Genomic analysis and pneumococcal population dynamics across PCV implementation in South Korea, 1997–2023

Streptococcus pneumoniae, a clinically significant pathogen, causes invasive diseases in children and older adults. Pneumococcal conjugate vaccines (PCVs) have substantially reduced the incidence of vaccine serotype (VT) pneumococcal diseases. However, serotype replacement, characterized by the emergence of non-vaccine serotypes (NVTs), presents a persistent challenge to disease prevention. To address this, we analysed 236 pneumococcal isolates collected in South Korea between 1997 and 2023, spanning both pre-and post-PCV13 periods. Whole-genome sequencing was performed to assess serotypes, antimicrobial resistance, virulence factors and global pneumococcal sequence clusters (GPSCs). Capsular switching events and the relationships among pneumococcal lineages, serotypes and disease invasiveness were also evaluated. Among the 37 identified serotypes, NVTs such as 23A, 15B/15C and 10A were dominant post-PCV13. Serotype 10A, associated with invasive pneumococcal diseases (IPDs), belonged to GPSC634-ST11189 and showed elevated minimum inhibitory concentrations for β-lactams. Capsular switching events were observed between VTs and NVTs, highlighting the adaptability of pneumococcal populations. Antimicrobial non-susceptibility was highest for azithromycin (82.7%), followed by tetracycline (76.5%) and co-trimoxazole (70.4%), with higher rates observed in the post-PCV13 period. Notably, amoxicillin (P=0.049) and meropenem (P=0.002) showed significant non-susceptibility in the post-PCV13 period. Virulence factors pspA and pfbA were associated with IPDs, while pilus islet PI-1-related genes were more frequent in non-invasive cases. These findings underscore the importance of genomic surveillance to monitor pneumococcal population dynamics and inform public health strategies. The inclusion of serotype 10A in the recently approved PCV20 offers promise for further reducing the global burden of IPDs, including in South Korea.