G. D. Brown, D. W. Denning, N. Gow, S. M. Levitz, M. G. Netea et al., Hidden killers: human fungal infections, Sci Transl Med, vol.4, pp.165-178, 2012.

A. Susca, G. Perrone, G. Cozzi, G. Stea, A. F. Logrieco et al., Multilocus sequence analysis of Aspergillus Sect. Nigri in dried vine fruits of worldwide origin, Int J Food Microbiol, vol.165, pp.163-168, 2013.

M. Oliveira, R. Almeida-paes, M. C. Gutierrez-galhardo, and R. M. Zancopé-oliveira, Molecular identification of the Sporothrix schenckii complex, Rev Iberoamer Micol, vol.31, pp.2-6, 2014.

E. Buommino, F. P. Nocera, A. Parisi, A. Rizzo, G. Donnarumma et al., Correlation between genetic variability and virulence factors in clinical strains of Malassezia pachydermatis of animal origin, New Microbiol, vol.39, pp.216-223, 2016.

M. Arabatzis, P. Abel, M. Kanellopoulou, D. Adamou, H. Alexandrouathanasoulis et al., Sequence-based identification, genotyping and EUCAST antifungal susceptibilities of Trichosporon clinical isolates from Greece, Clin Microbiol Infect, vol.20, pp.777-783, 2014.

D. R. Soll, The ins and outs of DNA fingerprinting the infectious fungi, Clin Microbiol Rev, vol.13, pp.332-370, 2000.

M. Diab-elschahawi, C. Forstner, F. Hagen, J. F. Meis, A. M. Lassnig et al., Microsatellite genotyping clarified conspicuous accumulation of Candida parapsilosis at a cardiothoracic surgery intensive care unit, J Clin Microbiol, vol.50, pp.1179-1191, 2012.

D. K. Chang, D. Metzgar, C. Wills, and C. R. Boland, Microsatellites in the eukaryotic DNA mismatch repair genes as modulators of evolutionary mutation rate, Genome Res, vol.11, pp.1145-1146, 2001.

R. Winter, J. Liebold, and E. Schwarz, The unresolved puzzle why alanine extensions cause disease, Biol Chem, vol.394, pp.951-963, 2013.

S. Kruglyak, R. T. Durrett, M. D. Schug, and C. F. Aquadro, Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations, Proc Natl Acad Sci U S A, vol.95, pp.10774-10778, 1998.

A. Grover, V. Aishwarya, and P. C. Sharma, Searching microsatellites in DNA sequences: approaches used and tools developed, Physiol Mol Biol Plants, vol.18, pp.11-19, 2012.

G. Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res, vol.27, pp.573-580, 1999.

W. S. Martins, D. Lucas, K. F. Neves, . De, and S. Bertioli, WebSat-a web software for microsatellite marker development, Bioinformation, vol.3, pp.282-283, 2009.

J. Costa, D. Garcia-hermoso, M. Olivi, O. Cabaret, C. Farrugia et al., Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus, J Microbiol Methods, vol.80, pp.306-309, 2010.

D. Garcia-hermoso, D. Bretagne, and S. , Typing Candida species using microsatellite length polymorphism and multilocus sequence typing, Methods Mol Biol, vol.1356, pp.199-214, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-02194784

J. M. Costa, O. Eloy, F. Botterel, G. Janbon, and S. Bretagne, Use of microsatellite markers and gene dosage to quantify gene copy numbers in Candida albicans, J Clin Microbiol, vol.43, pp.1387-1389, 2005.

H. A. De-valk, J. Meis, and C. Klaassen, Microsatellite based typing of Aspergillus fumigatus: strengths, pitfalls and solutions, J Microbiol Methods, vol.69, pp.268-272, 2007.

D. Garcia-hermoso, D. M. Maccallum, T. J. Lott, P. Sampaio, M. Serna et al., Multicenter collaborative study for standardization of Candida albicans genotyping using a polymorphic microsatellite marker, J Clin Microbiol, vol.48, pp.2578-2581, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00682520

H. A. De-valk, J. Meis, S. Bretagne, J. M. Costa, B. A. Lasker et al., Interlaboratory reproducibility of a microsatellite-based typing assay for Aspergillus fumigatus through the use of allelic ladders: proof of concept, Clin Microbiol Infect, vol.15, pp.180-187, 2009.

R. Urwin and M. Maiden, Multi-locus sequence typing: a tool for global epidemiology, Trends Microbiol, vol.11, pp.479-487, 2003.

A. Alanio, M. Olivi, O. Cabaret, F. Foulet, A. Bellanger et al., Correlation between Pneumocystis jirovecii mitochondrial genotypes and high and low fungal loads assessed by single nucleotide primer extension assay and quantitative real-time PCR, J Eukaryot Microbiol, vol.62, pp.650-656, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01294657

P. R. Hunter, A critical review of typing methods for Candida albicans and their applications, Crit Rev Microbiol, vol.17, pp.417-434, 1991.

C. Klaassen, MLST versus microsatellites for typing Aspergillus fumigatus isolates, Med Mycol, vol.47, issue.1, pp.27-33, 2009.

S. Brisse, C. Pannier, A. Angoulvant, T. De-meeus, L. Diancourt et al., Uneven distribution of mating types among genotypes of Candida glabrata isolates from clinical samples, Eukaryot Cell, vol.8, pp.287-295, 2009.

H. A. De-valk, J. Meis, I. M. Curfs, K. Muehlethaler, J. W. Mouton et al., Use of a novel panel of nine short tandem repeats for exact and high-resolution fingerprinting of Aspergillus fumigatus isolates, J Clin Microbiol, vol.43, pp.4112-4120, 2005.

J. M. Bain, A. Tavanti, A. D. Davidson, M. D. Jacobsen, D. Shaw et al., Multilocus sequence typing of the pathogenic fungus Aspergillus fumigatus, J Clin Microbiol, vol.45, pp.1469-1477, 2007.

D. Garcia-hermoso, O. Cabaret, G. Lecellier, M. Desnos-ollivier, D. Hoinard et al., Comparison of microsatellite length polymorphism and multilocus sequence typing for DNA-based typing of Candida albicans, J Clin Microbiol, vol.45, pp.3958-3963, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00321130

A. Enache-angoulvant, M. Bourget, S. Brisse, C. Stockman-pannier, L. Diancourt et al., Multilocus microsatellite markers for molecular typing of Candida glabrata: application to analysis of genetic relationships between bloodstream and digestive system isolates, J Clin Microbiol, vol.48, pp.4028-4034, 2010.

G. A. Pavlopoulos, T. G. Soldatos, A. Barbosa-silva, and R. Schneider, A reference guide for tree analysis and visualization, BioData Min, vol.3, 2010.

R. Agarwal, A. Chakrabarti, A. Shah, D. Gupta, J. F. Meis et al., Allergic bronchopulmonary aspergillosis: review of literature and proposal of new diagnostic and classification criteria, Clin Exp Allergy, vol.43, pp.850-873, 2013.

D. W. Denning, J. Cadranel, C. Beigelman-aubry, F. Ader, A. Chakrabarti et al., European Society for Clinical Microbiology and Infectious Diseases and European Respiratory Society, Eur Respir J, vol.47, pp.45-68, 2016.

O. Lortholary, J. Gangneux, K. Sitbon, B. Lebeau, F. De-monbrison et al., Epidemiological trends in invasive aspergillosis in France: the SAIF network, vol.17, pp.1882-1889, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00680990

E. Bart-delabesse, J. F. Humbert, E. Delabesse, and S. Bretagne, Microsatellite markers for typing Aspergillus fumigatus isolates, J Clin Microbiol, vol.36, pp.2413-2418, 1998.

E. Bart-delabesse, J. Sarfati, J. P. Debeaupuis, W. Van-leeuwen, A. Van-belkum et al., Comparison of restriction fragment length polymorphism, microsatellite length polymorphism, and random amplification of polymorphic DNA analyses for fingerprinting Aspergillus fumigatus isolates, J Clin Microbiol, vol.39, pp.2683-2686, 2001.

H. A. De-valk, J. Meis, B. E. De-pauw, P. J. Donnelly, and C. Klaassen, Comparison of two highly discriminatory molecular fingerprinting assays for analysis of multiple Aspergillus fumigatus isolates from patients with invasive aspergillosis, J Clin Microbiol, vol.45, pp.1415-1419, 2007.

L. Vanhee, F. Symoens, M. D. Jacobsen, H. J. Nelis, and T. Coenye, Comparison of multiple typing methods for Aspergillus fumigatus, Clin Microbiol Infect, vol.15, pp.643-650, 2009.

C. Klaassen, H. A. De-valk, S. A. Balajee, and J. Meis, Utility of CSP typing to sub-type clinical Aspergillus fumigatus isolates and proposal for a new CSP type nomenclature, J Microbiol Methods, vol.77, pp.292-296, 2009.

S. E. Kidd, N. Zulkepeli, N. Slavin, M. A. Morrissey, and C. O. , Utility of a proposed CSP typing nomenclature for Australian Aspergillus fumigatus isolates: identification of additional CSP types and suggested modifications, J Microbiol Methods, vol.78, pp.223-226, 2009.

S. A. Balajee, S. T. Tay, B. A. Lasker, S. F. Hurst, and A. P. Rooney, Characterization of a novel gene for strain typing reveals substructuring of Aspergillus fumigatus across North America, Eukaryot Cell, vol.6, pp.1392-1399, 2007.

S. F. Hurst, S. E. Kidd, C. O. Morrissey, E. Snelders, W. Melchers et al., Interlaboratory reproducibility of a single-locus sequence-based method for strain typing of Aspergillus fumigatus, J Clin Microbiol, vol.47, pp.1562-1564, 2009.

J. P. Debeaupuis, J. Sarfati, V. Chazalet, and J. P. Latgé, Genetic diversity among clinical and environmental isolates of Aspergillus fumigatus, Infect Immun, vol.65, pp.3080-3085, 1997.

V. Chazalet, J. P. Debeaupuis, J. Sarfati, J. Lortholary, P. Ribaud et al., Molecular typing of environmental and patient isolates of Aspergillus fumigatus from various hospital settings, J Clin Microbiol, vol.36, pp.1494-1500, 1998.

E. Bart-delabesse, C. Cordonnier, and S. Bretagne, Usefulness of genotyping with microsatellite markers to investigate hospital-acquired invasive aspergillosis, J Hosp Infect, vol.42, pp.321-327, 1999.

J. Menotti, J. Waller, O. Meunier, V. Letscher-bru, R. Herbrecht et al., Epidemiological study of invasive pulmonary aspergillosis in a haematology unit by molecular typing of environmental and patient isolates of Aspergillus fumigatus, J Hosp Infect, vol.60, pp.61-68, 2005.

R. Araujo, C. Pina-vaz, A. G. Rodrigues, A. Amorim, and L. Gusmão, Simple and highly discriminatory microsatellite-based multiplex PCR for Aspergillus fumigatus strain typing, Clin Microbiol Infect, vol.15, pp.260-266, 2009.

R. Araujo, A. Amorim, and L. Gusmão, Genetic diversity of Aspergillus fumigatus in indoor hospital environments, Med Mycol, vol.48, pp.832-838, 2010.

