“Just the Best Ones” combination: a new strategy for multi-epitope vaccine candidate based on immunoinformatics analysis to induce protective immunity against MRSA infection

Staphylococcus aureus is a major global health threat due to its increasing antibiotic resistance and high virulence, presenting serious challenges in healthcare. Currently, no effective vaccine exists to prevent its infections. In our study, we introduced a novel multi-epitope vaccine design method using immunoinformatics, named the “Just the Best Ones” strategy. This approach involved selecting the most promising T-cell and B-cell epitopes from 10 key proteins of S. aureus based on the pathogenic mechanism of the bacterium in the host, to create the Staphylococcus aureus Multi-Epitope Antigen (SAMEA) with optimal immunogenicity. Physicochemical and structural analyses confirmed SAMEA’s stability and suitable profiles for antigenicity, toxicity, and allergenicity. Molecular docking showed strong interactions between SAMEA and human TLR2, crucial for eliciting effective immune responses. Additionally, SAMEA was highly immunogenic and safe, generating a strong antibody response and excellent protection in mice. These results suggest that SAMEA is a promising multi-epitope vaccine candidate, highlighting the “Just the Best Ones” strategy’s effectiveness, and introducing a new direction in vaccine development against S. aureus infections. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major health threat due to its antibiotic resistance and ability to cause severe infections in humans and animals. Yet, no licensed vaccine is available. Here, we present a “Just the Best Ones” strategy that applies immunoinformatics to select the most protective epitopes from key S. aureus antigens. Using this approach, we developed a multi-epitope antigen (SAMEA) that proved safe, highly immunogenic, and protective in mice, particularly when combined with a bacterium-like particle adjuvant. These results highlight SAMEA as a promising MRSA vaccine candidate and indicate that this strategy may help guide vaccine development for other difficult pathogens. As it continues to be refined, this approach could facilitate more effective vaccines and improve the prevention of infectious diseases.