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Bohner F, Papp C, Takacs T, Varga M, Szekeres A, Nosanchuk JD, Vágvölgyi C, Tóth R, Gacser A. Acquired Triazole Resistance Alters Pathogenicity-Associated Features in Candida auris in an Isolate-Dependent Manner. J Fungi (Basel) 2023; 9:1148. [PMID: 38132749 PMCID: PMC10744493 DOI: 10.3390/jof9121148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Fluconazole resistance is commonly encountered in Candida auris, and the yeast frequently displays resistance to other standard drugs, which severely limits the number of effective therapeutic agents against this emerging pathogen. In this study, we aimed to investigate the effect of acquired azole resistance on the viability, stress response, and virulence of this species. Fluconazole-, posaconazole-, and voriconazole- resistant strains were generated from two susceptible C. auris clinical isolates (0381, 0387) and compared under various conditions. Several evolved strains became pan-azole-resistant, as well as echinocandin-cross-resistant. While being pan-azole-resistant, the 0381-derived posaconazole-evolved strain colonized brain tissue more efficiently than any other strain, suggesting that fitness cost is not necessarily a consequence of resistance development in C. auris. All 0387-derived evolved strains carried a loss of function mutation (R160S) in BCY1, an inhibitor of the PKA pathway. Sequencing data also revealed that posaconazole treatment can result in ERG3 mutation in C. auris. Despite using the same mechanisms to generate the evolved strains, both genotype and phenotype analysis highlighted that the development of resistance was unique for each strain. Our data suggest that C. auris triazole resistance development is a highly complex process, initiated by several pleiotropic factors.
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Affiliation(s)
- Flora Bohner
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Csaba Papp
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Tamas Takacs
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Mónika Varga
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - András Szekeres
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Joshua D. Nosanchuk
- Department of Medicine (Infectious Diseases), Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA;
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Csaba Vágvölgyi
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
| | - Attila Gacser
- Department of Microbiology, University of Szeged, 6726 Szeged, Hungary; (F.B.); (C.P.); (T.T.); (M.V.); (A.S.); (C.V.)
- HCEMM-USZ Fungal Pathogens Research Group, Department of Microbiology, University of Szeged, 6726 Szeged, Hungary
- HUN-REN-USZ Pathomechanisms of Fungal Infections Research Group, University of Szeged, 6726 Szeged, Hungary
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Escandón P, Lockhart SR, Chow NA, Chiller TM. Candida auris: a global pathogen that has taken root in Colombia. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:278-287. [PMID: 37721898 PMCID: PMC10599714 DOI: 10.7705/biomedica.7082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/17/2023] [Indexed: 09/20/2023]
Abstract
Candida auris has been recognized as an emerging multidrug-resistant pathogen with a significant public health burden, causing cases of invasive infection and colonization due to its persistence on inanimate surfaces, ability to colonize skin of some patients, and high transmissibility in healthcare settings. The first sporadic report of the isolation of this species from the ear canal of a patient in Asia was in 2009 and reports from other regions of the world soon followed. However, it was not until 2015 that global epidemiological alerts were communicated as a result of an increasing number of reports of invasive infections caused by C. auris in several countries. Colombia was soon added to this list in 2016 after an unusual increase in the number of C. haemulonii isolates was reported, later confirmed as C. auris. Since the issuing of a national alert by the Colombian National Institute of Health together with the Ministry of Health in 2016, the number of cases reported reached over 2,000 by 2022. Colombian isolates have not shown pan resistance to available antifungals, unlike C. auris strains reported in other regions of the world, which leaves patients in Colombia with therapeutic options for these infections. However, increasing fluconazole resistance is being observed. Whole-genome sequencing of Colombian C. auris isolates has enhanced molecular epidemiological data, grouping Colombian isolates in clade IV together with other South American isolates.
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Affiliation(s)
- Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, D.C., Colombia.
| | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta GA, USA.
| | - Nancy A Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta GA, USA.
| | - Tom M Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta GA, USA.
