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Xie J, Rybak JM, Martin-Vicente A, Guruceaga X, Thorn HI, Nywening AV, Ge W, Parker JE, Kelly SL, Rogers PD, Fortwendel JR. The sterol C-24 methyltransferase encoding gene, erg6, is essential for viability of Aspergillus species. Nat Commun 2024; 15:4261. [PMID: 38769341 PMCID: PMC11106247 DOI: 10.1038/s41467-024-48767-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
Triazoles, the most widely used class of antifungal drugs, inhibit the biosynthesis of ergosterol, a crucial component of the fungal plasma membrane. Inhibition of a separate ergosterol biosynthetic step, catalyzed by the sterol C-24 methyltransferase Erg6, reduces the virulence of pathogenic yeasts, but its effects on filamentous fungal pathogens like Aspergillus fumigatus remain unexplored. Here, we show that the lipid droplet-associated enzyme Erg6 is essential for the viability of A. fumigatus and other Aspergillus species, including A. lentulus, A. terreus, and A. nidulans. Downregulation of erg6 causes loss of sterol-rich membrane domains required for apical extension of hyphae, as well as altered sterol profiles consistent with the Erg6 enzyme functioning upstream of the triazole drug target, Cyp51A/Cyp51B. Unexpectedly, erg6-repressed strains display wild-type susceptibility against the ergosterol-active triazole and polyene antifungals. Finally, we show that erg6 repression results in significant reduction in mortality in a murine model of invasive aspergillosis. Taken together with recent studies, our work supports Erg6 as a potentially pan-fungal drug target.
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Affiliation(s)
- Jinhong Xie
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adela Martin-Vicente
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Xabier Guruceaga
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Harrison I Thorn
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ashley V Nywening
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
- Integrated Program in Biomedical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Wenbo Ge
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Josie E Parker
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Steven L Kelly
- Institute of Life Science, Swansea University Medical School, Swansea, Wales, UK
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jarrod R Fortwendel
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA.
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA.
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2
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Chen XF, Zhang H, Liu LL, Guo LN, Liu WJ, Liu YL, Li DD, Zhao Y, Zhu RY, Li Y, Dai RC, Yu SY, Li J, Wang T, Dou HT, Xu YC. Genome-wide analysis of in vivo-evolved Candida auris reveals multidrug-resistance mechanisms. Mycopathologia 2024; 189:35. [PMID: 38637433 DOI: 10.1007/s11046-024-00832-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/17/2024] [Indexed: 04/20/2024]
Abstract
Candida auris, an emerging and multidrug-resistant fungal pathogen, has led to numerous outbreaks in China. While the resistance mechanisms against azole and amphotericin B have been studied, the development of drug resistance in this pathogen remains poorly understood, particularly in in vivo-generated drug-resistant strains. This study employed pathogen whole-genome sequencing to investigate the epidemiology and drug-resistance mutations of C. auris using 16 strains isolated from two patients. Identification was conducted through Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and antimicrobial susceptibilities were assessed using broth microdilution and Sensititre YeastOne YO10. Whole-genome sequencing revealed that all isolates belonged to the South Asian lineage, displaying genetic heterogeneity. Despite low genetic variability among patient isolates, notable mutations were identified, including Y132F in ERG11 and A585S in TAC1b, likely linked to increased fluconazole resistance. Strains from patient B also carried F214L in TAC1b, resulting in a consistent voriconazole minimum inhibitory concentration of 4 µg/mL across all isolates. Furthermore, a novel frameshift mutation in the SNG1 gene was observed in amphotericin B-resistant isolates compared to susceptible ones. Our findings suggest the potential transmission of C. auris and emphasize the need to explore variations related to antifungal resistance. This involves analyzing genomic mutations and karyotypes, especially in vivo, to compare sensitive and resistant strains. Further monitoring and validation efforts are crucial for a comprehensive understanding of the mechanisms of drug resistance in C. auris.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Han Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ling-Li Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li-Na Guo
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wen-Jing Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ya-Li Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ding-Ding Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ying Zhao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ren-Yuan Zhu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Yi Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Rong-Chen Dai
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Shu-Ying Yu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Jin Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Tong Wang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hong-Tao Dou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
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Hoenigl M, Arastehfar A, Arendrup MC, Brüggemann R, Carvalho A, Chiller T, Chen S, Egger M, Feys S, Gangneux JP, Gold JAW, Groll AH, Heylen J, Jenks JD, Krause R, Lagrou K, Lamoth F, Prattes J, Sedik S, Wauters J, Wiederhold NP, Thompson GR. Novel antifungals and treatment approaches to tackle resistance and improve outcomes of invasive fungal disease. Clin Microbiol Rev 2024:e0007423. [PMID: 38602408 DOI: 10.1128/cmr.00074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Abstract
SUMMARYFungal infections are on the rise, driven by a growing population at risk and climate change. Currently available antifungals include only five classes, and their utility and efficacy in antifungal treatment are limited by one or more of innate or acquired resistance in some fungi, poor penetration into "sequestered" sites, and agent-specific side effect which require frequent patient reassessment and monitoring. Agents with novel mechanisms, favorable pharmacokinetic (PK) profiles including good oral bioavailability, and fungicidal mechanism(s) are urgently needed. Here, we provide a comprehensive review of novel antifungal agents, with both improved known mechanisms of actions and new antifungal classes, currently in clinical development for treating invasive yeast, mold (filamentous fungi), Pneumocystis jirovecii infections, and dimorphic fungi (endemic mycoses). We further focus on inhaled antifungals and the role of immunotherapy in tackling fungal infections, and the specific PK/pharmacodynamic profiles, tissue distributions as well as drug-drug interactions of novel antifungals. Finally, we review antifungal resistance mechanisms, the role of use of antifungal pesticides in agriculture as drivers of drug resistance, and detail detection methods for antifungal resistance.
