Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance

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 othe...

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Autores principales:	Ryan Kean, Christopher Delaney, Leighann Sherry, Andrew Borman, Elizabeth M. Johnson, Malcolm D. Richardson, Riina Rautemaa-Richardson, Craig Williams, Gordon Ramage
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Candida antifungal resistance biofilms efflux pumps gene expression Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/4e8e6da31ce94a6bbddbcc54a6233494
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spelling	oai:doaj.org-article:4e8e6da31ce94a6bbddbcc54a62334942021-11-15T15:25:50ZTranscriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance10.1128/mSphere.00334-182379-5042https://doaj.org/article/4e8e6da31ce94a6bbddbcc54a62334942018-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00334-18https://doaj.org/toc/2379-5042ABSTRACT 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 ~11.5-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. IMPORTANCE Fungal infections represent an important cause of human morbidity and mortality, particularly if the fungi adhere to and grow on both biological and inanimate surfaces as communities of cells (biofilms). Recently, a previously unrecognized yeast, Candida auris, has emerged globally that has led to widespread concern due to the difficulty in treating it with existing antifungal agents. Alarmingly, it is also able to grow as a biofilm that is highly resistant to antifungal agents, yet we are unclear about how it does this. Here, we used a molecular approach to investigate the genes that are important in causing the cells to be resistant within the biofilm. The work provides significant insights into the importance of efflux pumps, which actively pump out toxic antifungal drugs and therefore enhance fungal survival within a variety of harsh environments.Ryan KeanChristopher DelaneyLeighann SherryAndrew BormanElizabeth M. JohnsonMalcolm D. RichardsonRiina Rautemaa-RichardsonCraig WilliamsGordon RamageAmerican Society for MicrobiologyarticleCandidaantifungal resistancebiofilmsefflux pumpsgene expressionMicrobiologyQR1-502ENmSphere, Vol 3, Iss 4 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Candida antifungal resistance biofilms efflux pumps gene expression Microbiology QR1-502
spellingShingle	Candida antifungal resistance biofilms efflux pumps gene expression Microbiology QR1-502 Ryan Kean Christopher Delaney Leighann Sherry Andrew Borman Elizabeth M. Johnson Malcolm D. Richardson Riina Rautemaa-Richardson Craig Williams Gordon Ramage Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance
description	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 ~11.5-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. IMPORTANCE Fungal infections represent an important cause of human morbidity and mortality, particularly if the fungi adhere to and grow on both biological and inanimate surfaces as communities of cells (biofilms). Recently, a previously unrecognized yeast, Candida auris, has emerged globally that has led to widespread concern due to the difficulty in treating it with existing antifungal agents. Alarmingly, it is also able to grow as a biofilm that is highly resistant to antifungal agents, yet we are unclear about how it does this. Here, we used a molecular approach to investigate the genes that are important in causing the cells to be resistant within the biofilm. The work provides significant insights into the importance of efflux pumps, which actively pump out toxic antifungal drugs and therefore enhance fungal survival within a variety of harsh environments.
format	article
author	Ryan Kean Christopher Delaney Leighann Sherry Andrew Borman Elizabeth M. Johnson Malcolm D. Richardson Riina Rautemaa-Richardson Craig Williams Gordon Ramage
author_facet	Ryan Kean Christopher Delaney Leighann Sherry Andrew Borman Elizabeth M. Johnson Malcolm D. Richardson Riina Rautemaa-Richardson Craig Williams Gordon Ramage
author_sort	Ryan Kean
title	Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance
title_short	Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance
title_full	Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance
title_fullStr	Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance
title_full_unstemmed	Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance
title_sort	transcriptome assembly and profiling of <italic toggle="yes">candida auris</italic> reveals novel insights into biofilm-mediated resistance
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/4e8e6da31ce94a6bbddbcc54a6233494
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Transcriptome Assembly and Profiling of <italic toggle="yes">Candida auris</italic> Reveals Novel Insights into Biofilm-Mediated Resistance

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