Assessing the diagnostic accuracy of PCR-based detection of Streptococcus pneumoniae from nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: A Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study

The purpose of this study was to trace the diagnostic accuracy of PCR–based detection of S. pneumoniae, directly from nasopharyngeal (NP) swabs collected for respiratory virus studies. Though additional could be necessitated to increase the sensitivity of PCR–based detection, its high specificity indicated there was a value for pneumococcal surveillance. With many laboratories archiving specimens for influenza virus surveillance, this specimen type possibly yielded a non–culture–based method for pneumococcal surveillance.

Methods

• Active surveillance for community-acquired pneumonia (CAP) in hospitalised adults was carried out from December 2010 to 2013.
• The identification of pneumococcal CAP (CAP_Spn) was conducted through the urine antigen detection (UAD), identification of S. pneumoniae in sputum or blood cultures.
• S. pneumoniae was found in NP swabs, with the aid of lytA and cpsA real-time PCR.
• Serotyping was done through the conventional and real-time multiplex PCRs.
• For the purpose of serotyping, the Quellung reaction, PCR-based serotyping or a serotype-specific UAD was utilized.

Results

• The NP swab results were compared against CAP cases, where all pneumococcal tests were performed (n=434), or where at least one test was performed (n=1616).
• CAP_Spn was detected in 22.1% (96/434) and 14.9% (240/1616), respectively.
• The sensitivity of NP swab PCR for the detection of S. pneumoniae appeared to be poor for CAP_Spn (35.4% (34/96) and 34.17% (82/240)).
• However, high specificity was noted (99.4% (336/338) and 97.89% (1347/1376)).
• Among the positive NP swabs, a serotype could be deduced by PCR in 88.2% (30/34) and 93.9% (77/82), respectively.