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Affiliation(s)
- Martin Hoenigl
- Department of Internal Medicine, Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
- BiotechMed-Graz, Graz, Austria
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Maiken Cavling Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Roger Brüggemann
- Department of Pharmacy and Radboudumc Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise in Mycology, Nijmegen, The Netherlands
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sharon Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW South Wales Health Pathology, Westmead Hospital, Westmead, Australia
- The University of Sydney, Sydney, Australia
| | - Matthias Egger
- Department of Internal Medicine, Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
| | - Simon Feys
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Pierre Gangneux
- Centre National de Référence des Mycoses et Antifongiques LA-AspC Aspergilloses chroniques, European Excellence Center for Medical Mycology (ECMM EC), Centre hospitalier Universitaire de Rennes, Rennes, France
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) UMR_S 1085, Rennes, France
| | - Jeremy A W Gold
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andreas H Groll
- Department of Pediatric Hematology/Oncology and Infectious Disease Research Program, Center for Bone Marrow Transplantation, University Children's Hospital, Muenster, Germany
| | - Jannes Heylen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Jeffrey D Jenks
- Department of Public Health, Durham County, Durham, North Carolina, USA
- Department of Medicine, Division of Infectious Diseases, Duke University, Durham, North Carolina, USA
| | - Robert Krause
- Department of Internal Medicine, Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
- BiotechMed-Graz, Graz, Austria
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric Lamoth
- Department of Laboratory Medicine and Pathology, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Medicine, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Juergen Prattes
- Department of Internal Medicine, Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
- BiotechMed-Graz, Graz, Austria
| | - Sarah Sedik
- Department of Internal Medicine, Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
| | - Joost Wauters
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Nathan P Wiederhold
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - George R Thompson
- Department of Internal Medicine, Division of Infectious Diseases University of California-Davis Medical Center, Sacramento, California, USA
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, California, USA
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4
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Siopi M, Pachoulis I, Leventaki S, Spruijtenburg B, Meis JF, Pournaras S, Vrioni G, Tsakris A, Meletiadis J. Evaluation of the Vitek 2 system for antifungal susceptibility testing of Candida auris using a representative international panel of clinical isolates: overestimation of amphotericin B resistance and underestimation of fluconazole resistance. J Clin Microbiol 2024; 62:e0152823. [PMID: 38501836 PMCID: PMC11005389 DOI: 10.1128/jcm.01528-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Although the Vitek 2 system is broadly used for antifungal susceptibility testing of Candida spp., its performance against Candida auris has been assessed using limited number of isolates recovered from restricted geographic areas. We therefore compared Vitek 2 system with the reference Clinical and Laboratory Standards Institute (CLSI) broth microdilution method using an international collection of 100 C. auris isolates belonging to different clades. The agreement ±1 twofold dilution between the two methods and the categorical agreement (CA) based on the Centers for Disease Control and Prevention's (CDC's) tentative resistance breakpoints and Vitek 2-specific wild-type upper limit values (WT-ULVs) were determined. The CLSI-Vitek 2 agreement was poor for 5-flucytosine (0%), fluconazole (16%), and amphotericin B (29%), and moderate for voriconazole (61%), micafungin (67%), and caspofungin (81%). Significant interpretation errors were recorded using the CDC breakpoints for amphotericin B (31% CA, 69% major errors; MaEs) and fluconazole (69% CA, 31% very major errors; VmEs), but not for echinocandins (99% CA, 1% MaEs for both micafungin and caspofungin) for which the Vitek 2 allowed correct categorization of echinocandin-resistant FKS1 mutant isolates. Discrepancies were reduced when the Vitek 2 WT-ULV of 16 mg/L for amphotericin B (98% CA, 2% MaEs) and of 4 mg/L for fluconazole (96% CA, 1% MaEs, 3% VmEs) were used. In conclusion, the Vitek 2 system performed well for echinocandin susceptibility testing of C .auris. Resistance to fluconazole was underestimated whereas resistance to amphotericin B was overestimated using the CDC breakpoints of ≥32 and ≥2 mg/L, respectively. Vitek 2 minimun inhibitory concentrations (MICs) >4 mg/L indicated resistance to fluconazole and Vitek 2 MICs ≤16 mg/L indicated non-resistance to amphotericin B.
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Affiliation(s)
- Maria Siopi
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Molecular Microbiology and Immunology Laboratory, Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Ioannis Pachoulis
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Molecular Microbiology and Immunology Laboratory, Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Sevasti Leventaki
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Molecular Microbiology and Immunology Laboratory, Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Bram Spruijtenburg
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, the Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
| | - Jacques F. Meis
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany
| | - Spyros Pournaras
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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5
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Gregor JB, Gutierrez-Schultz VA, Hoda S, Baker KM, Saha D, Burghaze MG, Vazquez C, Burgei KE, Briggs SD. An expanded toolkit of drug resistance cassettes for Candida glabrata, Candida auris, and Candida albicans leads to new insights into the ergosterol pathway. mSphere 2023; 8:e0031123. [PMID: 37929964 PMCID: PMC10732037 DOI: 10.1128/msphere.00311-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE The increasing problem of drug resistance and emerging pathogens is an urgent global health problem that necessitates the development and expansion of tools for studying fungal drug resistance and pathogenesis. Prior studies in Candida glabrata, Candida auris, and Candida albicans have been mainly limited to the use of NatMX/SAT1 and HphMX/CaHyg for genetic manipulation in prototrophic strains and clinical isolates. In this study, we demonstrated that NatMX/SAT1, HphMX, KanMX, and/or BleMX drug resistance cassettes when coupled with a CRISPR-ribonucleoprotein (RNP)-based system can be efficiently utilized for deleting or modifying genes in the ergosterol pathway of C. glabrata, C. auris, and C. albicans. Moreover, the utility of these tools has provided new insights into ERG genes and their relationship to azole resistance in Candida. Overall, we have expanded the toolkit for Candida pathogens to increase the versatility of genetically modifying complex pathways involved in drug resistance and pathogenesis.
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Affiliation(s)
- Justin B. Gregor
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Smriti Hoda
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Kortany M. Baker
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Debasmita Saha
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Cynthia Vazquez
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Kendra E. Burgei
- 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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6
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Erturk Sengel B, Ekren BY, Sayin E, Cerikcioglu N, Sezerman U, Odabasi Z. Identification of Molecular and Genetic Resistance Mechanisms in a Candida auris Isolate in a Tertiary Care Center in Türkiye. Mycopathologia 2023; 188:929-936. [PMID: 37639054 DOI: 10.1007/s11046-023-00787-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Candida auris is a multidrug-resistant pathogen that causes nosocomial outbreaks and high mortality. We conducted this study to investigate the molecular mechanisms of antifungal resistance in our clinical isolate of C. auris with a high level of resistance to three main classes of antifungals. MATERIAL AND METHODS A clinical C. auris isolate was identified by MALDI-TOF MS and antifungal susceptibilities were determined by the Sensititre YeastOne YO10 panel. After sequencing the whole genome of the microorganism with Oxford Nanopore NGS Technologies, a phylogenetic tree was drawn as a cladogram to detect where the C. auris clade to this study's assembly belongs. RESULTS The C. auris isolate in this study (MaCa01) was determined to be a part of the clade I (South Asian). The resistance-related genes indicated that MaCa01 would most likely be highly resistant to fluconazole (CDR1, TAC1b, and ERG11), none or little resistant to amphotericin B (AmpB) and echinocandins, and sensitive to flucytosine. The mutations found in the above-mentioned genes in the Türkiye C. auris isolate reveals an antifungal resistance pattern. This molecular resistance pattern was found consistent with the interpretation of MIC values of the antifungals according to CDC tentative breakpoints. CONCLUSION We detected the well-known antifungal resistance mutations, responsible for azole resistance in C. auris. Despite no ERG2, ERG6, and FKS mutation identified, the isolate was found to be resistant to AmpB and caspofungin based on the CDC tentative breakpoints which could be related to unidentified mutations.
