The antimicrobial profile and phylogenomic analysis of serotype 1 Streptococcus pneumoniae in Indonesia
Serotype 1 pneumococcus is commonly associated with antimicrobial resistance and is a leading cause of respiratory infections and meningitis in infants, despite years of pneumococcal conjugate vaccine (PCV) immunization in Africa. This report provides a genome overview of serotype 1 Streptococcus pneumoniae, a rare serotype that colonized Indonesia before the introduction of PCV13, and shared the same strain as those commonly found in Africa. We conducted genomic analyses on the whole-genome sequencing data. In addition to sulfamethoxazole/trimethoprim resistance, we found transposon-mediated resistance to chloramphenicol and tetracycline, indicating multidrug resistance. The phylogenomic analysis revealed that serotype 1 from Indonesia was more closely related to isolates from Cambodia than to those from Africa. We identified virulence factor, competence, and quorum-sensing genes. This is a foundational study that describes a sequenced sample of serotype 1 pneumococcal carriage in Indonesia, uses a genomic approach, and compares it with other countries through phylogenomic analysis.
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