Diagnosis of Community-Acquired Pneumonia Due to Influenza or Respiratory Syncytial Virus: Evaluation of RT-PCR Sensitivity in Nasopharyngeal, Saliva, and Sputum Samples

Detection of viral RNA in nasopharyngeal (NP) samples by reverse transcription polymerase chain reaction (RT-PCR) is the standard diagnostic test for influenza or respiratory syncytial virus (RSV) in hospitalized patients with community-acquired pneumonia (CAP). This study compared the sensitivity of RT-PCR using NP swab, saliva, and sputum samples for the diagnosis of CAP due to influenza or RSV. A total of 60 patients were evaluated, of which 40 (67%) had influenza CAP, 19 (32%) had RSV CAP, and one patient (1%) had both RSV and influenza CAP. RT-PCR on NP swab, saliva, and sputum samples was performed using the Luminex ARIES platform. In patients with influenza CAP, the sensitivity was 34% for NP swabs, 68% for saliva, and 71% for sputum. In patients with RSV CAP, the sensitivity was 60% for NP swabs, 75% for saliva, and 85% for sputum. RT-PCR of nasopharyngeal swab samples was associated with a significant number of false negative results. A negative NP swab RT-PCR test should not be used to rule out CAP due to influenza or RSV. Saliva and sputum samples should be considered when performing a microbiological work-up in patients with suspected influenza or RSV CAP.