A. Alanio, G. Desoubeaux, C. Sarfati, S. Hamane, A. Bergeron et al., Real-time PCR assay-based strategy for differentiation between active Pneumocystis jirovecii pneumonia and colonization in immunocompromised patients, Clinical Microbiology and Infection, vol.17, issue.10, pp.1531-1537, 2011.
DOI : 10.1111/j.1469-0691.2010.03400.x
URL : https://hal.archives-ouvertes.fr/pasteur-01405252

A. Alanio, P. M. Hauser, K. Lagrou, W. J. Melchers, J. Helweg-larsen et al., ECIL guidelines for the diagnosis of Pneumocystis jirovecii pneumonia in patients with haematological malignancies and stem cell transplant recipients, J. Antimicrob. Chemother, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01405217

A. Alanio, M. Olivi, O. Cabaret, F. Foulet, A. Bellanger et al., Mitochondrial Genotypes and High and Low Fungal Loads Assessed by Single Nucleotide Primer Extension Assay and Quantitative Real-Time PCR, Journal of Eukaryotic Microbiology, vol.32, issue.5, pp.650-656, 2015.
DOI : 10.1111/jeu.12222
URL : https://hal.archives-ouvertes.fr/hal-01294657

J. M. Almeida, O. H. Cissé, Á. Fonseca, M. Pagni, and P. M. Hauser, Comparative genomics suggests primary homothallism of Pneumocystis species, pp.2250-02214, 2015.

J. B. Anderson, C. Wickens, M. Khan, L. E. Cowen, N. Federspiel et al., Infrequent Genetic Exchange and Recombination in the Mitochondrial Genome of Candida albicans, Journal of Bacteriology, vol.183, issue.3, pp.865-872, 2001.
DOI : 10.1128/JB.183.3.865-872.2001

B. Angulo, E. García-garcía, R. Martínez, A. Suárez-gauthier, E. Conde et al., A Commercial Real-Time PCR Kit Provides Greater Sensitivity than Direct Sequencing to Detect KRAS Mutations, The Journal of Molecular Diagnostics, vol.12, issue.3, pp.292-299, 2010.
DOI : 10.2353/jmoldx.2010.090139

C. M. Barr, M. Neiman, T. , and D. R. , Inheritance and recombination of mitochondrial genomes in plants, fungi and animals, New Phytologist, vol.359, issue.1, 2005.
DOI : 10.1111/j.1469-8137.2005.01492.x

C. W. Basse, Mitochondrial inheritance in fungi, Current Opinion in Microbiology, vol.13, issue.6, pp.712-719, 2010.
DOI : 10.1016/j.mib.2010.09.003

D. Beaudet, I. E. De-la-providencia, M. Labridy, A. Roy-bolduc, L. Daubois et al., Intraisolate Mitochondrial Genetic Polymorphism and Gene Variants Coexpression in Arbuscular Mycorrhizal Fungi, Genome Biology and Evolution, vol.7, issue.1, pp.218-227, 2015.
DOI : 10.1093/gbe/evu275

M. Belfort and R. J. Roberts, Homing endonucleases: keeping the house in order, Nucleic Acids Research, vol.25, issue.17, 1997.
DOI : 10.1093/nar/25.17.3379

F. Botterel, O. Cabaret, F. Foulet, C. Cordonnier, J. Costa et al., Clinical Significance of Quantifying Pneumocystis jirovecii DNA by Using Real-Time PCR in Bronchoalveolar Lavage Fluid from Immunocompromised Patients, Journal of Clinical Microbiology, vol.50, issue.2, pp.227-231, 1128.
DOI : 10.1128/JCM.06036-11

J. Brodin, M. Mild, C. Hedskog, E. Sherwood, T. Leitner et al., PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data, PLoS ONE, vol.16, issue.7, 2013.
DOI : 10.1371/journal.pone.0070388.s006

E. Catherinot, F. Lanternier, M. Bougnoux, M. Lecuit, L. Couderc et al., Pneumocystis jirovecii Pneumonia, Infectious Disease Clinics of North America, vol.24, issue.1, pp.107-138, 2010.
DOI : 10.1016/j.idc.2009.10.010

M. Chabé, E. Dei-cas, C. Creusy, L. Fleurisse, N. Respaldiza et al., Immunocompetent hosts as a reservoir of pneumocystis organisms: histological and rt-PCR data demonstrate active replication. Eur, J. Clin. Microbiol. Infect. Dis, vol.23, pp.89-97, 2004.

