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4. MULTI-LOCUS SEQUENCE TYPING AND PHYLOGENETICS OF CRYPTOCOCCUS NEOFORMANS AD HYBRIDS

Author

Cogliati, M, primary, Chidebelu, PE, additional, Hitchcock, M, additional, Chen, M, additional, Rickerts, V, additional, Ackermann, S, additional, Desnos Ollivier, M, additional, Inácio, J, additional, Nawrot, U, additional, Flore, M, additional, Kwon Chung, KJ, additional, Yang, D-H, additional, Firacative, C, additional, Puime, CA, additional, Escandon, P, additional, Bertout, S, additional, Roger, F, additional, and Xu, J, additional

Published
2023
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5. Identification, Prevalence and Susceptibility Profile of Candida Isolates at the Pasteur Institute in Côte D'ivoire from 2017 to 2019

Author

Bonouman Ira A.V., Mboh R., Roger F., Krasteva D., Bellet V., Koffi D., Noell J., Pottier C., Drakulovski P., Menan H., Toure O., Dosso M., Ranque S., and Bertout S.

Subjects
Marketing, Pharmacology, Organizational Behavior and Human Resource Management, Strategy and Management, Drug Discovery, Pharmaceutical Science
Abstract

This study was conducted in Côte d’Ivoire to determine the respective prevalence of Candida species and to study their susceptibility profile to antifungal agents to identify the emergence of resistance.This retrospective study was conducted from 2017 to 2019 at the Institute Pasteur of Côte d’Ivoire on patients with fungal disease. The yeasts isolated and identified in Côte d’Ivoire were subcultured on a chromogenic medium and identified with MALDI-TOF-MS. Sensitivity tests were performed using the CLSI method and evaluated by the M27. In total, 227 Candida spp. were isolated from 1941 patients. Most of the samples were vaginal swabs (120/228). Using the conventional method, C. albicans was prevalent (52.6%). There were mixtures of 2 to 4 species in 36.8% of the samples. Thus MALDI-TOF-MS identified in 315 isolates 13 distinct species, C. tropicalis was prevalent at 35.2%, and the species in both C. albicans and C. parapsilosis complexes were differentiated. This study highlights the hurdle of correct yeast identification in developing countries. The transition from conventional to modern MALDI-TOF based identification of these life-threatening opportunistic pathogens is mandatory and should be emphasised as a public health priority.

Published
2023
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7. Clonal population structure and genetic diversity of Candida albicans in AIDS patients from Abidjan (Cote d'Ivoire)

Author

Nebavi, F, Ayala, Francisco J, Renaud, F, Bertout, S, Eholie, S, Moussa, K, Mallie, M, and de Meeus, T

Subjects
clonality, molecular epidemiology, population genetics, candidiasis, asexual reproduction
Abstract

We have investigated the genotype at 14 enzyme-encoding loci in 275 isolates of the pathogenic yeast Candida albicans sampled from 42 HIV-positive patients (all but one with AIDS) from Abidjan (Cote d'Ivoire). We separately analyzed the following variables: patient, residence, age, gender, T cell count, hospitalization (yes or no), drug treatment, date of sampling, multilocus genotype, and serotype. The most important factors contributing to the genetic variability of C albicans are individual patient and gender. Our data manifest that the population size of the parasite is relatively small within each patient, although larger in women than in men, and that, at least for the patients involved in the study, the transmission rate of C albicans between human adults is very low. Most important is the inference that the prevailing mode of reproduction of C albicans in natural populations is clonal, so that sexual reproduction is extremely rare, if it occurs at all.

Published
2006

13. Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area

Author

Cogliati, M. Desnos-Ollivier, M. McCormick-Smith, I. Rickerts, V. Ferreira-Paim, K. Meyer, W. Boekhout, T. Hagen, F. Theelen, B. Inácio, J. Alonso, B. Colom, M.F. Trilles, L. Montagna, M.T. De Donno, A. Susever, S. Ergin, C. Velegraki, A. Ellabib, M.S. Nardoni, S. Macci, C. Trovato, L. Dipineto, L. Akcaglar, S. Mlinaric-Missoni, E. Bertout, S. Vencá, A.C.F. Sampaio, A.C. Criseo, G. Ranque, S. Çerikçioğlu, N. Marchese, A. Vezzulli, L. Ilkit, M. Pasquale, V. Polacheck, I. Lockhart, S.R.

