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

BACKGROUND: Salmonella enterica subspecies enterica is an important source of human foodborne illness, frequently via contaminated food animal products. Vaccination is a promisingly effective intervention to lower Salmonella loads in food animals, thus reducing food chain transmission. Currently-available commercial vaccines have limited cross protection across Salmonella serovars (> 2,600), indicating a need for novel vaccines with broad efficacy. In this study, an in silico reverse vaccinology (RV) pipeline comprehensively screened the proteome of Salmonella enterica serovar Typhimurium strain UK-1 for conserved proteins from poultry-associated, human-relevant Salmonella serovars and identified epitopes with predicted broad-spectrum protection for the design of a multiepitope vaccine construct (MEVC). RESULTS: The UK-1 proteome, excluding lipopolysaccharide-, flagellin-, and plasmid-associated proteins, was screened for proteins with pertinent properties including homology to five poultry-associated, human-relevant serovars (Enteritidis, Hadar, Infantis, Kentucky, and Uganda), representing Salmonella serogroups B-E. The resulting 101 proteins were evaluated for cytotoxic and helper T lymphocyte epitopes with strong binding to chicken-like human major histocompatibility complex alleles, high antigenicity, and 100% identity to ≥ 99% of the NCBI proteomes of the selected serovars (n = 90,800). Of the resulting 93 epitopes, 28 epitopes derived from 24 proteins were incorporated in an MEVC with epitope-type-associated linkers and a Salmonella flagellin adjuvant. In silico tools predicted immunological functions of the MEVC including TLR1/TLR2 binding, induction of classical cellular and humoral immune responses, and sequence homology (i.e. potential cross-protection) to a Salmonella outbreak dataset. CONCLUSIONS: A modified RV pipeline using a whole proteome approach targeting human-relevant, poultry-associated serovars identified previously recognized proteins with immunogenic and/or immunoprotective properties (suggestive of in vivo protein expression and immune stimulation), as well as eight novel proteins for vaccine target exploration. Our RV pipeline was further corroborated by 25 of the 28 MEVC epitopes demonstrating 100% sequence identity to > 90% of a PulseNet dataset of 135 outbreak-associated Salmonella serovars from various food sources. Although efficacy validation of the proposed MEVC requires in vivo or in vitro evaluation, the current study illustrates the utility of pairing target organisms with relevant datasets to in silico screen, assemble, and assess a multiepitope vaccine construct designed for predicted broad-spectrum protection.