1
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Smukowski Heil C. Loss of Heterozygosity and Its Importance in Evolution. J Mol Evol 2023; 91:369-377. [PMID: 36752826 PMCID: PMC10276065 DOI: 10.1007/s00239-022-10088-8] [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: 09/14/2022] [Accepted: 12/23/2022] [Indexed: 02/09/2023]
Abstract
Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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2
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Martínez AA, Lang GI. Identifying Targets of Selection in Laboratory Evolution Experiments. J Mol Evol 2023; 91:345-355. [PMID: 36810618 DOI: 10.1007/s00239-023-10096-2] [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: 12/07/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023]
Abstract
Adaptive evolution navigates a balance between chance and determinism. The stochastic processes of mutation and drift generate phenotypic variation; however, once mutations reach an appreciable frequency in the population, their fate is governed by the deterministic action of selection, enriching for favorable genotypes and purging the less-favorable ones. The net result is that replicate populations will traverse similar-but not identical-pathways to higher fitness. This parallelism in evolutionary outcomes can be leveraged to identify the genes and pathways under selection. However, distinguishing between beneficial and neutral mutations is challenging because many beneficial mutations will be lost due to drift and clonal interference, and many neutral (and even deleterious) mutations will fix by hitchhiking. Here, we review the best practices that our laboratory uses to identify genetic targets of selection from next-generation sequencing data of evolved yeast populations. The general principles for identifying the mutations driving adaptation will apply more broadly.
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Affiliation(s)
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
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3
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Laux K, Teixeira MDM, Barker B. Love in the time of climate change: A review of sexual reproduction in the order Onygenales. Fungal Genet Biol 2023; 167:103797. [PMID: 37100376 DOI: 10.1016/j.fgb.2023.103797] [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: 09/10/2022] [Revised: 02/02/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
Life-threatening infections caused by fungi in the order Onygenales have been rising over the last few decades. Increasing global temperature due to anthropogenic climate change is one potential abiotic selection pressure that may explain the increase in infections. The generation of genetically novel offspring with novel phenotypes through the process of sexual recombination could allow fungi to adapt to changing climate conditions. The basic structures associated with sexual reproduction have been identified in Histoplasma, Blastomyces, Malbranchea, and Brunneospora. However, for Coccidioides and Paracoccidioides, the actual structural identification of these processes has yet to be identified despite having genetic evidence that suggests sexual recombination is occurring in these organisms. This review highlights the importance of assessing sexual recombination in the order Onygenales as a means of understanding the mechanisms these organisms might employ to enhance fitness in the face of a changing climate and provides details regarding the known reproductive mechanisms in the Onygenales.
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Affiliation(s)
- Klaire Laux
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA.
| | - Marcus de Melo Teixeira
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA; Nùcleo de Medicina Tropical, University of Brasilia, Universitário Darcy Ribeiro, s/n -Asa Norte, Brasília, DF 70910-900, Brazil
| | - Bridget Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Bldg 56 Ste 210, Flagstaff, AZ 86011, USA.
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4
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Brown AJP. Fungal resilience and host-pathogen interactions: Future perspectives and opportunities. Parasite Immunol 2023; 45:e12946. [PMID: 35962618 PMCID: PMC10078341 DOI: 10.1111/pim.12946] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
We are constantly exposed to the threat of fungal infection. The outcome-clearance, commensalism or infection-depends largely on the ability of our innate immune defences to clear infecting fungal cells versus the success of the fungus in mounting compensatory adaptive responses. As each seeks to gain advantage during these skirmishes, the interactions between host and fungal pathogen are complex and dynamic. Nevertheless, simply compromising the physiological robustness of fungal pathogens reduces their ability to evade antifungal immunity, their virulence, and their tolerance against antifungal therapy. In this article I argue that this physiological robustness is based on a 'Resilience Network' which mechanistically links and controls fungal growth, metabolism, stress resistance and drug tolerance. The elasticity of this network probably underlies the phenotypic variability of fungal isolates and the heterogeneity of individual cells within clonal populations. Consequently, I suggest that the definition of the fungal Resilience Network represents an important goal for the future which offers the clear potential to reveal drug targets that compromise drug tolerance and synergise with current antifungal therapies.