L. Van-waeyenberghe, F. Pasmans, L. A. Beernaert, F. Haesebrouck, F. Vercammen et al., Microsatellite typing of avian clinical and environmental isolates of Aspergillus fumigatus, Avian Pathol, vol.40, pp.73-77, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00670235

L. Vanhee, F. Symoens, H. J. Nelis, and T. Coenye, Microsatellite typing of Aspergillus fumigatus isolates recovered from deep organ samples of patients with invasive aspergillosis, Diagn Microbiol Infect Dis, vol.62, pp.96-98, 2008.

S. Alvarez-perez, M. E. Garcia, E. Bouza, T. Peláez, and J. L. Blanco, Characterization of multiple isolates of Aspergillus fumigatus from patients: genotype, mating type and invasiveness, Med Mycol, vol.47, pp.601-608, 2009.

E. Rodriguez, F. Symoens, P. Mondon, M. Mallie, M. A. Piens et al., Combination of three typing methods for the molecular epidemiology of Aspergillus fumigatus infections. European Research Group on Biotype and Genotype of Aspergillus, J Med Microbiol, vol.48, pp.181-194, 1999.

G. Vidal, C. , U. A. Kirby, K. A. Marr, and K. A. , Epidemiology of invasive mold infections in allogeneic stem cell transplant recipients: biological risk factors for infection according to time after transplantation, Clin Infect Dis, vol.47, pp.1041-1050, 2008.

H. A. De-valk, C. Klaassen, J. Yntema, A. Hebestreit, M. Seidler et al., Molecular typing and colonization patterns of Aspergillus fumigatus in patients with cystic fibrosis, J Cyst Fibros, vol.8, pp.110-114, 2009.

L. Vanhee, F. Symoens, J. P. Bouchara, H. J. Nelis, and T. Coenye, Highresolution genotyping of Aspergillus fumigatus isolates recovered from chronically colonised patients with cystic fibrosis, Eur J Clin Microbiol Infect Dis, vol.27, pp.1005-1007, 2008.

K. A. Etienne, C. Subudhi, P. R. Chadwick, P. Settle, M. J. Magill et al., Investigation of a cluster of cutaneous aspergillosis in a neonatal intensive care unit, J Hosp Infect, vol.79, pp.344-348, 2011.

T. Pelaez, P. Munoz, J. Guinea, M. Valerio, M. Giannella et al., Outbreak of invasive aspergillosis after major heart surgery caused by spores in the air of the intensive care unit, Clin Infect Dis, vol.54, pp.24-31, 2012.

S. A. Balajee, H. A. De-valk, B. A. Lasker, J. Meis, and C. Klaassen, Utility of a microsatellite assay for identifying clonally related outbreak isolates of Aspergillus fumigatus, J Microbiol Methods, vol.73, pp.252-256, 2008.

R. Lavergne, T. Chouaki, F. Hagen, B. Toublanc, H. Dupont et al., Home environment as a source of life-threatening azole-resistant Aspergillus fumigatus in immunocompromised patients, Clin Infect Dis, vol.64, pp.76-78, 2017.

J. Chen, H. Li, R. Li, D. Bu, and Z. Wan, Mutations in the cyp51A gene and susceptibility to itraconazole in Aspergillus fumigatus serially isolated from a patient with lung aspergilloma, J Antimicrob Chemother, vol.55, pp.31-37, 2005.

B. Bellete, H. Raberin, J. Morel, P. Flori, J. Hafid et al., Acquired resistance to voriconazole and itraconazole in a patient with pulmonary aspergilloma, Med Mycol, vol.48, pp.197-200, 2010.

M. C. Arendrup, E. Mavridou, K. L. Mortensen, E. Snelders, N. Frimodt-møller et al., Development of azole resistance in Aspergillus fumigatus during azole therapy associated with change in virulence, PLoS One, vol.5, 2010.

S. Camps, J. Van-der-linden, Y. Li, E. J. Kuijper, J. T. Van-dissel et al., Rapid induction of multiple resistance mechanisms in Aspergillus fumigatus during azole therapy: a case study and review of the literature, Antimicrob Agents Chemother, vol.56, pp.10-16, 2012.

A. Alanio, O. Cabaret, E. Sitterlé, J. Costa, S. Brisse et al., Azole preexposure affects the Aspergillus fumigatus population in patients, Antimicrob Agents Chemother, vol.56, pp.4948-4950, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01405250

E. Snelders, H. Van-der-lee, J. Kuijpers, A. Rijs, J. Varga et al., Emergence of azole resistance in Aspergillus fumigatus and spread of a single resistance mechanism, Plos Med, vol.5, p.219, 2008.

E. Snelders, H. In-'t-veld, R. A. Rijs, A. J. Kema, G. H. Melchers et al., Possible environmental origin of resistance of Aspergillus fumigatus to medical triazoles, Appl Environ Microbiol, vol.75, pp.4053-4057, 2009.

P. E. Verweij, A. Chowdhary, W. Melchers, and J. F. Meis, Azole resistance in Aspergillus fumigatus: can we retain the clinical use of mold-active antifungal azoles?, Clin Infect Dis, vol.62, pp.362-368, 2016.

S. Camps, A. Rijs, C. Klaassen, J. F. Meis, C. M. O'gorman et al., Molecular epidemiology of Aspergillus fumigatus isolates harboring the TR34/L98H azole resistance mechanism, J Clin Microbiol, vol.50, pp.335-347, 2012.

J. Van-der-linden, S. Camps, G. A. Kampinga, J. Arends, Y. J. Debetsossenkopp et al., Aspergillosis due to voriconazole highly resistant Aspergillus fumigatus and recovery of genetically related resistant isolates from domiciles, Clin Infect Dis, vol.57, pp.513-520, 2013.

J. Steinmann, A. Hamprecht, M. Vehreschild, O. A. Cornely, D. Buchheidt et al., Emergence of azole-resistant invasive aspergillosis in HSCT recipients in Germany, J Antimicrob Chemother, vol.70, pp.1522-1526, 2015.

C. Klaassen, J. G. Gibbons, N. D. Fedorova, J. F. Meis, and A. Rokas, Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus, Mol Ecol, vol.21, pp.57-70, 2012.

A. Alanio, B. Denis, S. Hamane, E. Raffoux, P. De-la-tour et al., New therapeutic strategies for invasive aspergillosis in the era of azole resistance: how should the prevalence of azole resistance be defined?, J Antimicrob Chemother, vol.71, pp.2075-2078, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01405215

P. E. Verweij, P. Lestrade, W. Melchers, and J. F. Meis, Azole resistance surveillance in Aspergillus fumigatus: beneficial or biased?, J Antimicrob Chemother, vol.71, pp.2079-2082, 2016.

I. Hadrich, F. Makni, S. Neji, F. Cheikhrouhou, H. Sellami et al., A review molecular typing methods for Aspergillus flavus isolates, vol.172, pp.83-93, 2011.

G. Chamilos, M. Luna, R. E. Lewis, G. P. Bodey, R. Chemaly et al., Invasive fungal infections in patients with hematologic malignancies in a tertiary care cancer center: an autopsy study over a 15-year period, J Antimicrob Chemother, vol.91, pp.986-989, 1989.

L. Pagano, M. Caira, A. Nosari, M. T. Van-lint, A. Candoni et al., Fungal infections in recipients of hematopoietic stem cell transplants: results of the SEIFEM B-2004 studySorveglianza Epidemiologica Infezioni Fungine Nelle Emopatie Maligne, Clin Infect Dis, vol.45, pp.1161-1170, 2007.

T. M. Diaz-guerra, E. Mellado, M. Cuenca-estrella, L. Gaztelurrutia, J. I. Navarro et al., Genetic similarity among one Aspergillus flavus strain isolated from a patient who underwent heart surgery and two environmental strains obtained from the operating room, J Clin Microbiol, vol.38, pp.2419-2422, 2000.

Y. Myoken, T. Sugata, Y. Fujita, T. Kyo, M. Fujihara et al., Molecular epidemiology of invasive stomatitis due to Aspergillus flavus in patients with acute leukemia, J Oral Pathol Med, vol.32, pp.215-218, 2003.

M. J. James, B. A. Lasker, M. M. Mcneil, M. Shelton, D. W. Warnock et al., Use of a repetitive DNA probe to type clinical and environmental isolates of Aspergillus flavus from a cluster of cutaneous infections in a neonatal intensive care unit, J Clin Microbiol, vol.38, pp.3612-3618, 2000.

N. Tran-dinh and D. Carter, Characterization of microsatellite loci in the aflatoxigenic fungi Aspergillus flavus and Aspergillus parasiticus, Mol Ecol, vol.9, pp.2170-2172, 2000.

I. Hadrich, F. Makni, A. Ayadi, and S. Ranque, Microsatellite typing to trace Aspergillus flavus infections in a hematology unit, J Clin Microbiol, vol.48, pp.2396-2401, 2010.

S. Gheith, F. Saghrouni, A. Normand, W. Bannour, A. Khelif et al., Microsatellite typing of Aspergillus flavus strains in a Tunisian onco-hematology unit, Mycopathologia, vol.181, pp.175-184, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01459559

S. M. Rudramurthy, H. A. De-valk, A. Chakrabarti, J. Meis, and C. Klaassen, High resolution genotyping of clinical Aspergillus flavus isolates from India using microsatellites, PLoS One, vol.6, p.16086, 2011.

I. Hadrich, S. Neji, I. Drira, H. Trabelsi, N. Mahfoud et al., Microsatellite typing of Aspergillus flavus in patients with various clinical presentations of aspergillosis, Med Mycol, vol.51, pp.586-591, 2013.

I. Hadrich, I. Drira, S. Neji, N. Mahfoud, S. Ranque et al., Microsatellite typing of Aspergillus flavus from clinical and environmental avian isolates, J Med Microbiol, vol.62, pp.121-125, 2013.

I. Hadrich, I. Amouri, S. Neji, N. Mahfoud, S. Ranque et al., Genetic structure of Aspergillus flavus populations in human and Typing Fungi of Medical Importance Clinical Microbiology Reviews avian isolates, Eur J Clin Microbiol Infect Dis, vol.32, pp.277-282, 2013.

C. Lass-flörl, G. K. Mayr, A. Petzer, A. Gastl, G. Bonatti et al., Epidemiology and outcome of infections due to Aspergillus terreus: 10-year single centre experience, Br J Haematol, vol.131, pp.201-207, 2005.

W. J. Steinbach, D. K. Benjamin, D. P. Kontoyiannis, J. R. Perfect, I. Lutsar et al., Infections due to Aspergillus terreus: a multicenter retrospective analysis of 83 cases, Clin Infect Dis, vol.39, pp.192-198, 2004.

P. G. Pappas, B. D. Alexander, D. R. Andes, S. Hadley, C. A. Kauffman et al., Invasive fungal infections among organ transplant recipients: results of the Transplant-Associated Infection Surveillance Network (TRANSNET), Clin Infect Dis, vol.50, pp.1101-1111, 2010.

S. A. Balajee, R. Kano, J. W. Baddley, S. A. Moser, K. A. Marr et al., Molecular identification of Aspergillus species collected for the Transplant-Associated Infection Surveillance Network, J Clin Microbiol, vol.47, pp.3138-3141, 2009.

A. Rougeron, S. Giraud, B. Razafimandimby, J. F. Meis, and J. P. Bouchara, Different colonization patterns of Aspergillus terreus in patients with cystic fibrosis, Clin Microbiol Infect, vol.20, pp.327-333, 2014.

