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Dunaiski CM, Kock MM, Chan WY, Ismail A, Peters RPH. Molecular epidemiology and antimicrobial resistance of vaginal Candida glabrata isolates in Namibia. Med Mycol 2024; 62:myae009. [PMID: 38308518 DOI: 10.1093/mmy/myae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024] Open
Abstract
Candida glabrata is the most common non-albicans Candida species that causes vulvovaginal candidiasis (VVC). Given the intrinsically low susceptibility of C. glabrata to azole drugs, investigations into C. glabrata prevalence, fungal susceptibility profile, and molecular epidemiology are necessary to optimise the treatment of VVC. This molecular epidemiological study was conducted to determine antifungal drug profile, single nucleotide polymorphisms (SNPs) associated with phenotypic antifungal resistance and epidemic diversity of C. glabrata isolates from women with VVC in Namibia. Candida glabrata isolates were identified using phenotypic and molecular methods. Antifungal susceptibility of strains was determined for fluconazole, itraconazole, amphotericin B, and anidulafungin. Whole genome sequencing was used to determine SNPs in antifungal resistance genes and sequence type (ST) allocation. Among C. glabrata isolates, all (20/20; 100%) exhibited phenotypic resistance to the azole class antifungal drug, (fluconazole), and phenotypic susceptibility to the polyene class (amphotericin B), and the echinocandins (anidulafungin). Non-synonymous SNPs were identified in antifungal resistance genes of all fluconazole-resistant C. glabrata isolates including ERG6 (15%), ERG7 (15%), CgCDR1 (25%), CgPDR1 (60%), SNQ2 (10%), FKS1 (5.0%), FKS2 (5.0%), CgFPS1 (5.0%), and MSH2 (15%). ST15 (n = 8/20, 40%) was predominant. This study provides important insight into phenotypic and genotypic antifungal resistance across C. glabrata isolates from women with VVC in Namibia. In this study, azole resistance is determined by an extensive range of SNPs, while the observed polyene and echinocandin resistance-associated SNPs despite phenotypic susceptibility require further investigation.
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Affiliation(s)
- Cara M Dunaiski
- Namibia University of Sciences and Technology, Department of Health and Applied Sciences, Windhoek 10005, Namibia
- University of Pretoria, Department of Medical Microbiology, Pretoria 0001, South Africa
| | - Marleen M Kock
- University of Pretoria, Department of Medical Microbiology, Pretoria 0001, South Africa
- National Health Laboratory Service, Tshwane, Academic Division, Pretoria 3191, South Africa
| | - Wai Yin Chan
- Sequencing Core Facility, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0081, South Africa
- Right to care, Centurion 0157, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - Remco P H Peters
- University of Pretoria, Department of Medical Microbiology, Pretoria 0001, South Africa
- University of Cape Town, Division of Medical Microbiology, Cape Town 7701, South Africa
- Foundation for Professional Development, Research Unit, East London 5217, South Africa
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Li D, Wang L, Zhao Z, Bai C, Li X. A novel model for predicting deep-seated candidiasis due to Candida glabrata among cancer patients: A 6-year study in a cancer center of China. Med Mycol 2024; 62:myae010. [PMID: 38318635 DOI: 10.1093/mmy/myae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/16/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024] Open
Abstract
Followed by Candida albicans, Candida glabrata ranks as the second major species contributing to invasive candidiasis. Given the higher medical burden and lower susceptibility to azoles in C. glabrata infections, identifying these infections is critical. From 2016 to 2021, patients with deep-seated candidiasis due to C. glabrata and non-glabrata Candida met the criteria to be enrolled in the study. Clinical data were randomly divided into training and validation cohorts. A predictive model and nomogram were constructed using R software based on the stepwise algorithm and logistic regression. The performance of the model was assessed by the area under the receiver operating characteristic curve and decision curve analysis (DCA). A total of 197 patients were included in the study, 134 of them infected with non-glabrata Candida and 63 with C. glabrata. The predictive model for C. glabrata infection consisted of gastrointestinal cancer, co-infected with bacteria, diabetes mellitus, and kidney dysfunction. The specificity was 84.1% and the sensitivity was 61.5% in the validation cohort when the cutoff value was set to the same as the training cohort. Based on the model, treatment for patients with a high-risk threshold was better than 'treatment for all' in DCA, while opting low-risk patients out of treatment was also better than 'treatment for none' in opt-out DCA. The predictive model provides a rapid method for judging the probability of infections due to C. glabrata and will be of benefit to clinicians making decisions about therapy strategies.
