<i>In vitro</i> phenotyping results ordered by molecular type, VNI subtype, and high frequency MLST type.

<p>* CSF survival was not performed for one of the eight VNB isolates.</p><p><i>In vitro</i> phenotyping results ordered by molecular type, VNI subtype, and high frequency MLST type.</p

Median <i>in vitro</i> phenotyping values ordered by molecular type, VNI Subtype and high frequency MLST.

<p>Kruskal Wallis analysis performed on groups, and p values shown. Overall median is plotted in red. (A) Survival in <i>ex vivo</i> CSF, (B) Laccase Activity normalised to H99 reference strain, (C) <i>In vitro</i> phagocytosis of isolates by J774 cells (per 1 μl lysate).</p

Phylogenetic and Bayesian analysis of concatenated nucleotide sequences.

<p>(A) SplitsTree neighbour network shows diverse VNII and VNB, and clonal VNI clades. (B) Analysis of VNI clustering using StructureHARVESTER and ΔK shows optimal number of K clusters is 3. (C) Use of STRUCTURE allows VNI sequences to be subdivided into 3 distinct populations: VNI(a), VNI(b), VNI(c).</p

Clinical characteristics and survival of patients infected with different lineages of <i>C neoformans</i>.

<p>(A) Patient survival by molecular type; VNB isolates (n = 8) were associated with significantly worse outcome compared to VNI and VNII isolates at 70 days (p = 0.01) and 365 days (p = 0.003) follow-up in Cox’s proportional hazard survival analysis. (B) Patient survival by high frequency MLST type. (C) Number of patients with and without altered mental status by molecular group (% with altered mental status indicated above each bar). (D) Baseline fungal burden, showing variation by high frequency MLST type.</p

Assignment of MLST alleles, phylogeny and distribution of clinical isolates.

<p>Unrooted, ordered maximum likelihood tree (RAxML, GTR gamma, partitioned by loci) using concatenated nucleotide sequences from 7 loci and one representative sequence for each MLST type. Bootstrap values are shown for branches with greater than 60% agreement between replicates (1000 replicates). Also showing allele typing and MLST assignment for each sequence type, molecular type assignment according to phylogeny, and number of isolates belonging to each ST type.</p