Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections

Urinary tract infections are a common condition affecting people globally, with multidrug-resistant (MDR) Escherichia coli (E. coli) being a major causative agent. Antimicrobial susceptibility profiling was performed using the VITEK 2 automated system for 1254 E. coli isolates, revealing that 831(66.2%) isolates were determined as MDR E. coli. A significant resistance pattern was observed for nalidixic acid (86.04%), ampicillin (74.16%), ticarcillin (70.73%), cefalotin (65.23%), cefixime (62.68%), ciprofloxacin (55.18%), ceftriaxone (53.75%), amoxicillin-clavulanic acid (22.81%), ertapenem (7.18%), and fosfomycin (2.23%). Whole Genome Sequencing of Carbapenem-resistant E. coli (CREC)-CREC 3 (ST405), CREC 4 (ST448), and CREC 5 (ST167) was performed to determine genomic characteristics. CREC 3, CREC 4, and CREC 5 belong to the phylogroup D, B1, and A, respectively. The NDM-5 gene was common in all three isolates, with CTX-M-15 being present in CREC 3 and CREC 4. Virulence factors of CREC 3 (fliC, shuA), CREC 4 (spaS), CREC 5 (iucA, papH, papG, iucB, yigF), and plasmids (IncFIA, IncFIB) were identified to be significant. The use of pangenome analysis enhances our understanding of resistance traits of isolates ST167, ST405, and ST448, offering valuable insights into comparative genomics of uropathogenic MDR E. coli.