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Chedraoui C, Fattouh N, El Hachem S, Younes M, Khalaf RA. Induction of Antifungal Tolerance Reveals Genetic and Phenotypic Changes in Candida glabrata. J Fungi (Basel) 2025; 11:284. [PMID: 40278105 PMCID: PMC12028409 DOI: 10.3390/jof11040284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 01/22/2025] [Accepted: 02/14/2025] [Indexed: 04/26/2025] Open
Abstract
Candida glabrata is an opportunistic, pathogenic fungus that is increasingly isolated from hospitalized patients. The incidence of drug tolerance, heteroresistance, and resistance is on the rise due to an overuse of antifungal drugs. The aim of this study was to expose a sensitive C. glabrata strain to sequentially increasing concentrations of two antifungal drugs, fluconazole, an azole that targets ergosterol biosynthesis, or caspofungin, an echinocandin that targets cell wall glucan synthesis. Analysis of the drug-exposed isolates showed development of antifungal tolerance, chromosomal abnormalities, decreased adhesion, attenuated virulence, and an increase in efflux pump activity. Furthermore, whole genome sequencing of all isolates exposed to different concentrations of fluconazole or caspofungin was performed to determine mutations in key genes that could correlate with the observed phenotypes. Mutations were found in genes implicated in adhesion, such as in the AWP, PWP, and EPA family of genes. Isolates exposed to higher drug concentrations displayed more mutations than those at lower concentrations.
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Affiliation(s)
- Christy Chedraoui
- Department of Biological Sciences, Lebanese American University, Byblos P.O. Box 36, Lebanon; (C.C.); (N.F.); (S.E.H.); (M.Y.)
| | - Nour Fattouh
- Department of Biological Sciences, Lebanese American University, Byblos P.O. Box 36, Lebanon; (C.C.); (N.F.); (S.E.H.); (M.Y.)
- Department of Biology, Saint George University of Beirut, Beirut 1100-2807, Lebanon
| | - Setrida El Hachem
- Department of Biological Sciences, Lebanese American University, Byblos P.O. Box 36, Lebanon; (C.C.); (N.F.); (S.E.H.); (M.Y.)
| | - Maria Younes
- Department of Biological Sciences, Lebanese American University, Byblos P.O. Box 36, Lebanon; (C.C.); (N.F.); (S.E.H.); (M.Y.)
| | - Roy A. Khalaf
- Department of Biological Sciences, Lebanese American University, Byblos P.O. Box 36, Lebanon; (C.C.); (N.F.); (S.E.H.); (M.Y.)
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2
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Huang SJ, Song YH, Lv G, Liu JY, Zhao JT, Wang LL, Xiang MJ. Emergence of invasive candidiasis with multiple Candida species exhibiting azole and echinocandin resistance. Front Microbiol 2025; 16:1550894. [PMID: 40201445 PMCID: PMC11975943 DOI: 10.3389/fmicb.2025.1550894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Accepted: 03/04/2025] [Indexed: 04/10/2025] Open
Abstract
Background Invasive candidiasis (IC) is an increasingly common, expensive, and potentially fatal infection. However, IC caused by multiple Candida species is rarely reported in China. Herein, we revealed a complex IC caused by multiple Candida species, comprising the rare C. norvegensis, C. albicans, C. glabrata, and C. tropicalis. The resistance mechanism of azole and echinocandin resistance were explored further. Methods The isolates were confirmed using internal transcribed spacer (ITS) sequencing. The resistance mechanisms were investigated using PCR-based sequencing, quantitative real-time reverse transcription PCR, and rhodamine 6G efflux quantification. Results Antifungal susceptibility testing showed this complex infection was associated with cross-resistance to azole and echinocandin drugs. For C. glabrata, the acquired echinocandin resistance was likely caused by a novel mutational pattern (1,3-beta-D-glucan synthase subunits FKS1-S629P and FKS2-W1497stop) while the acquired azole resistance in C. glabrata RJ05 was related to complex mechanisms including enhanced efflux activity, pleiotropic drug resistance 1 (PDR1) mutation, and increased expression of Candida drug resistance 1 (CDR1) and CDR2. Additionally, the azole resistance of C. tropicalis was caused by two lanosterol 14-alpha demethylase (ERG11) mutations: Y132F and S154F. Conclusion Our study revealed a case of clinically complex, multiple Candida invasive infections, further uncovering the resistance mechanisms to azoles and echinocandins. These findings provide valuable references for the diagnosis and treatment of invasive candidiasis (IC) in clinical practice.
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Affiliation(s)
- Si-Jia Huang
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Hui Song
- The Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Geng Lv
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin-Yan Liu
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun-Tao Zhao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu-Ling Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming-Jie Xiang
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Wei K, Arlotto M, Overhulse JM, Dinh T, Zhou Y, Dupper NJ, Yang J, Kashemirov BA, Dawi H, Garnaud C, Bourgine G, Mietton F, Champleboux M, Larabi A, Hayat Y, Indorato R, Noirclerc‐Savoye M, Skoufias D, Cornet M, Rabut G, McKenna CE, Petosa C, Govin J. Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors With Antifungal Potential. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2404260. [PMID: 39821709 PMCID: PMC11904993 DOI: 10.1002/advs.202404260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 10/17/2024] [Indexed: 01/19/2025]
Abstract
The fungal Bromodomain and Extra-Terminal (BET) protein Bdf1 is a potential antifungal target against invasive fungal infections. However, the need to selectively inhibit both Bdf1 bromodomains (BDs) over human orthologs and the lack of molecular tools to assess on-target antifungal efficacy hamper efforts to develop Bdf1 BD inhibitors as antifungal therapeutics. This study reports a phenyltriazine compound that inhibits both Bdf1 BDs from the human fungal pathogen Candida glabrata with selectivity over the orthologous BDs from the human BET protein Brd4. On-target antifungal activity is established by devising two yeast-based inhibition assays: a growth assay using humanized Candida strains in which the Bdf1 BDs are replaced by their Brd4 counterparts, and a NanoBiT assay that evaluates the BD-mediated association of Bdf1 with chromatin. These assays additionally enable the discovery that BET inhibitor I-BET726 targets both Bdf1 BDs, inhibits the growth of a broad spectrum of Candida species, including antifungal-resistant clinical isolates, and displays efficacy in an invertebrate animal model of infection. These collective findings highlight the promising potential of Bdf1 BD inhibitors as an innovative class of antifungal therapeutics and the pivotal role of yeast-based assay development toward achieving this end.
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Affiliation(s)
- Kaiyao Wei
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
- Univ. Grenoble AlpesInsermCNRSInstitute for Advanced Biosciences (IAB)Grenoble38000France
| | - Marie Arlotto
- Univ. Grenoble AlpesInsermCNRSInstitute for Advanced Biosciences (IAB)Grenoble38000France
| | - Justin M. Overhulse
- Department of ChemistryDana and David Dornsife College of LettersArts, and SciencesUniversity of Southern CaliforniaUniversity Park CampusLos AngelesCA90089USA
| | - Tuan‐Anh Dinh
- Univ. Grenoble AlpesCNRSGrenoble INPCHU Grenoble Alpes, Laboratoire TIMCGrenoble38000France
| | - Yingsheng Zhou
- Department of ChemistryDana and David Dornsife College of LettersArts, and SciencesUniversity of Southern CaliforniaUniversity Park CampusLos AngelesCA90089USA
| | - Nathan J. Dupper
- Department of ChemistryDana and David Dornsife College of LettersArts, and SciencesUniversity of Southern CaliforniaUniversity Park CampusLos AngelesCA90089USA
| | - Jiayi Yang
- Department of ChemistryDana and David Dornsife College of LettersArts, and SciencesUniversity of Southern CaliforniaUniversity Park CampusLos AngelesCA90089USA
| | - Boris A. Kashemirov
- Department of ChemistryDana and David Dornsife College of LettersArts, and SciencesUniversity of Southern CaliforniaUniversity Park CampusLos AngelesCA90089USA
| | - Hasan Dawi
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
| | - Cécile Garnaud
- Univ. Grenoble AlpesCNRSGrenoble INPCHU Grenoble Alpes, Laboratoire TIMCGrenoble38000France
| | - Gaëlle Bourgine
- Univ. RennesCNRSINSERMInstitut de Génétique et Développement de Rennes (IGDR)UMR 6290, U1305Rennes35000France
| | - Flore Mietton
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
| | - Morgane Champleboux
- Univ. Grenoble AlpesInsermCNRSInstitute for Advanced Biosciences (IAB)Grenoble38000France
| | - Amédé Larabi
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
| | - Yordan Hayat
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
| | - Rose‐Laure Indorato
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
| | | | - Dimitrios Skoufias
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
| | - Muriel Cornet
- Univ. Grenoble AlpesCNRSGrenoble INPCHU Grenoble Alpes, Laboratoire TIMCGrenoble38000France
| | - Gwenaël Rabut
- Univ. RennesCNRSINSERMInstitut de Génétique et Développement de Rennes (IGDR)UMR 6290, U1305Rennes35000France
| | - Charles E. McKenna
- Department of ChemistryDana and David Dornsife College of LettersArts, and SciencesUniversity of Southern CaliforniaUniversity Park CampusLos AngelesCA90089USA
| | - Carlo Petosa
- Univ. Grenoble AlpesCEACNRSInstitut de Biologie Structurale (IBS)Grenoble38000France
| | - Jérôme Govin
- Univ. Grenoble AlpesInsermCNRSInstitute for Advanced Biosciences (IAB)Grenoble38000France
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Spettel K, Bumberger D, Kriz R, Frank S, Loy M, Galazka S, Suchomel M, Lagler H, Makristathis A, Willinger B. In vitro long-term exposure to chlorhexidine or triclosan induces cross-resistance against azoles in Nakaseomyces glabratus. Antimicrob Resist Infect Control 2025; 14:2. [PMID: 39849551 PMCID: PMC11755926 DOI: 10.1186/s13756-024-01511-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 12/16/2024] [Indexed: 01/30/2025] Open
Abstract
BACKGROUND Topical antiseptics are crucial for preventing infections and reducing transmission of pathogens. However, commonly used antiseptic agents have been reported to cause cross-resistance to other antimicrobials in bacteria, which has not yet been described in yeasts. This study aims to assess the in vitro efficacy of antiseptics against clinical and reference isolates of Candida albicans and Nakaseomyces glabratus, and whether prolonged exposure to antiseptics promotes the development of antifungal (cross)resistance. METHODS A high-throughput approach for in vitro resistance development was established to simultaneously expose 96 C. albicans and N. glabratus isolates to increasing concentrations of a given antiseptic - chlorhexidine, triclosan or octenidine. Susceptibility testing and whole genome sequencing of yeast isolates pre- and post-exposure were performed. RESULTS Long-term exposure to antiseptics does not result in the development of stable resistance to the antiseptics themselves. However, 50 N. glabratus isolates acquired resistance to azole antifungals after long-term exposure to triclosan or chlorhexidine, revealing newly acquired mutations in the PDR1 and PMA1 genes. CONCLUSIONS Chlorhexidine as well as triclosan, but not octenidine, were able to introduce selective pressure promoting resistance to azole antifungals. Although we assessed this phenomenon only in vitro, these findings warrant critical monitoring in clinical settings.
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Affiliation(s)
- Kathrin Spettel
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, 1090, Austria
- Section Biomedical Science, Health Sciences, FH Campus Wien University of Applied Sciences, Vienna, 1100, Austria
| | - Dominik Bumberger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Richard Kriz
- Section Biomedical Science, Health Sciences, FH Campus Wien University of Applied Sciences, Vienna, 1100, Austria
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, 1090, Austria
| | - Sarah Frank
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Madita Loy
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Sonia Galazka
- Division of Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety AGES, Vienna, 1220, Austria
| | - Miranda Suchomel
- Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, 1090, Austria
| | - Heimo Lagler
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, 1090, Austria
| | - Athanasios Makristathis
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, 1090, Austria
| | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, 1090, Austria.
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Ibe C, Otu A, Pohl CH. Mechanisms of resistance to cell wall and plasma membrane targeting antifungal drugs in Candida species isolated in Africa. Expert Rev Anti Infect Ther 2025; 23:91-104. [PMID: 39754518 DOI: 10.1080/14787210.2024.2448844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 12/05/2024] [Accepted: 12/29/2024] [Indexed: 01/06/2025]
Abstract
INTRODUCTION There is a rise in the emergence of multidrug resistant fungal pathogens worldwide, including in Africa. METHOD This systematic review summarized the published data on the mechanisms and epidemiology of antifungal resistance in Candida species in Africa between 2000 and early 2024. RESULT Seventeen reports from seven African countries were analyzed but due to the paucity of data, the prevalence of antifungal resistant Candida isolates in Africa could not be estimated. However, a total of 1376 (out of 2812) resistant isolates were documented with South Africa reporting the most. Candida auris was the most reported species with multidrug and pandrug resistant strains documented in South Africa. Generally, azoles but not posaconazole or isavuconazole, resistance was reported. Fluconazole resistant isolates harbored Erg11 Y132F, VF125LA and K177A/R/N335S/E343D substitutions, MRR1 gain of function mutations or efflux pump protein over expression. Resistance to members of the echinocandin family was also reported and Fks1 S639P substitution was observed. CONCLUSION The data highlight that the increasing Candida species resistance to cell wall and cell membrane active antifungals is a cause for serious concern in Africa. There is need to increase antifungal research capacity and mount epidemiological surveillance to determine the true scale of the problem. PROSPERO REGISTRATION NUMBER CRD42024550231.