Abstract

A total of 476 European isolates (310 Cryptococcus neoformans var. grubii, 150 C. neoformans var. neoformans, and 16 C. gattii species complex) from both clinical and environmental sources were analyzed by multi-locus sequence typing. Phylogenetic and population genetic analyses were performed. Sequence analysis identified 74 sequence types among C. neoformans var. neoformans (VNIV), 65 among C. neoformans var. grubii (56 VNI, 8 VNII, 1 VNB), and 5 among the C. gattii species complex (4 VGI and 1 VGIV) isolates. ST23 was the most frequent genotype (22%) among VNI isolates which were mostly grouped in a large clonal cluster including 50% of isolates. Among VNIV isolates, a predominant genotype was not identified. A high percentage of autochthonous STs were identified in both VNI (71%) and VNIV (96%) group of isolates. The 16 European C. gattii species complex isolates analyzed in the present study originated all from the environment and all belonged to a large cluster endemic in the Mediterranean area. Population genetic analysis confirmed that VNI group of isolates were characterized by low variability and clonal expansion while VNIV by a higher variability and a number of recombination events. However, when VNI and VNIV environmental isolates were compared, they showed a similar population structure with a high percentage of shared mutations and the absence of fixed mutations. Also linkage disequilibrium analysis reveals differences between clinical and environmental isolates showing a key role of PLB1 allele combinations in host infection as well as the key role of LAC1 allele combinations for survival of the fungus in the environment. The present study shows that genetic comparison of clinical and environmental isolates represents a first step to understand the genetic characteristics that cause the shift of some genotypes from a saprophytic to a parasitic life style. © 2019 Elsevier Inc.

Published
2019

14. Genotypes and population genetics of cryptococcus neoformans and

Author

Cogliati, M, Desnos-Ollivier, M, McCormick-Smith, I, Rickerts, V, Ferreira-Paim, K, Meyer, W, Boekhout, T, Hagen, F, Theelen, B, Inacio, J, Alonso, B, Colom, MF, Trilles, L, Montagna, MT, De Donno, A, Susever, S, Ergin, C, Velegraki, A, Ellabib, MS, Nardoni, S, Macci, C, Trovato, L, Dipineto, L, Akcaglar, S, Mlinaric-Missoni, E, Bertout, S, Venca, ACF, Sampaio, AC, Criseoa, G, Ranque, S, Cerikcioglu, N, Marchese, A, Vezzulli, L, Ilkit, M, Pasquale, V, Polacheck, I, and Lockhart, SR

Subjects
Europe, Cryptococcus neoformans, Cryptococcus gattii, MLST, Population genetics
Abstract

