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Urinary tract infections (UTIs) are one of the most common infections in the hospital environment and even though the diversity of microorganisms causing these infections is high, extra-intestinal pathogenic Escherichia coli (ExPEC) remains the most important etiological agent. The treatment of UTIs, is still a clinical challenge due antimicrobial resistance, mainly due to the presence of high-risk clones associated with multidrug-resistance and high virulence profiles that are spread worldwide. Thus, the characterization of these high-risk clones, particularly using molecular approaches can be used to improve the diagnostic and management of these infections. Hence, the objective of this study was to perform molecular characterization of Escherichia coli (ExPEC) isolates from urine samples of hospitalized patients, to identify high-risk clones, and to investigate the resistance and virulence profiles of these isolates. Our results showed that ExPEC high-risk clones are linked to the increase in antibiotic resistance in Rio de Janeiro, Brazil. Mobile genetic elements play an important role in the resistance and virulence profiles in these clones. The survival strategies of these clones also included the antibiotic heteroresistant profile and the production of bacteriocins. The combination of highly resistant and virulent profiles in these clones endangers the most vulnerable types of patients. Finally, this study indicates the need for better management of antibiotic use, diagnostic methods and more caution antibiotic prescription is required to reduce the spread of E. coli high-risk clones.

Comprehensive characterization of Escherichia coli isolated from urine samples of hospitalized patients in Rio de Janeiro, Brazil: the use of next generation sequencing technologies for resistance and virulence profiling and phylogenetic typing