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Affiliation(s)
- Chibuike Ibe
- Pathogenic Yeast Research Group, Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
- Department of Microbiology, Faculty of Biological Sciences, Abia State University, Uturu, Nigeria
| | - Akaninyene Otu
- Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Carolina Henritta Pohl
- Pathogenic Yeast Research Group, Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
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Conway TP, Vu BG, Beattie SR, Krysan DJ, Moye-Rowley WS. Similarities and distinctions in the activation of the Candida glabrata Pdr1 regulatory pathway by azole and non-azole drugs. mSphere 2024; 9:e0079224. [PMID: 39555934 DOI: 10.1128/msphere.00792-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 10/21/2024] [Indexed: 11/19/2024] Open
Abstract
Incidences of fluconazole (FLC) resistance among Candida glabrata clinical isolates are a growing issue in clinics. The pleiotropic drug response network in C. glabrata confers azole resistance and is defined primarily by the Zn2Cys6 zinc cluster-containing transcription factor Pdr1 and target genes such as CDR1, which encodes an ATP-binding cassette transporter protein thought to act as an FLC efflux pump. Mutations in the PDR1 gene that render the transcription factor hyperactive are the most common cause of fluconazole resistance among clinical isolates. The phenothiazine class drug fluphenazine and a molecular derivative, CWHM-974, which both exhibit antifungal properties, have been shown to induce the expression of Cdr1 in Candida spp. We have used a firefly luciferase reporter gene driven by the CDR1 promoter to demonstrate two distinct patterns of CDR1 promoter activation kinetics: gradual promoter activation kinetics that occur in response to ergosterol limitations imposed by exposure to azole and polyene class antifungals and a robust and rapid CDR1 induction occurring in response to the stress imposed by fluphenazines. We can attribute these different patterns of CDR1 induction as proceeding through the promoter region of this gene since this is the only segment of the gene included in the luciferase reporter construct. Genetic analysis indicates that the signaling pathways responsible for phenothiazine and azole induction of CDR1 overlap but are not identical. The short time course of phenothiazine induction suggests that these compounds may act more directly on the Pdr1 protein to stimulate its activity. IMPORTANCE Candida glabrata has emerged as the second-leading cause of candidiasis due, in part, to its ability to acquire high-level resistance to azole drugs, a major class of antifungal that acts to block the biosynthesis of the fungal sterol ergosterol. The presence of azole drugs causes the induction of a variety of genes involved in controlling susceptibility to this drug class, including drug transporters and ergosterol biosynthetic genes such as ERG11. We found that the presence of azole drugs leads to an induction of genes encoding drug transporters and ERG11, while exposure of C. glabrata cells to antifungals of the phenothiazine class of drugs caused a much faster and larger induction of drug transporters but not ERG11. Coupled with further genetic analyses of the effects of azole and phenothiazine drugs, our data indicate that these compounds are sensed and responded to differentially in the yeast cell.
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Affiliation(s)
- Thomas P Conway
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Bao Gia Vu
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Sarah R Beattie
- Department of Pediatrics, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Damian J Krysan
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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Zhang Y, Gong S, Xiong K, Yu X, Mo X, Su C, Lu Y. An alteration in the expression of cell wall structural proteins increases cell surface exposure of adhesins to promote virulence in Candida glabrata. mSphere 2024; 9:e0091024. [PMID: 39601558 DOI: 10.1128/msphere.00910-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Accepted: 11/04/2024] [Indexed: 11/29/2024] Open
Abstract
Candida glabrata is an opportunistic human fungal pathogen that causes superficial mucosal and life-threatening bloodstream infections in immunocompromised individuals. Remodeling in cell wall components has been extensively exploited by fungal pathogens to adapt to host-derived stresses, as well as immune evasion. How this process contributes to C. glabrata pathogenicity is less understood. Here, we applied RNA sequencing and an in vivo invasive infection model to elucidate the prompt response of C. glabrata during infection. Fungal transcriptomes show a dramatic alteration in the expression of Srp1/Tip1-family cell wall structural proteins during systemic infection. Deletion of all six genes in this family (TIR2-5 and AWP6-7) that are upregulated during infection leads to a significantly lower fungal burden in organs, as well as an attenuated virulence in the dextran sulfate sodium-induced colitis model. The tir2-5 awp6-7 sextuple mutant does not display any defect in response to host-derived stresses. Rather, deletion of all these six genes results in a lower cell surface exposure of an adhesin Epa1, which could contribute to its reduced adhesion to epithelial cells and cytotoxicity, as well as attenuated virulence. Our study reveals that cell wall remodeling triggered by the alteration in the expression of structural proteins is a key virulence attribute in C. glabrata that facilitates this fungus adhering to host cells and persisting in organs.IMPORTANCECandida glabrata is one of the most frequent causes of candidiasis after Candida albicans. While C. albicans has been extensively studied, the mechanisms of infection and invasion of C. glabrata have not been fully elucidated. Using an infection model of systemic candidiasis and RNA sequencing, we show that there is a dramatic change in the expression of Srp1/Tip1-family genes during infection. Deletion of all six Srp1/Tip1-family genes that are upregulated during infection decreases the amount of cell wall-localized Epa1, probably reflecting the reduced adherence to epithelial cells and attenuated virulence in the sextuple mutant. These data suggest that alterations in the expression of Srp1/Tip1-family structural proteins trigger cell wall remodeling that increases the cell surface exposure of adhesins, such as Epa1, to promote virulence. Our study provides a pathogenic mechanism associated with C. glabrata in ensuring its sustenance and survival during infection.
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Affiliation(s)
- Yaling Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shengwei Gong
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Kang Xiong
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiangtai Yu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xinreng Mo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chang Su
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Lu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
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Bautista C, Gagnon-Arsenault I, Utrobina M, Fijarczyk A, Bendixsen DP, Stelkens R, Landry CR. Hybrid adaptation is hampered by Haldane's sieve. Nat Commun 2024; 15:10319. [PMID: 39609385 PMCID: PMC11604976 DOI: 10.1038/s41467-024-54105-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 11/01/2024] [Indexed: 11/30/2024] Open
Abstract
Hybrids between species exhibit plastic genomic architectures that could foster or slow down their adaptation. When challenged to evolve in an environment containing a UV mimetic drug, yeast hybrids have reduced adaptation rates compared to parents. We find that hybrids and their parents converge onto similar molecular mechanisms of adaptation by mutations in pleiotropic transcription factors, but at a different pace. After 100 generations, mutations in these genes tend to be homozygous in the parents but heterozygous in the hybrids. We hypothesize that a lower rate of loss of heterozygosity (LOH) in hybrids could limit fitness gain. Using genome editing, we first demonstrate that mutations display incomplete dominance, requiring homozygosity to show full impact and to entirely circumvent Haldane's sieve, which favors the fixation of dominant mutations. Second, tracking mutations in earlier generations confirmed a different rate of LOH in hybrids. Together, these findings show that Haldane's sieve slows down adaptation in hybrids, revealing an intrinsic constraint of hybrid genomic architecture that can limit the role of hybridization in adaptive evolution.
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Affiliation(s)
- Carla Bautista
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada.
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Université Laval, Québec, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Université Laval, Québec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
| | - Mariia Utrobina
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Anna Fijarczyk
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Université Laval, Québec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
| | | | - Rike Stelkens
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada.
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Université Laval, Québec, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada.
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Saha D, Gregor JB, Hoda S, Eastman KE, Gutierrez-Schultz VA, Navarrete M, Wisecaver JH, Briggs SD. Candida glabrata maintains two HAP1 ohnologs, HAP1A and HAP1B, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions. mSphere 2024; 9:e0052424. [PMID: 39440948 PMCID: PMC11580460 DOI: 10.1128/msphere.00524-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 09/03/2024] [Indexed: 10/25/2024] Open
Abstract
Candida glabrata exhibits innate resistance to azole antifungal drugs but also has the propensity to rapidly develop clinical drug resistance. Azole drugs, which target Erg11, is one of the major classes of antifungals used to treat Candida infections. Despite their widespread use, the mechanism controlling azole-induced ERG gene expression and drug resistance in C. glabrata has primarily revolved around Upc2 and/or Pdr1. Phylogenetic and syntenic analyses revealed that C. glabrata, following a whole genome duplication event, maintained HAP1A and HAP1B, whereas Saccharomyces cerevisiae only retained the HAP1A ortholog, HAP1. In this study, we determined the function of two zinc cluster transcription factors, Hap1A and Hap1B, as direct regulators of ERG genes. In S. cerevisiae, Hap1, an ortholog of Hap1A, is a known transcription factor controlling ERG gene expression under aerobic and hypoxic conditions. Interestingly, deleting HAP1 or HAP1B in either S. cerevisiae or C. glabrata, respectively, showed altered susceptibility to azoles. In contrast, the strain deleted for HAP1A did not exhibit azole susceptibility. We also determined that the increased azole susceptibility in a hap1BΔ strain is attributed to decreased azole-induced expression of ERG genes, resulting in decreased levels of total ergosterol. Surprisingly, Hap1A protein expression is barely detected under aerobic conditions but is specifically induced under hypoxic conditions, where Hap1A is required for the repression of ERG genes. However, in the absence of Hap1A, Hap1B can compensate as a transcriptional repressor. Our study shows that Hap1A and Hap1B is utilized by C. glabrata to adapt to specific host and environmental conditions. IMPORTANCE Invasive and drug-resistant fungal infections pose a significant public health concern. Candida glabrata, a human fungal pathogen, is often difficult to treat due to its intrinsic resistance to azole antifungal drugs and its capacity to develop clinical drug resistance. Therefore, understanding the pathways that facilitate fungal growth and environmental adaptation may lead to novel drug targets and/or more efficacious antifungal therapies. While the mechanisms of azole resistance in Candida species have been extensively studied, the roles of zinc cluster transcription factors, such as Hap1A and Hap1B, in C. glabrata have remained largely unexplored until now. Our research shows that these factors play distinct yet crucial roles in regulating ergosterol homeostasis under azole drug treatment and oxygen-limiting growth conditions. These findings offer new insights into how this pathogen adapts to different environmental conditions and enhances our understanding of factors that alter drug susceptibility and/or resistance.
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Affiliation(s)
- Debasmita Saha
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Justin B. Gregor
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Smriti Hoda
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | | | | | - Mindy Navarrete
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Scott D. Briggs
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Institute for Cancer Research, West Lafayette, Indiana, USA
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10
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Mo X, Yu X, Cui H, Xiong K, Yang S, Su C, Lu Y. In vivo RNA sequencing reveals a crucial role of Fus3-Kss1 MAPK pathway in Candida glabrata pathogenicity. mSphere 2024; 9:e0071524. [PMID: 39475321 PMCID: PMC11580445 DOI: 10.1128/msphere.00715-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 10/14/2024] [Indexed: 11/22/2024] Open
Abstract
Candida glabrata is an important and increasingly common pathogen of humans, particularly in immunocompromised hosts. Despite this, little is known about how this fungus causes disease. Here, we applied RNA sequencing and an in vivo invasive infection model to identify the attributes that allow this organism to infect hosts. Fungal transcriptomes show a dramatic increase in the expression of Fus3 and Kss1, two mitogen-activated protein kinases (MAPKs), during invasive infection. We further demonstrate that they are both highly induced under a combination of serum and high CO2 conditions. Deletion of both FUS3 and KSS1, but neither gene alone, results in a reduced fungal burden in organs, as well as in the gastrointestinal tract in the DSS (Dextran Sulfate Sodium)-induced colitis model. Similarly, the defect in persistence in macrophages and attenuated adhesion to epithelial cells are observed when FUS3 and KSS1 are both disrupted. The fus3 kss1 double mutant also displays defects in the induction of virulence attributes such as genes required for iron acquisition and adhesion and in the anti-fungal drug tolerance. The putative downstream transcription factors Ste12 (1), Ste12 (2), Tec1, and Tec2 are found to be involved in the regulation of these virulence attributes. Collectively, our study indicates that an evolutionary conserved MAPK pathway, which regulates mating and filamentous growth in Saccharomyces cerevisiae, is critical for C. glabrata pathogenicity. IMPORTANCE The MAPK signaling pathway, mediated by closely related kinases Fus3 and Kss1, is crucial for controlling mating and filamentous growth in Saccharomyces cerevisiae, but this pathway does not significantly impact hyphal development and pathogenicity in Candida albicans, a commensal-pathogenic fungus of humans. Furthermore, deletion of Cpk1, the ortholog of Fus3 in pathogenic fungus Cryptococcus neoformans, has no effect on virulence. Here, we demonstrate that the MAPK pathway is crucial for the pathogenicity of Candida glabrata, a fungus that causes approximately one-third of cases of hematogenously disseminated candidiasis in the United States. This pathway regulates multiple virulence attributes including the induction of iron acquisition genes and adhesins, as well as persistence in macrophages and organs. Our work provides insights into C. glabrata pathogenesis and highlights an example in which regulatory rewiring of a conserved pathway confers a virulent phenotype in a pathogen.