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Affiliation(s)
- Ding Li
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Lin Wang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Zhihong Zhao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Changsen Bai
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Xichuan Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
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Huang YH, Lee YH, Lin CJ, Hsu LH, Chen YL. Deubiquitination module is critical for oxidative stress response and biofilm formation in Candida glabrata. Med Mycol 2023; 61:myad099. [PMID: 37844959 DOI: 10.1093/mmy/myad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/02/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023] Open
Abstract
Candidiasis is one of the most important fungal diseases and generally refers to diseases of the skin or mucosal tissues caused by Candida species. Candida glabrata is an opportunistic human fungal pathogen. Infection with C. glabrata has significantly increased due to innate antifungal drug tolerance and the ability to adhere to mucocutaneous surfaces. Spt-Ada-Gcn5 acetyltransferase complex contains two different post-translational modifications, histone acetylation (HAT) module and deubiquitination (DUB) module, which are decisive in gene regulation and highly conserved in eukaryotes. Previous research in our laboratory found that the HAT module ADA2 could regulate C. glabrata oxidative stress tolerance, drug tolerance, cell wall integrity, and virulence. However, the roles of the DUB module that is comprised of UBP8, SGF11, SGF73, and SUS1 genes in those phenotypes are not yet understood. In this study, we found that DUB module genes UBP8, SGF11, and SUS1, but not SGF73 positively regulate histone H2B DUB. Furthermore, ubp8, sgf11, and sus1 mutants exhibited decreased biofilm formation and sensitivity to cell wall-perturbing agent sodium dodecyl sulfate and antifungal drug amphotericin B. In addition, the sgf73 mutant showed increased biofilm formation but was susceptible to oxidative stresses, antifungal drugs, and cell wall perturbing agents. The ubp8, sgf11, and sus1 mutants showed marginal hypovirulence, whereas the sgf73 mutant exhibited virulence similar to the wild type in a murine systemic infection model. In conclusion, the C. glabrata DUB module plays distinct roles in H2B ubiquitination, oxidative stress response, biofilm formation, cell wall integrity, and drug tolerance, but exhibits minor roles in virulence.
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Affiliation(s)
- Yue-Han Huang
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Yi-Hang Lee
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Chi-Jan Lin
- Institute of Molecular Biology, National Chung Hsing University, 40227 Taichung, Taiwan
| | - Li-Hang Hsu
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
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Lin CJ, Yang SY, Hsu LH, Yu SJ, Chen YL. The Gcn5-Ada2-Ada3 histone acetyltransferase module has divergent roles in pathogenesis of Candida glabrata. Med Mycol 2023; 61:myad004. [PMID: 36715154 DOI: 10.1093/mmy/myad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/04/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Candida glabrata is an opportunistic fungal pathogen and the second most prevalent species isolated from candidiasis patients. C. glabrata has intrinsic tolerance to antifungal drugs and oxidative stresses and the ability to adhere to mucocutaneous surfaces. However, knowledge about the regulation of its virulence traits is limited. The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex modulates gene transcription by histone acetylation through the histone acetyltransferase (HAT) module comprised of Gcn5-Ada2-Ada3. Previously, we showed that the ada2 mutant was hypervirulent but displayed decreased tolerance to antifungal drugs and cell wall perturbing agents. In this study, we further characterized the functions of Ada3 and Gcn5 in C. glabrata. We found that single, double, or triple deletions of the HAT module, as expected, resulted in a decreased level of acetylation on histone H3 lysine 9 (H3K9) and defective growth. These mutants were more susceptible to antifungal drugs, oxidative stresses, and cell wall perturbing agents compared with the wild-type. In addition, HAT module mutants exhibited enhanced agar invasion and upregulation of adhesin and proteases encoding genes, whereas the biofilm formation of those mutants was impaired. Interestingly, HAT module mutants exhibited enhanced induction of catalases (CTA1) expression upon treatment with H2O2 compared with the wild-type. Lastly, although ada3 and gcn5 exhibited marginal hypervirulence, the HAT double and triple mutants were hypervirulent in a murine model of candidiasis. In conclusion, the HAT module of the SAGA complex plays unique roles in H3K9 acetylation, drug tolerance, oxidative stress response, adherence, and virulence in C. glabrata.
