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