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; David Lalloo; Cat 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
, David Lalloo
, Cat Anscombe
, L. T.H. Nhat
, J. Perfect

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

University of Oxford
University of Sydney
London School of Hygiene and Tropical Medicine
Mahidol University
Lao PDR
Cho Ray Hospital
University College London Hospitals NHS Foundation Trust
University of Toronto
Dignitas International
Duke University
Wellcome Trust
Wellcome Sanger Institute
University of Cambridge

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

47 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
Pages (from-to)	2035
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-10092-5
Publication status	Published - 2 May 2019

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Access to Document

10.1038/s41467-019-10092-5Licence: CC BY

S41467-019-10092-5Final published version, 1.24 MBLicence: CC BY

Cite this

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., 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), 2035. Article 2035. https://doi.org/10.1038/s41467-019-10092-5

@article{72bb4bd7556d478da25fd369647b124a,

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 David Lalloo and Cat Anscombe and Nhat, \{L. T.H.\} and J. Perfect and G. Dougan and S. Baker and S. Harris and Day, \{J. N.\}",

year = "2019",

month = may,

day = "2",

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

language = "English",

volume = "10",

pages = "2035",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

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, D, 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, pp. 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, David

AU - Anscombe, Cat

AU - Nhat, L. T.H.

AU - Perfect, J.

AU - Dougan, G.

AU - Baker, S.

AU - Harris, S.

AU - Day, J. N.

PY - 2019/5/2

Y1 - 2019/5/2

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.

U2 - 10.1038/s41467-019-10092-5

DO - 10.1038/s41467-019-10092-5

M3 - Article

SN - 2041-1723

VL - 10

SP - 2035

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 2035

ER -

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

Abstract

UN SDGs

Access to Document

Fingerprint

Cite this