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