R. Rajasingham, R. Smith, B. Park, J. Jarvis, N. Govender et al., Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis, The Lancet Infectious Diseases, vol.17, issue.8, pp.873-1473, 2017.
DOI : 10.1016/S1473-3099(17)30243-8

B. Park, K. Wannemuehler, B. Marston, N. Govender, P. Pappas et al., Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS, AIDS, vol.23, issue.4, pp.525-530, 2009.
DOI : 10.1097/QAD.0b013e328322ffac

D. Garcia-hermoso, G. Janbon, and F. Dromer, Epidemiological evidence for dormant Cryptococcus neoformans infection, Cryptococcus Neoformans, vol.37, pp.3204-3209, 1999.

A. Alanio, F. Vernel-pauillac, A. Sturny-leclère, and F. Dromer, Host Adaptation: Toward Biological Evidence of Dormancy, mBio, vol.6, issue.2, pp.2580-2594, 2015.
DOI : 10.1128/mBio.02580-14

URL : https://hal.archives-ouvertes.fr/pasteur-01405218

F. Chrétien, O. Lortholary, I. Kansau, S. Neuville, F. Gray et al., Infection after Fungemia, The Journal of Infectious Diseases, vol.186, issue.4, pp.522-530, 2002.
DOI : 10.1086/341564

J. Choi, A. Vogl, and J. Kronstad, Regulated expression of cyclic AMP-dependent protein kinase A reveals an influence on cell size and the secretion of virulence factors in Cryptococcus neoformans, Molecular Microbiology, vol.5, issue.4, pp.700-22717009, 2012.
DOI : 10.1016/j.femsyr.2004.04.004

S. Franzot, J. Mukherjee, R. Cherniak, L. Chen, J. Hamdan et al., Microevolution of a standard strain of Cryptococcus neoformans resulting in differences in virulence and other phenotypes, Infect Immun, vol.66, pp.89-97, 1998.

G. Hu, P. Cheng, A. Sham, J. Perfect, and J. Kronstad, during early murine pulmonary infection, Molecular Microbiology, vol.5, issue.6, pp.1456-1475, 2008.
DOI : 10.1164/ajrccm.149.2.8306026

A. Gerstein and K. Nielsen, virulence requires selection outside the human host, Yeast, vol.169, issue.4, pp.143-27862271, 2017.
DOI : 10.1007/s11046-009-9230-8

S. Brown, L. Campbell, and J. Lodge, Cryptococcus neoformans, a fungus under stress, Current Opinion in Microbiology, vol.10, issue.4, pp.320-325, 2007.
DOI : 10.1016/j.mib.2007.05.014

L. Wang and X. Lin, Morphogenesis in Fungal Pathogenicity: Shape, Size, and Surface, PLoS Pathogens, vol.109, issue.12, pp.1003027-23236274, 2012.
DOI : 10.1371/journal.ppat.1003027.g002

L. Okagaki, A. Strain, J. Nielsen, and C. Charlier, Cryptococcal cell morphology affects host cell interactions and pathogenicity, PLoS Pathog, vol.6, p.20585559, 2010.

O. Zaragoza, R. García-rodas, J. Nosanchuk, M. Cuenca-estrella, J. Rodríguez-tudela et al., Fungal Cell Gigantism during Mammalian Infection, PLoS Pathogens, vol.42, issue.6, pp.1000945-20585557, 2010.
DOI : 10.1371/journal.ppat.1000945.s009

G. Love, G. Boyd, and D. Greer, Large Cryptococcus neoformans isolated from brain abscess, J Clin Microbiol, vol.22, pp.1068-1070, 1985.

J. Cruickshank, R. Cavill, and M. Jelbert, Cryptococcus neoformans of unusual morphology, Appl Microbiol, vol.25, pp.309-312, 1973.

