The bacterium Streptococcus pneumoniae is a leading cause of human morbidity and mortality. With ever increasing antibiotic resistance rates and poor coverage of current vaccines, novel therapeutics and vaccines are urgently required. However, the mechanisms underlying the differences between localised vs invasive pneumococcal diseases are poorly understood. This is largely due to S. pneumoniae’s vast genetic diversity, as they are subdivided into 98 serotypes based on the capsular polysaccharide they produce, superimposed on >12000 clonal sequence types (ST) distinguished by multi-locus sequence typing. This poor understanding of underlying disease mechanisms is impeding novel treatment design.
Previously we showed that even closely related strains within the same serotype and clonal type can display variations in virulence, corresponding to their isolation site in humans. In murine intranasal challenge models, serotype 14 ST15 clinical isolates from the blood persisted in the lungs, while matching ear isolates were cleared from this niche. We recently showed that a single nucleotide polymorphism (SNP) in the raffinose pathway regulatory gene rafR accounts for significant differences in their disease progression. Swapping rafR alleles between these isolates led to a simultaneous switch in their disease profiles.
Using novel in vivo dual RNA-sequencing on infected murine lungs, we established that the rafR SNP extensively impacts both bacterial and host transcriptomes. A crucial role for IL-17 induced neutrophil recruitment was predicted, with IL-17 pathway genes upregulated in the strains cleared from the lungs. Indeed, single cell flow analysis showed the rafR SNP leads to massive recruitment of neutrophils in the lungs of the cleared strains, post-infection. Importantly, resulting disease outcomes were confirmed in murine intranasal challenges. Mice depleted of neutrophils or IL-17A had significantly higher bacterial loads in the lungs 24h post-challenge. Strikingly, the strains originally cleared from the lungs were now able to persist in this niche after neutrophil depletion, at the same levels as the non-neutrophil depleted invasive strains. Our findings elucidate disease mechanisms of S. pneumoniae, demonstrating how the wide impact of a single bacterial SNP leads to increased neutrophil recruitment post-infection in the lungs. This mechanism drives differential disease outcomes in clinical clonal isolates of S. pneumoniae.