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Chen XF, Zhang H, Liu LL, Guo LN, Liu WJ, Liu YL, Li DD, Zhao Y, Zhu RY, Li Y, Dai RC, Yu SY, Li J, Wang T, Dou HT, Xu YC. Genome-wide analysis of in vivo-evolved Candida auris reveals multidrug-resistance mechanisms. Mycopathologia 2024; 189:35. [PMID: 38637433 DOI: 10.1007/s11046-024-00832-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/17/2024] [Indexed: 04/20/2024]
Abstract
Candida auris, an emerging and multidrug-resistant fungal pathogen, has led to numerous outbreaks in China. While the resistance mechanisms against azole and amphotericin B have been studied, the development of drug resistance in this pathogen remains poorly understood, particularly in in vivo-generated drug-resistant strains. This study employed pathogen whole-genome sequencing to investigate the epidemiology and drug-resistance mutations of C. auris using 16 strains isolated from two patients. Identification was conducted through Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and antimicrobial susceptibilities were assessed using broth microdilution and Sensititre YeastOne YO10. Whole-genome sequencing revealed that all isolates belonged to the South Asian lineage, displaying genetic heterogeneity. Despite low genetic variability among patient isolates, notable mutations were identified, including Y132F in ERG11 and A585S in TAC1b, likely linked to increased fluconazole resistance. Strains from patient B also carried F214L in TAC1b, resulting in a consistent voriconazole minimum inhibitory concentration of 4 µg/mL across all isolates. Furthermore, a novel frameshift mutation in the SNG1 gene was observed in amphotericin B-resistant isolates compared to susceptible ones. Our findings suggest the potential transmission of C. auris and emphasize the need to explore variations related to antifungal resistance. This involves analyzing genomic mutations and karyotypes, especially in vivo, to compare sensitive and resistant strains. Further monitoring and validation efforts are crucial for a comprehensive understanding of the mechanisms of drug resistance in C. auris.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Han Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ling-Li Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li-Na Guo
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wen-Jing Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ya-Li Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ding-Ding Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ying Zhao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ren-Yuan Zhu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Yi Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Rong-Chen Dai
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Shu-Ying Yu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Jin Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Tong Wang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hong-Tao Dou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
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Yang F, Berman J. Beyond resistance: antifungal heteroresistance and antifungal tolerance in fungal pathogens. Curr Opin Microbiol 2024; 78:102439. [PMID: 38401284 DOI: 10.1016/j.mib.2024.102439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/18/2023] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
Fungal infections are increasing globally, causing alarmingly high mortality and economic burden. In addition to antifungal resistance, other more subtle drug responses appear to increase the likelihood of treatment failures. These responses include heteroresistance and tolerance, terms that are more well-defined for antibacterial drugs, but are also evident in pathogenic fungi. Here, we compare these antifungal responses with similarly named antibacterial responses, and we review recent advances in how we understand the routes by which antifungal heteroresistance and tolerance emerge.
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Affiliation(s)
- Feng Yang
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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Hui ST, Gifford H, Rhodes J. Emerging Antifungal Resistance in Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2024; 11:43-50. [PMID: 38725545 PMCID: PMC11076205 DOI: 10.1007/s40588-024-00219-8] [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] [Accepted: 02/09/2024] [Indexed: 05/12/2024]
Abstract
Purpose of Review Over recent decades, the number of outbreaks caused by fungi has increased for humans, plants (including important crop species) and animals. Yet this problem is compounded by emerging antifungal drug resistance in pathogenic species. Resistance develops over time when fungi are exposed to drugs either in the patient or in the environment. Recent Findings Novel resistant variants of fungal pathogens that were previously susceptible are evolving (such as Aspergillus fumigatus) as well as newly emerging fungal species that are displaying antifungal resistance profiles (e.g. Candida auris and Trichophyton indotineae). Summary This review highlights the important topic of emerging antifungal resistance in fungal pathogens and how it evolved, as well as how this relates to a growing public health burden.
