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Wu Y, Zou Y, Dai Y, Lu H, Zhang W, Chang W, Wang Y, Nie Z, Wang Y, Jiang X. Adaptive morphological changes link to poor clinical outcomes by conferring echinocandin tolerance in Candida tropicalis. PLoS Pathog 2025; 21:e1013220. [PMID: 40424325 DOI: 10.1371/journal.ppat.1013220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Accepted: 05/20/2025] [Indexed: 05/29/2025] Open
Abstract
Antibiotic tolerance, by which susceptible bacteria survive at high bactericide doses, is known to cause treatment failure in clinical practice. However, the impact of antifungal tolerance on clinical outcomes remains poorly understood. Here, we observed that candidemia cases caused by echinocandin-tolerant Candida tropicalis exhibited higher mortality rates during caspofungin treatment by conducting a comprehensive seven-year retrospective analysis. C. tropicalis develops tolerance to caspofungin by forming multicellular aggregates, a process linked to defects in cell division, both in vitro and in vivo. Our omics-based profiling results reveal that C. tropicalis develops tolerance through the intricate modulation of cell wall integrity and cell division pathways, particularly through the activation of chitin synthesis and the downregulation of cell division-related genes. The overexpression of cell division-related factor Ace2 can suppress the tolerance of C. tropicalis to caspofungin by delaying the formation of multicellular aggregates. Moreover, calcineurin inhibitors can suppress the tolerance of C. tropicalis by disrupting these adaptive molecular changes, thereby significantly enhancing the antifungal efficacy of caspofungin in a Galleria mellonella model. Collectively, our findings provide evidence that C. tropicalis acquires echinocandin tolerance through morphological alterations, and that inhibiting calcineurin may be a promising method to reduce this tolerance.
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Affiliation(s)
- Yongqin Wu
- Department of Clinical Laboratory, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, Anhui, China
| | - Yun Zou
- Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Dai
- Department of Clinical Laboratory, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Huaiwei Lu
- Department of Clinical Laboratory, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei Zhang
- Hefei Center for Disease Control and Prevention, Hefei, Anhui, China
| | - Wenjiao Chang
- Department of Clinical Laboratory, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Ying Wang
- Department of Clinical Laboratory, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhengchao Nie
- Department of Clinical Laboratory, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuanyuan Wang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xiaohua Jiang
- Center for Reproduction and Genetics, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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Banda-Flores IA, Torres-Tirado D, Mora-Montes HM, Pérez-Flores G, Pérez-García LA. Resilience in Resistance: The Role of Cell Wall Integrity in Multidrug-Resistant Candida. J Fungi (Basel) 2025; 11:271. [PMID: 40278091 PMCID: PMC12028102 DOI: 10.3390/jof11040271] [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: 02/05/2025] [Revised: 03/12/2025] [Accepted: 03/25/2025] [Indexed: 04/26/2025] Open
Abstract
The Candida species cell wall plays a pivotal role as a structural and functional barrier against external aggressors and as an intermediary in host-pathogen interactions. Candida species exhibit unique adaptations in their cell wall composition, with varying proportions of chitin, mannans, and β-glucans influenced by the environmental conditions and the morphological states. These components not only maintain cellular viability under osmotic, thermal, and chemical stress, but also serve as the key targets for novel antifungal strategies. MAPK signaling pathways, like the cell wall integrity pathway and the high-osmolarity glycerol pathway, play a crucial role in responding to cell wall stressors. Due to the rise of antifungal resistance and its clinical challenges, there is a need to identify new antifungal targets. This review discusses the recent advances in understanding the mechanisms underlying cell wall integrity, their impact on antifungal resistance and virulence, and their potential as therapeutic targets of C. albicans, N. glabratus, and C. auris.
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Affiliation(s)
- Iván A. Banda-Flores
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fracc. Rafael Curiel, Ciudad Valles 79060, San Luis Potosi, Mexico; (I.A.B.-F.); (D.T.-T.); (G.P.-F.)
| | - David Torres-Tirado
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fracc. Rafael Curiel, Ciudad Valles 79060, San Luis Potosi, Mexico; (I.A.B.-F.); (D.T.-T.); (G.P.-F.)
| | - Héctor M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, Col. Noria Alta, Guanajuato 36050, Guanajuato, Mexico;
| | - Gabriela Pérez-Flores
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fracc. Rafael Curiel, Ciudad Valles 79060, San Luis Potosi, Mexico; (I.A.B.-F.); (D.T.-T.); (G.P.-F.)
| | - Luis A. Pérez-García
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fracc. Rafael Curiel, Ciudad Valles 79060, San Luis Potosi, Mexico; (I.A.B.-F.); (D.T.-T.); (G.P.-F.)