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Affiliation(s)
- Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK
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5
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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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6
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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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7
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Avramovska O, Smith AC, Rego E, Hickman MA. Tetraploidy accelerates adaptation under drug selection in a fungal pathogen. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:984377. [PMID: 37746235 PMCID: PMC10512305 DOI: 10.3389/ffunb.2022.984377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/06/2022] [Indexed: 09/26/2023]
Abstract
Baseline ploidy significantly impacts evolutionary trajectories and, specifically, tetraploidy is associated with higher rates of adaptation relative to haploidy and diploidy. While the majority of experimental evolution studies investigating ploidy use the budding yeast Saccharomyces cerivisiae, the fungal pathogen Candida albicans is a powerful system to investigate ploidy dynamics, particularly in the context of acquiring antifungal drug resistance. C. albicans laboratory and clinical strains are predominantly diploid, but have been isolated as haploid and polyploid. Here, we evolved diploid and tetraploid C. albicans for ~60 days in the antifungal drug caspofungin. Tetraploid-evolved lines adapted faster than diploid-evolved lines and reached higher levels of caspofungin resistance. While diploid-evolved lines generally maintained their initial genome size, tetraploid-evolved lines rapidly underwent genome-size reductions and did so prior to caspofungin adaptation. While clinical resistance was largely due to mutations in FKS1, these mutations were caused by substitutions in diploid, and indels in tetraploid isolates. Furthermore, fitness costs in the absence of drug selection were significantly less in tetraploid-evolved lines compared to the diploid-evolved lines. Taken together, this work supports a model of adaptation in which the tetraploid state is transient but its ability to rapidly transition ploidy states improves adaptive outcomes and may drive drug resistance in fungal pathogens.
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Affiliation(s)
- Ognenka Avramovska
- Department of Biology, Emory University, Atlanta, GA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Amanda C. Smith
- Department of Biology, Emory University, Atlanta, GA, United States
- Division of Viral Disease, CDC Foundation, Atlanta, GA, United States
| | - Emily Rego
- Department of Biology, Emory University, Atlanta, GA, United States
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8
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Kukurudz RJ, Chapel M, Wonitowy Q, Adamu Bukari AR, Sidney B, Sierhuis R, Gerstein AC. Acquisition of cross-azole tolerance and aneuploidy in Candida albicans strains evolved to posaconazole. G3 (BETHESDA, MD.) 2022; 12:jkac156. [PMID: 35881695 PMCID: PMC9434289 DOI: 10.1093/g3journal/jkac156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/13/2022] [Indexed: 12/30/2022]
Abstract
A number of in vitro studies have examined the acquisition of drug resistance to the triazole fluconazole, a first-line treatment for many Candida infections. Much less is known about posaconazole, a newer triazole. We conducted the first in vitro experimental evolution of replicates from 8 diverse strains of Candida albicans in a high level of the fungistatic drug posaconazole. Approximately half of the 132 evolved replicates survived 50 generations of evolution, biased toward some of the strain backgrounds. We found that although increases in drug resistance were rare, increases in drug tolerance (the slow growth of a subpopulation of cells in a level of drug above the resistance level) were common across strains. We also found that adaptation to posaconazole resulted in widespread cross-tolerance to other azole drugs. Widespread aneuploidy was observed in evolved replicates from some strain backgrounds. Trisomy of at least one of chromosomes 3, 6, and R was identified in 11 of 12 whole-genome sequenced evolved SC5314 replicates. These findings document rampant evolved cross-tolerance among triazoles and highlight that increases in drug tolerance can evolve independently of drug resistance in a diversity of C. albicans strain backgrounds.
