1
|
Vande Zande P, Gautier C, Kawar N, Maufrais C, Metzner K, Wash E, Beach AK, Bracken R, Maciel EI, Pereira de Sá N, Fernandes CM, Solis NV, Del Poeta M, Filler SG, Berman J, Ene IV, Selmecki A. Step-wise evolution of azole resistance through copy number variation followed by KSR1 loss of heterozygosity in Candida albicans. PLoS Pathog 2024; 20:e1012497. [PMID: 39213436 DOI: 10.1371/journal.ppat.1012497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Antimicrobial drug resistance poses a global health threat, requiring a deeper understanding of the evolutionary processes that lead to its emergence in pathogens. Complex evolutionary dynamics involve multiple mutations that can result in cooperative or competitive (clonal interference) effects. Candida albicans, a major fungal pathogen, displays high rates of copy number variation (CNV) and loss of heterozygosity (LOH). CNV and LOH events involve large numbers of genes and could synergize during evolutionary adaptation. Understanding the contributions of CNV and LOH to antifungal drug adaptation is challenging, especially in the context of whole-population genome sequencing. Here, we document the sequential evolution of fluconazole tolerance and then resistance in a C. albicans isolate involving an initial CNV on chromosome 4, followed by an LOH on chromosome R that involves KSR1. Similar LOH events involving KSR1, which encodes a reductase in the sphingolipid biosynthesis pathway, were also detected in independently evolved fluconazole resistant isolates. We dissect the specific KSR1 codons that affect fluconazole resistance and tolerance. The combination of the chromosome 4 CNV and KSR1 LOH results in a >500-fold decrease in azole susceptibility relative to the progenitor, illustrating a compelling example of rapid, yet step-wise, interplay between CNV and LOH in drug resistance evolution.
Collapse
Affiliation(s)
- Pétra Vande Zande
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Cécile Gautier
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
| | - Nora Kawar
- Shmunis School of Biotechnology and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
- Institut Pasteur Bioinformatic Hub, Université Paris Cité, Paris, France
| | - Katura Metzner
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Elizabeth Wash
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Annette K Beach
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ryan Bracken
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eli Isael Maciel
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
| | - Nívea Pereira de Sá
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
| | - Caroline Mota Fernandes
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
| | - Norma V Solis
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, California, United States of America
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
- Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Veterans Administration Medical Center, Northport, New York, United States of America
| | - Scott G Filler
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, California, United States of America
- David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Judith Berman
- Shmunis School of Biotechnology and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Iuliana V Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| |
Collapse
|
2
|
Sprague JL, Schille TB, Allert S, Trümper V, Lier A, Großmann P, Priest EL, Tsavou A, Panagiotou G, Naglik JR, Wilson D, Schäuble S, Kasper L, Hube B. Candida albicans translocation through the intestinal epithelial barrier is promoted by fungal zinc acquisition and limited by NFκB-mediated barrier protection. PLoS Pathog 2024; 20:e1012031. [PMID: 38427950 PMCID: PMC10907035 DOI: 10.1371/journal.ppat.1012031] [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: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
The opportunistic fungal pathogen Candida albicans thrives on human mucosal surfaces as a harmless commensal, but frequently causes infections under certain predisposing conditions. Translocation across the intestinal barrier into the bloodstream by intestine-colonizing C. albicans cells serves as the main source of disseminated candidiasis. However, the host and microbial mechanisms behind this process remain unclear. In this study we identified fungal and host factors specifically involved in infection of intestinal epithelial cells (IECs) using dual-RNA sequencing. Our data suggest that host-cell damage mediated by the peptide toxin candidalysin-encoding gene ECE1 facilitates fungal zinc acquisition. This in turn is crucial for the full virulence potential of C. albicans during infection. IECs in turn exhibit a filamentation- and damage-specific response to C. albicans infection, including NFκB, MAPK, and TNF signaling. NFκB activation by IECs limits candidalysin-mediated host-cell damage and mediates maintenance of the intestinal barrier and cell-cell junctions to further restrict fungal translocation. This is the first study to show that candidalysin-mediated damage is necessary for C. albicans nutrient acquisition during infection and to explain how IECs counteract damage and limit fungal translocation via NFκB-mediated maintenance of the intestinal barrier.