A total of 476 European isolates (310 Cryptococcus neoformans var. grubii, 150 C. neoformans var. neoformans, and 16 C. gattii species complex) from both clinical and environmental sources were analyzed by multi-locus sequence typing. Phylogenetic and population genetic analyses were performed. Sequence analysis identified 74 sequence types among C. neoformans var. neoformans (VNIV), 65 among C. neoformans var. grubii (56 VNI, 8 VNII, 1 VNB), and 5 among the C. gattii species complex (4 VGI and 1 VGIV) isolates. ST23 was the most frequent genotype (22%) among VNI isolates which were mostly grouped in a large clonal cluster including 50% of isolates. Among VNIV isolates, a predominant genotype was not identified. A high percentage of autochthonous STs were identified in both VNI (71%) and VNIV (96%) group of isolates. The 16 European C. gattii species complex isolates analyzed in the present study originated all from the environment and all belonged to a large cluster endemic in the Mediterranean area. Population genetic analysis confirmed that VNI group of isolates were characterized by low variability and clonal expansion while VNIV by a higher variability and a number of recombination events. However, when VNI and VNIV environmental isolates were compared, they showed a similar population structure with a high percentage of shared mutations and the absence of fixed mutations. Also linkage disequilibrium analysis reveals differences between clinical and environmental isolates showing a key role of PLB1 allele combinations in host infection as well as the key role of LAC1 allele combinations for survival of the fungus in the environment. The present study shows that genetic comparison of clinical and environmental isolates represents a first step to understand the genetic characteristics that cause the shift of some genotypes from a saprophytic to a parasitic life style. C1 [Cogliati, Massimo] Univ Milan, Dip Sci Biomed Sallee, Via Pascal 36, I-20133 Milan, Italy. [Desnos-Ollivier, Marie] CNRS, UMR2000, Natl Reference Ctr Invas Mycoses & Antifungal, Inst Pasteur,Mol Mycol Unit, Paris, France. [McCormick-Smith, Ilka; Rickerts, Volker] Robert Koch Inst, Berlin, Germany. [Ferreira-Paim, Kennio; Meyer, Wieland] Univ Sydney, Marie Bashier Inst Emerging Infect Dis & Biosecur, Westmead Inst Med Res,Sydney Med Sch,Westmead Cli, Mol Mycol Res Lab,Ctr Infect Dis,Fac Med & Hlth,W, Westmead, NSW, Australia. [Ferreira-Paim, Kennio] Univ Fed Triangulo Mineiro, Dept Microbiol, Uberaba, MG, Brazil. [Boekhout, Teun; Hagen, Ferry; Theelen, Bart] Westerdijk Fungal Biodivers Inst, Utrecht, Netherlands. [Boekhout, Teun] Univ Amsterdam, IBED, Amsterdam, Netherlands. [Inacio, Joao; Alonso, Beatriz] Univ Brighton, Sch Pharm & Biomol Sci, Brighton, E Sussex, England. [Alonso, Beatriz] Hosp Gegorio Maranon, Inst Invest Sanitaria Gregorio Maranon IisGM, Madrid, Spain. [Colom, Maria F.] Univ Miguel Hernandez, Alicante, Spain. [Trilles, Luciana] Fundacao Oswaldo Cruz, FIOCRUZ, Rio De Janeiro, Brazil. [Montagna, Maria Teresa] Univ Bari Aldo Moro, Bari, Italy. [De Donno, Antonella] Univ Salento, DiSTeBA, Lecce, Italy. [Susever, Serdar] Cyprus Near East Univ, Nicosia, Cyprus. [Ergin, Cagri] Pamukkale Univ, Denizli, Turkey. [Velegraki, Aristea] Univ Athens, Med Sch, Athens, Greece. [Ellabib, Mohamed S.] Univ Tripoli, Med Coll, Tripoli, Libya. [Nardoni, Simona] Univ Pisa, Pisa, Italy. [Macci, Cristina] CNR, Res Inst Terr Ecosystems IRET, Pisa, Italy. [Trovato, Laura] Univ Catania, Catania, Italy. [Dipineto, Ludovico] Univ Napoli Federico II, Naples, Italy. [Akcaglar, Sevim] Uludag Univ, Sch Med, Bursa, Turkey. [Mlinaric-Missoni, Emilija] Croatian Natl Inst Publ Hlth, Zagreb, Croatia. [Bertout, Sebastien] Univ Montpellier, Unite Mixte Int Rech Translat Infect VIH & Malad, Montpellier, France. [Venca, Ana C. F.] Inst Higiene & Med Trop, Lisbon, Portugal. [Sampaio, Ana C.] Univ Tras os Montes & Alto Douro, CITAB, Quinta Prados, Vila Real, Portugal. [Criseoa, Giuseppe] Univ Messina, Dept Chem Biol Pharmaceut & Environm Sci, Messina, Italy. [Ranque, Stephane] Aix Marseille Univ, IHU Mediterranee Infect, AP HM, IRD,SSA,VITROME, Marseille, France. [Cerikcioglu, Nilgun] Marmara Univ, Sch Med, Istanbul, Turkey. [Marchese, Anna] Univ Genoa, IRCCS Policlin San Martino Genova, Sez Microbiol DISC, Genoa, Italy. [Vezzulli, Luigi] Univ Genoa, Dipartimento Sci Terra Ambiente & Vita DISTAV, Genoa, Italy. [Ilkit, Macit] Univ Cukurova Saricam, Adana, Turkey. [Pasquale, Vincenzo] Univ Napoli Parthenope, Naples, Italy. [Polacheck, Itzhack] Hadassah Hebrew Univ, Med Ctr, Jerusalem, Israel. [Lockhart, Shawn R.] Ctr Dis Control & Prevent, Atlanta, GA USA.

Published
2019

18. Corrigendum: Environmental distribution of Cryptococcus neoformans and C. gattii around the Mediterranean basin [FEMS, (2016), 16, 4] doi: http://dx.doi.org/10.1093/femsyr/fow045

Author

Cogliati M., D'Amicis R., Zani A., Montagna M. T., Caggiano G., De Giglio O., Balbino S., De Donno A., Serio F., Susever S., Ergin C., Velegraki A., Ellabib M. S., Nardoni S., Macci C., Oliveri S., Trovato L., Dipineto L., Rickerts V., McCormick-Smith I., Akcaglar S., Tore O., Mlinaric-Missoni E., Bertout S., Mallie M., Martins M. L., Venca A. C. F., Vieira M. L., Sampaio A. C., Pereira C., Criseo G., Romeo O., Ranque S., Al-Yasiri M. H. Y., Kaya M., Cerikcioglu N., Marchese A., Vezzulli L., Ilkit M., Desnos-Ollivier M., Pasquale V., Korem M., Polacheck I., Scopa A., Meyer W., Ferreira-Paim K., Hagen F., Theelen B., Boekhout T., Lockhart S. R., Tintelnot K., Tortorano A. M., Dromer F., Varma A., Kwon-Chung K. J., Inacio J., Alonso B., Colom M. F., Cogliati, M., D'Amicis, R., Zani, A., Montagna, M. T., Caggiano, G., De Giglio, O., Balbino, S., De Donno, A., Serio, F., Susever, S., Ergin, C., Velegraki, A., Ellabib, M. S., Nardoni, S., Macci, C., Oliveri, S., Trovato, L., Dipineto, L., Rickerts, V., McCormick-Smith, I., Akcaglar, S., Tore, O., Mlinaric-Missoni, E., Bertout, S., Mallie, M., Martins, M. L., Venca, A. C. F., Vieira, M. L., Sampaio, A. C., Pereira, C., Criseo, G., Romeo, O., Ranque, S., Al-Yasiri, M. H. Y., Kaya, M., Cerikcioglu, N., Marchese, A., Vezzulli, L., Ilkit, M., Desnos-Ollivier, M., Pasquale, V., Korem, M., Polacheck, I., Scopa, A., Meyer, W., Ferreira-Paim, K., Hagen, F., Theelen, B., Boekhout, T., Lockhart, S. R., Tintelnot, K., Tortorano, A. M., Dromer, F., Varma, A., Kwon-Chung, K. J., Inacio, J., Alonso, B., and Colom, M. F.

