Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans

P. M. Ashton; L. T. Thanh; P. H. Trieu; D. Van Anh; N. M. Trinh; J. Beardsley; F. Kibengo; W. Chierakul; D. A.B. Dance; S. Rattanavong; V. Davong; L. Q. Hung; N. V.V. Chau; N. L.N. Tung; A. K. Chan; G. E. Thwaites; D. G. Lalloo; C. Anscombe; L. T.H. Nhat; J. Perfect; G. Dougan; S. Baker; S. Harris; J. N. Day

doi:10.1038/s41467-019-10092-5

Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans

P. M. Ashton
, L. T. Thanh
, P. H. Trieu
, D. Van Anh
, N. M. Trinh
, J. Beardsley
, F. Kibengo
, W. Chierakul
, D. A.B. Dance
, S. Rattanavong
, V. Davong
, L. Q. Hung
, N. V.V. Chau
, N. L.N. Tung
, A. K. Chan
, G. E. Thwaites
, D. G. Lalloo
, C. Anscombe
, L. T.H. Nhat
, J. Perfect

G. Dougan, S. Baker, S. Harris, J. N. Day

Oxford University Clinical Research Unit
Nuffield Department of Medicine
University of Sydney
London School of Hygiene and Tropical Medicine
Mahidol University
Laos-Oxford-Mahosot-Wellcome Research Unit
Cho Ray Hospital
Hospital for Tropical Diseases
Sunnybrook Health Sciences Centre
Dignitas International
Liverpool School of Tropical Medicine
Duke University School of Medicine
Wellcome Trust
Wellcome Trust Sanger Institute
Department of Medicine

Research output: Contribution to journal › Article › peer-review

48 Citations (Scopus)

Abstract

Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.

Original language	English
Article number	2035
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-10092-5
Publication status	Published - 1 Dec 2019
Externally published	Yes

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SDG 3 Good Health and Well-being

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10.1038/s41467-019-10092-5

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Ashton, P. M., Thanh, L. T., Trieu, P. H., Van Anh, D., Trinh, N. M., Beardsley, J., Kibengo, F., Chierakul, W., Dance, D. A. B., Rattanavong, S., Davong, V., Hung, L. Q., Chau, N. V. V., Tung, N. L. N., Chan, A. K., Thwaites, G. E., Lalloo, D. G., Anscombe, C., Nhat, L. T. H., ... Day, J. N. (2019). Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans. Nature Communications, 10(1), Article 2035. https://doi.org/10.1038/s41467-019-10092-5

@article{e65900a874ff40379f774fcd77e02a4d,

title = "Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans",

abstract = "Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91\% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.",

author = "Ashton, \{P. M.\} and Thanh, \{L. T.\} and Trieu, \{P. H.\} and \{Van Anh\}, D. and Trinh, \{N. M.\} and J. Beardsley and F. Kibengo and W. Chierakul and Dance, \{D. A.B.\} and S. Rattanavong and V. Davong and Hung, \{L. Q.\} and Chau, \{N. V.V.\} and Tung, \{N. L.N.\} and Chan, \{A. K.\} and Thwaites, \{G. E.\} and Lalloo, \{D. G.\} and C. Anscombe and Nhat, \{L. T.H.\} and J. Perfect and G. Dougan and S. Baker and S. Harris and Day, \{J. N.\}",

note = "Publisher Copyright: {\textcopyright} 2019, The Author(s).",

year = "2019",

month = dec,

day = "1",

doi = "10.1038/s41467-019-10092-5",

language = "English",

volume = "10",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

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Ashton, PM, Thanh, LT, Trieu, PH, Van Anh, D, Trinh, NM, Beardsley, J, Kibengo, F, Chierakul, W, Dance, DAB, Rattanavong, S, Davong, V, Hung, LQ, Chau, NVV, Tung, NLN, Chan, AK, Thwaites, GE, Lalloo, DG, Anscombe, C, Nhat, LTH, Perfect, J, Dougan, G, Baker, S, Harris, S & Day, JN 2019, 'Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans', Nature Communications, vol. 10, no. 1, 2035. https://doi.org/10.1038/s41467-019-10092-5

TY - JOUR

T1 - Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans

AU - Ashton, P. M.

AU - Thanh, L. T.

AU - Trieu, P. H.

AU - Van Anh, D.

AU - Trinh, N. M.

AU - Beardsley, J.

AU - Kibengo, F.

AU - Chierakul, W.

AU - Dance, D. A.B.

AU - Rattanavong, S.

AU - Davong, V.

AU - Hung, L. Q.

AU - Chau, N. V.V.

AU - Tung, N. L.N.

AU - Chan, A. K.

AU - Thwaites, G. E.

AU - Lalloo, D. G.

AU - Anscombe, C.

AU - Nhat, L. T.H.

AU - Perfect, J.

AU - Dougan, G.

AU - Baker, S.

AU - Harris, S.

AU - Day, J. N.

PY - 2019/12/1

Y1 - 2019/12/1

N2 - Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.

AB - Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.

UR - https://www.scopus.com/pages/publications/85065201177

U2 - 10.1038/s41467-019-10092-5

DO - 10.1038/s41467-019-10092-5

M3 - Article

C2 - 31048698

AN - SCOPUS:85065201177

SN - 2041-1723

VL - 10

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 2035

ER -

Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans

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