R. García-rodas, A. Casadevall, J. Rodríguez-tudela, M. Cuenca-estrella, and O. Zaragoza, Cryptococcus neoformans Capsular Enlargement and Cellular Gigantism during Galleria mellonella Infection, PLoS ONE, vol.75, issue.9, pp.24485-21915338, 2011.
DOI : 10.1371/journal.pone.0024485.g008

O. Zaragoza and K. Nielsen, Titan cells in Cryptococcus neoformans: cells with a giant impact, Current Opinion in Microbiology, vol.16, issue.4, pp.409-413, 2013.
DOI : 10.1016/j.mib.2013.03.006

L. Okagaki, Y. Wang, E. Ballou, O. Meara, T. Bahn et al., ABSTRACT, Eukaryotic Cell, vol.10, issue.10, pp.1306-1316, 2011.
DOI : 10.1128/EC.05179-11

J. Crabtree, L. Okagaki, D. Wiesner, A. Strain, J. Nielsen et al., ABSTRACT, Infection and Immunity, vol.80, issue.11, pp.3776-3785, 2012.
DOI : 10.1128/IAI.00507-12

A. Gerstein, M. Fu, L. Mukaremera, Z. Li, K. Ormerod et al., ABSTRACT, mBio, vol.6, issue.5, pp.1340-1355, 2015.
DOI : 10.1128/mBio.01340-15

L. Okagaki and K. Nielsen, ABSTRACT, Eukaryotic Cell, vol.11, issue.6, pp.820-826, 2012.
DOI : 10.1128/EC.00121-12

Z. Li and K. Nielsen, Morphology Changes in Human Fungal Pathogens upon Interaction with the Host, Journal of Fungi, vol.7, issue.4, pp.66-29333431, 2017.
DOI : 10.1165/ajrcmb.22.6.3838

D. Souza, C. Yue, C. Alspaugh, and J. , Cyclic AMP-Dependent Protein Kinase Controls Virulence of the Fungal Pathogen Cryptococcus neoformans, Molecular and Cellular Biology, vol.21, issue.9, pp.3179-11287622, 2001.
DOI : 10.1128/MCB.21.9.3179-3191.2001

J. Kronstad, G. Hu, and J. Choi, Mycobiology, vol.63, issue.Pt 1, pp.143-50, 2011.
DOI : 10.1111/j.1365-2958.2006.05566.x

Y. Bahn and K. Jung, ABSTRACT, Eukaryotic Cell, vol.12, issue.12, pp.1564-1577, 2013.
DOI : 10.1128/EC.00218-13

G. Hu, B. Steen, T. Lian, A. Sham, N. Tam et al., Transcriptional Regulation by Protein Kinase A in Cryptococcus neoformans, PLoS Pathogens, vol.181, issue.3, pp.42-17367210, 2007.
DOI : 10.1371/journal.ppat.0030042.st006

J. Geddes, M. Caza, D. Croll, N. Stoynov, L. Foster et al., ABSTRACT, mBio, vol.7, issue.1, pp.1862-1877, 2016.
DOI : 10.1128/mBio.01862-15

A. Casadevall, M. Deshaw, M. Fan, F. Dromer, T. Kozel et al., Molecular and idiotypic analysis of antibodies to Cryptococcus neoformans glucuronoxylomannan, Infect Immun, vol.62, pp.3864-3872, 1994.

R. Cordero, B. Pontes, A. Guimarães, L. Martinez, J. Rivera et al., ABSTRACT, Infection and Immunity, vol.79, issue.12, pp.4990-5000, 2011.
DOI : 10.1128/IAI.05789-11

A. Alanio, M. Desnos-ollivier, and F. Dromer, Dynamics of Cryptococcus neoformans-Macrophage Interactions Reveal that Fungal Background Influences Outcome during Cryptococcal Meningoencephalitis in Humans, mBio, vol.2, issue.4, pp.158-169, 2011.
DOI : 10.1128/mBio.00158-11