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Affiliation(s)
- Chi-Jan Lin
- Institute of Molecular Biology, National Chung Hsing University, 40227 Taichung, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Sheng-Yung Yang
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Li-Hang Hsu
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Shang-Jie Yu
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
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Hajigholamreza H, Sharifzadeh A, Hassan J, Shokri H, Akbaripazouki A, Pakbin B, Tamai IA. Influence of menthol on biofilm formation, ergosterol content, and cell surface hydrophobicity of Candida glabrata. FEMS Microbiol Lett 2023; 370:fnad065. [PMID: 37429611 DOI: 10.1093/femsle/fnad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023] Open
Abstract
Resistance to synthetic antifungals has become one of the leading public health challenges around the world. Accordingly, novel antifungal products like naturally occurring molecules can be one of the potential ways to reach efficient curative approaches to control candidiasis. This work evaluated the effect of menthol on cell surface hydrophobicity (CSH), biofilm formation, growth, and ergosterol content of Candida glabrata, a yeast with a high resistance against antifungal agents. Disc diffusion method (susceptibility to synthetic antifungals), broth micro-dilution method (Susceptibility to menthol), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide reduction assay (biofilm formation), High-performance liquid chromatography (HPLC) technique (ergosterol content), and adherence to n-hexadecane (CSH) were employed to determine the influence of menthol against C. glabrata isolates. The minimum inhibitory concentration (MIC) range of menthol versus C. glabrata was 1250-5000 µg/mL (mean ± SD: 3375 ± 1375 µg/mL). The mean rate of C. glabrata biofilm formation was decreased up to 97.67%, 81.15%, 71.21%, 63.72%, 47.53%, 26.31%, and 0.051% at 625, 1250, 2500, 5000, 10 000, 20 000, and 40 000 µg/mL concentrations, respectively. The percentages of CSH were significant in groups treated with MIC/2 (17.51 ± 5.52%) and MIC/4 (26 ± 5.87%) concentrations of menthol. Also, the percentage changes in membrane ergosterol were 15.97%, 45.34%, and 73.40% at 0.125, 0.25, and 0.5 mg/mL concentrations of menthol, respectively, in comparison with untreated control. The results showed the menthol impact versus sessile and planktonic C. glabrata cells, and the interference with ergosterol content, CSH, and biofilm formation, which made it a potent natural antifungal.
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Affiliation(s)
- Hamid Hajigholamreza
- Department of Microbiology and immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1416634793, Iran
| | - Aghil Sharifzadeh
- Department of Microbiology and immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1416634793, Iran
| | - Jalal Hassan
- Division of Toxicology, Department of Comparative Bioscience, Faculty of Veterinary Medicine, University of Tehran, Tehran 1416634793, Iran
| | - Hojjatollah Shokri
- Department of Pathobiology, Faculty of Veterinary Medicine, Amol University of Special Modern Technologies, Amol 4615664616, Iran
| | - Ali Akbaripazouki
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 1416634793, Iran
| | - Babak Pakbin
- Werner Siemens Chair of Synthetic Biotechnology, Dept. of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748 Garching bei München, Germany
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, Sion 2 1950, Switzerland
| | - Iradj Ashrafi Tamai
- Department of Microbiology and immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran 1416634793, Iran
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6
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Abstract
Increased expression of the Candida glabrata CDR1 gene, encoding an ATP-binding cassette membrane transporter, is routinely observed in fluconazole-resistant isolates of this pathogenic yeast. CDR1 transcription has been well-documented to be due to activity of the Zn2Cys6 zinc cluster-containing transcription factor Pdr1. Gain-of-function mutations in the gene encoding this factor are the most commonly observed cause of fluconazole hyper-resistance in clinical isolates. We have recently found that the sterol-responsive transcription factor Upc2A also acts to control CDR1 transcription, providing a direct link between ergosterol biosynthesis and expression of Pdr1 target genes. While this earlier work implicated Upc2A as an activator of CDR1 transcription, our further analyses revealed the presence of a second Upc2A binding site that negatively regulated CDR1 expression. This Upc2A binding site designated a sterol-responsive element (SRE) was found to have significant lower affinity for Upc2A DNA-binding than the previously described SRE. This new SRE was designated SRE2 while the original, positively acting site was named SRE1. A mutant version of SRE2 prevented in vitro DNA-binding by recombinant Upc2A and, when introduced into the CDR1 promoter, caused decreased fluconazole susceptibility and increased CDR1 expression. This negative effect caused by loss of SRE2 was shown to be Pdr1 independent, consistent with the presence of at least one additional activator of CDR1 transcription. The ability of Upc2A to exert either positive or negative effects on gene expression resembles behavior of mammalian nuclear receptor proteins and reveals an unexpectedly complex nature for SRE effects on gene regulation.
