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

<i>Streptococcus pneumoniae</i> remains a leading respiratory pathogen for children and the elderly. In Taiwan, a national PCV13 catch-up vaccination programme for children began in March 2013. This study investigates the population structure and antimicrobial profiles of pneumococcal isolates in Taiwan from 2006 to 2022. A total of 1,343 <i>S</i>. <i>pneumoniae</i> isolates were collected biennially from 27 hospitals across 4 regions of Taiwan. All isolates were analysed for serotypes and antimicrobial resistance (AMR) profiles, and 137 isolates causing invasive pneumococcal diseases (IPDs) underwent whole-genome sequencing. In the post-PCV13 era (2014-2022), serotypes 15A, 23A, 19A, 19F and 6A predominated. The elderly populations showed an increased proportion of IPD in the post-PCV13 era. Among the 137 IPD isolates, GPSC1 (21.9%) was the primary lineage, consistently harbouring AMR genes. Serotype 15A within GPSC9 emerged rapidly, particularly in central Taiwan. In GPSC16, non-PCV13 serotype 15B/C increased significantly, replacing vaccine types. GPSC6 displayed frequent capsular switching, a unique phenomenon in Taiwan, driven by distinct recombination events post-2000. These findings underscore the importance of sustained genomic surveillance of <i>S. pneumoniae</i> in Taiwan to monitor age-related shifts in IPD burden and to track the expansion of persistent and highly adaptable lineages such as GPSC1 and GPSC6.