Abstract

The original article published in FEMS Yeast Research Vol. 16. Iss. 4; doi: http://dx.doi.org/10.1093/femsyr/fow045 This paper has been updated to correct a spelling error concerning an author name. It previously showed as Giuseppe Griseo, however the correct spelling is Giuseppe Criseo.

Published
2016

19. Fundamental niche prediction of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii in Europe

Author

Cogliati, M. Puccianti, E. Montagna, M.T. De Donno, A. Susever, S. Ergin, C. Velegraki, A. Ellabib, M.S. Nardoni, S. Macci, C. Trovato, L. Dipineto, L. Rickerts, V. Akcaglar, S. Mlinaric-Missoni, E. Bertout, S. Vencà, A.C.F. Sampaio, A.C. Criseo, G. Ranque, S. Çerikçioğlu, N. Marchese, A. Vezzulli, L. Ilkit, M. Desnos-Ollivier, M. Pasquale, V. Polacheck, I. Scopa, A. Meyer, W. Ferreira-Paim, K. Hagen, F. Boekhout, T. Dromer, F. Varma, A. Kwon-Chung, K.J. Inácio, J. Colom, M.F.

Subjects
parasitic diseases, bacterial infections and mycoses
Abstract

Fundamental niche prediction of Cryptococcus neoformans and Cryptococcus gattii in Europe is an important tool to understand where these pathogenic yeasts have a high probability to survive in the environment and therefore to identify the areas with high risk of infection. In this study, occurrence data for C. neoformans and C. gattii were compared by MaxEnt software with several bioclimatic conditions as well as with soil characteristics and land use. The results showed that C. gattii distribution can be predicted with high probability along the Mediterranean coast. The analysis of variables showed that its distribution is limited by low temperatures during the coldest season, and by heavy precipitations in the driest season. C. neoformans var. grubii is able to colonize the same areas of C. gattii but is more tolerant to cold winter temperatures and summer precipitations. In contrast, the C. neoformans var. neoformans map was completely different. The best conditions for its survival were displayed in sub-continental areas and not along the Mediterranean coasts. In conclusion, we produced for the first time detailed prediction maps of the species and varieties of the C. neoformans and C. gattii species complex in Europe and Mediterranean area. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd

Published
2017

20. Fundamental niche prediction of the pathogenic yeasts Cryptococcus

Author

Cogliati, M, Puccianti, E, Montagna, MT, De Donno, A, Susever, S, Ergin, C, Velegraki, A, Ellabib, MS, Nardoni, S, Macci, C, Trovato, L, Dipineto, L, Rickerts, V, Akcaglar, S, Mlinaric-Missoni, E, Bertout, S, Venca, ACF, Sampaio, AC, Criseo, G, Ranque, S, Cerikcioglu, N, Marchese, A, Vezzulli, L, Ilkit, M, Desnos-Ollivier, M, Pasquale, V, Polacheck, I, Scopa, A, Meyer, W, Ferreira-Paim, K, Hagen, F, Boekhout, T, Dromer, F, Varma, A, Kwon-Chung, KJ, Inacio, J, and Colom, MF

Subjects
parasitic diseases, bacterial infections and mycoses
Abstract

Fundamental niche prediction of Cryptococcus neoformans and Cryptococcus gattii in Europe is an important tool to understand where these pathogenic yeasts have a high probability to survive in the environment and therefore to identify the areas with high risk of infection. In this study, occurrence data for C. neoformans and C. gattii were compared by MaxEnt software with several bioclimatic conditions as well as with soil characteristics and land use. The results showed that C. gattii distribution can be predicted with high probability along the Mediterranean coast. The analysis of variables showed that its distribution is limited by low temperatures during the coldest season, and by heavy precipitations in the driest season. C. neoformans var. grubii is able to colonize the same areas of C. gattii but is more tolerant to cold winter temperatures and summer precipitations. In contrast, the C. neoformans var. neoformans map was completely different. The best conditions for its survival were displayed in sub-continental areas and not along the Mediterranean coasts. In conclusion, we produced for the first time detailed prediction maps of the species and varieties of the C. neoformans and C. gattii species complex in Europe and Mediterranean area.

