Phylogenomic Placement of American Southwest-Associated Clinical and Veterinary Isolates Expands Evidence for Distinct Cryptococcus gattii VGVI

Abstract

Whole-genome sequencing has advanced our understanding of the population structure of the pathogenic species complex Cryptococcus gattii, which has allowed for the phylogenomic specification of previously described major molecular type groupings and novel lineages. Recently, isolates collected in Mexico in the 1960s were determined to be genetically distant from other known molecular types and were classified as VGVI. We sequenced four clinical isolates and one veterinary isolate collected in the southwestern United States and Argentina from 2012 to 2021. Phylogenomic analysis groups these genomes with those of the Mexican VGVI isolates, expanding VGVI into a clade and establishing this molecular type as a clinically important population. These findings also potentially expand the known Cryptococcus ecological range with a previously unrecognized endemic area.

Keywords: Cryptococcus; VGVI; molecular type; phylogenomics; whole-genome sequencing.

Figure 1

Maximum parsimony phylogenies based on high confidence SNPs showing boxes around the isolates sequenced in this study. (A) This analysis of 24 genomes includes two to eight publicly available genomes from each of the major C. gattii molecular types. The tree covers 87.40% of the reference and comprises 1,733,389 polymorphic loci, with a consistency index of 0.88 and a retention index of 0.97. (B) The VGVI-only phylogeny includes all eight available genomes for this molecular type and comprises 1,123,371 polymorphic loci covering 91.88% of the reference genome. This phylogeny has a consistency index of 0.78 and a retention index of 0.73. The reference for both trees was AZ04665 draft assembly (17.5 Mbp N50: 185.1 Kbp). All branch bootstrap values equal 100, except where noted in red numerals.