Means for diagnosing, predicting or monitoring pneumocystis pneumonia

Abstract

The application relates to means for diagnosing, predicting or monitoring Pneumocystis pneumonia (PCP). The means of the application are also suitable for determining or predicting the efficacy of a drug or treatment against PCP in a human patient. The means of involve the detection and/or quantification, more particularly the quantification, of the RNA transcripts of two different P. jirovecii mitochondrial genes. The first of said two P. jirovecii mitochondrial genes is the P. jirovecii gene, the sequence of which codes for the Cytb protein or the P. jirovecii mitochondrial Small Sub-Unit (mtSSU) gene. The second of said two P. jirovecii mitochondrial genes is a P. jirovecii gene, the sequence of which transcribes into a P. jirovecii ribosomal RNA, e.g., be the mitochondrial P. jirovecii Large Sub-Unit (mtLSU) gene.

1 - 33 . (canceled) 
     
     
         34 . A kit suitable for diagnosing or predicting  PneumoCystis  Pneumonia (PCP) in a human patient, who is a  Pneumocystis jirovecii  carrier, or for determining or predicting the efficacy of a drug or treatment against PCP in a human patient, who is a  Pneumocystis jirovecii  carrier, wherein said kit comprises a reverse transcriptase, a polymerase, and oligonucleotides;
 wherein said oligonucleotides comprise a first primer pair and a second primer pair and/or a first probe and a second probe;   wherein said first primer pair and/or said first probe specifically hybridizes to the cDNA reverse transcripts of the RNA transcripts of a first  P. jirovecii  mitochondrial gene;   wherein said second primer pair and/or said second probe specifically hybridizes to the cDNA reverse transcripts of the RNA transcripts of a second  P. jirovecii  mitochondrial gene; and   wherein the first and the second  P. jirovecii  mitochondrial genes are different.   
     
     
         35 . The kit of  claim 34 , wherein the first mitochondrial gene codes for the Cytb protein. 
     
     
         36 . The kit of  claim 34 , wherein the first mitochondrial gene transcribes into a  P. jirovecii  ribosomal RNA. 
     
     
         37 . The kit of  claim 35 , wherein the second mitochondrial gene transcribes into a  P. jirovecii  ribosomal RNA. 
     
     
         38 . The kit of  claim 36 , wherein the second mitochondrial gene transcribes into a  P. jirovecii  ribosomal RNA. 
     
     
         39 . The kit of  claim 36 , wherein the first mitochondrial gene is the  P. jirovecii  mitochondrial Small Sub-Unit (mtSSU) gene. 
     
     
         40 . The kit of  claim 37 , wherein the second mitochondrial gene is the mitochondrial  P. jirovecii  Large Sub-Unit (mtLSU) gene. 
     
     
         41 . The kit of  claim 38 , wherein the second mitochondrial gene is the mitochondrial  P. jirovecii  Large Sub-Unit (mtLSU) gene. 
     
     
         42 . The kit of  claim 35 , wherein the first  P. jirovecii  mitochondrial gene comprises the sequence of SEQ ID NO: 29 or an RNA sequence that is of the same length as SEQ ID NO: 29 and is at least 95% identical to SEQ ID NO: 29. 
     
     
         43 . The kit of  claim 36 , wherein when the first  P. jirovecii  mitochondrial gene comprises the sequence of SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 24, or an RNA sequence that is of the same length as SEQ ID NO: 14, SEQ ID NO: 19, or SEQ ID NO: 24 and is at least 95% identical to SEQ ID NO: 14, SEQ ID NO: 19 or SEQ ID NO: 24, respectively. 
     
     
         44 . The kit of  claim 37 , wherein the second  P. jirovecii  mitochondrial gene is comprises the sequence of SEQ ID NO: 9, or an RNA sequence that is of the same length as SEQ ID NO: 9 and is at least 95% identical to SEQ ID NO: 9. 
     
     
         45 . The kit of  claim 38 , wherein the second  P. jirovecii  mitochondrial gene is comprises the sequence of SEQ ID NO: 9, or an RNA sequence that is of the same length as SEQ ID NO: 9 and is at least 95% identical to SEQ ID NO: 9. 
     
     
         46 . The kit of  claim 34 , wherein when the first  P. jirovecii  mitochondrial gene is the gene which codes for the Cytb protein, the quantification of the RNA transcripts of the first  P. jirovecii  mitochondrial gene is performed using a first probe that hybridizes to SEQ ID NO: 30 or to the complementary sequence thereof, without hybridizing to any of SEQ ID NO: 1, the sequence complementary to SEQ ID NO: 1, SEQ ID NO: 2 and the sequence complementary to SEQ ID NO: 2; and
 wherein when the first  P. jirovecii  mitochondrial gene is the mitochondrial  P. jirovecii  Small Sub-Unit (mtSSU) gene, the quantification of the RNA transcripts of the first  P. jirovecii  mitochondrial gene is performed using a first probe that hybridizes to SEQ ID NO: 15, or to the sequence complementary to SEQ ID NO: 15, or to SEQ ID NO: 20, or to the sequence complementary to SEQ ID NO: 20, or to SEQ ID NO: 25, or to the sequence complementary to SEQ ID NO: 25, without hybridizing to any of SEQ ID NO: 3, the sequence complementary to SEQ ID NO: 3, SEQ ID NO: 1 and the sequence complementary to SEQ ID NO: 1; and   wherein when the second  P. jirovecii  mitochondrial gene is the mitochondrial  P. jirovecii  Large Sub-Unit (mtLSU) gene, the quantification of the RNA transcripts of the second  P. jirovecii  mitochondrial gene is performed using a second probe that hybridizes to SEQ ID NO: 10 or to the sequence complementary to SEQ ID NO: 10, without hybridizing to any of SEQ ID NO: 3, the sequence complementary to SEQ ID NO: 3, SEQ ID NO: 2 and the sequence complementary to SEQ ID NO: 2.   
     
     
         47 . The kit of  claim 46 , wherein the second probe comprises SEQ ID NO: 13. 
     
     
         48 . The kit of  claim 46 , comprising a primer comprising SEQ ID NO: 11 and a primer comprising SEQ ID NO: 12.