title: Comparing the Yield of Nasopharyngeal Swabs, Nasal Aspirates, and Induced Sputum for Detection of Bordetella pertussis in Hospitalized Infants.
abstract: BACKGROUND
  Advances in molecular laboratory techniques are changing the landscape of Bordetella pertussis illness diagnosis. Polymerase chain reaction (PCR) assays have greatly improved the sensitivity detection and the turnaround time to diagnosis compared to culture. Moreover, different respiratory specimens, such as flocked nasopharyngeal swabs (NPSs), nasopharyngeal aspirates (NPAs), and induced sputum, have been used for B. pertussis detection, although there is limited head-to-head comparison to evaluating the PCR yield from the 3 sampling methods.
  
  
  METHODS
  Hospitalized infants <6 months of age who fulfilled a broad syndromic criteria of respiratory illness were tested for B. pertussis infection by PCR on paired NPSs and NPAs; or paired NPSs and induced sputum. An exploratory analysis of B. pertussis culture was performed on induced sputum specimens and in a subset of NPSs.
  
  
  RESULTS
  From November 2014 to May 2015, 484 infants with paired NPSs and NPAs were tested; 15 (3.1%) PCR-confirmed pertussis cases were identified, 13 of which were PCR positive on both samples, while 1 each were positive only on NPS or NPA. From March to October 2015, 320 infants had NPSs and induced sputum collected, and 11 (3.4%) pertussis cases were identified by PCR, including 8 (72.7%) positive on both samples, 1 (9.1%) only positive on NPS, and 2 (18.2%) only positive on induced sputum. The 3 types of specimens had similar negative predictive value >99% and sensitivity >83%. Compared to PCR, culture sensitivity was 60% in induced sputum and 40% in NPSs.
  
  
  CONCLUSIONS
  Flocked nasopharyngeal swabs, nasopharyngeal aspirates, and induced sputum performed similarly for the detection of B. pertussis infection in young infants by PCR.
authors.affiliation: Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.|Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand.
authors.forename: Marta C
authors.initials: MC
authors.lastname: Nunes
authors.affiliation: Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.|Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand.
authors.forename: Nasiha
authors.initials: N
authors.lastname: Soofie
authors.affiliation: Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.|Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand.
authors.forename: Sarah
authors.initials: S
authors.lastname: Downs
authors.affiliation: Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.|Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand.
authors.forename: Naume
authors.initials: N
authors.lastname: Tebeila
authors.affiliation: Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.|Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand.
authors.forename: Azwi
authors.initials: A
authors.lastname: Mudau
authors.affiliation: National Institute for Communicable Diseases, National Health Laboratory Service, Centre for Respiratory Diseases and Meningitis, Johannesburg, South Africa.
authors.forename: Linda
authors.initials: L
authors.lastname: de Gouveia
authors.affiliation: Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.|Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand.|National Institute for Communicable Diseases, National Health Laboratory Service, Centre for Respiratory Diseases and Meningitis, Johannesburg, South Africa.
authors.forename: Shabir A
authors.initials: SA
authors.lastname: Madhi
mesh_terms: D001886:Bordetella pertussis / Q000235:genetics / Q000302:isolation & purification; D060085:Coinfection; D005260:Female; D015658:HIV Infections; D006760:Hospitalization; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D009305:Nasopharynx / Q000382:microbiology*; D009666:Nose / Q000382:microbiology*; D011159:Population Surveillance; D013183:Sputum / Q000382:microbiology*; D014917:Whooping Cough / Q000175:diagnosis* / Q000453:epidemiology / Q000382:microbiology*
keywords: Bordetella pertussis; detection; induced sputum infants; nasopharyngeal aspirates; nasopharyngeal swabs