Streptococcus pneumoniae (the pneumococcus) is a leading cause of human mortality and morbidity, yet is more commonly carried asymptomatically in the human nasopharynx. However, the mechanisms underlying pneumococcal transition from commensal to pathogen are poorly understood, largely due to its vast genetic diversity. S. pneumoniae is subdivided into >90 serotypes based on the capsular polysaccharide they produce, which is superimposed on >12000 clonal types distinguished by multi-locus sequence typing. As current pneumococcal vaccines only protect against a maximum of 23 serotypes, and S. pneumoniae develops antibiotic resistance rapidly, new drug and vaccine targets are urgently needed.

Previous studies have shown that even closely related pneumococcal strains within the same serotype and sequence type (ST) can display variations in virulence, related to their isolation site in humans. Serotype 14 (ST15) and 3 (ST180) clinical isolates derived from the blood exhibited a tendency to cause septicaemia and/or pneumonia, while ear isolates caused otitis media and meningitis. Genomic comparisons performed between a blood and ear isolate, each from both ST15 and ST180, identified single nucleotide polymorphisms (SNPs) in the raffinose uptake genes rafR and rafK, respectively. Growth and qRT-PCR assays with raffinose as the sole carbon source showed that the blood isolates utilised raffinose more efficiently than the ear isolates, whereas there was no difference in ability to utilise glucose. Swapping rafR alleles between the ST15 blood and ear isolates led to a switch in the above in vitro characteristics. Strikingly, the rafR swapped strains also showed a simultaneous swap in the disease profiles between the blood and ear isolates. Now the rafR swapped blood isolate caused otitis media and meningitis significantly more than the rafR swapped ear isolate, which instead displayed an increased capacity to cause pneumonia. These results suggest that variations in the rafR sequence that affect the ability to utilise raffinose play a significant role in dictating tissue tropism and pneumococcal disease progression.