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2. 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

3. 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

4. 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

5. 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, Çağrı, Velegraki, A., and Çukurova Üniversitesi

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 N8 9313133 We thank Dr. Lockhart (CDC, Atalanta, USA) for critical reading of the manuscript and for his useful comments. Dr. Ferreira-Paim was supported by a CAPES Science without Borders visiting fellow (N8 9313133) from Brazil. We declare we have no conflict of interests.

Published
2017

6. 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

7. 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

9. 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

10. 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

11. 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

12. Assessment of nasal flora and respiratory function tests of bakery workers working under modern conditions

Author

Issever, H., primary, Hapcioglu, B., additional, Ozdilli, K., additional, Kocyigit, E., additional, Kaymakcalan, H., additional, Yegenoglu, Y., additional, Ozturk, O., additional, Agkoc, S., additional, Topuzoglu, A., additional, Onoglu, N., additional, Isik, E., additional, Susever, S., additional, Calak, B., additional, and Gurtekin, B., additional

Published
2005
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14. 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. Mallié, M. Martins, M.L. Vencà, 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. Inácio, J. Alonso, B. 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. © FEMS 2016. All rights reserved.

15. 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 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, Vencá ACF, Sampaio AC, Criseo G, Ranque S, Çerikçioğlu N, Marchese A, Vezzulli L, Ilkit M, Pasquale V, Polacheck I, and Lockhart SR

Subjects
Animals, Environmental Microbiology, Europe, Genetics, Population, Humans, Mediterranean Region, Multilocus Sequence Typing, Mycological Typing Techniques, Cryptococcus gattii genetics, Cryptococcus neoformans genetics, Genotype, Phylogeny
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., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Published
2019
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16. Fundamental niche prediction of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii in Europe.

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, Vencà ACF, Sampaio AC, 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 KJ, Inácio J, and Colom MF

Subjects
Cryptococcosis microbiology, Cryptococcus gattii metabolism, Cryptococcus neoformans metabolism, Europe, Mediterranean Region, Seasons, Soil chemistry, Weather, Cellular Microenvironment physiology, Cryptococcus gattii growth & development, Cryptococcus neoformans growth & development, Environmental Microbiology, Soil Microbiology
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
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17. An outbreak of Fusarium solani endophthalmitis after cataract surgery in an eye training and research hospital in Istanbul.

Author

Güngel H, Eren MH, Pınarcı EY, Altan C, Baylançiçek DO, Kara N, Gürsel T, Yegenoğlu Y, and Susever S

Subjects
Aged, Aged, 80 and over, Antifungal Agents administration & dosage, Cross Infection microbiology, Cross Infection pathology, Cross Infection therapy, Endophthalmitis microbiology, Endophthalmitis pathology, Endophthalmitis therapy, Eye Infections, Fungal microbiology, Eye Infections, Fungal pathology, Eye Infections, Fungal therapy, Female, Fusariosis microbiology, Fusariosis pathology, Fusariosis therapy, Fusarium genetics, Fusarium growth & development, Hospitals, Humans, Male, Middle Aged, Surgical Wound Infection epidemiology, Surgical Wound Infection microbiology, Surgical Wound Infection pathology, Surgical Wound Infection therapy, Vitrectomy, Cataract Extraction adverse effects, Cross Infection epidemiology, Disease Outbreaks, Endophthalmitis epidemiology, Eye Infections, Fungal epidemiology, Fusariosis epidemiology, Fusarium isolation & purification
Abstract

To report an outbreak of Fusarium solani endophthalmitis after uneventful cataract surgeries performed on the same day in the same operating room. Nine patients underwent phacoemulsification at 4th Clinic of Beyoglu Eye Training and Research Hospital in Istanbul. Cefuroxime axetyl was injected intracamerally from the same vial to all patients at the end of surgery. All patients developed acute postoperative endophthalmitis. Presentation, cultural studies, treatment, clinical responses and risk factors were evaluated. Cultural and DNA sequence findings revealed F. solani. Antifungal therapy was begun and pars plana vitrectomy, intraocular lens and capsule extraction were performed. Corneal involvement was correlated with old age and systemic disease. Fusarium solani should be considered in acute postoperative endophthalmitis. This infection can be controlled with early and aggressive combined antifungal and surgical treatment. The patients with corneal involvement had poor prognosis. It is important to use solutions prepared separately for each patient., (© 2011 Blackwell Verlag GmbH.)

Published
2011
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18. [Evaluation of the significance of molecular methods in the diagnosis of invasive fungal infections: comparison with conventional methods].

