Background: The emergence of fluoroquinolone (FQ) resistance in the Escherichia coli (E. coli) sequence type 131 (ST131) clone has become a major challenge in the management of urinary tract infections (UTIs). Chromosomal mutations and plasmid-mediated quinolone resistance (PMQR) determinants play an important role in FQ resistance.
Methods: This cross-sectional study was conducted in 2020 on 300 urine samples. It aimed to investigate the prevalence of chromosomal mutations, PMQR genes, including qnr and aac (6′)-Ib-cr, and efflux pumps among FQ-resistant ST131 and non-ST131 E. coli causing UTIs. Initially, the ST131 clone was detected using allele-specific PCR and confirmed by Multilocus Sequence Typing.
Results: Among 95 FQ-resistant E. coli isolates, 29 (30%) belonged to the ST131 clone. The most frequently detected PMQR genes in FQ-resistant isolates were aac (6′)-Ib-cr and qnrS. However, statistical analysis revealed a stronger association between aac (6′)-Ib-cr and the ST131 clone (62%; p < 0.03). The oqxA gene was the most prevalent efflux pump gene observed in both ST131 (n = 11; 38%) and non-ST131 (n = 16; 24%) isolates. Analysis of the gyrA and parC genes revealed a significantly higher frequency of mutations in ST131 compared with non-ST131. Double mutations, S80I + E84V, were significantly more prevalent in both gyrA (76% ST131 vs. 43% non-ST131; p = 0.004) and parC (55% ST131 vs. 26% non-ST131; p = 0.002). Notably, the substitution E84G was exclusive to non-ST131 isolates (n = 4). High-level resistance (MIC ≥ 32 μg/mL) was observed in 96.6% (28/29) of ST131 isolates compared with 65% (43/66) of non-ST131 isolates.
Conclusion: The double mutations confer high-level resistance to FQs in the ST131 clone. These findings regarding resistance mechanisms can guide infection control strategies.
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