Prevalence of fluoroquinolone-resistant and broad-spectrum cephalosporin-resistant community-acquired urinary tract infections in Rio de Janeiro: Impact of Escherichia coli genotypes ST69 and ST131

Uropathogenic Escherichia coli (UPEC) is the leading cause of community-acquired urinary tract infection (CA-UTI). The increasing prevalence of CA-UTI caused by UPEC strains resistant to broad-spectrum drugs complicates clinical management of these infections. Here we assessed the prevalence of antimicrobial drug resistance, genotypes and beta-lactamase genes among UPEC isolated from cases of CA-UTI in Rio de Janeiro, Brazil during November 2015 to determine if the prevalence of drug-resistant CA-UTI is determined by multiple genotypes of resistant UPEC or dissemination of key lineages of UPEC. Among 499 UPEC isolates, 98 (20%) were ciprofloxacin (CIP) resistant and 41 (8%) produced extended-spectrum beta-lactamase (ESBL). Sequence types (ST) 69 and 131 were the most common genotypes, representing 77 (15%) and 42 (8%) of all UPEC isolates, respectively. Of fluoroquinolone-resistant isolates, ST69 and ST131 together accounted for 57%, while of ESBL-producers, ST131 represented 21%. Only 5 (2%) of 255 susceptible isolates belonged to these STs (p < .001). bla(CTX-M-15) was detected in 17 (42%) of the 41 ESBL-producing isolates. Comparison with a collection of UPEC isolates obtained a decade earlier from the same community showed that a large proportion (60% and 25%, respectively) of the increase in CA-UTI caused by fluoroquinolone-resistant and ESBL-producing UPEC appears to be due to just two pandemic lineages ST131 and ST69. These findings indicate that much of the prevalence of broad-spectrum drug-resistant CA-UTI in Rio de Janeiro is due to a limited set of pandemic lineages of UPEC circulating in the community instead of multiple genotypes selected by antimicrobial agents.