Improving the identification of pneumonia pathogens by using the real-time polymerase chain reaction (qPCR) alongside culture methods.

Streptococcus pneumoniae, Haemophilus influenzae, and Klebsiella pneumoniae are among colonizers of the upper respiratory tract flora that can cause pneumonia upon invading the lungs. Molecular techniques have increasingly become the preferred diagnostic approach for detecting respiratory pathogens. However, sputum culture remains the standard diagnostic method for identifying respiratory pathogens in many underdeveloped and developing countries. In this cross-sectional perspective study, 94 sputum specimens were evaluated using both culture and an in-house multiplex qPCR assay. The multiplex qPCR demonstrated greater sensitivity, detecting pathogens in 79 specimens (84.04 %), compared with 32 specimens (31.37 %) identified by culture. The qPCR assay detected K. pneumoniae in 54 of 94 sputum samples, making it the most predominant bacterium, followed by S. pneumoniae (26/94), and H. influenzae (20/94). In contrast, culture detected S. pneumoniae, K. pneumoniae, and H. influenzae in 1, 14, and 3 cases, respectively. These findings support the integration of qPCR into the diagnostic routine alongside culture methods for respiratory samples, as the inclusion of qPCR methods enhances diagnostic sensitivity and accuracy, which are critical for effective patient management and treatment planning.