Biology and genetic diversity of Candida krusei isolates from fermented vegetables and clinical samples in China

Virulence. 2024 Dec;15(1):2411543. doi: 10.1080/21505594.2024.2411543. Epub 2024 Oct 17.

Abstract

Candida krusei, also known as Pichia kudriavzevii, is an emerging non-albicans Candida (NAC) species causing both superficial and deep-seated infections in humans. This fungal pathogen is inherently resistant to the first-line antifungal drug, fluconazole, and is widely distributed in natural environments such as soil, foods, vegetables, and fruits. In this study, we collected 86 C. krusei strains from clinical settings and traditional fermented vegetables from different areas of China. Compared to C. krusei strains from fermented vegetables, clinical isolates exhibited a higher ability to undergo filamentation and biofilm development, which could facilitate its host colonization and infections. Isolates from fermented vegetables showed higher resistance to several antifungal drugs including fluconazole, voriconazole, itraconazole, amphotericin B, and caspofungin, than clinical strains, while they were more susceptible to posaconazole than clinical strains. Although C. krusei has been thought to be a diploid organism, we found that one-fourth of clinical strains and the majority of isolates from fermented vegetables (87.5%) are triploid. Whole-genome sequencing and population genetic analyses demonstrated that isolates from clinical settings and fermented food are genetically associated, and distributed across a wide range of genetic clusters. Additionally, we found that six nucleotide substitutions at the promoter region of the ABC11 gene, encoding a multidrug efflux pump, could play a critical role in antifungal resistance in this species. Given the ubiquitous distribution of C. krusei strains in fermented vegetables and their genetic association with clinical strains, a One Health approach will be necessary to control the prevalence of this pathogen.

Keywords: Candida krusei; antifungal resistance; fermented food; genetic diversity; ploidy variation; population genetics.

MeSH terms

  • Antifungal Agents* / pharmacology
  • Biofilms / growth & development
  • Candida* / classification
  • Candida* / drug effects
  • Candida* / genetics
  • Candida* / isolation & purification
  • Candidiasis* / microbiology
  • China
  • Drug Resistance, Fungal / genetics
  • Fermentation
  • Fermented Foods / microbiology
  • Genetic Variation*
  • Humans
  • Microbial Sensitivity Tests*
  • Pichia / classification
  • Pichia / drug effects
  • Pichia / genetics
  • Pichia / isolation & purification
  • Vegetables* / microbiology
  • Whole Genome Sequencing

Substances

  • Antifungal Agents

Supplementary concepts

  • Pichia kudriavzevii

Grants and funding

This work was supported by the National Key Research and Development Program of China [grant no. 2021YFC2300400 to G.H., and no. 2022YFC2303000 to J.B.], National Natural Science Foundation of China [nos. 31930005 and 82272359 to G.H., nos. 32170193 and 32000018 to J.B., and 82202546 to Q.Z.], and Shanghai Science and Technology Innovation Action Plan 2023 “Basic Research Project” [23JC1404203 to GH]. The content is the sole responsibility of the authors and does not represent the views of the funders. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.