title: Development of a fast and low-cost qPCR assay for diagnosis of acute gas pharyngitis.
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.
  
  
  CONCLUSIONS
  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.
authors: ENGY Environmental and Energy Technologies Biotechnology Research and Development Limited Company, Istanbul, Turkey. mustafa.kolukirik@engy.com.tr.
authors: Mustafa
authors: M
authors: Kolukirik
authors: Infectious Diseases and Clinical Microbiology, Istanbul Medipol University, Istanbul, Turkey.
authors: Mesut
authors: http://orcid.org/0000-0001-8022-7325
authors: M
authors: Yılmaz
authors: Istanbul Technical University, Istanbul, Turkey.
authors: Orhan
authors: O
authors: Ince
authors: Istanbul Technical University, Istanbul, Turkey.
authors: Canan
authors: C
authors: Ketre
authors: Microbiology, Istanbul Medipol University, Istanbul, Turkey.
authors: Ayşe Istanbullu
authors: AI
authors: Tosun
authors: Bogazici University, Istanbul, Turkey.
authors: Bahar K
authors: BK
authors: Ince
mesh_terms: D002648:Child; D002675:Child, Preschool; D004269:DNA, Bacterial / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D010612:Pharyngitis / Q000175:diagnosis* / Q000382:microbiology; D010614:Pharynx / Q000382:microbiology; D060888:Real-Time Polymerase Chain Reaction / Q000191:economics / Q000379:methods / Q000592:standards*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013290:Streptococcal Infections / Q000175:diagnosis* / Q000382:microbiology; D013297:Streptococcus pyogenes / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D004269:DNA, Bacterial
keywords: Acute pharyngitis; Group A streptococci; Rapid antigen detection test; qPCR