title: Concordance between RT-PCR-based detection of respiratory viruses from nasal swabs collected for viral testing and nasopharyngeal swabs collected for bacterial testing.
abstract: BACKGROUND
  Epidemiologic studies of respiratory infections frequently rely on separate sample collections for the detection of bacteria and viruses. The requirement for two specimens presents cost, logistical, and acceptability challenges.
  
  
  OBJECTIVE
  To determine the agreement in detection of respiratory viruses using RT-PCR between two different types of samples collected on the same day: nasal swabs preserved in viral transport medium (NS) and nasopharyngeal swabs preserved in skim milk-tryptone-glucose-glycerol [STGG] medium (NP), the current standard for pneumococcal colonization studies.
  
  
  METHODS
  Paired NS and NP samples were collected between May 2009 and September 2011 as part of the RESPIRA-PERU study, a large prospective cohort of Andean children <3 years of age. NS samples used polyester swabs and viral transport medium whereas NP samples used rayon wire-handled swabs and STGG medium. Samples were tested for influenza, human metapneumovirus (MPV), respiratory syncytial virus (RSV), human rhinovirus (HRV), parainfluenza virus 3 (PIV3) and adenovirus (ADV) using real-time RT-PCR. We calculated the agreement, and compared cycle thresholds (CT) between NP and NS samples.
  
  
  RESULTS
  Among 226 paired NP-NS samples, we observed very high agreement with a Kappa statistic ranging from 0.71 for ADV to 0.97 for MPV. CT values were similar for both strategies.
  
  
  CONCLUSIONS
  NP samples preserved in STGG provide a simple and reliable strategy for identification of both pneumococcus and respiratory viruses. This single specimen collection strategy could be used for epidemiologic studies, especially in resource-limited settings. Furthermore, archived NP-STGG specimens from previous studies could be reliably tested by RT-PCR for viruses.
authors.affiliation: Department of Health Policy, Vanderbilt University School of Medicine, Nashville, TN, United States. Electronic address: Carlos.grijalva@vanderbilt.edu.
authors.forename: Carlos G
authors.initials: CG
authors.lastname: Grijalva
authors.affiliation: Department of Health Policy, Vanderbilt University School of Medicine, Nashville, TN, United States.
authors.forename: Marie R
authors.initials: MR
authors.lastname: Griffin
authors.affiliation: Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States.
authors.forename: Kathryn M
authors.initials: KM
authors.lastname: Edwards
authors.affiliation: Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States.
authors.forename: Monika
authors.initials: M
authors.lastname: Johnson
authors.affiliation: Instituto de Investigación Nutricional, Lima, Peru.
authors.forename: Ana I
authors.initials: AI
authors.lastname: Gil
authors.affiliation: Instituto de Investigación Nutricional, Lima, Peru.
authors.forename: Héctor
authors.initials: H
authors.lastname: Verástegui
authors.affiliation: Instituto de Investigación Nutricional, Lima, Peru.
authors.forename: Claudio F
authors.initials: CF
authors.lastname: Lanata
authors.affiliation: Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States.
authors.forename: John V
authors.initials: JV
authors.lastname: Williams
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D009305:Nasopharynx / Q000382:microbiology* / Q000821:virology*; D015203:Reproducibility of Results; D012141:Respiratory Tract Infections / Q000175:diagnosis / Q000382:microbiology* / Q000821:virology*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D014780:Viruses / Q000235:genetics / Q000302:isolation & purification
keywords: Children; Epidemiology; Nasal swab; Nasopharyngeal swab; Respiratory virus