Minimum spanning trees using the goeBURST algorithm showing MLST relationships among Asian C. neoformans var. <i>grubii</i> isolates.

<p>(A) Tree represents 476 <i>C</i>. <i>neoformans</i> var. <i>grubii</i> isolates from different countries. Each circle represents a unique genotype/sequence type (STs). The size of the circle corresponds to the number of isolates within that genotype. Different colors correspond to different countries; (B) Same as A, but now showing the genotypes from clinical and environmental sources; (C) Same as A and B, but with the addition of the genotypes of 179 <i>C</i>. <i>neoformans</i> var. <i>grubii</i> isolates from different continents (data from <a href="http://mlst.mycologylab.org" target="_blank">http://mlst.mycologylab.org</a> and previous reports by Cogliati <i>et al</i>., 2013 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072222#pone.0072222-Cogliati1" target="_blank">[44]</a> and Mihara <i>et al</i>., 2012 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072222#pone.0072222-Mihara1" target="_blank">[16]</a>).</p

Distribution of sequence types (STs) of <i>C</i>. <i>neoformans</i> var. <i>grubii</i> isolates according to HIV status of the patients.

<p>The predominant STs in each HIV status category are indicated in bold.</p

Primers used for MLST analysis of Asian <i>C</i>. <i>neoformans</i> var. <i>grubii</i> isolates.

<p>Primers used for MLST analysis of Asian <i>C</i>. <i>neoformans</i> var. <i>grubii</i> isolates.</p

Analysis of Molecular Variance (AMOVA) of Asian <i>C</i>. <i>neoformans</i> according to HIV status and geographical origin.

<p>Analysis of Molecular Variance (AMOVA) of Asian <i>C</i>. <i>neoformans</i> according to HIV status and geographical origin.</p

Unrooted Neighbor-joining phylogenetic analysis of the concatenated sequences of each sequence type (ST) found among the global isolates.

<p>Numbers at each branch indicate bootstrap values >50%, based on 1,000 replicates. Each color rectangle represents the geographic origin of isolates.</p

The MIC range, MIC₅₀, MIC₉₀, and geometric mean for 14 Hong Kong and all 476 <i>C</i>. <i>neoformans</i> isolates for seven antifungals.

<p>The MIC range, MIC₅₀, MIC₉₀, and geometric mean for 14 Hong Kong and all 476 <i>C</i>. <i>neoformans</i> isolates for seven antifungals.</p

DNA polymorphisms in each MLST locus and concatenated sequences of Asian <i>C</i>. <i>neoformans</i> var. <i>grubii</i> isolates.

<p>S: number of polymorphic sites.</p><p>π: nucleotide diversity.</p><p>θ_s: Watterson's θ per sequence.</p><p><i>k</i>: average number of nucleotide differences per sequence.</p><p>h: number of haplotypes.</p><p><i>H_d</i>: haplotype diversity.</p><p><i>D</i>, <i>F_D</i>, <i>F_F</i> and <i>F_s</i>: Tajima's D, Fu and Li's D*, Fu and Li's F* and Fu's Fs, respectively. The p value <0.05, *; <0.01, **; <0.001, ***.</p

Unrooted Neighbor-joining phylogenetic analysis of the concatenated MLST sequences found among Asian isolates.

<p>Numbers at each branch indicate bootstrap values >50%, based on 1,000 replicates. Each color rectangle represents the origin of isolates according to geographic origin, and clinical and environmental origin. Number inside each color rectangle indicates number of isolates.</p

Diagram showing DNA polymorphisms of <i>C.</i><i>neoformans</i> var. <i>grubii</i> from different Asian regions.

<p>(A) DNA polymorphism, genetic differentiation and gene flow; (B) same as A, but comparing African, American, Asian and European populations.</p

Distribution of sequence types (STs) of <i>C</i>. <i>neoformans</i> var. <i>grubii</i> isolates among different countries.

<p>The predominant STs in each country are indicated in bold.</p