URL : https://hal.archives-ouvertes.fr/pasteur-01405254

C. Chrisman, P. Albuquerque, A. Guimarães, E. Nieves, and A. Casadevall, Phospholipids Trigger Cryptococcus neoformans Capsular Enlargement during Interactions with Amoebae and Macrophages, PLoS Pathogens, vol.42, issue.5, pp.1002047-21637814, 2011.
DOI : 10.1371/journal.ppat.1002047.s004

P. Albuquerque, A. Nicola, E. Nieves, H. Paes, P. Williamson et al., Quorum sensingmediated , cell density-dependent regulation of growth and virulence in Cryptococcus neoformans, mBio, vol.5, pp.986-999, 2013.

C. Homer, D. Summers, A. Goranov, S. Clarke, D. Wiesner et al., Intracellular Action of a Secreted Peptide Required for Fungal Virulence, Cell Host & Microbe, vol.19, issue.6, pp.849-864, 2016.
DOI : 10.1016/j.chom.2016.05.001

G. Janbon, K. Ormerod, D. Paulet, E. Byrnes, V. Yadav et al., Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation, PLoS Genetics, vol.19, issue.4, pp.1004261-24743168, 2014.
DOI : 10.1371/journal.pgen.1004261.s023

URL : https://hal.archives-ouvertes.fr/hal-01204377

S. Arras, K. Ormerod, P. Erpf, M. Espinosa, A. Carpenter et al., Convergent microevolution of Cryptococcus neoformans hypervirulence in the laboratory and the clinic, Scientific Reports, vol.25, issue.Suppl 1, p.29263343, 2017.
DOI : 10.1006/meth.2001.1262

O. Meara, T. Alspaugh, and J. , The Cryptococcus neoformans Capsule: a Sword and a Shield, Clinical Microbiology Reviews, vol.25, issue.3, pp.387-408, 2012.
DOI : 10.1128/CMR.00001-12

R. Cordero and A. Casadevall, Functions of fungal melanin beyond virulence, Fungal Biology Reviews, vol.31, issue.2, p.99, 2017.
DOI : 10.1016/j.fbr.2016.12.003

J. Rhodes, C. Desjardins, S. Sykes, M. Beale, M. Vanhove et al., at the Global Population Level, Genetics, vol.207, issue.1, p.28679543, 2017.
DOI : 10.1534/genetics.117.203836

C. Desjardins, C. Giamberardino, S. Sykes, C. Yu, J. Tenor et al., Genome Research, vol.4, issue.7, pp.1207-1219, 2017.
DOI : 10.1038/ng.2310

I. Dambuza, T. Drake, A. Chapuis, L. Taylor-smith, N. Legrave et al., The Cryptococcus neoformans Titan cell is an inducible and regulated morphotype underlying pathogenesis, PLoS Pathog, vol.https, 2018.

N. Trevijano-contador, S. Rossi, H. Oliveira, . De, I. Llorente et al., Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals that require the activation of several transduction pathways, PLoS Pathog, vol.https, 2018.
DOI : 10.1101/193540

D. Wiesner, C. Specht, C. Lee, K. Smith, L. Mukaremera et al., Chitin Recognition via Chitotriosidase Promotes Pathologic Type-2 Helper T Cell Responses to Cryptococcal Infection, PLOS Pathogens, vol.8, issue.3, p.25764512, 2015.
DOI : 10.1371/journal.ppat.1004701.s012

V. Veses, A. Richards, and N. Gow, Vacuoles and fungal biology, Current Opinion in Microbiology, vol.11, issue.6, pp.503-510, 2008.
DOI : 10.1016/j.mib.2008.09.017

N. Zhang and L. Cao, Starvation signals in yeast are integrated to coordinate metabolic reprogramming and stress response to ensure longevity, Current Genetics, vol.3, issue.2, p.28444510, 2017.
DOI : 10.1098/rsob.120137

