Abstract
In 2017, 553,000 clinical cases of Streptococcus pneumoniae 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 S. pneumoniae population over the past 10 years in China, we collected 418 S. pneumoniae 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%, n=160) and GPSC1 (60.8%, n=254) as the predominant serotype and lineage, respectively. We found that the majority (64.8%, n=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%, n=373). Almost all (94.3%, n=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% (n=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 S. pneumoniae 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 S. pneumoniae isolates in Suzhou, China. Therefore, increasing the uptake of PCVs by including PCV13 in the NIP would lead to significant benefits for child health.
| Original language | English |
|---|---|
| Article number | 001398 |
| Journal | Microbial Genomics |
| Volume | 11 |
| Issue number | 6 |
| Early online date | 2 Jun 2025 |
| DOIs | |
| Publication status | Published - 2 Jun 2025 |
Bibliographical note
For the purposes of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission.Data Availability Statement
Genome sequences are deposited in the GenBank (Bioproject, PRJNA1154805); the accession number and a phylogenetic snapshot are available at https://microreact.org/project/gps2-china. Data can also be found and downloaded through Monocle (https://data-viewer.monocle.sanger.ac.uk/project/gps). Metadata of the pneumococcal isolates in this study is submitted as a supplementary file. The authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files.Acknowledgements
Special thanks to the researchers and clinicians who were involved in sample collection in China. We would like to thank all members of the Global Pneumococcal Sequencing Consortium for their contributions to create this rich global dataset. We are also grateful for the technical support from the Wellcome Sanger Institute Pathogen Informatics team. Finally, we would like to thank Dr Lesley McGee at the CDC for her valuable comments and feedback on the manuscript.Funding
This study was co-funded by the National Natural Science Foundation of China (82272381 and 82472322). The authors thank the GPS project funded by the Bill and Melinda Gates Foundation (grant code INV-003570) and the Wellcome Trust (grant reference 206194).
Keywords
- Global Pneumococcal Sequencing project
- invasive
- multidrug resistance
- pneumococcal conjugate vaccine (PCV)
- Streptococcus pneumoniae
ASJC Scopus subject areas
- Epidemiology
- Microbiology
- Molecular Biology
- Genetics
