Design of a novel chimeric multi-epitope vaccine construct against Staphylococcus lugdunensis using pan-genome analysis and immunoinformatics approaches

Abstract Staphylococcus lugdunensis has emerged as an increasingly important opportunistic pathogen associated with invasive infections and rising antimicrobial resistance, creating a need for new preventive approaches. In this study, a reverse-vaccinology strategy integrated with immunoinformatics analyses was applied to genomic datasets derived from 29 complete genomes. Pan-genome evaluation identified 1689 conserved core proteins, from which four surface-associated proteins were prioritized as potential vaccine targets based on their predicted antigenic properties and favorable safety profiles. Predicted epitopes derived from these proteins were assembled into a multi-epitope vaccine construct. Computational assessment predicted broad global population coverage of 99.47% of the selected epitopes used for multi-epitope vaccine design together with favorable physicochemical properties, including predicted solubility and a low instability index of 15.54. Molecular docking analyses predicted favorable interactions between the vaccine construct and TLR2 and TLR4. Furthermore, 100 ns molecular dynamics simulations suggested that the receptor–vaccine complexes maintained overall conformational stability throughout the simulation period. Computational immune simulations predicted adaptive immune responses characterized by antibody production, cellular immune responses, and immunological memory formation. Collectively, these computational findings suggest that the proposed multi-epitope vaccine construct represents a promising candidate for further experimental validation as a potential preventive strategy against S. lugdunensis .