Genetic and phenotypic intra-species variation in Candida albicans

Abstract

Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity.

Budding off: bringing functional genomics toCandida albicans

“…Although C. albicans is typically isolated as a diploid, it is also capable of propagating in the haploid or tetraploid states [22,40]. Furthermore, as noted above, aneuploid cells carrying an abnormal complement of chromosomes are frequently found among clinical C. albicans strains [11,[41][42][43], suggesting they can provide a selective advantage in some host contexts. Indeed, C. albicans exposure to the most frequently administered antifungal fluconazole induces aneuploidy in vitro [44], and resistance in the clinic is associated with an extra isochromosome of chromosome 5 in a subset of strains [42,43,45,46].…”

“…To provide a more detailed analysis of genotypic and phenotypic diversity within C. albicans, a recent study [11] sequenced 21 clinical C. albicans isolates representing seven divergent MLST types [19]. The average nucleotide diversity between any two sequenced strains was 0.37%, with 6069 (98.1%) of the genes shared by any two isolates.…”

“…NGS offers many advantages over the SNP-CGH approach including: increased genome coverage, greater sensitivity and the ability to assess strains independent of genetic background [11,39,56,57]. Techniques such as restriction-site-associated DNA sequencing (RAD-Seq) are also emerging, primarily because they dramatically reduce the cost of karyotyping fungal strains by NGS [58,59].…”

“…Among all 21 strains, 461 genes (7.4%) were disrupted in at least 1 strain compared with 57 genes (0.86%) disrupted by nonsense mutations among 71 sequenced Saccharomyces cerevisiae and Saccharomyces paradoxus isolates [27]. Genes with the highest indicators of positive selection encoded cell wall proteins (PGAs), secreted virulence factors (SAP5 and PEP3) and regulators of filamentous growth (FGRs) [11]. The greatest variation in gene copy number was associated with repetitive elements such as the TAR1 gene within the rDNA array and the TLOs in subtelomeric regions.…”

“…CGH arrays were used to determine both the chromosome copy number and the allelic composition, the latter allowing the identification of LOH events [49,51]. LOH occurs frequently in C. albicans [11,[51][52][53], although less so than in diploid S. cerevisiae strains [54], and often influences clinically relevant phenotypes. For example, loss of a low-activity TAC1 allele and gain of a hyperactive allele increased fluconazole resistance in C. albicans [45,55].…”