Chromosomal mutations that accompany qnr in clinical isolates of Escherichia coli

•Elevated expression of efflux pumps accompanies topoisomerase mutations.•AcrA is the predominant overexpressed efflux pump.•Other PMQR genes often accompanied qnr in clinical strains.•In one Escherichia coli clinical strain the ciprofloxacin minimum inhibitory concentration (MIC) reached 1024 µg/mL.•A range of resistance mechanisms occurs in clinical isolates with and without qnr genes.