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

Transcriptional profiling of azole-resistant Candida parapsilosis strains

Open access
Silva, A. P., Miranda, I. M., Guida, A., Synnott, J., Rocha, R., Silva, R., Amorim, A., Pina-Vaz, C. +2 more·2011·Antimicrobial Agents and Chemotherapy

Abstract

Herein we describe the changes in the gene expression profile of Candida parapsilosis associated with the acquisition of experimentally induced resistance to azole antifungal drugs. Three resistant strains of C. parapsilosis were obtained following prolonged in vitro exposure of a susceptible clinical isolate to constant concentrations of fluconazole, voriconazole, or posaconazole. We found that after incubation with fluconazole or voriconazole, strains became resistant to both azoles but not to posaconazole, although susceptibility to this azole decreased, whereas the strain incubated with posaconazole displayed resistance to the three azoles. The resistant strains obtained after exposure to fluconazole and to voriconazole have increased expression of the transcription factor MRR1, the major facilitator transporter MDR1, and several reductases and oxidoreductases. Interestingly, and similarly to what has been described in C. albicans, upregulation of MRR1 and MDR1 is correlated with point mutations in MRR1 in the resistant strains. The resistant strain obtained after exposure to posaconazole shows upregulation of two transcription factors (UPC2 and NDT80) and increased expression of 13 genes involved in ergosterol biosynthesis. This is the first study addressing global molecular mechanisms underlying azole resistance in C. parapsilosis; the results suggest that similarly to C. albicans, tolerance to azoles involves the activation of efflux pumps and/or increased ergosterol synthesis.

AI snapshot

Written from the paper’s full text.

TL;DR

This study generated three azole-resistant Candida parapsilosis strains in vitro and used microarray profiling to show that fluconazole/voriconazole resistance involves MRR1/MDR1 efflux upregulation, while posaconazole resistance involves UPC2/NDT80 and ergosterol biosynthesis genes. It is described as the first study addressing global molecular mechanisms underlying azole resistance in C. parapsilosis.

Key findings

  • After 60 days of exposure to fluconazole (16 μg/ml), voriconazole (2 μg/ml), or posaconazole (1 μg/ml), resistant strains BC014RFLC and BC014RVRC had MICs of 128 μg/ml FLC, 4 μg/ml VRC, and 0.5 μg/ml PSC; BC014RPSC had MICs of 128 μg/ml FLC, 16 μg/ml VRC, and 32 μg/ml PSC. Resistance was stable after 60 days without drug, with no MIC decrease greater than 1 dilution.
  • Microarray analysis found differential expression (FC > 2, P < 0.05) of 1,128 genes (595 upregulated, 533 downregulated) in BC014RFLC, 210 genes (138 upregulated, 72 downregulated) in BC014RVRC, and 598 genes (341 upregulated, 257 downregulated) in BC014RPSC.
  • BC014RFLC and BC014RVRC shared 130 differentially regulated genes, representing 62% of total genes in BC014RVRC; these included increased expression of MRR1, MDR1, and several reductases/oxidoreductases. MDR1 was upregulated 19.43-fold in BC014RFLC and 40.22-fold in BC014RVRC, but unchanged in BC014RPSC; MRR1 upregulation correlated with point mutations in MRR1.
  • BC014RPSC showed upregulation of transcription factors UPC2 and NDT80 and increased expression of 13 genes involved in ergosterol biosynthesis; GO analysis found sterol biosynthesis overrepresented (19/409 cluster frequency vs 32/5,085 background, corrected P = 1.17E−10).

Methods

  • A single azole-susceptible clinical isolate, C. parapsilosis BC014S, was subcultured daily for 60 days in RPMI 1640 with constant fluconazole, voriconazole, or posaconazole, generating BC014RFLC, BC014RVRC, and BC014RPSC. MICs were determined by CLSI M27-A3/M27-S3, with population analysis and stability testing after 60 days without antifungal drug.
  • RNA from overnight YEPD cultures without antifungal drugs was profiled on Agilent C. parapsilosis microarrays (GPL13192) covering 5,834 putative ORFs, with four biological replicates per experiment including two dye swaps. Data were analyzed with Limma, Loess normalization, and thresholds of FC > 2 and adjusted P < 0.05; selected genes were confirmed by RT-qPCR, and MRR1, UPC2, and NDT80 were sequenced. Raw data are in GEO accession GSE27409.