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Affiliation(s)
- Xinreng Mo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiangtai Yu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hao Cui
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Kang Xiong
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shan Yang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chang Su
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Lu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
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11
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Hwang IJ, Kwon YJ, Lim HJ, Hong KH, Lee H, Yong D, Won EJ, Byun SA, Lee GY, Kim SH, Song ES, Shin JH. Nosocomial transmission of fluconazole-resistant Candida glabrata bloodstream isolates revealed by whole-genome sequencing. Microbiol Spectr 2024; 12:e0088324. [PMID: 39162519 PMCID: PMC11448407 DOI: 10.1128/spectrum.00883-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/22/2024] [Indexed: 08/21/2024] Open
Abstract
The clonal transmission of fluconazole-resistant Candida glabrata isolates within hospitals has seldom been analyzed by whole-genome sequencing (WGS). We performed WGS on 79 C. glabrata isolates, comprising 31 isolates from three premature infants with persistent C. glabrata bloodstream infection despite antifungal treatment in the same neonatal intensive care unit (NICU) in 2022 and 48 (27 fluconazole-resistant and 21 fluconazole-susceptible dose-dependent) bloodstream isolates from 48 patients in 15 South Korean hospitals from 2010 to 2022. Phylogenetic analysis based on WGS single-nucleotide polymorphisms (SNPs) distinguished the 79 isolates according to multilocus sequence typing (MLST) (17 sequence type [ST]3, 13 ST7, two ST22, 41 ST26, four ST55, and two ST59 isolates) and unveiled two possible clusters of nosocomial transmission among ST26 isolates. One cluster from two premature infants with overlapping NICU hospitalizations in 2022 encompassed 15 fluconazole-resistant isolates harboring pleiotropic drug-resistance transcription factor (Pdr1p) P258L (13 isolates) or N1086I (two isolates), together with 10 fluconazole-susceptible dose-dependent isolates lacking Pdr1p SNPs. The other cluster indicated unforeseen clonal transmission of fluconazole-resistant bloodstream isolates among five patients (four post-lung transplantation and one with diffuse interstitial lung disease) in the same hospital over 8 months. Among these five isolates, four obtained after exposure to azole antifungals harbored distinct Pdr1p SNPs (N1091D, E388Q, K365E, and R376Q). The findings reveal the transmission patterns of clonal bloodstream isolates of C. glabrata among patients undergoing antifungal treatment, exhibiting different levels of fluconazole susceptibility or distinct Pdr1p SNP profiles. IMPORTANCE The prevalence of fluconazole-resistant bloodstream infections caused by Candida glabrata is increasing globally, but the transmission of these resistant strains within hospitals has rarely been documented. Through whole-genome sequencing and epidemiological analyses, this study identified two potential clusters of C. glabrata bloodstream infections within the same hospital, revealing the transmission of clonal C. glabrata strains with different levels of fluconazole susceptibility or distinct transcription factor pleiotropic drug resistance protein 1 (Pdr1p) single-nucleotide polymorphism profiles among patients receiving antifungal therapy.
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Affiliation(s)
- In Ji Hwang
- Department of Pediatrics, Chonnam National University Medical School, Gwangju, South Korea
| | - Yong Jun Kwon
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Ha Jin Lim
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Eun Jeong Won
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Seung A Byun
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Ga Yeong Lee
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Soo Hyun Kim
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Eun Song Song
- Department of Pediatrics, Chonnam National University Medical School, Gwangju, South Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
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12
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Zhang H, Jin P, Kong Y, Jia C, Qiao P, Dong Y, Zhou Y, Hu J, Yang Z, Jung G. Mutations across Diverse Domains of CjXDR1 Lead to Multidrug Resistance in Clarireedia jacksonii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39352294 DOI: 10.1021/acs.jafc.4c05106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Recently, Clarireedia jacksonii has emerged as a significant pathogen threatening turfgrass, and its escalating resistance to multiple drugs often undermines field interventions. This study highlighted the critical role of the fungus-specific transcription factor CjXDR1 (formerly ShXDR1) in regulating multidrug resistance (MDR) in C. jacksonii. This was demonstrated through experiments involving CjXDR1-knockout and CjXDR1-complemented strains. Our sequence analysis revealed five mutations in CjXDR1: G445D, K453E, S607F, D676H, and V690A. All five gain-of-function (GOF) mutations were confirmed to directly contribute to MDR against three different classes of fungicides (propiconazole: demethylation inhibitor, boscalid: succinate dehydrogenase inhibitor, and iprodione: dicarboximide) using the genetic transformation system and in vitro fungicide-sensitivity assay. Comparative transcriptome analysis revealed that CjXDR1 and its GOF mutations led to the overexpression of downstream genes encoding a Phase I metabolizing enzyme (CYP68) and two Phase III transporters (CjPDR1 and CjAtrD) previously reported. Knockout mutants of CYP68, CjPDR1, CjAtrD, and double-knockout mutants of CjPDR1 and CjAtrD exhibited increased sensitivity to all three fungicides tested. Among these, the CYP68-knockout mutants displayed the highest sensitivity to propiconazole, while the CjPDR1 knockout mutant exhibited significantly increased sensitivity to all three fungicides. Double-knockout mutants of CjPDR1 and CjAtrD displayed greater sensitivity than the single knockouts. In conclusion, multiple GOF mutants in CjXDR1 contribute to MDR by upregulating the expression of CjPDR1, CjAtrD, and CYP68. This study enhances our understanding of the molecular mechanisms underlying MDR in plant pathogenic fungi, providing valuable insights into GOF mutation structures and advancing the development of antifungal drugs.
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Affiliation(s)
- Huangwei Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Peiyuan Jin
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yixuan Kong
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Chenchen Jia
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Panpan Qiao
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yinglu Dong
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxin Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210095, China
| | - Jian Hu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhimin Yang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Geunhwa Jung
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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13
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Eliaš D, Tóth Hervay N, Černáková L, Gbelská Y. Changes in Ergosterol Biosynthesis Alter the Response to Cycloheximide, 4-Nitroquinoline-N-Oxide, Weak Organic Acids, and Virulence in Candida glabrata. J Fungi (Basel) 2024; 10:669. [PMID: 39452621 PMCID: PMC11508597 DOI: 10.3390/jof10100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/10/2024] [Accepted: 09/24/2024] [Indexed: 10/26/2024] Open
Abstract
The ERG6 gene encodes the sterol C24-methyltransferase converting zymosterol to fecosterol in the ergosterol biosynthetic pathway. Here, we extend the results of functional analysis of the CgERG6 gene, which was previously shown to modulate drug susceptibility in Candida glabrata mutant cells, by demonstrating that its deletion leads to increased susceptibility to cycloheximide, 4-nitroquinoline-N-oxide and weak organic acids, and such effects are associated with attenuated virulence. Together with abrogated efflux of drug substrates by CgCdr1p and CgPdr12p, the Cgerg6Δ mutation leads to reduced cell surface hydrophobicity and decreased virulence of the mutant cells of C. glabrata. The absence of CgErg6p impacts the lipid organization and function of the plasma membrane, resulting in non-specific permeability and abrogation of normal function of membrane-bound proteins accompanied by decreased virulence in Cgerg6Δ cells. Galleria mellonella larvae were used as a non-vertebrate animal host model to determine differences in the virulence potential of C. glabrata strains (parental strain and the Cgerg6Δ deletion mutant). We found that Cgerg6Δ mutant strain attenuated in virulence caused 25-30% survival of larvae compared with parental strain.
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Affiliation(s)
| | - Nora Tóth Hervay
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Yvetta Gbelská
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
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14
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Conway TP, Vu BG, Beattie SR, Krysan DJ, Moye-Rowley WS. Similarities and distinctions in the activation of the Candida glabrata Pdr1 regulatory pathway by azole and non-azole drugs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613905. [PMID: 39345512 PMCID: PMC11429959 DOI: 10.1101/2024.09.19.613905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Incidences of fluconazole (FLC) resistance among Candida glabrata clinical isolates is a growing issue in clinics. The pleiotropic drug response (PDR) network in C. glabrata confers azole resistance and is defined primarily by the Zn2Cys6 zinc cluster-containing transcription factor Pdr1 and target genes such as CDR1, that encodes an ATP-binding cassette transporter protein thought to act as a FLC efflux pump. Mutations in the PDR1 gene that render the transcription factor hyperactive are the most common cause of fluconazole resistance among clinical isolates. The phenothiazine class drug fluphenazine and a molecular derivative, CWHM-974, which both exhibit antifungal properties, have been shown to induce the expression of Cdr1 in Candida spp. We have used a firefly luciferase reporter gene driven by the CDR1 promoter to demonstrate two distinct patterns of CDR1 promoter activation kinetics: gradual promoter activation kinetics that occur in response to ergosterol limitations imposed by exposure to azole and polyene class antifungals and a robust and rapid CDR1 induction occurring in response to the stress imposed by fluphenazines. We can attribute these different patterns of CDR1 induction as proceeding through the promoter region of this gene since this is the only segment of the gene included in the luciferase reporter construct. Genetic analysis indicates that the signaling pathways responsible for phenothiazine and azole induction of CDR1 overlap but are not identical. The short time course of phenothiazine induction suggests that these compounds may act more directly on the Pdr1 protein to stimulate its activity.
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Affiliation(s)
| | - Bao Gia Vu
- Present address: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Sarah R. Beattie
- Departments of Molecular Physiology and Biophysics and Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Damian J. Krysan
- Departments of Molecular Physiology and Biophysics and Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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15
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Conway TP, Simonicova L, Moye-Rowley WS. Overlapping coactivator function is required for transcriptional activation by the Candida glabrata Pdr1 transcription factor. Genetics 2024; 228:iyae115. [PMID: 39028831 PMCID: PMC11791784 DOI: 10.1093/genetics/iyae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/21/2024] Open
Abstract
Azole resistance in the pathogenic yeast Candida glabrata is a serious clinical complication and increasing in frequency. The majority of resistant organisms have been found to contain a substitution mutation in the Zn2Cys6 zinc cluster-containing transcription factor Pdr1. These mutations typically lead to this factor driving high, constitutive expression of target genes like the ATP-binding cassette transporter-encoding gene CDR1. Overexpression of Cdr1 is required for the observed elevated fluconazole resistance exhibited by strains containing one of these hyperactive PDR1 alleles. While the identity of hyperactive PDR1 alleles has been extensively documented, the mechanisms underlying how these gain-of-function (GOF) forms of Pdr1 lead to elevated target gene transcription are not well understood. We have used a tandem affinity purification-tagged form of Pdr1 to identify coactivator proteins that biochemically purify with the wild-type and 2 different GOF forms of Pdr1. Three coactivator proteins were found to associate with Pdr1: the SWI/SNF complex Snf2 chromatin remodeling protein and 2 different components of the SAGA complex, Spt7 and Ngg1. We found that deletion mutants lacking either SNF2 or SPT7 exhibited growth defects, even in the absence of fluconazole challenge. To overcome these issues, we employed a conditional degradation system to acutely deplete these coactivators and determined that loss of either coactivator complex, SWI/SNF or SAGA, caused defects in Pdr1-dependent transcription. A double degron strain that could be depleted for both SWI/SNF and SAGA exhibited a profound defect in PDR1 autoregulation, revealing that these complexes work together to ensure high-level Pdr1-dependent gene transcription.