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Affiliation(s)
- Rebekah J Kukurudz
- Department of Microbiology, The University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Madison Chapel
- Department of Microbiology, The University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Quinn Wonitowy
- Department of Microbiology, The University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Brooke Sidney
- Department of Microbiology, The University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Riley Sierhuis
- Department of Microbiology, The University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Aleeza C Gerstein
- Department of Microbiology, The University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Statistics, The University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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9
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Handelman M, Osherov N. Experimental and in-host evolution of triazole resistance in human pathogenic fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:957577. [PMID: 37746192 PMCID: PMC10512370 DOI: 10.3389/ffunb.2022.957577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/19/2022] [Indexed: 09/26/2023]
Abstract
The leading fungal pathogens causing systemic infections in humans are Candida spp., Aspergillus fumigatus, and Cryptococcus neoformans. The major class of antifungals used to treat such infections are the triazoles, which target the cytochrome P450 lanosterol 14-α-demethylase, encoded by the ERG11 (yeasts)/cyp51A (molds) genes, catalyzing a key step in the ergosterol biosynthetic pathway. Triazole resistance in clinical fungi is a rising concern worldwide, causing increasing mortality in immunocompromised patients. This review describes the use of serial clinical isolates and in-vitro evolution toward understanding the mechanisms of triazole resistance. We outline, compare, and discuss how these approaches have helped identify the evolutionary pathways taken by pathogenic fungi to acquire triazole resistance. While they all share a core mechanism (mutation and overexpression of ERG11/cyp51A and efflux transporters), their timing and mechanism differs: Candida and Cryptococcus spp. exhibit resistance-conferring aneuploidies and copy number variants not seen in A. fumigatus. Candida spp. have a proclivity to develop resistance by undergoing mutations in transcription factors (TAC1, MRR1, PDR5) that increase the expression of efflux transporters. A. fumigatus is especially prone to accumulate resistance mutations in cyp51A early during the evolution of resistance. Recently, examination of serial clinical isolates and experimental lab-evolved triazole-resistant strains using modern omics and gene editing tools has begun to realize the full potential of these approaches. As a result, triazole-resistance mechanisms can now be analyzed at increasingly finer resolutions. This newfound knowledge will be instrumental in formulating new molecular approaches to fight the rapidly emerging epidemic of antifungal resistant fungi.
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Affiliation(s)
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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10
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Brettner L, Ho WC, Schmidlin K, Apodaca S, Eder R, Geiler-Samerotte K. Challenges and potential solutions for studying the genetic and phenotypic architecture of adaptation in microbes. Curr Opin Genet Dev 2022; 75:101951. [PMID: 35797741 DOI: 10.1016/j.gde.2022.101951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
All organisms are defined by the makeup of their DNA. Over billions of years, the structure and information contained in that DNA, often referred to as genetic architecture, have been honed by a multitude of evolutionary processes. Mutations that cause genetic elements to change in a way that results in beneficial phenotypic change are more likely to survive and propagate through the population in a process known as adaptation. Recent work reveals that the genetic targets of adaptation are varied and can change with genetic background. Further, seemingly similar adaptive mutations, even within the same gene, can have diverse and unpredictable effects on phenotype. These challenges represent major obstacles in predicting adaptation and evolution. In this review, we cover these concepts in detail and identify three emerging synergistic solutions: higher-throughput evolution experiments combined with updated genotype-phenotype mapping strategies and physiological models. Our review largely focuses on recent literature in yeast, and the field seems to be on the cusp of a new era with regard to studying the predictability of evolution.
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11
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Sharma D, Denmat SHL, Matzke NJ, Hannan K, Hannan RD, O'Sullivan JM, Ganley ARD. A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations. Genomics 2022; 114:110430. [PMID: 35830947 DOI: 10.1016/j.ygeno.2022.110430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/23/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations.