Limitations

  • The paper does not include a dedicated limitations section.
  • Evident from the text: resistance was induced in vitro from a single susceptible clinical isolate (BC014S), so findings may not represent clinical azole-resistant C. parapsilosis populations or in vivo resistance development.
  • Evident from the text: transcriptome profiling was performed on strains grown without antifungal drugs, measuring constitutive changes rather than acute drug exposure; one posaconazole array failed quality control and was discarded as an outlier.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1128/aac.01127-10

Cites

80 of 80 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 19 cited sources checked · 0 supported · 0 flagged

  • Findingown data
    § RESULTS AND DISCUSSION

    In BC014RPSC, GO terms associated with sterol biosynthesis, response to chemical synthesis, and response to drugs are overrepresented.

    “whereas in the BC014RPSC strain, GO terms associated with sterol biosynthesis, response to chemical synthesis, and response to drugs are overrepresented”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • Findingown data
    § RESULTS AND DISCUSSION

    Population analysis demonstrated the homogeneous nature of the population for all three resistant strains, excluding the possibility that a mixture of susceptible and resistant clones was present in the final cultures.

    “Population analysis clearly demonstrated the homogeneous nature of the population for all strains (data not shown), excluding the possibility that a mixture of susceptible and resistant clones is present in the final cultures.”
    Quote in the paperSubstantial claim
  • Findingown data
    § RESULTS AND DISCUSSION

    In BC014RVRC, the GO term associated with response to chemical stimulus is overrepresented.

    “In BC014RVRC, the GO term associated with response to chemical stimulus is overrepresented”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • Findingown data
    § Abstract

    Upregulation of MRR1 and MDR1 is correlated with point mutations in MRR1 in the resistant strains.

    “Interestingly, and similarly to what has been described in C. albicans, upregulation of MRR1 and MDR1 is correlated with point mutations in MRR1 in the resistant strains.”
    Quote in the paperSubstantial claim
  • Findingown data
    § Abstract

    Three resistant C. parapsilosis strains were obtained after prolonged in vitro exposure of a susceptible clinical isolate to constant concentrations of fluconazole, voriconazole, or posaconazole.

    “Three resistant strains of C. parapsilosis were obtained following prolonged in vitro exposure of a susceptible clinical isolate to constant concentrations of fluconazole, voriconazole, or posaconazole.”
    • Also stated in: § MATERIALS AND METHODS · plain
      “In summary, three resistant strains were generated from the initial susceptible strain, strain BC014S, which were designated BC014RFLC, BC014RVRC, and BC014RPSC.”
    Quote in the paperSubstantial claim
  • May combine two claims. 15
  • Classified as probably not a substantial claim. 14
  • May combine two claims.

    Findingown data
    § Abstract

    The resistant strains obtained after exposure to fluconazole and voriconazole have increased expression of the transcription factor MRR1, the major facilitator transporter MDR1, and several reductases and oxidoreductases.

    “The resistant strains obtained after exposure to fluconazole and to voriconazole have increased expression of the transcription factor MRR1, the major facilitator transporter MDR1, and several reductases and oxidoreductases.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data
    § RESULTS AND DISCUSSION

    Azoles impaired the expression of genes involved in multiple cellular processes, resulting in a pleiotropic effect upon gene expression.

    “Azoles impaired the expression of genes involved in multiple cellular processes, resulting in a pleiotropic effect upon gene expression.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • May combine two claims.

    Findingown data
    § Abstract

    The resistant strain obtained after exposure to posaconazole shows upregulation of two transcription factors (UPC2 and NDT80) and increased expression of 13 genes involved in ergosterol biosynthesis.

    “The resistant strain obtained after exposure to posaconazole shows upregulation of two transcription factors (UPC2 and NDT80) and increased expression of 13 genes involved in ergosterol biosynthesis.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data
    § RESULTS AND DISCUSSION

    Expression of MDR1 is upregulated by 19.43-fold in BC014RFLC and 40.22-fold in BC014RVRC, confirmed by RT-qPCR, whereas its expression in BC014RPSC remained unchanged.