Collapse
Affiliation(s)
- Jakob L. Sprague
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Tim B. Schille
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
| | - Stefanie Allert
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Verena Trümper
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Adrian Lier
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Peter Großmann
- Department of Microbiome Dynamics, Hans-Knöll-Institute, Jena, Germany
| | - Emily L. Priest
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Antzela Tsavou
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Gianni Panagiotou
- Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
- Department of Microbiome Dynamics, Hans-Knöll-Institute, Jena, Germany
- Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Julian R. Naglik
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Duncan Wilson
- Medical Research Council, Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - Sascha Schäuble
- Department of Microbiome Dynamics, Hans-Knöll-Institute, Jena, Germany
| | - Lydia Kasper
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
- Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| |
Collapse
|
3
|
Ali B, Kumar M, Kumar P, Chauhan A, Usmani SA, Rudramurthy SM, Meis JF, Chakrabarti A, Singh A, Gaur NA, Mondal AK, Prasad R. Sphingolipid diversity in Candida auris: unraveling interclade and drug resistance fingerprints. FEMS Yeast Res 2024; 24:foae008. [PMID: 38444195 PMCID: PMC10941814 DOI: 10.1093/femsyr/foae008] [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: 11/08/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
In this study, we explored the sphingolipid (SL) landscape in Candida auris, which plays pivotal roles in fungal biology and drug susceptibility. The composition of SLs exhibited substantial variations at both the SL class and molecular species levels among clade isolates. Utilizing principal component analysis, we successfully differentiated the five clades based on their SL class composition. While phytoceramide (PCer) was uniformly the most abundant SL class in all the isolates, other classes showed significant variations. These variations were not limited to SL class level only as the proportion of different molecular species containing variable number of carbons in fatty acid chains also differed between the isolates. Also a comparative analysis revealed abundance of ceramides and glucosylceramides in fluconazole susceptible isolates. Furthermore, by comparing drug-resistant and susceptible isolates within clade IV, we uncovered significant intraclade differences in key SL classes such as high PCer and low long chain base (LCB) content in resistant strains, underscoring the impact of SL heterogeneity on drug resistance development in C. auris. These findings shed light on the multifaceted interplay between genomic diversity, SLs, and drug resistance in this emerging fungal pathogen.
Collapse
Affiliation(s)
- Basharat Ali
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, 122413, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohit Kumar
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, 122413, India
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - Praveen Kumar
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, 122413, India
| | - Anshu Chauhan
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, 122413, India
| | - Sana Akhtar Usmani
- Department of Biochemistry, University of Lucknow, Lucknow, 226007 India
| | | | - Jacques F Meis
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, 50931 Germany
| | | | - Ashutosh Singh
- Department of Biochemistry, University of Lucknow, Lucknow, 226007 India
| | - Naseem A Gaur
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - Alok K Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rajendra Prasad
- Amity Institute of Integrative Science and Health and Amity Institute of Biotechnology, Amity University Gurgaon, Haryana, 122413, India
| |
Collapse
|
4
|
Matos GS, Fernandes CM, Del Poeta M. Role of sphingolipids in the host-pathogen interaction. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159384. [PMID: 37673393 PMCID: PMC11218662 DOI: 10.1016/j.bbalip.2023.159384] [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: 02/07/2023] [Revised: 06/21/2023] [Accepted: 07/05/2023] [Indexed: 09/08/2023]
Abstract
Fungal pathogens have been under the spotlight as their expanding geographic range combined with their potential harm to vulnerable populations turns them into increasingly threats to public health. Therefore, it is ultimately important to unveil the mechanisms associated with their infection process for further new treatment discovery. With this purpose, sphingolipid-based research has gained attention over the last years as these molecules have key properties that can regulate fungal pathogenicity. Here we discuss some of these properties as well as their role in fungal diseases, focusing on the subgroup of glycosphingolipids, as they represent promising molecules for drug discovery and for the development of fungal vaccines.