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Abstract
The field of molecular embryology started around 1990 by identifying new genes and analyzing their functions in early vertebrate embryogenesis. Those genes encode transcription factors, signaling molecules, their regulators, etc. Most of those genes are relatively highly expressed in specific regions or exhibit dramatic phenotypes when ectopically expressed or mutated. This review focuses on one of those genes, Lim1/Lhx1, which encodes a transcription factor. Lim1/Lhx1 is a member of the LIM homeodomain (LIM-HD) protein family, and its intimate partner, Ldb1/NLI, binds to two tandem LIM domains of LIM-HDs. The most ancient LIM-HD protein and its partnership with Ldb1 were innovated in the metazoan ancestor by gene fusion combining LIM domains and a homeodomain and by creating the LIM domain-interacting domain (LID) in ancestral Ldb, respectively. The LIM domain has multiple interacting interphases, and Ldb1 has a dimerization domain (DD), the LID, and other interacting domains that bind to Ssbp2/3/4 and the boundary factor, CTCF. By means of these domains, LIM-HD-Ldb1 functions as a hub protein complex, enabling more intricate and elaborate gene regulation. The common, ancestral role of LIM-HD proteins is neuron cell-type specification. Additionally, Lim1/Lhx1 serves crucial roles in the gastrula organizer and in kidney development. Recent studies using Xenopus embryos have revealed Lim1/Lhx1 functions and regulatory mechanisms during development and regeneration, providing insight into evolutionary developmental biology, functional genomics, gene regulatory networks, and regenerative medicine. In this review, we also discuss recent progress at unraveling participation of Ldb1, Ssbp, and CTCF in enhanceosomes, long-distance enhancer-promoter interactions, and trans-interactions between chromosomes.
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Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.
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Carolus H, Pierson S, Muñoz JF, Subotić A, Cruz RB, Cuomo CA, Van Dijck P. Genome-Wide Analysis of Experimentally Evolved Candida auris Reveals Multiple Novel Mechanisms of Multidrug Resistance. mBio 2021; 12:e03333-20. [PMID: 33820824 PMCID: PMC8092288 DOI: 10.1128/mbio.03333-20] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
Candida auris is globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome-wide evolution of MDR in C. auris obtained through serial in vitro exposure to azoles, polyenes, and echinocandins. We show the stepwise accumulation of copy number variations and novel mutations in genes both known and unknown in antifungal drug resistance. Echinocandin resistance was accompanied by a codon deletion in FKS1 hot spot 1 and a substitution in FKS1 "novel" hot spot 3. Mutations in ERG3 and CIS2 further increased the echinocandin MIC. Decreased azole susceptibility was linked to a mutation in transcription factor TAC1b and overexpression of the drug efflux pump Cdr1, a segmental duplication of chromosome 1 containing ERG11, and a whole chromosome 5 duplication, which contains TAC1b The latter was associated with increased expression of ERG11, TAC1b, and CDR2 but not CDR1 The simultaneous emergence of nonsense mutations in ERG3 and ERG11 was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross-resistance. A mutation in MEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential for and diversity of MDR development in C. auris, even in a clade until now not associated with MDR (clade II), stressing its clinical importance and the urge for future research.IMPORTANCECandida auris is a recently discovered human fungal pathogen and has shown an alarming potential for developing multi- and pan-resistance toward all classes of antifungals most commonly used in the clinic. Currently, C. auris has been globally recognized as a nosocomial pathogen of high concern due to this evolutionary potential. So far, this is the first study in which the stepwise progression of multidrug resistance (MDR) in C. auris is monitored in vitro Multiple novel mutations in known resistance genes and genes previously not or vaguely associated with drug resistance reveal rapid MDR evolution in a C. auris clade II isolate. Additionally, this study shows that in vitro experimental evolution can be a powerful tool to discover new drug resistance mechanisms, although it has its limitations.
