Genotypic analysis of uropathogenic Escherichia coli to understand factors that impact the prevalence of β-lactam-resistant urinary tract infections in a community.

Abstract

To determine the contribution of specific uropathogenic Escherichia coli (UPEC) lineages, drug resistance genes, and plasmid incompatibility/replicon (Inc) groups to the prevalence of β-lactam-resistant urinary tract infections (UTIs) in a university community. Urine samples were consecutively collected and cultured over a 2-year period from patients presenting to a university health centre with symptoms of UTI. Isolated UPEC were subtyped by multilocus sequence typing and fimH typing, and tested by PCR and sequencing for β-lactamase genes and plasmid Inc groups. Among 273 UPEC isolates, 85 (31%) were ampicillin-resistant (AMP-R) and 188 (69%) were susceptible to all β-lactam drugs (AMP-S). Six lineages accounted for two-thirds of the isolates: ST95 (21%), ST69 (11%), ST420 (11%), ST73 (10%), ST127 (8%), and ST404 (3%). ST69 and ST404 were associated with AMP-R (P=0.003, P=0.0005), while ST420 and ST127 were associated with AMP-S (P<0.0001, P=0.027). ST95 contained four fimH types; the ST95/f-6 sublineage was more frequently identified among the AMP-R population (P = 0.009), while the ST95/f-47 sublineage was more frequently identified among the AMP-S population (P=0.007). The most common β-lactamase gene was blaTEM, which was identified in 81 (95%) AMP-R isolates. IncFIB, IncFIA, and IncB/O type plasmids were the most commonly identified types, and were associated with β-lactam resistance (P<0.001 for all). These observations indicate that the prevalence of β-lactam-resistant UTIs in this community was largely determined by a limited set of circulating UPEC STs and sublineages, carrying TEM β-lactamase genes that were likely encoded on one of three Inc type plasmids.