Streptococcus pneumoniae remains a leading cause of invasive diseases such as pneumonia, sepsis, and meningitis, especially among children and the elderly. While pneumococcal conjugate vaccines (PCVs) have significantly reduced the burden of vaccine-covered serotypes, non-vaccine types (NVTs) have emerged, reshaping the epidemiological landscape.
To better understand this shift, we conducted whole-genome sequencing (WGS) of invasive pneumococcal isolates collected between 2006 and 2022 through the national TSAR program, in collaboration with the Wellcome Sanger Institute. WGS offers high-resolution insights that traditional serotyping cannot provide—it enables precise identification of capsular switching events, clonal lineage definitions, resistance determinants, and genetic recombination patterns critical for monitoring vaccine-driven evolution.
Our findings revealed two key dynamics: the clonal expansion of NVTs (such as serotype 15B/C in GPSC16), and frequent capsular switching in vaccine-type clones (especially GPSC6). These events reflect adaptive responses to vaccine pressure. Multidrug-resistant lineages such as GPSC1 and GPSC9 remain prevalent in the elderly, raising concerns over treatment options.
These results highlight the limitations of current serotype-based vaccine strategies. With the high genetic plasticity of S. pneumoniae, future vaccine development should consider protein-based or universal vaccines to ensure broader and more durable protection. WGS will continue to be an essential tool for genomic surveillance and vaccine policy guidance in Taiwan.