Differential detection of bacterial pathogens from patients with community acquired pneumonia by multiplex real-time polymerase chain reaction (PCR)

Abstract

Community acquired pneumonia (CAP) is a common infectious disease associated with significant morbidity and mortality in both developing and developed countries. Streptococcus pneumoniae remains the predominant cause of CAP followed by atypical pathogens (Mycoplasma pneumoniae, Chlamydophila pneumoniae and Legionella pneumophila). Burkholderia pseudomallei is also noy an uncommon cause of pneumonia especially in endemic areas including Southeast Asia and Northern Australia. The etiologic diagnosis of CAP remains an uneasy task, with the causative organisms often identified in as few as 30-50% of cases. This is mainly due to difficulties and/or delay in obtaining results usually associated with the conventional diagnostic methods of culture and serology. The recent development of molecular diagnostic techniques offers a highly sensitive, specific and rapid etiologic diagnosis of CAP, supporting traditional laboratory methods and aids in early selection and administration of more appropriate antibiotics. This study was designed to develop, optimize and evaluate multiplex real-time PCR as a method for simultaneous differential detection of five bacterial pathogens commonly causing CAP. Two multiplex real time PCR assays with a satisfactory degree of sensitivity and specificity were successfully developed. Duplex real time PCR was developed for differential detection of Streptococcus pneumoniae and Burkholderia pseudomallei, and triplex real time PCR for differential detection of atypical bacterial pathogens (Mycoplasma pneumoniae, Chlamydophila pneumoniae and Legionella pneumophila). 91 clinical samples (46 blood and 45 respiratory samples) were collected from 46 adult patients admitted to Hospital Tengku Ampuan Afzan (HTAA)/ Kuantan with primary diagnosis of pneumonia over a period of six months. These samples were analyzed by both multiplex real time PCR assays in addition to conventional methods. The microbial etiology of CAP could be established for 39.1% (18/46) of the patients by conventional methods and this figure was increased to 65.2% (30/46) with the additional use of multiplex real-time PCR. The most frequently detected pathogens were Streptococcus pneumoniae (21.7%), followed by Klebsiella pneumoniae (17.3%), Burkholderia pseudomallei (13%), Pseudomonas aeruginosa (6.5%), Mycoplasma pneumoniae (6.5%), Chlamydophila pneumoniae (4.3%) and E.coli (4.3%). Legionella pneumophila, Haemophilus infuenzae, Acinetobacter lwoffii and Acinetobacter baumannii were detected in one case each (2.2% for each). In conclusion, it was demonstrated that multiplex real-time PCR is useful in identifying CAP causative agents. By supplementing traditional diagnostic methods with real-time PCR, a higher microbial detection rate was achieved for both typical and atypical pneumonias. Further prospective studies are needed to establish standardized real-time PCR methods that are robust and simple enough to be used outside the setting of research laboratories i.e. in diagnostic reference and hospital-based laboratories.