Real-Time PCR Of Oropharyngeal Swabs Diagnoses Pneumonia in Adults

A lack of sensitive tests and difficulties obtaining representative samples contribute to the challenge in identifying etiology in pneumonia. Upper respiratory tract swabs can be easily collected and analyzed with real-time polymerase chain reaction (rtPCR).

The microbial etiology of pneumonia often remains undetected despite extensive diagnostic testing. Blood cultures lack sensitivity and obtaining representative lower respiratory tract samples can be challenging. An etiologic diagnosis allows targeted antimicrobial treatment, a matter of increasing importance as resistance rates increase.


Medical scientists at the University of Iceland (Reykjavik, Iceland) prospectively collected oropharyngeal swabs from 239 adults admitted to hospital with pneumonia. Blood cultures were collected, incubated and cultured using standard methods. Urine antigen testing (UAT) for Streptococcus pneumoniae (SP) was performed using a commercially available kit, the BinaxNOW Streptococcus pneumoniae (Alere, Waltham, MA, USA). An oropharyngeal swab sample using sterile rayon tipped swabs, (COPAN Italia, Brescia, Italy) was collected for rtPCR.

The team extracted nucleic acid from 200 μL specimens and rtPCR was performed with an ABI 7900 384-well system (Applied Biosystems, Foster City, CA, USA). The specificity of rtPCR for SP and Haemophilus influenzae (HI) was tested using reference samples containing S. mitis, S. oralis and S. sanguinis, and H. haemolyticus and H. parainfluenzae respectively. No cross-reaction was noted with either comparison. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of rtPCR for SP and HI were calculated using combined and separate results from sputum (SP and HI) and blood cultures (SP only), and urine antigen analysis (SP only) as a reference “gold standard”.

When the investigators compared the rtPCR with conventional testing for S. pneumoniae in 57 patients with all tests available, this resulted in a sensitivity of 87 %,a specificity of 79 %, PPV equalled 59 % and the NPV was 94 %, and for 67 H. influenzae patients, the sensitivity was, 75 %, specificity 80 %, PPV 45 % and NPV 94 %. When patients with prior antimicrobial exposure were excluded sensitivity improved: 92 % for S. pneumoniae and 80 % for H. influenzae. Receiver operating characteristic curve analysis demonstrated for S. pneumoniae: AUC = 0.65 and for H. influenzae: AUC = 0.86. Using rtPCR SP was identified in 61 (25.5 %) cases and HI in 50 (20.9 %).

The authors concluded that analysis of oropharyngeal swabs using rtPCR proved both reasonably sensitive and specific for diagnosing pneumonia caused by S. pneumoniae and H. influenzae. This method may be a useful diagnostic adjunct to other methods and of special value in patients unable to provide representative lower airway samples. The study was published online on November 7, 2016, in the European Journal of Clinical Microbiology & Infectious Diseases.

Related Links:
University of Iceland
Alere
COPAN Italia
Applied Biosystems