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Tian S, Wu Y, Li H, Rong C, Wu N, Chu Y, Jiang N, Zhang J, Shang H. Evolutionary accumulation of FKS1 mutations from clinical echinocandin-resistant Candida auris. Emerg Microbes Infect 2024; 13:2377584. [PMID: 38989545 PMCID: PMC11265302 DOI: 10.1080/22221751.2024.2377584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
INTRODUCTION Drug resistance to echinocandins, first-line drugs used to treat Candida auris infection, is rapidly emerging. However, the accumulation of mutations in genes other than FKS1 (before an isolate develops to resistance via FKS1 mutations), remains poorly understood. Methods: Four clinical cases and 29 isolates associated with the incremental process of echinocandin resistance were collected and analyzed using antifungal drug susceptibility testing and genome sequencing to assess the evolution of echinocandin resistance. FINDINGS Six echinocandin minimum inhibitory concentration (MIC)-elevated C. auris strains and seven resistant strains were isolated from the urinary system of patients receiving echinocandin treatment. Meanwhile, phylogenetic analyses illustrated that the echinocandin-resistant strains were closely related to other strains in the same patient. Genomic data revealed that the echinocandin-resistant strains had FKS1 mutations. Furthermore, three categories (ECN-S/E/R) of non-synonymous mutant SNP genes (such as RBR3, IFF6, MKC1, MPH1, RAD2, and MYO1) in C. auris appeared to be associated with the three-stage-evolutionary model of echinocandin resistance in C. glabrata: cell wall stress, drug adaptation, and genetic escape (FKS mutation). INTERPRETATION Echinocandin-resistant C. auris undergoes spatial and temporal phase changes closely related to echinocandin exposure, particularly in the urinary system. These findings suggest that FKS1 mutations mediate an evolutionary accumulation of echinocandin resistance followed by modulation of chromosome remodelling and DNA repair processes that ultimately lead to FKS1 hot spot mutations and the development of drug resistance. This study provides an in-depth exploration of the molecular pathways involved in the evolution of Candida auris echinocandin resistance.
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Affiliation(s)
- Sufei Tian
- National Clinical Research Center for Laboratory Medicine, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Yusheng Wu
- National Clinical Research Center for Laboratory Medicine, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Hailong Li
- National Clinical Research Center for Laboratory Medicine, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, People’s Republic of China
- NHC Key Laboratory of AIDS Prevention and Treatment, The First Hospital of China Medical University, China Medical University, Shenyang, People’s Republic of China
| | - Chen Rong
- National Clinical Research Center for Laboratory Medicine, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Na Wu
- Department of Infectious Diseases, the First Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Yunzhuo Chu
- National Clinical Research Center for Laboratory Medicine, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Ning Jiang
- National Clinical Research Center for Laboratory Medicine, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Jingping Zhang
- Department of Infectious Diseases, the First Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Hong Shang
- National Clinical Research Center for Laboratory Medicine, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, People’s Republic of China
- NHC Key Laboratory of AIDS Prevention and Treatment, The First Hospital of China Medical University, China Medical University, Shenyang, People’s Republic of China
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Dakalbab S, Hamdy R, Holigová P, Abuzaid EJ, Abu-Qiyas A, Lashine Y, Mohammad MG, Soliman SSM. Uniqueness of Candida auris cell wall in morphogenesis, virulence, resistance, and immune evasion. Microbiol Res 2024; 286:127797. [PMID: 38851008 DOI: 10.1016/j.micres.2024.127797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Candida auris has drawn global attention due to its alarming multidrug resistance and the emergence of pan resistant strains. C. auris poses a significant risk in nosocomial candidemia especially among immunocompromised patients. C. auris showed unique virulence characteristics associated with cell wall including cell polymorphism, adaptation, endurance on inanimate surfaces, tolerance to external conditions, and immune evasion. Notably, it possesses a distinctive cell wall composition, with an outer mannan layer shielding the inner 1,3-β glucan from immune recognition, thereby enabling immune evasion and drug resistance. This review aimed to comprehend the association between unique characteristics of C. auris's cell wall and virulence, resistance mechanisms, and immune evasion. This is particularly relevant since the fungal cell wall has no human homology, providing a potential therapeutic target. Understanding the complex interactions between the cell wall and the host immune system is essential for devising effective treatment strategies, such as the use of repurposed medications, novel therapeutic agents, and immunotherapy like monoclonal antibodies. This therapeutic targeting strategy of C. auris holds promise for effective eradication of this resilient pathogen.
