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Title: Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans
Authors: 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
Dignitas International
Cho Ray Hospital
London School of Hygiene & Tropical Medicine
University of Cambridge
The University of Sydney
Wellcome Trust
Liverpool School of Tropical Medicine
University of Toronto
Mahidol University
Nuffield Department of Clinical Medicine
Duke University
Wellcome Sanger Institute
MRC/UVRI and LSHTM Uganda Research Unit
Wellcome Trust Research Unit
Oxford University Clinical Research Unit
Keywords: Biochemistry, Genetics and Molecular Biology;Chemistry
Issue Date: 1-Dec-2019
Citation: Nature Communications. Vol.10, No.1 (2019)
Abstract: © 2019, The Author(s). 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.
ISSN: 20411723
Appears in Collections:Scopus 2019

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