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Affiliation(s)
- Bao Gia Vu
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Elias D, Hervay NT, Jacko J, Morvova M, Valachovic M, Gbelska Y. Erg6p is essential for antifungal drug resistance, plasma membrane properties and cell wall integrity in Candida glabrata. FEMS Yeast Res 2022; 21:6680247. [PMID: 36047961 DOI: 10.1093/femsyr/foac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
ERG6 gene encodes C-24 methyltransferase, one of the specific enzymes that differ in mammalian and yeast sterol biosynthesis. To explore the function of CgErg6p in the yeast pathogen Candida glabrata, we have constructed the Cgerg6Δ deletion mutant. We found that C. glabrata cells lacking CgErg6p exhibit reduced susceptibility to both antifungal azoles and polyenes. The reduced content of ergosterol in the Cgerg6 deletion mutant was accompanied by increased expression of genes encoding the last steps of the ergosterol biosynthetic pathway. The absence of CgErg6p leads to plasma membrane hyperpolarization and decrease in its fluidity compared to the parental C. glabrata strain. The absence of sterols containing C-24 alkyls influenced the susceptibility of Cgerg6Δ mutant cells to alkali metal cations and several other metabolic inhibitors. Our results thus show that sterols lacking C-24 alkyls are not sufficient substitutes for maintaining yeast plasma membrane function. The absence of CgErg6p influences also the cell wall integrity and calcineurin signaling in C. glabrata.
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Affiliation(s)
- Daniel Elias
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
| | - Nora Toth Hervay
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
| | - Juraj Jacko
- Faculty of Mathematics, Physics and Informatics, Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Mlynska dolina, 842 48 Bratislava, Slovak Republic
| | - Marcela Morvova
- Faculty of Mathematics, Physics and Informatics, Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Mlynska dolina, 842 48 Bratislava, Slovak Republic
| | - Martin Valachovic
- Institute of Animal Biochemistry and Genetics CBS SAS, Dubravska cesta 9, 840 05 BratislavaSlovak Republic
| | - Yvetta Gbelska
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
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Schrevens S, Sanglard D. A novel Candida glabrata doxycycline-inducible system for in vitro/in vivo use. FEMS Yeast Res 2022; 22:6680246. [PMID: 36047937 PMCID: PMC9508828 DOI: 10.1093/femsyr/foac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Candida glabrata is an important pathogen causing superficial to invasive disease in human. Conditional expression systems are helpful in addressing the function of genes and especially when they can be applied to in vivo studies. Tetracycline-dependent regulation systems have been used in diverse fungi to turn-on (Tet-on) or turn-off (Tet-off) gene expression either in vitro but also in vivo in animal models. Up to now, only a Tet-off expression has been constructed for gene expression in C. glabrata. Here, we report a Tet-on gene expression system which can be used in vitro and in vivo in any C. glabrata genetic background. This system was used in a mice model of systemic infection to demonstrate that the general amino acid permease Gap1 is important for C. glabrata virulence.
