Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Nat Commun. 2024 Sep 27;15(1):8401. doi: 10.1038/s41467-024-52459-3.
Invasive pneumococcal disease (IPD) due to non-vaccine serotypes after the introduction of pneumococcal conjugate vaccines (PCV) remains a global concern. This study used pathogen genomics to evaluate changes in invasive pneumococcal lineages before, during and after vaccine introduction in South Africa. We included genomes (N = 3104) of IPD isolates from individuals aged <18 years (2005-20), spanning four periods: pre-PCV, PCV7, early-PCV13, and late-PCV13. Significant incidence reductions occurred among vaccine-type lineages in the late-PCV13 period compared to the pre-PCV period. However, some vaccine-type lineages continued to cause invasive disease and showed increasing effective population size trends in the post-PCV era. A significant increase in lineage diversity was observed from the PCV7 period to the early-PCV13 period (Simpson's diversity index: 0.954, 95% confidence interval 0.948-0.961 vs 0.965, 0.962-0.969) supporting intervention-driven population structure perturbation. Increases in the prevalence of penicillin, erythromycin, and multidrug resistance were observed among non-vaccine serotypes in the late-PCV13 period compared to the pre-PCV period. In this work we highlight the importance of continued genomic surveillance to monitor disease-causing lineages post vaccination to support policy-making and future vaccine designs and considerations.
在肺炎球菌结合疫苗（PCV）引入后，非疫苗血清型导致的侵袭性肺炎球菌病（IPD）仍然是一个全球性问题。本研究使用病原体基因组学来评估南非在疫苗引入之前、期间和之后侵袭性肺炎球菌谱系的变化。我们包括了来自年龄<18 岁（2005-20 年）个体的 IPD 分离株的基因组（N=3104），跨越四个时期：PCV7 之前、PCV7 期间、PCV13 早期和 PCV13 晚期。与 PCV7 之前的时期相比，PCV13 晚期的疫苗型谱系的发病率显著降低。然而，一些疫苗型谱系继续导致侵袭性疾病，并在 PCV 后时代显示出有效种群大小趋势的增加。从 PCV7 时期到 PCV13 早期，谱系多样性显著增加（辛普森多样性指数：0.954，95%置信区间 0.948-0.961 与 0.965，0.962-0.969），支持干预驱动的种群结构扰动。与 PCV7 之前的时期相比，在 PCV13 晚期，非疫苗血清型的青霉素、红霉素和多药耐药性的流行率增加。在这项工作中，我们强调了继续进行基因组监测以监测疫苗接种后导致疾病的谱系的重要性，以支持决策制定和未来的疫苗设计和考虑。