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Affiliation(s)
- Diksha Sharma
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sylvie Hermann-Le Denmat
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross D Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168, Australia
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand; Maurice Wilkins Center, University of Auckland, New Zealand; MRC Lifecourse Unit, University of Southampton, United Kingdom; Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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12
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Experimental Evolution of Multidrug Resistance in Neurospora crassa under Antifungal Azole Stress. J Fungi (Basel) 2022; 8:jof8020198. [PMID: 35205952 PMCID: PMC8875772 DOI: 10.3390/jof8020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
Multidrug resistance, defined as the resistance to multiple drugs in different categories, has been an increasing serious problem. Limited antifungal drugs and the rapid emergence of antifungal resistance prompt a thorough understanding of how the occurrence of multidrug resistance develops and which mechanisms are involved. In this study, experimental evolution was performed under single-azole-drug stress with the model filamentous fungus Neurospora crassa. By about 30 weeks of continuous growth on agar plates containing ketoconazole or voriconazole with weekly transfer, four evolved multidrug-resistant strains 30thK1, 30thK2, 26thV1, and 24thV2 were obtained. Compared to the ancestral strain, all four strains increased resistance not only to commonly used azoles, including ketoconazole, voriconazole, itraconazole, fluconazole, and triadimefon, but also to antifungal drugs in other categories, including terbinafine (allylamine), amorolfine (morpholine), amphotericin B (polyene), polyoxin B (chitin synthesis inhibitor), and carbendazim (β-tubulin inhibitor). After 8 weeks of growth on agar plates without antifungal drugs with weekly transfer, these evolved strains still displayed multidrug-resistant phenotype, suggesting the multidrug resistance could be stably inherited. Transcriptional measurement of drug target genes and drug transporter genes and deletion analysis of the efflux pump gene cdr4 in the evolved strains suggest that overexpression of cdr4 played a major role in the resistance mechanisms for azoles and terbinafine in the evolved strains, particularly for 30thK2 and 26thV1, and evolved drug-resistant strains had less intracellular ketoconazole accumulation and less disruption of ergosterol accumulations under ketoconazole stress compared to wild type. Mutations specifically present in evolved drug-resistant strains were identified by genome re-sequencing, and drug susceptibility test of knockout mutants for most of mutated genes suggests that mutations in 16 genes, functionally novel in drug resistance, potentially contribute to multidrug resistance in evolved strains.
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13
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Ottilie S, Luth MR, Hellemann E, Goldgof GM, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, Abraham M, Tarsio M, LeBlanc E, Whitesell L, Schenken J, Gunawan F, Patel R, Smith J, Love MS, Williams RM, McNamara CW, Gerwick WH, Ideker T, Suzuki Y, Wirth DF, Lukens AK, Kane PM, Cowen LE, Durrant JD, Winzeler EA. Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol 2022; 5:128. [PMID: 35149760 PMCID: PMC8837787 DOI: 10.1038/s42003-022-03076-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
In vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in Saccharomyces cerevisiae. Sequence analysis identified many genes contributing to the resistance phenotype as well as numerous amino acids in potential targets that may play a role in compound binding. Our work shows that compound-target pairs can be conserved across multiple species. The set of 25 most frequently mutated genes was enriched for transcription factors, and for almost 25 percent of the compounds, resistance was mediated by one of 100 independently derived, gain-of-function SNVs found in a 170 amino acid domain in the two Zn2C6 transcription factors YRR1 and YRM1 (p < 1 × 10−100). This remarkable enrichment for transcription factors as drug resistance genes highlights their important role in the evolution of antifungal xenobiotic resistance and underscores the challenge to develop antifungal treatments that maintain potency. Ottilie et al. employ an experimental evolution approach to investigate the role of transcription factors in yeast chemical resistance. Most emergent mutations in resistant strains were enriched in transcription factor coding genes, highlighting their importance in drug resistance.
