title: Detection of Pneumocystis jirovecii by two staining methods and two quantitative PCR assays.
abstract: BACKGROUND
  Pneumocystis jirovecii is an opportunistic pathogen that causes pneumonia, particularly in immunodeficient hosts.
  
  
  METHODS
  We retrospectively compared the results obtained by two staining methods (toluidine blue and calcofluor white) and two quantitative (q) real time PCR assays for the detection of P. jirovecii in bronchoalveolar lavage (BAL) specimens. For the qPCR assays, we used newly selected probes and primers targeting the Kex-1 gene, which codes for a serine endoprotease, and compared the results to those from the published assay targeting the beta-tubulin gene.
  
  
  RESULTS
  A total of 1,843 BAL specimens were analyzed microscopically in parallel, and 74 (4.0%) were found to be positive with both stains, 23 (1.2%) were positive only with the toluidine blue stain, and six (0.3%) only with the calcofluor stain (p = 0.003). Of these, a selection of 186 consecutive BAL fluid samples were tested by qPCR using the respective different primer pairs. 21 of the 186 samples (11.3%) were microscopically positive with both stains as well as qPCR positive after 18-31 cycles (corresponding to 5.24 x 10(6) copies/ml to 640 copies/ml of native BAL) using the Kex-1 primer pair and between 21-33 cycles using the beta-tubulin assay. A good correlation between semi-quantitative microscopy and the number of PCR cycles needed for a positive signal was noted. Of the remaining 165 samples, 153 (82%) were both microscopically and PCR negative (PCR with the two sets of primers); the remaining 12 samples (7%) were Kex-1-based PCR positive (from cycles 33 to 41, corresponding to 160 copies/ml of BAL or less) but microscopically negative. Of these latter samples, ten (6%) were also positive (from cycles 34 to 38) with the primers targeting the beta-tubulin gene. Taking microscopy as a reference, the sensitivity of qPCR targeting the Kex-1 gene was 100%, and the specificity was 92.4%.
  
  
  CONCLUSIONS
  The sensitive qPCR analysis proved to be a rapid and reliable method to detect P. jirovecii in BAL.
authors.affiliation: Medical Direction, University Hospitals of Geneva, 24 rue Micheli-du-Crest, 1211, Geneva 14, Switzerland. peter.rohner@diogenes.hcuge.ch
authors.forename: P
authors.initials: P
authors.lastname: Rohner
authors.forename: V
authors.initials: V
authors.lastname: Jacomo
authors.forename: R
authors.initials: R
authors.lastname: Studer
authors.forename: J
authors.initials: J
authors.lastname: Schrenzel
authors.forename: J-D
authors.initials: JD
authors.lastname: Graf
mesh_terms: D001483:Base Sequence; D001557:Benzenesulfonates; D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology*; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D006801:Humans; D008297:Male; D045363:Pneumocystis carinii / Q000235:genetics / Q000302:isolation & purification*; D011020:Pneumonia, Pneumocystis / Q000175:diagnosis*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012189:Retrospective Studies; D012680:Sensitivity and Specificity; D012697:Serine Endopeptidases / Q000235:genetics; D013194:Staining and Labeling / Q000379:methods*; D014048:Tolonium Chloride; D014404:Tubulin / Q000235:genetics
chemical_list: D001557:Benzenesulfonates; D004271:DNA, Fungal; D014404:Tubulin; D014048:Tolonium Chloride; C007061:C.I. Fluorescent Brightening Agent 28; C470926:Kex1 protein, Pneumocystis jirovecii; D012697:Serine Endopeptidases