The study describes the first isolation of multidrug-resistant (MDR) ST16, ST131 (Esc), and subsp. steigerwaltii ST93 ( complex [ECC]) in Sri Lanka. Eight MDR strains of uropathogenic Enterobacterales isolated from hospital acquired urinary tract infections (UTIs) were analyzed using genomic sequencing and comparative genomics. Isolates carried multiple carbapenemase, AmpC, and ESBL (extended-spectrum β-lactamase) genes. ECC manifested both and . The strains harbored fimbrial genes that facilitate pathogenesis of UTI. Several extraintestinal pathogenic associated virulence genes were identified in Esc. The efflux pump gene, , and the T6SS gene cluster were detected in ECC. Many antimicrobial resistance (AMR) and virulence genes were identified associated with mobile genetic elements. ISEcp1 flanked upstream of . The carbapenemase genes were carried on ColKP3 plasmids and were associated with ISEcp1. In Esc, the AMR gene and virulence gene were found on an IncF plasmid replicon. In the AMR genes and tetB present on IncR plasmid replicons and were associated with the insertion sequence IS6100. In Kp5, and coexisted and were flanked by ISEcl. AMR gene clusters, conferring resistance to multiple antimicrobial classes, flanked by mobile elements were identified in seven isolates.
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