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Affiliation(s)
- Salam Dakalbab
- Research Institute for Medical and Health sciences, University of Sharjah, P.O. Box, Sharjah 27272, United Arab Emirates; College of Medicine, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Rania Hamdy
- Research Institute for Science and Engineering (RISE), University of Sharjah, Sharjah 27272, United Arab Emirates; Faculty of Pharmacy, Zagazig University, P.O. Box 44519, Egypt
| | | | - Eman J Abuzaid
- Research Institute for Medical and Health sciences, University of Sharjah, P.O. Box, Sharjah 27272, United Arab Emirates
| | - Ameera Abu-Qiyas
- Research Institute for Medical and Health sciences, University of Sharjah, P.O. Box, Sharjah 27272, United Arab Emirates
| | - Yasmina Lashine
- Research Institute for Medical and Health sciences, University of Sharjah, P.O. Box, Sharjah 27272, United Arab Emirates; Faculty of Pharmacy, Zagazig University, P.O. Box 44519, Egypt
| | - Mohammad G Mohammad
- Research Institute for Medical and Health sciences, University of Sharjah, P.O. Box, Sharjah 27272, United Arab Emirates; Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Sameh S M Soliman
- Research Institute for Medical and Health sciences, University of Sharjah, P.O. Box, Sharjah 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
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5
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Borgio JF, Almandil NB, Selvaraj P, John JS, Alquwaie R, AlHasani E, Alhur NF, Aldahhan R, AlJindan R, Almohazey D, Almofty S, Dhas TS, AbdulAzeez S. The Potential of Dutasteride for Treating Multidrug-Resistant Candida auris Infection. Pharmaceutics 2024; 16:810. [PMID: 38931930 PMCID: PMC11207579 DOI: 10.3390/pharmaceutics16060810] [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: 04/24/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Novel antifungal drugs are urgently needed to treat candidiasis caused by the emerging fungal multidrug-resistant pathogen Candida auris. In this study, the most cost-effective drug repurposing technology was adopted to identify an appropriate option among the 1615 clinically approved drugs with anti-C. auris activity. High-throughput virtual screening of 1,3-beta-glucanosyltransferase inhibitors was conducted, followed by an analysis of the stability of 1,3-beta-glucanosyltransferase drug complexes and 1,3-beta-glucanosyltransferase-dutasteride metabolite interactions and the confirmation of their activity in biofilm formation and planktonic growth. The analysis identified dutasteride, a drug with no prior antifungal indications, as a potential medication for anti-auris activity in seven clinical C. auris isolates from Saudi Arabian patients. Dutasteride was effective at inhibiting biofilm formation by C. auris while also causing a significant reduction in planktonic growth. Dutasteride treatment resulted in disruption of the cell membrane, the lysis of cells, and crushed surfaces on C. auris, and significant (p-value = 0.0057) shrinkage in the length of C. auris was noted at 100,000×. In conclusion, the use of repurposed dutasteride with anti-C. auris potential can enable rapid recovery in patients with difficult-to-treat candidiasis caused by C. auris and reduce the transmission of nosocomial infection.
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Affiliation(s)
- J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (N.F.A.); (R.A.)
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Prathas Selvaraj
- Entomology Research Unit (ERU), Department of Zoology, St. Xavier’s College (Autonomous), Palayamkottai, Affiliated to Manonmaniam Sundaranar University, Tirunelveli 627002, Tamil Nadu, India; (P.S.); (J.S.J.)
| | - J. Sherlin John
- Entomology Research Unit (ERU), Department of Zoology, St. Xavier’s College (Autonomous), Palayamkottai, Affiliated to Manonmaniam Sundaranar University, Tirunelveli 627002, Tamil Nadu, India; (P.S.); (J.S.J.)
| | - Rahaf Alquwaie
- Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia or (R.A.); or (E.A.)
| | - Eman AlHasani
- Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia or (R.A.); or (E.A.)
| | - Norah F. Alhur
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (N.F.A.); (R.A.)
| | - Razan Aldahhan
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (N.F.A.); (R.A.)
| | - Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 40017, Saudi Arabia;
| | - Dana Almohazey
- Department of Stem Cell Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (D.A.); (S.A.)
| | - Sarah Almofty
- Department of Stem Cell Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (D.A.); (S.A.)
| | - T. Stalin Dhas
- Centre for Ocean Research (DST—FIST Sponsored Centre), MoES-Earth Science & Technology Cell, Sathyabama Institute of Science and Technology, Chennai 600119, India;
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (N.F.A.); (R.A.)
