Streptococcus pneumoniae (the pneumococcus) is the most common cause of community-acquired pneumonia. However, it is also commonly found as an asymptomatic coloniser of the upper respiratory tract. It is not clear how this pathogen may change from the colonisation state to causing disease. This study investigated nasopharyngeal swabs and lung aspirates collected from pneumonia patients as part of ongoing surveillance in The Gambia, along with pneumococcal isolates obtained from these clinical samples. Our aim was to elucidate the molecular processes by which the pneumococcus can transition from the carriage to infection state, and identify potential genes involved in the pathogenesis of pneumococcal pneumonia. Genomic analysis revealed three non-silent genomic variations: two substitutions (202G>A in rpoC and -18G>T in psaB) and one insertion (469insC in glnA). Transcriptomic changes were examined using RNA extracted directly from clinical samples by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and the 2-DDCt method. We found that ply (pneumolysin), nanA (neuraminidase A), yeeN (putative virulence regulator), and psaB (manganese transporter) were upregulated (> 4-fold) in lung aspirates compared with nasopharyngeal swabs; whereas spxB (pyruvate oxidase) and eno (enolase) were downregulated (2- to 168-fold). For cpsA (capsule), luxS (quorum sensing), endA (DNA-entry nuclease), and lytA (autolysin), disparate expression patterns were observed across serotypes, ranging from 23-fold downregulation to 57-fold upregulation. Upregulations or downregulations of the ten genes were also seen in vitro when comparing expression in artificial sputum with nose-like media. However, direction and/or magnitude from the in vitro results were not always consistent with those in the clinical samples. In addition, limited upregulations or downregulations (both <4-fold) were seen in the same ten genes when pneumonia patients were compared with healthy controls using nasopharyngeal swabs. This is the first study investigating pneumococcal gene expression using samples collected directly from patients. These findings indicate the critical role that the host plays during pneumococcal pneumonia, and provide new insights into the complex process of pneumonia pathogenesis.