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

Background: Streptococcus pneumoniae remains a leading cause of morbidity and mortality among children under five, causing an estimated 300,000 deaths annually worldwide. Despite widespread implementation of pneumococcal conjugate vaccines (PCVs), serotype 19F, a vaccine serotype (VT), continues to persist in several high-burden settings, including South Africa. While its persistence has been documented, the evolutionary and spatial mechanisms underpinning continued circulation remain poorly understood. We investigated the evolutionary history and fine-scale spatial dynamics of predominant serotype 19F lineages within the Drakenstein Child Health Study (DCHS) to better understand the processes maintaining persistence in a highly vaccinated population. Methods: We analysed whole-genome sequences from 617 serotype 19F carriage isolates collected from infants enrolled in the DCHS, Cape Town, South Africa (2012-2017). To investigate long-term evolutionary dynamics, local genomes were combined with publicly available South African serotype 19F genomes from the Global Pneumococcal Sequencing (GPS) project. Bayesian molecular dating and complementary spatial genetic analyses were used to investigate lineage evolution and fine-scale transmission dynamics. Results: Three Global Pneumococcal Sequence Clusters (GPSC205, GPSC1, and GPSC21) accounted for 98% of all serotype 19F isolates. GPSC1 and GPSC21 exhibited significant temporal signal with the evolutionary rate of 10.3 and 5.6 substitutions per year, respectively, whereas GPSC205 showed no measurable molecular clock signal. Relative risk (RR) analyses demonstrated significant spatial clustering of isolates belonging to the same lineage within 1 km (RR = 1.32 (95% CI: 1.09-1.80)). However, genetic similarity showed a weak relationship with geographic proximity (r = 0.063, p = 0.0004), and geographic distances between isolate pairs remained largely unchanged across divergence times, indicating extensive genetic mixing across the study area. Conclusions: Persistence of pneumococcal serotype 19F appears to be driven by the long-term co-circulation of successful lineages rather than sustained expansion of geographically restricted clones. Integrating evolutionary and spatial genomic analyses provides a more comprehensive understanding of VTs' persistence and may strengthen genomic surveillance in highly vaccinated populations.