Clonal expansion of global pneumococcal sequence cluster 3 within serotype 8 after 13-valent pneumococcal conjugate vaccine introduction, South Africa

Abstract

Background . Serotype 8 has emerged as a common non-vaccine serotype causing invasive pneumococcal disease (IPD) in children and adults globally after the introduction of pneumococcal conjugate vaccines (PCV). We aimed to determine serotype 8 incidence and genomic epidemiology in South Africa. Methods . From national, laboratory-based surveillance for IPD in South Africa, we calculated the incidence of serotype 8 and global pneumococcal sequence cluster 3 (GPSC3) before and after PCV introduction. We performed phylodynamic analysis of genomes from clonal complex (CC) 53 and described South African isolates in the context of a global collection of serotype 8 and GPSC3 genomes. Results. Compared to the pre-PCV period, serotype 8 incidence increased in the late-PCV13 period among children <5 years [incidence rate ratio (IRR) 2.3, 95% confidence interval (CI) 1.3–4.1] and adults >64 years (2.8, 1.1–8.3). Similarly, GPSC3 rates increased among children <5 years (IRR 2.4, 95% CI 1.4–4.3) and individuals of all ages (1.7, 1.3–2.1). Serotype 8 CC53 population dynamics predicted at least five clonal expansions since the most recent common ancestor in 1929 (credible interval 1919–1937), with future predictions showing increases in the effective population size despite remaining largely susceptible to first-line treatment. Serotype 8 CC53 isolates from South Africa had a clonal structure when contextualized within a global collection of serotype 8 and GPSC3 genomes. Conclusion. Serotype 8 invasive disease incidence increased in South Africa after PCV introduction. Predictions showed sustained increases over time. Since South Africa switched to a lower-valency PCV10 (Pneumosil, Serum Institute of India) that does not include serotype 8 in 2024, continued surveillance will be crucial to inform PCV policy-making.