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Affiliation(s)
- Thomas P Conway
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Lucia Simonicova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - W 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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16
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Koren V, Ben-Zeev E, Voronov I, Fridman M. Chiral Fluorescent Antifungal Azole Probes Detect Resistance, Uptake Dynamics, and Subcellular Distribution in Candida Species. JACS AU 2024; 4:3157-3169. [PMID: 39211628 PMCID: PMC11350599 DOI: 10.1021/jacsau.4c00479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
Azoles are essential for fungal infection treatment, yet the increasing resistance highlights the need for innovative diagnostic tools and strategies to revitalize this class of antifungals. We developed two enantiomers of a fluorescent antifungal azole probe (1 S and 1 R ), analyzing 60 Candida strains via live-cell microscopy. A database of azole distribution images in strains of Candida albicans, Candida glabrata, and Candida parapsilosis, among the most important pathogenic Candida species, was established and analyzed. This analysis revealed distinct populations of yeast cells based on the correlation between fluorescent probe uptake and cell diameter. Varied uptake levels and subcellular distribution patterns were observed in C. albicans, C. glabrata, and C. parapsilosis, with the latter displaying increased localization to lipid droplets. Comparison of the more potent fluorescent antifungal azole probe enantiomer 1 S with the moderately potent enantiomer 1 R highlighted time-dependent differences in the uptake profiles. The former displayed a marked elevation in uptake after approximately 150 min, indicating the time required for significant cell permeabilization to occur and its association with the azole's antifungal activity potency. Divergent uptake levels between susceptible and high efflux-based azole-resistant strains were detected, offering a rapid diagnostic approach for identifying azole resistance. This study highlights unique insights achievable through fluorescent antifungal azole probes, unraveling the complexities of azole resistance, subcellular dynamics, and uptake within fungal pathogens.
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Affiliation(s)
- Vlad Koren
- School
of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Efrat Ben-Zeev
- Ilana
and Pascal Mantoux Institute for Bioinformatics and Nancy and Stephen
Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ivan Voronov
- School
of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School
of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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17
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Chen PY, Huang YS, Chuang YC, Wang JT, Sheng WH, Chen YC, Chang SC. Implication of genotypes for prognosis of Candida glabrata bloodstream infections. J Antimicrob Chemother 2024; 79:2008-2016. [PMID: 38906829 PMCID: PMC11290879 DOI: 10.1093/jac/dkae200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Genotyping isolates of a specific pathogen may demonstrate unique patterns of antimicrobial resistance, virulence or outcomes. However, evidence for genotype-outcome association in Candida glabrata is scarce. We aimed to characterize the mycological and clinical relevance of genotypes on C. glabrata bloodstream infections (BSIs). METHODS Non-duplicated C. glabrata blood isolates from hospitalized adults were genotyped by MLST, and further clustered by the unweighted pair group method with arithmetic averages (UPGMA). A clonal complex (CC) was defined by UPGMA similarities of >90%. Antifungal susceptibility testing was performed by a colorimetric microdilution method and interpreted following CLSI criteria. RESULTS Of 48 blood isolates evaluated, 13 STs were identified. CC7 was the leading CC (n = 14; 29.2%), including 13 ST7. The overall fluconazole and echinocandin resistance rates were 6.6% and 0%, respectively. No specific resistance patterns were associated with CC7 or other CCs. Charlson comorbidity index (adjusted OR, 1.49; 95% CI, 1.05-3.11) was the only predictor for CC7. By multivariable Cox regression analyses, CC7 was independently associated with 28 day mortality [adjusted HR (aHR), 3.28; 95% CI, 1.31-8.23], even after considering potential interaction with neutropenia (aHR, 3.41; 95% CI, 1.23-9.42; P for interaction, 0.24) or limited to 34 patients with monomicrobial BSIs (aHR, 2.85; 95% CI, 1.15-7.08). Also, the Kaplan-Meier estimate showed greater mortality with CC7 (P = 0.003). Fluconazole resistance or echinocandin therapy had no significant impact on mortality. CONCLUSIONS Our data suggested comorbid patients were at risk of developing CC7 BSIs. Further, CC7 was independently associated with worse outcomes.
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Affiliation(s)
- Pao-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan
| | - Yu-Shan Huang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan
| | - Yu-Chung Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
| | - Jann-Tay Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Taipei City, Taiwan
| | - Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- Department of Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan
| | - Yee-Chun Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Taipei City, Taiwan
- Department of Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- Department of Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan
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18
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Ror S, Stamnes MA, Moye-Rowley WS. Gene-specific transcriptional activation by the Aspergillus fumigatus AtrR factor requires a conserved C-terminal domain. mSphere 2024; 9:e0042524. [PMID: 38975761 PMCID: PMC11288021 DOI: 10.1128/msphere.00425-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Treatment of fungal infections associated with the filamentous fungus Aspergillus fumigatus is becoming more problematic as this organism is developing resistance to the main chemotherapeutic drug at an increasing rate. Azole drugs represent the current standard-of-care in the treatment of aspergillosis with this drug class acting by inhibiting a key step in the biosynthesis of the fungal sterol ergosterol. Azole compounds block the activity of the lanosterol α-14 demethylase, encoded by the cyp51A gene. A common route of azole resistance involves an increase in transcription of cyp51A. This transcriptional increase requires the function of a Zn2Cys6 DNA-binding domain-containing transcription activator protein called AtrR. AtrR was identified through its action as a positive regulator of expression of an ATP-binding cassette transporter (abcC/cdr1B here called abcG1). Using both deletion and alanine scanning mutagenesis, we demonstrate that a conserved C-terminal domain in A. fumigatus is required for the expression of abcG1 but dispensable for cyp51A transcription. This domain is also found in several other fungal pathogen AtrR homologs consistent with a conserved gene-selective function of this protein segment being conserved. Using RNA sequencing (RNA-seq), we find that this gene-specific transcriptional defect extends to several other membrane transporter-encoding genes including a second ABC transporter locus. Our data reveal that AtrR uses at least two distinct mechanisms to induce gene expression and that normal susceptibility to azole drugs cannot be provided by maintenance of wild-type expression of the ergosterol biosynthetic pathway when ABC transporter expression is reduced. IMPORTANCE Aspergillus fumigatus is the primary human filamentous fungal pathogen. The principal chemotherapeutic drug used to control infections associated with A. fumigatus is the azole compound. These drugs are well-tolerated and effective, but resistance is emerging at an alarming rate. Most resistance is associated with mutations that lead to overexpression of the azole target enzyme, lanosterol α-14 demethylase, encoded by the cyp51A gene. A key regulator of cyp51A gene expression is the transcription factor AtrR. Very little is known of the molecular mechanisms underlying the effect of AtrR on gene expression. Here, we use deletion and clustered amino acid substitution mutagenesis to map a region of AtrR that confers gene-specific activation on target genes of this transcription factor. This region is highly conserved across AtrR homologs from other pathogenic species arguing that its importance in transcriptional regulation is maintained across evolution.
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Affiliation(s)
- Shivani Ror
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - W. Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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19
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Pham D, Sivalingam V, Tang HM, Montgomery JM, Chen SCA, Halliday CL. Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches. J Fungi (Basel) 2024; 10:447. [PMID: 39057332 PMCID: PMC11278267 DOI: 10.3390/jof10070447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Varsha Sivalingam
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Helen M. Tang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - James M. Montgomery
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
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20
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Saha D, Gregor JB, Hoda S, Eastman KE, Navarrete M, Wisecaver JH, Briggs SD. Candida glabrata maintains two Hap1 homologs, Zcf27 and Zcf4, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599910. [PMID: 38979343 PMCID: PMC11230168 DOI: 10.1101/2024.06.20.599910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Candida glabrata exhibits innate resistance to azole antifungal drugs but also has the propensity to rapidly develop clinical drug resistance. Azole drugs, which target Erg11, is one of the three major classes of antifungals used to treat Candida infections. Despite their widespread use, the mechanism controlling azole-induced ERG gene expression and drug resistance in C. glabrata has primarily revolved around Upc2 and/or Pdr1. In this study, we determined the function of two zinc cluster transcription factors, Zcf27 and Zcf4, as direct but distinct regulators of ERG genes. Our phylogenetic analysis revealed C. glabrata Zcf27 and Zcf4 as the closest homologs to Saccharomyces cerevisiae Hap1. Hap1 is a known zinc cluster transcription factor in S. cerevisiae in controlling ERG gene expression under aerobic and hypoxic conditions. Interestingly, when we deleted HAP1 or ZCF27 in either S. cerevisiae or C. glabrata, respectively, both deletion strains showed altered susceptibility to azole drugs, whereas the strain deleted for ZCF4 did not exhibit azole susceptibility. We also determined that the increased azole susceptibility in a zcf27Δ strain is attributed to decreased azole-induced expression of ERG genes, resulting in decreased levels of total ergosterol. Surprisingly, Zcf4 protein expression is barely detected under aerobic conditions but is specifically induced under hypoxic conditions. However, under hypoxic conditions, Zcf4 but not Zcf27 was directly required for the repression of ERG genes. This study provides the first demonstration that Zcf27 and Zcf4 have evolved to serve distinct roles allowing C. glabrata to adapt to specific host and environmental conditions.
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Affiliation(s)
| | | | | | | | | | | | - Scott D Briggs
- Department of Biochemistry
- Purdue University Institute for Cancer Research
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21
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Fattouh N, Husni R, Finianos M, Bitar I, Khalaf RA. Adhesive and biofilm-forming Candida glabrata Lebanese hospital isolates harbour mutations in subtelomeric silencers and adhesins. Mycoses 2024; 67:e13750. [PMID: 38813959 DOI: 10.1111/myc.13750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND The prevalence of Candida glabrata healthcare-associated infections is on the rise worldwide and in Lebanon, Candida glabrata infections are difficult to treat as a result of their resistance to azole antifungals and their ability to form biofilms. OBJECTIVES The first objective of this study was to quantify biofilm biomass in the most virulent C. glabrata isolates detected in a Lebanese hospital. In addition, other pathogenicity attributes were evaluated. The second objective was to identify the mechanisms of azole resistance in those isolates. METHODS A mouse model of disseminated systemic infection was developed to evaluate the degree of virulence of 41 azole-resistant C. glabrata collected from a Lebanese hospital. The most virulent isolates were further evaluated alongside an isolate having attenuated virulence and a reference strain for comparative purposes. A DNA-sequencing approach was adopted to detect single nucleotide polymorphisms (SNPs) leading to amino acid changes in proteins involved in azole resistance and biofilm formation. This genomic approach was supported by several phenotypic assays. RESULTS All chosen virulent isolates exhibited increased adhesion and biofilm biomass compared to the isolate having attenuated virulence. The amino acid substitutions D679E and I739N detected in the subtelomeric silencer Sir3 are potentially involved- in increased adhesion. In all isolates, amino acid substitutions were detected in the ATP-binding cassette transporters Cdr1 and Pdh1 and their transcriptional regulator Pdr1. CONCLUSIONS In summary, increased adhesion led to stable biofilm formation since mutated Sir3 could de-repress adhesins, while decreased azole susceptibility could result from mutations in Cdr1, Pdh1 and Pdr1.
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Affiliation(s)
- Nour Fattouh
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
- Department of Biology, Saint George University of Beirut, Beirut, Lebanon
| | - Rola Husni
- School of Medicine, Lebanese American University, Beirut, Lebanon
- Lebanese American University Medical Center, Rizk Hospital, Beirut, Lebanon
| | - Marc Finianos
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Roy A Khalaf
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
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22
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López-Marmolejo AL, Hernández-Chávez MJ, Gutiérrez-Escobedo G, Selene Herrera-Basurto M, Mora-Montes HM, De Las Peñas A, Castaño I. Microevolution of Candida glabrata (Nakaseomyces glabrata) during an infection. Fungal Genet Biol 2024; 172:103891. [PMID: 38621582 DOI: 10.1016/j.fgb.2024.103891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/27/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Candida glabrata (Nakaseomyces glabrata) is an emergent and opportunistic fungal pathogen that colonizes and persists in different niches within its human host. In this work, we studied five clinical isolates from one patient (P7), that have a clonal origin, and all of which come from blood cultures except one, P7-3, obtained from a urine culture. We found phenotypic variation such as sensitivity to high temperature, oxidative stress, susceptibility to two classes of antifungal agents, and cell wall porosity. Only isolate P7-3 is highly resistant to the echinocandin caspofungin while the other four isolates from P7 are sensitive. However, this same isolate P7-3, is the only one that displays susceptibility to fluconazole (FLC), while the rest of the isolates are resistant to this antifungal. We sequenced the PDR1 gene which encodes a transcription factor required to induce the expression of several genes involved in the resistance to FLC and found that all the isolates encode for the same Pdr1 amino acid sequence except for the last isolate P7-5, which contains a single amino acid change, G1099C in the putative Pdr1 transactivation domain. Consistent with the resistance to FLC, we found that the CDR1 gene, encoding the main drug efflux pump in C. glabrata, is highly overexpressed in the FLC-resistant isolates, but not in the FLC-sensitive P7-3. In addition, the resistance to FLC observed in these isolates is dependent on the PDR1 gene. Additionally, we found that all P7 isolates have a different proportion of cell wall carbohydrates compared to our standard strains CBS138 and BG14. In P7 isolates, mannan is the most abundant cell wall component, whereas β-glucan is the most abundant component in our standard strains. Consistently, all P7 isolates have a relatively low cell wall porosity compared to our standard strains. These data show phenotypic and genotypic variability between clonal isolates from different niches within a single host, suggesting microevolution of C. glabrata during an infection.