V. Nizet and R. Johnson, Interdependence of hypoxic and innate immune responses, Nature Reviews Immunology, vol.105, issue.9, pp.609-617, 2009.
DOI : 10.4049/jimmunol.177.8.4962

N. Grahl, K. Shepardson, D. Chung, and R. Cramer, ABSTRACT, Eukaryotic Cell, vol.11, issue.5, pp.560-570, 2012.
DOI : 10.1128/EC.00031-12

N. Grahl, S. Puttikamonkul, J. Macdonald, M. Gamcsik, L. Ngo et al., In vivo Hypoxia and a Fungal Alcohol Dehydrogenase Influence the Pathogenesis of Invasive Pulmonary Aspergillosis, PLoS Pathogens, vol.198, issue.7, pp.1002145-21811407, 2011.
DOI : 10.1371/journal.ppat.1002145.s006

C. Chun, O. Liu, and H. Madhani, A Link between Virulence and Homeostatic Responses to Hypoxia during Infection by the Human Fungal Pathogen Cryptococcus neoformans, PLoS Pathogens, vol.98, issue.2, pp.22-17319742, 2007.
DOI : 10.1371/journal.ppat.0030022.st005

H. Lee, Y. Chang, G. Nardone, and K. Kwon-chung, TUP1 disruption in Cryptococcus neoformans uncovers a peptide-mediated density-dependent growth phenomenon that mimics quorum sensing, Molecular Microbiology, vol.16, issue.3, pp.591-17462010, 2007.
DOI : 10.1111/j.1365-2958.2004.04234.x

F. Dromer, J. Salamero, A. Contrepois, C. Carbon, and P. Yeni, Production, characterization, and antibody specificity of a mouse monoclonal antibody reactive with Cryptococcus neoformans capsular polysaccharide, Infect Immun, vol.55, pp.742-748, 1987.

S. Zebedee, R. Koduri, J. Mukherjee, S. Mukherjee, S. Lee et al., Mouse-human immunoglobulin G1 chimeric antibodies with activities against Cryptococcus neoformans., Antimicrobial Agents and Chemotherapy, vol.38, issue.7, pp.1507-7979280, 1994.
DOI : 10.1128/AAC.38.7.1507

E. Mcclelland, A. Nicola, R. Prados-rosales, and A. Casadevall, Ab binding alters gene expression in Cryptococcus neoformans and directly modulates fungal metabolism, Journal of Clinical Investigation, vol.120, issue.4, pp.1355-1361, 2010.
DOI : 10.1172/JCI38322DS1

S. Geunes-boyer, M. Beers, J. Perfect, J. Heitman, and J. Wright, ABSTRACT, Infection and Immunity, vol.80, issue.7, pp.2444-2453, 2012.
DOI : 10.1128/IAI.05613-11

D. Sanglard, F. Ischer, D. Calabrese, M. De-micheli, and J. Bille, Multiple resistance mechanisms to azole antifungals in yeast clinical isolates, Drug Resistance Updates, vol.1, issue.4, pp.25510-1016, 1998.
DOI : 10.1016/S1368-7646(98)80006-X

A. Loyse, F. Dromer, J. Day, O. Lortholary, and T. Harrison, Flucytosine and cryptococcosis: time to urgently address the worldwide accessibility of a 50-year-old antifungal, Journal of Antimicrobial Chemotherapy, vol.113, issue.3, pp.2435-2444, 2013.
DOI : 10.7326/0003-4819-113-3-183

C. Bian, C. Xu, J. Ruan, K. Lee, T. Burke et al., Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation, The EMBO Journal, vol.17, issue.14, pp.2829-2842, 2011.
DOI : 10.1093/emboj/17.11.3155

Z. Li, J. Bi, Y. J. Pan, J. Sun, Z. Zhu et al., ABSTRACT, Applied and Environmental Microbiology, vol.78, issue.1, pp.21-27, 2011.
DOI : 10.1128/AEM.06072-11

