In silico development of a cross-protective, multiepitope Salmonella vaccine against clinically- relevant and poultry-associated serovars

Background Non-typhoidal Salmonella enterica subspecies enterica (NTS) is an important source of human foodborne illness, 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 across Salmonella serovars (> 2,600), 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 and plasmid-associated proteins, was screened for proteins with relevant properties including homology to five poultry-associated and human-relevant serovars (Enteritidis, Hadar, Infantis, Kentucky, and Uganda), representing Salmonella serogroups B-E. The resulting 101 proteins were evaluated for cytotoxic and helper lymphocyte epitopes with strong binding to chicken-like human major histocompatibility complex alleles, high antigenicity, and 100% identity to ≥ 99% of the NCBI proteomes (n = 90,800) for each of the selected serovars. Twenty-eight epitopes representing 24 proteins were incorporated in a MEVC with epitope-type-associated linkers and a Salmonella flagellin adjuvant. Immunological predictions for the MEVC included 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 reverse vaccinology pipeline using a whole genome approach targeting clinically-relevant, poultry-associated serovars was validated by not only identifying previously recognized proteins with immunogenic, immunoprotective and/or attenuation properties (n = 16), but also unique proteins (n = 8) for vaccine target exploration. Our reverse vaccinology pipeline was further corroborated by 25/28 MEVC epitopes demonstrating 100% sequence identity to > 90% of a PulseNet dataset of 135 outbreak-associated Salmonella serovars from various food animal sources, 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.