L. Chatre and M. Ricchetti, Are mitochondria the Achilles??? heel of the Kingdom Fungi?, Current Opinion in Microbiology, vol.20, 2014.
DOI : 10.1016/j.mib.2014.05.001

X. J. Chen, R. A. Butow, B. Chevalier, R. J. Monnat, . Jr et al., The organization and inheritance of the mitochondrial genome, Homing Endonucleases and Inteins Nucleic Acids and Molecular Biology, pp.815-825, 1708.
DOI : 10.1016/S1567-7249(02)00006-5

F. Choukri, J. Menotti, C. Sarfati, J. C. Lucet, G. Nevez et al., Pneumonia, Clinical Infectious Diseases, vol.51, issue.3, pp.259-265, 1086.
DOI : 10.1086/653933

J. R. Christie, T. M. Schaerf, and M. Beekman, Selection against Heteroplasmy Explains the Evolution of Uniparental Inheritance of Mitochondria, PLOS Genetics, vol.78, issue.2, 2015.
DOI : 10.1371/journal.pgen.1005112.s056

O. H. Cissé, J. M. Almeida, Á. Fonseca, A. A. Kumar, J. Salojärvi et al., Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl, mBio, vol.4, issue.3, pp.55-68, 1128.
DOI : 10.1128/mBio.00055-13

O. H. Cissé, M. Pagni, and P. M. Hauser, De Novo Assembly of the Pneumocystis jirovecii Genome from a Single Bronchoalveolar Lavage Fluid Specimen from a Patient, mBio, vol.4, issue.1, pp.428-0041200428, 2012.
DOI : 10.1128/mBio.00428-12

O. H. Cissé, M. Pagni, and P. M. Hauser, Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss Are members of the fungal genus Pneumocystis (a) Commensals, (b) Opportunists, (c) Pathogens, or (d) All of the Above? PLoS Pathog, Genome Biol. Evol, vol.6, 1938.

M. T. Cushion, K. , and S. P. , Assembly and Annotation of Pneumocystis jirovecii from the Human Lung Microbiome, mBio, vol.4, issue.2, pp.224-237, 2013.
DOI : 10.1128/mBio.00224-13

M. G. De-boer, L. E. Bruijnesteijn-van-coppenraet, A. Gaasbeek, S. P. Berger, L. B. Gelinck et al., An Outbreak of Pneumocystis jiroveci Pneumonia with 1 Predominant Genotype among Renal Transplant Recipients: Interhuman Transmission or a Common Environmental Source?, Clinical Infectious Diseases, vol.44, issue.9, pp.1143-1149, 1086.
DOI : 10.1086/513198

M. G. De-boer, J. W. De-fijter, and F. P. Kroon, Outbreaks and clustering of Pneumocystis pneumonia in kidney transplant recipients: a systematic review, Med. Mycol, vol.49, pp.673-680, 2011.

B. Dujon, Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci, Cell, vol.2080, pp.185-197, 1980.

F. Esteves, J. Gaspar, D. Sousa, B. Antunes, F. Mansinho et al., Clinical Relevance of Multiple Single-Nucleotide Polymorphisms in Pneumocystis jirovecii Pneumonia: Development of a Multiplex PCR-Single-Base-Extension Methodology, Journal of Clinical Microbiology, vol.49, issue.5, pp.1810-1815, 2011.
DOI : 10.1128/JCM.02303-10

A. S. Evans, Causation and disease: the Henle-Koch postulates revisited, Yale J. Biol. Med, vol.49, pp.175-195, 1976.
DOI : 10.1007/978-1-4615-3024-4

S. Falkow, Molecular Koch's Postulates Applied to Microbial Pathogenicity, Clinical Infectious Diseases, vol.10, issue.Supplement 2, pp.274-276, 1988.
DOI : 10.1093/cid/10.Supplement_2.S274

E. S. Fritsch, C. D. Chabbert, B. Klaus, and L. M. Steinmetz, A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast, Genetics, vol.198, issue.2, pp.755-771, 2014.
DOI : 10.1534/genetics.114.166637

F. Gigliotti, A. G. Harmsen, W. , and T. W. , Characterization of Transmission of Pneumocystis carinii f. sp. muris through Immunocompetent BALB/c Mice, Infection and Immunity, vol.71, issue.7, pp.3852-3856, 2003.
DOI : 10.1128/IAI.71.7.3852-3856.2003