Published
2017

21. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus

Author

Hagen, F., Lumbsch, H.T., Arsenijevic, V.A., Badali, H., Bertout, S., Billmyre, R.B., Bragulat, M.R., Cabanes, F.J., Carbia, M., Chakrabarti, A, Chaturvedi, S., Chaturvedi, V., Chen, M., Chowdhary, A., Colom, M.F., Cornely, O.A., Crous, P.W., Cuetara, M.S., Diaz, M.R., Espinel-Ingroff, A., Fakhim, H., Falk, R., Fang, W., Herkert, P.F., Rodriguez, C., Fraser, J.A., Gene, J., Guarro, J., Idnurm, A., Illnait-Zaragozi, M.T., Khan, Z., Khayhan, K., Kolecka, A., Kurtzman, C.P., Lagrou, K., Liao, W., Linares, C., Meis, J.F.G.M., Nielsen, K., Nyazika, T.K., Pan, W., Pekmezovic, M., Polacheck, I., Posteraro, B., Queiroz Telles, F.F. de, Romeo, O., Sanchez, M., Sampaio, A., Sanguinetti, M., Sriburee, P., Sugita, T., Taj-Aldeen, S.J., Takashima, M., Taylor, J.W., Theelen, B., Tomazin, R., Verweij, P.E., Wahyuningsih, R., Wang, P., Boekhout, T., Hagen, F., Lumbsch, H.T., Arsenijevic, V.A., Badali, H., Bertout, S., Billmyre, R.B., Bragulat, M.R., Cabanes, F.J., Carbia, M., Chakrabarti, A, Chaturvedi, S., Chaturvedi, V., Chen, M., Chowdhary, A., Colom, M.F., Cornely, O.A., Crous, P.W., Cuetara, M.S., Diaz, M.R., Espinel-Ingroff, A., Fakhim, H., Falk, R., Fang, W., Herkert, P.F., Rodriguez, C., Fraser, J.A., Gene, J., Guarro, J., Idnurm, A., Illnait-Zaragozi, M.T., Khan, Z., Khayhan, K., Kolecka, A., Kurtzman, C.P., Lagrou, K., Liao, W., Linares, C., Meis, J.F.G.M., Nielsen, K., Nyazika, T.K., Pan, W., Pekmezovic, M., Polacheck, I., Posteraro, B., Queiroz Telles, F.F. de, Romeo, O., Sanchez, M., Sampaio, A., Sanguinetti, M., Sriburee, P., Sugita, T., Taj-Aldeen, S.J., Takashima, M., Taylor, J.W., Theelen, B., Tomazin, R., Verweij, P.E., Wahyuningsih, R., Wang, P., and Boekhout, T.

Abstract

Contains fulltext : 177602.pdf (publisher's version ) (Open Access), Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.

Published
2017

22. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus

Author

Lorenz, M, Hagen, F, Lumbsch, HT, Arsenijevic, VA, Badali, H, Bertout, S, Billmyre, RB, Rosa Bragulat, M, Javier Cabanes, F, Carbia, M, Chakrabarti, A, Chaturvedi, S, Chaturvedi, V, Chen, M, Chowdhary, A, Colom, M-F, Cornely, OA, Crous, PW, Cuetara, MS, Diaz, MR, Espinel-Ingroff, A, Fakhim, H, Falk, R, Fang, W, Herkert, PF, Ferrer Rodriguez, C, Fraser, JA, Gene, J, Guarro, J, Idnurm, A, Illnait-Zaragozi, M-T, Khan, Z, Khayhan, K, Kolecka, A, Kurtzman, CP, Lagrou, K, Liao, W, Linares, C, Meis, JF, Nielsen, K, Nyazika, TK, Pan, W, Pekmezovic, M, Polacheck, I, Posteraro, B, Telles Filho, FDQ, Romeo, O, Sanchez, M, Sampaio, A, Sanguinetti, M, Sriburee, P, Sugita, T, Taj-Aldeen, SJ, Takashima, M, Taylor, JW, Theelen, B, Tomazin, R, Verweij, PE, Wahyuningsih, R, Wang, P, Boekhoutiii, T, Lorenz, M, Hagen, F, Lumbsch, HT, Arsenijevic, VA, Badali, H, Bertout, S, Billmyre, RB, Rosa Bragulat, M, Javier Cabanes, F, Carbia, M, Chakrabarti, A, Chaturvedi, S, Chaturvedi, V, Chen, M, Chowdhary, A, Colom, M-F, Cornely, OA, Crous, PW, Cuetara, MS, Diaz, MR, Espinel-Ingroff, A, Fakhim, H, Falk, R, Fang, W, Herkert, PF, Ferrer Rodriguez, C, Fraser, JA, Gene, J, Guarro, J, Idnurm, A, Illnait-Zaragozi, M-T, Khan, Z, Khayhan, K, Kolecka, A, Kurtzman, CP, Lagrou, K, Liao, W, Linares, C, Meis, JF, Nielsen, K, Nyazika, TK, Pan, W, Pekmezovic, M, Polacheck, I, Posteraro, B, Telles Filho, FDQ, Romeo, O, Sanchez, M, Sampaio, A, Sanguinetti, M, Sriburee, P, Sugita, T, Taj-Aldeen, SJ, Takashima, M, Taylor, JW, Theelen, B, Tomazin, R, Verweij, PE, Wahyuningsih, R, Wang, P, and Boekhoutiii, T

