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The emergence of antibiotic-resistant microorganisms is a significant concern in global health. Antibiotic resistance is attributed to various virulent factors and genetic elements. This study investigated the virulence factors of <i>Staphylococcus aureus</i> to create an mRNA-based vaccine that could help prevent antibiotic resistance. Distinct strains of the bacteria were selected for molecular identification of virulence genes, such as <i>spa</i>, <i>fmhA</i>, <i>lukD</i>, and <i>hla-D</i>, which were performed utilizing PCR techniques. DNA extraction from samples of <i>Staphylococcus aureus</i> was conducted using the Cetyl Trimethyl Ammonium Bromide (CTAB) method, which was confirmed and visualized using a gel doc; 16S rRNA was utilized to identify the bacterial strains, and primers of <i>spa</i>, <i>lukD</i>, <i>fmhA</i>, and <i>hla-D</i> genes were employed to identify the specific genes. Sequencing was carried out at Applied Bioscience International (ABI) in Malaysia. Phylogenetic analysis and alignment of the strains were subsequently constructed. We also performed an in silico analysis of the <i>spa</i>, <i>fmhA</i>, <i>lukD</i>, and <i>hla-D</i> genes to generate an antigen-specific vaccine. The virulence genes were translated into proteins, and a chimera was created using various linkers. The mRNA vaccine candidate was produced utilizing 18 epitopes, linkers, and an adjuvant, known as RpfE, to target the immune system. Testing determined that this design covered 90% of the population conservancy. An in silico immunological vaccine simulation was conducted to verify the hypothesis, including validating and predicting secondary and tertiary structures and molecular dynamics simulations to evaluate the vaccine’s long-term viability. This vaccine design may be further evaluated through in vivo and in vitro testing to assess its efficacy.