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Bing J, Guan Z, Zheng T, Ennis CL, Nobile CJ, Chen C, Chu H, Huang G. Rapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection. Nat Commun 2024; 15:2381. [PMID: 38493178 PMCID: PMC10944540 DOI: 10.1038/s41467-024-46786-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Candida auris has become a serious threat to public health. The mechanisms of how this fungal pathogen adapts to the mammalian host are poorly understood. Here we report the rapid evolution of an adaptive C. auris multicellular aggregative morphology in the murine host during systemic infection. C. auris aggregative cells accumulate in the brain and exhibit obvious advantages over the single-celled yeast-form cells during systemic infection. Genetic mutations, specifically de novo point mutations in genes associated with cell division or budding processes, underlie the rapid evolution of this aggregative phenotype. Most mutated C. auris genes are associated with the regulation of cell wall integrity, cytokinesis, cytoskeletal properties, and cellular polarization. Moreover, the multicellular aggregates are notably more recalcitrant to the host antimicrobial peptides LL-37 and PACAP relative to the single-celled yeast-form cells. Overall, to survive in the host, C. auris can rapidly evolve a multicellular aggregative morphology via genetic mutations.
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Affiliation(s)
- Jian Bing
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Zhangyue Guan
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Tianhong Zheng
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Craig L Ennis
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, 95343, USA
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95343, USA
- Health Sciences Research Institute, University of California, Merced, Merced, CA, 95343, USA
| | - Changbin Chen
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China.
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China.
| | - Guanghua Huang
- Shanghai Institute of Infectious Disease and Biosecurity, Department of infectious diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China.
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Santana DJ, Zhao G, O’Meara TR. The many faces of Candida auris: Phenotypic and strain variation in an emerging pathogen. PLoS Pathog 2024; 20:e1012011. [PMID: 38427609 PMCID: PMC10906884 DOI: 10.1371/journal.ppat.1012011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024] Open
Abstract
Candida auris is an emerging fungal pathogen with unusual evolutionary history-there are multiple distinct phylogeographic clades showing a near simultaneous transition from a currently unknown reservoir to nosocomial pathogen. Each of these clades has experienced different selective pressures over time, likely resulting in selection for genotypes with differential fitness or phenotypic consequences when introduced to new environments. We also observe diversification within clades, providing additional opportunities for phenotypic differences. These differences can have large impacts on pathogenic potential, drug resistance profile, evolutionary trajectory, and transmissibility. In recent years, there have been significant advances in our understanding of strain-specific behavior in other microbes, including bacterial and fungal pathogens, and we have an opportunity to take this strain variation into account when describing aspects of C. auris biology. Here, we critically review the literature to gain insight into differences at both the strain and clade levels in C. auris, focusing on phenotypes associated with clinical disease or transmission. Our goal is to integrate clinical and epidemiological perspectives with molecular perspectives in a way that would be valuable for both audiences. Identifying differences between strains and understanding which phenotypes are strain specific will be crucial for understanding this emerging pathogen, and an important caveat when describing the analysis of a singular isolate.
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Affiliation(s)
- Darian J. Santana
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Guolei Zhao
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Teresa R. O’Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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8
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Pelletier C, Shaw S, Alsayegh S, Brown AJP, Lorenz A. Candida auris undergoes adhesin-dependent and -independent cellular aggregation. PLoS Pathog 2024; 20:e1012076. [PMID: 38466738 PMCID: PMC10957086 DOI: 10.1371/journal.ppat.1012076] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 03/21/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Candida auris is a fungal pathogen of humans responsible for nosocomial infections with high mortality rates. High levels of resistance to antifungal drugs and environmental persistence mean these infections are difficult to treat and eradicate from a healthcare setting. Understanding the life cycle and the genetics of this fungus underpinning clinically relevant traits, such as antifungal resistance and virulence, is of the utmost importance to develop novel treatments and therapies. Epidemiological and genomic studies have identified five geographical clades (I-V), which display phenotypic and genomic differences. Aggregation of cells, a phenotype primarily of clade III strains, has been linked to reduced virulence in some infection models. The aggregation phenotype has thus been associated with conferring an advantage for (skin) colonisation rather than for systemic infection. However, strains with different clade affiliations were compared to infer the effects of different morphologies on virulence. This makes it difficult to distinguish morphology-dependent causes from clade-specific or even strain-specific genetic factors. Here, we identify two different types of aggregation: one induced by antifungal treatment which is a result of a cell separation defect; and a second which is controlled by growth conditions and only occurs in strains with the ability to aggregate. The latter aggregation type depends on an ALS-family adhesin which is differentially expressed during aggregation in an aggregative C. auris strain. Finally, we demonstrate that macrophages cannot clear aggregates, suggesting that aggregation might after all provide a benefit during systemic infection and could facilitate long-term persistence in the host.