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Affiliation(s)
- Sui Ting Hui
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Hugh Gifford
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Johanna Rhodes
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Medical Microbiology, Radboudumc, the Netherlands
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Zhou X, Hilk A, Solis NV, Hogan BM, Bierbaum TA, Filler SG, Burrack LS, Selmecki A. Erg251 has complex and pleiotropic effects on azole susceptibility, filamentation, and stress response phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583770. [PMID: 38496635 PMCID: PMC10942443 DOI: 10.1101/2024.03.06.583770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Ergosterol is essential for fungal cell membrane integrity and growth, and numerous antifungal drugs target ergosterol. Inactivation or modification of ergosterol biosynthetic genes can lead to changes in antifungal drug susceptibility, filamentation and stress response. Here, we found that the ergosterol biosynthesis gene ERG251 is a hotspot for point mutations during adaptation to antifungal drug stress within two distinct genetic backgrounds of Candida albicans. Heterozygous point mutations led to single allele dysfunction of ERG251 and resulted in azole tolerance in both genetic backgrounds. This is the first known example of point mutations causing azole tolerance in C. albicans. Importantly, single allele dysfunction of ERG251 in combination with recurrent chromosome aneuploidies resulted in bona fide azole resistance. Homozygous deletions of ERG251 caused increased fitness in low concentrations of fluconazole and decreased fitness in rich medium, especially at low initial cell density. Dysfunction of ERG251 resulted in transcriptional upregulation of the alternate sterol biosynthesis pathway and ZRT2, a Zinc transporter. Notably, we determined that overexpression of ZRT2 is sufficient to increase azole tolerance in C. albicans. Our combined transcriptional and phenotypic analyses revealed the pleiotropic effects of ERG251 on stress responses including cell wall, osmotic and oxidative stress. Interestingly, while loss of either allele of ERG251 resulted in similar antifungal drug responses, we observed functional divergence in filamentation regulation between the two alleles of ERG251 (ERG251-A and ERG251-B) with ERG251-A exhibiting a dominant role in the SC5314 genetic background. Finally, in a murine model of systemic infection, homozygous deletion of ERG251 resulted in decreased virulence while the heterozygous deletion mutants maintain their pathogenicity. Overall, this study provides extensive genetic, transcriptional and phenotypic analysis for the effects of ERG251 on drug susceptibility, fitness, filamentation and stress responses.
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Affiliation(s)
- Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Audrey Hilk
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Norma V. Solis
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Bode M. Hogan
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Tessa A. Bierbaum
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Laura S. Burrack
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
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5
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Spruijtenburg B, Ahmad S, Asadzadeh M, Alfouzan W, Al-Obaid I, Mokaddas E, Meijer EFJ, Meis JF, de Groot T. Whole genome sequencing analysis demonstrates therapy-induced echinocandin resistance in Candida auris isolates. Mycoses 2023; 66:1079-1086. [PMID: 37712885 DOI: 10.1111/myc.13655] [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: 08/01/2023] [Revised: 08/30/2023] [Accepted: 09/02/2023] [Indexed: 09/16/2023]
Abstract
Candida auris is an emerging, multidrug-resistant yeast, causing outbreaks in healthcare facilities. Echinocandins are the antifungal drugs of choice to treat candidiasis, as they cause few side effects and resistance is rarely found. Previously, immunocompromised patients from Kuwait with C. auris colonisation or infection were treated with echinocandins, and within days to months, resistance was reported in urine isolates. To determine whether the development of echinocandin resistance was due to independent introductions of resistant strains or resulted from intra-patient resistance development, whole genome sequencing (WGS) single-nucleotide polymorphism (SNP) analysis was performed on susceptible (n = 26) and echinocandin-resistant (n = 6) isolates from seven patients. WGS SNP analysis identified three distinct clusters differing 17-127 SNPs from two patients, and the remaining isolates from five patients, respectively. Sequential isolates within patients had a maximum of 11 SNP differences over a time period of 1-10 