A global epidemic serotype 14 <i>Streptococcus pneumoniae</i> switching to non-vaccine types

<i>Streptococcus pneumoniae</i> 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 <i>cps</i> gene locus that has been flagged globally as serotypes of concern. In this study, we collected 166 <i>S</i>. <i>pneumoniae</i> clinical isolates and analyzed the serotypes of isolates to evaluate vaccine effectiveness. Additionally, we identified multidrug-resistant NVT <i>S. pneumoniae</i> 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 <i>cps, pbp1a,</i> and additional key factors, including the DNA uptake-related gene <i>comC</i>. 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 <i>Streptococcus pneumoniae</i> 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 <i>S. pneumoniae</i> under selective pressure exerted by vaccination, offering novel insights into strategies for the prevention and control of <i>S. pneumoniae</i> and the optimization of vaccine deployment.