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Affiliation(s)
- Chloe Pelletier
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Sophie Shaw
- Centre for Genome-Enabled Biology and Medicine (CGEBM), University of Aberdeen, Aberdeen, United Kingdom
| | - Sakinah Alsayegh
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, United Kingdom
| | | | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, United Kingdom
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Malavia-Jones D, Farrer RA, Stappers MH, Edmondson MB, Borman AM, Johnson EM, Lipke PN, Gow NA. Strain and temperature dependent aggregation of Candida auris is attenuated by inhibition of surface amyloid proteins. Cell Surf 2023; 10:100110. [PMID: 37559873 PMCID: PMC10407437 DOI: 10.1016/j.tcsw.2023.100110] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Candida auris is a multi-drug resistant human fungal pathogen that has become a global threat to human health due to its drug resistant phenotype, persistence in the hospital environment and propensity for patient to patient spread. Isolates display variable aggregation that may affect the relative virulence of strains. Therefore, dissection of this phenotype has gained substantial interest in recent years. We studied eight clinical isolates from four different clades (I-IV); four of which had a strongly aggregating phenotype and four of which did not. Genome analysis identified polymorphisms associated with loss of cell surface proteins were enriched in weakly-aggregating strains. Additionally, we identified down-regulation of chitin synthase genes involved in the synthesis of the chitinous septum. Characterisation of the cells revealed no ultrastructural defects in cytokinesis or cell separation in aggregating isolates. Strongly and weakly aggregating strains did not differ in net surface charge or in cell surface hydrophobicity. The capacity for aggregation and for adhesion to polystyrene microspheres were also not correlated. However, aggregation and extracellular matrix formation were all increased at higher growth temperatures, and treatment with the amyloid protein inhibitor Thioflavin-T markedly attenuated aggregation. Genome analysis further indicated strain specific differences in the genome content of GPI-anchored proteins including those encoding genes with the potential to form amyloid proteins. Collectively our data suggests that aggregation is a complex strain and temperature dependent phenomenon that may be linked in part to the ability to form extracellular matrix and cell surface amyloids.
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Affiliation(s)
- Dhara Malavia-Jones
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rhys A. Farrer
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Mark H.T. Stappers
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Matt B. Edmondson
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew M. Borman
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- UKHSA Mycology Reference Laboratory, National Infection Services, UKHSA South West Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Elizabeth M. Johnson
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- UKHSA Mycology Reference Laboratory, National Infection Services, UKHSA South West Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Peter N. Lipke
- Biology Department, Brooklyn College of City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Neil A.R. Gow
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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10
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Silva LN, Ramos LS, Oliveira SSC, Magalhães LB, Cypriano J, Abreu F, Macedo AJ, Branquinha MH, Santos ALS. Development of Echinocandin Resistance in Candida haemulonii: An Emergent, Widespread, and Opportunistic Fungal Pathogen. J Fungi (Basel) 2023; 9:859. [PMID: 37623630 PMCID: PMC10455776 DOI: 10.3390/jof9080859] [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: 07/21/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
Echinocandins, used for the prevention and treatment of invasive fungal infections, have led to a rise in breakthrough infections caused by resistant Candida species. Among these species, those belonging to the Candida haemulonii complex are rare multidrug-resistant (MDR) yeasts that are frequently misidentified but have emerged as significant healthcare-associated pathogens causing invasive infections. The objectives of this study were to investigate the evolutionary pathways of echinocandin resistance in C. haemulonii by identifying mutations in the FKS1 gene and evaluating the impact of resistance on fitness. After subjecting a MDR clinical isolate of C. haemulonii (named Ch4) to direct selection using increasing caspofungin concentrations, we successfully obtained an isolate (designated Ch4'r) that exhibited a high level of resistance, with MIC values exceeding 16 mg/L for all tested echinocandin drugs (caspofungin, micafungin, and anidulafungin). Sequence analysis revealed a specific mutation in the resistant Ch4'r strain, leading to an arginine-histidine amino acid substitution (R1354H), occurring at the G4061A position of the HS2 region of the FKS1 gene. Compared to the wild-type strain, Ch4'r exhibited significantly reduced growth proliferation, biofilm formation capability, and phagocytosis ratio, indicating a decrease in fitness. Transmission electron microscopy analysis revealed alterations in cell wall components, with a notable increase in cell wall thickness. The resistant strain also exhibited higher amounts (2.5-fold) of chitin, a cell wall-located molecule, compared to the wild-type strain. Furthermore, the resistant strain demonstrated attenuated virulence in the Galleria mellonella larval model. The evolved strain Ch4'r maintained its resistance profile in vivo since the treatment with either caspofungin or micafungin did not improve larval survival or reduce the fungal load. Taken together, our findings suggest that the acquisition of pan-echinocandin resistance occurred rapidly after drug exposure and was associated with a significant fitness cost in C. haemulonii. This is particularly concerning as echinocandins are often the first-line treatment option for MDR Candida species.
