The Prevalence of Fluoroquinolone Resistance Mechanisms in Colonizing Escherichia coli Isolates from Hospitalized Patients

Background: Fluoroquinolones (FQs) are the most commonly prescribed antimicrobials. The epidemiology of fecal colonization with Escherichia coli demonstrating reduced susceptibility to FQs remains unclear.  

Objective: 1) to characterize GI tract colonization due to E. coli with reduced susceptibility to FQs among the hospitalized patient population using continuous enrollment of hospitalized patients over a three year time period; 2) to comprehensively characterize the resistance genotypes and phenotypes of fecal E. coli isolates with reduced susceptibility to FQs in this patient population.

Methods:   Over a three year period, all patients hospitalized >3 days were approached for fecal sampling. All E. coli with reduced susceptibility to FQs (MIC ≥0.125μg/mL to levofloxacin) were identified. We characterized gyrA and parC mutations and organic solvent tolerance. Isolates were compared using pulsed field gel electrophoresis.

Results: Among the 353 subjects, the median age was 56 (interquartile range = 48-65) and 187 (53.0%) were male. Of 353 subjects colonized with E. coli demonstrating reduced FQ susceptibility, 300 (85%) had ≥ 1 gyrA mutation, 161 (45.6%) had ≥ 1 parC mutation, and 171 (48.6%) demonstrated organic solvent tolerance. Of the 353 study isolates, 217 (61.5%) demonstrated a levofloxacin MIC ≥8 μg/ml. The mean number of total mutations (i.e., gyrA + parC) for E. coli isolates with a levofloxacin MIC ≥8 μg/ml vs. <8.0 μg/ml was 2.70 and 0.82, respectively (p<0.001). Among all 353 E. coli isolates, 306 (86.7%) demonstrated a nalidixic acid MIC in the non-susceptible range (i.e., ≥16 μg/ml). Of the 136 E. coli isolates with a levofloxacin MIC ≤8 μg/ml, 90 (66.2%) demonstrated a nalidixic acid MIC ≥16 μg/ml. There were significant differences across study years in the proportion of E. coli isolates demonstrating various mechanisms of resistance. For example, the proportion of isolates with at least one gyrA mutation was 18/20 (90%) in 2004; 67/71 (94.4%) in 2005; 113/146 (77.4%) in 2006; and 102/116 (87.9%) in 2007 (p=0.005). Similarly, the proportion of isolates with at least one parC mutation was 11/20 (55.0%) in 2004; 37/71 (52.1%) in 2005; 74/146 (50.7%) in 2006; and 39/116 (33.6%) in 2007 (p=0.02). Finally, the proportion of isolates exhibiting organic solvent tolerance was 5/20 (25%) in 2004; 26/71 (36.6%) in 2005; 79/145 (54.5%)  in 2006; and 61/116 (52.6%) in 2007 (p=0.02).  There was little evidence for clonal spread of isolates.

Conclusions: GI tract colonization with E. coli demonstrating reduced susceptibility to levofloxacin is common. Although 40% of study isolates exhibited a levofloxacin MIC <8 μg/ml (and would thus be missed by current CLSI breakpoints), nalidixic acid resistance may be a useful marker for detection of such isolates. Significant temporal changes occurred in the proportion of isolates exhibiting various resistance mechanisms.