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Affiliation(s)
- Buket Erturk Sengel
- Department of Infectious Disease and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Türkiye.
| | - Berkay Yekta Ekren
- Department of Bioistatistics and Medical Informatics, Graduate School of Health Sciences, Acibadem University, Istanbul, Türkiye
| | - Elvan Sayin
- Department of Medical Microbiology, Marmara University School of Medicine, Istanbul, Türkiye
| | - Nilgun Cerikcioglu
- Department of Medical Microbiology, Marmara University School of Medicine, Istanbul, Türkiye
| | - Ugur Sezerman
- Department of Bioistatistics and Medical Informatics, Graduate School of Health Sciences, Acibadem University, Istanbul, Türkiye
| | - Zekaver Odabasi
- Department of Infectious Disease and Clinical Microbiology, Marmara University School of Medicine, Istanbul, Türkiye
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7
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Abstract
During recent decades, the emergence of pathogenic fungi has posed an increasing public health threat, particularly given the limited number of antifungal drugs available to treat invasive infections. In this Review, we discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, driven by global health-care transmission and possibly facilitated by climate change; azole-resistant Aspergillus fumigatus, driven by the selection facilitated by azole fungicide use in agricultural and other settings; and Trichophyton indotineae, driven by the under-regulated use of over-the-counter high-potency corticosteroid-containing antifungal creams. The diversity of the fungi themselves and the drivers of their emergence make it clear that we cannot predict what might emerge next. Therefore, vigilance is critical to monitoring fungal emergence, as well as the rise in overall antifungal resistance.
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Affiliation(s)
- Shawn R Lockhart
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Jeremy A W Gold
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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8
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Boyce KJ. The Microevolution of Antifungal Drug Resistance in Pathogenic Fungi. Microorganisms 2023; 11:2757. [PMID: 38004768 PMCID: PMC10673521 DOI: 10.3390/microorganisms11112757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The mortality rates of invasive fungal infections remain high because of the limited number of antifungal drugs available and antifungal drug resistance, which can rapidly evolve during treatment. Mutations in key resistance genes such as ERG11 were postulated to be the predominant cause of antifungal drug resistance in the clinic. However, recent advances in whole genome sequencing have revealed that there are multiple mechanisms leading to the microevolution of resistance. In many fungal species, resistance can emerge through ERG11-independent mechanisms and through the accumulation of mutations in many genes to generate a polygenic resistance phenotype. In addition, genome sequencing has revealed that full or partial aneuploidy commonly occurs in clinical or microevolved in vitro isolates to confer antifungal resistance. This review will provide an overview of the mutations known to be selected during the adaptive microevolution of antifungal drug resistance and focus on how recent advances in genome sequencing technology have enhanced our understanding of this process.
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Affiliation(s)
- Kylie J Boyce
- School of Science, RMIT University, Melbourne, VIC 3085, Australia
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9
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Abstract
Candida auris is a multidrug-resistant fungal pathogen that presents a serious threat to global human health. Since the first reported case in 2009 in Japan, C. auris infections have been reported in more than 40 countries, with mortality rates between 30% and 60%. In addition, C. auris has the potential to cause outbreaks in health care settings, especially in nursing homes for elderly patients, owing to its efficient transmission via skin-to-skin contact. Most importantly, C. auris is the first fungal pathogen to show pronounced and sometimes untreatable clinical drug resistance to all known antifungal classes, including azoles, amphotericin B, and echinocandins. In this review, we explore the causes of the rapid spread of C. auris. We also highlight its genome organization and drug resistance mechanisms and propose future research directions that should be undertaken to curb the spread of this multidrug-resistant pathogen.
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Affiliation(s)
- Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India;
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Kusum Jain
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India;
| | - Neeraj Chauhan
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
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10
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Asadzadeh M, Alfouzan W, Parker JE, Meis JF, Kelly SL, Joseph L, Ahmad S. Molecular Characterization and Sterol Profiles Identify Nonsynonymous Mutations in ERG2 as a Major Mechanism Conferring Reduced Susceptibility to Amphotericin B in Candida kefyr. Microbiol Spectr 2023; 11:e0147423. [PMID: 37358415 PMCID: PMC10434000 DOI: 10.1128/spectrum.01474-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/01/2023] [Indexed: 06/27/2023] Open
Abstract
The molecular basis of reduced susceptibility to amphotericin B (rs-AMB) among any yeasts is poorly defined. Genetic alterations in genes involved in ergosterol biosynthesis and total cell sterols were investigated among clinical Candida kefyr isolates. C. kefyr isolates (n = 81) obtained from 74 patients in Kuwait and identified by phenotypic and molecular methods were analyzed. An Etest was initially used to identify isolates with rs-AMB. Specific mutations in ERG2 and ERG6 involved in ergosterol biosynthesis were detected by PCR sequencing. Twelve selected isolates were also tested by the SensiTitre Yeast One (SYO), and total cell sterols were evaluated by gas chromatography-mass spectrometry and ERG3 and ERG11 sequencing. Eight isolates from 8 patients showed rs-AMB by Etest, including 2 isolates with additional resistance to fluconazole or to all three antifungals. SYO correctly identified 8 of 8 rs-AMB isolates. A nonsynonymous mutation in ERG2 was detected in 6 of 8 rs-AMB isolates but also in 3 of 73 isolates with a wild-type AMB pattern. One rs-AMB isolate contained a deletion (frameshift) mutation in ERG2. One or more nonsynonymous mutations was detected in ERG6 in 11 of 81 isolates with the rs-AMB or wild-type AMB pattern. Among 12 selected isolates, 2 and 2 isolates contained a nonsynonymous mutation(s) in ERG3 and ERG11, respectively. Ergosterol was undetectable in 7 of 8 rs-AMB isolates, and the total cell sterol profiles were consistent with loss of ERG2 function in 6 rs-AMB isolates and loss of ERG3 activity in another rs-AMB isolate. Our data showed that ERG2 is a major target conferring rs-AMB in clinical C. kefyr isolates. IMPORTANCE Some yeast species exhibit intrinsic resistance or rapidly acquire resistance to azole antifungals. Despite >50 years of clinical use, resistance to amphotericin B (AMB) among yeast species has been extremely rarely reported until recently. Reduced susceptibility to AMB (rs-AMB) among yeast species is, therefore, a matter of serious concern due to the availability of only four classes of antifungal drugs. Recent studies in Candida glabrata, Candida lusitaniae, and Candida auris have identified ERG genes involved in ergosterol biosynthesis as the major targets conferring rs-AMB. The results of this study also show that nonsynonymous mutations in ERG2 impair its function, abolish ergosterol from C. kefyr, and confer rs-AMB. Thus, rapid detection of rs-AMB among clinical isolates will help in proper management of invasive C. kefyr infections.
