Assessing the diagnostic accuracy of PCR-based detection ofStreptococcus pneumoniaefrom 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

Abstract

Study designDetection and serotyping of Streptococcus pneumoniae are important to assess the impact of pneumococcal vaccines. This study describes the diagnostic accuracy of PCR-based detection of S. pneumoniae directly from nasopharyngeal (NP) swabs collected for respiratory virus studies.MethodsActive surveillance for community-acquired pneumonia (CAP) in hospitalised adults was performed from December 2010 to 2013. Detection of pneumococcal CAP (CAPSpn) was performed by urine antigen detection (UAD), identification of S. pneumoniae in sputum or blood cultures. S. pneumoniae was detected in NP swabs using lytA and cpsA real-time PCR, and serotyping was performed using conventional and real-time multiplex PCRs. For serotyping, the Quellung reaction, PCR-based serotyping or a serotype-specific UAD was used.ResultsNP 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). CAPSpn was identified in 22.1% (96/434) and 14.9% (240/1616), respectively. The sensitivity of NP swab PCR for the detection of S. pneumoniae was poor for CAPSpn (35.4% (34/96) and 34.17% (82/240)), but high specificity was observed (99.4% (336/338) and 97.89% (1347/1376)). Of the positive NP swabs, a serotype could be deduced by PCR in 88.2% (30/34) and 93.9% (77/82), respectively.ConclusionsWhile further optimisation may be needed to increase the sensitivity of PCR-based detection, its high specificity suggests there is a value for pneumococcal surveillance. With many laboratories archiving specimens for influenza virus surveillance, this specimen type could provide a non-culture-based method for pneumococcal surveillance.

Multiplex polymerase chain reaction detection of Streptococcus pneumoniae and Haemophilus influenzae and their antibiotic resistance in patients with community-acquired pneumonia from southwest Iran

“…This study revealed a 100% sensitivity of M-PCR in detection of H. influenzae and S. pneumoniae compared to culture method. In contrast to the current research, Gillis et al [ 26 ] showed that PCR based method had poor sensitivity in detection of S. pneumoniae in nasopharyngeal swabs of CAP patients. This discrepancy may be due to the differences in sample types, as we used sputum samples in the current study.…”

Utility of Polymerase Chain Reaction in Nasopharyngeal Swabs for Identifying Respiratory Bacteria Causing Community-Acquired Pneumonia

“…However, the magnitude of the PPA increase in our study was lower, supporting the use of a cutoff at ≥10 4 copies/mL in NP for S. pneumoniae diagnostic to keep a high NPA. ( 15 – 17 ). To our knowledge, our study is the first that evaluates different RT-PCR cutoffs in NP for H. influenzae .…”

“…Although molecular tests in NP swabs are accepted for viruses and atypical bacteria such as Mycoplasma pneumoniae and Chlamydia pneumoniae ( 14 ), few studies evaluated their performance on upper respiratory tract samples (URT) for the most common bacterial causes of community-acquired LRTIs, such as Streptococcus pneumoniae , Haemophilus influenzae , and Moraxella catarrhalis . Four studies evaluated identification of S. pneumoniae by real-time PCR (RT-PCR) in NP specimen of patients with community-acquired pneumonia (CAP) with negative percent agreements (NPA) of >90% but with wide differences in positive percent agreement (PPA; 35% to 82%) using standard microbiological tests as gold standard ( 15 – 18 ). No study evaluated the validity of PCR in the NP swabs for other bacteria.…”

Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods

“…The development of molecular methods and increasing knowledge of S. pneumoniae virulence determinants together with a better understanding of genetic diversity of pneumococci and other Mitis streptococci led to proposing several targets for PCR and real-time PCR in order to improve species identification among Mitis streptococci, especially concerning their questionable representatives. As PCR-based approaches do not require cultured microorganisms, they find also an application in the direct detection of pneumococci in clinical materials [55,56], including polymicrobial samples [57][58][59][60].…”