    “Expression of MDR1 is upregulated by 19.43- and 40.22-fold (confirmed by RT-qPCR; Fig. 4) in BC014RFLC and BC014RVRC strains, whereas its expression in the BC014RPSC strain remained unchanged.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • May combine two claims.

    Findingown data
    § RESULTS AND DISCUSSION

    Clusters 1, 2, and 3 contain genes with increased expression in BC014RFLC and BC014RVRC strains; cluster 3 showed the greatest changes in gene expression.

    “Clusters 1, 2, and 3 contain genes with increased expression in BC014RFLC and BC014RVRC strains; cluster 3 showed the greatest changes in gene expression”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • May combine two claims.

    Findingown data
    § Abstract

    The strains obtained after exposure to fluconazole or voriconazole became resistant to both fluconazole and voriconazole but not to posaconazole, although susceptibility to posaconazole decreased (posaconazole MIC increased 4 dilutions).

    “We found that after incubation with fluconazole or voriconazole, strains became resistant to both azoles but not to posaconazole, although susceptibility to this azole decreased”
    • Also stated in: § RESULTS AND DISCUSSION · plain
      “Strains obtained after exposure to either fluconazole (BC014RFLC) or voriconazole (BC014RVOR) acquired resistance to both drugs, but not to posaconazole, although the posaconazole MIC value increased 4 dilutions.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data
    § RESULTS AND DISCUSSION

    All three induced resistant strains maintained a stable resistance pattern after subculturing in the absence of antifungal drugs for 60 days, with no decrease greater than 1 dilution in MIC values.

    “All three induced resistant strains maintained a stable resistance pattern after they were subcultured in the absence of antifungal drugs for 60 days. No decrease greater than 1 dilution was found in MIC values (data not shown).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data
    § RESULTS AND DISCUSSION

    130 genes were differentially regulated in both BC014RFLC and BC014RVRC, representing 62% of total genes in BC014RVRC.

    “Because BC014RFLC and BC014RVRC strains displayed similar resistance profiles, the genes that were differentially regulated in both were identified (130 genes, representing 62% of total genes in BC014RVRC).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • May combine two claims.

    Findingown data
    § RESULTS AND DISCUSSION

    In BC014RFLC, up to 13% of upregulated genes were associated with RNA metabolic processes and ribosome biogenesis and 10% were associated with translation.

    “However, in the BC014RFLC strain, up to 13% of the upregulated genes were associated with RNA metabolic processes and ribosome biogenesis and 10% were associated with translation”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • May combine two claims.

    Findingown data
    § RESULTS AND DISCUSSION

    Microarray analysis identified differential expression (FC > 2, P < 0.05) of 1,128 genes (595 upregulated and 533 downregulated) in BC014RFLC, 210 genes (138 upregulated and 72 downregulated) in BC014RVRC, and 598 genes (341 upregulated and 257 downregulated) in BC014RPSC.

    “Microarray analysis identified differential expression (FC > 2, P < 0.05) of 1,128 (595 upregulated and 533 downregulated), 210 (138 upregulated and 72 downregulated), and 598 (341 upregulated and 257 downregulated) genes in BC014RFLC, BC014RVRC, and BC014RPSC strains, respectively”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Duplicate probes within each array can be considered technical replicates.
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation
    § INTRODUCTION

    The authors previously described the in vitro development of stable azole resistance in C. parapsilosis, which was induced rapidly following fluconazole exposure or more slowly when exposed to posaconazole.

    “We previously described the in vitro development of stable azole resistance in C. parapsilosis, which was induced rapidly following fluconazole exposure or more slowly when it was exposed to posaconazole (PSC) (47).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [47]

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation
    § INTRODUCTION

    Point mutations in genes coding for the target enzyme, reducing azole target affinity, are a mechanism of azole resistance in Candida species.

    “point mutations in genes coding for the target enzyme, reducing azole target affinity (61)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [61]

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation
    § INTRODUCTION

    Previous studies with C. albicans, C. dubliniensis, and C. tropicalis demonstrated that resistance to fluconazole can be promoted following repeated in vitro exposure to the drug.