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Affiliation(s)
- Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Josie E. Parker
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands
- Center of Expertise in Mycology, Radboudumc, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands
- Department of Internal Medicine, Excellence Center for Medical Mycology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Steven L. Kelly
- Institute of Life Science, Faculty of Health, Medicine and Life Sciences, Swansea University, Swansea, Wales, United Kingdom
| | - Leena Joseph
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
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Ben Abid F, Salah H, Sundararaju S, Dalil L, Abdelwahab AH, Salameh S, Ibrahim EB, Almaslmani MA, Tang P, Perez-Lopez A, Tsui CKM. Molecular characterization of Candida auris outbreak isolates in Qatar from patients with COVID-19 reveals the emergence of isolates resistant to three classes of antifungal drugs. Clin Microbiol Infect 2023; 29:1083.e1-1083.e7. [PMID: 37116861 PMCID: PMC10132836 DOI: 10.1016/j.cmi.2023.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/08/2023] [Accepted: 04/22/2023] [Indexed: 04/30/2023]
Abstract
OBJECTIVES During the COVID-19 pandemic in Qatar, many patients who were severely ill were colonized and infected by Candida auris, an invasive multidrug-resistant yeast pathogen that spreads through nosocomial transmission within healthcare facilities. Here, we investigated the molecular epidemiology of these C. auris isolates and the mechanisms associated with antifungal drug resistance. METHODS Whole genomes of 76 clinical C. auris isolates, including 65 from patients with COVID-19 collected from March 2020 to June 2021, from nine major hospitals were sequenced on Illumina NextSeq. Single nucleotide polymorphisms were used to determine their epidemiological patterns and mechanisms for antifungal resistance. The data were compared with those published prior to the COVID-19 pandemic from 2018 to 2020 in Qatar. RESULTS Genomic analysis revealed low genetic variability among the isolates from patients with and without COVID-19, confirming a clonal outbreak and ongoing dissemination of C. auris among various healthcare facilities. Based on antifungal susceptibility profiles, more than 70% (22/28) of isolates were resistant to both fluconazole and amphotericin B. Variant analysis revealed the presence of multi-antifungal resistant isolates with prominent amino acid substitutions: Y132F in ERG11 and V704L in CDR1 linked to reduced azole susceptibility and the emergence of echinocandin resistance samples bearing mutations in FKS1 in comparison with pre-COVID-19 pandemic samples. One sample (CAS109) was resistant to three classes of antifungal drugs with a unique premature stop codon in ERG3 and novel mutations in CDR2, which may be associated with elevated amphotericin B and azole resistance. DISCUSSION Candida auris isolates from patients with COVID-19 and from most patient samples without COVID-19 in Qatar were highly clonal. The data demonstrated the emergence of multidrug-resistant strains that carry novel mutations linked to enhanced resistance to azoles, echinocandins, and amphotericin B. Understanding the epidemiology and drug resistance will inform the infection control strategy and drug therapy.
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Affiliation(s)
- Fatma Ben Abid
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar; Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Lamya Dalil
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Ayman H Abdelwahab
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Sarah Salameh
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar; Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Emad B Ibrahim
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Muna A Almaslmani
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Patrick Tang
- Weill Cornell Medicine-Qatar, Doha, Qatar; Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Andres Perez-Lopez
- Weill Cornell Medicine-Qatar, Doha, Qatar; Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar.
| | - Clement K M Tsui
- Weill Cornell Medicine-Qatar, Doha, Qatar; Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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12
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Abstract
Fungal pathogens are a severe public health problem. The leading causative agents of systemic fungal infections include species from the Candida, Cryptococcus, and Aspergillus genera. As opportunistic pathogens, these fungi are generally harmless in healthy hosts; however, they can cause significant morbidity and mortality in immunocompromised patients. Despite the profound impact of pathogenic fungi on global human health, the current antifungal armamentarium is limited to only three major classes of drugs, all of which face complications, including host toxicity, unfavourable pharmacokinetics, or limited spectrum of activity. Further exacerbating this issue is the growing prevalence of antifungal-resistant infections and the emergence of multidrug-resistant pathogens. In this review, we discuss the diverse strategies employed by leading fungal pathogens to evolve antifungal resistance, including drug target alterations, enhanced drug efflux, and induction of cellular stress response pathways. Such mechanisms of resistance occur through diverse genetic alterations, including point mutations, aneuploidy formation, and epigenetic changes given the significant plasticity observed in many fungal genomes. Additionally, we highlight recent literature surrounding the mechanisms governing resistance in emerging multidrug-resistant pathogens including Candida auris and Candida glabrata. Advancing our knowledge of the molecular mechanisms by which fungi adapt to the challenge of antifungal exposure is imperative for designing therapeutic strategies to tackle the emerging threat of antifungal resistance.
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Affiliation(s)
- Yunjin Lee
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1 Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1 Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1 Canada
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Oliva A, De Rosa FG, Mikulska M, Pea F, Sanguinetti M, Tascini C, Venditti M. Invasive Candida infection: epidemiology, clinical and therapeutic aspects of an evolving disease and the role of rezafungin. Expert Rev Anti Infect Ther 2023; 21:957-975. [PMID: 37494128 DOI: 10.1080/14787210.2023.2240956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023]
Abstract
INTRODUCTION Invasive Candida Infections (ICIs) have undergone a series of significant epidemiological, pathophysiological, and clinical changes during the last decades, with a shift toward non-albicans species, an increase in the rate of exogenous infections and clinical manifestations ranging from candidemia to an array of highly invasive and life-threatening clinical syndromes. The long-acting echinocandin rezafungin exhibits potent in-vitro activity against most wild-type and azole-resistant Candida spp. including C.auris. AREAS COVERED The following topics regarding candidemia only and ICIs were reviewed and addressed: i) pathogenesis; ii) epidemiology and temporal evolution of Candida species; iii) clinical approach; iv) potential role of the novel long-acting rezafungin in the treatment of ICIs. EXPERT OPINION Authors' expert opinion focused on considering the potential role of rezafungin in the evolving context of ICIs. Rezafungin, which combines a potent in-vitro activity against Candida species, including azole-resistant strains and C.auris, with a low likelihood of drug-drug interactions and a good safety profile, may revolutionize the treatment of candidemia/ICI. Indeed, it may shorten the length of hospital stays when clinical conditions allow and extend outpatient access to treatment of invasive candidiasis, especially when prolonged treatment duration is expected.
