title: Detection of group a streptococcal pharyngitis by quantitative PCR.
abstract: BACKGROUND
  Group A streptococcus (GAS) is the most common bacterial cause of sore throat. School-age children bear the highest burden of GAS pharyngitis. Accurate diagnosis is difficult: the majority of sore throats are viral in origin, culture-based identification of GAS requires 24-48 hours, and up to 15% of children are asymptomatic throat carriers of GAS. The aim of this study was to develop a quantitative polymerase chain reaction (qPCR) assay for detecting GAS pharyngitis and assess its suitability for clinical diagnosis.
  
  
  METHODS
  Pharyngeal swabs were collected from children aged 3-18 years (n = 91) and adults (n = 36) located in the Melbourne area who presented with sore throat. Six candidate PCR assays were screened using a panel of reference isolates, and two of these assays, targeting speB and spy1258, were developed into qPCR assays. The qPCR assays were compared to standard culture-based methods for their ability to detect GAS pharyngitis. GAS isolates from culture positive swabs underwent emm-typing. Clinical data were used to calculate McIsaac scores as an indicator of disease severity.
  
  
  RESULTS
  Twenty-four of the 127 samples (18.9%) were culture-positive for GAS, and all were in children (26%). The speB qPCR had 100% sensitivity and 100% specificity compared with gold-standard culture, whereas the spy1258 qPCR had 87% sensitivity and 100% specificity. Nine different emm types were found, of which emm 89, 3, and 28 were most common. Bacterial load as measured by qPCR correlated with culture load. There were no associations between symptom severity as indicated by McIsaac scores and GAS bacterial load.
  
  
  CONCLUSIONS
  The speB qPCR displayed high sensitivity and specificity and may be a useful tool for GAS pharyngitis diagnosis and research.
authors.affiliation: Pneumococcal Research, Murdoch Childrens Research Institute, Parkville, VIC, Australia. eileen.dunne@mcri.edu.au
authors.forename: Eileen M
authors.initials: EM
authors.lastname: Dunne
authors.forename: Julia L
authors.initials: JL
authors.lastname: Marshall
authors.forename: Ciara A
authors.initials: CA
authors.lastname: Baker
authors.forename: Jayne
authors.initials: J
authors.lastname: Manning
authors.forename: Gena
authors.initials: G
authors.lastname: Gonis
authors.forename: Margaret H
authors.initials: MH
authors.lastname: Danchin
authors.forename: Pierre R
authors.initials: PR
authors.lastname: Smeesters
authors.forename: Catherine
authors.initials: C
authors.lastname: Satzke
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Steer
mesh_terms: D000293:Adolescent; D001426:Bacterial Proteins / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D005098:Exotoxins / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D058889:Molecular Typing / Q000379:methods; D010612:Pharyngitis / Q000175:diagnosis / Q000453:epidemiology / Q000382:microbiology*; D010614:Pharynx / Q000382:microbiology; D011446:Prospective Studies; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D018709:Statistics, Nonparametric; D013290:Streptococcal Infections / Q000175:diagnosis / Q000453:epidemiology / Q000382:microbiology*; D013297:Streptococcus pyogenes / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D014739:Victoria / Q000453:epidemiology
chemical_list: D001426:Bacterial Proteins; D005098:Exotoxins; C027951:erythrogenic toxin