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Table 4 Performance of respiratory Pneumocystis PCR for the diagnosis of PJP*

From: Pneumocystis jirovecii pneumonia in intensive care units: a multicenter study by ESGCIP and EFISG

Population

PJP (TP/total)

No PJP (TN/total)

Sensitivity % (95% CI)

Specificity % (95% CI)

PPV % (95% CI)

NPV % (95% CI)

LR + (95% CI)

LR- (95% CI)

Diagnosis of presumptive/proven PJP

        

All respiratory Pneumocystis PCR**

111/111

373/439

100 (97–100)

85 (81–88)

63 (55–70)

100 (99–100)

6.7 (5.3–8.3)

0.0 §

Sputum Pneumocystis PCR***

10/10

19/28

100 (69–100)

68 (48–84)

53 (29–76)

100 (82–100)

3.1 (1.8–5.3)

0.0 §

Tracheal aspirate Pneumocystis PCR***

10/10

63/74

100 (69–100)

85 (75–92)

48 (26–70)

100 (94–100)

6.7 (3.9–11.6)

0.0 §

BALF Pneumocystis PCR***

95/95

299/351

100 (96–100)

85 (81–89)

65 (56–72)

100 (99–100)

6.8 (5.3–8.7)

0.0 §

Diagnosis of proven PJP****

        

Pneumocystis PCR vs. microscopy (ref) *****

27/27

100/163

100 (87–100)

61 (53–69)

30 (21–41)

100 (96–100)

2.6 (2.1–3.1)

0.0 §

  1. BALF, bronchoalveolar lavage fluid; CI, confidence interval; LR−, negative likelihood ratio; LR+, positive likelihood ratio; NPV, negative predictive value; PCR, polymerase chain reaction; PJP, Pneumocystis jirovecii pneumonia; PPV, positive predictive value; TN, true negative; TP, true positive
  2. *Quantitative or qualitative Pneumocystis PCR (according to locally implemented laboratory developed tests or commercial assays, for details see Additional file 1: Table S1) on respiratory specimens (sputum, tracheal aspirate, and/or bronchoalveolar lavage fluid). Patients with neither a “PJP” nor a “no PJP” diagnosis (i.e., “diagnosis inconclusive”, see study methods) were conservatively classified as “no PJP” to reduce overestimation of the diagnostic performance of Pneumocystis PCR (a higher frequency of DNA detection was indeed registered in patients with inconclusive diagnosis than in the entire “no PJP” population)
  3. **The criterion for PCR positivity was defined as the detection of Pneumocystis DNA in any respiratory specimen (sputum, tracheal aspirate, and/or bronchoalveolar lavage fluid). For reference definitions of presumptive and proven PJP see methods
  4. ***Not mutually exclusive since some patients underwent Pneumocystis PCR testing on different types of respiratory samples (sputum, tracheal aspirate, and/or BALF)
  5. ****Evaluated in the subgroup of patients tested for Pneumocystis microscopy (Crystal Violet, May-Grünwald-Giemsa, Wright-Giemsa, Rapid Giemsa-like stains, Direct Fluorescent Antibody, Methenamine Silver, or Toluidine Blue O according to local procedures) on respiratory specimens
  6. *****Positivity of microscopy as reference was defined as at least one positive tested sample/s (sputum, tracheal aspirate, and/or bronchoalveolar lavage fluid)
  7. §No false negatives in the tested sample (consider the presence of incorporation bias, see methods)
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Critical Care

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