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Affiliation(s)
- Alessandra Oliva
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Francesco Giuseppe De Rosa
- Department of Medical Sciences, University of Turin, Infectious Diseases, City of Health and Sciences, Turin, Italy
| | - Malgorzata Mikulska
- Division of Infectious Diseases Department of Health Sciences (DISSAL), University of Genoa IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Federico Pea
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Clinical Pharmacology Unit, Department for Integrated Infectious Risk Management, IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy
| | - Maurizio Sanguinetti
- Department of Laboratory Sciences and Infectious Diseases, Fondazione Policlinico Universitario "A. Gemelli"; IRCCS, Università Cattolica Del Sacro Cuore, Rome, Italy
| | - Carlo Tascini
- Infectious Diseases Clinic: Department of Medical Area (DAME), University of Udine, Udine, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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Gregor JB, Gutierrez-Schultz VA, Hoda S, Baker KM, Saha D, Burghaze MG, Briggs SD. Expanding the toolkit for genetic manipulation and discovery in Candida species using a CRISPR ribonucleoprotein-based approach. bioRxiv 2023:2023.06.16.545382. [PMID: 37398038 PMCID: PMC10312801 DOI: 10.1101/2023.06.16.545382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The World Health Organization recently published the first list of priority fungal pathogens highlighting multiple Candida species including C. glabrata, C. albicans, and C. auris. The use of CRISPR-Cas9 and auxotrophic C. glabrata and C. albicans strains have been instrumental in the study of these fungal pathogens. Dominant drug resistance cassettes are also critical for genetic manipulation and eliminate the concern of altered virulence when using auxotrophic strains. However, genetic manipulation has been mainly limited to the use of two drug resistance cassettes, NatMX and HphMX. Using an in vitro assembled CRISPR-Cas9 ribonucleoprotein (RNP)-based system and 130-150 bp homology regions for directed repair, we expand the drug resistance cassettes for Candida to include KanMX and BleMX, commonly used in S. cerevisiae. As a proof of principle, we demonstrated efficient deletion of ERG genes using KanMX and BleMX. We also showed the utility of the CRISPR-Cas9 RNP system for generating double deletions of genes in the ergosterol pathway and endogenous epitope tagging of ERG genes using an existing KanMX cassette. This indicates that CRISPR-Cas9 RNP can be used to repurpose the S. cerevisiae toolkit. Furthermore, we demonstrated that this method is effective at deleting ERG3 in C. auris using a codon optimized BleMX cassette and effective at deleting the epigenetic factor, SET1, in C. albicans using a recyclable SAT1. Using this expanded toolkit, we discovered new insights into fungal biology and drug resistance.
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Affiliation(s)
| | | | | | | | | | | | - Scott D. Briggs
- Department of Biochemistry
- Purdue University Institute for Cancer Research
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15
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Madaan K, Bari VK. Emerging Role of Sphingolipids in Amphotericin B Drug Resistance. Microb Drug Resist 2023. [PMID: 37327022 DOI: 10.1089/mdr.2022.0353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Invasive fungal infections in humans are common in people with compromised immune systems and are difficult to treat, resulting in high mortality. Amphotericin B (AmB) is one of the main antifungal drugs available to treat these infections. AmB binds with plasma membrane ergosterol, causing leakage of cellular ions and promoting cell death. The increasing use of available antifungal drugs to combat pathogenic fungal infections has led to the development of drug resistance. AmB resistance is not very common and is usually caused by changes in the amount or type of ergosterol or changes in the cell wall. Intrinsic AmB resistance occurs in the absence of AmB exposure, whereas acquired AmB resistance can develop during treatment. However, clinical resistance arises due to treatment failure with AmB and depends on multiple factors such as the pharmacokinetics of AmB, infectious fungal species, and host immune status. Candida albicans is a common opportunistic pathogen that can cause superficial infections of the skin and mucosal surfaces, thrush, to life-threatening systemic or invasive infections. In addition, immunocompromised individuals are more susceptible to systemic infections caused by Candida, Aspergillus, and Cryptococcus. Several antifungal drugs with different modes of action are used to treat systemic to invasive fungal infections and are approved for clinical use in the treatment of fungal diseases. However, C. albicans can develop a variety of defenses against antifungal medications. In fungi, plasma membrane sphingolipid molecules could interact with ergosterol, which can lead to the alteration of drug susceptibilities such as AmB. In this review, we mainly summarize the role of sphingolipid molecules and their regulators in AmB resistance.
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Affiliation(s)
- Kashish Madaan
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, India
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Siopi M, Peroukidou I, Beredaki MI, Spruijtenburg B, de Groot T, Meis JF, Vrioni G, Tsakris A, Pournaras S, Meletiadis J. Overestimation of Amphotericin B Resistance in Candida auris with Sensititre YeastOne Antifungal Susceptibility Testing: a Need for Adjustment for Correct Interpretation. Microbiol Spectr 2023; 11:e0443122. [PMID: 37036351 PMCID: PMC10269614 DOI: 10.1128/spectrum.04431-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Significant variation in minimal inhibitory concentrations (MIC) has been reported for amphotericin B (AMB) and C. auris, depending on the antifungal susceptibility testing (AFST) method. Although the Sensititre YeastOne (SYO) is widely used in routine laboratory testing, data regarding its performance for the AFST of C. auris are scarce. We tested AMB against 65 C. auris clinical isolates with the SYO and the reference methodology by the Clinical and Laboratory Standards Institute (CLSI). The essential agreement (EA, ±1 dilution) between the two methods and the categorical agreement (CA) based on the Centers for Disease Control and Prevention (CDC)'s tentative breakpoint of MIC ≥ 2 mg/L were determined. The SYO wild type upper limit value (WT-UL) was determined using the ECOFFinder. The modal (range) CLSI growth inhibitory MIC was lower than the SYO colorimetric MIC [1(0.25-1) versus 2(1-8) mg/L, respectively]). The CLSI-colorimetric SYO EA was 29% and the CA was 11% (89% major errors; MaE). MaE were reduced when the SYO WT-UL of 8 mg/L was used (0% MaE). Alternatively, the use of SYO growth inhibition endpoints of MIC-1 (75% growth inhibition) or MIC-2 (50% growth inhibition) resulted in 88% CA with 12% MaE and 97% CA with 3% MaE, respectively. In conclusion, SYO overestimated AMB resistance in C. auris isolates when colorimetric MICs, as per SYO instructions and the CDC breakpoint of 2 mg/L, were used. This can be improved either by using the method-specific WT-UL MIC of 8 mg/L for colorimetric MICs or by determining growth inhibition MIC endpoints, regardless of the color. IMPORTANCE Candida auris is an emerging and frequently multidrug-resistant fungal pathogen that accounts for life-threatening invasive infections and nosocomial outbreaks worldwide. Reliable AF is important for the choice of the optimal treatment. Commercial methods are frequently used without prior vigorous assessment. Resistance to AMB was over-reported with the commercial colorimetric method Sensititre YeastOne (SYO). SYO produced MICs that were 1 to 2 twofold dilutions higher than those of the reference CLSI method, resulting in 89% MaE. MaE were reduced using a SYO-specific colorimetric wild type upper limit MIC value of 8 mg/L (0%) or a 50% growth inhibition endpoint (3%).
