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Abstract
Microbial antibiotic resistance is caused by chromosomal mutations in the genes encoding the drug targets, increased expression of efflux pumps, adopting alternative metabolic pathways, and / or acquisition of plasmid-borne genes. For flouroquinolones, chromosomal mutations in the genes encoding topoisomerases II and IV, and increased expression of multidrug efflux pump AcrAB-TolC proved to be most common. In this study, multiplex PCR protocols were designed for high-throughput sequencing of quinolone resistance determining regions of topoisomerases genes (gyrA, parC, and parE) and/or the multidrug efflux pump AcrAB expression regulation systems (acrRAB, marRAB, and soxSR). These protocols were applied to sequence samples from 5 sub-populations of E. coli clinical isolates. These sub-populations were classified according to susceptibility pattern to levofloxacin as follows; highly resistant (HR), resistant (R), intermediate (I), reduced-susceptible (RS), and susceptible (S). All (HR), isolates had mutations in the 6 genes with two 2supermutator3 isolates harboring 13 mutations on the 6 genes