance and plasmid-mediated quinolone resistance among E. coli and K. pneumoniae in Onitsha highlights the urgent need for routine molecular surveillance. Incorporating genotypic screening into resistance monitoring programs is critical for guiding effective antimicrobial stewardship and preserving therapeutic options.