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Affiliation(s)
- S Schrevens
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
| | - D Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
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Salazar SB, Pinheiro MJF, Sotti-Novais D, Soares AR, Lopes MM, Ferreira T, Rodrigues V, Fernandes F, Mira NP. Disclosing azole resistance mechanisms in resistant Candida glabrata strains encoding wild-type or gain-of-function CgPDR1 alleles through comparative genomics and transcriptomics. G3 (Bethesda) 2022; 12:jkac110. [PMID: 35532173 PMCID: PMC9258547 DOI: 10.1093/g3journal/jkac110] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 04/25/2022] [Indexed: 12/03/2022]
Abstract
The pathogenic yeast Candida glabrata is intrinsically resilient to azoles and rapidly acquires resistance to these antifungals, in vitro and in vivo. In most cases azole-resistant C. glabrata clinical strains encode hyperactive CgPdr1 variants, however, resistant strains encoding wild-type CgPDR1 alleles have also been isolated, although remaining to be disclosed the underlying resistance mechanism. In this study, we scrutinized the mechanisms underlying resistance to azoles of 8 resistant clinical C. glabrata strains, identified along the course of epidemiological surveys undertaken in Portugal. Seven of the strains were found to encode CgPdr1 gain-of-function variants (I392M, E555K, G558C, and I803T) with the substitutions I392M and I803T being herein characterized as hyper-activating mutations for the first time. While cells expressing the wild-type CgPDR1 allele required the mediator subunit Gal11A to enhance tolerance to fluconazole, this was dispensable for cells expressing the I803T variant indicating that the CgPdr1 interactome is shaped by different gain-of-function substitutions. Genomic and transcriptomic profiling of the sole azole-resistant C. glabrata isolate encoding a wild-type CgPDR1 allele (ISTB218) revealed that under fluconazole stress this strain over-expresses various genes described to provide protection against this antifungal, while also showing reduced expression of genes described to increase sensitivity to these drugs. The overall role in driving the azole-resistance phenotype of the ISTB218 C. glabrata isolate played by these changes in the transcriptome and genome of the ISTB218 isolate are discussed shedding light into mechanisms of resistance that go beyond the CgPdr1-signalling pathway and that may alone, or in combination, pave the way for the acquisition of resistance to azoles in vivo.
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Affiliation(s)
- Sara B Salazar
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Maria Joana F Pinheiro
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Danielle Sotti-Novais
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Ana R Soares
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro 3810, Portugal
| | - Maria M Lopes
- Departamento de Microbiologia e Imunologia, Faculdade de Farmácia da Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Teresa Ferreira
- Laboratório de Microbiologia, Hospital Dona Estefânia (Centro Hospitalar Universitário Lisboa Central), Lisboa 1169-045, Portugal
| | - Vitória Rodrigues
- Seção de Microbiologia, Laboratório SYNLAB—Lisboa, Grupo SYNLAB Portugal, Lisboa 1070-061, Portugal
| | - Fábio Fernandes
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
| | - Nuno P Mira
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico—Department of Bioengineering, Universidade de Lisboa, Lisboa 1049-001, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1049-001, Portugal
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10
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Helmstetter N, Chybowska AD, Delaney C, Da Silva Dantas A, Gifford H, Wacker T, Munro C, Warris A, Jones B, Cuomo CA, Wilson D, Ramage G, Farrer RA. Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets. Genetics 2022; 221:iyac031. [PMID: 35199143 PMCID: PMC9071574 DOI: 10.1093/genetics/iyac031] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Candida glabrata is the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabrata from across Scotland are highly genetically diverse, including at least 19 separate sequence types that have been recovered previously in globally diverse locations, and 1 newly discovered sequence type. Several sequence types had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every sequence type including enrichment for epithelial adhesins thought to facilitate fungal adhesin to human epithelial cells. In patent microevolution was identified from 7 sets of recurrent cases of candidiasis, revealing an enrichment for nonsynonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected epithelial adhesins genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4 and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole minimum inhibitory concentration. In addition to nuclear genome diversity, the C. glabrata mitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein-encoding genes in all nonreference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabrata population that may impact virulence and drug resistance, and 2 major mechanisms generating this diversity: microevolution and genetic exchange/recombination.
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Affiliation(s)
- Nicolas Helmstetter
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | | | - Christopher Delaney
- School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Hugh Gifford
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Theresa Wacker
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Carol Munro
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Adilia Warris
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Brian Jones
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | | | - Duncan Wilson
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Gordon Ramage
- School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rhys A Farrer
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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11
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Saguez C, Viterbo D, Descorps-Declère S, Cormack BP, Dujon B, Richard GF. Functional variability in adhesion and flocculation of yeast megasatellite genes. Genetics 2022; 221:iyac042. [PMID: 35274698 PMCID: PMC9071537 DOI: 10.1093/genetics/iyac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Abstract
Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogen Candida glabrata. They are encoded in genes involved in cell-cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete several Candida glabrata megasatellite-containing genes and found that 2 of them were positively involved in adhesion to epithelial cells, whereas 3 genes negatively controlled adhesion. Two of the latter, CAGL0B05061g or CAGL0A04851g, were also negative regulators of yeast-to-yeast adhesion, making them central players in controlling Candida glabrata adherence properties. Using a series of synthetic Saccharomyces cerevisiae strains in which the FLO1 megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to epithelial cells or to invade agar. Finally, to understand how megasatellites were initially created and subsequently expanded, an experimental evolution system was set up, in which modified yeast strains containing different megasatellite seeds were grown in bioreactors for more than 200 generations and selected for their ability to sediment at the bottom of the culture tube. Several flocculation-positive mutants were isolated. Functionally relevant mutations included general transcription factors as well as a 230-kbp segmental duplication.