months. The majority of isolates with reduced susceptibility displayed unique FKS1 substitutions including a novel FKS1M690V substitution, and nearly all were genetically related, ranging from only three to six SNP differences compared to susceptible isolates from the same patient. Resistant isolates from three patients shared the common FKS1S639F substitution; however, WGS analysis did not suggest a common source. These findings strongly indicate that echinocandin resistance is induced during antifungal treatment. Future studies should determine whether such echinocandin-resistant strains are capable of long-term colonisation, cause subsequent breakthrough candidiasis, have a propensity to cross-infect other patients, or remain viable for longer time periods in the hospital environment.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Center of Expertise for Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Microbiology Unit, Department of Laboratory Medicine, Farwania Hospital, Kuwait City, Kuwait
| | - Inaam Al-Obaid
- Department of Microbiology, Al-Sabah Hospital, Shuwaikh, Kuwait
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Department of Microbiology, Ibn-Sina Hospital, Shuwaikh, Kuwait
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Center of Expertise for Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F Meis
- Center of Expertise for Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Center of Expertise for Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
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6
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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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7
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Boyce KJ. The Microevolution of Antifungal Drug Resistance in Pathogenic Fungi. Microorganisms 2023; 11:2757. [PMID: 38004768 PMCID: PMC10673521 DOI: 10.3390/microorganisms11112757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The mortality rates of invasive fungal infections remain high because of the limited number of antifungal drugs available and antifungal drug resistance, which can rapidly evolve during treatment. Mutations in key resistance genes such as ERG11 were postulated to be the predominant cause of antifungal drug resistance in the clinic. However, recent advances in whole genome sequencing have revealed that there are multiple mechanisms leading to the microevolution of resistance. In many fungal species, resistance can emerge through ERG11-independent mechanisms and through the accumulation of mutations in many genes to generate a polygenic resistance phenotype. In addition, genome sequencing has revealed that full or partial aneuploidy commonly occurs in clinical or microevolved in vitro isolates to confer antifungal resistance. This review will provide an overview of the mutations known to be selected during the adaptive microevolution of antifungal drug resistance and focus on how recent advances in genome sequencing technology have enhanced our understanding of this process.
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Affiliation(s)
- Kylie J Boyce
- School of Science, RMIT University, Melbourne, VIC 3085, Australia
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8
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Selmecki A. Recurrent copy number variations in the human fungal pathogen Candida parapsilosis. mBio 2023; 14:e0071323. [PMID: 37787545 PMCID: PMC10653803 DOI: 10.1128/mbio.00713-23] [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] [Indexed: 10/04/2023] Open
Abstract
Candida parapsilosis is an opportunistic fungal pathogen with increasing incidence in hospital settings worldwide; however, we lack a comprehensive understanding of the mechanisms promoting its virulence and drug resistance. Bergin et al. systematically quantify the frequency and effect of copy number variation (CNV) across 170 diverse clinical and environmental isolates of C. parapsilosis (Bergin SA, Zhao F, Ryan AP, Müller CA, Nieduszynski CA, Zhai B, Rolling T, Hohl TM, Morio F, Scully J, Wolfe KH, Butler G, 2022, mBio, https://doi.org/10.1128/mbio.01777-22). Using a combination of both short- and long-read whole genome sequencing techniques, they determine the structure and copy number of two CNVs that arose recurrently throughout the evolution of these isolates. Each CNV predominantly amplifies one coding sequence (ARR3 or RTA3); however, the amplitude and recombination breakpoints are variable across the isolates. Amplification of RTA3 correlates with drug resistance and deletion causes drug susceptibility. This study highlights the need for further research into the mechanisms and dynamics of CNV formation and the impact of these CNVs on virulence and drug resistance across diverse fungal pathogens.
