Computational Design and Immunoinformatic Analysis of a Broad-Spectrum Edible Multi-Epitope Vaccine Against Salmonella for Poultry

Salmonellosis remains a persistent threat to global food safety and poultry productivity, compounded by rising antimicrobial resistance. Here, we report the in silico design and immunoinformatic validation of a broad-spectrum, edible multi-epitope vaccine targeting conserved adhesion and biofilm-associated proteins (FimH, AgfA, SefA, SefD, and MrkD) of Salmonella spp. Two constructs were engineered by integrating cytotoxic (CTL) and helper (HTL) epitopes with β-defensin-3 (HBD-3) or lipopolysaccharide (LPS) adjuvants, optimized for expression in Chlorella vulgaris. Structural modeling confirmed native-like folding (z-scores −2.58 and −5.22) and high stability indices. Molecular docking and dynamics revealed that the LPS-adjuvanted construct (Construct 2) forms a highly stable complex with Toll-like receptor 3 (HADDOCK score −63.4; desolvation energy −50.2 kcal/mol), indicating potent innate immune activation. Immune simulations predicted strong IgM-to-IgG class switching and durable humoral responses, consistent with effective antigen clearance. Codon optimization achieved high adaptability for algal expression (CAI = 0.93; GC ≈ 65%), supporting scalable microalgae-based production. Compared with current parenteral vaccines, offering a low-cost, non-invasive way to curb Salmonella in poultry, this edible vaccine platform reduces dependence on antibiotics. Our approach, which combines computational vaccinology with a safe-by-design sustainable biomanufacturing perspective, outlines a One Health framework for advancing antimicrobial stewardship and food safety.