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Affiliation(s)
- Ana L López-Marmolejo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José No. 2055, Col. Lomas 4a Sección, San Luis Potosí CP 78216, Mexico
| | - Marco J Hernández-Chávez
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José No. 2055, Col. Lomas 4a Sección, San Luis Potosí CP 78216, Mexico
| | - Guadalupe Gutiérrez-Escobedo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José No. 2055, Col. Lomas 4a Sección, San Luis Potosí CP 78216, Mexico
| | - M Selene Herrera-Basurto
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José No. 2055, Col. Lomas 4a Sección, San Luis Potosí CP 78216, Mexico
| | - Héctor M Mora-Montes
- Departamento de Biología, División de Ciencias Naturales, Universidad de Guanajuato, Noria Alta s/n Col. Noria Alta, Guanajuato, Gto CP36050, Mexico
| | - Alejandro De Las Peñas
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José No. 2055, Col. Lomas 4a Sección, San Luis Potosí CP 78216, Mexico
| | - Irene Castaño
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José No. 2055, Col. Lomas 4a Sección, San Luis Potosí CP 78216, Mexico
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23
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Conway TP, Simonicova L, Moye-Rowley WS. Overlapping coactivator function is required for transcriptional activation by the Candida glabrata Pdr1 transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595833. [PMID: 38853834 PMCID: PMC11160619 DOI: 10.1101/2024.05.24.595833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Azole resistance in the pathogenic yeast Candida glabrata is a serious clinical complication and increasing in frequency. The majority of resistant organisms have been found to contain a substitution mutation in the Zn2Cys6 zinc cluster-containing transcription factor Pdr1. These mutations typically lead to this factor driving high, constitutive expression of target genes like the ATP-binding cassette transporter-encoding gene CDR1 . Overexpression of Cdr1 is required for the observed elevated fluconazole resistance exhibited by strains containing one of these hyperactive PDR1 alleles. While the identity of hyperactive PDR1 alleles has been extensively documented, the mechanisms underlying how these gain-of-function (GOF) forms of Pdr1 lead to elevated target gene transcription are not well understood. We have used a tandem affinity purification (TAP)-tagged form of Pdr1 to identify coactivator proteins that biochemically purify with the wild-type and two different GOF forms of Pdr1. Three coactivator proteins were found to associate with Pdr1: the SWI/SNF complex Snf2 chromatin remodeling protein and two different components of the SAGA complex, Spt7 and Ngg1. We found that deletion mutants lacking either SNF2 or SPT7 exhibited growth defects, even in the absence of fluconazole challenge. To overcome these issues, we employed a conditional degradation system to acutely deplete these coactivators and determined that loss of either coactivator complex, SWI/SNF or SAGA, caused defects in Pdr1-dependent transcription. A double degron strain that could be depleted for both SWI/SNF and SAGA exhibited a profound defect in PDR1 autoregulation, revealing that these complexes work together to ensure high level Pdr1-dependent gene transcription.
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24
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Ror S, Stamnes MA, Moye-Rowley WS. Loss of a conserved C-terminal region of the Aspergillus fumigatus AtrR transcriptional regulator leads to a gene-specific defect in target gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595332. [PMID: 38826412 PMCID: PMC11142210 DOI: 10.1101/2024.05.22.595332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Treatment of fungal infections associated with the filamentous fungus Aspergillus fumigatus is becoming more problematic as this organism is developing resistance to the main chemotherapeutic drug at an increasing rate. Azole drugs represent the current standard-of-care in treatment of aspergillosis with this drug class acting by inhibiting a key step in biosynthesis of the fungal sterol ergosterol. Azole compounds block the activity of the lanosterol α-14 demethylase, encoded by the cyp51A gene. A common route of azole resistance involves an increase in transcription of cyp51A. This transcriptional increase requires the function of a Zn2Cys6 DNA-binding domain-containing transcription activator protein called AtrR. AtrR was identified through its action as a positive regulator of expression of an ATP-binding cassette transporter (abcC/cdr1B here called abcG1). Using both deletion and alanine scanning mutagenesis, we demonstrate that a conserved C-terminal domain in A. fumigatus is required for expression of abcG1 but dispensable for cyp51A transcription. This domain is also found in several other fungal pathogen AtrR homologues consistent with a conserved gene-selective function of this protein segment being conserved. Using RNA-seq, we find that this gene-specific transcriptional defect extends to several other membrane transporter-encoding genes including a second ABC transporter locus. Our data reveal that AtrR uses at least two distinct mechanisms to induce gene expression and that normal susceptibility to azole drugs cannot be provided by maintenance of wild-type expression of the ergosterol biosynthetic pathway when ABC transporter expression is reduced.
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Affiliation(s)
- Shivani Ror
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Mark A Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - W 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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25
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Maroc L, Shaker H, Shapiro RS. Functional genetic characterization of stress tolerance and biofilm formation in Nakaseomyces ( Candida) glabrata via a novel CRISPR activation system. mSphere 2024; 9:e0076123. [PMID: 38265239 PMCID: PMC10900893 DOI: 10.1128/msphere.00761-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
The overexpression of genes frequently arises in Nakaseomyces (formerly Candida) glabrata via gain-of-function mutations, gene duplication, or aneuploidies, with important consequences on pathogenesis traits and antifungal drug resistance. This highlights the need to develop specific genetic tools to mimic and study genetic amplification in this important fungal pathogen. Here, we report the development, validation, and applications of the first clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) system in N. glabrata for targeted genetic overexpression. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in N. glabrata, and further assess optimal guide RNA targeting for robust overexpression. We demonstrate the applications of CRISPRa to overexpress genes involved in fungal pathogenesis and drug resistance and detect corresponding phenotypic alterations in these key traits, including the characterization of novel phenotypes. Finally, we capture strain variation using our CRISPRa system in two commonly used N. glabrata genetic backgrounds. Together, this tool will expand our capacity for functional genetic overexpression in this pathogen, with numerous possibilities for future applications.IMPORTANCENakaseomyces (formerly Candida) glabrata is an important fungal pathogen that is now the second leading cause of candidiasis infections. A common strategy that this pathogen employs to resist antifungal treatment is through the upregulation of gene expression, but we have limited tools available to study this phenomenon. Here, we develop, optimize, and apply the use of CRISPRa as a means to overexpress genes in N. glabrata. We demonstrate the utility of this system to overexpress key genes involved in antifungal susceptibility, stress tolerance, and biofilm growth. This tool will be an important contribution to our ability to study the biology of this important fungal pathogen.
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Affiliation(s)
- Laetitia Maroc
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Hajer Shaker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
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26
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Misas E, Seagle E, Jenkins EN, Rajeev M, Hurst S, Nunnally NS, Bentz ML, Lyman MM, Berkow E, Harrison LH, Schaffner W, Markus TM, Pierce R, Farley MM, Chow NA, Lockhart SR, Litvintseva AP. Genomic description of acquired fluconazole- and echinocandin-resistance in patients with serial Candida glabrata isolates. J Clin Microbiol 2024; 62:e0114023. [PMID: 38265207 PMCID: PMC10865870 DOI: 10.1128/jcm.01140-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/29/2023] [Indexed: 01/25/2024] Open
Abstract
Candida glabrata is one of the most common causes of systemic candidiasis, often resistant to antifungal medications. To describe the genomic context of emerging resistance, we conducted a retrospective analysis of 82 serially collected isolates from 33 patients from population-based candidemia surveillance in the United States. We used whole-genome sequencing to determine the genetic relationships between isolates obtained from the same patient. Phylogenetic analysis demonstrated that isolates from 29 patients were clustered by patient. The median SNPs between isolates from the same patient was 30 (range: 7-96 SNPs), while unrelated strains infected four patients. Twenty-one isolates were resistant to echinocandins, and 24 were resistant to fluconazole. All echinocandin-resistant isolates carried a mutation either in the FKS1 or FKS2 HS1 region. Of the 24 fluconazole-resistant isolates, 17 (71%) had non-synonymous polymorphisms in the PDR1 gene, which were absent in susceptible isolates. In 11 patients, a genetically related resistant isolate was collected after recovering susceptible isolates, indicating in vivo acquisition of resistance. These findings allowed us to estimate the intra-host diversity of C. glabrata and propose an upper boundary of 96 SNPs for defining genetically related isolates, which can be used to assess donor-to-host transmission, nosocomial transmission, or acquired resistance. IMPORTANCE In our study, mutations associated to azole resistance and echinocandin resistance were detected in Candida glabrata isolates using a whole-genome sequence. C. glabrata is the second most common cause of candidemia in the United States, which rapidly acquires resistance to antifungals, in vitro and in vivo.
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Affiliation(s)
- E. Misas
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - E. Seagle
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - E. N. Jenkins
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- ASRT, Inc., Atlanta, Georgia, USA
| | - M. Rajeev
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - S. Hurst
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - N. S. Nunnally
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M. L. Bentz
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M. M. Lyman
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - E. Berkow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L. H. Harrison
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - W. Schaffner
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - T. M. Markus
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - R. Pierce
- Oregon Public Health Division, Oregon Health Authority, Portland, USA
| | - M. M. Farley
- Emory University School of Medicine, Decatur, Georgia, USA
| | - N. A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - S. R. Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - A. P. Litvintseva
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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27
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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] [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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Arastehfar A, Daneshnia F, Hovhannisyan H, Cabrera N, Ilkit M, Desai JV, Gabaldón T, Shor E, Perlin DS. A multidimensional assessment of in-host fitness costs of drug resistance in the opportunistic fungal pathogen Candida glabrata. FEMS Yeast Res 2024; 24:foae035. [PMID: 39545363 PMCID: PMC11631428 DOI: 10.1093/femsyr/foae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/28/2024] [Accepted: 11/11/2024] [Indexed: 11/17/2024] Open
Abstract
Drug-resistant microbes typically carry mutations in genes involved in critical cellular functions and may therefore be less fit under drug-free conditions than susceptible strains. Candida glabrata is a prevalent opportunistic yeast pathogen with a high rate of fluconazole resistance (FLZR), echinocandin resistance (ECR), and multidrug resistance (MDR) relative to other Candida. However, the fitness of C. glabrata MDR isolates, particularly in the host, is poorly characterized, and studies of FLZR isolate fitness have produced contradictory findings. Two important host niches for C. glabrata are macrophages, in which it survives and proliferates, and the gut. Herein, we used a collection of clinical and lab-derived C. glabrata isolates to show that FLZR C. glabrata isolates are less fit inside macrophages than susceptible isolates and that this fitness cost is reversed by acquiring ECR mutations. Interestingly, dual-RNAseq revealed that macrophages infected with drug-resistant isolates mount an inflammatory response whereas intracellular drug-resistant cells downregulate processes required for in-host adaptation. Furthermore, drug-resistant isolates were outcompeted by their susceptible counterparts during gut colonization and in infected kidneys, while showing comparable fitness in the spleen. Collectively, our study shows that macrophage-rich organs, such as the spleen, favor the retention of MDR isolates of C. glabrata.
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Affiliation(s)
- Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, United States
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, United States
- Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
| | - Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, United States
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, United States
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam1012 WX, The Netherlands
| | - Hrant Hovhannisyan
- Life Sciences Programme, Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Nathaly Cabrera
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, United States
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, 01330 Adana, Turkey
| | - Jigar V Desai
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, United States
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC 20057, United States
| | - Toni Gabaldón
- Life Sciences Programme, Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, United States
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ 07110, United States
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, United States
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC 20057, United States
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ 07110, United States
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29
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Wang Y, Xu J, Ben Abid F, Salah H, Sundararaju S, Al Ismail K, Wang K, Sara Matthew L, Taj-Aldeen S, Ibrahim EB, Tang P, Perez-Lopez A, Tsui CKM. Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata ( Nakaseomyces glabrata) isolates causing invasive infections. Microb Genom 2024; 10:001179. [PMID: 38226964 PMCID: PMC10868614 DOI: 10.1099/mgen.0.001179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world.