F. Gigliotti, W. , and T. W. , Pneumocystis, Cold Spring Harbor Perspectives in Medicine, vol.4, issue.12, 2012.
DOI : 10.1101/cshperspect.a019828

M. Gits-muselli, M. Peraldi, N. De-castro, V. Delcey, J. Menotti et al., New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards, PLOS ONE, vol.29, issue.5, 2015.
DOI : 10.1371/journal.pone.0125763.s004
URL : https://hal.archives-ouvertes.fr/pasteur-01405228

P. Haugen, D. M. Simon, and D. Bhattacharya, The natural history of group I introns, Trends in Genetics, vol.21, issue.2, 2005.
DOI : 10.1016/j.tig.2004.12.007

P. M. Hauser, The development of a typing method for an uncultivable microorganism: the example of Pneumocystis jirovecii, Infection, Genetics and Evolution, vol.4, issue.3, pp.199-203, 2004.
DOI : 10.1016/j.meegid.2004.01.011

P. M. Hauser, D. S. Blanc, J. Bille, A. Nahimana, and P. Francioli, Carriage of Pneumocystis carinii by immunosuppressed patients and molecular typing of the organisms, AIDS, vol.14, issue.4, pp.461-463, 2000.
DOI : 10.1097/00002030-200003100-00022

P. M. Hauser, D. S. Blanc, P. Sudre, E. Senggen-manoloff, A. Nahimana et al., Genetic diversity of Pneumocystis carinii in HIV-positive and -negative patients as revealed by PCR???SSCP typing, AIDS, vol.15, issue.4, pp.461-466, 2001.
DOI : 10.1097/00002030-200103090-00004

J. Helweg-larsen, B. Lundgren, and J. D. Lundgren, Heterogeneity and Compartmentalization of Pneumocystis carinii f. sp. hominis Genotypes in Autopsy Lungs, Journal of Clinical Microbiology, vol.39, issue.10, 2001.
DOI : 10.1128/JCM.39.10.3789-3792.2001

A. Jacquier and B. Dujon, An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene, Cell, vol.41, issue.2, pp.383-394, 1985.
DOI : 10.1016/S0092-8674(85)80011-8

L. Gal, S. Damiani, C. Rouillé, A. Grall, A. Tréguer et al., A Cluster of Pneumocystis Infections Among Renal Transplant Recipients: Molecular Evidence of Colonized Patients as Potential Infectious Sources of Pneumocystis jirovecii, Clinical Infectious Diseases, vol.54, issue.7, pp.62-71, 2012.
DOI : 10.1093/cid/cir996

L. Meliani, M. Develoux, M. Marteau-miltgen, D. Magne, V. Barbu et al., Real Time Quantitative PCR Assay for Pneumocystis jirovecii Detection, The Journal of Eukaryotic Microbiology, vol.86, issue.s1, 2003.
DOI : 10.1111/j.1550-7408.2003.tb00670.x

J. H. Meuwissen, I. Tauber, A. D. Leeuwenberg, P. J. Beckers, and M. Sieben, Parasitologic and Serologic Observations of Infection with Pneumocystis in Humans, Journal of Infectious Diseases, vol.136, issue.1, pp.43-49, 1977.
DOI : 10.1093/infdis/136.1.43

S. Mori and M. Sugimoto, Pneumocystis jirovecii infection: an emerging threat to patients with rheumatoid arthritis, Rheumatology, vol.51, issue.12, pp.2120-2130, 2012.
DOI : 10.1093/rheumatology/kes244

A. Morris, N. , and K. A. , Colonization by Pneumocystis jirovecii and Its Role in Disease, Clinical Microbiology Reviews, vol.25, issue.2, pp.297-317, 2012.
DOI : 10.1128/CMR.00013-12
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346301

A. Nahimana, P. Francioli, D. S. Blanc, J. Bille, A. E. Wakefield et al., Determination of the Copy Number of the Nuclear rDNA and Beta-tubulin Genes of Pneumocystis carinii f. sp. hominis Using PCR Multicompetitors, The Journal of Eukaryotic Microbiology, vol.45, issue.4, pp.368-372, 2000.
DOI : 10.1016/0022-1759(93)90104-F

A. Nahimana, M. Rabodonirina, J. Bille, P. Francioli, and P. M. Hauser, Mutations of Pneumocystis jirovecii Dihydrofolate Reductase Associated with Failure of Prophylaxis, Antimicrobial Agents and Chemotherapy, vol.48, issue.11, 2004.
DOI : 10.1128/AAC.48.11.4301-4305.2004

C. M. Parobek, L. Y. Jiang, J. C. Patel, M. J. Alvarez-martinez, J. M. Miro et al., 10 years' experience of infection in GIMEMA centres Multilocus microsatellite genotyping array for investigation of genetic epidemiology of Pneumocystis jirovecii, Pneumocystis carinii pneumonia in patients with malignant haematological diseases, pp.379-386, 1128.

