Pan-genome study underling the extent of genomic variation of invasive Streptococcus pneumoniae in Malawi

Streptococcus pneumoniae is a common cause of acute bacterial infections in Malawi. Understanding the underlying molecular mechanisms of the pathogen’s invasive behavior is crucial for designing new therapeutic strategies. We conducted a pan-genome analysis to identify potential virulence genes in S. pneumoniae by comparing the gene pool of the isolates from carriers’ nasopharyngeal secretions to isolates from the blood and cerebrospinal fluid of patients. We identified 56 serotypes in the cohort. Most serotypes showed a similar prevalence in carriage and disease groups. However, serotypes 1, 5, and 12F were disproportionately more commonly detected in specimens from patients compared to the carriage group, as expected, given the known invasiveness of these serotypes. These serotypes were genetically distinct from other isolates of other serotypes. The lack of genes from a genomic island known as RD8a was the most pronounced difference between serotypes 1, 5, and 12F compared to significantly prevalent serotypes in the nasopharynx. Genes in RD8a are involved in binding to epithelial cells and performing aerobic respiration to synthesize ATP through oxidative phosphorylation. The absence of RD8a from serotypes 1, 5, and 12F may result in a short duration in the nasopharynx, theoretically because of decreased capacity to bind to epithelial cells and access free oxygen molecules for aerobic respiration (needed to maintain the carriage state). Available ATP may be lower in isolates without RD8a, like serotypes 1, 5, and 12F, causing them to alternatively use phosphotransferase systems to transport carbohydrates since these transporters use phosphoenolpyruvate as the energy source instead of ATP. In conclusion, serotypes 1, 5, and 12F, the most prevalent invasive pneumococcal strains in Malawi, showed a considerable genetic distinction from other strains that may explain their invasiveness. Author summary Despite introducing the pneumococcal conjugate vaccine in 2011, Streptococcus pneumoniae remains a major cause of bacterial infection in Malawi. Whilst some pneumococcal strains harmlessly colonize the nasopharynx, others find their way into normally sterile sites, such as lungs, blood, and nervous system, resulting in serious illness. We found specific pneumococcal strains the most invasive in Malawi, they had a short colonization period and were genetically distinct from other strains. Their remarkable genetic divergence included the absence of several genes involved in aerobic respiration and the presence of genes that contribute to ATP-independent carbohydrate transport. The presence or absence of these genes may be one of the underlying causes of their high invasiveness with a short colonization period. This hypothesis could make these genes potential candidate targets for future therapeutic strategies. We hypothesized that the specific gene gain and/or loss in invasive vs. other serotypes are possibly associated with invasive pneumococcal disease development. ### Competing Interest Statement The authors have declared no competing interest.