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Pneumocystis jirovecii  is an unculturable fungus and the causative agent of  Pneumocystis  pneumonia, a life-threatening opportunistic infection. Although molecular diagnosis is often based on the detection of  mtLSU rRNA  mitochondrial gene, the number of copies of mitochondrial genes had not been investigated. We developed and optimized six real-time PCR assays in order to determine the copy number of four mitochondrial genes ( mtSSU rRNA ,  mtLSU rRNA ,  NAD1 , and  CYTB ) in comparison to nuclear genome ( DHPS  and  HSP70 ) and tested 84 bronchoalveolar fluids of patients at different stages of the infection. Unexpectedly, we found that copy number of mitochondrial genes varied from gene to gene with  mtSSU rRNA  gene being more represented (37 copies) than  NAD1  (23 copies),  mtLSU rRNA  (15 copies) and  CYTB  (6 copies) genes compared to nuclear genome. Hierarchical clustering analysis (HCA) allowed us to define five major clusters, significantly associated with fungal load ( p  = 0.029), in which copy number of mitochondrial genes was significantly different among them. More importantly, copy number of  mtLSU rRNA ,  NAD1 , and  CYTB  but not  mtSSU rRNA  differed according to  P. jirovecii  physiological state with a decreased number of copies when the fungal load is low. This suggests the existence of a mixture of various subspecies of mtDNA that can harbor different amplification rates. Overall, we revealed here an unexpected variability of  P. jirovecii  mtDNA copy number that fluctuates according to  P. jirovecii ’s physiological state, except for mtSSU that is the most stable and the most present mitochondrial gene.

Copy Number Variation of Mitochondrial DNA Genes in Pneumocystis jirovecii According to the Fungal Load in BAL Specimens