Abstract

Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.

Published
2017

23. Importance of resolving fungal nomenclature: the case of multiple pathogenic species in the Cryptococcus genus

Author

Universitat Rovira i Virgili, Hagen F, Lumbsch H, Arsenijevic V, Badali H, Bertout S, Billmyre R, Bragulat M, Cabañes F, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom M, Cornely O, Crous P, Cuétara M, Diaz M, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert P, Rodríguez C, Fraser J, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi M, Khan Z, Khayhan K, Kolecka A, Kurtzman C, Lagrou K, Liao W, Linares C, Meis J, Nielsen K, Nyazika T, Universitat Rovira i Virgili, and Hagen F, Lumbsch H, Arsenijevic V, Badali H, Bertout S, Billmyre R, Bragulat M, Cabañes F, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom M, Cornely O, Crous P, Cuétara M, Diaz M, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert P, Rodríguez C, Fraser J, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi M, Khan Z, Khayhan K, Kolecka A, Kurtzman C, Lagrou K, Liao W, Linares C, Meis J, Nielsen K, Nyazika T

Abstract

© 2017 Hagen et al. Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi .org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature C. neoformans species complex and C. gattii species complex. Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.

Published
2017

24. Environmental distribution of Cryptococcus neoformans and C. gattii around the Mediterranean basin

Author

Cogliati M, D'Amicis R, Zani A, Montagna MT, Caggiano G, De Giglio O, Balbino S, De Donno A, Serio F, Susever S, Ergin C, Velegraki A, Ellabib MS, Nardoni S, Macci C, Oliveri S, Trovato L, Dipineto L, Rickerts V, McCormick-Smith I, Akcaglar S, Tore O, Mlinaric-Missoni E, Bertout S, Mallié M, Martins MD, Vencà AC, Vieira ML, Sampaio AC, Pereira C, Criseo G, Romeo O, Ranque S, Al-Yasiri MH, Kaya M, Cerikcioglu N, Marchese A, Vezzulli L, Ilkit M, Desnos-Ollivier M, Pasquale V, Korem M, and Polacheck I

Subjects
Cryptococcus gattii/classification/genetics/*isolation & purification, Cryptococcus neoformans/classification/genetics/*isolation & purification, Environmental Microbiology, Genotype, Mediterranean Region, Molecular Typing, Mycological Typing Techniques, Trees/*microbiology
Abstract

In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012-2015. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia, 10% of Olea, Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus, four Ceratonia, two Pinus and two Olea trees. Cryptococcus neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates, VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts.

Published
2016

25. Environmental distribution of Cryptococcus neoformans and Cryptococcus gattii around the Mediterranean basin

Author

Cogliati, M, D'Amicis, R, Zani, A, Montagna, Mt, Caggiano, G, De Giglio, O, Balbino, S, De Donno, A, Serio, F, Susever, S, Ergin, C, Velegraki, A, Ellabib, Ms, Nardoni, S, Macci, C, Oliveri, Salvatore, Trovato, L, Dipineto, L, Rickerts, V, McCormick Smith, I, Akcaglar, S, Tore, O, Mlinaric Missoni, E, Bertout, S, Mallié, M, Martins, Md, Vencà, Ac, Vieira, Ml, Sampaio, Ac, Pereira, C, Griseo, G, Romeo, O, Ranque, S, Al Yasiri MH, Kaya, M, Cerikcioglu, N, Marchese, A, Vezzulli, L, Ilkit, M, Desnos Ollivier, M, Pasquale, V, Korem, M, Polacheck, I, Scopa, A, Meyer, W, Ferreira Paim, K, Hagen, F, Theelen, B, Boekhout, T, Lockhart, Sr, Tintelnot, K, Tortorano, Am, Dromer, F, Varma, A, Kwon Chung KJ, Inácio, J, Alonso, B, and Colom, M. F.

