Mutation rate and evolution of fluoroquinolone resistance in Escherichia coli isolates from patients with urinary tract infections

Abstract

Escherichia coli strains from patients with uncomplicated urinary tract infections were examined by DNA sequencing for fluoroquinolone resistance-associated mutations in six genes: gyrA, gyrB, parC, parE, marOR, and acrR. The 54 strains analyzed had a susceptibility range distributed across 15 dilutions of the fluoroquinolone MICs. There was a correlation between the fluoroquinolone MIC and the number of resistance mutations that a strain carried, with resistant strains having mutations in two to five of these genes. Most resistant strains carried two mutations in gyrA and one mutation in parC. In addition, many resistant strains had mutations in parE, marOR, and/or acrR. No (resistance) mutation was found in gyrB. Thus, the evolution of fluoroquinolone resistance involves the accumulation of multiple mutations in several genes. The spontaneous mutation rate in these clinical strains varied by 2 orders of magnitude. A high mutation rate correlated strongly with a clinical resistance phenotype. This correlation suggests that an increased general mutation rate may play a significant role in the development of high-level resistance to fluoroquinolones by increasing the rate of accumulation of rare new mutations.

FIG. 1.

Correlation of norfloxacin and ciprofloxacin MICs for 54 clinical E. coli UTI isolates. NCCLS breakpoints for norfloxacin and ciprofloxacin are indicated with arrows.

FIG. 2.

Relative mutation rates of 54 clinical E. coli UTI isolates as a function of norfloxacin MICs. All values are relative to the rifampin resistance mutation rate of antibiotic-susceptible strain Nu14 (5 × 10⁻⁹), which was set equal to 1. NCCLS breakpoints for norfloxacin susceptibility and resistance are indicated with arrows.

FIG. 3.

Percentage of E. coli UTI strains in the susceptible and resistant groups (defined by NCCLS breakpoints) that have a mutation rate greater than or equal to that of Nu14 (set equal to 1), as indicated on the x axis. Data for all strains with a mutation rate up to those indicated on the x axis are included. Few strains had higher mutation rates and do not fit this linear plot.

FIG. 4.

Number of fluoroquinolone resistance-associated mutations (see text for definition) per strain as a function of fluoroquinolone susceptibility and resistance (defined by NCCLS breakpoints).