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Affiliation(s)
- Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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9
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Gabaldón T. Nothing makes sense in drug resistance except in the light of evolution. Curr Opin Microbiol 2023; 75:102350. [PMID: 37348192 DOI: 10.1016/j.mib.2023.102350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 06/24/2023]
Abstract
Our ability to fight infectious diseases is being increasingly compromised due to the emergence and spread of pathogens that become resistant to one or several drugs. This phenomenon is ubiquitous among pathogens and has parallels in cancer treatment. Given the urgency of the problem, there is a need for a paradigm shift in drug therapy toward one in which the objective to prevent the evolution of drug resistance is considered alongside the main objective of eliminating the infection or tumor. Here, I stress the importance of considering an evolutionary perspective to achieve this goal, and review recent advances in this direction, including therapies that exploit the fitness trade-offs of resistance.
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Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain.
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10
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Vande Zande P, Zhou X, Selmecki A. The Dynamic Fungal Genome: Polyploidy, Aneuploidy and Copy Number Variation in Response to Stress. Annu Rev Microbiol 2023; 77:341-361. [PMID: 37307856 PMCID: PMC10599402 DOI: 10.1146/annurev-micro-041320-112443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fungal species have dynamic genomes and often exhibit genomic plasticity in response to stress. This genome plasticity often comes with phenotypic consequences that affect fitness and resistance to stress. Fungal pathogens exhibit genome plasticity in both clinical and agricultural settings and often during adaptation to antifungal drugs, posing significant challenges to human health. Therefore, it is important to understand the rates, mechanisms, and impact of large genomic changes. This review addresses the prevalence of polyploidy, aneuploidy, and copy number variation across diverse fungal species, with special attention to prominent fungal pathogens and model species. We also explore the relationship between environmental stress and rates of genomic changes and highlight the mechanisms underlying genotypic and phenotypic changes. A comprehensive understanding of these dynamic fungal genomes is needed to identify novel solutions for the increase in antifungal drug resistance.
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Affiliation(s)
- Pétra Vande Zande
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
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11
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Ambrosio FJ, Scribner MR, Wright SM, Otieno JR, Doughty EL, Gorzalski A, Siao DD, Killian S, Hua C, Schneider E, Tran M, Varghese V, Libuit KG, Pandori M, Sevinsky JR, Hess D. TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization. Front Public Health 2023; 11:1198213. [PMID: 37593727 PMCID: PMC10428623 DOI: 10.3389/fpubh.2023.1198213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens. Methods TheiaEuk was designed using containerized components and written in the workflow description language (WDL) to facilitate deployment on the cloud-based open bioinformatics platform Terra. This species-agnostic workflow enables the analysis of fungal genomes without requiring coding, thereby reducing the entry barrier for laboratory scientists. To demonstrate the usefulness of this pipeline, an ongoing outbreak of C. auris in southern Nevada was investigated. We performed whole-genome sequence analysis of 752 new C. auris isolates from this outbreak. Furthermore, TheiaEuk was utilized to observe the accumulation of mutations in the FKS1 gene over the course of the outbreak, highlighting the utility of TheiaEuk as a monitor of emerging public health threats when combined with whole-genome sequencing surveillance of fungal pathogens. Results A primary result of this work is a curated fungal database containing 5,667 unique genomes representing 245 species. TheiaEuk also incorporates taxon-specific submodules for specific species, including clade-typing for Candida auris (C. auris). In addition, for several fungal species, it performs dynamic reference genome selection and variant calling, reporting mutations found in genes currently associated with antifungal resistance (FKS1, ERG11, FUR1). Using genome assemblies from the ATCC Mycology collection, the taxonomic identification module used by TheiaEuk correctly assigned genomes to the species level in 126/135 (93.3%) instances and to the genus level in 131/135 (97%) of instances, and provided zero false calls. Application of TheiaEuk to actual specimens obtained in the course of work at a local public health laboratory resulted in 13/15 (86.7%) correct calls at the species level, with 2/15 called at the genus level. It made zero incorrect calls. TheiaEuk accurately assessed clade type of Candida auris in 297/302 (98.3%) of instances. Discussion TheiaEuk demonstrated effectiveness in identifying fungal species from whole genome sequence. It further showed accuracy in both clade-typing of C. auris and in the identification of mutations known to associate with drug resistance in that organism.
