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.
TSAR Publications：
1. Cheng HR, Kuo SC, Lai JF, Wu HC, Chen FJ, Sytwu HK, Lo SW, Bentley SD, Huang YC. Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022. Microb Genom. 2025 Sep;11(9):001498. doi: 10.1099/mgen.0.001498. PMID: 40924938; PMCID: PMC12452192.
2. Wu CJ, Lai JF, Huang IW, Shiau YR, Wang HY, Lauderdale TL. Serotype Distribution and Antimicrobial Susceptibility of Streptococcus pneumoniae in Pre- and Post- PCV7/13 Eras, Taiwan, 2002-2018. Front Microbiol. 2020 Oct 22;11:557404. doi: 10.3389/fmicb.2020.557404. PMID: 33193140; PMCID: PMC7642986.