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Affiliation(s)
- Yue Wang
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Fatma Ben Abid
- Department of Medicine, Division of Infectious Diseases, Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar
| | - Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Khalil Al Ismail
- Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar
| | - Kun Wang
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Saad Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Emad B. Ibrahim
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Patrick Tang
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Andres Perez-Lopez
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Clement K. M. Tsui
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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30
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Schikora-Tamarit MÀ, Gabaldón T. Recent gene selection and drug resistance underscore clinical adaptation across Candida species. Nat Microbiol 2024; 9:284-307. [PMID: 38177305 PMCID: PMC10769879 DOI: 10.1038/s41564-023-01547-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024]
Abstract
Understanding how microbial pathogens adapt to treatments, humans and clinical environments is key to infer mechanisms of virulence, transmission and drug resistance. This may help improve therapies and diagnostics for infections with a poor prognosis, such as those caused by fungal pathogens, including Candida. Here we analysed genomic variants across approximately 2,000 isolates from six Candida species (C. glabrata, C. auris, C. albicans, C. tropicalis, C. parapsilosis and C. orthopsilosis) and identified genes under recent selection, suggesting a highly complex clinical adaptation. These involve species-specific and convergently affected adaptive mechanisms, such as adhesion. Using convergence-based genome-wide association studies we identified known drivers of drug resistance alongside potentially novel players. Finally, our analyses reveal an important role of structural variants and suggest an unexpected involvement of (para)sexual recombination in the spread of resistance. Our results provide insights on how opportunistic pathogens adapt to human-related environments and unearth candidate genes that deserve future attention.
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Affiliation(s)
- Miquel Àngel Schikora-Tamarit
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- Centro Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
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31
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Bohner F, Papp C, Takacs T, Varga M, Szekeres A, Nosanchuk JD, Vágvölgyi C, Tóth R, Gacser A. Acquired Triazole Resistance Alters Pathogenicity-Associated Features in Candida auris in an Isolate-Dependent Manner. J Fungi (Basel) 2023; 9:1148. [PMID: 38132749 PMCID: PMC10744493 DOI: 10.3390/jof9121148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Fluconazole resistance is commonly encountered in Candida auris, and the yeast frequently displays resistance to other standard drugs, which severely limits the number of effective therapeutic agents against this emerging pathogen. In this study, we aimed to investigate the effect of acquired azole resistance on the viability, stress response, and virulence of this species. Fluconazole-, posaconazole-, and voriconazole- resistant strains were generated from two susceptible C. auris clinical isolates (0381, 0387) and compared under various conditions. Several evolved strains became pan-azole-resistant, as well as echinocandin-cross-resistant. While being pan-azole-resistant, the 0381-derived posaconazole-evolved strain colonized brain tissue more efficiently than any other strain, suggesting that fitness cost is not necessarily a consequence of resistance development in C. auris. All 0387-derived evolved strains carried a loss of function mutation (R160S) in BCY1, an inhibitor of the PKA pathway. Sequencing data also revealed that posaconazole treatment can result in ERG3 mutation in C. auris. Despite using the same mechanisms to generate the evolved strains, both genotype and phenotype analysis highlighted that the development of resistance was unique for each strain. Our data suggest that C. auris triazole resistance development is a highly complex process, initiated by several pleiotropic factors.
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Affiliation(s)
- Flora Bohner
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Csaba Papp
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Tamas Takacs
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Mónika Varga
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - András Szekeres
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Joshua D. Nosanchuk
- Department of Medicine (Infectious Diseases), Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA;
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Csaba Vágvölgyi
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Attila Gacser
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
- HCEMM-USZ Fungal Pathogens Research Group, Department of Microbiology, University of Szeged, 6726 Szeged, Hungary
- HUN-REN-USZ Pathomechanisms of Fungal Infections Research Group, University of Szeged, 6726 Szeged, Hungary
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32
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Czajka KM, Venkataraman K, Brabant-Kirwan D, Santi SA, Verschoor C, Appanna VD, Singh R, Saunders DP, Tharmalingam S. Molecular Mechanisms Associated with Antifungal Resistance in Pathogenic Candida Species. Cells 2023; 12:2655. [PMID: 37998390 PMCID: PMC10670235 DOI: 10.3390/cells12222655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
Candidiasis is a highly pervasive infection posing major health risks, especially for immunocompromised populations. Pathogenic Candida species have evolved intrinsic and acquired resistance to a variety of antifungal medications. The primary goal of this literature review is to summarize the molecular mechanisms associated with antifungal resistance in Candida species. Resistance can be conferred via gain-of-function mutations in target pathway genes or their transcriptional regulators. Therefore, an overview of the known gene mutations is presented for the following antifungals: azoles (fluconazole, voriconazole, posaconazole and itraconazole), echinocandins (caspofungin, anidulafungin and micafungin), polyenes (amphotericin B and nystatin) and 5-fluorocytosine (5-FC). The following mutation hot spots were identified: (1) ergosterol biosynthesis pathway mutations (ERG11 and UPC2), resulting in azole resistance; (2) overexpression of the efflux pumps, promoting azole resistance (transcription factor genes: tac1 and mrr1; transporter genes: CDR1, CDR2, MDR1, PDR16 and SNQ2); (3) cell wall biosynthesis mutations (FKS1, FKS2 and PDR1), conferring resistance to echinocandins; (4) mutations of nucleic acid synthesis/repair genes (FCY1, FCY2 and FUR1), resulting in 5-FC resistance; and (5) biofilm production, promoting general antifungal resistance. This review also provides a summary of standardized inhibitory breakpoints obtained from international guidelines for prominent Candida species. Notably, N. glabrata, P. kudriavzevii and C. auris demonstrate fluconazole resistance.
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Affiliation(s)
- Karolina M. Czajka
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
| | - Krishnan Venkataraman
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
| | | | - Stacey A. Santi
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Chris Verschoor
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Vasu D. Appanna
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
| | - Ravi Singh
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Deborah P. Saunders
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Sujeenthar Tharmalingam
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
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33
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Gale AN, Pavesic MW, Nickels TJ, Xu Z, Cormack BP, Cunningham KW. Redefining pleiotropic drug resistance in a pathogenic yeast: Pdr1 functions as a sensor of cellular stresses in Candida glabrata. mSphere 2023; 8:e0025423. [PMID: 37358297 PMCID: PMC10449514 DOI: 10.1128/msphere.00254-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 06/27/2023] Open
Abstract
Candida glabrata is a prominent opportunistic fungal pathogen of humans. The increasing incidence of C. glabrata infections is attributed to both innate and acquired resistance to antifungals. Previous studies suggest the transcription factor Pdr1 and several target genes encoding ABC transporters are critical elements of pleiotropic defense against azoles and other antifungals. This study utilizes Hermes transposon insertion profiling to investigate Pdr1-independent and Pdr1-dependent mechanisms that alter susceptibility to the frontline antifungal fluconazole. Several new genes were found to alter fluconazole susceptibility independent of Pdr1 (CYB5, SSK1, SSK2, HOG1, TRP1). A bZIP transcription repressor of mitochondrial function (CIN5) positively regulated Pdr1 while hundreds of genes encoding mitochondrial proteins were confirmed as negative regulators of Pdr1. The antibiotic oligomycin activated Pdr1 and antagonized fluconazole efficacy likely by interfering with mitochondrial processes in C. glabrata. Unexpectedly, disruption of many 60S ribosomal proteins also activated Pdr1, thus mimicking the effects of the mRNA translation inhibitors. Cycloheximide failed to fully activate Pdr1 in a cycloheximide-resistant Rpl28-Q38E mutant. Similarly, fluconazole failed to fully activate Pdr1 in a strain expressing a low-affinity variant of Erg11. Fluconazole activated Pdr1 with very slow kinetics that correlated with the delayed onset of cellular stress. These findings are inconsistent with the idea that Pdr1 directly senses xenobiotics and support an alternative hypothesis where Pdr1 senses cellular stresses that arise only after engagement of xenobiotics with their targets. IMPORTANCE Candida glabrata is an opportunistic pathogenic yeast that causes discomfort and death. Its incidence has been increasing because of natural defenses to our common antifungal medications. This study explores the entire genome for impacts on resistance to fluconazole. We find several new and unexpected genes can impact susceptibility to fluconazole. Several antibiotics can also alter the efficacy of fluconazole. Most importantly, we find that Pdr1-a key determinant of fluconazole resistance-is not regulated directly through binding of fluconazole and instead is regulated indirectly by sensing the cellular stresses caused by fluconazole blockage of sterol biosynthesis. This new understanding of drug resistance mechanisms could improve the outcomes of current antifungals and accelerate the development of novel therapeutics.
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Affiliation(s)
- Andrew N Gale
- Department of Biology, Johns Hopkins University , Baltimore, Maryland, USA
| | - Matthew W Pavesic
- Department of Biology, Johns Hopkins University , Baltimore, Maryland, USA
| | - Timothy J Nickels
- Department of Biology, Johns Hopkins University , Baltimore, Maryland, USA
| | - Zhuwei Xu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine , Baltimore, Maryland, USA
| | - Brendan P Cormack
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine , Baltimore, Maryland, USA
| | - Kyle W Cunningham
- Department of Biology, Johns Hopkins University , Baltimore, Maryland, USA
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34
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Franconi I, Rizzato C, Poma N, Tavanti A, Lupetti A. Candida parapsilosis sensu stricto Antifungal Resistance Mechanisms and Associated Epidemiology. J Fungi (Basel) 2023; 9:798. [PMID: 37623569 PMCID: PMC10456088 DOI: 10.3390/jof9080798] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Fungal diseases cause millions of deaths per year worldwide. Antifungal resistance has become a matter of great concern in public health. In recent years rates of non-albicans species have risen dramatically. Candida parapsilosis is now reported to be the second most frequent species causing candidemia in several countries in Europe, Latin America, South Africa and Asia. Rates of acquired azole resistance are reaching a worrisome threshold from multiple reports as in vitro susceptibility testing is now starting also to explore tolerance and heteroresistance to antifungal compounds. With this review, the authors seek to evaluate known antifungal resistance mechanisms and their worldwide distribution in Candida species infections with a specific focus on C. parapsilosis.
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Affiliation(s)
- Iacopo Franconi
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno, 37, 56127 Pisa, Italy; (I.F.); (C.R.)
| | - Cosmeri Rizzato
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno, 37, 56127 Pisa, Italy; (I.F.); (C.R.)
| | - Noemi Poma
- Department of Biology, University of Pisa, Via San Zeno, 37, 56127 Pisa, Italy; (N.P.); (A.T.)
| | - Arianna Tavanti
- Department of Biology, University of Pisa, Via San Zeno, 37, 56127 Pisa, Italy; (N.P.); (A.T.)
| | - Antonella Lupetti
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno, 37, 56127 Pisa, Italy; (I.F.); (C.R.)
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35
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Chew KL, Achik R, Osman NH, Octavia S, Teo JWP. Genomic epidemiology of human candidaemia isolates in a tertiary hospital. Microb Genom 2023; 9:mgen001047. [PMID: 37440287 PMCID: PMC10438824 DOI: 10.1099/mgen.0.001047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/17/2023] [Indexed: 07/14/2023] Open
Abstract
Invasive candida infections are significant infections that may occur in vulnerable patients with high rates of mortality or morbidity. Drug-resistance rates also appear to be on the rise which further complicate treatment options and outcomes. The aims of this study were to describe the prevalence, molecular epidemiology, and genetic features of Candida bloodstream isolates in a hospital setting. The resistance mechanisms towards the two most commonly administered antifungals, fluconazole and anidulafungin, were determined. Blood culture isolates between 1 January 2018 and 30 June 2021 positive for Candida spp. were included. Susceptibility testing was performed using Etest. Whole-genome-sequencing was performed using Illumina NovaSeq with bioinformatics analysis performed. A total of 203 isolates were sequenced: 56 C. glabrata, 53 C. tropicalis, 44 C. albicans, 36 C. parapsilosis complex (consisting of C. parapsilosis, C. orthopsilosis, and C. metapsilosis), six C. krusei, five C. dubliniensis, and three C. auris. A single cluster of azole-resistant C. tropicalis, and four clusters of C. parapsilosis isolates were observed, suggesting possible transmission occurring over several years. We found 11.3%, and 52.7 % of C. tropicalis and C. parapsilosis, respectively, clustered with other isolates, suggesting exogenous sources may play a significant role of transmission, particularly for C. parapsilosis. The clusters spanned over several years suggesting the possibility of environmental reservoirs contributing to the spread. Limited clonality was seen for C. albicans. Several sequence types appeared to be dominant for C. glabrata, however the SNP differences varied widely, indicating absence of sustained transmission.
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Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Rosemini Achik
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Nurul Hudaa Osman
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Sophie Octavia
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Jeanette W. P. Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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36
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Osset-Trénor P, Pascual-Ahuir A, Proft M. Fungal Drug Response and Antimicrobial Resistance. J Fungi (Basel) 2023; 9:jof9050565. [PMID: 37233275 DOI: 10.3390/jof9050565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Antifungal resistance is a growing concern as it poses a significant threat to public health. Fungal infections are a significant cause of morbidity and mortality, especially in immunocompromised individuals. The limited number of antifungal agents and the emergence of resistance have led to a critical need to understand the mechanisms of antifungal drug resistance. This review provides an overview of the importance of antifungal resistance, the classes of antifungal agents, and their mode of action. It highlights the molecular mechanisms of antifungal drug resistance, including alterations in drug modification, activation, and availability. In addition, the review discusses the response to drugs via the regulation of multidrug efflux systems and antifungal drug-target interactions. We emphasize the importance of understanding the molecular mechanisms of antifungal drug resistance to develop effective strategies to combat the emergence of resistance and highlight the need for continued research to identify new targets for antifungal drug development and explore alternative therapeutic options to overcome resistance. Overall, an understanding of antifungal drug resistance and its mechanisms will be indispensable for the field of antifungal drug development and clinical management of fungal infections.
