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

Massimo Cogliati, Marie Desnos-Ollivier, Ilka McCormick-Smith, Volker Rickerts, Kennio Ferreira-Paim, Wieland Meyer, Teun Boekhout, Ferry Hagen, Bart Theelen, Joäo Inácio, Beatriz Alonso, Maria F. Colom, Luciana Trilles, Maria Teresa Montagna, Antonella De Donno, Serdar Susever, Cagri Ergin, Aristea Velegraki, Mohamed S. Ellabib, Simona Nardoni & 17 others Cristina Macci, Laura Trovato, Ludovico Dipineto, Sevim Akcaglar, Emilija Mlinaric-Missoni, Sebastien Bertout, Ana C.F. Vencá, Ana C. Sampaio, Giuseppe Criseo, Stéphane Ranque, Nilgün Çerikçioğlu, Anna Marchese, Luigi Vezzulli, Macit Ilkit, Vincenzo Pasquale, Itzhack Polacheck, Shawn R. Lockhart

Research output: Contribution to journalArticleResearchpeer-review

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.

Original languageEnglish
Pages (from-to)16-29
Number of pages14
JournalFungal Genetics and Biology
Volume129
DOIs
Publication statusPublished - 3 Apr 2019

Fingerprint

Cryptococcus gattii
Cryptococcus neoformans
Population Genetics
Genotype
Alleles
Mutation
Linkage Disequilibrium
Genetic Recombination
Sequence Analysis
Life Style
Fungi
Infection
Population

Keywords

  • Cryptococcus gattii
  • Cryptococcus neoformans
  • Europe
  • MLST
  • Population genetics

Cite this

Cogliati, M., Desnos-Ollivier, M., McCormick-Smith, I., Rickerts, V., Ferreira-Paim, K., Meyer, W., ... Lockhart, S. R. (2019). Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area. Fungal Genetics and Biology, 129, 16-29. https://doi.org/10.1016/j.fgb.2019.04.001
Cogliati, Massimo ; Desnos-Ollivier, Marie ; McCormick-Smith, Ilka ; Rickerts, Volker ; Ferreira-Paim, Kennio ; Meyer, Wieland ; Boekhout, Teun ; Hagen, Ferry ; Theelen, Bart ; Inácio, Joäo ; Alonso, Beatriz ; Colom, Maria F. ; Trilles, Luciana ; Montagna, Maria Teresa ; De Donno, Antonella ; Susever, Serdar ; Ergin, Cagri ; Velegraki, Aristea ; Ellabib, Mohamed S. ; Nardoni, Simona ; Macci, Cristina ; Trovato, Laura ; Dipineto, Ludovico ; Akcaglar, Sevim ; Mlinaric-Missoni, Emilija ; Bertout, Sebastien ; Vencá, Ana C.F. ; Sampaio, Ana C. ; Criseo, Giuseppe ; Ranque, Stéphane ; Çerikçioğlu, Nilgün ; Marchese, Anna ; Vezzulli, Luigi ; Ilkit, Macit ; Pasquale, Vincenzo ; Polacheck, Itzhack ; Lockhart, Shawn R. / Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area. In: Fungal Genetics and Biology. 2019 ; Vol. 129. pp. 16-29.
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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.",
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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 & Lockhart, SR 2019, 'Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area', Fungal Genetics and Biology, vol. 129, pp. 16-29. https://doi.org/10.1016/j.fgb.2019.04.001

Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area. / Cogliati, Massimo; Desnos-Ollivier, Marie; McCormick-Smith, Ilka; Rickerts, Volker; Ferreira-Paim, Kennio; Meyer, Wieland; Boekhout, Teun; Hagen, Ferry; Theelen, Bart; Inácio, Joäo; Alonso, Beatriz; Colom, Maria F.; Trilles, Luciana; Montagna, Maria Teresa; De Donno, Antonella; Susever, Serdar; Ergin, Cagri; Velegraki, Aristea; Ellabib, Mohamed S.; Nardoni, Simona; Macci, Cristina; Trovato, Laura; Dipineto, Ludovico; Akcaglar, Sevim; Mlinaric-Missoni, Emilija; Bertout, Sebastien; Vencá, Ana C.F.; Sampaio, Ana C.; Criseo, Giuseppe; Ranque, Stéphane; Çerikçioğlu, Nilgün; Marchese, Anna; Vezzulli, Luigi; Ilkit, Macit; Pasquale, Vincenzo; Polacheck, Itzhack; Lockhart, Shawn R.

In: Fungal Genetics and Biology, Vol. 129, 03.04.2019, p. 16-29.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area

AU - Cogliati, Massimo

AU - Desnos-Ollivier, Marie

AU - McCormick-Smith, Ilka

AU - Rickerts, Volker

AU - Ferreira-Paim, Kennio

AU - Meyer, Wieland

AU - Boekhout, Teun

AU - Hagen, Ferry

AU - Theelen, Bart

AU - Inácio, Joäo

AU - Alonso, Beatriz

AU - Colom, Maria F.

AU - Trilles, Luciana

AU - Montagna, Maria Teresa

AU - De Donno, Antonella

AU - Susever, Serdar

AU - Ergin, Cagri

AU - Velegraki, Aristea

AU - Ellabib, Mohamed S.

AU - Nardoni, Simona

AU - Macci, Cristina

AU - Trovato, Laura

AU - Dipineto, Ludovico

AU - Akcaglar, Sevim

AU - Mlinaric-Missoni, Emilija

AU - Bertout, Sebastien

AU - Vencá, Ana C.F.

AU - Sampaio, Ana C.

AU - Criseo, Giuseppe

AU - Ranque, Stéphane

AU - Çerikçioğlu, Nilgün

AU - Marchese, Anna

AU - Vezzulli, Luigi

AU - Ilkit, Macit

AU - Pasquale, Vincenzo

AU - Polacheck, Itzhack

AU - Lockhart, Shawn R.

PY - 2019/4/3

Y1 - 2019/4/3

N2 - 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.

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KW - Cryptococcus gattii

KW - Cryptococcus neoformans

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KW - MLST

KW - Population genetics

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