In silico design and evaluation of a cross-protective, multiepitope vaccine against outbreak-associated Salmonella

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

Submitted to: Conference Research Workers Disease Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 10/20/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: OBJECTIVE: Non-typhoidal Salmonella enterica subspecies enterica (NTS) is an important source of foodborne illness and is estimated to cause 1.35 million illnesses, 26,500 hospitalizations, and 420 deaths annually in the United States by the Centers for Disease Control and Prevention (CDC). The Interagency Food Safety Analytics Collaboration estimates that contaminated food animal meat from chickens and turkeys represents 18.6% and 5.5%, respectively, of foodborne NTS infections. Vaccination is a potentially effective intervention to lower NTS loads in food animals, thus reducing food chain transmission. A limitation of currently available commercial vaccines is cross protection against multiple Salmonella serovars (>2,600), thereby indicating a need for improved vaccine design. Multiepitope vaccines designed using reverse vaccinology tools can be created with statistically selected, antigenic epitopes and screened/evaluated in silico. This study focused on six clinically- and poultry-related NTS serovars to design a cross-protective, multiepitope vaccine construct (MEVC); the MEVC was evaluated in silico for predicted cross-protection against CDC PulseNet outbreak-associated Salmonella isolates. METHODS: Reverse vaccinology tools identified non-LPS and non-flagellar antigenic outer membrane/extracellular/periplasmic chromosomal proteins in the Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1 strain (UK-1) genome. These proteins were assessed for immunogenic, antigenic, non-toxic, and hydrophilic epitopes that had homology against six clinically- and poultry-related NTS serovars from serogroups B-E: Typhimurium (B), Infantis (C1), Kentucky (C2), Hadar (C2), Enteritidis (D) and Uganda (E). These epitopes were used to create a MEVC with cytotoxic T-cell (CTL), helper T-cell (HTL) epitopes along with HTL/CTL epitopes predicted to have linear B-cell (LBL) attributes. Presence of the epitopes within PulseNet outbreak-associated genomes was determined with BLAST. Finally, the MEVC was evaluated for physiochemical properties as well as tertiary structure prediction, refinement, and validation. RESULTS: The reverse vaccinology pipeline resulted in 105 epitopes representing 54 proteins. The nine most antigenic CTL and HTL epitopes along with all LBL epitopes (3 CTL, 6 HTL) were incorporated in a MEVC using epitope-type-associated linkers described in the literature. Each of the selected MEVC epitopes, representing 24 proteins, was compared to sequence assemblies of PulseNet outbreak-associated isolates (n=33,672) representing 142 Salmonella serovars; BLAST results showed 19 out of 28 MEVC epitopes had 100% identity and coverage against greater than 99% of the PulseNet outbreak-associated isolates. Following the addition of a Salmonella flagellin adjuvant via the EAAK linker, construct evaluation revealed the MEVC to be stable, relatively thermostable, and the predicted tertiary structure model passed defined validation metric thresholds. CONCLUSIONS: A subtractive proteomics and immunoinformatic approach was employed using various reverse vaccinology tools to create and evaluate a Salmonella MEVC. Six poultry- and clinically-related NTS serovars were used in the epitope evaluation phase, and the resulting MEVC has predicted cross-protective properties to a variety of Salmonella serovars based on sequence homology to outbreak isolates from the PulseNet database. This study shows the utility of reverse vaccinology to identify, assemble, assess, and validate predicted effectiveness of a vaccine design in silico when target organisms are paired with relevant datasets.