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Affiliation(s)
- Paloma Osset-Trénor
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas IBMCP, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas IBMCP, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, 46010 Valencia, Spain
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Gale AN, Pavesic MW, Nickels TJ, Xu Z, Cormack BP, Cunningham KW. Redefining Pleiotropic Drug Resistance in a Pathogenic Yeast: Pdr1 Functions as a Sensor of Cellular Stresses in Candida glabrata. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539747. [PMID: 37214952 PMCID: PMC10197522 DOI: 10.1101/2023.05.07.539747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Candida glabrata is a prominent opportunistic fungal pathogen of humans. The increasing incidence of C. glabrata infections is attributed to both innate and acquired resistance to antifungals. Previous studies suggest the transcription factor Pdr1 and several target genes encoding ABC transporters are critical elements of pleiotropic defense against azoles and other antifungals. This study utilizes Hermes transposon insertion profiling to investigate Pdr1-independent and Pdr1-dependent mechanisms that alter susceptibility to the frontline antifungal fluconazole. Several new genes were found to alter fluconazole susceptibility independent of Pdr1 ( CYB5 , SSK1 , SSK2 , HOG1 , TRP1 ). A bZIP transcription repressor of mitochondrial function ( CIN5 ) positively regulated Pdr1 while hundreds of genes encoding mitochondrial proteins were confirmed as negative regulators of Pdr1. The antibiotic oligomycin activated Pdr1 and antagonized fluconazole efficacy likely by interfering with mitochondrial processes in C. glabrata . Unexpectedly, disruption of many 60S ribosomal proteins also activated Pdr1, thus mimicking the effects of the mRNA translation inhibitors. Cycloheximide failed to fully activate Pdr1 in a cycloheximide-resistant Rpl28-Q38E mutant. Similarly, fluconazole failed to fully activate Pdr1 in a strain expressing a low-affinity variant of Erg11. Fluconazole activated Pdr1 with very slow kinetics that correlated with the delayed onset of cellular stress. These findings are inconsistent with the idea that Pdr1 directly senses xenobiotics and support an alternative hypothesis where Pdr1 senses cellular stresses that arise only after engagement of xenobiotics with their targets. Importance Candida glabrata is an opportunistic pathogenic yeast that causes discomfort and death. Its incidence has been increasing because of natural defenses to our common antifungal medications. This study explores the entire genome for impacts on resistance to fluconazole. We find several new and unexpected genes can impact susceptibility to fluconazole. Several antibiotics can also alter the efficacy of fluconazole. Most importantly, we find that Pdr1 - a key determinant of fluconazole resistance - is not regulated directly through binding of fluconazole and instead is regulated indirectly by sensing the cellular stresses caused by fluconazole blockage of sterol biosynthesis. This new understanding of drug resistance mechanisms could improve the outcomes of current antifungals and accelerate the development of novel therapeutics.
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Alastruey-Izquierdo A, Martín-Galiano AJ. The challenges of the genome-based identification of antifungal resistance in the clinical routine. Front Microbiol 2023; 14:1134755. [PMID: 37152754 PMCID: PMC10157239 DOI: 10.3389/fmicb.2023.1134755] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
The increasing number of chronic and life-threatening infections caused by antimicrobial resistant fungal isolates is of critical concern. Low DNA sequencing cost may facilitate the identification of the genomic profile leading to resistance, the resistome, to rationally optimize the design of antifungal therapies. However, compared to bacteria, initiatives for resistome detection in eukaryotic pathogens are underdeveloped. Firstly, reported mutations in antifungal targets leading to reduced susceptibility must be extensively collected from the literature to generate comprehensive databases. This information should be complemented with specific laboratory screenings to detect the highest number possible of relevant genetic changes in primary targets and associations between resistance and other genomic markers. Strikingly, some drug resistant strains experience high-level genetic changes such as ploidy variation as much as duplications and reorganizations of specific chromosomes. Such variations involve allelic dominance, gene dosage increments and target expression regime effects that should be explicitly parameterized in antifungal resistome prediction algorithms. Clinical data indicate that predictors need to consider the precise pathogen species and drug levels of detail, instead of just genus and drug class. The concomitant needs for mutation accuracy and assembly quality assurance suggest hybrid sequencing approaches involving third-generation methods will be utilized. Moreover, fatal fast infections, like fungemia and meningitis, will further require both sequencing and analysis facilities are available in-house. Altogether, the complex nature of antifungal resistance demands extensive sequencing, data acquisition and processing, bioinformatic analysis pipelines, and standard protocols to be accomplished prior to genome-based protocols are applied in the clinical setting.
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Affiliation(s)
- Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Center for Biomedical Research in Network in Infectious Diseases (CIBERINFEC-CB21/13/00105), Instituto de Salud Carlos III, Madrid, Spain
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39
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Simonicova L, Moye-Rowley WS. Characterizing Candida glabrata Pdr1, a Hyperactive Transcription Factor Involved in Azole Resistance. Methods Mol Biol 2023; 2658:169-179. [PMID: 37024701 DOI: 10.1007/978-1-0716-3155-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
This chapter illustrates how to prepare isogenic strains carrying gain-of-function forms of transcription factor Pdr1 in the human pathogen Candida glabrata. Simple steps are described that lead from a characterized plasmid-borne PDR1-GOF allele to its integration into the yeast genome in a markerless manner. Pdr1-GOF strains constructed by this approach are suitable for virulence studies in an animal host.
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Affiliation(s)
- Lucia Simonicova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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40
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Galocha M, Viana R, Pais P, Silva-Dias A, Cavalheiro M, Miranda IM, Van Ende M, Souza CS, Costa C, Branco J, Soares CM, Van Dijck P, Rodrigues AG, Teixeira MC. Genomic evolution towards azole resistance in Candida glabrata clinical isolates unveils the importance of CgHxt4/6/7 in azole accumulation. Commun Biol 2022; 5:1118. [PMID: 36271293 PMCID: PMC9587243 DOI: 10.1038/s42003-022-04087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
The increasing prevalence of candidosis caused by Candida glabrata is related to its ability to acquire azole resistance. Although azole resistance mechanisms are well known, the mechanisms for azole import into fungal cells have remained obscure. In this work, we have characterized two hexose transporters in C. glabrata and further investigate their role as potential azole importers. Three azole susceptible C. glabrata clinical isolates were evolved towards azole resistance and the acquired resistance phenotype was found to be independent of CgPDR1 or CgERG11 mutations. Through whole-genome sequencing, CgHXT4/6/7 was found to be mutated in the three evolved strains, when compared to their susceptible parents. CgHxt4/6/7 and the 96% identical CgHxt6/7 were found to confer azole susceptibility and increase azole accumulation in C. glabrata cells, strikingly rescuing the susceptibility phenotype imposed by CgPDR1 deletion, while the identified loss-of-function mutation in CgHXT4/6/7, leads to increased azole resistance. In silico docking analysis shows that azoles display a strong predicted affinity for the glucose binding site of CgHxt4/6/7. Altogether, we hypothesize that hexose transporters, such as CgHxt4/6/7 and CgHxt6/7, may constitute a family of azole importers, involved in clinical drug resistance in fungal pathogens, and constituting promising targets for improved antifungal therapy. Mutations in the hexose transporter, CgHXT4/6/7, contribute to increased antifungal (azole) resistance in the fungal pathogen, Candida glabrata, potentially by influencing azole accumulation.
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Affiliation(s)
- Mónica Galocha
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisbon, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Romeu Viana
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisbon, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisbon, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Silva-Dias
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Mafalda Cavalheiro
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisbon, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel M Miranda
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal.,Cardiovascular R&D Center, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Mieke Van Ende
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Caio S Souza
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Catarina Costa
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisbon, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Branco
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Acácio G Rodrigues
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal. .,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal.
| | - Miguel C Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal. .,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisbon, Portugal. .,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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41
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Bhakt P, Raney M, Kaur R. The SET-domain protein CgSet4 negatively regulates antifungal drug resistance via the ergosterol biosynthesis transcriptional regulator CgUpc2a. J Biol Chem 2022; 298:102485. [PMID: 36108742 PMCID: PMC9576903 DOI: 10.1016/j.jbc.2022.102485] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/27/2022] Open
Abstract
Invasive fungal infections, which pose a serious threat to human health, are increasingly associated with a high mortality rate and elevated health care costs, owing to rising resistance to current antifungals and emergence of multidrug-resistant fungal species. Candida glabrata is the second to fourth common cause of Candida bloodstream infections. Its high propensity to acquire resistance toward two mainstream drugs, azoles (inhibit ergosterol biosynthesis) and echinocandins (target cell wall), in clinical settings, and its inherent low azole susceptibility render antifungal therapy unsuccessful in many cases. Here, we demonstrate a pivotal role for the SET {suppressor of variegation 3 to 9 [Su(var)3-9], enhancer of zeste [E(z)], and trithorax (Trx)} domain-containing protein, CgSet4, in azole and echinocandin resistance via negative regulation of multidrug transporter-encoding and ergosterol biosynthesis (ERG) genes through the master transcriptional factors CgPdr1 and CgUpc2A, respectively. RNA-Seq analysis revealed that C. glabrata responds to caspofungin (CSP; echinocandin antifungal) stress by downregulation and upregulation of ERG and cell wall organization genes, respectively. Although CgSet4 acts as a repressor of the ergosterol biosynthesis pathway via CgUPC2A transcriptional downregulation, the CSP-induced ERG gene repression is not dependent on CgSet4, as CgSet4 showed diminished abundance on the CgUPC2A promoter in CSP-treated cells. Furthermore, we show a role for the last three enzymes of the ergosterol biosynthesis pathway, CgErg3, CgErg5, and CgErg4, in antifungal susceptibility and virulence in C. glabrata. Altogether, our results unveil the link between ergosterol biosynthesis and echinocandin resistance and have implications for combination antifungal therapy.
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Affiliation(s)
- Priyanka Bhakt
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Mayur Raney
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Rupinder Kaur
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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42
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Vu BG, Moye-Rowley WS. Nonidentical function of Upc2A binding sites in the Candida glabrata CDR1 promoter. Genetics 2022; 222:iyac135. [PMID: 36063046 PMCID: PMC9526049 DOI: 10.1093/genetics/iyac135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/15/2022] [Indexed: 01/04/2023] Open
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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43
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Edlind T, Katiyar S. Intrinsically High Resistance of Candida glabrata to Hydrogen Peroxide and Its Reversal in a Fluconazole-Resistant Mutant. Antimicrob Agents Chemother 2022; 66:e0072122. [PMID: 35916516 PMCID: PMC9487529 DOI: 10.1128/aac.00721-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Tom Edlind
- MicrobiType LLC, Wyndmoor, Pennsylvania, USA
| | - Santosh Katiyar
- Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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Artemisinin Targets Transcription Factor PDR1 and Impairs Candida glabrata Mitochondrial Function. Antioxidants (Basel) 2022; 11:antiox11101855. [PMID: 36290580 PMCID: PMC9598568 DOI: 10.3390/antiox11101855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
A limited number of antifungal drugs, the side-effect of clinical drugs and the emergence of resistance create an urgent need for new antifungal treatment agents. High-throughput drug screening and in-depth drug action mechanism analyzation are needed to address this problem. In this study, we identified that artemisinin and its derivatives possessed antifungal activity through a high-throughput screening of the FDA-approved drug library. Subsequently, drug-resistant strains construction, a molecular dynamics simulation and a transcription level analysis were used to investigate artemisinin’s action mechanism in Candida glabrata. Transcription factor pleiotropic drug resistance 1 (PDR1) was an important determinant of artemisinin’s sensitivity by regulating the drug efflux pump and ergosterol biosynthesis pathway, leading to mitochondrial dysfunction. This dysfunction was shown by a depolarization of the mitochondrial membrane potential, an enhancement of the mitochondrial membrane viscosity and an upregulation of the intracellular ROS level in fungi. The discovery shed new light on the development of antifungal agents and understanding artemisinin’s action mechanism.