P. M. Rath, S. Kamphoff, and R. Ansorg, Value of different methods for the characterisation of Aspergillus terreus strains, J Med Microbiol, vol.48, pp.161-166, 1999.

F. Symoens, J. P. Bouchara, S. Heinemann, and N. Nolard, Molecular typing of Aspergillus terreus isolates by random amplification of polymorphic DNA, J Hosp Infect, vol.44, pp.273-280, 2000.

C. Lass-florl, P. Rath, D. Niederwieser, G. Kofler, R. Würzner et al., Aspergillus terreus infections in haematological malignancies: molecular epidemiology suggests association with inhospital plants, J Hosp Infect, vol.46, pp.31-35, 2000.

C. Neal, A. O. Richardson, S. F. Hurst, A. M. Tortorano, M. A. Viviani et al., Global population structure of Aspergillus terreus inferred by ISSR typing reveals geographical subclustering, BMC Microbiol, vol.11, p.203, 2011.

M. Lackner, S. Coassin, M. Haun, U. Binder, F. Kronenberg et al., Geographically predominant genotypes of Aspergillus terreus species complex in Austria: a microsatellite typing study, Clin Microbiol Infect, vol.22, pp.270-276, 2016.

S. Kathuria, C. Sharma, P. K. Singh, P. Agarwal, K. Agarwal et al., Molecular epidemiology and in-vitro antifungal susceptibility of Aspergillus terreus species complex isolates in Delhi, India: evidence of genetic diversity by amplified fragment length polymorphism and microsatellite typing, PLoS One, vol.10, 2015.

K. O'donnell, A. P. Rooney, R. H. Proctor, D. W. Brown, S. P. Mccormick et al., Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria, Fungal Genet Biol, vol.52, pp.20-31, 2013.

N. S. Chandra, E. G. Wulff, A. C. Udayashankar, B. P. Nandini, S. R. Niranjana et al., Prospects of molecular markers in Fusarium species diversity, Appl Microbiol Biotechnol, vol.90, pp.1625-1639, 2011.

D. C. Chang, G. B. Grant, O. Donnell, K. Wannemuehler, K. A. Noble-wang et al., Fusarium Keratitis Investigation Team. 2006. Multistate outbreak of Fusarium keratitis associated with use of a contact lens solution, JAMA, vol.296, pp.953-963

K. O'donnell, D. A. Sutton, A. Fothergill, D. Mccarthy, M. G. Rinaldi et al., Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex, J Clin Microbiol, vol.46, pp.2477-2490, 2008.

K. O'donnell, D. A. Sutton, M. G. Rinaldi, C. Gueidan, P. W. Crous et al., Novel multilocus sequence typing scheme reveals high genetic diversity of human pathogenic members of the Fusarium incarnatum-F. equiseti and F. chlamydosporum species complexes within the United States, J Clin Microbiol, vol.47, pp.3851-3861, 2009.

K. O'donnell, D. A. Sutton, M. G. Rinaldi, B. Sarver, S. A. Balajee et al., Internet-accessible DNA sequence database for identifying fusaria from human and animal infections, J Clin Microbiol, vol.48, pp.3708-3718, 2010.

D. Short, K. O'donnell, U. Thrane, K. F. Nielsen, N. Zhang et al., Phylogenetic relationships among members of the Fusarium solani species complex in human infections and the descriptions of F. keratoplasticum sp. nov. and F. petroliphilum stat. nov, Fungal Genet Biol, vol.53, pp.59-70, 2013.

K. O'donnell, B. Sarver, M. Brandt, D. C. Chang, J. Noble-wang et al., Phylogenetic diversity and microsphere array-based genotyping of human pathogenic Fusaria, including isolates from the multistate contact lens-associated U.S. keratitis outbreaks of 2005 and, J Clin Microbiol, vol.45, pp.2235-2248, 2006.

R. Jureen, T. H. Koh, G. Wang, L. Chai, A. L. Tan et al., Use of multiple methods for genotyping Fusarium during an outbreak of contact lens associated fungal keratitis in Singapore, BMC Infect Dis, vol.8, p.92, 2008.

C. M. Scheel, S. F. Hurst, G. Barreiros, T. Akiti, M. Nucci et al., Molecular analyses of Fusarium isolates recovered from a cluster of invasive mold infections in a Brazilian hospital, BMC Infect Dis, vol.13, p.49, 2013.

D. P. Short, K. O'donnell, N. Zhang, J. H. Juba, and D. M. Geiser, Widespread occurrence of diverse human pathogenic types of the fungus Fusarium detected in plumbing drains, J Clin Microbiol, vol.49, pp.4264-4272, 2011.

M. Bogale, B. D. Wingfield, M. J. Wingfield, and E. T. Steenkamp, Simple sequence repeat markers for species in the Fusarium oxysporum complex, Mol Ecol Notes, vol.5, pp.622-624, 2005.

K. Y. Leyva-madrigal, C. P. Larralde-corona, C. L. Calderon-vazquez, and I. E. Maldonado-mendoza, Genome distribution and validation of novel microsatellite markers of Fusarium verticillioides and their transferability to other Fusarium species, J Microbiol Methods, vol.101, pp.18-23, 2014.

J. E. Demers and M. D. Jimenez-gasco, Evolution of nine microsatellite loci in the fungus Fusarium oxysporum, J Mol Evol, vol.82, pp.27-37, 2015.

M. Lackner, F. Hagen, J. F. Meis, G. Van-den-ende, A. Vu et al., Susceptibility and diversity in the therapy-refractory genus Scedosporium, Antimicrob Agents Chemother, vol.58, pp.5877-5885, 2014.

K. J. Cortez, E. Roilides, F. Quiroz-telles, J. Meletiadis, C. Antachopoulos et al., Infections caused by Scedosporium spp, Clin Microbiol Rev, vol.21, pp.157-197, 2008.

A. Harun, H. Perdomo, F. Gilgado, S. Chen, J. Cano et al., Genotyping of Scedosporium species: a review of molecular approaches, Med Mycol, vol.47, pp.406-414, 2009.

A. Bernhardt, L. Sedlacek, S. Wagner, C. Schwarz, B. Würstl et al., Multilocus sequence typing of Scedosporium apiospermum and Pseudallescheria boydii isolates from cystic fibrosis patients, J Cyst Fibros, vol.12, pp.592-598, 2013.

A. Defontaine, R. Zouhair, B. Cimon, J. Carrère, E. Bailly et al., Genotyping study of Scedosporium apiospermum isolates from patients with cystic fibrosis, J Clin Microbiol, vol.40, pp.2108-2114, 2002.

R. Zouhair, A. Defontaine, C. Ollivier, B. Cimon, F. Symoens et al., Typing of Scedosporium apiospermum by multilocus enzyme electrophoresis and random amplification of polymorphic DNA, J Med Microbiol, vol.50, pp.925-932, 2001.

L. Delhaes, A. Harun, S. Chen, Q. Nguyen, M. Slavin et al., Molecular typing of Australian Scedosporium isolates showing genetic variability and numerous S. aurantiacum, Emerg Infect Dis, vol.14, pp.282-290, 2008.

A. Harun, C. Serena, F. Gilgado, C. Sca, and W. Meyer, Scedosporium aurantiacum is as virulent as S. prolificans, and shows strain-specific virulence differences, in a mouse model, Med Mycol, vol.48, issue.1, pp.45-51, 2010.

M. Lackner, A. Rezusta, M. C. Villuendas, M. P. Palacian, J. F. Meis et al., Infection and colonisation due to Scedosporium in northern Spain. An in vitro antifungal susceptibility and molecular epidemiology study of 60 isolates, Mycoses, vol.54, issue.3, pp.12-21, 2011.

M. Solé, J. Cano, J. L. Rodriguez-tudela, J. Pontòn, D. A. Sutton et al., Molecular typing of clinical and environmental isolates of Scedosporium prolificans by inter-simplesequence-repeat polymerase chain reaction, Med Mycol, vol.41, pp.293-300, 2003.

A. Tavanti, N. A. Gow, M. C. Maiden, F. C. Odds, and D. J. Shaw, Genetic evidence for recombination in Candida albicans based on haplotype analysis, Fungal Genet Biol, vol.41, pp.553-562, 2004.

H. Chibana, J. L. Beckerman, and P. T. Magee, Fine-resolution physical mapping of genomic diversity in Candida albicans, Genome Res, vol.10, pp.1865-1877, 2000.

A. Selmecki, A. Forche, and J. Berman, Genomic plasticity of the human fungal pathogen Candida albicans, Eukaryot Cell, vol.9, pp.991-1008, 2010.

S. R. Lockhart, J. J. Fritch, A. S. Meier, K. Schroppel, T. Srikantha et al., Colonizing populations of Candida albicans are clonal in origin but undergo microevolution through C1 fragment reorganization as demonstrated by DNA fingerprinting and C1 sequencing, J Clin Microbiol, vol.33, pp.1501-1509, 1995.

M. E. Bougnoux, D. Diogo, N. François, B. Sendid, S. Veirmeire et al., Multilocus sequence typing reveals intrafamilial transmission and microevolutions of Candida albicans isolates from the human digestive tract, J Clin Microbiol, vol.44, pp.1810-1820, 2006.

F. C. Odds, A. D. Davidson, M. D. Jacobsen, A. Tavanti, J. A. Whyte et al., Candida albicans strain maintenance, replacement, and microvariation demonstrated by multilocus sequence typing, J Clin Microbiol, vol.44, pp.3647-3658, 2006.

C. Pujol, S. Joly, B. Nolan, T. Srikantha, and D. R. Soll, Microevolutionary changes in Candida albicans identified by the complex Ca3 fingerprinting probe involve insertions and deletions of the full-length repetitive sequence RPS at specific genomic sites, Microbiology, vol.145, pp.2635-2646, 1999.

F. Saghrouni, B. Abdeljelil, J. Boukadida, J. , B. Said et al., Molecular methods for strain typing of Candida albicans: a review, J Appl Microbiol, vol.114, pp.1559-1574, 2013.

B. A. Mcmanus and D. C. Coleman, Molecular epidemiology, phylogeny and evolution of Candida albicans, Infect Genet Evol, vol.21, pp.166-178, 2014.

S. Bretagne, J. M. Costa, C. Besmond, R. Carsique, and R. Calderone, Microsatellite polymorphism in the promoter sequence of the elongation factor 3 gene of Candida albicans as the basis for a typing system, J Clin Microbiol, vol.35, pp.1777-1780, 1997.

F. Botterel, C. Desterke, C. Costa, and S. Bretagne, Analysis of microsatellite markers of Candida albicans used for rapid typing, J Clin Microbiol, vol.39, pp.4076-4081, 2001.

P. Sampaio, L. Gusmão, C. Alves, C. Pina-vaz, A. Amorim et al., Highly polymorphic microsatellite for identification of Candida albicans strains, J Clin Microbiol, vol.41, pp.552-557, 2003.

P. Sampaio, L. Gusmão, A. Correia, C. Alves, A. G. Rodrigues et al., New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes, J Clin Microbiol, vol.43, pp.3869-3876, 2005.

F. Dalle, N. Franco, J. Lopez, O. Vagner, D. Caillot et al., Comparative genotyping of Candida albicans bloodstream and nonbloodstream isolates at a polymorphic microsatellite locus, J Clin Microbiol, vol.38, pp.4554-4559, 2000.