Author

Susever S and Yeğenoğlu Y

Subjects
Aspergillus fumigatus genetics, Aspergillus fumigatus growth & development, Candida genetics, Candida growth & development, Candida isolation & purification, Candidiasis, Invasive microbiology, Cryptococcosis microbiology, Cryptococcus neoformans genetics, Cryptococcus neoformans growth & development, DNA, Fungal chemistry, DNA, Fungal isolation & purification, Humans, Immunosuppression Therapy, Invasive Pulmonary Aspergillosis microbiology, Polymerase Chain Reaction, Sensitivity and Specificity, Aspergillus fumigatus isolation & purification, Candida classification, Candidiasis, Invasive diagnosis, Cryptococcosis diagnosis, Cryptococcus neoformans isolation & purification, Invasive Pulmonary Aspergillosis diagnosis
Abstract

Direct microscopy and culture methods are still valuable standard conventional methods for the diagnosis of infections caused by true or opportunistic fungal pathogens, especially in high risk patients. However, some of the problems concerning the application and interpretation of those methods, indicate a need for more rapid, practical and reliable tests with high sensitivity and specificity. This study was conducted to compare the results obtained by molecular methods with the results of conventional methods performed simultaneously for the detection and identification of causative fungi in clinical samples. Clinical samples [24 bronchoalveolar lavage (BAL); 14 blood; 5 peritoneal, 4 pleural and 1 pericardial fluids; 1 cerebrospinal fluid (CSF), 1 urine] from 50 immunosuppressed patients were included in the study. All of the samples were cultivated on Sabouraud dextrose and brain-heart infusion agar media and incubated at 30°C and 37°C for 30 days. Samples other than blood were stained with 10-15% KOH + calcofluor white and examined by direct microscopy. Conventional identification of the isolates were performed by using basic morphological and biochemical characteristics. The isolation of fungal DNAs for polymerase chain reaction (PCR) was achieved by classical phenol-chloroform-isoamylalcohol procedure (9-10 hours) and commercial DNA extraction kit (6-7 hours) and general and species-specific primers (multiplex) from ITS1, ITS2, ITS3, ITS4, 5.8S rDNA and 28S rDNA regions were chosen for amplification. In PCR results, 550 base-paired (bp) bands obtained with universal primers were evaluated as fungal DNA positivity, and 273 bp, 320 bp, 423 bp, 357 bp, 136 bp and 385 bp bands with species-specific primers were evaluated as Candida albicans, Candida parapsilosis, Candida glabrata, Candida tropicalis, Cryptococcus neoformans and Aspergillus fumigatus positivities, respectively. Seventeen (34%) of the 50 samples yielded fungal growth on culture (C.albicans in 12 BAL, 3 blood, 1 urine sample, and C.parapsilosis in 1 urine), while seven BAL out of 36 (19.4%) non-blood samples gave positive result by direct microscopy. Of the samples 27 (54%) were found positive by PCR. All of the 17 culture positive samples were also found PCR positive, and all of the 23 culture negative samples were also found PCR negative. However, fungal DNAs were detected by PCR in 10 of the samples (5 BAL, 4 peritoneal fluids, 1 CSF) which were negative by direct microscopy and culture methods. These fungi were identified as C.albicans (n= 8), C.parapsilosis (n= 1, from peritonal fluid) and C.neoformans (n= 1, from CSF) by multiplex PCR. No samples yielded PCR negative, culture positive result. All of those 10 PCR positive, culture negative samples belonged to patients who were under antifungal treatment. The detection of C.neoformans DNA from CSF sample of a patient with suspected cryptococcosis only with PCR provided the chance for rapid therapy. In statistical evaluation, the concordance between culture and PCR methods were found significantly high (k= 0.61; p< 0.001), whereas it was minimal (k= 0.24; p< 0.001) between direct microscopy and PCR. When considering culture as the reference method, the sensitivity and specificity of PCR were estimated as 100% and 69.7%, respectively. In addition, multiplex PCR was as successful as culture and conventional identification methods in the identification of all fungal species. As a result, without disregarding conventional methods, use of PCR might be recommended for the identification of fungal species on the basis of clinical status of the patient and conditions of the laboratory.

Published
2011

19. Prevalence, susceptibility profile and proteinase production of yeasts causing vulvovaginitis in Turkish women.

Author

Ozcan SK, Budak F, Yucesoy G, Susever S, and Willke A

Subjects
Adult, Amphotericin B pharmacology, Candida isolation & purification, Candida metabolism, Candidiasis, Vulvovaginal epidemiology, Female, Fluconazole pharmacology, Humans, Itraconazole pharmacology, Microbial Sensitivity Tests, Prevalence, Risk Factors, Turkey epidemiology, Antifungal Agents pharmacology, Candida drug effects, Candida enzymology, Candidiasis, Vulvovaginal microbiology, Peptide Hydrolases biosynthesis
Abstract

