J. Perlroth, B. Choi, and B. Spellberg, Nosocomial fungal infections: epidemiology, diagnosis, and treatment, Medical Mycology, vol.45, issue.4, pp.321-346, 2007.
DOI : 10.1080/13693780701218689

A. Borst, M. Raimer, D. Warnock, C. Morrison, and B. Arthington-skaggs, Rapid Acquisition of Stable Azole Resistance by Candida glabrata Isolates Obtained before the Clinical Introduction of Fluconazole, Antimicrobial Agents and Chemotherapy, vol.49, issue.2, pp.783-787, 2005.
DOI : 10.1128/AAC.49.2.783-787.2005

D. Warnock, J. Burke, N. Cope, E. Johnson, and N. Fraunhofer, FLUCONAZOLE RESISTANCE IN CANDIDA GLABRATA, The Lancet, vol.332, issue.8623, p.1310, 1988.
DOI : 10.1016/S0140-6736(88)92919-4

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC188100

D. Sanglard, F. Ischer, D. Calabrese, P. Majcherczyk, and J. Bille, The ATP binding cassette transporter gene CgCDR1 from Candida glabrata is involved in the resistance of clinical isolates to azole antifungal agents, Antimicrob Agents Chemother, vol.43, pp.2753-2765, 1999.

A. Roetzer, T. Gabaldon, and C. Schuller, From Saccharomyces cerevisiae???to Candida glabrata???in a few easy steps: important adaptations for an opportunistic pathogen, FEMS Microbiology Letters, vol.314, issue.1, pp.1-9, 2011.
DOI : 10.1111/j.1574-6968.2010.02102.x

J. Shin, M. Chae, J. Song, S. Jung, and D. Cho, Changes in Karyotype and Azole Susceptibility of Sequential Bloodstream Isolates from Patients with Candida glabrata Candidemia, Journal of Clinical Microbiology, vol.45, issue.8, pp.2385-2391, 2007.
DOI : 10.1128/JCM.00381-07

O. Bader, A. Schwarz, E. Kraneveld, M. Tangwattanchuleeporn, and P. Schmidt, Gross karyotypic and phenotypic alterations among different progenies of the Candida glabrata CBS138/ATCC2001 reference strain, PLoS One, vol.7, 2012.

S. Polakova, C. Blume, J. Zarate, M. Mentel, and D. Jorck-ramberg, Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata, Proceedings of the National Academy of Sciences, vol.49, issue.4, pp.2688-2693, 2009.
DOI : 10.1099/00207713-49-4-1925

P. Mann, P. Mcnicholas, A. Chau, R. Patel, and C. Mendrick, Impact of Antifungal Prophylaxis on Colonization and Azole Susceptibility of Candida Species, Antimicrobial Agents and Chemotherapy, vol.53, issue.12, pp.5026-5034, 2009.
DOI : 10.1128/AAC.01031-09

H. Vanden-bossche, P. Marichal, F. Odds, L. Jeune, L. Coene et al., Characterization of an azole-resistant Candida glabrata isolate., Antimicrobial Agents and Chemotherapy, vol.36, issue.12, pp.2602-2610, 1992.
DOI : 10.1128/AAC.36.12.2602

Z. Woodman and C. Williamson, HIV molecular epidemiology: transmission and adaptation to human populations, Current Opinion in HIV and AIDS, vol.4, issue.4, pp.247-252, 2009.
DOI : 10.1097/COH.0b013e32832c0672

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351078

W. Ziebuhr, K. Ohlsen, H. Karch, T. Korhonen, and J. Hacker, Evolution of bacterial pathogenesis, Cellular and Molecular Life Sciences (CMLS), vol.56, issue.9-10, pp.719-728, 1999.
DOI : 10.1007/s000180050018

J. Morschhauser, G. Kohler, W. Ziebuhr, G. Blum-oehler, and U. Dobrindt, Evolution of microbial pathogens, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.355, issue.1397, pp.695-704, 2000.
DOI : 10.1098/rstb.2000.0609

A. Maurelli, Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens, FEMS Microbiology Letters, vol.267, issue.1, pp.1-8, 2007.
DOI : 10.1111/j.1574-6968.2006.00526.x

I. Jacobsen, S. Brunke, K. Seider, T. Schwarzmuller, and A. Firon, Candida glabrata Persistence in Mice Does Not Depend on Host Immunosuppression and Is Unaffected by Fungal Amino Acid Auxotrophy, Infection and Immunity, vol.78, issue.3, pp.1066-1077, 2010.
DOI : 10.1128/IAI.01244-09

