Aneuploidy, polyploidy, and loss of heterozygosity distinguish serial bloodstream isolates of Candida albicans

Supplemental data for Aneuploidy, polyploidy, and loss of heterozygosity distinguish serial bloodstream isolates of Candida albicans. Candida albicans is an important opportunistic fungal pathogen with extensive genomic variation. We performed comparative genomic and phenotypic analysis of 101 C. albicans bloodstream isolates collected from 55 patients in the Twin Cities region of Minnesota, including serial isolates from 19 patients. We analyzed the phylogenetic relationships of these isolates relative to 199 globally-collected public C. albicans genomes. This study’s regional isolates span the phylogenetic diversity of C. albicans; 6 isolates represent novel outliers to known clades. While all serial isolates from the same patient clustered together phylogenetically, we observed extensive large-scale genomic variation between serial isolates including polyploidy, aneuploidy, copy number variation, loss of heterozygosity, and chromosomal rearrangements. We demonstrated how a heterozygous ERG251 variant drives azole tolerance in a clinical isolate from a patient with a history of recurrent infections. Using serial isolates, we demonstrated that polyploidy provides an adaptive advantage in the presence of fluconazole despite the absence of overt antifungal drug resistance. Our analysis of closely matched serial isolates reveals the genomic plasticity of C. albicans during invasive infections and identifies variation driving antifungal drug tolerance.The Illumina whole genome sequencing data is deposited at the NCBI SRA, Bioproject ID PRJNA1068683.Supplemental Figure S1: Maximum-likelihood, midpoint-rooted phylogenetic tree with 101 new isolates (this study) and 199 publicly available genomesSupplemental Figure S2: LOH patterns distinguish unrelated strainsSupplemental Figure S3: Single allele ERG251 dysfunction does not have a significant fitness cost and complementation of WT ERG251 allele increases azole sensitivitySupplemental Figure S4: Evidence for reciprocal translocation between Chr2 and Chr6 in isolate 60Supplemental Figure S5: Uncropped karyotype gels and Southern blotsSupplemental Figure S6: Deletion of orf19.4069 (and dubious orf19.4070) in clinical isolates from multiple phylogenetic cladesSupplemental Table S1: Strain table with MIC, SMG, MLST, clade, genome heterozygositySupplemental Table S2: Publicly availabe genomes analyzed in this studySupplemental Table S3: Pearson's correlation of heterozygosity and phenotypesSupplemental Table S4: Aneuploid isolate FACS and estimated relative copy number by read depth analysisSupplemental Table S5: CNV size, breakpoints and associated repeat regionsSupplemental Table S6: Gene amplifications and deletionsSupplemental Table S7: Primers used for WT ERG251 transformationSupplemental Table S8: CFU counts for Figure 7Archive of analysis scripts: 2024_Candida_albicans_MEC_analysis_github_files