Enterobacter hormaechei is a significant nosocomial pathogen associated with multidrug resistance. This study investigates high-risk clones isolated from tertiary care hospitals using whole-genome sequencing (WGS). The findings reveal diverse resistance genes, mobile genetic elements, and virulence factors contributing to its pathogenicity. Comparative genomics identified clonal relationships and novel plasmids driving antimicrobial resistance. These results highlight the urgent need for stringent infection control policies and novel therapeutic approaches to combat E. hormaechei-associated infections.Enterobacter hormaechei is a significant nosocomial pathogen associated with multidrug resistance. This study investigates high-risk clones isolated from tertiary care hospitals using whole-genome sequencing (WGS). The findings reveal diverse resistance genes, mobile genetic elements, and virulence factors contributing to its pathogenicity. Comparative genomics identified clonal relationships and novel plasmids driving antimicrobial resistance. These results highlight the urgent need for stringent infection control policies and novel therapeutic approaches to combat E. hormaechei-associated infections.