K. Seider, S. Brunke, L. Schild, N. Jablonowski, and D. Wilson, The Facultative Intracellular Pathogen Candida glabrata Subverts Macrophage Cytokine Production and Phagolysosome Maturation, The Journal of Immunology, vol.187, issue.6, pp.3072-3086, 2011.
DOI : 10.4049/jimmunol.1003730

R. Kaur, B. Ma, and B. Cormack, A family of glycosylphosphatidylinositol-linked aspartyl proteases is required for virulence of Candida glabrata, Proceedings of the National Academy of Sciences, vol.3, issue.14-15, pp.7628-7633, 2007.
DOI : 10.1016/S1286-4579(01)01496-4

A. Roetzer, N. Gratz, P. Kovarik, and C. Schuller, survival during phagocytosis, Cellular Microbiology, vol.16, issue.Part 19, pp.199-216, 2010.
DOI : 10.1111/j.1462-5822.2009.01391.x

V. Otto and D. Howard, Further studies on the intracellular behavior of Torulopsis glabrata, Infect Immun, vol.14, pp.433-438, 1976.

J. Steenbergen, J. Nosanchuk, S. Malliaris, and A. Casadevall, Cryptococcus neoformans Virulence Is Enhanced after Growth in the Genetically Malleable Host Dictyostelium discoideum, Infection and Immunity, vol.71, issue.9, pp.4862-4872, 2003.
DOI : 10.1128/IAI.71.9.4862-4872.2003

A. Casadevall, Evolution of Intracellular Pathogens, Annual Review of Microbiology, vol.62, issue.1, pp.19-33, 2008.
DOI : 10.1146/annurev.micro.61.080706.093305

D. Magditch, T. Liu, C. Xue, and A. Idnurm, DNA Mutations Mediate Microevolution between Host-Adapted Forms of the Pathogenic Fungus Cryptococcus neoformans, PLoS Pathogens, vol.8, issue.10, p.1002936, 2012.
DOI : 10.1371/journal.ppat.1002936.s007

A. Ensminger, Y. Yassin, A. Miron, and R. Isberg, Experimental Evolution of Legionella pneumophila in Mouse Macrophages Leads to Strains with Altered Determinants of Environmental Survival, PLoS Pathogens, vol.2, issue.103, p.1002731, 2012.
DOI : 10.1371/journal.ppat.1002731.s001

M. Miskinyte, A. Sousa, R. Ramiro, J. De-sousa, and J. Kotlinowski, The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages, PLoS Pathogens, vol.15, issue.12, p.1003802, 2013.
DOI : 10.1371/journal.ppat.1003802.s018

S. Lachke, S. Joly, K. Daniels, and D. Soll, Phenotypic switching and filamentation in Candida glabrata, Microbiology, vol.148, issue.9, pp.2661-2674, 2002.
DOI : 10.1099/00221287-148-9-2661

T. Schwarzmüller, B. Ma, E. Hiller, F. Istel, and M. Tscherner, Systematic Phenotyping of a Large-Scale Candida glabrata Deletion Collection Reveals Novel Antifungal Tolerance Genes, PLoS Pathogens, vol.39, issue.6, p.1004211, 2014.
DOI : 10.1371/journal.ppat.1004211.s022

I. Jacobsen, K. Grosse, A. Berndt, and B. Hube, Pathogenesis of Candida albicans Infections in the Alternative Chorio-Allantoic Membrane Chicken Embryo Model Resembles Systemic Murine Infections, PLoS ONE, vol.29, issue.Pt 8, p.19741, 2011.
DOI : 10.1371/journal.pone.0019741.s002

B. Dujon, D. Sherman, G. Fischer, P. Durrens, and S. Casaregola, Genome evolution in yeasts, Nature, vol.316, issue.6995, pp.35-44, 2004.
DOI : 10.1093/nar/gkg056

URL : https://hal.archives-ouvertes.fr/hal-00104411

A. De-las-penas, S. Pan, I. Castano, J. Alder, and R. Cregg, Virulence-related surface glycoproteins in the yeast pathogen Candida glabrata are encoded in subtelomeric clusters and subject to RAP1- and SIR-dependent transcriptional silencing, Genes & Development, vol.17, issue.18, pp.2245-2258, 2003.
DOI : 10.1101/gad.1121003

A. Thierry, B. Dujon, and G. Richard, Megasatellites: a new class of large tandem repeats discovered in the pathogenic yeast Candida glabrata, Cellular and Molecular Life Sciences, vol.48, issue.5, pp.671-676, 2010.
DOI : 10.1007/s00018-009-0216-y

URL : https://hal.archives-ouvertes.fr/pasteur-01370699

J. Shaw, P. Mol, B. Bowers, S. Silverman, and M. Valdivieso, The function of chitin synthases 2 and 3 in the Saccharomyces cerevisiae cell cycle, The Journal of Cell Biology, vol.114, issue.1, pp.111-123, 1991.
DOI : 10.1083/jcb.114.1.111

