1
|
Daneshnia F, Floyd DJ, Ryan AP, Ghahfarokhy PM, Ebadati A, Jusuf S, Munoz J, Jeffries NE, Elizabeth Yvanovich E, Apostolopoulou A, Perry AM, Lass-Flörl C, Birinci A, Hilmioğlu-Polat S, Ilkit M, Butler G, Nobile CJ, Arastehfar A, Mansour MK. Evaluation of outbreak persistence caused by multidrug-resistant and echinocandin-resistant Candida parapsilosis using multidimensional experimental and epidemiological approaches. Emerg Microbes Infect 2024; 13:2322655. [PMID: 38380673 PMCID: PMC10916928 DOI: 10.1080/22221751.2024.2322655] [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: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Candida parapsilosis is known to cause severe and persistent outbreaks in clinical settings. Patients infected with multidrug-resistant C. parapsilosis (MDR Cp) isolates were identified in a large Turkish hospital from 2017-2020. We subsequently identified three additional patients infected with MDR Cp isolates in 2022 from the same hospital and two echinocandin-resistant (ECR) isolates from a single patient in another hospital. The increasing number of MDR and ECR isolates contradicts the general principle that the severe fitness cost associated with these phenotypes could prevent their dominance in clinical settings. Here, we employed a multidimensional approach to systematically assess the fitness costs of MDR and ECR C. parapsilosis isolates. Whole-genome sequencing revealed a novel MDR genotype infecting two patients in 2022. Despite severe in vitro defects, the levels and tolerances of the biofilms of our ECR and MDR isolates were generally comparable to those of susceptible wild-type isolates. Surprisingly, the MDR and ECR isolates showed major alterations in their cell wall components, and some of the MDR isolates consistently displayed increased tolerance to the fungicidal activities of primary human neutrophils and were more immunoevasive during exposure to primary human macrophages. Our systemic infection mouse model showed that MDR and ECR C. parapsilosis isolates had comparable fungal burden in most organs relative to susceptible isolates. Overall, we observed a notable increase in the genotypic diversity and frequency of MDR isolates and identified MDR and ECR isolates potentially capable of causing persistent outbreaks in the future.
Collapse
Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel J. Floyd
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam P. Ryan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Pegah Mosharaf Ghahfarokhy
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Arefeh Ebadati
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Sebastian Jusuf
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Julieta Munoz
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | | | | | - Anna Apostolopoulou
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin M. Perry
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Cornelia Lass-Flörl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Innsbruck, Austria
| | - Asuman Birinci
- Department of Medical Microbiology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Türkiye
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael K. Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
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; 37:e0007423. [PMID: 38602408 DOI: 10.1128/cmr.00074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
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
| |
Collapse
|
3
|
Hartuis S, Ourliac-Garnier I, Robert E, Albassier M, Duchesne L, Beaufils C, Kuhn J, Le Pape P, Morio F. Precise genome editing underlines the distinct contributions of mutations in ERG11, ERG3, MRR1, and TAC1 genes to antifungal resistance in Candida parapsilosis. Antimicrob Agents Chemother 2024:e0002224. [PMID: 38624217 DOI: 10.1128/aac.00022-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/21/2024] [Indexed: 04/17/2024] Open
Abstract
Candida parapsilosis has recently emerged as a major threat due to the worldwide emergence of fluconazole-resistant strains causing clonal outbreaks in hospitals and poses a therapeutic challenge due to the limited antifungal armamentarium. Here, we used precise genome editing using CRISPR-Cas9 to gain further insights into the contribution of mutations in ERG11, ERG3, MRR1, and TAC1 genes and the influence of allelic dosage to antifungal resistance in C. parapsilosis. Seven of the most common amino acid substitutions previously reported in fluconazole-resistant clinical isolates (including Y132F in ERG11) were engineered in two fluconazole-susceptible C. parapsilosis lineages (ATCC 22019 and STZ5). Each mutant was then challenged in vitro against a large array of antifungals, with a focus on azoles. Any possible change in virulence was also assessed in a Galleria mellonella model. We successfully generated a total of 19 different mutants, using CRISPR-Cas9. Except for R398I (ERG11), all remaining amino acid substitutions conferred reduced susceptibility to fluconazole. However, the impact on fluconazole in vitro susceptibility varied greatly according to the engineered mutation, the stronger impact being noted for G583R acting as a gain-of-function mutation in MRR1. Cross-resistance with newer azoles, non-medical azoles, but also non-azole antifungals such as flucytosine, was occasionally noted. Posaconazole and isavuconazole remained the most active in vitro. Except for G583R, no fitness cost was associated with the acquisition of fluconazole resistance. We highlight the distinct contributions of amino acid substitutions in ERG11, ERG3, MRR1, and TAC1 genes to antifungal resistance in C. parapsilosis.