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Affiliation(s)
- Sabine Ottilie
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Madeline R Luth
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Erich Hellemann
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Gregory M Goldgof
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Eddy Vigil
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Prianka Kumar
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Andrea L Cheung
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Miranda Song
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Karla P Godinez-Macias
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Krypton Carolino
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Jennifer Yang
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Gisel Lopez
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Matthew Abraham
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
| | - Emmanuelle LeBlanc
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Jake Schenken
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Felicia Gunawan
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Reysha Patel
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Joshua Smith
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA
| | - Melissa S Love
- Calibr, a division of The Scripps Research Institutes, La Jolla, CA, 92037, USA
| | - Roy M Williams
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA.,Aspen Neuroscience, San Diego, CA, 92121, USA
| | - Case W McNamara
- Calibr, a division of The Scripps Research Institutes, La Jolla, CA, 92037, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA, 92037, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yo Suzuki
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Amanda K Lukens
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, NY, 13210, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, Gilman Dr, La Jolla, CA, 92093, USA.
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14
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Ksiezopolska E, Schikora-Tamarit MÀ, Beyer R, Nunez-Rodriguez JC, Schüller C, Gabaldón T. Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata. Curr Biol 2021; 31:5314-5326.e10. [PMID: 34699784 PMCID: PMC8660101 DOI: 10.1016/j.cub.2021.09.084] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/20/2021] [Accepted: 09/29/2021] [Indexed: 01/25/2023]
Abstract
Fungal infections are a growing medical concern, in part due to increased resistance to one or multiple antifungal drugs. However, the evolutionary processes underpinning the acquisition of antifungal drug resistance are poorly understood. Here, we used experimental microevolution to study the adaptation of the yeast pathogen Candida glabrata to fluconazole and anidulafungin, two widely used antifungal drugs with different modes of action. Our results show widespread ability of rapid adaptation to one or both drugs. Resistance, including multidrug resistance, is often acquired at moderate fitness costs and mediated by mutations in a limited set of genes that are recurrently and specifically mutated in strains adapted to each of the drugs. Importantly, we uncover a dual role of ERG3 mutations in resistance to anidulafungin and cross-resistance to fluconazole in a subset of anidulafungin-adapted strains. Our results shed light on the mutational paths leading to resistance and cross-resistance to antifungal drugs.
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Affiliation(s)
- Ewa Ksiezopolska
- Barcelona Supercomputing Centre (BSC-CNS), Life Sciences Department, Jordi Girona 29, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), Mechanisms of Disease Program, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Miquel Àngel Schikora-Tamarit
- Barcelona Supercomputing Centre (BSC-CNS), Life Sciences Department, Jordi Girona 29, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), Mechanisms of Disease Program, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Reinhard Beyer
- Institute of Microbial Genetics and Core Facility Bioactive Substances: Screening and Analysis, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 24, 3430 Tulln an der Donau, Austria
| | - Juan Carlos Nunez-Rodriguez
- Barcelona Supercomputing Centre (BSC-CNS), Life Sciences Department, Jordi Girona 29, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), Mechanisms of Disease Program, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Christoph Schüller
- Institute of Microbial Genetics and Core Facility Bioactive Substances: Screening and Analysis, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 24, 3430 Tulln an der Donau, Austria
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Life Sciences Department, Jordi Girona 29, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), Mechanisms of Disease Program, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain.