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Affiliation(s)
- Maria Siopi
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilektra Peroukidou
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria-Ioanna Beredaki
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Spyros Pournaras
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, “Attikon” University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Affiliation(s)
- Cheshta Sharma
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - David Kadosh
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
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Chen X, Jia X, Bing J, Zhang H, Hong N, Liu Y, Xi H, Wang W, Liu Z, Zhang Q, Li L, Kang M, Xiao Y, Yang B, Lin Y, Xu H, Fan X, Huang J, Gong J, Xu J, Xie X, Yang W, Zhang G, Zhang J, Kang W, Wang H, Hou X, Xiao M, Xu Y. Clonal Dissemination of Antifungal-Resistant Candida haemulonii, China. Emerg Infect Dis 2023; 29:576-584. [PMID: 36823029 PMCID: PMC9973686 DOI: 10.3201/eid2903.221082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Candida haemulonii, a relative of C. auris, frequently shows antifungal resistance and is transmissible. However, molecular tools for genotyping and investigating outbreaks are not yet established. We performed genome-based population analysis on 94 C. haemulonii strains, including 58 isolates from China and 36 other published strains. Phylogenetic analysis revealed that C. haemulonii can be divided into 4 clades. Clade 1 comprised strains from China and other global strains; clades 2-4 contained only isolates from China, were more recently evolved, and showed higher antifungal resistance. Four regional epidemic clusters (A, B, C, and D) were identified in China, each comprising ≥5 cases (largest intracluster pairwise single-nucleotide polymorphism differences <50 bp). Cluster A was identified in 2 hospitals located in the same city, suggesting potential intracity transmissions. Cluster D was resistant to 3 classes of antifungals. The emergence of more resistant phylogenetic clades and regional dissemination of antifungal-resistant C. haemulonii warrants further monitoring.
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Giacobbe DR, Mikulska M, Vena A, Di Pilato V, Magnasco L, Marchese A, Bassetti M. Challenges in the diagnosis and treatment of candidemia due to multidrug-resistant Candida auris. Front Fungal Biol 2023; 4:1061150. [PMID: 37746122 PMCID: PMC10512377 DOI: 10.3389/ffunb.2023.1061150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/16/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Malgorzata Mikulska
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Antonio Vena
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Laura Magnasco
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Anna Marchese
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- Unità di Microbiologia, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Matteo Bassetti
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Leibovici L. An open call to join the CMI editorial team: editor in fungal infections. Clin Microbiol Infect 2023; 29:125-126. [PMID: 36503115 DOI: 10.1016/j.cmi.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
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Toepfer S, Lackner M, Keniya MV, Monk BC. Functional Expression of Recombinant Candida auris Proteins in Saccharomyces cerevisiae Enables Azole Susceptibility Evaluation and Drug Discovery. J Fungi (Basel) 2023; 9. [PMID: 36836283 DOI: 10.3390/jof9020168] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Candida auris infections are difficult to treat due to acquired drug resistance against one or multiple antifungal drug classes. The most prominent resistance mechanisms in C. auris are overexpression and point mutations in Erg11, and the overexpression of efflux pump genes CDR1 and MDR1. We report the establishment of a novel platform for molecular analysis and drug screening based on acquired azole-resistance mechanisms found in C. auris. Constitutive functional overexpression of wild-type C. auris Erg11, Erg11 with amino acid substitutions Y132F or K143R and the recombinant efflux pumps Cdr1 and Mdr1 has been achieved in Saccharomyces cerevisiae. Phenotypes were evaluated for standard azoles and the tetrazole VT-1161. Overexpression of CauErg11 Y132F, CauErg11 K143R, and CauMdr1 conferred resistance exclusively to the short-tailed azoles Fluconazole and Voriconazole. Strains overexpressing the Cdr1 protein were pan-azole resistant. While CauErg11 Y132F increased VT-1161 resistance, K143R had no impact. Type II binding spectra showed tight azole binding to the affinity-purified recombinant CauErg11 protein. The Nile Red assay confirmed the efflux functions of CauMdr1 and CauCdr1, which were specifically inhibited by MCC1189 and Beauvericin, respectively. CauCdr1 exhibited ATPase activity that was inhibited by Oligomycin. The S. cerevisiae overexpression platform enables evaluation of the interaction of existing and novel azole drugs with their primary target CauErg11 and their susceptibility to drug efflux.
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22
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Abstract
Purpose of Review Candida auris, a recently recognized yeast pathogen, has become a major public health threat due to the problems associated with its accurate identification, intrinsic and acquired resistance to antifungal drugs, and its potential to easily contaminate the environment causing clonal outbreaks in healthcare facilities. These outbreaks are associated with high mortality rates particularly among older patients with multiple comorbidities under intensive care settings. The purpose of this review is to highlight strategies that are being adapted to prevent transmission of C. auris in healthcare settings. Recent Findings Colonized patients shed C. auris into their environment which contaminates surrounding equipment. It resists elimination even by robust decontamination procedures and is easily transmitted to new patients during close contact resulting in outbreaks. Efforts are being made to rapidly identify C. auris-infected/C. auris-colonized patients, to determine its susceptibility to antifungals, and to perform effective cleaning and decontamination of the environment and isolation of colonized patients to prevent further transmission. Summary Rapid and accurate identification of hospitalized patients infected/colonized with C. auris, rapid detection of its susceptibility patterns, and appropriate use of infection control measures can help to contain the spread of this highly pathogenic yeast in healthcare settings and prevent/control outbreaks.