    “Previous studies with C. albicans (38), C. dubliniensis (59), and C. tropicalis (9) demonstrated that resistance to fluconazole can be promoted following repeated in vitro exposure to the drug.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [38] source

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    • cites [59]

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    • cites [9] source

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  • Classified as probably not a substantial claim.

    Study design and conductnone given
    § MATERIALS AND METHODS

    In each microarray experiment, four biological replicates (including two dye swaps) were prepared.

    “In each experiment, four biological replicates (including two dye swaps) were prepared.”
    • Also stated in: § MATERIALS AND METHODS · plain
      “In each experiment, four biological replicates were performed.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data
    § Abstract

    Tolerance to azoles in C. parapsilosis, similarly to C. albicans, involves the activation of efflux pumps and/or increased ergosterol synthesis.

    “the results suggest that similarly to C. albicans, tolerance to azoles involves the activation of efflux pumps and/or increased ergosterol synthesis.”
    • Also stated in: § INTRODUCTION · hedged
      “Our results suggest that, similar to C. albicans, C. parapsilosis acquires resistance to azoles either through upregulation of the MDR1 multidrug transporter family or via increased expression of the sterol biosynthetic pathway.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation
    § INTRODUCTION

    Increased production of the azole target enzyme is a mechanism of azole resistance in Candida species.

    “increased production of the azole target enzyme (23, 27, 63)”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [23] source

      Not checked in the free run.

    • cites [27] source

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    • cites [63] source

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  • Classified as probably not a substantial claim.

    Study design and conductnone given
    § MATERIALS AND METHODS

    Only RNA samples yielding 28S rRNA/18S rRNA ratios ranging from 1.6 to 2.2 and showing absence of degradation were used in subsequent analyses.

    “Only samples yielding 28S rRNA/18S rRNA ratios ranging from 1.6 to 2.2 and showing the absence of degradation were used in subsequent analyses.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation
    § INTRODUCTION

    Failure to accumulate the drug intracellularly may be caused by lack of drug penetration due to changes in membrane lipids and sterols or by active efflux of drugs, particularly from overexpression of CDR1, CDR2, and MDR1.

    “failure to accumulate the drug intracellularly, which may be caused by the lack of drug penetration, due to changes in membrane lipids and sterols (28), or by active efflux of drugs, resulting particularly from overexpression of the CDR1, CDR2, and MDR1 genes (3, 38, 62, 73)”
    Quote in the paperNot a substantial claim0 of 5 sources checked
    • cites [28]

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    • cites [3]

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    • cites [38] source

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    • cites [62]

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    • cites [73] source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation
    § MATERIALS AND METHODS

    The C. parapsilosis ATCC 22019 type strain was used for quality control of antifungal susceptibility testing.

    “The C. parapsilosis ATCC 22019 type strain from the American Type Culture Collection was used for quality control of antifungal susceptibility testing, as recommended (15, 16).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [15]

      Not checked in the free run.

    • cites [16]

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductcitation
    § MATERIALS AND METHODS

    Quality controls were performed to assess the good quality of the arrays and to verify the presence of any chromosomal bias expression.

    “Quality controls were performed in order to assess the good quality of the arrays and to verify the presence of any chromosomal bias expression (7) (data not shown).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [7]

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given
    § MATERIALS AND METHODS

    Only probes with a fold change greater than 2 and an adjusted P value less than 0.05 were used in analyses.

    “Only probes with a fold change (FC) of greater than 2 and an adjusted P value of less than 0.05 were used in analyses.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data
    § MATERIALS AND METHODS

    Raw microarray data and the description of the array were deposited in the Gene Expression Omnibus Database under accession number GSE27409.

    “Raw microarray data and the description of the array have been deposited in the Gene Expression Omnibus Database under accession number GSE27409 (superseries).”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Study design and conductcitation
    § MATERIALS AND METHODS

    MIC values of fluconazole, voriconazole, and posaconazole were determined according to the CLSI M27-A3 protocol and M27-S3 supplement.

    “MIC values of FLC, VRC, and PSC were determined according to the M27-A3 protocol and the M27-S3 supplement of the Clinical and Laboratory Standards Institute (CLSI) (15, 16).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [15]

      Not checked in the free run.

