Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names

PLoS Pathogens
Alexander P DouglassKenneth H Wolfe

Abstract

We investigated genomic diversity of a yeast species that is both an opportunistic pathogen and an important industrial yeast. Under the name Candida krusei, it is responsible for about 2% of yeast infections caused by Candida species in humans. Bloodstream infections with C. krusei are problematic because most isolates are fluconazole-resistant. Under the names Pichia kudriavzevii, Issatchenkia orientalis and Candida glycerinogenes, the same yeast, including genetically modified strains, is used for industrial-scale production of glycerol and succinate. It is also used to make some fermented foods. Here, we sequenced the type strains of C. krusei (CBS573T) and P. kudriavzevii (CBS5147T), as well as 30 other clinical and environmental isolates. Our results show conclusively that they are the same species, with collinear genomes 99.6% identical in DNA sequence. Phylogenetic analysis of SNPs does not segregate clinical and environmental isolates into separate clades, suggesting that C. krusei infections are frequently acquired from the environment. Reduced resistance of strains to fluconazole correlates with the presence of one gene instead of two at the ABC11-ABC1 tandem locus. Most isolates are diploid, but one-quarter are trip...Continue Reading

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Datasets Mentioned

BETA
SRP139056
SRP139299

Methods Mentioned

BETA
RNAseq
RNA-seq
Illumina sequencing
flow cytometry
genotyping

Software Mentioned

SAMtools
DNAMAN
MUMmer
BWA
Pilon
STRUCTURE
MAFFT
Picard Tools
Burrows
PhyML

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