Clonal Composition and Community Clustering of Drug-Susceptible and -Resistant Escherichia coli Isolates from Bloodstream Infections

Abstract

ABSTRACTMultidrug-resistantEscherichia colistrains belonging to a single lineage frequently account for a large proportion of extraintestinalE. coliinfections in many parts of the world. However, limited information exists on the community prevalence and clonal composition of drug-susceptibleE. colistrains. Between July 2007 and September 2010, we analyzed all consecutively collected Gram-negative bacterial isolates from patients with bloodstream infection (BSI) admitted to a public hospital in San Francisco for drug susceptibility and associated drug resistance genes. TheE. coliisolates were genotyped forfimHsingle nucleotide polymorphisms (SNPs) and multilocus sequence types (MLSTs). Among 539 isolates,E. coliaccounted for 249 (46%); 74 (30%) of them were susceptible to all tested drugs, and 129 (52%) were multidrug resistant (MDR). Only five MLST genotypes accounted for two-thirds of theE. coliisolates; the most common were ST131 (23%) and ST95 (18%). Forty-seven (92%) of 51 ST131 isolates, as opposed to only 8 (20%) of 40 ST95 isolates, were MDR (P< 0.0001). The Simpson's diversity index for drug-susceptible ST genotypes was 87%, while the index for MDR ST genotypes was 81%. ST95 strains were comprised of fourfimHtypes, and one of these (f-6) accounted for 67% of the 21 susceptible isolates (P< 0.003). A large proportion (>70%) of both MDR and susceptibleE. coliBSI isolates represented community-onset infections. These observations show that factors other than the selective pressures of antimicrobial agents used in hospitals contribute to community-onset extraintestinal infections caused by clonal groups ofE. coliregardless of their drug resistance.