F. Dalle, L. Dumont, N. Franco, D. Mesmacque, D. Caillot et al., Genotyping of Candida albicans oral strains from healthy individuals by polymorphic microsatellite locus analysis, J Clin Microbiol, vol.41, pp.2203-2205, 2003.

F. Dalle, I. Lafon, L. 'ollivier, C. Ferrant, E. Sicard et al., A prospective analysis of the genotypic diversity and dynamics of the Candida albicans colonizing flora in neutropenic patients with de novo acute leukemia, J Antimicrob Chemother, vol.93, pp.581-587, 2008.

M. E. Bougnoux, A. Tavanti, C. Bouchier, N. A. Gow, A. Magnier et al., Collaborative consensus for optimized multilocus sequence typing of Candida albicans, J Clin Microbiol, vol.41, pp.5265-5266, 2003.

M. E. Bougnoux, S. Morand, and C. D'enfert, Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans, J Clin Microbiol, vol.40, pp.1290-1297, 2002.

A. Tavanti, N. A. Gow, S. Senesi, M. C. Maiden, and F. C. Odds, Optimization and validation of multilocus sequence typing for Candida albicans, J Clin Microbiol, vol.41, pp.3765-3776, 2003.

T. J. Lott and R. T. Scarborough, Development of a MLST-biased SNP microarray for Candida albicans, Fungal Genet Biol, vol.45, pp.803-811, 2008.

A. Tavanti, A. Lupetti, E. Ghelardi, V. Corsini, P. Davini et al., Molecular monitoring of Candida albicans infections in liver transplant recipients, Eur J Clin Microbiol Infect Dis, vol.20, pp.544-553, 2001.

F. Stephan, M. S. Bah, C. Desterke, S. Rezaiguia-delclaux, F. Foulet et al., Molecular diversity and routes of colonization of Candida albicans in a surgical intensive care unit, as studied using microsatellite markers, Clin Infect Dis, vol.35, pp.1477-1483, 2002.

O. Eloy, S. Marque, F. Botterel, F. Stephan, J. M. Costa et al., Uniform distribution of three Candida albicans microsatellite markers in two French ICU populations supports a lack of nosocomial cross-contamination, BMC Infect Dis, vol.6, p.162, 2006.

S. Beretta, J. P. Fulgencio, A. Enache-angoulvant, C. Bernard, M. El et al., Application of microsatellite typing for the investigation of a cluster of cases of Candida albicans candidaemia, Clin Microbiol Infect, vol.12, pp.674-676, 2006.

A. W. Al-aidan, W. Goessens, N. Lemmens-den-toom, A. , M. Van-belkum et al., Microevolution in genomic short sequence repeats of Candida albicans in non-neutropenic patients, Yeast, vol.24, pp.155-160, 2007.

M. Bougnoux, G. Kac, P. Aegerter, C. Enfert, and J. Fagon, Candidemia and candiduria in critically ill patients admitted to intensive care units in France: incidence, molecular diversity, management and outcome, Intensive Care Med, vol.34, pp.292-299, 2008.

P. R. Cliff, J. A. Sandoe, J. Heritage, and R. C. Barton, Use of multilocus sequence typing for the investigation of colonisation by Candida albicans in intensive care unit patients, J Hosp Infect, vol.69, pp.24-32, 2008.

E. S. Song, J. H. Shin, H. C. Jang, M. J. Choi, S. H. Kim et al., Multilocus sequence typing for the analysis of clonality among Candida albicans strains from a neonatal intensive care unit, Med Mycol, vol.52, pp.653-658, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01522528

K. Wu, T. Luo, L. Li, Q. Zhang, J. Zhu et al., Multilocus sequence typing of pathogenic Candida albicans isolates collected from a teaching hospital in Shanghai, China: a molecular epidemiology study, PLoS One, vol.10, 2015.

L. Albano, S. Bretagne, M. Mamzer-bruneel, I. Kacso, M. Desnos-ollivier et al., Evidence that graft-site candidiasis after kidney transplantation is acquired during organ recovery: a multicenter Typing Fungi of Medical Importance Clinical Microbiology Reviews study in France, Clin Infect Dis, vol.48, pp.194-202, 2009.

D. A. Da-matta, A. S. Melo, T. Guimaraes, J. P. Frade, T. J. Lott et al., Multilocus sequence typing of sequential Candida albicans isolates from patients with persistent or recurrent fungemia, Med Mycol, vol.48, pp.757-762, 2010.

M. D. Jacobsen, A. D. Duncan, J. Bain, E. M. Johnson, J. R. Naglik et al., Mixed Candida albicans strain populations in colonized and infected mucosal tissues, FEMS Yeast Res, vol.8, pp.1334-1338, 2008.

J. H. Shin, M. E. Bougnoux, D. 'enfert, C. Kim, S. H. Moon et al., Genetic diversity among Korean Candida albicans bloodstream isolates: assessment by multilocus sequence typing and restriction endonuclease analysis of genomic DNA by use of BssHII, J Clin Microbiol, vol.49, pp.2572-2577, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01524601

B. A. Mcmanus, E. Mcgovern, G. P. Moran, C. M. Healy, J. Nunn et al., Microbiological screening of Irish patients with autoimmune polyendocrinopathy-candidiasisectodermal dystrophy reveals persistence of Candida albicans strains, gradual reduction in susceptibility to azoles, and incidences of clinical signs of oral candidiasis without culture evidence, J Clin Microbiol, vol.49, pp.1879-1889, 2011.

M. Baixench, N. Aoun, M. Desnos-ollivier, D. Garcia-hermoso, S. Bretagne et al., Acquired resistance to echinocandins in Candida albicans: case report and review, J Antimicrob Chemother, vol.59, pp.1076-1083, 2007.

F. C. Odds, Molecular phylogenetics and epidemiology of Candida albicans, Future Microbiol, vol.5, pp.67-79, 2010.

F. C. Odds, M. Bougnoux, D. J. Shaw, J. M. Bain, A. D. Davidson et al., Molecular phylogenetics of Candida albicans, Eukaryot Cell, vol.6, pp.1041-1052, 2007.

C. L'ollivier, C. Labruère, A. Jebrane, M. Bougnoux, C. Enfert et al., Using a multi-locus microsatellite typing method improved phylogenetic distribution of Candida albicans isolates but failed to demonstrate association of some genotype with the commensal or clinical origin of the isolates, Infect Genet Evol, vol.12, pp.1949-1957, 2012.

D. J. Sullivan, G. P. Moran, and D. C. Coleman, Candida dubliniensis: ten years on, FEMS Microbiol Lett, vol.253, pp.9-17, 2005.

B. A. Mcmanus, D. C. Coleman, G. Moran, E. Pinjon, D. Diogo et al., Multilocus sequence typing reveals that the population structure of Candida dubliniensis is significantly less divergent than that of Candida albicans, J Clin Microbiol, vol.46, pp.652-664, 2008.

M. A. Nunn, S. M. Schaefer, M. A. Petrou, and J. R. Brown, Environmental source of Candida dubliniensis, Emerg Infect Dis, vol.13, pp.747-750, 2007.

B. A. Mcmanus, D. J. Sullivan, G. P. Moran, D. 'enfert, C. Bougnoux et al., Genetic differences between avian and human isolates of Candida dubliniensis, Emerg Infect Dis, vol.15, pp.1467-1470, 2009.
URL : https://hal.archives-ouvertes.fr/pasteur-01525025

C. P. Kurtzman, J. W. Fell, and T. Boekhout, The yeasts, a taxonomic study, 2011.

M. A. Pfaller, L. Boyken, R. J. Hollis, J. Kroeger, S. A. Messer et al., Wild-type MIC distributions and epidemiological cutoff values for the echinocandins and Candida spp, J Clin Microbiol, vol.48, pp.52-56, 2010.

M. A. Pfaller, D. J. Diekema, D. L. Gibbs, V. A. Newell, J. F. Meis et al., Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2005: an 8.5-year analysis of susceptibilities of Candida species and other yeast species to fluconazole and voriconazole determined by CLSI standardized disk diffusion testing, J Clin Microbiol, vol.45, pp.1735-1745, 2007.

M. A. Pfaller, D. J. Diekema, R. N. Jones, S. A. Messer, R. J. Hollis et al., Trends in antifungal susceptibility of Candida spp. isolated from pediatric and adult patients with bloodstream infections: SENTRY Antimicrobial Surveillance Program, J Clin Microbiol, vol.40, pp.852-856, 1997.

O. Lortholary, M. Desnos-ollivier, K. Sitbon, A. Fontanet, S. Bretagne et al., Recent exposure to caspofungin or fluconazole influences the epidemiology of candidemia: a prospective multicenter study involving 2,441 patients, Antimicrob Agents Chemother, vol.55, pp.532-538, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00818523

O. Lortholary, C. Renaudat, K. Sitbon, Y. Madec, L. Denoeud-ndam et al., Worrisome trends in incidence and mortality of candidemia in intensive care units, Intensive Care Med, vol.40, pp.1303-1312, 2002.
URL : https://hal.archives-ouvertes.fr/pasteur-01405246

T. De-meeus, F. Renaud, E. Mouveroux, J. Reynes, G. Galeazzi et al., Genetic structure of Candida glabrata populations in AIDS and non-AIDS patients, J Clin Microbiol, vol.40, pp.2199-2206, 2002.

A. R. Dodgson, C. Pujol, M. A. Pfaller, D. W. Denning, and D. R. Soll, Evidence for recombination in Candida glabrata, Fungal Genet Biol, vol.42, pp.233-243, 2005.

B. P. Cormack and S. Falkow, Efficient homologous and illegitimate recombination in the opportunistic yeast pathogen Candida glabrata, Genetics, vol.151, pp.979-987, 1999.

A. R. Dodgson, C. Pujol, D. W. Denning, D. R. Soll, and A. J. Fox, Multilocus sequence typing of Candida glabrata reveals geographically enriched clades, J Clin Microbiol, vol.41, pp.5709-5717, 2003.

T. J. Lott, J. P. Frade, and S. R. Lockhart, Multilocus sequence type analysis reveals both clonality and recombination in populations of Candida glabrata bloodstream isolates from U.S. surveillance studies, Eukaryot Cell, vol.9, pp.619-625, 2010.

T. J. Lott, J. P. Frade, G. M. Lyon, N. Iqbal, and S. R. Lockhart, Bloodstream and non-invasive isolates of Candida glabrata have similar population structures and fluconazole susceptibilities, Med Mycol, vol.50, pp.136-142, 2012.

F. Foulet, N. Nicolas, O. Eloy, F. Botterel, J. C. Gantier et al., Microsatellite marker analysis as a typing system for Candida glabrata, J Clin Microbiol, vol.43, pp.4574-4579, 2005.

F. Grenouillet, L. Millon, J. M. Bart, S. Roussel, I. Biot et al., Multiple-locus variable-number tandem-repeat analysis for rapid typing of Candida glabrata, J Clin Microbiol, vol.45, pp.3781-3784, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00341434

S. Abbes, H. Sellami, A. Sellami, F. Makni, N. Mahfoudh et al., Microsatellite analysis and susceptibility to FCZ of Candida glabrata invasive isolates in Sfax Hospital, Tunisia. Med Mycol, vol.49, pp.10-15, 2011.