Published
2016

26. African ST173 Cryptococcus deuterogattiistrains are commonly less susceptible to fluconazole: An unclear mechanism of resistance

Author

Bertout, S., Roger, F., Drakulovski, P., Martin, A.S., Gouveia, T., Kassi, F., Menan, H., Krasteva, D., Delaporte, E., and Bellet, V.

Abstract

•All Ivorian Cryptococcus deuterogattiiisolates were identified as ST173 by MLST.•64.3% (18/28) of isolates had a fluconazole (FCZ) MIC of ≥16μg/mL.•FCZ exposure increased AFR1mRNA expression, especially in isolates with high FCZ MICs.•Resistance mechanisms described in Cryptococcus neoformanswere not involved in C. deuterogattiiST173 isolates.

Published
2020
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27. Environmental survey of Cryptococcus neoformans and C. gattii in European and Mediterranean area

Author

Cogliati, M., Colom, M. F., Hagen, F., Boekhout, T., Ilkit, M. M., Velegraki, A., Lockhart, S. R., Montagna, M. T., Tintelnot, K., Rickerts, V., Kwon-chung, K. J., Akcaglar, S., Tore, O., Oliveri, S., Trovato, L. C., Susever, S., Ergin, C., Mitchell, T. G., Marchese, A., Vezzulli, L., Kaya, M., Cerikcioglu, N., Korem, M., Polacheck, I., De Donno, A., Ranque, S., Criseo, G., Tortorano, A. M., D’Amicis, R., Bertout, S., Maillé, M., Dipineto, L., Pasquale, V., Dromer, F., Desnosollivier, M., Nardoni, S., Macci, C. P., Scopa, A., Trilles, L., Meyer, W., Firacative, C., Ellabib, M. S., Kronstad, J., and Bartlett, K. H. Mlinaric-missoni E.

Published
2014

29. Clonality structure in Candida dubliniensis

Author

Badoc, C., De Meeûs, Thierry, Bertout, S., Odds, F.C., Mallié, M., and Bastide, J.M.

Subjects
GENETIQUE DE POPULATION, MYCOSE, EPIDEMIOLOGIE, STRUCTURE GENETIQUE, SIDA, REPRODUCTION ASEXUEE, CLONE, POLYMORPHISME GENETIQUE, VARIABILITE GENETIQUE, MALADIE OPPORTUNISTE, GENOTYPE
Published
2002

45. A Candida albicans strain with high MIC for caspofungin and no FKS1 mutations exhibits a high chitin content and mutations in two chitinase genes.

Author

Drakulovski, P., Dunyach, C., Bertout, S., Reynes, J., and Malliéé, M.

Abstract

We studied the cell wall of a Candida albicans laboratory mutant exhibiting a high minimum inhibitory concentration (MIC; 8 μμg ml−−1) for caspofungin without bearing FKS1 mutations. This strain showed a reduced level of ßß 1,3 D glucan (0.43××) and a higher chitin content (2.3××) than a control strain even when grown without caspofungin. No significant over- or under-expression of chitin synthase or chitinase genes was observed. However, point mutations were detected in the chitinase 2 and 3 genes. These mutations, which may affect the enzymatic activity of the encoded protein products involved in the degradation of the chitin, could have led to an increased concentration of that component, allowing the strain to compensate for its low ßß 1,3 D glucan content and the effect of caspofungin. [ABSTRACT FROM AUTHOR]

Published
2011
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46. Comparison of the Sensititre YeastOne® dilution method with the Clinical Laboratory Standards Institute (CLSI) M27-A3 microbroth dilution reference method for determining MIC of eight antifungal agents on 102 yeast strains

Author

Bertout, S., Dunyach, C., Drakulovski, P., Reynes, J., and Mallié, M.

Subjects
*DILUTION, *MICROBIAL sensitivity tests, *PATHOLOGICAL laboratories, *CRYPTOCOCCUS, *ANTIFUNGAL agents, *YEAST
Abstract

Abstract: The Clinical Laboratory Standards Institute ([CLSI] formerly NCCLS) reference broth microdilution testing method (protocol M27-A3) was compared with a commercially available methods (Sensititre YeastOne®) by testing two quality control strains and 102 isolates of Candida sp. and Cryptococcus sp. against fluconazole, itraconazole, ketoconazole, posaconazole, voriconazole, flucytosin, amphotericin B and caspofungin. Minimal inhibitory concentrations (MIC) endpoints were determined after 24h of incubation for Sensititre YeastOne® and after 24 and 48h for CLSI microdilution method. Essential agreements between methods vary from 70.6 to 92.2%. Categorical agreements vary from 94.1% for 5FC to 72.6% for AMB. Sensititre YeastOne® reading appears to be useful for avoiding very major errors and this confirms the interest of this method for evaluating new antifungals activity in vitro. [Copyright &y& Elsevier]

Published
2011
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47. Sensibilité comparée par CLSI, EUCAST, E-test et ATB® Fungus 2 des souches de Candida sp. isolées au cours d’une enquête épidémiologique sur les candidémies dans des hôpitaux non ...

