title: Evaluation of yield of currently available diagnostics by sample type to optimize detection of respiratory pathogens in patients with a community-acquired pneumonia.
abstract: BACKGROUND
  For the detection of respiratory pathogens, the sampling strategy may influence the diagnostic yield. Ideally, samples from the lower respiratory tract are collected, but they are difficult to obtain.
  
  
  OBJECTIVE
  In this study, we compared the diagnostic yield in sputum and oropharyngeal samples (OPS) for the detection of respiratory pathogens in patients with community-acquired pneumonia (CAP), with the objective to optimize our diagnostic testing algorithm.
  
  
  METHODS
  Matched sputum samples, OPS, blood cultures, serum, and urine samples were taken from patients (>18 years) with CAP and tested for the presence of possible respiratory pathogens using bacterial cultures, PCR for 17 viruses and five bacteria and urinary antigen testing.
  
  
  RESULTS
  When using only conventional methods, that is, blood cultures, sputum culture, urinary antigen tests, a pathogen was detected in 49·6% of patients (n = 57). Adding molecular detection assays increased the yield to 80%. A pathogen was detected in 77 of the 115 patients in OPS or sputum samples by PCR. The sensitivity of the OPS was lower than that of the sputum samples (57% versus 74%). In particular, bacterial pathogens were more often detected in sputum samples. The sensitivity of OPS for the detection of most viruses was higher than in sputum samples (72% versus 66%), except for human rhinovirus and respiratory syncytial virus.
  
  
  CONCLUSIONS
  Addition of PCR on both OPS and sputum samples significantly increased the diagnostic yield. For molecular detection of bacterial pathogens, a sputum sample is imperative, but for detection of most viral pathogens, an OPS is sufficient.
authors: Laboratory of Medical Microbiology and Immunology, St. Elisabeth Hospital, Tilburg, The Netherlands; Department of Medical Microbiology, Albert Schweitzer Hospital, Dordrecht, The Netherlands.
authors: Elisabeth G W
authors: EG
authors: Huijskens
authors: John W A
authors: JW
authors: Rossen
authors: Jan A J W
authors: JA
authors: Kluytmans
authors: Adri G M
authors: AG
authors: van der Zanden
authors: Marion
authors: M
authors: Koopmans
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001769:Blood / Q000382:microbiology / Q000821:virology; D019411:Clinical Laboratory Techniques / Q000379:methods*; D015331:Cohort Studies; D017714:Community-Acquired Infections / Q000175:diagnosis* / Q000209:etiology; D003955:Diagnostic Tests, Routine / Q000379:methods*; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009960:Oropharynx / Q000382:microbiology / Q000821:virology; D011014:Pneumonia / Q000175:diagnosis* / Q000209:etiology; D011446:Prospective Studies; D012680:Sensitivity and Specificity; D013183:Sputum / Q000382:microbiology / Q000821:virology; D014556:Urine / Q000382:microbiology / Q000821:virology; D055815:Young Adult
keywords: Community-acquired pneumonia; oropharyngeal swabs; real-time PCR; respiratory virus; sputum samples; yield
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