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Affiliation(s)
| | | | | | | | | | | | | | - Steve Killian
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | - Chi Hua
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Emily Schneider
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Michael Tran
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Vici Varghese
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV, United States
| | | | - David Hess
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
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Fayed B, Lazreg IK, AlHumaidi RB, Qasem MAAA, Alajmy BMGN, Bojbarah FMAM, Senok A, Husseiny MI, Soliman SSM. Intra-clade Heterogeneity in Candida auris: Risk of Management. Curr Microbiol 2023; 80:295. [PMID: 37486431 DOI: 10.1007/s00284-023-03416-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
Candida auris has emerged as a significant nosocomial fungal pathogen with a high risk of pathogenicity. Since the initial detection of C. auris in 2009, it gained lots of attention with a recent alert by the Centers for Disease Control and Prevention (CDC) due to its high infectivity and drug resistance. Several studies showed the capability of C. auris to secrete lytic enzymes, germinate, and form a biofilm that eventually results in interactions with the host cells, leading to serious infections. Other studies demonstrated a decrease in susceptibility of C. auris strains to available antifungals, which may be caused by mutations within the target genes, or the drug efflux pumps. However, the contribution of C. auris heterogeneity in pathogenicity and drug resistance is not well studied. Here, we shed light on the factors contributing to the development of heterogeneity in C. auris. These include phenotypic changes, biofilm formation, mechanisms of drug resistance, host invasion, mode of transmission, and expression of virulence factors. C. auris exhibits different phenotypes, particularly aggregative, and non-aggregative forms that play an important role in fungal heterogeneity, which significantly affects drug resistance and pathogenicity. Collectively, heterogeneity in C. auris significantly contributes to ineffective treatment, which in turn affects the fungal pathogenicity and drug resistance. Therefore, understanding the underlying reasons for C. auris heterogeneity and applying effective antifungal stewardship could play a major role in controlling this pathogen.
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Affiliation(s)
- Bahgat Fayed
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Chemistry of Natural and Microbial Products, National Research Centre, Cairo, Egypt
| | - Imene K Lazreg
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Razan B AlHumaidi
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Maryam A A A Qasem
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Bashayir M Gh N Alajmy
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Fatemh M A M Bojbarah
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Building 14 Dubai Healthcare City, P.O.Box 505055, Dubai, UAE
| | - Mohamed I Husseiny
- Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Sameh S M Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
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Proctor DM, Drummond RA, Lionakis MS, Segre JA. One population, multiple lifestyles: Commensalism and pathogenesis in the human mycobiome. Cell Host Microbe 2023; 31:539-553. [PMID: 37054674 PMCID: PMC10155287 DOI: 10.1016/j.chom.2023.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/12/2023] [Accepted: 02/23/2023] [Indexed: 04/15/2023]
Abstract
Candida auris and Candida albicans can result in invasive fungal diseases. And yet, these species can stably and asymptomatically colonize human skin and gastrointestinal tracts. To consider these disparate microbial lifestyles, we first review factors shown to influence the underlying microbiome. Structured by the damage response framework, we then consider the molecular mechanisms deployed by C. albicans to switch between commensal and pathogenic lifestyles. Next, we explore this framework with C. auris to highlight how host physiology, immunity, and/or antibiotic receipt are associated with progression from colonization to infection. While treatment with antibiotics increases the risk that an individual will succumb to invasive candidiasis, the underlying mechanisms remain unclear. Here, we describe several hypotheses that may explain this phenomenon. We conclude by highlighting future directions integrating genomics with immunology to advance our understanding of invasive candidiasis and human fungal disease.