Author

Rieu, P., Eloy, O., Bertout, S., Mallié, M., Bain, P., and Blanc, V.

Subjects
CANDIDIASIS, PUBLIC health, INFECTIOUS disease transmission, MICROBIOLOGY
Abstract

Copyright of Journal of Medical Mycology / Journal de Mycologie Médicale is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2009
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48. Antifungal Susceptibility of 205 Candidaspp. Isolated Primarily during Invasive Candidiasis and Comparison of the Vitek 2 System with the CLSI Broth Microdilution and Etest Methods

Author

Bourgeois, N., Dehandschoewercker, L., Bertout, S., Bousquet, P.-J., Rispail, P., and Lachaud, L.

Abstract

ABSTRACTInfections due to Candidaspp. are frequent, particularly in immunocompromised and intensive care unit patients. Antifungal susceptibility tests are now required to optimize antifungal treatment given the emergence of acquired antifungal resistance in some Candidaspecies. An antifungal susceptibility automated method, the Vitek 2 system (VK2), was evaluated. VK2 was compared to the CLSI broth microdilution reference method and the Etest procedure. For this purpose, 205 clinical isolates of Candidaspp., including 11 different species, were tested for fluconazole, voriconazole, and amphotericin B susceptibility. For azoles, essential agreement ranged from 25% to 100%, depending on the method used and the Candidaspecies tested. Categorical agreements for all of the species averaged 92.2% and ranged from 14.3 to 100%, depending on the 24-h or 48-h MIC reading by the Etest and CLSI methods and on the Candidaspecies. Results obtained for Candida albicansshowed excellent categorical and essential agreements with the two comparative methods. For Candida glabrata, the essential agreement was high with the CLSI method but low with the Etest method, and several very major errors in interpretation were observed between VK2 and the Etest method for both azoles. Low MICs of fluconazole were obtained for all of the Candida kruseiisolates, but the VK2 expert software corrected all of the results obtained to resistant. Amphotericin B results showed MICs of =1 mg/liter for 201 (VK2), 190 (CLSI), and 202 (Etest) isolates. The AST-YS01 Vitek 2 card system (bioMe´rieux) is a reliable and practical standardized automated antifungal susceptibility test. Nevertheless, more assays are needed to better evaluate C. glabratafluconazole sensitivity.

Published
2010
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49. Typing of Saccharomyces cerevisiaeClinical Strains by Using Microsatellite Sequence Polymorphism

Author

Malgoire, J. Y., Bertout, S., Renaud, F., Bastide, J. M., and Mallie´, M.

Abstract

ABSTRACTIt seems that S. cerevisiae, which was thought for about 30 years to be a nonpathogenic yeast, should now be considered an opportunistic pathogen. In this study, we estimated the discrimination ability of the microsatellite sequence amplification technique within a sample of clinical and reference S. cerevisiaestrains and S. boulardiireference strains.

Published
2005
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50. Genetic Polymorphism of Aspergillus fumigatusin Clinical Samples from Patients with Invasive Aspergillosis: Investigation Using Multiple Typing Methods

Author

Bertout, S., Renaud, F., Barton, R., Symoens, F., Burnod, J., Piens, M.-A., Lebeau, B., Viviani, M.-A., Chapuis, F., Bastide, J.-M., Grillot, R., and Mallie´, M.

Abstract

ABSTRACTThe genotypes of 52 strains of Aspergillus fumigatusisolated from 12 patients with invasive aspergillosis were investigated using three typing methods (random amplified polymorphic DNA, sequence-specific DNA polymorphism, and microsatellite polymorphism) combined with multilocus enzyme electrophoresis. Isolates were from patients hospitalized in three different geographic areas (Lyon, France; Grenoble, France; and Milan, Italy). In each case, the genetic polymorphism of several colonies (two to five) within the first respiratory clinical sample was studied. For the 52 isolates tested, random amplified polymorphic DNA identified 8 different genotypes, sequence-specific DNA polymorphism identified 9 different types, and microsatellite polymorphism identified 14 types. A combination of these results with multilocus enzyme electrophoresis study identified 25 different types within the sample studied. We identified 3 patients (of the 12 studied) who carried a single genotype; 6 patients were infected by two genotypes, 1 patient had four genotypes, while the last patient had five. A combination of typing methods provided better discrimination than the use of a single method. Typing methods revealed a population structure within each geographical site, suggesting that the epidemiology of A. fumigatusshould be considered separately for each of these geographic areas. This study demonstrates the usefulness of combining several typing methods in reaching an understanding of the epidemiology of A. fumigatusand clarifies whether it is sufficient to type one isolate from each specimen to determine the strain involved in invasive aspergillosis.

Published
2001
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