Molecular characterization of multidrug-resistant Escherichia coli isolated from human urine infections with their antibiogram profile

Abstract

Urinary tract infections (UTIs) are the leading cause of hospitalization due to bacterial infection, and the frequency of multidrug-resistant Escherichia coli isolates from these infections is increasing worldwide. The current study aims to isolate and characterize antibiotic-resistant Escherichia coli and their antibiogram typing from urine samples of humans. From April to December 2019, a total of 60 human urine samples were collected aseptically and treated to primary isolation by propagation in nutrient broth followed by culture on various agar media. Gram’s staining, string techniques, biochemical characterization, PCR, and Sanger sequencing were performed to confirm E. coli. The Kirby-Bauer disk diffusion technique was used to test the susceptibility of all bacterial strains to thirteen typically prescribed antibiotics. The overall prevalence of E. coli in UTIs was 66.67%. Three variations were noted in E. coli, all of which were single substitutions (A>T, C>T, and T>A). Phylogenetic analysis of the 16S rRNA revealed that the E. coli discovered in this study belonged to the genus Escherichia, but was distinct from those identified in other countries. The antibiograms revealed that all the isolates (100%) were resistant to penicillin, ampicillin, and amoxicillin; 94.87% to doxycycline; 79.16% to gentamycin; 75.48% to ciprofloxacin; 73.07% to erythromycin; 71.66% to levofloxacin; 47.36% to ceftriaxone; and 46.66% to tetracycline. In contrast, all E. coli strains were sensitive to amikacin (95%), vancomycin (92.50%), and azithromycin (92.50%). People with a urinary tract infection (UTI) often have multidrug-resistant E. coli in their urine samples, which calls for a one-health strategy to deal with this rapidly changing condition.