S. Abbes, H. Sellami, A. Sellami, I. Hadrich, I. Amouri et al., Candida glabrata strain relatedness by new microsatellite markers, Eur J Clin Microbiol Infect Dis, vol.31, pp.83-91, 2012.

S. R. Lockhart, S. Joly, C. Pujol, J. D. Sobel, M. A. Pfaller et al., Development and verification of fingerprinting probes for Candida glabrata, Microbiology, vol.143, pp.3733-3746, 1997.

S. Katiyar, E. Shiffrin, C. Shelton, K. Healey, J. Vermitsky et al., Evaluation of polymorphic locus sequence typing for Candida glabrata epidemiology, J Clin Microbiol, vol.54, pp.1042-1050, 2016.

S. Delliere, K. Healey, M. Gits-muselli, B. Carrara, A. Barbaro et al., Fluconazole and echinocandin resistance of Candida glabrata correlates better with antifungal drug exposure rather than with MSH2 mutator genotype in a french cohort of patients harboring low rates of resistance, Front Microbiol, vol.7, 2016.

K. R. Healey, Y. Zhao, W. B. Perez, S. R. Lockhart, J. D. Sobel et al., Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance, Nat Commun, vol.7, 2016.

M. H. Al-yasiri, N. , L. 'ollivier, C. Lachaud, L. Bourgeois et al., Opportunistic fungal pathogen Candida glabrata circulates between humans and yellow-legged gulls, Sci Rep, vol.6, p.36157, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01455795

O. Leroy, J. Gangneux, P. Montravers, J. P. Mira, F. Gouin et al., Epidemiology, management, and risk factors for death of invasive Candida infections in critical care: a multicenter, prospective, observational study in France, Crit Care Med, vol.37, pp.1612-1618, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00676899

D. L. Horn, D. Neofytos, E. J. Anaissie, J. A. Fishman, W. J. Steinbach et al., Epidemiology and outcomes of candidemia in 2019 patients: data from the prospective antifungal therapy alliance registry, Clin Infect Dis, vol.48, pp.1695-1703, 2009.

A. Chakrabarti, S. S. Chatterjee, K. L. Rao, M. M. Zameer, M. R. Shivaprakash et al., Recent experience with fungaemia: change in species distribution and azole resistance, Scand J Infect Dis, vol.41, pp.275-284, 2009.

S. E. Massey, G. Moura, P. Beltrao, R. Almeida, J. R. Garey et al., Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp, Genome Res, vol.13, pp.544-557, 2003.

G. Butler, M. D. Rasmussen, M. F. Lin, M. A. Santos, S. Sakthikumar et al., Evolution of pathogenicity and sexual reproduction in eight Candida genomes, Nature, vol.459, pp.657-662, 2009.

B. N. Doebbeling, R. J. Hollis, H. D. Isenberg, R. P. Wenzel, and M. A. Pfaller, Restriction fragment analysis of a Candida tropicalis outbreak of sternal wound infections, J Clin Microbiol, vol.29, pp.1268-1270, 1991.

B. N. Doebbeling, P. F. Lehmann, R. J. Hollis, L. C. Wu, A. F. Widmer et al., Comparison of pulsed-field gel electrophoresis with isoenzyme profiles as a typing system for Candida tropicalis, Clin Infect Dis, vol.16, pp.377-383, 1993.

K. W. Chen, Y. C. Chen, Y. H. Lin, H. H. Chou, and S. Y. Li, The molecular epidemiology of serial Candida tropicalis isolates from ICU patients as revealed by multilocus sequence typing and pulsed-field gel electrophoresis, Infect Genet Evol, vol.9, pp.912-920, 2009.

J. Zhang, R. J. Hollis, and M. A. Pfaller, Variations in DNA subtype and antifungal susceptibility among clinical isolates of Candida tropicalis, Diagn Microbiol Infect Dis, vol.27, issue.97, pp.2-3, 1997.

A. Chowdhary, K. Becker, W. Fegeler, H. C. Gugnani, L. Kapoor et al., An outbreak of candidemia due to Candida tropicalis in a neonatal intensive care unit, Mycoses, vol.46, pp.287-292, 2003.

A. Tavanti, A. D. Davidson, E. M. Johnson, M. C. Maiden, D. J. Shaw et al., Multilocus sequence typing for differentiation of strains of Candida tropicalis, J Clin Microbiol, vol.43, pp.5593-5600, 2005.

M. D. Jacobsen, A. D. Davidson, S. Y. Li, D. J. Shaw, N. A. Gow et al., Molecular phylogenetic analysis of Candida tropicalis isolates by multilocus sequence typing, Fungal Genet Biol, vol.45, pp.1040-1042, 2008.

M. M. Magri, M. S. Gomes-gouvea, V. L. De-freitas, A. L. Motta, M. L. Moretti et al., Multilocus sequence typing of Candida tropicalis shows the presence of different clonal clusters and fluconazole susceptibility profiles in sequential isolates from candidemia patients in Sao Paulo, Brazil, J Clin Microbiol, vol.51, pp.268-277, 2013.

M. Desnos-ollivier, S. Bretagne, C. Bernede, V. Robert, D. Raoux et al., Clonal population of flucytosine-resistant Candida tropicalis from blood cultures, Emerg Infect Dis, vol.14, pp.557-565, 2008.

H. H. Chou, H. J. Lo, K. W. Chen, M. H. Liao, and S. Y. Li, Multilocus sequence typing of Candida tropicalis shows clonal cluster enriched in isolates with resistance or trailing growth of fluconazole, Diagn Microbiol Infect Dis, vol.58, pp.427-433, 2007.

R. N. Seervai, S. Jones, M. P. Hirakawa, A. M. Porman, and R. J. Bennett, Parasexuality and ploidy change in Candida tropicalis, Eukaryot Cell, vol.12, pp.1629-1640, 2013.

F. Botterel, F. Foulet, P. Legrand, A. M. Soria, C. Farrugia et al., Yeast contamination of kidney, liver and cardiac preservation solutions before graft: need for standardisation of microbial evaluation, J Hosp Infect, vol.76, pp.52-55, 2010.

M. Desnos-ollivier, S. Bretagne, D. Raoux, D. Hoinard, F. Dromer et al., Mutations in the fks1 gene in Candida albicans, C. tropicalis, and C. krusei correlate with elevated caspofungin MICs uncovered in AM3 medium using the method of the European Committee on Antibiotic Susceptibility Testing, Antimicrob Agents Chemother, vol.52, pp.3092-3098, 2008.

Y. Wu, H. Zhou, C. J. Li, W. Bian, F. et al., Multilocus microsatellite markers for molecular typing of Candida tropicalis isolates, BMC Microbiol, vol.14, p.245, 2014.

X. Fan, M. Xiao, P. Liu, S. Chen, F. Kong et al., Novel polymorphic multilocus microsatellite markers to distinguish Candida tropicalis isolates, PLoS One, vol.11, 2016.

M. A. Lachance, T. Boekhout, G. Scorzetti, J. W. Fell, and C. P. Kurtzman, The yeasts, a taxonomic study, pp.987-1278, 1923.

A. A. Lattif, P. K. Mukherjee, J. Chandra, K. Swindell, S. R. Lockhart et al., Characterization of biofilms formed by Candida parapsilosis, C. metapsilosis, and C. orthopsilosis, Int J Med Microbiol, vol.300, pp.265-270, 2010.

R. Hernandez-castro, S. Arroyo-escalante, E. M. Carrillo-casas, D. Moncadabarron, E. Alvarez-verona et al., Outbreak of Candida parapsilosis in a neonatal intensive care unit: a health care workers source, Eur J Pediatr, vol.169, pp.783-787, 2010.

E. Reiss, B. A. Lasker, T. J. Lott, C. M. Bendel, D. A. Kaufman et al., Genotyping of Candida parapsilosis from three neonatal intensive care units (NICUs) using a panel of five multilocus microsatellite markers: broad genetic diversity and a cluster of related strains in one NICU, Infect Genet Evol, vol.12, pp.1654-1660, 2012.

E. C. Van-asbeck, Y. C. Huang, A. N. Markham, K. V. Clemons, and D. A. Stevens, Candida parapsilosis fungemia in neonates: genotyping results suggest healthcare workers hands as source, and review of published studies, Mycopathologia, vol.164, pp.287-293, 2007.

H. Pinhati, L. A. Casulari, A. Souza, R. A. Siqueira, C. Damasceno et al., Outbreak of candidemia caused by fluconazole resistant Candida parapsilosis strains in an intensive care unit, BMC Infect Dis, vol.16, p.443, 2016.

A. Tavanti, A. D. Davidson, N. Gow, M. Maiden, and F. C. Odds, Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III, J Clin Microbiol, vol.43, pp.284-292, 2005.

E. C. Van-asbeck, K. V. Clemons, and D. A. Stevens, Candida parapsilosis: a review of its epidemiology, pathogenesis, clinical aspects, typing and antimicrobial susceptibility, Crit Rev Microbiol, vol.35, pp.283-309, 2009.

A. Tavanti, L. Hensgens, S. Mogavero, L. Majoros, S. Senesi et al., Genotypic and phenotypic properties of Candida parapsilosis sensu strictu strains isolated from different geographic regions and body sites, BMC Microbiol, vol.10, p.203, 2010.

L. P. Pryszcz, T. Németh, A. Gácser, and T. Gabaldón, Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies, Genome Biol Evol, vol.6, pp.1069-1078, 2014.

B. A. Lasker, G. Butler, and T. J. Lott, Molecular genotyping of Candida parapsilosis group I clinical isolates by analysis of polymorphic microsatellite markers, J Clin Microbiol, vol.44, pp.750-759, 2006.

R. Sabino, P. Sampaio, L. Rosado, D. A. Stevens, K. V. Clemons et al., New polymorphic microsatellite markers able to distinguish among, 2010.

, Candida parapsilosis sensu stricto isolates, J Clin Microbiol, vol.48, pp.1677-1682

R. Sabino, P. Sampaio, C. Carneiro, L. Rosado, and C. Pais, Isolates from hospital environments are the most virulent of the Candida parapsilosis complex, BMC Microbiol, vol.11, p.180, 2011.

R. Sabino, P. Sampaio, L. Rosado, Z. Videira, F. Grenouillet et al., Analysis of clinical and environmental Candida parapsilosis isolates by microsatellite genotyping-a tool for hospital infection surveillance, Clin Microbiol Infect, vol.21, 2015.

A. Brillowska-dabrowska, T. Schon, S. Pannanusorn, N. Lonnbro, L. Bernhoff et al., A nosocomial outbreak of Candida parapsilosis in southern Sweden verified by genotyping, Scand J Infect Dis, vol.41, pp.135-142, 2009.

E. Reissa, B. A. Lasker, N. J. Iqbal, M. James, and A. Ba, Molecular epidemiology of Candida parapsilosis sepsis from outbreak investigations in neonatal intensive care units, Infect Genet Evol, vol.8, pp.103-109, 2008.

A. Carlotti, R. Grillot, A. Couble, and J. Villard, Typing of Candida krusei clinical isolates by restriction endonuclease analysis and hybridization with CkF1,2 DNA probe, J Clin Microbiol, vol.32, pp.1691-1699, 1994.

