Our research group at the Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) in Islamabad’s lush green campus specializes in microbial genomics and pangenomics to combat infectious disease threats. We employ integrative genomic approaches to study pathogen evolution, transmission dynamics, and antimicrobial resistance (AMR) patterns through large-scale analysis of microbial genomes and pangenomes. Our work focuses particularly on decoding the core and accessory genome elements that drive virulence and resistance in multidrug-resistant pathogens circulating in both healthcare and community settings. We develop innovative bioinformatics tools and databases for genomic surveillance, enabling real-time tracking of emerging pathogens through whole genome sequencing and pangenome analysis. Additionally, we combine reverse vaccinology with machine learning approaches to predict potential vaccine targets and therapeutic candidates, bridging the gap between microbial genomics and translational solutions for infectious disease control. Our research aims to address the growing global AMR crisis while advancing genomic technologies for pathogen monitoring and intervention strategies.