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15
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Hu L, Yang X, Yin J, Rong X, Huang X, Yu P, He Z, Liu Y. Combination of AgNPs and Domiphen is Antimicrobial Against Biofilms of Common Pathogens. Int J Nanomedicine 2021; 16:7181-7194. [PMID: 34712048 PMCID: PMC8547768 DOI: 10.2147/ijn.s334133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Purpose The aim was to evaluate the antimicrobial potential of AgNPs synthesized with Artemisia argyi leaf extract and investigate the antimicrobial synergistic effects of AgNPs combined with domiphen and provide an efficient and broad-spectrum combination drug strategy. Methods AgNPs synthesized with Artemisia argyi leaf extract were studied using UV–vis spectroscopy, FTIR spectroscopy and particle size analysis. Then, Artemisia argyi leaf extract-synthesized AgNPs and domiphen were tested against Acinetobacter baumannii (ATCC 19606), Staphylococcus aureus (ATCC 6538), Escherichia coli (8099) and Candida albicans (ATCC 10231), respectively. Then, we explore synergistic antimicrobial effect and synergistic anti-biofilm effect through combined drug susceptibility test and combined drug minimum biofilm eradication concentration (MBEC50) test. Results Characteristic absorption bands of AgNPs were found near 430 nm in the UV–vis spectrum. Particle size analysis results revealed that the average particle size of Artemisia argyi leaf extract-synthesized AgNPs was 77.6 nm. Artemisia argyi leaf extract-synthesized AgNPs showed high antimicrobial activity against the above four strains. Minimum inhibitory concentration (MIC) of Artemisia argyi leaf extract-synthesized AgNPs against strains was 1 μg/mL for Acinetobacter baumannii, 2 μg/mL for Staphylococcus aureus, Escherichia coli and Candida albicans. MBEC50 of Artemisia argyi leaf extract-synthesized AgNPs against strains was 2 μg/mL for Acinetobacter baumannii, 4 μg/mL for Staphylococcus aureus, 1/2 μg/mL for Escherichia coli and 2 μg/mL for Candida albicans. The combination of Artemisia argyi leaf extract-synthesized AgNPs and domiphen has synergistic antimicrobial effect and synergistic anti-biofilm effect. Fractional inhibitory concentration (FIC) was ≤0.5. Conclusion Artemisia argyi leaf extract-synthesized AgNPs had antimicrobial activity against the above four strains. The combination of Artemisia argyi leaf extract-synthesized AgNPs and domiphen has synergistic antimicrobial effects to reduce the dosage of each antimicrobial drugs. Artemisia argyi leaf extract-synthesized AgNPs and domiphen have synergistic anti-biofilm effects.
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Affiliation(s)
- Longhao Hu
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Xi Yang
- School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China.,Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Jing Yin
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Xuan Rong
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Xinlei Huang
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Peiquan Yu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Zhiqiang He
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Yi Liu
- Department of Biophysics, School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China.,School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China.,Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
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16
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Voit T, Cieplik F, Regensburger J, Hiller KA, Gollmer A, Buchalla W, Maisch T. Spatial Distribution of a Porphyrin-Based Photosensitizer Reveals Mechanism of Photodynamic Inactivation of Candida albicans. Front Med (Lausanne) 2021; 8:641244. [PMID: 34350191 PMCID: PMC8326406 DOI: 10.3389/fmed.2021.641244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
The antimicrobial photodynamic therapy (aPDT) is a promising approach for the control of microbial and especially fungal infections such as mucosal mycosis. TMPyP [5,10,15, 20-tetrakis(1-methylpyridinium-4-yl)-porphyrin tetra p-toluenesulfonate] is an effective photosensitizer (PS) that is commonly used in aPDT. The aim of this study was to examine the localization of TMPyP in Candida albicans before and after irradiation with visible light to get information about the cellular mechanism of antifungal action of the photodynamic process using this PS. Immediately after incubation of C. albicans with TMPyP, fluorescence microscopy revealed an accumulation of the PS in the cell envelope. After irradiation with blue light the complete cell showed red fluorescence, which indicates, that aPDT is leading to a damage in the cell wall with following influx of PS into the cytosol. Incubation of C. albicans with Wheat Germ Agglutinin (WGA) could confirm the cell wall as primary binding site of TMPyP. The finding that the porphyrin accumulates in the fungal cell wall and does not enter the interior of the cell before irradiation makes it unlikely that resistances can emerge upon aPDT. The results of this study may help in further development and modification of PS in order to increase efficacy against fungal infections such as those caused by C. albicans.
