Pneumo-Typer: integrated genomic surveillance tool for capsule genotype, serotype and sequence type in Streptococcus pneumoniae informs vaccine strategies

Background Streptococcus pneumoniae persists as a leading global pathogen, with current capsule-based vaccines like PCV13 offering limited coverage against its extensive serotype diversity (> 100 serotypes). This restricted coverage drives the emergence of non-vaccine serotypes. Moreover, vaccine efficacy is further compromised by immune evasion caused by capsule genotype (CapT) variations within vaccine-covered serotypes, while existing genome-based tools lack robust analytical capabilities for CapT. Results We developed Pneumo-Typer, a CapT visualization tool enabling rapid identification of CapT variations in S. pneumoniae. Application to 17,407 publicly available genomes from the NCBI database revealed widespread CapT variations across vaccine-covered serotypes, providing critical insights for optimizing vaccine formulations. In addition, Pneumo-Typer integrates high-accuracy serotype prediction (98.44% accuracy across 93 serotypes) and multilocus sequence typing (ST), facilitating comprehensive genomic surveillance. Besides, CapT and ST information can assist in serotype determination. Pneumo-Typer enables integrated analysis of serotype-CapT-ST relationships, demonstrating that while most serotypes associate with multiple STs and CapTs, ST and CapT lineages evolve independently. Strikingly, multi-serotype serogroups exhibited pronounced CapT diversity, suggesting evolutionary processes driving serogroup expansion through CapT plasticity. Conclusions In summary, Pneumo-Typer is an integrated platform for genomic surveillance of pneumococcal populations. By resolving previously underexplored serotype-CapT-ST linkages, the tool provides a framework for next-generation vaccine design, emphasizing the need for vaccine formulations that address both serotype replacement and CapT-driven immune evasion.