Clonal Analysis of Streptococcus pneumoniae in Clinical Specimens

We examined sputum specimens collected from hospitalized adults in Indonesia who were clinically diagnosed with CAP. This study initially aimed to detect unidentified pathogens responsible for causing CAP using real-time polymerase chain reactions (PCR) and metagenomic shotgun sequencing (metagenomics) to complement conventional culture. Upon further examination, we focus on Streptococcus pneumoniae (pneumococcus) detection as the foremost etiology of CAP from the bacteria group. We compare culture, real-time PCR, and shotgun metagenomics for the detection of pneumococcus. We found one sample of pneumococcus positive by culture and had the lowest CT by real-time PCR; the metagenomics result presented homogenous sequences after mapping back to the S. pneumoniae reference strain. This finding indicates pneumococcus in this sample originated from a single clone lineage. Thus, we performed advanced analysis on the clonality of the pneumococcus positive samples.