Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages.

Streptococcus pneumoniae remains a major global health threat, causing diseases ranging from mild respiratory infections to severe conditions like pneumonia, sepsis, and meningitis. Although pneumococcal conjugate vaccines (PCVs), including PCV7, PCV10, and PCV13 have significantly reduced disease burden, especially in children, S. pneumoniae continues to exhibit high serotype and genetic diversity. Whole-genome sequencing (WGS) analysis offers high-resolution insights into clonal lineages and multidrug-resistant strains. However, genomic data on Malaysian isolates remain limited. This study characterized the whole genome features and comparative profiles of seven invasive S. pneumoniae isolates from two tertiary hospitals in Malaysia. WGS analyses described serotype, sequence type (ST), antimicrobial resistance determinant genes, pan-genome structure, and recombination events. The average genome size was ∼2.12 Mbp, with 1 988-2 205 coding sequences. WGS-based MLST identified five sequence types (ST236, ST320, ST386, ST671, ST695), with ST236 linked to serotypes 19A and 19F related to PMEN clones Taiwan19F-14 and CC271. Core genome analysis with 35 global reference strains revealed three major clades. Notably, isolates TSP95, SSP45, and SSP46 clustered closely with strains from South Korea, suggesting a long-term persistence of ST320 over a decade. Recombination analysis identified both shared and isolate-specific events, forming distinct phylogenetic clusters. Extensive shared recombination was observed in several isolates, while others displayed isolate-specific events, indicating ongoing genetic diversification. These findings underscore the critical role of recombination in shaping pneumococcal population structure, evolution, and adaptation.