In this study the prevalence of vulvovaginal candidiasis (VVC), antifungal susceptibility and proteinase production of isolated Candida species were investigated. Vaginal swabs were collected from symptomatic women with vulvovaginitis attending the Obstetrics and Gynecology Clinic of Kocaeli University, Turkey. The relation between risk factors, such as pregnancy, diabetes mellitus, antibiotic and corticosteroid use, history of sexually transmitted diseases and contraceptive methods, was recorded. Candida spp. were identified by conventional methods, then evaluated for proteinase secretion in a medium containing casein. Antifungal susceptibility was determined according to the NCCLS microdilution method. The prevalence of women with vulvovaginitis was 35.7% (170/6080) and 16% (28/170) of them were diagnosed as VVC. Candida albicans was the dominant species: 21 (75%), followed by 4 C. glabrata (14%), 2 C. tropicalis (7%), and one C. krusei (3.5%). All isolates were susceptible to fluconazole, itraconazole and amphotericin B, except one C. krusei, one C. glabrata and one C. albicans that were resistant to fluconazole. Proteinase production was determined in 19 (90.5%) C. albicans and in all C. tropicalis isolates. Proteinase activity was not associated with antifungal resistance. No association was found between risk factors and VVC.

Published
2006
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20. In vitro susceptibility of yeasts isolated from patients in intensive care units to fluconazole and amphotericin B during a 3-year period.

Author

Kucukates E, Erturan Z, Susever S, and Yegenoglu Y

Subjects
Candida drug effects, Candida isolation & purification, Cardiac Care Facilities, Cohort Studies, Female, Humans, Intensive Care Units, Male, Microbial Sensitivity Tests, Middle Aged, Mycoses prevention & control, Species Specificity, Turkey, Yeasts isolation & purification, Amphotericin B pharmacology, Antifungal Agents pharmacology, Fluconazole pharmacology, Mycoses microbiology, Yeasts drug effects
Abstract

Fungal infections have increased dramatically in recent years and candidemia is a major risk factor for morbidity and mortality in intensive care units (ICUs). Candidemia has been considered to be a nosocomial infection that is strongly associated with neutropenia, recent surgery or presence of intravascular lines, and previous colonization is an independent risk factor. We evaluated the in vitro efficacy of fluconazole and amphotericin B against yeasts isolated from various clinical specimens of colonized or infected patients treated in the ICUs of the Institute of Cardiology, Istanbul University. A total of 1397 ICU patients were treated at the Institute of Cardiology between January 2000 and December 2002. A total of 117 yeasts isolated from 97 patients were included in this study. These ICU patients were hospitalized for a mean of 29 days. All yeasts were identified by conventional methods and using the API (20C AUX, ID 32C) system (Bio Meriéux, France). Susceptibility to fluconazole and amphotericin B was evaluated using the E-test (AB Biodisk, Solna, Sweden). The most commonly isolated yeast was Candida albicans (72.6%), followed by Candida tropicalis (16.2%), Candida kefyr, Candida krusei, Candida parapsilosis, Trichosporon mucoides and Geotrichum spp. Fluconazole and amphotericin B MIC90 values were 0.75 microg/ml; 0.19 microg/ml and 1 microg/ml; 0.38 microg/ml for C. albicans and C. tropicalis, respectively. All Geotrichum spp. were found to be susceptible-dose dependent (SDD) (MIC=16-32 microg/ml) to fluconazole. Two C. albicans, two C. tropicalis, one C. krusei and one Geotrichum spp. had a MIC value of > or = 0.38 microg/ml for amphotericin B. The rate of colonization was 3.36% (47/1397). Only 10 (0.71%) patients out of a total of 1397 developed candidemia during the period of the investigation. Of these, 7 (70%) were caused by non-albicans Candida spp.

Published
2005
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21. Effect of some antibiotics on pigmentation in Serratia marcescens.

Author

Anğ-Küçüker M, Büyükbaba-Boral O, Tolun V, Törümküney D, Susever S, and Anğ O

Subjects
Animals, Keratitis microbiology, Keratitis pathology, Lethal Dose 50, Mice, Mice, Inbred BALB C, Microbial Sensitivity Tests, Pigmentation drug effects, Serratia marcescens metabolism, Virulence, Anti-Bacterial Agents pharmacology, Prodigiosin biosynthesis, Serratia Infections microbiology, Serratia marcescens drug effects, Serratia marcescens pathogenicity
Abstract

Serratia marcescens is characterized by its ability to produce a red pigment called prodigiosin. It is well known that there are some substances affecting pigmentation in bacteria. Cefoxitin, erythromycin, tobramycin, co-trimoxazole, imipenem and nitrofurantoin were found to have an inhibitory effect on pigmentation in a S. marcescens strain isolated from urine. It was also shown that the LD50 dose determined by inoculation of eight-week-old BALB/c mice with serial dilutions of overnight cultures of pigmented and nonpigmented variants was lower (LD50 = 300 x 10(3.94)) in the nonpigmented variant than in the pigmented one (LD50 = 300 x 10(5.58)). In addition, the Sereny test showed that in contrast to the pigmented variant, the nonpigmented variant caused keratitis in guinea pig eye.

Published
2000
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