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Affiliation(s)
- Laura N. Silva
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (L.N.S.); (L.S.R.); (S.S.C.O.); (L.B.M.); (M.H.B.)
| | - Lívia S. Ramos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (L.N.S.); (L.S.R.); (S.S.C.O.); (L.B.M.); (M.H.B.)
| | - Simone S. C. Oliveira
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (L.N.S.); (L.S.R.); (S.S.C.O.); (L.B.M.); (M.H.B.)
| | - Lucas B. Magalhães
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (L.N.S.); (L.S.R.); (S.S.C.O.); (L.B.M.); (M.H.B.)
| | - Jefferson Cypriano
- Laboratório de Biologia Celular e Magnetotaxia & Unidade de Microscopia Multiusuário, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (J.C.); (F.A.)
| | - Fernanda Abreu
- Laboratório de Biologia Celular e Magnetotaxia & Unidade de Microscopia Multiusuário, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (J.C.); (F.A.)
| | - Alexandre J. Macedo
- Laboratório de Biofilmes e Diversidade Microbiana, Centro de Biotecnologia e Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90010-150, Brazil;
| | - Marta H. Branquinha
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (L.N.S.); (L.S.R.); (S.S.C.O.); (L.B.M.); (M.H.B.)
- Programa de Pós-Graduação em Bioquímica (PPGBq), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-853, Brazil
| | - André L. S. Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil; (L.N.S.); (L.S.R.); (S.S.C.O.); (L.B.M.); (M.H.B.)
- Programa de Pós-Graduação em Bioquímica (PPGBq), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-853, Brazil
- Rede Micologia RJ—Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro 21941-902, Brazil
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11
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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: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [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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Amatuzzi RF, Zamith-Miranda D, Munhoz da Rocha IF, Lucena ACR, de Toledo Martins S, Streit R, Staats CC, Trentin G, Almeida F, Rodrigues ML, Nosanchuk JD, Alves LR. Caspofungin Affects Extracellular Vesicle Production and Cargo in Candida auris. J Fungi (Basel) 2022; 8:990. [PMID: 36294557 PMCID: PMC9605528 DOI: 10.3390/jof8100990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/15/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022] Open
Abstract
Antifungal resistance has become more frequent, either due to the emergence of naturally resistant species or the development of mechanisms that lead to resistance in previously susceptible species. Among these fungal species of global threat, Candida auris stands out for commonly being highly resistant to antifungal drugs, and some isolates are pan-resistant. The rate of mortality linked to C. auris infections varies from 28% to 78%. In this study, we characterized C. auris extracellular vesicles (EVs) in the presence of caspofungin, an echinocandin, which is the recommended first line antifungal for the treatment of infections due to this emerging pathogen. Furthermore, we also analyzed the protein and RNA content of EVs generated by C. auris cultivated with or without treatment with caspofungin. We observed that caspofungin led to the increased production of EVs, and treatment also altered the type and quantity of RNA molecules and proteins enclosed in the EVs. There were distinct classes of RNAs in the EVs with ncRNAs being the most identified molecules, and tRNA-fragments (tRFs) were abundant in each of the strains studied. We also identified anti-sense RNAs, varying from 21 to 55 nt in length. The differentially abundant mRNAs detected in EVs isolated from yeast subjected to caspofungin treatment were related to translation, nucleosome core and cell wall. The differentially regulated proteins identified in the EVs produced during caspofungin treatment were consistent with the results observed with the RNAs, with the enriched terms being related to translation and cell wall. Our study adds new information on how an echinocandin can affect the EV pathway, which is associated with the yeast cell being able to evade treatment and persist in the host. The ability of C. auris to efficiently alter the composition of EVs may represent a mechanism for the fungus to mitigate the effects of antifungal agents.