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Affiliation(s)
- Cyril Saguez
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
- Present address: Abolis Biotechnologies, 5 Rue Henri Desbruères, Evry 91030, France
| | - David Viterbo
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
| | - Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Paris F-75015, France
| | - Brendan P Cormack
- Department of Molecular Biology & Genetics, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Bernard Dujon
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
| | - Guy-Franck Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
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12
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Abstract
Invasive candidiasis, the most frequent healthcare-associated invasive fungal infection, is commonly caused by Candida albicans. However, in recent years other antifungal-resistant Candida species—namely Candida glabrata and Candidaauris—have emerged as a serious matter of concern. Much of our understanding of the mechanisms regulating antifungal resistance and tolerance relies on studies utilizing C. albicans, C. glabrataand the model yeast Saccharomyces cerevisiae. ‘Omics studies have been used to describe alterations in metabolic, genomic and transcriptomic expression profiles upon antifungal treatment of fungal cells. The physiological changes identified by these approaches could significantly affect fungal fitness in the host and survival during antifungal challenge, as well as provide further understanding of clinical resistance. Thus, this review aims to comparatively address ‘omics data for C. albicans, C. glabrata andS. cerevisiae published from 2000 to 2021 to identify what these technologies can tell us regarding cellular responses to antifungal therapy. We will also highlight possible effects on pathogen survival and identify future avenues for antifungal research.
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Affiliation(s)
- Gabriela Fior Ribeiro
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
| | - Eszter Denes
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
| | - Helen Heaney
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
| | - Delma S Childers
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
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13
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Kumari S, Kumar M, Khandelwal NK, Pandey AK, Bhakt P, Kaur R, Prasad R, Gaur NA. A homologous overexpression system to study roles of drug transporters in Candida glabrata. FEMS Yeast Res 2020; 20:foaa032. [PMID: 32490522 PMCID: PMC7611192 DOI: 10.1093/femsyr/foaa032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/02/2020] [Indexed: 12/21/2022] Open
Abstract
Considering the relevance of drug transporters belonging to ABC and MFS superfamilies in pathogenic Candida species, there has always been a need to have an overexpression system where these membrane proteins for functional analysis could be expressed in a homologous background. We could address this unmet need by constructing a highly drug-susceptible Candida glabrata strain deleted in seven dominant ABC transporters genes such as CgSNQ2, CgAUS1, CgCDR1, CgPDH1, CgYCF1, CgYBT1 and CgYOR1 and introduced a GOF mutation in transcription factor (TF) CgPDR1 leading to a hyper-activation of CgCDR1 locus. The expression system was validated by overexpressing four GFP tagged ABC (CgCDR1, CgPDH1, CaCDR1 and ScPDR5) and an MFS (CgFLR1) transporters genes facilitated by an engineered expression plasmid to integrate at the CgCDR1 locus. The properly expressed and localized transporters were fully functional, as was revealed by their several-fold increased drug resistance, growth kinetics, localization studies and efflux activities. The present homologous system will facilitate in determining the role of an individual transporter for its substrate specificity, drug efflux, pathogenicity and virulence traits without the interference of other major transporters.
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Affiliation(s)
- Sonam Kumari
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Mohit Kumar
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University, Gurgaon, 122413, Haryana, India and
| | - Nitesh Kumar Khandelwal
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ajay Kumar Pandey
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Priyanka Bhakt
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, Telangana, India
| | - Rupinder Kaur
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, Telangana, India
| | - Rajendra Prasad
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University, Gurgaon, 122413, Haryana, India and
| | - Naseem A. Gaur
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
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