Metzner, K. M. | bioRxiv Science

bioRxiv2026

CRISPR-activation reveals key resistance genes and vulnerabilities of copy number variants in Candida albicans

Changes in gene copy number are an extremely important source of variation and are frequently observed during the acquisition of drug resistance. The opportunistic human fungal pathogen Candida albicans frequently adapts to antifungal drugs via large copy number variations (CNVs) that amplify hundreds of genes simultaneously. Despite the recurrent amplification of CNVs across diverse clinical isolates, the genes that contribute to drug resistance are not known. Additionally, by amplifying many genes, CNVs might result in cross-adaptation or fitness trade-offs to multiple environments, which has major implications for how CNVs are expected to contribute to adaptation in complex environments like a mammalian host. We use CRISPR-activation to systematically assay the fitness effects of individually overexpressing [~]800 genes in four genetically diverse isolates across eight physiologically relevant environments. We identify 198 genes with significant fitness effects in at least one environment in one or more genetic backgrounds. We identify novel genes with positive fitness effects in two different classes of antifungal drug and observe frequent gene-by-environment interactions for the fitness effects of gene overexpression. Additive fitness effects of individual gene overexpression are a significant predictor of the fitness of multiple isolates with CNVs and can explain fitness trade-offs observed between classes of antifungal drug for the CNV isolates. These findings identify genes that increase fitness in drug and those that create vulnerabilities in CNV isolates and can help inform treatment of isolates adapting to antifungal drug via CNVs.

microbiology↗

bioRxiv2022

Human commensal Candida albicans strains demonstrate substantial within-host diversity and retained pathogenic potential

Candida albicans is a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen. C. albicans is remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is unclear how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we undertook an examination of commensal isolates from healthy donors with a goal of identifying site-specific phenotypic adaptation and genetic variation associated with these phenotypes. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverse C. albicans strains, and that this genetic diversity includes both SNVs and structural rearrangements. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterized ZMS1 transcription factor that was sufficient to drive hyper invasion into agar. However, our commensal strains retained the capacity to cause disease in systemic models of infection, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity of C. albicans and suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.

microbiology↗