S. Nagahashi, M. Sudoh, N. Ono, R. Sawada, and E. Yamaguchi, Characterization of Chitin Synthase 2 of Saccharomyces cerevisiae.: IMPLICATION OF TWO HIGHLY CONSERVED DOMAINS AS POSSIBLE CATALYTIC SITES, Journal of Biological Chemistry, vol.270, issue.23, pp.13961-13967, 1995.
DOI : 10.1074/jbc.270.23.13961

M. Kamran, A. Calcagno, H. Findon, E. Bignell, and M. Jones, Inactivation of Transcription Factor Gene ACE2 in the Fungal Pathogen Candida glabrata Results in Hypervirulence, Eukaryotic Cell, vol.3, issue.2, pp.546-552, 2004.
DOI : 10.1128/EC.3.2.546-552.2004

J. Vazquez, G. Peng, J. Sobel, L. Steele-moore, and P. Schuman, Species Isolates Recovered from Human Immunodeficiency Virus???Infected Women Receiving Fluconazole Prophylaxis, Clinical Infectious Diseases, vol.33, issue.7, pp.1069-1075, 2001.
DOI : 10.1086/322641

S. Ferrari, F. Ischer, D. Calabrese, B. Posteraro, and M. Sanguinetti, Gain of Function Mutations in CgPDR1 of Candida glabrata Not Only Mediate Antifungal Resistance but Also Enhance Virulence, PLoS Pathogens, vol.1, issue.1, p.1000268, 2009.
DOI : 10.1371/journal.ppat.1000268.s008

K. Seider, A. Heyken, A. Luttich, P. Miramon, and B. Hube, Interaction of pathogenic yeasts with phagocytes: survival, persistence and escape, Current Opinion in Microbiology, vol.13, issue.4, pp.392-400, 2010.
DOI : 10.1016/j.mib.2010.05.001

J. Brieland, D. Essig, C. Jackson, D. Frank, and D. Loebenberg, Comparison of Pathogenesis and Host Immune Responses to Candida glabrata and Candida albicans in Systemically Infected Immunocompetent Mice, Infection and Immunity, vol.69, issue.8, pp.5046-5055, 2001.
DOI : 10.1128/IAI.69.8.5046-5055.2001

J. Ju, C. Polhamus, K. Marr, S. Holland, and J. Bennett, Efficacies of Fluconazole, Caspofungin, and Amphotericin B in Candida glabrata-Infected p47phox-/- Knockout Mice, Antimicrobial Agents and Chemotherapy, vol.46, issue.5, pp.1240-1245, 2002.
DOI : 10.1128/AAC.46.5.1240-1245.2002

P. Brockert, S. Lachke, T. Srikantha, C. Pujol, and R. Galask, Phenotypic Switching and Mating Type Switching of Candida glabrata at Sites of Colonization, Infection and Immunity, vol.71, issue.12, pp.7109-7118, 2003.
DOI : 10.1128/IAI.71.12.7109-7118.2003

C. Lin, Y. Chen, H. Lo, K. Chen, and S. Li, Assessment of Candida glabrata Strain Relatedness by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing, Journal of Clinical Microbiology, vol.45, issue.8, pp.2452-2459, 2007.
DOI : 10.1128/JCM.00699-07

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1951215

H. Muller, A. Thierry, J. Coppee, C. Gouyette, and C. Hennequin, Genomic polymorphism in the population of Candida glabrata: Gene copy-number variation and chromosomal translocations, Fungal Genetics and Biology, vol.46, issue.3, pp.264-276, 2009.
DOI : 10.1016/j.fgb.2008.11.006

A. Thierry, C. Bouchier, B. Dujon, and G. Richard, Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata, Nucleic Acids Research, vol.36, issue.18, pp.5970-5982, 2008.
DOI : 10.1093/nar/gkn594

A. Luettich, S. Brunke, B. Hube, and I. Jacobsen, Serial Passaging of Candida albicans in Systemic Murine Infection Suggests That the Wild Type Strain SC5314 Is Well Adapted to the Murine Kidney, PLoS ONE, vol.154, issue.5, 2013.
DOI : 10.1371/journal.pone.0064482.s002

J. Neilson, M. Ivey, and G. Bulmer, Cryptococcus neoformans: pseudohyphal forms surviving culture with Acanthamoeba polyphaga, Infect Immun, vol.20, pp.262-266, 1978.

B. Fries, D. Goldman, R. Cherniak, R. Ju, and A. Casadevall, Phenotypic switching in Cryptococcus neoformans results in changes in cellular morphology and glucuronoxylomannan structure, Infect Immun, vol.67, pp.6076-6083, 1999.