Collapse
Affiliation(s)
- Gabriel Soares Matos
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | | | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA; Institute of Chemical Biology and Drug Discovery (ICB&DD), Stony Brook, NY, USA; Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, NY, USA; Veterans Administration Medical Center, Northport, NY, USA.
| |
Collapse
|
5
|
Alabi PE, Gautier C, Murphy TP, Gu X, Lepas M, Aimanianda V, Sello JK, Ene IV. Small molecules restore azole activity against drug-tolerant and drug-resistant Candida isolates. mBio 2023; 14:e0047923. [PMID: 37326546 PMCID: PMC10470600 DOI: 10.1128/mbio.00479-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/13/2023] [Indexed: 06/17/2023] Open
Abstract
Each year, fungi cause more than 1.5 billion infections worldwide and have a devastating impact on human health, particularly in immunocompromised individuals or patients in intensive care units. The limited antifungal arsenal and emerging multidrug-resistant species necessitate the development of new therapies. One strategy for combating drug-resistant pathogens is the administration of molecules that restore fungal susceptibility to approved drugs. Accordingly, we carried out a screen to identify small molecules that could restore the susceptibility of pathogenic Candida species to azole antifungals. This screening effort led to the discovery of novel 1,4-benzodiazepines that restore fluconazole susceptibility in resistant isolates of Candida albicans, as evidenced by 100-1,000-fold potentiation of fluconazole activity. This potentiation effect was also observed in azole-tolerant strains of C. albicans and in other pathogenic Candida species. The 1,4-benzodiazepines selectively potentiated different azoles, but not other approved antifungals. A remarkable feature of the potentiation was that the combination of the compounds with fluconazole was fungicidal, whereas fluconazole alone is fungistatic. Interestingly, the potentiators were not toxic to C. albicans in the absence of fluconazole, but inhibited virulence-associated filamentation of the fungus. We found that the combination of the potentiators and fluconazole significantly enhanced host survival in a Galleria mellonella model of systemic fungal infection. Taken together, these observations validate a strategy wherein small molecules can restore the activity of highly used anti-infectives that have lost potency. IMPORTANCE In the last decade, we have been witnessing a higher incidence of fungal infections, due to an expansion of the fungal species capable of causing disease (e.g., Candida auris), as well as increased antifungal drug resistance. Among human fungal pathogens, Candida species are a leading cause of invasive infections and are associated with high mortality rates. Infections by these pathogens are commonly treated with azole antifungals, yet the expansion of drug-resistant isolates has reduced their clinical utility. In this work, we describe the discovery and characterization of small molecules that potentiate fluconazole and restore the susceptibility of azole-resistant and azole-tolerant Candida isolates. Interestingly, the potentiating 1,4-benzodiazepines were not toxic to fungal cells but inhibited their virulence-associated filamentous growth. Furthermore, combinations of the potentiators and fluconazole decreased fungal burdens and enhanced host survival in a Galleria mellonella model of systemic fungal infections. Accordingly, we propose the use of novel antifungal potentiators as a powerful strategy for addressing the growing resistance of fungi to clinically approved drugs.
Collapse
Affiliation(s)
- Philip E. Alabi
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Cécile Gautier
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
| | - Thomas P. Murphy
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Xilin Gu
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Mathieu Lepas
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Molecular Mycology Unit, Paris, France
| | - Vishukumar Aimanianda
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Molecular Mycology Unit, Paris, France
| | - Jason K. Sello
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, Paris, France
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| |
Collapse
|
6
|
Druseikis M, Mottola A, Berman J. The Metabolism of Susceptibility: Clearing the FoG Between Tolerance and Resistance in Candida albicans. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:36-46. [DOI: 10.1007/s40588-023-00189-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
|
7
|
Sprague JL, Kasper L, Hube B. From intestinal colonization to systemic infections: Candida albicans translocation and dissemination. Gut Microbes 2022; 14:2154548. [PMID: 36503341 PMCID: PMC9746630 DOI: 10.1080/19490976.2022.2154548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Candida species are the most prevalent cause of invasive fungal infections, of which Candida albicans is the most common. Translocation across the epithelial barrier into the bloodstream by intestinal-colonizing C. albicans cells serves as the main source for systemic infections. Understanding the fungal mechanisms behind this process will give valuable insights on how to prevent such infections and keep C. albicans in the commensal state in patients with predisposing conditions. This review will focus on recent developments in characterizing fungal translocation mechanisms, compare what we know about enteric bacterial pathogens with C. albicans, and discuss the different proposed hypotheses for how C. albicans enters and disseminates through the bloodstream immediately following translocation.
Collapse
Affiliation(s)
- Jakob L. Sprague
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany,Contact: Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Beutenbergstrasse 11a, 07745Jena, Germany
| | - Lydia Kasper
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| |
Collapse
|