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In South Africa,  Cryptococcus neoformans  is the most common cause of adult meningitis. We performed multi locus sequence typing and fluconazole susceptibility testing of clinical  C. neoformans  isolates collected from 251 South African patients with cryptococcosis through national surveillance from 2005 to 2009. We examined the association between clinical characteristics of patients and genotype, and the effect of genotype on in-hospital mortality. We performed whole genome phylogenetic analysis of fifteen  C. neoformans  isolates with the molecular type VNB and tested their virulence in a  Galleria mellonella  model. Most isolates had the molecular type VNI (206/251, 82%), followed by VNII (25/251, 10%), VNB (15/251, 6%), and VNIV (5/251, 2%); 67 sequence types were identified. There were no differences in fluconazole minimum inhibitory concentration (MIC) values among molecular types and the majority of strains had low MIC values (MIC 50  of 1 µg/mL and MIC 90  of 4 µg/mL). Males were almost twice as likely of being infected with a non-VNI genotype (adjusted odds ratio [OR]: 1.65, 95% confidence interval [CI]: 0.25–10.99;  p  = 0.61). Compared to patients infected with a VNI genotype, those with a non-VNI genotype had a 50% reduced adjusted odds of dying in hospital (95% CI: 0.03–7.57;  p  = 0.62). However, for both these analyses, our estimates had wide confidence intervals spanning 1 with large  p -values. Fifteen VNB strains were not as virulent in a  G. mellonella  larval model as the H99 reference strain. A majority of these VNB strains belonged to the VNBII clade and were very closely related by phylogenetic analysis.

Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005–2009