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Merdan O, Şişman AS, Aksoy SA, Kızıl S, Tüzemen NÜ, Yılmaz E, Ener B. Investigation of the Defective Growth Pattern and Multidrug Resistance in a Clinical Isolate of Candida glabrata Using Whole-Genome Sequencing and Computational Biology Applications. Microbiol Spectr 2022; 10:e0077622. [PMID: 35867406 PMCID: PMC9430859 DOI: 10.1128/spectrum.00776-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022] Open
Abstract
Candida glabrata is increasingly isolated from blood cultures, and multidrug-resistant isolates have important implications for therapy. This study describes a cholesterol-dependent clinical C. glabrata isolate (ML72254) that did not grow without blood (containing cholesterol) on routine mycological media and that showed azole and amphotericin B (AmB) resistance. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and whole-genome sequencing (WGS) were used for species identification. A modified Etest method (Mueller-Hinton agar supplemented with 5% sheep blood) was used for antifungal susceptibility testing. WGS data were processed via the Galaxy platform, and the genomic variations of ML72254 were retrieved. A computational biology workflow utilizing web-based applications (PROVEAN, AlphaFold Colab, and Missense3D) was constructed to predict possible deleterious effects of these missense variations on protein functions. The predictive ability of this workflow was tested with previously reported missense variations in ergosterol synthesis genes of C. glabrata. ML72254 was identified as C. glabrata sensu stricto with MALDI-TOF, and WGS confirmed this identification. The MICs of fluconazole, voriconazole, and amphotericin B were >256, >32, and >32 μg/mL, respectively. A novel frameshift mutation in the ERG1 gene (Pro314fs) and many missense variations were detected in the ergosterol synthesis genes. None of the missense variations in the ML72254 ergosterol synthesis genes were deleterious, and the Pro314fs mutation was identified as the causative molecular change for a cholesterol-dependent and multidrug-resistant phenotype. This study verified that web-based computational biology solutions can be powerful tools for examining the possible impacts of missense mutations in C. glabrata. IMPORTANCE In this study, a cholesterol-dependent C. glabrata clinical isolate that confers azole and AmB resistance was investigated using artificial intelligence (AI) technologies and cloud computing applications. This is the first of the known cholesterol-dependent C. glabrata isolate to be found in Turkey. Cholesterol-dependent C. glabrata isolates are rarely isolated in clinical samples; they can easily be overlooked during routine laboratory procedures. Microbiologists therefore need to be alert when discrepancies occur between microscopic examination and growth on routine media. In addition, because these isolates confer antifungal resistance, patient management requires extra care.
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Affiliation(s)
- Osman Merdan
- Department of Medical Microbiology, Faculty of Medicine, Bursa Uludağ University, Bursa, Turkey
| | - Ayşe Sena Şişman
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Bursa Uludağ University, Bursa, Turkey
| | - Seçil Ak Aksoy
- İnegöl Vocational School, Bursa Uludağ University, Bursa, Turkey
| | - Samet Kızıl
- Department of Medical Microbiology, Faculty of Medicine, Bursa Uludağ University, Bursa, Turkey
| | - Nazmiye Ülkü Tüzemen
- Department of Medical Microbiology, Faculty of Medicine, Bursa Uludağ University, Bursa, Turkey
| | - Emel Yılmaz
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Bursa Uludağ University, Bursa, Turkey
| | - Beyza Ener
- Department of Medical Microbiology, Faculty of Medicine, Bursa Uludağ University, Bursa, Turkey
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Daneshnia F, Hilmioğlu Polat S, Ilkit M, Shor E, de Almeida Júnior JN, Favarello LM, Colombo AL, Arastehfar A, Perlin DS. Determinants of fluconazole resistance and the efficacy of fluconazole and milbemycin oxim combination against Candida parapsilosis clinical isolates from Brazil and Turkey. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:906681. [PMID: 37746198 PMCID: PMC10512262 DOI: 10.3389/ffunb.2022.906681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/11/2022] [Indexed: 09/26/2023]
Abstract
Fluconazole-resistant Candida parapsilosis (FLZR-CP) outbreaks are a growing public health concern and have been reported in numerous countries. Patients infected with FLZR-CP isolates show fluconazole therapeutic failure and have a significantly increased mortality rate. Because fluconazole is the most widely used antifungal agent in most regions with outbreaks, it is paramount to restore its antifungal activity. Milbemycin oxim (MOX), a well-known canine endectocide, is a potent efflux pump inhibitor that significantly potentiates the activity of fluconazole against FLZR C. glabrata and C. albicans. However, the FLZ-MOX combination has not been tested against FLZR-CP isolates, nor is it known whether MOX may also potentiate the activity of echinocandins, a different class of antifungal drugs. Furthermore, the extent of involvement of efflux pumps CDR1 and MDR1 and ergosterol biosynthesis enzyme ERG11 and their link with gain-of-function (GOF) mutations in their transcription regulators (TAC1, MRR1, and UPC2) are poorly characterized among FLZR-CP isolates. We analyzed 25 C. parapsilosis isolates collected from outbreaks in Turkey and Brazil by determining the expression levels of CDR1, MDR1, and ERG11, examining the presence of potential GOF mutations in their transcriptional regulators, and assessing the antifungal activity of FLZ-MOX and micafungin-MOX against FLZR and multidrug-resistant (MDR) C. parapsilosis isolates. ERG11 was found to be universally induced by fluconazole in all isolates, while expression of MDR1 was unchanged. Whereas mutations in MRR1 and UPC2 were not detected, CDR1 was overexpressed in three Brazilian FLZR-CP isolates, which also carried a novel TAC1L518F mutation. Of these three isolates, one showed increased basal expression of CDR1, while the other two overexpressed CDR1 only in the presence of fluconazole. Interestingly, MOX showed promising antifungal activity against FLZR isolates, reducing the FLZ MIC 8- to 32-fold. However, the MOX and micafungin combination did not exert activity against an MDR C. parapsilosis isolate. Collectively, our study documents that the mechanisms underpinning FLZR are region specific, where ERG11 mutations were the sole mechanism of FLZR in Turkish FLZR-CP isolates, while simultaneous overexpression of CDR1 was observed in some Brazilian counterparts. Moreover, MOX and fluconazole showed potent synergistic activity, while the MOX-micafungin combination showed no synergy.
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Affiliation(s)
- Farnaz Daneshnia
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Turkey
| | - Erika Shor
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Hackensack Meridian School of Medicine, Nutley, NJ, United States
| | - João Nobrega de Almeida Júnior
- Laboratorio de Micologia Medica (LIM 53), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Central (LIM 03), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Larissa M. Favarello
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Arnaldo Lopes Colombo
- Department of Medicine, Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Amir Arastehfar
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Hackensack Meridian School of Medicine, Nutley, NJ, United States
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, United States
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47
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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, MD.) 2022; 12:jkac110. [PMID: 35532173 PMCID: PMC9258547 DOI: 10.1093/g3journal/jkac110] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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48
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Schrevens S, Durandau E, Tran VDT, Sanglard D. Using in vivo transcriptomics and RNA enrichment to identify genes involved in virulence of Candida glabrata. Virulence 2022; 13:1285-1303. [PMID: 35795910 PMCID: PMC9348041 DOI: 10.1080/21505594.2022.2095716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Candida species are the most commonly isolated opportunistic fungal pathogens in humans. Candida albicans causes most of the diagnosed infections, closely followed by Candida glabrata. C. albicans is well studied, and many genes have been shown to be important for infection and colonization of the host. It is however less clear how C. glabrata infects the host. With the help of fungal RNA enrichment, we here investigated for the first time the transcriptomic profile of C. glabrata during urinary tract infection (UTI) in mice. In the UTI model, bladders and kidneys are major target organs and therefore fungal transcriptomes were addressed in these organs. Our results showed that, next to adhesins and proteases, nitrogen metabolism and regulation play a vital role during C. glabrata UTI. Genes involved in nitrogen metabolism were upregulated and among them we show that DUR1,2 (urea amidolyase) and GAP1 (amino acid permease) were important for virulence. Furthermore, we confirmed the importance of the glyoxylate cycle in the host and identified MLS1 (malate synthase) as an important gene necessary for C. glabrata virulence. In conclusion, our study shows with the support of in vivo transcriptomics how C. glabrata adapts to host conditions.
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Affiliation(s)
- Sanne Schrevens
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
| | - Eric Durandau
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
| | - Van Du T Tran
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
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49
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Schikora-Tamarit MÀ, Gabaldón T. Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens. Biochem Soc Trans 2022; 50:1259-1268. [PMID: 35713390 PMCID: PMC9246328 DOI: 10.1042/bst20211123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 02/06/2023]
Abstract
Fungal pathogens pose an increasingly worrying threat to human health, food security and ecosystem diversity. To tackle fungal infections and improve current diagnostic and therapeutic tools it is necessary to understand virulence and antifungal drug resistance mechanisms in diverse species. Recent advances in genomics approaches have provided a suitable framework to understand these phenotypes, which ultimately depend on genetically encoded determinants. In this work, we review how the study of genome sequences has been key to ascertain the bases of virulence and drug resistance traits. We focus on the contribution of comparative genomics, population genomics and directed evolution studies. In addition, we discuss how different types of genomic mutations (small or structural variants) contribute to intraspecific differences in virulence or drug resistance. Finally, we review current challenges in the field and anticipate future directions to solve them. In summary, this work provides a short overview of how genomics can be used to understand virulence and drug resistance in fungal pathogens.
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Affiliation(s)
- Miquel Àngel Schikora-Tamarit
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain
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50
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Shahi G, Kumar M, Khandelwal NK, Banerjee A, Sarkar P, Kumari S, Esquivel BD, Chauhan N, Chattopadhyay A, White TC, Gaur NA, Singh A, Prasad R. Inositol Phosphoryl Transferase, Ipt1, Is a Critical Determinant of Azole Resistance and Virulence Phenotypes in Candida glabrata. J Fungi (Basel) 2022; 8:jof8070651. [PMID: 35887407 PMCID: PMC9322651 DOI: 10.3390/jof8070651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 12/10/2022] Open
Abstract
In this study, we have specifically blocked a key step of sphingolipid (SL) biosynthesis in Candida glabrata by disruption of the orthologs of ScIpt1 and ScSkn1. Based on their close homology with S. cerevisiae counterparts, the proteins are predicted to catalyze the addition of a phosphorylinositol group onto mannosyl inositolphosphoryl ceramide (MIPC) to form mannosyl diinositolphosphoryl ceramide (M(IP)2C), which accounts for the majority of complex SL structures in S. cerevisiae membranes. High throughput lipidome analysis confirmed the accumulation of MIPC structures in ΔCgipt1 and ΔCgskn1 cells, albeit to lesser extent in the latter. Noticeably, ΔCgipt1 cells showed an increased susceptibility to azoles; however, ΔCgskn1 cells showed no significant changes in the drug susceptibility profiles. Interestingly, the azole susceptible phenotype of ΔCgipt1 cells seems to be independent of the ergosterol content. ΔCgipt1 cells displayed altered lipid homeostasis, increased membrane fluidity as well as high diffusion of radiolabeled fluconazole (3H-FLC), which could together influence the azole susceptibility of C. glabrata. Furthermore, in vivo experiments also confirmed compromised virulence of the ΔCgipt1 strain. Contrarily, specific functions of CgSkn1 remain unclear.
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Affiliation(s)
- Garima Shahi
- Amity Institute of Biotechnology and Integrative Science and Health, Amity University Gurgaon, Gurgaon 122412, India; (G.S.); (M.K.); (A.B.)
| | - Mohit Kumar
- Amity Institute of Biotechnology and Integrative Science and Health, Amity University Gurgaon, Gurgaon 122412, India; (G.S.); (M.K.); (A.B.)
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.K.); (N.A.G.)
| | | | - Atanu Banerjee
- Amity Institute of Biotechnology and Integrative Science and Health, Amity University Gurgaon, Gurgaon 122412, India; (G.S.); (M.K.); (A.B.)
| | - Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India; (P.S.); (A.C.)
| | - Sonam Kumari
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.K.); (N.A.G.)
| | - Brooke D. Esquivel
- School of Biological and Chemical Sciences, University of Missouri at Kansas City, Kansas City, MO 64110, USA; (B.D.E.); (T.C.W.)
| | - Neeraj Chauhan
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA;
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India; (P.S.); (A.C.)
| | - Theodore C. White
- School of Biological and Chemical Sciences, University of Missouri at Kansas City, Kansas City, MO 64110, USA; (B.D.E.); (T.C.W.)
| | - Naseem A. Gaur
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.K.); (N.A.G.)
| | - Ashutosh Singh
- Department of Biochemistry, University of Lucknow, Lucknow 226007, India
- Correspondence: (A.S.); (R.P.)
| | - Rajendra Prasad
- Amity Institute of Biotechnology and Integrative Science and Health, Amity University Gurgaon, Gurgaon 122412, India; (G.S.); (M.K.); (A.B.)
- Correspondence: (A.S.); (R.P.)
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