Predominance of blaNDM- and blaIMP-Harboring Escherichia coli Belonging to Clonal Complexes 131 and 23 in a Major University Hospital

<i>Background and Objectives</i>: Carbapenem resistance is a growing global challenge for healthcare, and, therefore, monitoring its prevalence and patterns is crucial for implementing targeted interventions to mitigate its impact on patient outcomes and public health. This study aimed to determine the prevalence of carbapenem resistance among <i>Escherichia coli</i> (<i>E. coli</i>) strains in the largest tertiary care hospital of the capital territory of Pakistan and to characterize the isolates for the presence of antimicrobial resistance genes. Additionally, the most prevalent sequence types were analyzed. <i>Materials and Methods</i>: A total of 15,467 clinical samples were collected from November 2020 to May 2022, underwent antimicrobial susceptibility testing, and were analyzed for antimicrobial resistance genes through conventional PCR and sequence typing using MLST. <i>Results</i>: In carbapenem-resistant <i>E. coli</i> (CR-EC), 74.19% of isolates harbored the <i>bla</i>_NDM gene, with <i>bla</i>_NDM-1 (66.96%), <i>bla</i>_NDM-5 (12.17%), and <i>bla</i>_NDM-7 (20.87%) variants detected. Additionally, <i>bla</i>_IMP was found in 25.81% and <i>bla</i>_OXA-48 in 35.48% of isolates. The presence of <i>bla</i>_CTX-M15 and <i>bla</i>_TEM was identified in 83.87% and 73.55% of CR-EC isolates, respectively, while <i>arm</i>A and <i>rmt</i>B were detected in 40% and 65.16% of isolates, respectively. Colistin and tigecycline were the most effective drugs against CR-EC isolates, with both showing an MIC₅₀ of 0.5 µg/mL. The MIC₉₀ for colistin was 1 µg/mL, while for tigecycline, it was 2 µg/mL. MLST analysis revealed that the CR-EC isolates belonged to ST131 (24.52%), ST2279 (23.87%), ST3499 (16.13%), ST8051 (15.48%), ST8900 (9.68%), ST3329 (7.10%), ST88 (1.94%), and ST6293 (1.29%). The ST131 complex (70.97%) was the most prevalent, harboring 95.65% of the <i>bla</i>_NDM gene, while the ST23 complex (18.06%) harbored 62.50% of the <i>bla</i>_IMP gene. <i>Conclusions</i>: Implementing large-scale surveillance studies to monitor the spread of specific pathogens, along with active infection control policies, is crucial for the effective containment and prevention of future epidemics.