Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates

Area of Science:

• Medical Mycology
• Genomics
• Antimicrobial Resistance

Background:

• Candida glabrata is a significant fungal pathogen known for rapid antifungal resistance development.
• Azole treatments induce resistance in C. glabrata, involving multidrug efflux transporters and PDR1 mutations.
• PDR1 mutations can also enhance fungal virulence in host organisms.

Purpose of the Study:

• To compare the genomes of azole-susceptible and azole-resistant Candida glabrata clinical isolates.
• To identify genetic variations, including mutations and rearrangements, that may contribute to antifungal resistance and host adaptation.
• To investigate the role of specific genes, such as PDR1 and MSH2, in the evolution of resistance.

Main Methods:

• Whole-genome sequencing of two sequential C. glabrata isolates (DSY562 and DSY565) using PacBio technology.
• Comparative genomic analysis against a reference genome (CBS138) and between the clinical isolates.
• Identification of single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and other genomic features.

Main Results:

• PacBio sequencing generated high-quality genome assemblies for both isolates, revealing high similarity.
• Comparative analysis identified significant genome rearrangements compared to the reference CBS138, but limited differences between the clinical strains.
• Unique features included retrotransposons and a substantial number of adhesin-like genes, with minor variations in coding regions, including the PDR1 mutation in the resistant isolate.
• A DNA mismatch repair allele of MSH2 was identified, consistent with a hyper-mutator phenotype and accumulated mutations.

Conclusions:

• This is the first study to compare genomes of sequential C. glabrata clinical isolates using PacBio technology.
• Despite host pressure and azole therapy, the genomes of sequential isolates exhibited limited variations.
• The findings suggest that major genomic alterations are not the primary driver of resistance evolution in this context, with potential roles for subtle genetic changes and existing genetic machinery.