Collapse
Affiliation(s)
- Sophie Hartuis
- Nantes Université, CHU Nantes, Cibles et Médicaments des Infections et de l'Immunité, Nantes, France
| | | | - Estelle Robert
- Nantes Université, Cibles et Médicaments des Infections et de l'Immunité, Nantes, France
| | - Marjorie Albassier
- Nantes Université, Cibles et Médicaments des Infections et de l'Immunité, Nantes, France
| | - Léa Duchesne
- Department Public Health, Nantes Université, CHU Nantes, Nantes, France
| | - Clara Beaufils
- Nantes Université, Cibles et Médicaments des Infections et de l'Immunité, Nantes, France
| | - Joséphine Kuhn
- Nantes Université, Cibles et Médicaments des Infections et de l'Immunité, Nantes, France
| | - Patrice Le Pape
- Nantes Université, CHU Nantes, Cibles et Médicaments des Infections et de l'Immunité, Nantes, France
| | - Florent Morio
- Nantes Université, CHU Nantes, Cibles et Médicaments des Infections et de l'Immunité, Nantes, France
| |
Collapse
|
4
|
Lass-Flörl C, Kanj SS, Govender NP, Thompson GR, Ostrosky-Zeichner L, Govrins MA. Invasive candidiasis. Nat Rev Dis Primers 2024; 10:20. [PMID: 38514673 DOI: 10.1038/s41572-024-00503-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Invasive candidiasis is an important fungal disease caused by Candida albicans and, increasingly, non-albicans Candida pathogens. Invasive Candida infections originate most frequently from endogenous human reservoirs and are triggered by impaired host defences. Signs and symptoms of invasive candidiasis are non-specific; candidaemia is the most diagnosed manifestation, with disseminated candidiasis affecting single or multiple organs. Diagnosis poses many challenges, and conventional culture techniques are frequently supplemented by non-culture-based assays. The attributable mortality from candidaemia and disseminated infections is ~30%. Fluconazole resistance is a concern for Nakaseomyces glabratus, Candida parapsilosis, and Candida auris and less so in Candida tropicalis infection; acquired echinocandin resistance remains uncommon. The epidemiology of invasive candidiasis varies in different geographical areas and within various patient populations. Risk factors include intensive care unit stay, central venous catheter use, broad-spectrum antibiotics use, abdominal surgery and immune suppression. Early antifungal treatment and central venous catheter removal form the cornerstones to decrease mortality. The landscape of novel therapeutics is growing; however, the application of new drugs requires careful selection of eligible patients as the spectrum of activity is limited to a few fungal species. Unanswered questions and knowledge gaps define future research priorities and a personalized approach to diagnosis and treatment of invasive candidiasis is of paramount importance.
Collapse
Affiliation(s)
- Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, ECMM Excellence Centres of Medical Mycology, Medical University of Innsbruck, Innsbruck, Austria.
