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

Authors: Ashton, P M and Thanh, L T and Trieu, P H and Van Anh, D and Trinh, N M and Beardsley, J and Kibengo, F and Chierakul, W and Dance, D A B and Rattanavong, S and Davong, V 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 Anscombe, C and Nhat, L T H and Perfect, J and Dougan, G and Baker, S and Harris, S and Day, J N

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.

Journal: Nature communications
DOI: 10.1038/s41467-019-10092-5
Year: 2019

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