A global epidemic serotype 14 Streptococcus pneumoniae switching to non-vaccine types.

Streptococcus pneumoniae infection is a leading cause of bacterial pneumonia worldwide, contributing to both invasive pneumococcal diseases and non-invasive diseases. Following the introduction of pneumococcal conjugate vaccines (PCV7, PCV10, and PCV13), a significant decrease in the prevalence of vaccine-type pneumococci has been observed, while the prevalence of non-vaccine-type (NVT) pneumococci has increased. This shift has been evident in both disease incidence and nasopharyngeal carriage. Serotype switching refers to the alteration or exchange of the serotype-related cps gene locus that has been flagged globally as serotypes of concern. In this study, we collected 166 S. pneumoniae clinical isolates and analyzed the serotypes of isolates to evaluate vaccine effectiveness. Additionally, we identified multidrug-resistant NVT S. pneumoniae isolates that recently emerged within the epidemic CC876 complex, a pandemic serotype 14 clone. More importantly, we identified a serotype 15B/ST4749 strain, which might have been generated through a serotype-switch event from serotype 14/ST4749. Mapping the genomic recombination sites within the serotype 15B/ST4749 progeny revealed a donated fragment encompassing cps, pbp1a, and additional key factors, including the DNA uptake-related gene comC. More importantly, as a strain that is already prevalent, the novel NVT strain possesses the potential to become a global pandemic strain.IMPORTANCEThe study employed high-throughput sequencing to analyze Streptococcus pneumoniae isolates from Xiamen Children's Hospital, China, to evaluate vaccine effectiveness in light of serotype changes and documented the occurrence of a serotype switch (from 14 to 15B) between vaccine-type and non-vaccine-type serotypes in the ST4749 strain. This observation indicates a genomic recombination and adaptive response of S. pneumoniae under selective pressure exerted by vaccination, offering novel insights into strategies for the prevention and control of S. pneumoniae and the optimization of vaccine deployment.