| | - Souha S Kanj
- Infectious Diseases Division, and Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nelesh P Govender
- Faculty of Health Sciences, University of the Witwatersrand and National Institute for Communicable Diseases, Johannesburg, South Africa
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - George R Thompson
- UC Davis Health Medical Center, Division of Infectious Diseases, Sacramento, CA, USA
| | | | - Miriam Alisa Govrins
- Institute of Hygiene and Medical Microbiology, ECMM Excellence Centres of Medical Mycology, Medical University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
5
|
McTaggart LR, Eshaghi A, Hota S, Poutanen SM, Johnstone J, De Luca DG, Bharat A, Patel SN, Kus JV. First Canadian report of transmission of fluconazole-resistant Candida parapsilosis within two hospital networks confirmed by genomic analysis. J Clin Microbiol 2024; 62:e0116123. [PMID: 38112529 PMCID: PMC10793253 DOI: 10.1128/jcm.01161-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023] Open
Abstract
Candida parapsilosis is a common cause of non-albicans candidemia. It can be transmitted in healthcare settings resulting in serious healthcare-associated infections and can develop drug resistance to commonly used antifungal agents. Following a significant increase in the percentage of fluconazole (FLU)-nonsusceptible isolates from sterile site specimens of patients in two Ontario acute care hospital networks, we used whole genome sequence (WGS) analysis to retrospectively investigate the genetic relatedness of isolates and to assess potential in-hospital spread. Phylogenomic analysis was conducted on all 19 FLU-resistant and seven susceptible-dose dependent (SDD) isolates from the two hospital networks, as well as 13 FLU susceptible C. parapsilosis isolates from the same facilities and 20 isolates from patients not related to the investigation. Twenty-five of 26 FLU-nonsusceptible isolates (resistant or SDD) and two susceptible isolates from the two hospital networks formed a phylogenomic cluster that was highly similar genetically and distinct from other isolates. The results suggest the presence of a persistent strain of FLU-nonsusceptible C. parapsilosis causing infections over a 5.5-year period. Results from WGS were largely comparable to microsatellite typing. Twenty-seven of 28 cluster isolates had a K143R substitution in lanosterol 14-α-demethylase (ERG11) associated with azole resistance. As the first report of a healthcare-associated outbreak of FLU-nonsusceptible C. parapsilosis in Canada, this study underscores the importance of monitoring local antimicrobial resistance trends and demonstrates the value of WGS analysis to detect and characterize clusters and outbreaks. Timely access to genomic epidemiological information can inform targeted infection control measures.
Collapse
Affiliation(s)
| | | | - Susy Hota
- Infection Prevention and Control Department, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Susan M. Poutanen
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, University Health Network/Sinai Health, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennie Johnstone
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Infection Prevention and Control Department, Sinai Health, Toronto, Ontario, Canada
| | - Domenica G. De Luca
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Samir N. Patel
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Julianne V. Kus
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
6
|
Franconi I, Lupetti A. In Vitro Susceptibility Tests in the Context of Antifungal Resistance: Beyond Minimum Inhibitory Concentration in Candida spp. J Fungi (Basel) 2023; 9:1188. [PMID: 38132789 PMCID: PMC10744879 DOI: 10.3390/jof9121188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Antimicrobial resistance is a matter of rising concern, especially in fungal diseases. Multiple reports all over the world are highlighting a worrisome increase in azole- and echinocandin-resistance among fungal pathogens, especially in Candida species, as reported in the recently published fungal pathogens priority list made by WHO. Despite continuous efforts and advances in infection control, development of new antifungal molecules, and research on molecular mechanisms of antifungal resistance made by the scientific community, trends in invasive fungal diseases and associated antifungal resistance are on the rise, hindering therapeutic options and clinical cures. In this context, in vitro susceptibility testing aimed at evaluating minimum inhibitory concentrations, is still a milestone in the management of fungal diseases. However, such testing is not the only type at a microbiologist's disposal. There are other adjunctive in vitro tests aimed at evaluating fungicidal activity of antifungal molecules and also exploring tolerance to antifungals. This plethora of in vitro tests are still left behind and performed only for research purposes, but their role in the context of invasive fungal diseases associated with antifungal resistance might add resourceful information to the clinical management of patients. The aim of this review was therefore to revise and explore all other in vitro tests that could be potentially implemented in current clinical practice in resistant and difficult-to-treat cases.
Collapse
Affiliation(s)
- Iacopo Franconi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
- Mycology Unit, Pisa University Hospital, 56126 Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
- Mycology Unit, Pisa University Hospital, 56126 Pisa, Italy
| |
Collapse
|