Hamza Arshad Dar, Arslan Saleem Chughtai, Ali Hyder Baig, Kashif Asghar
Salmonella enterica serovar Typhi (S. Typhi) is the aetiologic agent of typhoid fever in humans. The burden of typhoid is highest in low- and middle-income countries such as Pakistan. Moreover, the increasing emergence of antibiotic-resistant and hypervirulent S. Typhi strains highlights the need for deeper genomic understanding as current treatment regimens become progressively less effective. Therefore, this study analyzed publicly available S. Typhi genomes from Pakistan to characterize genomic diversity, sequence types, plasmid content, and antimicrobial resistance and virulence profiles. Subsequently, pangenome analysis identified conserved core proteins, which were screened via reverse vaccinology to prioritize potential vaccine candidates. Analysis of 71 high-quality S. Typhi genomes identified ST-1 and ST-2 as the predominant sequence types, a finding aligned with global trends. While plasmids were detected in 32% (n = 23) of isolates, these strains exhibited significantly higher antimicrobial resistance and virulence factor gene counts compared to plasmid-free strains (p < 0.05). All isolates were found to have the aac(6')-Iaa gene. The isolates harbored Salmonella Pathogenicity Islands (SPIs), including SPI-1 through SPI-10 and SPI-12. Pangenome analysis revealed an open pangenome, with calculated pangenome size of 5912 and core genome size of 3849. Reverse vaccinology analysis prioritized three broad-spectrum S. Typhi antigens STY1784, STY1830, and STY2871 as prime vaccine candidates, with support from cross-pathogen data in the literature. Additionally, our study identified nine antigenic, strong-binding, promiscuous HLA class I epitopes. This study provides updated genomic insights into circulating S. Typhi in Pakistan and proposes novel, computationally validated vaccine targets, laying a crucial foundation for subsequent experimental investigation.