Development of a fast and low-cost qPCR assay for diagnosis of acute gas pharyngitis


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Kolukirik M., YILMAZ M., İnce O., Ketre C., Tosun A. I., Ince B. K.

Annals of Clinical Microbiology and Antimicrobials, vol.15, no.1, 2016 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 15 Issue: 1
  • Publication Date: 2016
  • Doi Number: 10.1186/s12941-016-0162-0
  • Journal Name: Annals of Clinical Microbiology and Antimicrobials
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Keywords: Group A streptococci, Acute pharyngitis, qPCR, Rapid antigen detection test
  • Istanbul Medipol University Affiliated: Yes

Abstract

Background: Group A streptococci (GAS) are the most common bacterial cause of acute pharyngitis and account for 15-30 % of cases of acute pharyngitis in children and 5-10 % of cases in adults. In this study, a real-time quantitative PCR (qPCR) based GAS detection assay in pharyngeal swab specimens was developed. Methods: The qPCR assay was compared with the gold standard bacterial culture and a rapid antigen detection test (RADT) to evaluate its clinical performance in 687 patients. The analytical sensitivity of the assay was 240 cfu/swab. Forty-five different potential cross-reacting organisms did not react with the test. Four different laboratories for the reproducibility studies were in 100 % (60/60) agreement for the contrived GAS positive and negative swab samples. Results: The relative sensitivities of the RADT and the qPCR test were 55.9 and 100 %; and the relative specificities were 100 and 96.3 %, respectively. Duration of the total assay for 24 samples including pre-analytical processing and analysis changed between 42 and 55 min depending on the type of qPCR instrument used. A simple DNA extraction method and a low qPCR volume made the developed assay an economical alternative for the GAS detection. Conclusion: We showed that the developed qPCR test is rapid, cheap, sensitive and specific and therefore can be used to replace both antigen detection and culture for diagnosis of acute GAS pharyngitis.