Abstract

We investigated the pathogenesis of pneumococcal pneumonia using clinical specimens collected for pneumonia surveillance in The Gambia. Lung aspirates and nasopharyngeal swabs from 31 patients were examined by culture, qPCR, whole genome sequencing, serotyping, and reverse transcription qPCR. Five lung aspirates cultured pneumococci, with a matching strain identified in the nasopharynx. Three virulence genes including ply (pneumolysin) were upregulated >20-fold in the lung compared with the nasopharynx. Nasopharyngeal pneumococcal density was higher in pediatric pneumonia patients compared with controls (p <0.0001). Findings suggest that changes in pneumococcal gene expression occurring in the lung environment may be important in pathogenesis.