Phenotypic and Genomic Evolution in Candida albicans during Long-term Pathologic Interaction in Patients with Chronic Mucocutaneous Candidiasis

Abstract

Background The Candida albicans genome displays a high level of plasticity. Point mutations or large-scale genetic changes, including aneuploidies or large-range loss-of-heterozygosity (LOH) events, can occur in vitro and in vivo under different stress conditions. Chronic Mucocutaneous Candidiasis (CMC) is a complex and rare case of primary immunodeficiency in humans, characterized by chronic non-invasive C. albicans infections of the skin and mucosae. CMC is an interesting model of long-term and pathologic interactions between C. albicans and the host, possibly leading to genomic evolution. Methods Sixty-three C. albicans strains isolated from the mouth, skin, vagina and nails from 11 patients with CMC and their family were studied using Multi Locus Sequence Typing (MLST) and extensive phenotypic analysis. We sequenced the genomes of 27 isolates (Illumina Hiseq-100 bp reads) selected to represent different patients, anatomical sites and time of sampling. SNPs were detected using GATK and selected with the recommended filters. Post-treatment analysis was performed using dedicated scripts to analyze Copy Number Variations (CNVs), SNP density and distal LOH per chromosome. Results The 63 strains were distributed within 4 clades and each patient was infected over time with strains sharing a unique or closely related MLST patterns. These strains exhibited an extensive phenotypic variability in terms of growth rates, filamentation, stress resistance and susceptibility to antifungal agents. The whole genome sequencing of the 27 strains (104 X coverage on average) allowed to cover about 99.4 % of the reference SC5314 genome. While genomes are heterozygous, many LOH tracts were found in each strain, but no aneuploidy event was detected by CNV analysis. Characterization of genetic changes in 6 strains isolated from the mouth of one patient over 7 years revealed appearance and fixation of LOH events. Among the 38,000 SNPs shared by all the 6 strains, 74 were predicted to have a significant impact on proteins. Furthermore, while the strains were closely related, about 5,000 transient or recurrent SNPs were observed between the strains. Conclusion Altogether, these findings show extensive variations both at the genomic and phenotypic levels in C. albicans strains during chronic infection in CMC patients and suggest that CMC could be an interesting model for the study of C. albicans genomic evolution.