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Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022

Hsueh-Chien Raymond Cheng1, Shu-Chen Kuo2, Jui-Fen Lai2

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Microbial Genomics
|September 9, 2025
PubMed

Insights

Pneumococcal isolates in Taiwan show shifts after PCV13 vaccination, with increased invasive pneumococcal disease (IPD) in the elderly and the rise of specific serotypes and lineages like GPSC1 and GPSC6.

Area of Science:

  • Microbiology
  • Genomics
  • Epidemiology

Background:

  • Streptococcus pneumoniae is a major cause of respiratory illness in children and the elderly.
  • Taiwan implemented a national PCV13 vaccination program for children in March 2013.
  • Understanding pneumococcal population dynamics and antimicrobial resistance is crucial for public health.

Purpose of the Study:

  • To investigate the population structure and antimicrobial resistance profiles of S. pneumoniae isolates in Taiwan from 2006 to 2022.
  • To analyze serotype distribution and genetic lineages before and after the PCV13 vaccination program.
  • To identify emerging and persistent pneumococcal strains and their characteristics.

Main Methods:

  • Collection of 1,343 S. pneumoniae isolates biennially from 27 hospitals across Taiwan.
  • Analysis of serotypes and antimicrobial resistance (AMR) profiles for all isolates.
  • Whole-genome sequencing of 137 isolates causing invasive pneumococcal diseases (IPDs).

Main Results:

  • Post-PCV13 era (2014-2022) saw predominance of serotypes 15A, 23A, 19A, 19F, and 6A.
  • Elderly populations experienced an increased proportion of IPD post-PCV13.
  • GPSC1 was the primary lineage among IPD isolates, consistently harboring AMR genes.
  • Serotype 15A within GPSC9 emerged rapidly, especially in central Taiwan.
  • GPSC16 showed a significant increase in non-PCV13 serotype 15B/C.
  • GPSC6 exhibited frequent capsular switching, a unique phenomenon in Taiwan.

Conclusions:

  • Sustained genomic surveillance of S. pneumoniae in Taiwan is essential.
  • Monitoring age-related shifts in IPD burden is critical.
  • Tracking the expansion of adaptable lineages like GPSC1 and GPSC6 is important for public health strategies.

Keywords:
Global Pneumococcal Sequence Cluster (GPSC)Streptococcus pneumoniaeTaiwaninvasive pneumococcal disease (IPD)whole-genome sequencing

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