Geographical structure and evolutionary trajectories of Streptococcus pneumoniae serotype 19F lineages in South Africa

BackgroundPneumococcal disease causes approximately 505,000 deaths annually in children under 5 and disproportionately affects vulnerable groups, including the elderly and immunocompromised individuals. Despite the success of pneumococcal conjugate vaccines (PCVs) in reducing disease burden, residual vaccine 19F persists in carriage and disease. We used whole genome sequences and geological data to understand the spread dynamics of serotype 19F lineages in South Africa. MethodsWe obtained 617 serotype 19F carriage isolates from infants enrolled in the Drakenstein Child Health Study (DCHS), Cape Town, South Africa (2012 to 2017). Whole-genome sequencing was performed using the Illumina HiSeq. We utilized genomic and geological data to assess the spread dynamics of pneumococcal serotype 19F. ResultsThe most predominant 19F lineages were GPSC205 (50%; n= 309), GPSC1 (36%; n= 220), and GPSC21 (12%; n= 76). Temporal signal and a correlation between genetic and geographic distance were generally weak. We observed the geographical structure within one kilometre in a study area of approximately eight kilometres. We found that the homogenization time pneumococcal 19F serotype was immediate. ConclusionsSerotype 19F transmission in the Drakenstein operates under a quasi-endemic equilibrium, which is likely maintained by sustained carriage, overlapping social networks, and repeated reintroductions within households and communities. Therefore, the homogenization observed is not necessarily evidence of exceptional transmission velocity; it could be of prolonged persistence in a tightly connected host population, a hallmark of serotype 19F resilience under vaccine pressure.