Molecular Characterisation and Population Structure Determination of Streptococcus pneumoniae in South Africa using Whole-Genome Analysis

Abstract

Pneumococcal conjugate vaccines (PCV) have effectively reduced overall invasive pneumococcal disease (IPD) and antibiotic-nonsusceptible IPD in many countries. Ongoing invasive disease due to residual vaccine-targeted serotypes (VT) and non-vaccine serotypes (NVT) after PCV introduction remains a global concern. In South Africa, seven-valent PCV (PCV7) was introduced in 2009 and was replaced by 13-valent PCV (PCV13) in 2011. We aimed to evaluate changes in IPD lineages and antibiotic-nonsusceptibility before and after PCV introduction in South Africa. We analysed 54,199 IPD cases reported from 2005–2020 as part of the national, laboratory- based surveillance program. A randomly selected subset of approximately 4800 isolates underwent whole-genome sequencing. We determined in silico serotypes, sequence types, global pneumococcal sequence cluster (GPSC) lineages, and antimicrobial resistance determinants from the genomes of 4669 isolates. Vaccine periods were defined as pre-PCV (2005–2008), PCV7 (2009–2010), early-PCV13 (2011–2014), and late-PCV13 (2015–2020). Penicillin multidrug resistance (penicillin-MDR) was defined as nonsusceptibility to penicillin plus ≥2 other antibiotic classes. Other MDR was defined as nonsusceptibility to ≥3 antibiotic classes. Vaccine-type and non-vaccine-type lineages were defined as expressing ≥50% VTs and >50% NVTs, respectively, before PCV introduction. In silico serotype and lineage diversity trends were determined using Simpson’s diversity index (SDI). vii Significant incidence reductions occurred among vaccine-type lineages in the late-PCV13 period compared to the pre-PCV period. The five most common serotypes in the late-PCV13 period were NVTs 8, 12F, 15B/C, and residual VTs 19A and 19F, mainly expressed by GPSC3 (non-vaccine-type lineage), GPSC26 and GPSC56 (non-vaccine-type and vaccine- type), GPSC48 (non-vaccine-type), GPSC17 (vaccine-type), and GPSC1/21 (vaccine-types), respectively. Compared to the baseline period, significantly higher serotype diversity estimates were observed in the early-PCV13 period, with the highest estimate occurring during the PCV13 introduction year (2011, SDI 0.993, 95% confidence interval [CI] 0.991– 0.995). A significant increase in lineage diversity was also observed from the PCV7 period to the early-PCV13 period (SDI: 0.954, 95% CI 0.948–0.961 vs 0.965, 0.962–0.969) supporting intervention-driven population structure perturbation. Overall antibiotic-nonsusceptible IPD declined across the study period. Residual PCV13 serotypes 19A and 19F contributed 44% (977/2236) of penicillin-cotrimoxazole or penicillin-MDR IPD in the late-PCV13 period. Among NVTs, serotypes 10A, 15A, 15B/C, 16F, 23B, and 35B were common causes (61.9%, 545/881) of penicillin-cotrimoxazole or penicillin-MDR IPD after PCV13 introduction in children and adults. Overall, NVT 8 was the most common cause of IPD after PCV13 introduction with significant incidence increases among children ≤5 years (incidence rate ratio 2.3, 95% CI 1.3–4.1) and adults >64 years (2.8, 1.1–8.3) when comparing pre-PCV versus late-PCV13 periods. NVT 8 (GPSC3, sequence type 53) IPD was predicted to continue increasing despite remaining largely susceptible to first-line treatment. Incidence of IPD declined in all ages in South Africa after PCV introduction. Similarly, overall nonsusceptible IPD declined in the post-PCV era. Vaccine-type lineages, particularly those expressing VTs 19A (GPSC17) and 19F (GPSC21) continued to circulate after PCV introduction and were important contributors to penicillin-nonsusceptible IPD in addition to viii some pre-existing non-vaccine-type lineages. GPSC3 (NVT 8) caused substantial disease in children and adults in the post-PCV era. In 2024, South Africa switched to a lower-valency vaccine PCV10 (Pneumosil, Serum Institute of India). Given the expansion of non-vaccine- type lineages and the persistence of vaccine-type lineages that are predominantly expressing their NVT counterparts following PCV use, it is crucial to monitor the impact of this switch on the pneumococcal population structure and AMR to inform future PCV formulation considerations.