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Affiliation(s)
- Thomas Voit
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany.,Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany.,Private Practice, Kaufbeuren, Germany
| | - Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | | | - Karl-Anton Hiller
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Anita Gollmer
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Wolfgang Buchalla
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Tim Maisch
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
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17
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Nishimoto AT, Sharma C, Rogers PD. Molecular and genetic basis of azole antifungal resistance in the opportunistic pathogenic fungus Candida albicans. J Antimicrob Chemother 2021; 75:257-270. [PMID: 31603213 DOI: 10.1093/jac/dkz400] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Candida albicans is an opportunistic yeast and the major human fungal pathogen in the USA, as well as in many other regions of the world. Infections with C. albicans can range from superficial mucosal and dermatological infections to life-threatening infections of the bloodstream and vital organs. The azole antifungals remain an important mainstay treatment of candidiasis and therefore the investigation and understanding of the evolution, frequency and mechanisms of azole resistance are vital to improving treatment strategies against this organism. Here the organism C. albicans and the genetic changes and molecular bases underlying the currently known resistance mechanisms to the azole antifungal class are reviewed, including up-regulated expression of efflux pumps, changes in the expression and amino acid composition of the azole target Erg11 and alterations to the organism's typical sterol biosynthesis pathways. Additionally, we update what is known about activating mutations in the zinc cluster transcription factor (ZCF) genes regulating many of these resistance mechanisms and review azole import as a potential contributor to azole resistance. Lastly, investigations of azole tolerance in C. albicans and its implicated clinical significance are reviewed.
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Affiliation(s)
- Andrew T Nishimoto
- Department of Clinical Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Cheshta Sharma
- Department of Clinical Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - P David Rogers
- Department of Clinical Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
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18
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Pezzotti G, Asai T, Adachi T, Ohgitani E, Yamamoto T, Kanamura N, Boschetto F, Zhu W, Zanocco M, Marin E, Bal BS, McEntire BJ, Makimura K, Mazda O, Nishimura I. Antifungal activity of polymethyl methacrylate/Si 3N 4 composites against Candida albicans. Acta Biomater 2021; 126:259-276. [PMID: 33727194 DOI: 10.1016/j.actbio.2021.03.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/16/2022]
Abstract
Previous studies using gram-positive and -negative bacteria demonstrated that hydrolysis of silicon nitride (Si3N4) in aqueous suspensions elutes nitrogen and produces gaseous ammonia while buffering pH. According to immunochemistry assays, fluorescence imaging, and in situ Raman spectroscopy, we demonstrate here that the antipathogenic surface chemistry of Si3N4 can be extended to polymethylmethacrylate (PMMA) by compounding it with a minor fraction (~8 vol.%) of Si3N4 particles without any tangible loss in bulk properties. The hydrolytic products, which were eluted from partly exposed Si3N4 particles at the composite surface, exhibited fungicidal action against Candida albicans. Using a specific nitrative stress sensing dye and highly resolved fluorescence micrographs, we observed in situ congestion of peroxynitrite (ONOO-) radicals in the mitochondria of the Candida cells exposed to the PMMA/Si3N4 composite, while these radicals were absent in the mitochondria of identical cells exposed to monolithic PMMA. These in situ observations suggest that the surface chemistry of Si3N4 mimics the antifungal activity of macrophages, which concurrently produce NO radicals and superoxide anions (O2•-) resulting in the formation of candidacidal ONOO-. The fungicidal properties of PMMA/Si3N4 composites could be used in dental appliances to inhibit the uncontrolled growth of Candida albicans and ensuing candidiasis while being synergic with chemoprophylaxis. STATEMENT OF SIGNIFICANCE: In a follow-up of previous studies of gram-positive and gram-negative bacteria, we demonstrate here that the antipathogenic surface chemistry of Si3N4 could be extended to polymethylmethacrylate (PMMA) containing a minor fraction (~8 vol.%) of Si3N4 particles without tangible loss in bulk properties. Hydrolytic products eluted from Si3N4 particles at the composite surface exhibited fungicidal action against Candida albicans. Highly resolved fluorescence microscopy revealed congestion of peroxynitrite (ONOO-) radicals in the mitochondria of the Candida cells exposed to the PMMA/Si3N4 composite, while radicals were absent in the mitochondria of identical cells exposed to monolithic PMMA. The fungicidal properties of PMMA/Si3N4 composites could be used in dental appliances to inhibit uncontrolled growth of Candida albicans and ensuing candidiasis in synergy with chemoprophylaxis.