R. Shemer, Z. Weissman, N. Hashman, and D. Kornitzer, A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei, Microbiology, vol.147, pp.2021-2028, 2001.

M. D. Jacobsen, N. A. Gow, M. C. Maiden, D. J. Shaw, and F. C. Odds, Strain typing and determination of population structure of Candida krusei by multilocus sequence typing, J Clin Microbiol, vol.45, pp.317-323, 2007.

E. Tavernier, M. Desnos-ollivier, F. Honeyman, M. Srour, A. Fayard et al., Development of echinocandin resistance in Candida krusei isolates following exposure to micafungin and caspofungin in a BM transplant unit, Bone Marrow Transplant, vol.50, pp.158-160, 2015.

B. J. Park, K. A. Wannemuehler, B. J. Marston, N. Govender, P. G. Pappas et al., Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS, AIDS, vol.23, pp.525-530, 2009.

M. A. Viviani, M. Cogliati, M. C. Esposto, K. Lemmer, K. Tintelnot et al., Molecular analysis of 311 Cryptococcus neoformans isolates from a 30-month ECMM survey of cryptococcosis in Europe, FEMS Yeast Res, vol.6, pp.614-619, 2006.

F. Dromer, S. Mathoulin-pélissier, O. Launay, and O. Lortholary, Determinants of disease presentation and outcome during cryptococcosis: the CryptoA/D study, Plos Med, vol.4, p.21, 2007.

K. J. Kwon-chung, T. Boekhout, J. W. Fell, and M. Diaz, Proposal to conserve the name Cryptococcus gattii against C. hondurianus and C. bacillisporus (Basidiomycota, Hymenomycetes, Tremellomycetiadae), Taxon, vol.51, pp.804-806, 2002.

S. Chen, T. M. Korman, M. A. Slavin, D. Marriott, K. Byth et al., Australia and New Zealand Mycoses Interest Group (ANZMIG) Cryptococcus Study. 2013. Antifungal therapy and management of complications of cryptococcosis due to Cryptococcus gattii, Clin Infect Dis, vol.57, pp.543-551

F. Hagen, K. Khayhan, B. Theelen, A. Kolecka, I. Polacheck et al., Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex, Fungal Genet Biol, vol.78, pp.16-48, 2015.

K. J. Kwon-chung, J. E. Bennett, B. L. Wickes, W. Meyer, C. A. Cuomo et al., The case for adopting the "species complex" nomenclature for the etiologic agents of cryptococcosis, vol.2, pp.357-373, 2017.

W. Meyer, F. Gilgado, P. Ngamskulrungroj, L. Trilles, F. Hagen et al., Molecular typing of the Cryptococcus neoformans/Cryptococcus gattii species complex, Cryptococcus: from human pathogen to model yeast, pp.327-357, 2011.

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

T. Boekhout, A. Van-belkum, A. C. Leenders, H. A. Verbrugh, P. Mukamurangwa et al., Molecular typing of Cryptococcus neoformans: taxonomic and epidemiological aspects, Int J Syst Bacteriol, vol.47, pp.432-442, 1997.

F. Dromer, A. Varma, O. Ronin, S. Mathoulin, and B. Dupont, Molecular typing of Cryptococcus neoformans serotype D clinical isolates, J Clin Microbiol, vol.32, pp.2364-2371, 1994.

T. C. Sorrell, S. C. Chen, P. Ruma, W. Meyer, T. J. Pfeiffer et al., Concordance of clinical and environmental isolates of Cryptococcus neoformans var. gattii by random amplification of polymorphic DNA analysis and PCR fingerprinting, J Clin Microbiol, vol.34, pp.1253-1260, 1996.

T. Boekhout, B. Theelen, M. Diaz, J. W. Fell, W. C. Hop et al., Hybrid genotypes in the pathogenic yeast Cryptococcus neoformans, Microbiology, vol.147, pp.891-907, 2001.

M. Bovers, F. Hagen, E. E. Kuramae, M. R. Diaz, L. Spanjaard et al., Unique hybrids between the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii, FEMS Yeast Res, vol.6, pp.599-607, 2006.

M. Bovers, F. Hagen, E. E. Kuramae, H. L. Hoogveld, F. Dromer et al., AIDS patient death caused by novel Cryptococcus neoformans ? C. gattii hybrid, Emerg Infect Dis, vol.14, pp.1105-1108, 2008.

W. Meyer, D. M. Aanensen, T. Boekhout, M. Cogliati, M. R. Diaz et al., Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii, Med Mycol, vol.47, pp.561-570, 2009.

P. Ngamskulrungroj, F. Gilgado, J. Faganello, A. P. Litvintseva, A. L. Leal et al., Genetic diversity of the Cryptococcus species complex suggests that Cryptococcus gattii deserves to have varieties, PLoS One, vol.4, 2009.

F. Hagen, M. T. Illnait-zaragozi, K. H. Bartlett, D. Swinne, E. Geertsen et al., In vitro antifungal susceptibilities and amplified fragment length polymorphism genotyping of a worldwide collection of 350 clinical, veterinary, and environmental Cryptococcus gattii isolates, Antimicrob Agents Chemother, vol.54, pp.5139-5145, 2010.

M. Bovers, F. Hagen, E. E. Kuramae, and T. Boekhout, Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing, Fungal Genet Biol, vol.45, pp.400-421, 2008.

W. Meyer, A. Castañeda, S. Jackson, M. Huynh, and E. Castañeda, Molecular typing of IberoAmerican Cryptococcus neoformans isolates, Emerg Infect Dis, vol.9, pp.189-195, 2003.

S. E. Kidd, F. Hagen, R. L. Tscharke, M. Huynh, K. H. Bartlett et al., A rare genotype of Cryptococcus gattii caused the cryptococcosis outbreak on Vancouver Island (British Columbia, Canada), Proc Natl Acad Sci U S A, vol.101, pp.17258-17263, 2004.

L. M. Hoang, J. A. Maguire, P. Doyle, M. Fyfe, and D. L. Roscoe, Cryptococcus neoformans infections at Vancouver Hospital and Health Sciences Centre (1997-2002): epidemiology, microbiology and histopathology, J Med Microbiol, vol.53, pp.935-940, 2004.

C. Stephen, S. Lester, W. Black, M. Fyfe, and S. Raverty, Multispecies outbreak of cryptococcosis on southern Vancouver Island, British Columbia, Can Vet J, vol.43, pp.792-794, 2002.

J. A. Fraser, S. S. Giles, E. C. Wenink, S. G. Geunes-boyer, J. R. Wright et al., Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak, Nature, vol.437, pp.1360-1364, 2005.

S. E. Kidd, H. Guo, K. H. Bartlett, J. Xu, and J. W. Kronstad, Comparative gene genealogies indicate that two clonal lineages of Cryptococcus gattii in British Columbia resemble strains from other geographical areas, Eukaryot Cell, vol.4, pp.1629-1638, 2005.

A. P. Litvintseva, R. Thakur, R. Vilgalys, and T. G. Mitchell, Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana, Genetics, vol.172, pp.2223-2238, 2006.

H. Karaoglu, C. M. Lee, D. Carter, and W. Meyer, Development of polymorphic microsatellite markers for Cryptococcus neoformans, 2008.

, Mol Ecol Resourc, vol.8, pp.1136-1138

A. Hanafy, S. Kaocharoen, A. Jover-botella, M. Katsu, S. Iida et al., Multilocus microsatellite typing for Cryptococcus neoformans var. grubii, Med Mycol, vol.46, pp.685-696, 2008.

M. Illnait-zaragozi, G. F. Martínez-machín, C. M. Fernández-andreu, T. Boekhout, J. Meis et al., Microsatellite typing of clinical and environmental Cryptococcus neoformans var. grubii isolates from Cuba shows multiple genetic lineages, PLoS One, vol.5, 2010.

A. P. Litvintseva and T. G. Mitchell, Most environmental isolates of Cryptococcus neoformans var. grubii (serotype A) are not lethal for mice, Infect Immun, vol.77, pp.3188-3195, 2009.

F. Hagen, M. Illnait-zaragozi, J. F. Meis, W. Chew, I. Curfs-breuker et al., Extensive genetic diversity within the Dutch clinical Cryptococcus neoformans population, J Clin Microbiol, vol.50, pp.1918-1926, 2012.

R. P. Igreja, M. Lazéra, B. Wanke, M. Galhardo, S. E. Kidd et al., Molecular epidemiology of Cryptococcus neoformans isolates from AIDS patients of the Brazilian city, Med Mycol, vol.42, pp.229-238, 2004.

M. Desnos-ollivier, S. Patel, D. Raoux-barbot, J. Heitman, F. Dromer et al., Cryptococcosis serotypes impact outcome and provide evidence of Cryptococcus neoformans speciation, vol.6, p.311, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01178954

M. Desnos-ollivier, S. Patel, A. R. Spaulding, C. Charlier, D. Garcia-hermoso et al., Mixed infections and in vivo evolution in the human fungal pathogen Cryptococcus neoformans, vol.1, pp.91-101, 2010.

D. L. Wiesner, O. Moskalenko, J. M. Corcoran, T. Mcdonald, M. A. Rolfes et al., Cryptococcal genotype influences immunologic response and human clinical outcome after meningitis, vol.3, pp.196-208, 2012.

A. Alanio, F. Vernel-pauillac, A. Sturny-leclère, and F. Dromer, Cryptococcus neoformans host adaptation: toward biological evidence of dormancy, vol.6, pp.2580-2594, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01405218

M. A. Beale, W. Sabiiti, E. J. Robertson, K. M. Fuentes-cabrejo, O. 'hanlon et al., Genotypic diversity is associated with clinical outcome and phenotype in cryptococcal meningitis across southern Africa, PLoS Negl Trop Dis, vol.9, 2015.

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, vol.2, pp.158-169, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01405254

M. K. Mansour, J. M. Vyas, and S. M. Levitz, Dynamic virulence: real-time assessment of intracellular pathogenesis links Cryptococcus neoformans phenotype with clinical outcome, vol.2, pp.217-228, 2011.

Y. H. Choi, P. Ngamskulrungroj, A. Varma, E. Sionov, S. M. Hwang et al., Prevalence of the VNIc genotype of Cryptococcus neoformans in non-HIV-associated cryptococcosis in the Republic of Korea, FEMS Yeast Res, vol.10, pp.769-778, 2010.

J. Chen, A. Varma, M. R. Diaz, A. P. Litvintseva, K. K. Wollenberg et al., Cryptococcus neoformans strains and infection in apparently immunocompetent patients, China. Emerg Infect Dis, vol.14, pp.755-762, 2008.

J. N. Day, T. N. Hoang, A. V. Duong, C. T. Hong, P. T. Diep et al., Most cases of cryptococcal meningitis in HIV-uninfected patients in Vietnam are due to a distinct amplified fragment length polymorphism-defined cluster of Cryptococcus neoformans var. grubii VN1, J Clin Microbiol, vol.49, pp.658-664, 2011.

C. Firacative, L. Trilles, and W. Meyer, MALDI-TOF MS enables the rapid identification of the major molecular types within the Cryptococcus neoformans/C. gattii species complex, PLoS One, vol.7, 2012.

F. Gigliotti and T. W. Wright, Pneumocystis: where does it live?, PLoS Pathog, vol.8, 2012.

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, Clin Infect Dis, vol.32, pp.855-861, 2001.