URL : https://hal.archives-ouvertes.fr/hal-00232969

S. Gish, E. Maier, B. Haynes, F. Santiago-tirado, D. Srikanta et al., ABSTRACT, mBio, vol.7, issue.2, pp.313-329, 2016.
DOI : 10.1128/mBio.00313-16

J. Vandamme, D. Castermans, and J. Thevelein, Molecular mechanisms of feedback inhibition of protein kinase A on intracellular cAMP accumulation, Cellular Signalling, vol.24, issue.8, pp.1610-1618, 2012.
DOI : 10.1016/j.cellsig.2012.04.001

Y. Chen, R. Farrer, C. Giamberardino, S. Sakthikumar, A. Jones et al., Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii. mBio, pp.166-183, 2017.

K. Mccluskey, A. Wiest, and M. Plamann, The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research, Journal of Biosciences, vol.47, issue.1, pp.119-126, 2010.
DOI : 10.1007/s12038-010-0014-6

Y. Wang, P. Aisen, and A. Casadevall, Melanin, melanin " ghosts, " and melanin composition in Cryptococcus neoformans, Infect Immun, vol.64, pp.2420-2424, 1996.

I. Banks, C. Specht, M. Donlin, K. Gerik, S. Levitz et al., Eukaryotic Cell, vol.4, issue.11, pp.1902-1912, 2005.
DOI : 10.1128/EC.4.11.1902-1912.2005

R. Tanaka, H. Taguchi, K. Takeo, M. Miyaji, and K. Nishimura, by flow cytometry, Medical Mycology, vol.3, issue.5, pp.299-301, 1996.
DOI : 10.1016/0003-2697(89)90065-1

URL : https://hal.archives-ouvertes.fr/hal-01663398

S. Ingavale, Y. Chang, H. Lee, C. Mcclelland, M. Leong et al., Importance of Mitochondria in Survival of Cryptococcus neoformans Under Low Oxygen Conditions and Tolerance to Cobalt Chloride, PLoS Pathogens, vol.4, issue.9, pp.1000155-18802457, 2008.
DOI : 10.1371/journal.ppat.1000155.s002

E. Mcclelland, U. Ramagopal, J. Rivera, J. Cox, A. Nakouzi et al., A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals, PLOS Pathogens, vol.53, issue.9, pp.1005849-27583447, 2016.
DOI : 10.1371/journal.ppat.1005849.s008

S. Arras, J. Chitty, K. Blake, B. Schulz, and J. Fraser, A Genomic Safe Haven for Mutant Complementation in Cryptococcus neoformans, PLOS ONE, vol.27, issue.Suppl 1, pp.122916-25856300, 2015.
DOI : 10.1371/journal.pone.0122916.s004

URL : https://doi.org/10.1371/journal.pone.0122916

J. Rhodes, M. Beale, M. Vanhove, J. Jarvis, S. Kannambath et al., A population genomics approach to assessing the genetic basis of within-host microevolution underlying recurrent cryptococcal meningitis infection, G3 Genes, vol.https, 2016.

H. Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, 1303.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data, Genome Research, vol.20, issue.9, pp.1297-1303, 2010.
DOI : 10.1101/gr.107524.110

P. Cingolani, A. Platts, L. Wang, M. Coon, T. Nguyen et al., A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff, Fly, vol.8, issue.2, pp.80-92, 2012.
DOI : 10.1101/gr.4086505

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.57, issue.9, pp.1312-1313, 2014.
DOI : 10.1080/10635150802429642

URL : https://academic.oup.com/bioinformatics/article-pdf/30/9/1312/17345185/btu033.pdf

F. De-chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop et al., Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, vol.9, issue.7, pp.690-696, 2012.
DOI : 10.1038/nmeth.1924

, The Kappa Statistic in Reliability Studies: Use, Interpretation, and Sample Size Requirements, Phys Ther, vol.https, 2005.