Karakterisasi Genomik, Gen Resistensi Antibiotik dan Gen pspK pada Isolat Non-Typeable Streptococcus pneumoniae

Abstract

Streptococcus pneumoniae (pneumokokus) merupakan bakteri penyebab pneumonia, sepsis, dan meningitis pada anak-anak dan orang tua yang memiliki lebih dari 100 serotipe berdasarkan struktur kapsul polisakarida (CPS). Tetapi hanya <30 serotipe yang termasuk dalam vaksin pneumokokus. Non-Typeable S. pneumoniae (NTSPn) merupakan isolat non-vaksin dengan gen pspK sebagai salah satu gen penanda. Penelitian ini bertujuan mengkarakterisasi genom, gen resistensi antibiotik, dan gen pspK pada isolat NTSPn dari sampel swab nasofaring di Indonesia. Metode yang digunakan meliputi kultur, identifikasi bakteri, ekstraksi DNA, whole genome sequencing (WGS), dan visualisasi dengan elektron mikroskop. Analisis data genom dilakukan dengan pipeline ASA3P, PathogenWatch, Genoscope, dan DNA features. Dari 536 data WGS, terdapat 42 isolat yang teridentifkasi sebagai NTSPn, sebanyak 40 isolat merupakan sequence type baru, Isolat NTSPn menunjukan resistensi tertinggi pada co-trimoxazole sebesar 78,6% (n=35) dan eritromicin sebesar 66,7% (n=28). Prevalensi gen pspK cukup tinggi sebesar 35% (n=15).

Streptococcus pneumoniae (pneumococcus) is a leading bacterial pathogen causing pneumonia, sepsis, and meningitis in children and the elderly. It possesses more than 100 serotypes based on the structure of its capsular polysaccharide (CPS), yet fewer than 30 serotypes are included in current pneumococcal vaccines. Non-typeable S. pneumoniae (NTSPn) refers to non-vaccine isolates, with the pspK gene recognized as one of their genetic markers. This study aimed to characterize the genome, antibiotic resistance genes, and pspK gene in NTSPn isolates collected from nasopharyngeal swab samples in Indonesia. The methods included bacterial culture, identification, DNA extraction, whole genome sequencing (WGS), and visualization by electron microscopy. Genomic data were analyzed using ASA3P, PathogenWatch, Genoscope, and DNA feature pipelines. Of 536 WGS datasets, 42 isolates were identified as NTSPn based on CPS locus analysis, with 40 of them representing novel sequence types. The NTSPn isolates exhibited the highest resistance to co-trimoxazole (78.6%, n=35) and erythromycin (66.7%, n=28). The prevalence of the pspK gene was relatively high at 35% (n=15).