Genomic Characterization of Fluoroquinolones Resistance Determinants in Pseudomonas aeruginosa Clinical Isolates

Abstract

Pseudomonas aeruginosa has an increasing fluoroquinolones resistance rate globally and the surveillance for identifying the resistance mechanisms is low in countries like Pakistan. This study detects the genotypic mechanisms associated with fluoroquinolones resistance and evaluates if these genotypic mechanisms were associated with fluoroquinolones susceptibility. The Whole Genome Sequencing (WGS) of 77 isolates was performed by Illumina short reads sequencing, collected from three different hospitals in Pakistan during the time of 2016 and 2017. The antibiotic susceptibility testing (AST) was performed by Kirby-Bauer disk diffusion method in which fluoroquinolones resistance was high, with 71% isolates resistant to ciprofloxacin and 75% isolates resistant to levofloxacin. The genomes analysis revealed that the fluoroquinolone resistance was largely mediated by mutations in Quinolone Resistance Determining Regions (QRDRs) and regulatory genes of efflux pumps along with the possession of acquired genes. The resistance determinants identified were further compared with antibiotic susceptibility of ciprofloxacin and levofloxacin to check the association between phenotype and genotype. Moreover, comparison of zone sizes from AST with resistance mechanisms revealed that possession of multiple resistance mechanisms (mutations in QRDRs, efflux pumps upregulation and acquired fluoroquinolones resistance genes) collectively contribute to fluoroquinolones resistance suggesting that multiple resistance mechanisms adopted by these clinical isolates ensures their survival against same antibiotics