Analysis of antifungal resistance genes in Candida albicans and Candida glabrata using next generation sequencing

Spettel, Kathrin; Barousch, Wolfgang; Makristathis, Athanasios; Zeller, Iris; Nehr, Marion; Selitsch, Brigitte; Lackner, Michaela; Rath, Peter-Michael; Steinmann, Joerg; Willinger, Birgit

doi:10.1371/journal.pone.0210397

Cited by 86Antifungal resistance and susceptibilityFungal and yeast genetics researchFungal Plant Pathogen Control

Analysis of antifungal resistance genes in Candida albicans and Candida glabrata using next generation sequencing

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Spettel, Kathrin, Barousch, Wolfgang, Makristathis, Athanasios, Zeller, Iris, Nehr, Marion, Selitsch, Brigitte, Lackner, Michaela, Rath, Peter-Michael +2 more·2019·PLoS ONE

DOI 10.1371/journal.pone.0210397PMC PMC6328131

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Abstract

INTRODUCTION/OBJECTIVES: An increase in antifungal resistant Candida strains has been reported in recent years. The aim of this study was to detect mutations in resistance genes of azole-resistant, echinocandin-resistant or multi-resistant strains using next generation sequencing technology, which allows the analysis of multiple resistance mechanisms in a high throughput setting. METHODS: Forty clinical Candida isolates (16 C. albicans and 24 C. glabrata strains) with MICs for azoles and echinocandins above the clinical EUCAST breakpoint were examined. The genes ERG11, ERG3, TAC1 and GSC1 (FKS1) in C. albicans, as well as ERG11, CgPDR1, FKS1 and FKS2 in C. glabrata were sequenced. RESULTS: Fifty-four different missense mutations were identified, 13 of which have not been reported before. All nine echinocandin-resistant Candida isolates showed mutations in the hot spot (HS) regions of FKS1, FKS2 or GSC1. In ERG3 two homozygous premature stop codons were identified in two highly azole-resistant and moderately echinocandin-resistant C. albicans strains. Seven point mutations in ERG11 were determined in azole-resistant C. albicans whereas in azole-resistant C. glabrata, no ERG11 mutations were detected. In 10 out of 13 azole-resistant C. glabrata, 12 different potential gain-of-function mutations in the transcription factor CgPDR1 were verified, which are associated with an overexpression of the efflux pumps CDR1/2. CONCLUSION: This study showed that next generation sequencing allows the thorough investigation of a large number of isolates more cost efficient and faster than conventional Sanger sequencing. Targeting different resistance genes and a large sample size of highly resistant strains allows a better determination of the relevance of the different mutations, and to differentiate between causal mutations and polymorphisms.

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The overlap between CandidaMine variants and two datasets of previously described drug resistance mutations (SENTRY database and PDR1 mutations from the literature) was low, comparable to that found in this work.
“In order to test this we calculated the overlap between CandidaMine variants and two datasets of previously described drug resistance-mutations: the SENTRY database6 and a set of described PDR1 mutations from the literature.71, 72, 73 This yielded low overlaps as well, comparable to those found in our work (Figure S5A).”
From Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata (2021) · cites this paper as [73]

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Authors: Spettel, K., Barousch, W., Makristathis, A., Zeller, I., Nehr, M., Selitsch, B., Lackner, M., Rath, P.-M., Steinmann, J., & Willinger, B.
Affiliations: Medical University of Vienna (AT)
Innsbruck Medical University (AT)
Essen University Hospital (DE)
Paracelsus Medizinische Privatuniversität (DE)
Corresponding author: Willinger, Birgit
ORCID: Spettel, Kathrin
Makristathis, Athanasios
Selitsch, Brigitte
Lackner, Michaela
Rath, Peter-Michael
Steinmann, Joerg
Willinger, Birgit
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2019-01-10
Volume: 14
Issue: 1
Pages: e0210397
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0210397
PMC: PMC6328131
OpenAlex: W2910178341
Cited by: 86
References: 49
Citations by year: 2026: 7 · 2025: 10 · 2024: 11 · 2023: 9 · 2022: 14 · 2021: 19 · 2020: 13 · 2019: 3
FWCI: 9.39
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: PLoS ONE (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Funders: Pfizer
Topics: Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Fungal Plant Pathogen Control
Keywords: antifungal resistance, Candida albicans, Candida glabrata, azole resistance, echinocandin resistance, multidrug resistance, ERG11, ERG3, FKS1, FKS2, efflux pumps, missense mutations, clinical isolates, resistance gene mutations
MeSH terms: Antifungal Agents, Candida albicans, Microbial Sensitivity Tests, Mutation, Sequence Analysis, DNA, Computational Biology, Drug Resistance, Fungal, Candida glabrata

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Analysis of antifungal resistance genes in Candida albicans and Candida glabrata using next generation sequencing

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