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Affiliation(s)
- Suhail Ahmad
- Faculty of Medicine, Department of Microbiology, Kuwait University, PO Box: 24923, 13110 Safat, Kuwait
| | - Mohammad Asadzadeh
- Faculty of Medicine, Department of Microbiology, Kuwait University, PO Box: 24923, 13110 Safat, Kuwait
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23
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Rybak JM, Cuomo CA, Rogers PD. The molecular and genetic basis of antifungal resistance in the emerging fungal pathogen Candida auris. Curr Opin Microbiol 2022; 70:102208. [PMID: 36242897 PMCID: PMC10364995 DOI: 10.1016/j.mib.2022.102208] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 01/25/2023]
Abstract
Fungal infections are responsible for significant morbidity and mortality. Resistance to the limited number of agents in the antifungal armamentarium among pathogenic fungi represents a growing public health threat. Particularly concerning is the emerging fungal pathogen Candida auris that frequently exhibits resistance to the triazole class of antifungals and amphotericin B, and for which isolates resistant to all of the major antifungal classes have been reported. In this brief review, we provide an overview of what is currently known about the molecular and genetic basis for antifungal resistance in this fungal pathogen.
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Affiliation(s)
- Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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24
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Khatoon R, Sharma S, Vishwakarma P, Saini A, Aggarwal P, Lynn AM, Prakash A, Prasad R, Banerjee A. Genomic landscape of the DHA1 family in Candida auris and mapping substrate repertoire of CauMdr1. Appl Microbiol Biotechnol 2022. [PMID: 36184687 DOI: 10.1007/s00253-022-12189-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 11/02/2022]
Abstract
The last decade has witnessed the rise of an extremely threatening healthcare-associated multidrug-resistant non-albicans Candida (NAC) species, Candida auris. Since besides target alterations, efflux mechanisms contribute maximally to antifungal resistance, it is imperative to investigate their contributions in this pathogen. Of note, within the major facilitator superfamily (MFS) of efflux pumps, drug/H+ antiporter family 1 (DHA1) has been established as a predominant contributor towards xenobiotic efflux. Our study provides a complete landscape of DHA1 transporters encoded in the genome of C. auris. This study identifies 14 DHA1 transporters encoded in the genome of the pathogen. We also construct deletion and heterologous overexpression strains for the most important DHA1 drug transporter, viz., CauMdr1 to map the spectrum of its substrates. While the knockout strain did not show any significant changes in the resistance patterns against most of the tested substrates, the ortholog when overexpressed in a minimal background Saccharomyces cerevisiae strain, AD1-8u-, showed significant enhancement in the minimum inhibitory concentrations (MICs) against a large panel of antifungal molecules. Altogether, the present study provides a comprehensive template for investigating the role of DHA1 members of C. auris in antifungal resistance mechanisms. KEY POINTS: • Fourteen putative DHA1 transporters are encoded in the Candida auris genome. • Deletion of the CauMDR1 gene does not lead to major changes in drug resistance. • CauMdr1 recognizes and effluxes numerous xenobiotics, including prominent azoles.
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Gow NAR, Johnson C, Berman J, Coste AT, Cuomo CA, Perlin DS, Bicanic T, Harrison TS, Wiederhold N, Bromley M, Chiller T, Edgar K. The importance of antimicrobial resistance in medical mycology. Nat Commun 2022; 13:5352. [PMID: 36097014 PMCID: PMC9466305 DOI: 10.1038/s41467-022-32249-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/22/2022] [Indexed: 01/08/2023] Open
Abstract
Prior to the SARS-CoV-2 pandemic, antibiotic resistance was listed as the major global health care priority. Some analyses, including the O'Neill report, have predicted that deaths due to drug-resistant bacterial infections may eclipse the total number of cancer deaths by 2050. Although fungal infections remain in the shadow of public awareness, total attributable annual deaths are similar to, or exceeds, global mortalities due to malaria, tuberculosis or HIV. The impact of fungal infections has been exacerbated by the steady rise of antifungal drug resistant strains and species which reflects the widespread use of antifungals for prophylaxis and therapy, and in the case of azole resistance in Aspergillus, has been linked to the widespread agricultural use of antifungals. This review, based on a workshop hosted by the Medical Research Council and the University of Exeter, illuminates the problem of antifungal resistance and suggests how this growing threat might be mitigated.
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Affiliation(s)
- Neil A R Gow
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Carolyn Johnson
- Medical Research Council, Polaris House, Swindon, SN2 1FL, UK.
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 418 Britannia Building, Ramat Aviv, 69978, Israel
| | - Alix T Coste
- Microbiology Institute, University Hospital Lausanne, rue du Bugnon 48, 1011, Lausanne, Switzerland
| | - Christina A Cuomo
- (CAC) Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian health, Nutley, NJ, 07110, USA
| | - Tihana Bicanic
- Institute of Infection and Immunity, St George's University of London, London, SW17 0RE, UK
- Clinical Academic Group in Infection, St George's University Hospitals NHS Foundation Trust, London, SW17 0QT, UK
| | - Thomas S Harrison
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK
- Institute of Infection and Immunity, St George's University of London, London, SW17 0RE, UK
- Clinical Academic Group in Infection, St George's University Hospitals NHS Foundation Trust, London, SW17 0QT, UK
| | - Nathan Wiederhold
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Mike Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, CTF Building, 46 Grafton Street, Manchester, M13 9NT, UK
| | - Tom Chiller
- Center for Disease Control and Prevention Mycotic Disease Branch 1600 Clifton Rd, MSC-09, Atlanta, 30333, GA, USA
| | - Keegan Edgar
- Center for Disease Control and Prevention Mycotic Disease Branch 1600 Clifton Rd, MSC-09, Atlanta, 30333, GA, USA
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Shivarathri R, Jenull S, Chauhan M, Singh A, Mazumdar R, Chowdhary A, Kuchler K, Chauhan N. Comparative Transcriptomics Reveal Possible Mechanisms of Amphotericin B Resistance in Candida auris. Antimicrob Agents Chemother 2022; 66:e0227621. [PMID: 35652307 PMCID: PMC9211394 DOI: 10.1128/aac.02276-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/11/2022] [Indexed: 12/27/2022] Open
Abstract
Candida auris is an emerging multidrug-resistant human fungal pathogen often refractory to treatment by all classes of antifungal drugs. Amphotericin B (AmB) is a fungicidal drug that, despite its toxic side effects, remains a drug of choice for the treatment of drug-resistant fungal infections, including those caused by C. auris. However, the molecular mechanisms underlying AmB resistance are poorly understood. In this study, we present data that suggests membrane lipid alterations and chromatin modifications are critical processes that may contribute to or cause adaptive AmB resistance in clinical C. auris isolates. To determine the plausible cause of increased AmB resistance, we performed RNA-seq of AmB-resistant and sensitive C. auris isolates. Remarkably, AmB-resistant strains show a pronounced enrichment of genes involved in lipid and ergosterol biosynthesis, adhesion, drug transport as well as chromatin remodeling. The transcriptomics data confirm increased adhesion and reduced lipid membrane permeability of AmB-resistant strains compared to the sensitive isolates. The AmB-resistant strains also display hyper-resistance to cell wall perturbing agents, including Congo red, calcofluor white and caffeine. Additionally, we noticed an increased phosphorylation of Mkc1 cell integrity MAP kinase upon AmB treatment. Collectively, these data identify differences in the transcriptional landscapes of AmB-resistant versus AmB-sensitive isolates and provide a framework for the mechanistic understanding of AmB resistance in C. auris.
