Genomic analysis of invasive and non-invasive disease-causing Streptococcus pneumoniae isolated from children between 2014 and 2023 in Suzhou, China

In 2017, 553,000 clinical cases of <i>Streptococcus pneumoniae</i> in children were reported in China, although the pneumococcal conjugate vaccine (PCV), which targets the pneumococcal capsule, is not included in the Chinese National Immunization Program (NIP) for children. Therefore, the PCV uptake rate is very low. To investigate the <i>S. pneumoniae</i> population over the past 10 years in China, we collected 418 S. <i>pneumoniae</i> isolates from children with pneumococcal diseases in Suzhou, China, 2014-2023, and whole-genome sequenced them. A total of 27 serotypes expressed by 36 Global Pneumococcal Sequence Clusters (GPSCs) that encompassed 72 sequence types were identified, with serotype 19F (38.3%, <i>n</i>=160) and GPSC1 (60.8%, <i>n</i>=254) as the predominant serotype and lineage, respectively. We found that the majority (64.8%, <i>n</i>=271) of samples represented serotypes that are covered by the GSK 10-valent PCV (PCV10) formulation and that even more were covered by the SII PCV10 formulation (89.2%, <i>n</i>=373). Almost all (94.3%, <i>n</i>=394) samples represented serotypes that are included within the 13-valent PCV (PCV13) vaccine formulation. This suggests that the inclusion of the PCV in the NIP would lead to significant benefits for child health. Also, we observed that no significant differences were seen in the serotypes or lineages in cases of invasive and non-invasive pneumococcal diseases.Additionally, we investigated the prevalence of antimicrobial resistance within the population and found that 99.8% (<i>n</i>=417) of isolates were predicted to be resistant to at least one antibiotic tested. This again supports the need to increase PCV uptake to prevent infections with antibiotic-resistant <i>S. pneumoniae</i> and to reduce the number of infections in general, consequently lowering the consumption of antibiotics. In summary, the PCV13 vaccine could potentially cover over 90% of invasive and non-invasive <i>S. pneumoniae</i> isolates in Suzhou, China. Therefore, increasing the uptake of PCVs by including PCV13 in the NIP would lead to significant benefits for child health.