L. R. Bishop and J. A. Kovacs, Quantitation of anti-Pneumocystis jirovecii antibodies in healthy persons and immunocompromised patients, J Infect Dis, vol.187, pp.1844-1848, 2003.

S. L. Peglow, A. G. Smulian, M. J. Linke, C. L. Pogue, S. Nurre et al., Serologic responses to Pneumocystis carinii antigens in health and disease, J Infect Dis, vol.161, pp.296-306, 1990.

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.

J. H. Meuwissen, I. Tauber, A. D. Leeuwenberg, P. J. Beckers, and M. Sieben, Parasitologic and serologic observations of infection with Pneumocystis in humans, J Infect Dis, vol.136, pp.43-49, 1977.

A. Morris and K. A. Norris, Colonization by Pneumocystis jirovecii and its role in disease, Clin Microbiol Rev, vol.25, pp.13-25, 2012.

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, pp.461-463, 2000.

F. Gigliotti, A. G. Harmsen, and T. W. Wright, Characterization of transmission of Pneumocystis carinii f. sp. muris through immunocompetent BALB/c mice, Infect Immun, vol.71, pp.3852-3856, 2003.

A. Dumoulin, E. Mazars, N. Seguy, D. Gargallo-viola, S. Vargas et al., Transmission of Pneumocystis carinii disease from immunocompetent contacts of infected hosts to susceptible hosts, Eur J Clin Microbiol Infect Dis, vol.19, pp.671-678, 2000.

V. Schildgen, S. Mai, S. Khalfaoui, J. Lusebrink, M. Pieper et al., Pneumocystis jirovecii can be productively cultured in differentiated CuFi-8 airway cells, mBio, vol.5, pp.1186-1200, 2014.

F. Choukri, J. Menotti, C. Sarfati, J. C. Lucet, G. Nevez et al., Quantification and spread of Pneumocystis jirovecii in the surrounding air of patients with Pneumocystis pneumonia, Clin Infect Dis, vol.51, pp.259-265, 2010.

M. T. Cushion, M. J. Linke, A. Ashbaugh, T. Sesterhenn, M. S. Collins et al., Echinocandin treatment of Pneumocystis pneumonia in rodent models depletes cysts leaving trophic burdens that cannot transmit the infection, PLoS One, vol.5, 2010.

P. M. Hauser, P. Francioli, J. Bille, A. Telenti, and D. S. Blanc, Typing of Pneumocystis carinii f. sp. hominis by single-strand conformation polymorphism of four genomic regions, J Clin Microbiol, vol.35, pp.3086-3091, 1997.

P. M. Hauser, P. Francioli, J. Bille, A. Telenti, and D. S. Blanc, Typing of Pneumocystis carinii sp.f. hominis by PCR-SSCP of four genomic regions, J Eukaryot Microbiol, vol.44, p.16, 1997.

A. Nahimana, D. S. Blanc, P. Francioli, J. Bille, and P. M. Hauser, Typing of Pneumocystis carinii f. sp. hominis by PCR-SSCP to indicate a high frequency of co-infections, J Med Microbiol, vol.49, pp.753-758, 2000.

M. J. Struelens, Consensus guidelines for appropriate use and Typing Fungi of Medical Importance Clinical Microbiology Reviews evaluation of microbial epidemiologic typing systems, Clin Microbiol Infect, vol.2, pp.2-11, 1996.

R. U. Pliquett, A. Asbe-vollkopf, P. M. Hauser, L. L. Presti, K. P. Hunfeld et al., A Pneumocystis jirovecii pneumonia outbreak in a single kidney-transplant center: role of cytomegalovirus co-infection, Eur J Clin Microbiol Infect Dis, vol.31, pp.2429-2437, 2012.

S. Gianella, L. Haeberli, B. Joos, B. Ledergerber, R. P. Wüthrich et al., Molecular evidence of interhuman transmission in an outbreak of Pneumocystis jirovecii pneumonia among renal transplant recipients, Transplant Infect Dis, vol.12, pp.1-10, 2010.

S. Schmoldt, R. Schuhegger, T. Wendler, I. Huber, H. Söllner et al., Molecular evidence of nosocomial Pneumocystis jirovecii transmission among 16 patients after kidney transplantation, J Clin Microbiol, vol.46, pp.966-971, 2008.

C. Maitte, M. Leterrier, L. Pape, P. Miegeville, M. Morio et al., Multilocus sequence typing of Pneumocystis jirovecii from clinical samples: how many and which loci should be used?, J Clin Microbiol, vol.51, pp.2843-2849, 2013.

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, Clin Infect Dis, vol.54, pp.62-71, 2012.

M. Rabodonirina, P. Vanhems, S. Couray-targe, R. Gillibert, C. Ganne et al., Molecular evidence of interhuman transmission of Pneumocystis pneumonia among renal transplant recipients hospitalized with HIV-infected patients, Emerg Infect Dis, vol.10, pp.1766-1773, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00427683

P. M. Hauser, The development of a typing method for an uncultivable microorganism: the example of Pneumocystis jirovecii, Infect Genet Evol, vol.4, pp.199-203, 2004.

J. Lu and C. Lee, Pneumocystis pneumonia, J Formos Med Assoc, vol.107, pp.60199-60199, 2008.

F. Esteves, J. Gaspar, T. Marques, R. Leite, F. Antunes et al., Identification of relevant single-nucleotide polymorphisms in Pneumocystis jirovecii: relationship with clinical data, Clin Microbiol Infect, vol.16, pp.878-884, 2010.

F. Esteves, M. A. Montes-cano, C. De-la-horra, M. C. Costa, E. J. Calderón et al., Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain, Clin Microbiol Infect, vol.14, pp.356-362, 2008.

C. Ripamonti, A. Orenstein, G. Kutty, L. Huang, R. Schuhegger et al., Restriction fragment length polymorphism typing demonstrates substantial diversity among Pneumocystis jirovecii isolates, J Infect Dis, vol.200, pp.1616-1622, 2009.

L. Ma, G. Kutty, Q. Jia, H. Imamichi, L. Huang et al., Analysis of variation in tandem repeats in the intron of the major surface glycoprotein expression site of the human form of Pneumocystis carinii, J Infect Dis, vol.186, pp.1647-1654, 2002.

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, J Infect Dis, vol.174, pp.141-156, 1996.

J. Helweg-larsen, C. H. Lee, J. S. Hsueh, J. Y. Benfield, T. L. Hansen et al., Clinical correlation of variations in the internal transcribed spacer regions of rRNA genes in Pneumocystis carinii f.sp. hominis, AIDS, vol.15, pp.451-459, 2001.

O. Matos and F. Esteves, Epidemiology and clinical relevance of Pneumocystis jirovecii Frenkel, 1976 dihydropteroate synthase gene mutations, Parasite, vol.17, pp.219-232, 2010.

P. M. Hauser, A. Nahimana, P. Taffé, R. Weber, P. Francioli et al., Interhuman transmission as a potential key parameter for geographical variation in the prevalence of Pneumocystis jirovecii dihydropteroate synthase mutations, Clin Infect Dis, vol.51, pp.28-33, 2010.

A. Alanio, P. M. Hauser, K. Lagrou, W. Melchers, J. Helweg-larsen et al., The European Organization for Research and Treatment of Cancer (EORTC), the Immunocompromised Host Society (ICHS) and The European LeukemiaNet (ELN). 2016. ECIL guidelines for the diagnosis of Pneumocystis jirovecii pneumonia in patients with haematological malignancies and stem cell transplant recipients, 5th European Conference on Infections in Leukemia (ECIL-5), a joint venture of The European Group for Blood and Marrow Transplantation (EBMT), vol.71, pp.2386-2396

C. M. Parobek, L. Y. Jiang, J. C. Patel, M. J. Alvarez-martinez, J. M. Miro et al., Multilocus microsatellite genotyping array for investigation of genetic epidemiology of Pneumocystis jirovecii, J Clin Microbiol, vol.52, pp.1391-1399, 2014.

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.10, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01405228

A. Alanio, M. Gits-muselli, S. Mercier-delarue, F. Dromer, and S. Bretagne, Diversity of Pneumocystis jirovecii during infection revealed by ultradeep pyrosequencing, Front Microbiol, vol.7, p.733, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01405203

Y. Gräser, J. Scott, and R. Summerbell, The new species concept in dermatophytes-a polyphasic approach, Mycopathologia, vol.166, pp.239-256, 2008.

M. Gits-muselli, M. Benderdouche, S. Hamane, A. Mingui, F. De-chauvin et al., Continuous increase of Trichophyton tonsurans as a cause of tinea capitis in the urban area of Paris, France: a 5-year-long study, Med Mycol, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01405212

C. Viguié-vallanet, M. Serre, L. Masliah, and C. Tourte-schaefer, Epidemic of Trichophyton tonsurans tinea capitis in a nursery school in the southern suburbs of Paris, Ann Dermatol Venereol, vol.132, pp.432-438, 2005.

J. Shroba, C. Olson-burgess, B. Preuett, and A. Sm, A large outbreak of Trichophyton tonsurans among health care workers in a pediatric hospital, Am J Infect Control, vol.37, pp.43-48, 2009.

M. Ilkit, A. Saracli, M. Kurdak, H. Turac-bicer, A. Yuksel et al., Clonal outbreak of Trichophyton tonsurans tinea capitis gladiatorum among wrestlers in Adana, Turkey. Med Mycol, vol.48, pp.480-485, 2010.

O. Coulibaly, M. A. Thera, R. Piarroux, O. K. Doumbo, and S. Ranque, High dermatophyte contamination levels in hairdressing salons of a West African suburban community, Mycoses, vol.58, pp.65-68, 2015.

S. M. Abdel-rahman, T. Sugita, G. M. González, D. Ellis, M. Arabatzis et al., Divergence among an international population of Trichophyton tonsurans isolates, Mycopathologia, vol.169, pp.1-13, 2010.

S. M. Abdel-rahman, B. Preuett, and A. Gaedigk, Multilocus genotyping identifies infections by multiple strains of Trichophyton tonsurans, J Clin Microbiol, vol.45, pp.1949-1953, 2007.

J. Yu, Z. Wan, W. Chen, W. Wang, and R. Li, Molecular typing study of the Microsporum canis strains isolated from an outbreak of tinea capitis in a school, Mycopathologia, vol.157, pp.37-41, 2004.

J. Cano, A. Rezusta, M. Solé, J. Gil, M. C. Rubio et al., Inter-single-sequence-repeat-PCR typing as a new tool for identification of Microsporum canis strains, J Dermatol Sci, vol.39, pp.17-21, 2005.

N. Vanittanakom, C. Cooper, M. C. Fisher, and T. Sirisanthana, Penicillium marneffei infection and recent advances in the epidemiology and molecular biology aspects, Clin Microbiol Rev, vol.19, pp.95-110, 2006.

B. A. Lasker, Nucleotide sequence-based analysis for determining the molecular epidemiology of Penicillium marneffei, J Clin Microbiol, vol.44, pp.3145-3153, 2006.

M. C. Fisher, S. De-hoog, and N. V. Akom, A highly discriminatory multilocus microsatellite typing (MLMT) system for Penicillium marneffei, Mol Ecol Notes, vol.4, pp.515-518, 2004.

