In silico design and evaluation of a candidate multiepitope Salmonella vaccine construct targeting broad-spectrum protection in poultry

Authors: BRADSHAW II, DAVID - Oak Ridge Institute For Science And Education (ORISE); Monson, Melissa; Bearson, Bradley; Bearson, Shawn

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/8/2026
Publication Date: 6/25/2026
Citation: Bradshaw II, D.J., Monson, M.S., Bearson, B.L., Bearson, S.M. 2026. In silico design and evaluation of a candidate multiepitope Salmonella vaccine construct targeting broad-spectrum protection in poultry. BMC Genomics. https://doi.org/10.1186/s12864-026-13056-4.
DOI: https://doi.org/10.1186/s12864-026-13056-4

Interpretive Summary: Salmonella sickens over 1 million Americans each year and causes the costliest foodborne illness in the United States. Food-producing animals can have Salmonella in their intestinal tract, but Salmonella typically does not cause disease in these animals, resulting in unrecognized spread to neighboring animals and contamination of the environment as well as the nation’s food supply during processing. With greater than 2,600 serotypes of Salmonella, vaccines that cross-protect against multiple Salmonella serotypes are needed by farmers that raise food-producing animals. A computer modeling approach called reverse vaccinology was used to identify antigenic regions (sites where antibodies bind) from Salmonella proteins of clinically relevant and poultry-associated serotypes to design a vaccine that protects against multiple Salmonella serotypes. Cross-protection of the vaccine construct was predicted by comparing the sequence of the vaccine to greater than 33,000 genome sequences from 135 Salmonella serotypes associated with human foodborne outbreaks. The data provide a vaccine design requested by livestock and poultry producers to reduce Salmonella in their food-producing animals, thereby enhancing food safety and improving profitability by reducing recall risk of Salmonella-contaminated products.

Technical Abstract: Background: Non-typhoidal Salmonella enterica subspecies enterica (NTS) is an important source of foodborne illness in humans, frequently via contaminated food animal products. Vaccination is a promisingly effective intervention to lower NTS loads in food animals, thus reducing food chain transmission. Currently available commercial vaccines have limited cross protection against multiple Salmonella serovars (>2,600), thereby indicating a need for improved vaccine design. Multiepitope vaccines designed using reverse vaccinology tools are created with statistically selected, antigenic epitopes and evaluated in silico. In the current study, a modified reverse vaccinology pipeline was employed to screen for epitopes in the Salmonella enterica serovar Typhimurium strain UK-1 proteome for design of a cross-protective, multiepitope vaccine construct (MEVC) against Salmonella for poultry. Results: The UK-1 proteome, excluding immunovariable and immunodominant lipopolysaccharide- and flagellin-associated proteins as well as plasmid-associated proteins, was screened for proteins with various relevant properties including positive homology to five poultry-associated and human-relevant serovars (Enteritidis, Hadar, Infantis, Kentucky, and Uganda), representing four Salmonella serogroups (B-E). The resulting 101 proteins were evaluated for cytotoxic (CTL) and helper lymphocyte (Th) epitopes with strong binding to chicken-like human major histocompatibility complex alleles, high antigenicity, non-toxicity, hydrophilicity, and 100% identity to = 99% of the NCBI proteomes (n = 90,800) for each of the selected serovars. Twenty-eight epitopes (9 CTL, 9 HTL, and 10 CTL/Th epitopes with linear B lymphocyte properties) representing 24 proteins were incorporated in a MEVC with epitope-type-associated linkers and a Salmonella flagellin adjuvant. Conclusions: A modified reverse vaccinology pipeline using a whole genome approach targeting clinically-relevant, poultry-associated serovars from serogroup B-E was validated by not only identifying previously recognized proteins/epitopes with immunogenic, immunoprotective and/or attenuation properties (n=21), but also unique proteins (n=7) for vaccine target exploration. Further corroboration of our RV pipeline approach was supported by 24/28 epitopes in the MEVC demonstrating 100% sequence identity to >90% of a PulseNet dataset of 135 outbreak-associated Salmonella serovars, thereby illustrating the utility of reverse vaccinology to identify, assemble, assess, and validate predicted efficacy of a vaccine design in silico when target organisms are paired with relevant validation datasets.