ArticleFunctional & integrative genomics2026
Integrated genomic analysis of Salmonella Typhi from Pakistan: Antimicrobial resistance determinants, pangenome structure, and reverse vaccinology-driven vaccine target discovery.
Article in Functional & integrative genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Indexed as
Identifiers
42616173What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.