Whole genome sequencing and phenotypic characterization of Escherichia coli causing urinary tract infection in hospitalized patients in Rio de Janeiro hospitals: high prevalence of multidrug resistance

Urinary tract infections (UTIs) are frequently caused by Escherichia coli. Their increasing resistance to a broad-spectrum of antibiotics challenges treatment of infections, especially if caused by extended spectrum beta-lactamase (ESBL)-producing variants. Particularly, E. coli ST131 is commonly linked to community and nosocomial infections caused by multidrug- resistant (MDR) isolates leading to complicated infections, including UTIs. In contrast, E. coli ST69, also often associated with UTIs, seems to remain susceptible to antibiotics as cephalosporin. Although extensively studied worldwide, little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we comprehensively characterized E. coli isolated from urine samples of patients hospitalized at the University and three private hospitals in Rio de Janeiro using whole genome sequencing (WGS). Our results showed a high prevalence of E. coli ST131 and ST69, but other clones, namely ST73, ST648, ST405 and ST10, were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. One group consisted of isolates belonging to ST131, ST648 and ST405, showing a high resistance rate to all antimicrobial classes tested and a second group including isolates belonging to ST10, ST73, ST69 were susceptible to antibiotics. ST69 normally resistant to aminoglycosides appeared to be susceptible in the majority of our isolates. The majority of ST131 isolates belonged to serotype O25:H4 and were found to be ESBL producing. They were associated with more complicated UTIs, most likely due to their high resistance rate to different antimicrobial classes. Surprisingly, in this study isolates from patients in private hospitals were more often found to be MDR than isolates from patients in the University hospital. In conclusion, despite the diversity of E. coli isolates causing UTIs, ST found to be most prevalent worldwide were also found to be prevalent in Brazil.