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Affiliation(s)
- Diana M Proctor
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Rebecca A Drummond
- Institute of Immunology & Immunotherapy, Institute of Microbiology & Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Sharma C, Kadosh D. Perspective on the origin, resistance, and spread of the emerging human fungal pathogen Candida auris. PLoS Pathog 2023; 19:e1011190. [PMID: 36952448 PMCID: PMC10035752 DOI: 10.1371/journal.ppat.1011190] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Affiliation(s)
- Cheshta Sharma
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - David Kadosh
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
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15
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Todd RT, Soisangwan N, Peters S, Kemp B, Crooks T, Gerstein A, Selmecki A. Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in Candida albicans. Mol Biol Evol 2023; 40:6989826. [PMID: 36649220 PMCID: PMC9887641 DOI: 10.1093/molbev/msad009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Invasive fungal infections are a leading global cause of human mortality. Only three major classes of antifungal drugs are widely used, and resistance to all three classes can arise rapidly. The most widely prescribed antifungal drug, fluconazole, disseminates rapidly and reaches a wide range of concentrations throughout the body. The impact of drug concentration on the spectrum and effect of mutations acquired during adaptation is not known for any fungal pathogen, and how the specific level of a given stress influences the distribution of beneficial mutations has been poorly explored in general. We evolved 144 lineages from three genetically distinct clinical isolates of Candida albicans to four concentrations of fluconazole (0, 1, 8, and 64 μg/ml) and performed comprehensive phenotypic and genomic comparisons of ancestral and evolved populations. Adaptation to different fluconazole concentrations resulted in distinct adaptive trajectories. In general, lineages evolved to drug concentrations close to their MIC50 (the level of drug that reduces growth by 50% in the ancestor) tended to rapidly evolve an increased MIC50 and acquired distinct segmental aneuploidies and copy number variations. By contrast, lineages evolved to drug concentrations above their ancestral MIC50 tended to acquire a different suite of mutational changes and increased in drug tolerance (the ability of a subpopulation of cells to grow slowly above their MIC50). This is the first evidence that different concentrations of drug can select for different genotypic and phenotypic outcomes in vitro and may explain observed in vivo drug response variation.
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Affiliation(s)
- Robert T Todd
- Present address: Department of Biology, Bard College, Annandale-on-Hudson, New York
| | | | - Sam Peters
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Bailey Kemp
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Taylor Crooks
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Aleeza Gerstein
- Department of Microbiology, The University of Manitoba, Winnipeg, Manitoba, Canada,Department of Statistics, The University of Manitoba, Winnipeg, Manitoba, Canada
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Ahmad S, Asadzadeh M. Strategies to Prevent Transmission of Candida auris in Healthcare Settings. CURRENT FUNGAL INFECTION REPORTS 2023; 17:36-48. [PMID: 36718372 PMCID: PMC9878498 DOI: 10.1007/s12281-023-00451-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2022] [Indexed: 01/27/2023]
Abstract
Purpose of Review Candida auris, a recently recognized yeast pathogen, has become a major public health threat due to the problems associated with its accurate identification, intrinsic and acquired resistance to antifungal drugs, and its potential to easily contaminate the environment causing clonal outbreaks in healthcare facilities. These outbreaks are associated with high mortality rates particularly among older patients with multiple comorbidities under intensive care settings. The purpose of this review is to highlight strategies that are being adapted to prevent transmission of C. auris in healthcare settings. Recent Findings Colonized patients shed C. auris into their environment which contaminates surrounding equipment. It resists elimination even by robust decontamination procedures and is easily transmitted to new patients during close contact resulting in outbreaks. Efforts are being made to rapidly identify C. auris-infected/C. auris-colonized patients, to determine its susceptibility to antifungals, and to perform effective cleaning and decontamination of the environment and isolation of colonized patients to prevent further transmission. Summary Rapid and accurate identification of hospitalized patients infected/colonized with C. auris, rapid detection of its susceptibility patterns, and appropriate use of infection control measures can help to contain the spread of this highly pathogenic yeast in healthcare settings and prevent/control outbreaks.
