Means for diagnosing, predicting or monitoring Pneumocystis pneumonia

An in vitro method for diagnosing whether a human patient, who is a Pneumocystis jirovecii carrier, has Pneumocystis pneumonia (PCP) or is at an elevated risk of developing PCP, the method comprising:

• A) providing a sample comprising RNA obtained from the respiratory tract of a human patient by a process comprising extracting and/or purifying the RNA material of a biological sample from the respiratory tract of the human patient in the presence of an RNA extraction internal control;
• B) quantifying in the sample RNA transcripts of a first P. jirovecii mitochondrial gene, wherein the first mitochondrial gene codes for the Cytb protein or transcribes into a P. jirovecii ribosomal RNA;
• and
• C) quantifying in the sample RNA transcripts of a second P. jirovecii mitochondrial gene, wherein the second mitochondrial gene transcribes into a P. jirovecii ribosomal RNA;
• wherein the quantification of B) and C) is performed by (cDNA) reverse-transcription and PCR amplification;
• wherein the first and the second P. jirovecii mitochondrial genes are different;
• wherein a ratio of the value of quantification of the RNA transcripts of the first P. jirovecii mitochondrial gene to the value of quantification of the RNA transcripts of the second P. jirovecii mitochondrial gene that is equal to or lower than a threshold value indicates that the human patient has PCP or an elevated risk of developing PCP;
• wherein a ratio of the value of quantification of the RNA transcripts of the first P. jirovecii mitochondrial gene to the value of quantification of the RNA transcripts of the second P. jirovecii mitochondrial gene that is higher than the threshold value indicates that the human patient does not have PCP or an elevated risk of developing PCP;
• wherein the threshold value has been predetermined by comparing the values, or the distribution of the values, that the ratio of the value of quantification of the RNA transcripts of the first P. jirovecii mitochondrial gene to the value of quantification of the RNA transcripts of the second P. jirovecii mitochondrial gene takes in reference human cohorts of P. jirovecii carriers, who have been pre-established as a function of their status of
• P. jirovecii carriers, who have or develop PCP, or
• P. jirovecii carriers, who do not have and do not develop PCP.