P. M. AshtonL. T. ThanhP. H. TrieuD. Van AnhN. M. TrinhJ. BeardsleyF. KibengoW. ChierakulD. A.B. DanceS. RattanavongV. DavongL. Q. HungN. V.V. ChauN. L.N. TungA. K. ChanG. E. ThwaitesD. G. LallooC. AnscombeL. T.H. NhatJ. PerfectG. DouganS. BakerS. HarrisJ. N. DayDignitas InternationalCho Ray HospitalLondon School of Hygiene & Tropical MedicineUniversity of CambridgeThe University of SydneyUCLWellcome TrustLiverpool School of Tropical MedicineUniversity of TorontoMahidol UniversityNuffield Department of Clinical MedicineDuke UniversityWellcome Sanger InstituteMRC/UVRI and LSHTM Uganda Research UnitWellcome Trust Research UnitOxford University Clinical Research Unit2020-01-272020-01-272019-12-01Nature Communications. Vol.10, No.1 (2019)204117232-s2.0-85065201177https://repository.li.mahidol.ac.th/handle/20.500.14594/50024© 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.Mahidol UniversityBiochemistry, Genetics and Molecular BiologyChemistryArticleSCOPUS10.1038/s41467-019-10092-5