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Affiliation(s)
- Rafaela F. Amatuzzi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
| | - Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Aline C. R. Lucena
- Laboratory for Applied Sciences and Technology in Health, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
| | - Sharon de Toledo Martins
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
| | - Rodrigo Streit
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil
| | - Charley C. Staats
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, Brazil
| | - Gabriel Trentin
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirao Preto 14040-900, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirao Preto 14040-900, Brazil
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
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13
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Jenull S, Shivarathri R, Tsymala I, Penninger P, Trinh PC, Nogueira F, Chauhan M, Singh A, Petryshyn A, Stoiber A, Chowdhary A, Chauhan N, Kuchler K. Transcriptomics and Phenotyping Define Genetic Signatures Associated with Echinocandin Resistance in Candida auris. mBio 2022; 13:e0079922. [PMID: 35968956 PMCID: PMC9426441 DOI: 10.1128/mbio.00799-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Candida auris emerged as a human fungal pathogen only during the past decade. Remarkably, C. auris displays high degrees of genomic diversity and phenotypic plasticity, with four major clades causing hospital outbreaks with high mortality and morbidity rates. C. auris can show clinical resistance to all classes of antifungal drugs, including echinocandins that are usually recommended as first-line therapies for invasive candidiasis. Here, we exploit transcriptomics coupled with phenotypic profiling to characterize a set of clinical C. auris isolates displaying pronounced echinocandin resistance (ECN-R). A hot spot mutation in the echinocandin FKS1 target gene is present in all resistant isolates. Moreover, ECN-R strains share a core signature set of 362 genes differentially expressed in ECN-R isolates. Among others, mitochondrial gene expression and genes affecting cell wall function appear to be the most prominent, with the latter correlating well with enhanced adhesive traits, increased cell wall mannan content, and altered sensitivity to cell wall stress of ECN-R isolates. Moreover, ECN-R phenotypic signatures were also linked to pathogen recognition and interaction with immune cells. Hence, transcriptomics paired with phenotyping is a suitable tool to predict resistance and fitness traits as well as treatment outcomes in pathogen populations with complex phenotypic diversity. IMPORTANCE The surge in antimicrobial drug resistance in some bacterial and fungal pathogens constitutes a significant challenge to health care facilities. The emerging human fungal pathogen Candida auris has been particularly concerning, as isolates can display pan-antifungal resistance traits against all drugs, including echinocandins. However, the mechanisms underlying this phenotypic diversity remain poorly understood. We identify transcriptomic signatures in C. auris isolates resistant to otherwise fungicidal echinocandins. We identify a set of differentially expressed genes shared by resistant strains compared to unrelated susceptible isolates. Moreover, phenotyping demonstrates that resistant strains show distinct behaviors, with implications for host-pathogen interactions. Hence, this work provides a solid basis to identify the mechanistic links between antifungal multidrug resistance and fitness costs that affect the interaction of C. auris with host immune defenses.
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Affiliation(s)
- Sabrina Jenull
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Raju Shivarathri
- 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
| | - Irina Tsymala
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
| | - Philipp Penninger
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
| | - Phan-Canh Trinh
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
| | - Filomena Nogueira
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
- CCRI-St. Anna Children’s Cancer Research Institute, Vienna, Austria
| | - Manju 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
| | - Ashutosh Singh
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Andriy Petryshyn
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
| | - Anton Stoiber
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
| | - Anuradha Chowdhary
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - 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
| | - Karl Kuchler
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, Vienna, Austria
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14
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The RNA Content of Fungal Extracellular Vesicles: At the “Cutting-Edge” of Pathophysiology Regulation. Cells 2022; 11:cells11142184. [PMID: 35883627 PMCID: PMC9318717 DOI: 10.3390/cells11142184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
The role of extracellular vesicles (EVs) in interkingdom communication is widely accepted, and their role in intraspecies communication has been strengthened by recent research. Based on the regulation promoted by EV-associated molecules, the interactions between host and pathogens can reveal different pathways that ultimately affect infection outcomes. As a great part of the regulation is ascribable to RNA contained in EVs, many studies have focused on profiling RNAs in fungal and host EVs, tracking their accumulation during infection, and identifying potential target genes. Herein, we overview the main classes of RNA contained in fungal EVs and the biological processes regulated by these molecules, portraying a state-of-the-art picture of RNAs loaded in fungal EVs, while also raising several questions to drive future investigations. Our compiled data show unambiguously that EVs act as key elements in signaling pathways, and play a crucial role in pathosystems. A complete understanding of the processes that govern RNA content loading and trafficking, and its effect on recipient cells, will lead to improved technologies to ward off infectious agents that threaten human health.