    • cites [16]

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given
    § MATERIALS AND METHODS

    For each RT-qPCR, five replicates for each strain were integrated, and the signal obtained for each gene was normalized with the TUB4 signal.

    “For each real-time quantitative PCR (RT-qPCR), five replicates for each strain were integrated.”
    • Also stated in: § MATERIALS AND METHODS · plain
      “The signal obtained for each gene was normalized with the TUB4 signal.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data
    § MATERIALS AND METHODS

    One array in the posaconazole experiment did not pass quality control and was discarded as an outlier.

    “One of the arrays in the posaconazole experiment did not pass our quality control and it was therefore discarded as an outlier.”
    Quote in the paperNot a substantial claim
25 of 25
  • The paper relies on this without support.

    There are scarce data regarding mechanisms of azole resistance in C. parapsilosis.

    “However, there are still scarce data regarding mechanisms of azole resistance in C. parapsilosis.”
  • The authors state this as an assumption.

    Duplicate probes within each array can be considered technical replicates.

    “Duplicate probes within each array were considered technical replicates. This assumption allows full advantage of the platform design to be taken by analyzing the within-array replicate spots using a pooled correlation method.”
2 of 2

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Resistance to azoles in C. parapsilosis has been attributed to mutations in MRR1 and ERG11 (Y132F alone or with R398I), and overexpression of CDR1, MDR1, and ERG11.

    “Resistance to azoles in C. parapsilosis has been attributed to mutations in the transcription factor gene MRR1 [84] and ERG11 (Y132F, either alone or in combination with an R398I) [85,86,87], and overexpression of CDR1, MDR1, and ERG11 [85,86,88].”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Voriconazole-resistant strain has two identifiers

    Minor

    The results call the strain obtained after voriconazole exposure BC014RVOR, whereas the methods identify that strain as BC014RVRC.

1 of 1

Cites

Flagged first, then by citations

Research works printed but not linked: 3

  1. AzanzaJ. R. Garcia-QuetglasE. SadabaB.. 2007. Pharmacology of azoles. Rev. Iberoam. Micol. 24:223–227.(In Spanish.)
  2. Clinical Laboratory Standards Institute 2008. Reference method for broth dilution antifungal susceptibility testing of yeasts, 3rd ed. Approved standard M27-A3. Clinical and Laboratory Standards Institute, Wayne, PA.
  3. Clinical Laboratory Standards Institute. 2008. Reference method for broth dilution antifungal susceptibility testing of yeasts. Third informational supplement: document M27-S3. Clinical and Laboratory Standards Institute, Wayne, PA.

Cited by

Sorted by citations

Authors
Silva, A. P., Miranda, I. M., Guida, A., Synnott, J., Rocha, R., Silva, R., Amorim, A., Pina-Vaz, C., Butler, G., & Rodrigues, A. G.
Affiliations
  • Universidade do Porto (PT)
  • University College Dublin (IE)
  • Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal
Venue
Antimicrobial Agents and Chemotherapy
Published
2011-07
Volume
55
Issue
7
Pages
3546-3556
ISSN
  • 0066-4804 (ISSN-L)
  • 1098-6596
OpenAlex
W2115530382
Cited by
86
References
80
Citations by year
2026: 4 · 2025: 3 · 2024: 1 · 2023: 7 · 2022: 7 · 2021: 5 · 2020: 9 · 2019: 5 · 2018: 8 · 2017: 9 · 2016: 7 · 2015: 6 · 2014: 5 · 2013: 4 · 2012: 4
FWCI
3.02
Type
journal article
Language
en
Open access
Locations
  • Antimicrobial Agents and Chemotherapy (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Science Foundation Ireland
  • University College Dublin
  • Universidade do Porto
  • Fundação para a Ciência e a Tecnologia
  • European Social Fund
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
Candida parapsilosis, azole resistance, fluconazole, voriconazole, posaconazole, gene expression profiling, MRR1, MDR1, efflux pumps, ergosterol biosynthesis, UPC2, Ndt80, antifungal resistance, transcription factor mutations
MeSH terms
Antifungal Agents, Azoles, Candida, Fungal Proteins, Microbial Sensitivity Tests, Pyrimidines, Triazoles, Fluconazole, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Drug Resistance, Fungal, Voriconazole

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