J. C. Peterson and M. T. Cushion, Pneumocystis: not just pneumonia, Current Opinion in Microbiology, vol.8, issue.4, 2005.
DOI : 10.1016/j.mib.2005.06.010

L. L. Pifer, W. T. Hughes, S. Stagno, and D. Woods, Pneumocystis carinii infection: evidence for high prevalence in normal and immunosuppressed children, Pediatrics, vol.61, pp.35-41, 1978.

S. F. Queener, V. Cody, J. Pace, P. Torkelson, and A. Gangjee, Trimethoprim Resistance of Dihydrofolate Reductase Variants from Clinical Isolates of Pneumocystis jirovecii, Antimicrobial Agents and Chemotherapy, vol.57, issue.10, pp.4990-499801161, 2013.
DOI : 10.1128/AAC.01161-13

A. B. Reid, S. C. Chen, and L. J. Worth, Pneumocystis jirovecii pneumonia in non-HIV-infected patients, Current Opinion in Infectious Diseases, vol.24, issue.6, pp.534-544, 2011.
DOI : 10.1097/QCO.0b013e32834cac17

F. Roblot, L. Moal, G. Godet, C. Hutin, P. Texereau et al., Pneumocystis carinii pneumonia in patients with hematologic malignancies: a descriptive study, Journal of Infection, vol.47, issue.1, pp.19-27, 2003.
DOI : 10.1016/S0163-4453(03)00038-0

A. I. Saeed, N. K. Bhagabati, J. C. Braisted, W. Liang, V. Sharov et al., [9] TM4 Microarray Software Suite, Methods Enzymol, vol.411, issue.06, pp.134-193, 2006.
DOI : 10.1016/S0076-6879(06)11009-5

V. Schildgen, S. Mai, S. Khalfaoui, J. Lüsebrink, M. Pieper et al., Pneumocystis jirovecii Can Be Productively Cultured in Differentiated CuFi-8 Airway Cells, mBio, vol.5, issue.3, pp.1186-1200, 2014.
DOI : 10.1128/mBio.01186-14

S. Song, Z. F. Pursell, W. C. Copeland, M. J. Longley, T. A. Kunkel et al., DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mutagenesis through reduced replication fidelity, Proceedings of the National Academy of Sciences, vol.102, issue.14, pp.4990-4995, 2005.
DOI : 10.1073/pnas.0500253102

S. Tasaka and H. Tokuda, Pneumocystis jirovecii pneumonia in non-HIV-infected patients in the era of novel immunosuppressive therapies, Journal of Infection and Chemotherapy, vol.18, issue.6, pp.793-806, 2012.
DOI : 10.1007/s10156-012-0453-0

A. G. Tsolaki, R. F. Miller, A. P. Underwood, S. Banerji, and A. E. Wakefield, Genetic Diversity at the Internal Transcribed Spacer Regions of the rRNA Operon among Isolates of Pneumocystis carinii from AIDS Patients with Recurrent Pneumonia, Journal of Infectious Diseases, vol.174, issue.1, pp.141-156, 1996.
DOI : 10.1093/infdis/174.1.141

S. L. Vargas, W. T. Hughes, M. E. Santolaya, A. V. Ulloa, C. A. Ponce et al., Search for Primary Infection by Pneumocystis carinii in a Cohort of Normal, Healthy Infants, Clinical Infectious Diseases, vol.32, issue.6, pp.855-861, 2001.
DOI : 10.1086/319340

G. Wissmann, R. Morilla, I. Martín-garrido, V. Friaza, N. Respaldiza et al., Pneumocystis jirovecii colonization in patients treated with infliximab, European Journal of Clinical Investigation, vol.14, issue.3, pp.343-348, 2010.
DOI : 10.1111/j.1365-2362.2010.02415.x