Pneumo-Typer: a high-throughput capsule genotype visualization tool with integrated serotype and sequence type prediction for Streptococcus pneumoniae

Streptococcus pneumoniae remains a significant global pathogen, with capsule-based vaccines targeting only a subset of over 100 serotypes. Accurate serotyping is critical for evaluating vaccine impact and optimizing capsule formulations. While whole-genome sequencing (WGS)-based methods achieve high serotyping accuracy, they often struggle to identify serotype variants with altered capsule loci that may evade vaccine-induced immunity. Here, we present Pneumo-Typer, a high-throughput tool for capsule genotype (CapT) visualization, enabling rapid identification of isolates with capsular gene variations, including mutations and horizontal gene transfer. In addition, Pneumo-Typer integrates serotype and sequence type (ST) prediction, achieving 98.44% accuracy in predicting 93 serotypes across 17,683 genomes. Our analysis reveals substantial serotypes linked to multiple STs and CapTs, with STs and CapTs demonstrating relative evolutionary independence and limited CapT variation during ST expansion. Within multi-serotype serogroups, we observe striking CapT diversity, providing insights into the evolutionary dynamics of serogroup formation. These findings underscore the utility of Pneumo-Typer for epidemiological surveillance and vaccine design, contributing to efforts to mitigate the global burden of S. pneumoniae.