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Affiliation(s)
- Hans Carolus
- VIB Center for Microbiology, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - José F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ana Subotić
- VIB Center for Microbiology, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Rita B Cruz
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Patrick Van Dijck
- VIB Center for Microbiology, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
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Misas E, Chow NA, Gómez OM, Muñoz JF, McEwen JG, Litvintseva AP, Clay OK. Mitochondrial Genome Sequences of the Emerging Fungal Pathogen Candida auris. Front Microbiol 2020; 11:560332. [PMID: 33193142 PMCID: PMC7652928 DOI: 10.3389/fmicb.2020.560332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/30/2020] [Indexed: 11/25/2022] Open
Abstract
Candida auris is an emerging fungal pathogen capable of causing invasive infections in humans. Since its first appearance around 1996, it has been isolated in countries spanning five continents. C. auris is a yeast that has the potential to cause outbreaks in hospitals, can survive in adverse conditions, including dry surfaces and high temperatures, and has been frequently misidentified by traditional methods. Furthermore, strains have been identified that are resistant to two and even all three of the main classes of antifungals currently in use. Several nuclear genome assemblies of C. auris have been published representing different clades and continents, yet until recently, the mitochondrial genomes (mtDNA chromosomes) of this species and the closely related species of C. haemulonii, C. duobushaemulonii, and C. pseudohaemulonii had not been analyzed in depth. We used reads from PacBio and Illumina sequencing to obtain a de novo reference assembly of the mitochondrial genome of the C. auris clade I isolate B8441 from Pakistan. This assembly has a total size of 28.2 kb and contains 13 core protein-coding genes, 25 tRNAs and the 12S and 16S ribosomal subunits. We then performed a comparative analysis by aligning Illumina reads of 129 other isolates from South Asia, Japan, South Africa, and South America with the B8441 reference. The clades of the phylogenetic tree we obtained from the aligned mtDNA sequences were consistent with those derived from the nuclear genome. The mitochondrial genome revealed a generally low genetic variation within clades, although the South Asian clade displayed two sub-branches including strains from both Pakistan and India. In particular, the 86 isolates from Colombia and Venezuela had mtDNA sequences that were all identical at the base level, i.e., a single conserved haplotype or mitochondrial background that exhibited characteristic differences from the Pakistan reference isolate B8441, such as a unique 25-nt insert that may affect function.
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Affiliation(s)
- Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Wisconsin One Health Consortium, Universidad Nacional de Colombia, Medellín, Colombia
| | - Nancy A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Oscar M. Gómez
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Microbiology, Universidad de Antioquia, Medellín, Colombia
- Genoma CES, Universidad CES, Medellín, Colombia
| | - José F. Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Translational Microbiology and Emerging Diseases, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Antifungal Resistance in Candida auris: Molecular Determinants. Antibiotics (Basel) 2020; 9:antibiotics9090568. [PMID: 32887362 PMCID: PMC7558570 DOI: 10.3390/antibiotics9090568] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 02/06/2023] Open
Abstract
Since Candida auris integrates strains resistant to multiple antifungals, research has been conducted focused on knowing which molecular mechanisms are involved. This review aims to summarize the results obtained in some of these studies. A search was carried out by consulting websites and online databases. The analysis indicates that most C. auris strains show higher resistance to fluconazole, followed by amphotericin B, and less resistance to 5-fluorocytosine and caspofungin. In C. auris, antifungal resistance to amphotericin B has been linked to an overexpression of several mutated ERG genes that lead to reduced ergosterol levels; fluconazole resistance is mostly explained by mutations identified in the ERG11 gene, as well as a higher number of copies of this gene and the overexpression of efflux pumps. For 5-fluorocytosine, it is hypothesized that the resistance is due to mutations in the FCY2, FCY1, and FUR1 genes. Resistance to caspofungin has been associated with a mutation in the FKS1 gene. Finally, resistance to each antifungal is closely related to the type of clade to which the strain belongs.
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Misas E, Escandón P, McEwen JG, Clay OK. The LUFS domain, its transcriptional regulator proteins, and drug resistance in the fungal pathogen Candida auris. Protein Sci 2020; 28:2024-2029. [PMID: 31503375 DOI: 10.1002/pro.3727] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023]
Abstract
The LUFS domain (LUG/LUH, Flo8, single-strand DNA-binding protein [SSBP]) is a well-conserved and apparently ancient region found in diverse proteins and taxa. This domain, which has as its most obvious structural feature a series of three helices, has been identified in transcriptional regulator proteins of animals, plants, and fungi. Recently, in these pages (Wang et al., Protein Sci., 2019, 28:788-793), the first crystal structure of a LUFS domain was reported, for the human SSBP2, a transcriptional repressor. We briefly address how the new insights into LUFS structures might contribute to a better understanding of an important transcriptional activator of yeasts that contains the LUFS domain, Flo8, and consider how a focus on the LUFS domain and its variation could help us to understand etiologies of drug resistance in a recently emerged pathogenic fungus, Candida auris.
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Affiliation(s)
- Elizabeth Misas
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia.,Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Juan G McEwen
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia.,School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Oliver K Clay
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia.,Translational Microbiology and Emerging Diseases (MICROS), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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