Genomic and statistical models to characterize Streptococcus pneumoniae transmission patterns in Malawi

Controlling the carriage and transmission of Streptococcus pneumoniae in children from high-burden settings is critical for disease prevention. To investigate the rate and drivers of transmission following pneumococcal conjugate vaccine (PCV) introduction, we estimated evolutionary divergence times using whole-genome sequences of S. pneumoniae from 1,617 children in Blantyre, Malawi (2015–2019). The cohort included PCV13-vaccinated children aged 2–7 years and unvaccinated children aged 5–10 years who were vaccine ineligible at the time of rollout into routine use. Using generalized additive mixed models and relative risk frameworks that incorporated household geospatial distances, we found that pneumococcal lineages spread widely across Blantyre within ~4 years, with transmission most likely between neighbouring households. Logistic regression and random forest models identified higher transmission risk among preschool-aged children in densely populated, higher socioeconomic areas. Recent transmission events were primarily associated with expanding, non-vaccine serotype lineages that were non-susceptible to penicillin. These findings highlight the potential for extended valency PCVs to reduce the spread of disease-causing and antimicrobial-resistant pneumococcal lineages among preschool-aged children, particularly in high-density areas – thereby strengthening herd protection for vulnerable groups such as young infants and individuals living with HIV.