A genetic interaction screen in Streptococcus pneumoniae identifies functionally redundant vaccine candidate proteins CbpC and CbpJ

Streptococcus pneumoniae is a Gram-positive bacterium that asymptomatically colonizes the nasopharynx and can disseminate to sterile sites resulting in pneumococcal diseases such as pneumonia, otitis media, bacteremia, and meningitis. Due to increased incidence of invasive disease caused by serotypes that are not included in available polysaccharide vaccines, there is a need for a broadly protective protein vaccine to complement the polysaccharide based vaccines. To limit immune escape such a vaccine would ideally target proteins that are essential for virulence. However, the genetic robustness of S. pneumoniae results in few surface exposed proteins being essential for virulence. Here we carried out a genetic interaction screen to identify functionally redundant surface protein pairs that could be used as bivalent protein vaccines, based on the observation that together, these protein pairs are essential for virulence. We identified four pairs of functionally redundant surface proteins that displayed a significant competitive disadvantage during murine pneumococcal pneumonia. Immunization with the most attenuated pair, CbpC and CbpJ, resulted in production of high titers of specific antibodies and a modest increased median survival times of mice challenged with pneumococcal pneumonia. This study demonstrates a method to identify essential pairs of surface-associated virulence proteins that could be widely applied to many bacterial pathogens. IMPORTANCEInfection by Streptococcus pneumoniae can result in life-threatening illness. Current licensed polysaccharide vaccines only protect against serotypes that are present in the vaccine - at most 23 serotypes of the total 100 identified, circulating serotypes. There remains a need for a widely protective protein vaccine that is effective against most circulating strains of S. pneumoniae. The significance of our research is in developing a method to identify functionally redundant protein pairs as potential vaccine candidates, which could inform the development of effective bivalent protein vaccines for many bacterial pathogens.