Complete genome sequence data of Streptococcus pneumoniae serotype 17F isolated in Malaysia

This study reports the genomic insights into a Streptococcus pneumoniae serotype 17F isolate in Malaysia (IMRCC/SS430/25), collected from an adult patient with aspiration pneumonia in 2025. Phenotypic identification revealed characteristic alpha-haemolytic colonies and optochin susceptibility. Species identity as S. pneumoniae was further verified by bile solubility testing and the 17F serotype was confirmed using the Quellung reaction. The isolate was subjected to whole-genome sequencing using the Oxford Nanopore platform. The assembly yielded a highly accurate, single circular contig of 2,065,967 bp with 100% completeness and 48× coverage. In silico typing assigned the genome to ST2355 within the globally disseminated GPSC10 cluster. Antimicrobial susceptibility testing demonstrated resistance to erythromycin, azithromycin, clindamycin, and tetracycline. This phenotypic profile was concordant with genomic screening which identified the ermB and tetM_8 genes responsible for macrolide-lincosamide-streptogramin B (MLSB) and tetracycline resistance respectively. The penicillin-binding protein allelic profile (pbp1a: 79, pbp2b: 26, pbp2x: 194) predicted uniform susceptibility to beta-lactam antibiotics shown by phenotypic testing of amoxicillin-clavulanate and penicillin. Phylogenomic characterization identified the Malaysian isolate within the predominant global ST2355 clade of GPSC10, clustering alongside isolates from Nepal, the United Kingdom, Bangladesh, and the United States. This study demonstrates the utility of combining routine clinical microbiology with high-resolution genomic surveillance to resolve lineage relationship, reveal underlying resistance mechanisms, and confirm genotype-phenotype concordance.