Genomic characterization of invasive Streptococcus pneumoniae isolates from a southern Taiwan medical centre, 2015–2023

Since the introduction of pneumococcal conjugate vaccines, the incidence of invasive pneumococcal disease (IPD) among children has decreased significantly. The distribution of IPD cases has shifted towards other vulnerable populations, including older adults and individuals with pre-existing medical conditions. Alongside this shift, there has also been a concurrent change in pneumococcal serotype distribution. Studies on the distribution of pneumococcal serotypes and antibiotic resistance patterns in the post-pneumococcal conjugate vaccine era, particularly following the coronavirus disease 2019 (COVID-19) pandemic, remain limited in the Asia-Pacific region. This study aims to investigate patient characteristics, pneumococcal serotype and antibiotic resistance profiles predicted by whole-genome sequencing among IPD patients in a public medical centre in southern Taiwan. A total of 61 IPD isolates were collected between 2015 and 2023. Serotype and antibiotic resistance were determined using whole-genome sequencing. The results showed that 47.5% of cases were in patients aged 65 years and older and 34.3% of cases involved patients with comorbid malignancy. The serotypes included in the 13-valent pneumococcal conjugate vaccine (PCV13) comprised 52.5% of the isolates. Overall, 26.2% of isolates were non-susceptible to penicillin (non-meningitis breakpoint). For the PCV13 serotypes, the non-susceptible rate to penicillin (non-meningitis breakpoint) was 43.8%. Phylogenetic analysis suggested recent emergence of a multi-drug resistant serotype34/ST9395 lineage. These findings suggest that the older adult population and those with pre-existing medical conditions, particularly malignancy, could benefit from targeted prevention efforts.