D. Maccallum, H. Findon, C. Kenny, G. Butler, and K. Haynes, Different Consequences of ACE2 and SWI5 Gene Disruptions for Virulence of Pathogenic and Nonpathogenic Yeasts, Infection and Immunity, vol.74, issue.9, pp.5244-5248, 2006.
DOI : 10.1128/IAI.00817-06

O. 'conallain, C. Doolin, M. Taggart, C. Thornton, F. Butler et al., Regulated nuclear localisation of the yeast transcription factor Ace2p controls expression of chitinase (CTS1) in Saccharomyces cerevisiae, Mol Gen Genet, vol.262, pp.275-282, 1999.

P. Dohrmann, G. Butler, K. Tamai, S. Dorland, and J. Greene, Parallel pathways of gene regulation: homologous regulators SWI5 and ACE2 differentially control transcription of HO and chitinase., Genes & Development, vol.6, issue.1, pp.93-104, 1992.
DOI : 10.1101/gad.6.1.93

M. Lorenz, J. Bender, and G. Fink, Transcriptional Response of Candida albicans upon Internalization by Macrophages, Eukaryotic Cell, vol.3, issue.5, pp.1076-1087, 2004.
DOI : 10.1128/EC.3.5.1076-1087.2004

S. Hummert, C. Hummert, A. Schroter, B. Hube, and S. Schuster, Game theoretical modelling of survival strategies of Candida albicans inside macrophages, Journal of Theoretical Biology, vol.264, issue.2, pp.312-318, 2010.
DOI : 10.1016/j.jtbi.2010.01.022

C. Charlier, K. Nielsen, S. Daou, M. Brigitte, and F. Chretien, Evidence of a Role for Monocytes in Dissemination and Brain Invasion by Cryptococcus neoformans, Infection and Immunity, vol.77, issue.1, pp.120-127, 2009.
DOI : 10.1128/IAI.01065-08

C. Maffei, L. Mirels, R. Sobel, K. Clemons, and D. Stevens, Cytokine and Inducible Nitric Oxide Synthase mRNA Expression during Experimental Murine Cryptococcal Meningoencephalitis, Infection and Immunity, vol.72, issue.4, pp.2338-2349, 2004.
DOI : 10.1128/IAI.72.4.2338-2349.2004

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC375146

C. Csank and K. Haynes, displays pseudohyphal growth, FEMS Microbiology Letters, vol.189, issue.1, pp.115-120, 2000.
DOI : 10.1111/j.1574-6968.2000.tb09216.x

P. Vandeputte, G. Tronchin, T. Berges, C. Hennequin, and D. Chabasse, Reduced Susceptibility to Polyenes Associated with a Missense Mutation in the ERG6 Gene in a Clinical Isolate of Candida glabrata with Pseudohyphal Growth, Antimicrobial Agents and Chemotherapy, vol.51, issue.3, pp.982-990, 2007.
DOI : 10.1128/AAC.01510-06

URL : https://hal.archives-ouvertes.fr/hal-00273771

I. Jacobsen, K. Grosse, S. Slesiona, B. Hube, and A. Berndt, Embryonated Eggs as an Alternative Infection Model To Investigate Aspergillus fumigatus Virulence, Infection and Immunity, vol.78, issue.7, pp.2995-3006, 2010.
DOI : 10.1128/IAI.00268-10

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897382

C. Hoffman and F. Winston, A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformaion of Escherichia coli, Gene, vol.57, issue.2-3, pp.267-272, 1987.
DOI : 10.1016/0378-1119(87)90131-4

G. Schönian, O. Meusel, H. Tietz, W. Meyer, and Y. Graser, Identification of clinical strains of Candida albicans by DNA fingerprinting with the polymerase chain reaction, Mycoses, vol.158, issue.Suppl. I, pp.171-179, 1993.
DOI : 10.1111/j.1439-0507.1993.tb00746.x

L. Rosas-hernandez, A. Juarez-reyes, O. Arroyo-helguera, D. Las-penas, A. Pan et al., yKu70/yKu80 and Rif1 Regulate Silencing Differentially at Telomeres in Candida glabrata, Eukaryotic Cell, vol.7, issue.12, pp.2168-2178, 2008.
DOI : 10.1128/EC.00228-08

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593182

J. Sambrook and D. Russell, Molecular Cloning -A Laboratory Manual. Cold Spring Harbor, 2001.

S. Ossowski, K. Schneeberger, R. Clark, C. Lanz, and N. Warthmann, Sequencing of natural strains of Arabidopsis thaliana with short reads, Genome Research, vol.18, issue.12, pp.2024-2033, 2008.
DOI : 10.1101/gr.080200.108