Preliminary genomic assessment of invasive Streptococcus pneumoniae serotype 3 isolates in Malaysia

Streptococcus pneumoniae is a pathogen responsible for invasive pneumococcal disease (IPD) among young children, the elderly, and immunocompromised individuals. The polysaccharide capsule is a main virulence factor that defines pneumococcal serotypes, among which serotype 3 is highly invasive and associated with severe clinical outcomes. Experience from countries that implemented pneumococcal conjugate vaccines (PCVs) earlier have demonstrated a shift in serotype distribution, with a notable increase in serotype 3 following vaccine rollout. Given the persistence of serotype 3 despite widespread vaccination, genomic studies have been conducted in different countries to better understand the serotype. This pilot study utilizes whole genome sequencing (WGS) analysis to provide preliminary insights into the population structure and resistance profiles of serotype 3 clones in Malaysia. Five S. pneumoniae serotype 3 isolates were recovered from blood specimens of Malaysian pediatric patients with invasive pneumococcal infections between 2022 and 2023. All isolates were confirmed as serotype 3 by phenotypic testing and genomic identification. Whole genome sequencing that involved Illumina NovaSeq6000 sequencing platform generated 470, 029–779, 194 reads, with > 35 mean Phred score, average GC content of 39–40%, and ≥ 99. 9% genome completeness. Genomic analyses revealed genome sizes ranging from 1. 94 to 2. 00 Mb, comprising 56 to 80 contigs, with N50 values ranging from 64, 020 to 103, 653 bp. Genomic characterization based on single nucleotide polymorphism (SNP) identified three distinct lineages in Malaysia: GPSC12/ST180, GPSC43/ST6011, and GPSC83/ST1377. Antimicrobial susceptibility testing identified a multidrug-resistant GPSC43/ST6011 isolate, resistant to erythromycin, clindamycin, tetracycline, and trimethoprim–sulfamethoxazole, corresponding to the presence of ermB, tetM₁2, and mutations in folA and folP. The remaining isolates were phenotypically susceptible to all tested antimicrobials without resistance determinants detected in the genomes. Despite variation in penicillin-binding protein (pbp) gene profiles, all isolates remained susceptible to beta-lactam antibiotics. The study presents a preliminary genomic characterization of invasive serotype 3 S. pneumoniae in Malaysia. The identification of distinct lineages and a multidrug-resistant clone highlight the value of genomic data in understanding local pneumococcal epidemiology. A nationwide genomic surveillance is important to monitor emerging high-risk clones and antimicrobial resistome to combat invasive diseases caused by serotype 3 S. pneumoniae in Malaysia.