High-throughput antigen discovery using Functional Genomic Vaccinology (FGV) identifies protective Streptococcus pneumoniae vaccine candidates

The discovery of protective antigens remains a major bottleneck in bacterial vaccine development. To overcome this limitation, we present Functional Genomic Vaccinology (FGV), a high-throughput antigen discovery platform integrating genome-wide antigen prediction, proteome-scale screening, and experimental immunogenicity validation to identify protective bacterial antigens. Using FGV, 222 conserved S. pneumoniae proteins are expressed in vitro, incorporated into a protein microarray, and coupled to magnetic beads for mouse vaccination. Protein array analysis shows significant IgG responses in 40% of the screened proteins. Antigen-specific responses measured in human sera guide the prioritisation of 22 candidates, which undergo further studied for their serological and Th17 responses. Four antigens combined in a multicomponent vaccine induces protection from pneumonia and sepsis in mice, with epitope mapping revealing potential protective sites for each protein. These results establish FGV as a scalable, experimentally driven approach for bacterial vaccine discovery and demonstrate its applicability in developing protective pneumococcal vaccines.