X. Huang, G. He, S. Lu, Y. Liang, and L. Xi, Role of Rhizomys pruinosus as a natural animal host of Penicillium marneffei in Guangdong, China. Microb Biotechnol, vol.8, pp.659-664, 2015.

C. Cao, L. Liang, W. Wang, H. Luo, S. Huang et al., Common reservoirs for Penicillium marneffei infection in humans and rodents, China. Emerg Infect Dis, vol.17, pp.209-214, 2011.

M. C. Fisher, D. Aanensen, D. Hoog, and N. Vanittanakom, Multilocus microsatellite typing system for Penicillium marneffei reveals spatially structured populations, J Clin Microbiol, vol.42, pp.5065-5069, 2004.

N. C. Bahr, S. Antinori, L. J. Wheat, and G. A. Sarosi, Histoplasmosis infections worldwide: thinking outside of the Ohio River valley, Curr Trop Med Rep, vol.2, pp.70-80, 2015.

J. P. Woods, Histoplasma capsulatum molecular genetics, pathogenesis, and responsiveness to its environment, Fungal Genet Biol, vol.35, pp.81-97, 2002.

. Kwon-chung, . Kj, and J. Bennett, Histoplasmosis, Medical mycology, pp.464-513, 1992.

L. S. Damasceno, T. M. Leitao, M. L. Taylor, M. M. Muniz, and R. M. Zancope-oliveira, The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review, Eur J Clin Microbiol Infect Dis, vol.35, pp.19-27, 2016.

T. Kasuga, J. W. Taylor, and T. J. White, Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling, J Clin Microbiol, vol.37, pp.653-663, 1999.

K. Benedict and R. K. Mody, Epidemiology of Histoplasmosis outbreaks, Emerg Infect Dis, vol.22, pp.370-378, 2016.

T. Vite-garín, D. A. Estrada-bárcenas, J. Cifuentes, and M. L. Taylor, The importance of molecular analyses for understanding the genetic diversity of Histoplasma capsulatum: an overview, Rev Iberoamer Micol, vol.31, pp.11-15, 2014.

M. Saccente and G. L. Woods, Clinical and laboratory update on blastomycosis, Clin Microbiol Rev, vol.23, pp.56-65, 2010.

K. D. Reed, J. K. Meece, J. R. Archer, and A. T. Peterson, Ecologic niche modeling of Blastomyces dermatitidis in Wisconsin, PLoS One, vol.3, 2008.

J. K. Meece, J. L. Anderson, M. C. Fisher, D. A. Henk, B. L. Sloss et al., Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, based on 27 polymorphic microsatellite markers, Appl Environ Microbiol, vol.77, pp.5123-5131, 2011.

M. J. Mccullough, A. F. Disalvo, K. V. Clemons, P. Park, and D. A. Stevens, Molecular epidemiology of Blastomyces dermatitidis, Clin Infect Dis, vol.30, pp.328-335, 2000.

J. K. Meece, J. L. Anderson, B. S. Klein, T. D. Sullivan, S. L. Foley et al., Genetic diversity in Blastomyces dermatitidis: implications for PCR detection in clinical and environmental samples, Med Mycol, vol.48, pp.285-290, 2010.

J. K. Meece, J. L. Anderson, S. Gruszka, B. L. Sloss, B. Sullivan et al., Variation in clinical phenotype of human infection among genetic groups of Blastomyces dermatitidis, J Infect Dis, vol.207, pp.814-822, 2013.

D. R. Matute, J. G. Mcewen, R. Puccia, B. A. Montes, G. San-blas et al., Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies, Mol Biol Evol, vol.23, pp.65-73, 2006.

D. R. Matute, V. E. Sepulveda, L. M. Quesada, G. H. Goldman, J. W. Taylor et al., Microsatellite analysis of three phylogenetic species of Paracoccidioides brasiliensis, J Clin Microbiol, vol.44, pp.2153-2157, 2006.

M. M. Teixeira, R. C. Theodoro, M. J. De-carvalho, L. Fernandes, H. C. Paes et al., Phylogenetic analysis reveals a high level of speciation in the Paracoccidioides genus, Mol Phylogenet Evol, vol.52, pp.273-283, 2009.

M. M. Teixeira, R. C. Theodoro, G. Nino-vega, E. Bagagli, and M. S. Felipe, Paracoccidioides species complex: ecology, phylogeny, sexual reproduction, and virulence, PLoS Pathog, vol.10, 2014.

E. Brummer, E. Castaneda, and A. Restrepo, Paracoccidioidomycosis: an update, Clin Microbiol Rev, vol.6, pp.89-117, 1993.

B. J. Manns, B. W. Baylis, S. J. Urbanski, A. P. Gibb, and H. R. Rabin, Paracoccidioidomycosis: case report and review, Clin Infect Dis, vol.23, pp.1026-1032, 1996.

R. Martinez, Epidemiology of paracoccidioidomycosis, Rev Inst Med Trop Sao Paulo, vol.57, pp.11-20, 2015.

M. Franco, Host-parasite relationships in paracoccidioidomycosis, J Med Vet Mycol, vol.25, pp.5-18, 1987.

E. Bagagli, A. Sano, K. I. Coelho, S. Alquati, M. Miyaji et al., Isolation of Paracoccidioides brasiliensis from armadillos (Dasypus noveminctus) captured in an endemic area of paracoccidioidomycosis, Am J Trop Med Hyg, vol.58, pp.505-512, 1998.

G. G. Corredor, L. A. Peralta, J. H. Castano, J. S. Zuluaga, B. Henao et al., The nakedtailed armadillo Cabassous centralis (Miller 1899): a new host to Paracoccidioides brasiliensis. Molecular identification of the isolate, Med Mycol, vol.43, pp.275-280, 2005.

D. E. Neafsey, B. M. Barker, T. J. Sharpton, J. E. Stajich, D. J. Park et al., Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control, Genome Res, vol.20, pp.938-946, 2010.

B. M. Barker, K. A. Jewell, S. Kroken, and M. J. Orbach, The population biology of Coccidioides: epidemiologic implications for disease outbreaks, Ann N Y Acad Sci, vol.1111, pp.147-163, 2007.

R. E. Laniado-laborin, Expanding understanding of epidemiology of coccidioidomycosis in the Western hemisphere, Ann N Y Acad Sci, vol.1111, pp.19-34, 2007.

D. Greene, G. Koenig, M. C. Fisher, and J. W. Taylor, Soil isolation and molecular identification of Coccidioides immitis, Mycologia, vol.92, pp.406-410, 2000.

C. Nguyen, B. M. Barker, S. Hoover, D. E. Nix, N. M. Ampel et al., Recent advances in our understanding of the environmental, epidemiological, immunological, and clinical dimensions of coccidioidomycosis, Clin Microbiol Rev, vol.26, pp.505-525, 2013.

C. R. Zimmermann, C. J. Snedker, and D. Pappagianis, Characterization of Coccidioides immitis isolates by restriction fragment length polymorphisms, J Clin Microbiol, vol.32, pp.3040-3042, 1994.

A. Burt, B. M. Dechairo, G. L. Koenig, D. A. Carter, T. J. White et al., Molecular markers reveal differentiation among isolates of Coccidioides immitis from California, Arizona and Texas, Mol Ecol, vol.6, pp.781-786, 1997.

V. Koufopanou, A. Burt, and J. W. Taylor, Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis, Proc Natl Acad Sci U S A, vol.94, pp.5478-5482, 1997.

M. C. Fisher, B. Rannala, V. Chaturvedi, and J. W. Taylor, Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections, Proc Natl Acad Sci U S A, vol.99, pp.9067-9071, 2002.

K. Jewell, R. Cheshier, and G. D. Cage, Genetic diversity among clinical Coccidioides spp. isolates in Arizona, Med Mycol, vol.46, pp.449-455, 2008.

J. A. Luna-isaac, R. Muniz-salazar, R. C. Baptista-rosas, L. M. Enriquez-paredes, L. R. Castanon-olivares et al., Genetic analysis of the endemic Typing Fungi of Medical Importance Clinical Microbiology Reviews fungal pathogens Coccidioides posadasii and Coccidioides immitis in Mexico, Med Mycol, vol.52, pp.156-166, 2014.

Y. Chen, A. E. Frazzitta, A. P. Litvintseva, C. Fang, T. G. Mitchell et al., Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing, Fungal Genet Biol, vol.75, pp.64-71, 2015.

J. D. Gillece, J. M. Schupp, S. A. Balajee, J. Harris, T. Pearson et al., Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity, PLoS One, vol.6, 2011.

W. Meyer, Cryptococcus gattii in the age of whole-genome sequencing, vol.6, pp.1761-1776, 2015.

R. A. Farrer, C. A. Desjardins, S. Sakthikumar, S. Gujja, S. Saif et al., Genome evolution and innovation across the four major lineages of Cryptococcus gattii, mBio, vol.6, pp.868-883, 2015.

A. P. Litvintseva, M. E. Brandt, R. K. Mody, and S. R. Lockhart, Investigating fungal outbreaks in the 21st century, PLoS Pathog, vol.11, 2015.

D. M. Engelthaler, T. Chiller, J. A. Schupp, J. Colvin, S. M. Beckstrom-sternberg et al., Next-generation sequencing of Coccidioides immitis isolated during cluster investigation, Emerg Infect Dis, vol.17, pp.227-232, 2011.

A. P. Litvintseva, N. Marsden-haug, S. Hurst, H. Hill, L. Gade et al., Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington State soil associated with recent human infection, Clin Infect Dis, vol.60, pp.1-3, 2015.

A. P. Litvintseva, S. Hurst, L. Gade, M. A. Frace, R. Hilsabeck et al., Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections, J Clin Microbiol, vol.52, pp.936-950, 2014.

K. A. Etienne, J. Gillece, R. Hilsabeck, J. M. Schupp, R. Colman et al., Whole genome sequence typing to investigate the Apophysomyces outbreak following a tornado in, PLoS One, vol.7, 2011.

S. Vaux, A. Criscuolo, M. Desnos-ollivier, L. Diancourt, C. Tarnaud et al., Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen, vol.5, pp.2309-2323, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01484251

A. Alanio, D. Garcia-hermoso, A. Criscuolo, M. Legrand, M. Chaouat et al., Whole genome sequencing to investigate an outbreak of mucormycosis in a burn unit, Mycoses, vol.58, p.23, 2015.

S. C. Lee, R. B. Billmyre, A. Li, S. Carson, S. M. Sykes et al., Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt, vol.5, pp.1390-1404, 2014.

S. Camps, B. E. Dutilh, M. C. Arendrup, A. Rijs, E. Snelders et al., Discovery of a hapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing, PLoS One, vol.7, 2012.

A. Abdolrasouli, J. Rhodes, M. A. Beale, F. Hagen, T. R. Rogers et al., Genomic context of azole resistance mutations in Aspergillus fumigatus determined using whole-genome sequencing, mBio, vol.6, pp.536-551, 2015.

K. L. Ormerod, C. A. Morrow, E. Chow, I. R. Lee, S. Arras et al., Comparative genomics of serial isolates of Cryptococcus neoformans reveals gene associated with carbon utilization and virulence, Bethesda), vol.3, pp.675-686, 2013.

E. J. Feil, Small change: keeping pace with microevolution, Nat Rev Microbiol, vol.2, pp.483-495, 2004.