Loss of RafE impairs raffinose utilization and increases early pneumococcal burden in mice

Streptococcus pneumoniae (the pneumococcus) is one of the most common bacterial causes of middle ear infections (otitis media) in children. These infections are highly prevalent but can be persistent and challenging to treat. The pneumococcus is a highly genetically diverse organism, but the precise molecular factors that drive infection of the ear are not fully understood. Bacterial metabolic capacity is known to play an important role in infection. Here, we explored the metabolic capacity of two serotype 3 isolates of S. pneumoniae obtained from the middle ear of children with otitis media. Serotype 3 is a clinically relevant serotype of concern due to its inadequate control despite its inclusion in pneumococcal conjugate vaccines. We identified one strain as unable to metabolize raffinose, and by coupling genomic and phenotypic methods, we showed that this metabolic defect was likely due to a premature stop codon in the gene encoding the raffinose-family oligosaccharide utilization system ABC transporter substrate-binding protein (rafE). Using a S. pneumoniae D39 serotype 2 strain as a model, we showed that construction of a rafE deletion or introduction of the variant gene resulted in an increase in the number of pneumococci in the ears of mice, suggesting that this may promote transit to, or survival at, this site. This work provides further evidence of variation at the raffinose utilization locus in pneumococci and an association with distinct virulence phenotypes. Together, this aids our understanding of these infections and may have implications for the design of new therapies and vaccines.IMPORTANCEStreptococcus pneumoniae is a bacterium that lives in the nose of healthy people but can cause a range of infections in the lungs, ears, brain, and blood. In this study, we explore how S. pneumoniae acquires nutrients and proliferates inside different sites of the body. We found that nutrient uptake pathways can differ between strains, and this changes how they infect different sites. The significance of our research is in understanding how these bacteria survive in different parts of the body, which is important for developing new ways of preventing or treating disease.