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15
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Kim J, Oh SH, Rodriguez-Bobadilla R, Vuong VM, Hubka V, Zhao X, Hoyer LL. Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family. Front Cell Infect Microbiol 2022; 12:836632. [PMID: 35372132 PMCID: PMC8975586 DOI: 10.3389/fcimb.2022.836632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Abstract
The fungal cell wall, comprised primarily of protein and polymeric carbohydrate, maintains cell structure, provides protection from the environment, and is an important antifungal drug target. Pir proteins (proteins with internal repeats) are linked to cell wall β-1,3-glucan and are best studied in Saccharomyces cerevisiae. Sequential deletion of S. cerevisiae PIR genes produces strains with increasingly notable cell wall damage. However, a true null mutant lacking all five S. cerevisiae PIR genes was never constructed. Because only two PIR genes (PIR1, PIR32) were annotated in the Candida albicans genome, the initial goal of this work was to construct a true Δpir/Δpir null strain in this species. Unexpectedly, the phenotype of the null strain was almost indistinguishable from its parent, leading to the search for other proteins with Pir function. Bioinformatic approaches revealed nine additional C. albicans proteins that share a conserved Pir functional motif (minimally DGQ). Examination of the protein sequences revealed another conserved motif (QFQFD) toward the C-terminal end of each protein. Sequence similarities and presence of the conserved motif(s) were used to identify a set of 75 proteins across 16 fungal species that are proposed here as Pir proteins. The Pir family is greatly expanded in C. albicans and C. dubliniensis compared to other species and the orthologs are known to have specialized function during chlamydospore formation. Predicted Pir structures showed a conserved core of antiparallel beta-sheets and sometimes-extensive loops that contain amino acids with the potential to form linkages to cell wall components. Pir phylogeny demonstrated emergence of specific ortholog groups among the fungal species. Variation in gene expression patterns was noted among the ortholog groups during growth in rich medium. PIR allelic variation was quite limited despite the presence of a repeated sequence in many loci. Results presented here demonstrate that the Pir family is larger than previously recognized and lead to new hypotheses to test to better understand Pir proteins and their role in the fungal cell wall.
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Affiliation(s)
- Jisoo Kim
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Soon-Hwan Oh
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | | | - Vien M. Vuong
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Vit Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Xiaomin Zhao
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Lois L. Hoyer
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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16
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Munhoz da Rocha IF, Martins ST, Amatuzzi RF, Zamith-Miranda D, Nosanchuk JD, Rodrigues ML, Alves LR. Cellular and Extracellular Vesicle RNA Analysis in the Global Threat Fungus Candida auris. Microbiol Spectr 2021; 9:e0153821. [PMID: 34908466 PMCID: PMC8672890 DOI: 10.1128/spectrum.01538-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 12/18/2022] Open
Abstract
Emerging and reemerging pathogens are a worldwide concern, and it is predicted that these microbes will cause severe outbreaks. Candida auris affects people with weakened immune systems, particularly those who are hospitalized or are in health care facilities. Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all domains of life. EVs can deliver functional molecules to target cells, including proteins and nucleic acids, especially RNA molecules. EVs from several pathogenic fungi species play diverse biological roles related to cell-cell communication and pathogen-host interaction. In this study, we describe a data set which we produced by sequencing the RNA content of EVs from C. auris under normal growth conditions and in the presence of the antifungal caspofungin, a first-line drug to treat this fungus. To generate a more complete data set for future comparative studies, we also sequenced the RNA cellular content of EVs under the same conditions. This data set addresses a previously unexplored area of fungal biology regarding cellular small RNA and EV RNA. Our data will provide a molecular basis for the study of the aspects associated with antifungal treatment, gene expression response, and EV composition in C. auris. These data will also allow the exploration of small RNA content in the fungal kingdom and might serve as an informative basis for studies on the mechanisms by which molecules are directed to fungal EVs. IMPORTANCE Candida auris, a relevant emerging human-pathogenic yeast, is the first fungus to be called a global public health threat by the WHO. This is because of its rapid spread on all inhabited continents, together with its extremely high frequency of drug and multidrug resistance. In our study, we generated a large data set for 3 distinct strains of C. auris and obtained cellular small RNA fraction as well as extracellular vesicle RNA (EV-RNA) during normal growth conditions and after treatment with caspofungin, the first-line drug used to treat C. auris infection.
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Affiliation(s)
| | - Sharon T. Martins
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
| | - Rafaela F. Amatuzzi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
| | - Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
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