Genomic and phenotypic characterization of a multidrug-resistant Streptococcus pneumoniae 19Â F ST320 isolate from a pediatric SARS-CoV-2 case in Yogyakarta, Indonesia

Multidrug-resistant Streptococcus pneumoniae remains a major concern in Southeast Asia, yet genomic data from Indonesia are limited. Among 19 pediatric patients with suspected COVID-19 in Yogyakarta, we identified a single pneumococcal isolate, GD-BC-10, from a SARS-CoV-2 positive child. The isolate was serotyped as 19 F and was assigned to sequence type (ST) 320, which is a member of the globally disseminated clonal complex (CC) 320/271. This 19 F strain exhibits resistance to multiple drug classes, including β-lactams, macrolides, tetracyclines, lincosamides, and folate-pathway inhibitors. Whole genome sequencing revealed resistance determinants characteristic of ST320 isolates within the CC320/271 lineage, defined by the 13-11-16 allelic combination across pbp1a, pbp2b, and pbp2x, together with erm(B), mef(A), tet(M), and folA/folP determinants. Virulence profiling identified a wide array of adhesion and immune-evasion factors including both PI-1 and PI-2 pilus islets, consistent with high-fitness of pediatric lineages. Although derived from a single carrier, the genomic and phenotypic features of this isolate reflect the persistence of high-risk 19 F clones in Indonesia. These findings emphasize the need for strengthened genomic surveillance and targeted genotypic assays to support pneumococcal monitoring in pediatric clinical settings. © The Author(s) 2026.