Characteristics of the included studies.

<p>Abbreviations: BMT, bone marrow transplants; CA, cancer; CD, corticosteroid dependent; CS, colorimeric staining; CA, cancer; HIV, hunman immunodeficiency virus; HM, haematological malignancies; IFS, immunofluorescent staining; Non-AIDS, non-acquired immune deficiency syndrome; NR, not reported; OD, other diseases; OT, organ transplantation; SOC, solid organ malignancies; SLE, systemic lupus erythematosus; WG, wegener’s granulomatosis; Y, yes.</p

SROC curve shows summary operating sensitivity and specificity with confidence and prediction contours.

<p>SROC curve with confidence and prediction regions around mean operating sensitivity and specificity point analyses of PCR assays in BALF for the diagnosis of PJP. Abbreviations: AUC, area under curve; SENS, sensitivity; SPEC, specificity; SROC curve, summary receiver operating (SROC) curve.</p

Technical details methods of the PCR in the included studies.

<p>Abbreviations: DHPS, dihydroperoate synthase; ITS, internal transcribed spacer; mt LSU rRNA, mitochondrial large-subunit ribosomal RNA; mt rRNA, mitochondrial ribosomal RNA; NR, not reported; qPCR, quantitative polymerase chain reaction; RT-PCR, reverse transcriptase -polymerase chain reaction; TD-PCR, a single-round touchdown PCR; Y, yes.</p

Forest plots of the sensitivity and specificity of BALF-PCR for the diagnosis of PJP.

<p>The circles in squares and the horizontal lines represent the point estimate and 95% confidence interval for each included study and the diamond represents the pooled estimate.</p

Summary of the methodological quality assessment of the included studies according to QUADAS-2 criteria.

<p>Data was carried out using a bar graph showing the percentages of the 16 studies that met the criteria (Yes), did not meet the criteria (No), and did not provide adequate relevant data (Unclear).</p

Subgroup analyses of PCR in BAL fluid for the diagnosis of PJP.

<p>The use of regression methods to incorporate the effect of covarying factors on summary measures of performance to explore between-study heterogeneity. We did not find statistically significant except nested-PCR * (P<0.001). Abbreviations: 95% CI, 95% confidence interval; comEX, commercial extraction; DHPS, dihydroperoate synthase; IFS, immunofluorescent staining; LRT Chi, likelihood ratio Chi; mt-rRNA, mitochondrial ribosomal RNA; qPCR, quantitative polymerase chain reaction.</p

Fagan’s nomogram for calculating post-test probabilities (PTPs).

<p>Lines were drawn from the prior probability on the left through the likelihood ratios in the center and extended to the posterior probabilities on the right, which demonstrates that BALF-PCR is very informative raising probability of PJP to over 3-fold when positive from 20% and lowering the probability of disease to as low as 0.5% when negative.</p

Flow diagram of the process of selecting included studies.

<p>This flow-diagram shows 398 references identified, after screening all of the titles and abstracts, 71 articles were selected for full-text review. Ultimately, 16 studies that were included in the meta-analysis, 55 studies were excluded for various reasons.</p