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Genomic and phenotypic characterization of a multidrug-resistant Streptococcus pneumoniae 19 F ST320 isolate from a

Tiara Putri1,2, Budi Setiadi Daryono3, Endah Retnaningrum4

  • 1The Doctoral Program, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia.

Scientific Reports
|April 24, 2026
PubMed

Insights

Multidrug-resistant Streptococcus pneumoniae, a significant threat in Southeast Asia, was identified in an Indonesian child. This 19F strain (ST320) shows extensive drug resistance, highlighting the need for genomic surveillance.

Area of Science:

  • Microbiology
  • Genomics
  • Epidemiology

Background:

  • Multidrug-resistant Streptococcus pneumoniae (MDR-SP) poses a significant public health challenge, particularly in Southeast Asia.
  • Genomic data on MDR-SP in Indonesia are scarce, limiting effective monitoring and control strategies.

Purpose of the Study:

  • To characterize the genomic and phenotypic features of a multidrug-resistant Streptococcus pneumoniae isolate from Indonesia.
  • To assess the potential public health implications of this isolate within the context of pediatric infections.

Main Methods:

  • Whole genome sequencing (WGS) of the pneumococcal isolate GD-BC-10.
  • Serotyping and sequence typing (ST) analysis.
  • Antimicrobial resistance profiling and virulence factor analysis.

Main Results:

  • A 19F Streptococcus pneumoniae isolate, designated GD-BC-10, was identified in a SARS-CoV-2-positive child in Yogyakarta, Indonesia.
  • The isolate belonged to sequence type 320 (ST320), part of the globally disseminated clonal complex (CC) 320/271, and exhibited resistance to multiple drug classes (β-lactams, macrolides, tetracyclines, lincosamides, folate-pathway inhibitors).
  • Genomic analysis revealed specific resistance determinants (erm(B), mef(A), tet(M), folA/folP) and virulence factors (PI-1, PI-2 pilus islets) consistent with high fitness.

Conclusions:

  • The characterized 19F ST320 strain reflects the persistence of high-risk pneumococcal clones in Indonesia.
  • Findings underscore the critical need for enhanced genomic surveillance and targeted genotypic assays for pneumococcal monitoring in pediatric populations.
Keywords:
Streptococcus pneumoniaeMultidrug resistancePediatric COVID-19Serotype 19FWhole-genome sequencing

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