Comparison of lower and upper respiratory tract specimens for the detection of respiratory viruses and atypical pneumonia pathogens by multiplex real-time polymerase chain reaction.

Multiplex respiratory polymerase chain reaction (PCR) testing allows for the rapid and reliable identification of viral, bacterial and fungal causative agents of respiratory tract infections. Traditionally, PCR testing is performed on nose and throat swabs which are easy to collect and are accessible to most patients; however, many commercial kits have several additional validated specimen types including sputum and bronchial washings. These specimens may be more representative of the lower respiratory tract (LRT) environment. The current study aimed to investigate the performance of PCR when testing LRT specimens to detect viral, bacterial and fungal causative agents of pneumonia in an adult inpatient population, using the AusDiagnostics Respiratory Pathogens 24-well multiplex assay. A total of 189 LRT specimens qualified for testing and had a positivity rate of 47% (89/189). Positive LRT specimens were paired, where available, to an upper respiratory tract (URT) specimen collected within 2 weeks. In 81% (21/26) of cases, the LRT specimen had an earlier cycle threshold (CT) value than the URT specimen. There were 16 instances where a target was detected in the LRT specimen but not detected in the URT specimen. This study provides evidence that sample type may be crucial for the optimal performance of multiplex PCR assays, especially in detecting infections with lower pathogen burden. We suggest that the multiplex PCR testing of sputum and other LRT specimens would increase the detection rate and accuracy of diagnosis of respiratory tract infections and pneumonia. LRT specimens are a superior representative of the respiratory tract environment and site of infection and should be tested in addition to, or in place of, a URT specimen where possible.