Transcriptome assembly and profiling of Candida auris reveals novel insights into biofilm-mediated resistance

Ryan Kean, Christopher Delaney, Leighann Sherry, Andrew Borman, Elizabeth M. Johnson, Malcolm D. Richardson, Riina Rautemaa-Richardson, Craig Williams, Gordon Ramage

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Abstract

Candida auris has emerged as a significant global nosocomial pathogen. This is primarily due to its antifungal resistance profile but also its capacity to form adherent biofilm communities on a range of clinically important substrates. While we have a comprehensive understanding of how other Candida species resist and respond to antifungal challenge within the sessile phenotype, our current understanding of C. auris biofilm-mediated resistance is lacking. In this study, we are the first to perform transcriptomic analysis of temporally developing C. auris biofilms, which were shown to exhibit phase- and antifungal class-dependent resistance profiles. A de novo transcriptome assembly was performed, where sequenced sample reads were assembled into an ar12611.5-Mb transcriptome consisting of 5,848 genes. Differential expression (DE) analysis demonstrated that 791 and 464 genes were upregulated in biofilm formation and planktonic cells, respectively, with a minimum 2-fold change. Adhesin-related glycosylphosphatidylinositol (GPI)-anchored cell wall genes were upregulated at all time points of biofilm formation. As the biofilm developed into intermediate and mature stages, a number of genes encoding efflux pumps were upregulated, including ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transporters. When we assessed efflux pump activity biochemically, biofilm efflux was greater than that of planktonic cells at 12 and 24 h. When these were inhibited, fluconazole sensitivity was enhanced 4- to 16-fold. This study demonstrates the importance of efflux-mediated resistance within complex C. auris communities and may explain the resistance of C. auris to a range of antimicrobial agents within the hospital environment.
Original languageEnglish
JournalmSphere
Volume3
DOIs
Publication statusPublished - 11 Jul 2018

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Kean, R., Delaney, C., Sherry, L., Borman, A., Johnson, E. M., Richardson, M. D., Rautemaa-Richardson, R., Williams, C., & Ramage, G. (2018). Transcriptome assembly and profiling of Candida auris reveals novel insights into biofilm-mediated resistance. mSphere, 3. https://doi.org/10.1128/mSphere.00334-18