Phylogenetic Characterization and Quinolone Resistance Gene Profiling of Escherichia coli Strains Causing Urinary Tract Infections in Women in Cotonou, Benin

Abstract

Study Design and Aims: Quinolones and fluoroquinolones are among the most widely used classes of antibiotics in therapy. The emergence of plasmid-mediated quinolone resistance (PMQR) mechanisms complicates treatment, and although cases have been reported in several countries around the world, there is a lack of data in Benin. It is essential to periodically establish the prevalence of resistance in order to better guide treatment strategies and prevent the spread of resistance. This study aimed to characterize the E. coli strains isolated from the urine of women in Cotonou, focusing on their phylogenetic background and resistance to antimicrobial treatments. Place and Duration of Study: This work was carried out from February to December 2020 at the Laboratory of Integrative Biology for Therapeutic Innovation (BioInov), Faculty of Science and Technology, University of Abomey-Calavi, Benin. Methodology: Antimicrobial susceptibility testing was performed against 10 antibiotics from four major classes: beta-lactams (Amoxicillin + clavulanic acid, Aztreonam, Ceftriaxone, Imipenem, Cefixime), fluoroquinolones (Ciprofloxacin), aminoglycosides (Amikacin, Netilmicin), and nitrofurans. Simplex PCR was used to detect plasmid-mediated quinolone resistance genes (Qnr) and to determine phylogenetic groups using specific markers (ChuA, YjaA, and TSPE4.C2). Results: Among the Twenty (20) uropathogenic E. coli (UPEC) isolates were included in this study, 45% carried at least one Qnr gene. QnrB was detected in 66.66% and QnrS in 77.77% of these positive strains. The antibiotic resistance profile of isolates carrying the Qnr genes showed high resistance to ciprofloxacin, trimethoprim/sulfamethoxazole, cefixime, and aztreonam (77.77%). Phylogenetic classification revealed that group D was the most prevalent (55%), followed by group A (35%) and group B1 (10%). Notably, group B2, which is often associated with extra-intestinal pathogenic E. coli, was completely absent. Conclusion: In summary, the detection of resistance and Qnr genes in Benin highlights the need to strengthen surveillance and adjust therapeutic strategies to limit the impact of multidrug-resistant UPEC. Despite the small sample size, which limits the generalizability of the results, this study provides valuable preliminary data for the local molecular epidemiology of quinolone resistance.