title: Detection of respiratory viruses and bacteria in children using a twenty-two target reverse-transcription real-time PCR (RT-qPCR) panel.
abstract: BACKGROUND
  Rapid detection of the wide range of viruses and bacteria that cause respiratory infection in children is important for patient care and antibiotic stewardship. We therefore designed and evaluated a ready-to-use 22 target respiratory infection reverse-transcription real-time polymerase chain reaction (RT-qPCR) panel to determine if this would improve detection of these agents at our pediatric hospital.
  
  
  METHODS
  RT-qPCR assays for twenty-two target organisms were dried-down in individual wells of 96 well plates and saved at room temperature. Targets included 18 respiratory viruses and 4 bacteria. After automated nucleic acid extraction of nasopharyngeal aspirate (NPA) samples, rapid qPCR was performed. RT-qPCR results were compared with those obtained by the testing methods used at our hospital laboratories.
  
  
  RESULTS
  One hundred fifty-nine pediatric NPA samples were tested with the RT-qPCR panel. One or more respiratory pathogens were detected in 132/159 (83%) samples. This was significantly higher than the detection rate of standard methods (94/159, 59%) (P<0.001). This difference was mainly due to improved RT-qPCR detection of rhinoviruses, parainfluenza viruses, bocavirus, and coronaviruses. The panel internal control assay performance remained stable at room temperature storage over a two-month testing period.
  
  
  CONCLUSIONS
  The RT-qPCR panel was able to identify pathogens in a high proportion of respiratory samples. The panel detected more positive specimens than the methods in use at our hospital. The pre-made panel format was easy to use and rapid, with results available in approximately 90 minutes. We now plan to determine if use of this panel improves patient care and antibiotic stewardship.
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
authors.forename: Chelsey
authors.initials: C
authors.lastname: Ellis
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
authors.forename: Amita
authors.initials: A
authors.lastname: Misir
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
authors.forename: Charles
authors.initials: C
authors.lastname: Hui
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
authors.forename: Mona
authors.initials: M
authors.lastname: Jabbour
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Barrowman
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Langill
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Bowes
authors.affiliation: Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada. slinger@cheo.on.ca.|Children's Hospital of Eastern Ontario, University of Ottawa, 401 Smyth Rd, Ottawa, ON, K1H 8L1, Canada. slinger@cheo.on.ca.
authors.forename: Robert
authors.initials: R
authors.lastname: Slinger
mesh_terms: D001419:Bacteria / Q000302:isolation & purification; D002648:Child; D006801:Humans; D008828:Microbiological Techniques; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000382:microbiology* / Q000821:virology; D012189:Retrospective Studies; D014780:Viruses / Q000302:isolation & purification
keywords: bacterial infections; pediatric; polymerase chain reaction; respiratory infectious diseases; viral infections