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Affiliation(s)
- Suhail Ahmad
- Faculty of Medicine, Department of Microbiology, Kuwait University, PO Box: 24923, 13110 Safat, Kuwait
| | - Mohammad Asadzadeh
- Faculty of Medicine, Department of Microbiology, Kuwait University, PO Box: 24923, 13110 Safat, Kuwait
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Directed Evolution Detects Supernumerary Centric Chromosomes Conferring Resistance to Azoles in Candida auris. mBio 2022; 13:e0305222. [PMID: 36445083 PMCID: PMC9765433 DOI: 10.1128/mbio.03052-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Candida auris exhibits resistance to multiple antifungal drug classes and sterilization agents, posing threats to the immunocompromised worldwide. Among the four major geographical clades, the East Asian clade 2 isolates of C. auris are mostly drug susceptible. In this study, we experimentally evolved one such drug-susceptible isolate for multiple generations in the presence of the antifungal compound fluconazole and analyzed changes in the karyotype, DNA sequence, and gene expression profiles in three evolved drug-resistant isolates. Next-generation sequencing and electrophoretic karyotyping confirm the presence of segmental aneuploidy as supernumerary chromosomes originating from centromere-inclusive chromosomal duplication events in two such cases. A 638-kb region and a 675-kb region, both of which originated from chromosome 5 and contained its centromere region, are instances of supernumerary chromosome formation identified in two evolved fluconazole-resistant isolates. Loss of the supernumerary chromosomes from the drug-resistant isolates results in a complete reversal of fluconazole susceptibility. Transcriptome analysis of the third isolate identified overexpression of drug efflux pumps as a possible non-aneuploidy-driven mechanism of drug resistance. Together, this study reveals how both aneuploidy-driven and aneuploidy-independent mechanisms may operate in parallel in an evolving population of C. auris in the presence of an antifungal drug, in spite of starting from the same strain grown under similar conditions, to attain various levels of fluconazole resistance. IMPORTANCE Fungal pathogens develop drug resistance through multiple pathways by acquiring gene mutations, increasing the copy number of genes, or altering gene expression. In this study, we attempt to understand the mechanisms of drug resistance in the recently emerged superbug, C. auris. One approach to studying this aspect is identifying various mechanisms operating in drug-resistant clinical isolates. An alternative approach is to evolve a drug-susceptible isolate in the presence of an antifungal compound and trace the changes that result in drug resistance. Here, we evolve a drug-susceptible isolate of C. auris in the laboratory in the presence of a widely used antifungal compound, fluconazole. In addition to the already known changes like overexpression of drug efflux pumps, this study identifies a novel mechanism of azole resistance by the emergence of additional chromosomes through segmental duplication of chromosomal regions, including centromeres. The centric supernumerary chromosome helps stable amplification of a set of genes with an extra copy to confer fluconazole resistance.
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Drug Resistance and Evolvability in an Emerging Human Fungal Pathogen. mBio 2022; 13:e0187622. [PMID: 35980032 PMCID: PMC9600676 DOI: 10.1128/mbio.01876-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Over the past decade, Candida auris has emerged as a highly transmissible human fungal pathogen. Because of its ability to transmit between patients in hospitals and its ability to rapidly develop drug resistance, C. auris presents unique challenges. However, at a genetic and genomic level we still understand relatively little about how drug resistance develops in this pathogen. Burrack et al. use experimental evolution and whole-genome sequencing to identify mutations correlated with fluconazole resistance in C. auris. They identify interesting genomic features, including highly plastic subtelomeric regions and whole chromosomal and segmental aneuploidies. Excitingly, they also identify the first example of a hypermutator strain in C. auris. In comparison with the model human fungal pathogen Candida albicans, C. auris is more likely to undergo mutation and less likely to undergo copy number variation in response to drug selection, which may be linked to differences in base ploidy level.
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