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Affiliation(s)
- Raju Shivarathri
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Sabrina Jenull
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Medical University of Vienna, Vienna, Austria
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Manju Chauhan
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Ashutosh Singh
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rounik Mazumdar
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Karl Kuchler
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Neeraj Chauhan
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
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Al-Obaid I, Asadzadeh M, Ahmad S, Alobaid K, Alfouzan W, Bafna R, Emara M, Joseph L. Fatal Breakthrough Candidemia in an Immunocompromised Patient in Kuwait Due to Candida auris Exhibiting Reduced Susceptibility to Echinocandins and Carrying a Novel Mutation in Hotspot-1 of FKS1. J Fungi (Basel) 2022; 8:jof8030267. [PMID: 35330269 PMCID: PMC8953900 DOI: 10.3390/jof8030267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022] Open
Abstract
Candida auris is an emerging yeast pathogen that has recently caused major outbreaks in healthcare facilities worldwide. Clinical C. auris isolates are usually resistant to fluconazole and readily develop resistance to echinocandins and amphotericin B (AMB) during treatment. We describe here an interesting case of C. auris infection in an immunocompromised patient who had previously received AMB and caspofungin treatment. Subsequently, C. auris was isolated from tracheal (tracheostomy) secretions and twice from urine and all three isolates were susceptible to AMB and micafungin. The patient received a combination therapy with AMB and caspofungin. Although the C. auris was cleared from the urine, the patient subsequently developed breakthrough candidemia and the bloodstream isolate exhibited a reduced susceptibility to micafungin and also showed the presence of a novel (S639T) mutation in hotspot-1 of FKS1. Interestingly, C. auris from the tracheal (tracheostomy) secretions recovered one and four days later exhibited a reduced susceptibility to micafungin and S639Y and S639T mutations in hotspot-1 of FKS1, respectively. Although the treatment was changed to voriconazole, the patient expired. Our case highlights a novel FKS1 mutation and the problems clinicians are facing to treat invasive C. auris infections due to inherent or developing resistance to multiple antifungal drugs and limited antifungal armamentarium.
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Affiliation(s)
- Inaam Al-Obaid
- Department of Microbiology, Al-Sabah Hospital, Shuwaikh 70031, Kuwait; (I.A.-O.); (R.B.); (M.E.)
| | - Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; (M.A.); (W.A.); (L.J.)
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; (M.A.); (W.A.); (L.J.)
- Correspondence: ; Tel.: +00965-2463-6503
| | - Khaled Alobaid
- Department of Microbiology, Mubarak Al-Kabeer Hospital, Jabriya 46300, Kuwait;
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; (M.A.); (W.A.); (L.J.)
| | - Ritu Bafna
- Department of Microbiology, Al-Sabah Hospital, Shuwaikh 70031, Kuwait; (I.A.-O.); (R.B.); (M.E.)
| | - Maha Emara
- Department of Microbiology, Al-Sabah Hospital, Shuwaikh 70031, Kuwait; (I.A.-O.); (R.B.); (M.E.)
| | - Leena Joseph
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; (M.A.); (W.A.); (L.J.)
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28
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Asadzadeh M, Mokaddas E, Ahmad S, Abdullah AA, de Groot T, Meis JF, Shetty SA. Molecular characterisation of Candida auris isolates from immunocompromised patients in a tertiary-care hospital in Kuwait reveals a novel mutation in FKS1 conferring reduced susceptibility to echinocandins. Mycoses 2021; 65:331-343. [PMID: 34953089 DOI: 10.1111/myc.13419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/17/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Candida auris is an emerging, potentially multidrug-resistant pathogen that exhibits clade-specific resistance to fluconazole and also develops resistance to echinocandins and amphotericin B easily. This study analysed 49 C auris isolates for alterations in hotspot-1 and hotspot-2 of FKS1 for the detection of mutations conferring reduced susceptibility to echinocandins. METHODS C auris isolates (n = 49) obtained from 18 immunocompromised patients during June 2016-December 2018 were analysed. Antifungal susceptibility testing was performed by Etest and broth microdilution-based MICRONAUT-AM assay. Mutations in hotspot-1 and hotspot-2 regions of FKS1 were detected by PCR sequencing and fingerprinting of the isolates was done by short tandem repeat typing. RESULTS The patients had multiple comorbidities/risk factors for Candida spp. infection including cancer/leukaemia/lymphoma/myeloma (n = 16), arterial/central line (n = 17), urinary catheter (n = 17), mechanical ventilation (n = 14) and major surgery (n = 9) and received antifungal drugs as prophylaxis and/or empiric treatment. Seven patients developed C auris candidemia/breakthrough candidemia, nine patients had candiduria with/without candidemia and four patients developed surgical site/respiratory infection. Resistance to fluconazole and amphotericin B was detected in 44 and four isolates, respectively. Twelve C auris isolates from eight patients showed reduced susceptibility to echinocandins. Seven isolates contained hostspot-1 mutations and three isolates from a candidemia patient contained R1354H mutation in hotspot-2 of FKS1. Ten patients died, five were cured, two were lost to follow-up and treatment details for one patient were not available. CONCLUSIONS Our findings describe development of a novel mutation in FKS1 conferring reduced susceptibility to echinocandins in one patient during treatment and unfavourable clinical outcome for many C auris-infected patients.
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Affiliation(s)
- Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait.,Microbiology Department, Ibn Sina Hospital, Shuwaikh, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | | | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.,Center of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.,Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba, Brazil
| | - Shama A Shetty
- Microbiology Department, Ibn Sina Hospital, Shuwaikh, Kuwait
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