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19
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Changes in DMI, SDHI, and QoI Fungicide Sensitivity in the Estonian Zymoseptoria tritici Population between 2019 and 2020. Microorganisms 2021; 9:microorganisms9040814. [PMID: 33921542 PMCID: PMC8070593 DOI: 10.3390/microorganisms9040814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
Zymoseptoria tritici (Zt) populations adapt under the selection pressure of fungicides applied for disease control. The primary objective of this study was to assess fungicide sensitivity in the Estonian Zt population. A total of 282 Zt isolates from 2019 and 2020 were tested for sensitivity to azoles (DMIs; prothioconazole-desthio, epoxiconazole, mefentrifluconazole) and succinate dehydrogenase inhibitors (SDHIs; boscalid, fluxapyroxad). The efficacy of the tested fungicides varied considerably between the Estonian counties, but the Zt population is mainly sensitive to DMIs. Additionally, the frequencies of CYP51 gene alterations varied; D134G, V136C, A379G, and S524T had increased, but V136A and I381V showed a moderate decrease in 2020 in comparison to 2019. Sensitivity to SDHIs was stable, but boscalid was less effective than fluxapyroxad. SdhC gene mutations C-T33N, C-T34N, and C-N86S were common, but not linked with SDHI fungicide sensitivity assay results. Otherwise, mutation B-N225I in the SdhB subunit occurred in isolates with reduced sensitivity to SDHIs. Sensitivity to strobilurins was evaluated by the mutation G143A in the CytB gene, which was present in nearly half of the population. The data presented confirm the ongoing evolution of fungicide sensitivity in the Zt population in Estonia and highlight the importance of knowledge-based decisions for optimizing anti-resistance strategies in the field.
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20
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The Disinfectant Effect of Modified Hydrothermal Nanotitania Extract on Candida albicans. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6617645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Candida albicans is a pathogenic yeast typically associated with diseases such as HIV, AIDS, and other immunocompromised conditions. It is rarely the cause of fatalities and is commonly treated with drugs administered orally or intravenously. In this experiment, Candida albicans was tested with an extract of modified hydrothermal nanotitania to identify whether the material is capable of inhibiting the organism’s growth. The extract was mixed with the Candida albicans in a culture media preparation to determine whether the organisms were able to grow. The test showed that modified hydrothermal nanotitania inhibits the growth of this organism.
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21
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Bermas A, Geddes-McAlister J. Experimental Evolution of Antifungal Resistance in Cryptococcus neoformans. ACTA ACUST UNITED AC 2020; 59:e116. [PMID: 32986290 DOI: 10.1002/cpmc.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cryptococcus neoformans, an opportunistic yeast-like fungal pathogen, has demonstrated resistance to all major classes of antifungals used to treat cryptococcal meningitis. However, combatting this fungal disease is an ongoing challenge among clinicians due to the evolution of antifungal-resistant strains. The limited availability of clinically approved antifungals has heightened the urgency to investigate the molecular mechanisms underscoring resistance. Studying how a fungal pathogen evolves to an antifungal drug in vitro using experimental evolution provides a simple, yet powerful approach to study the mechanisms of antifungal resistance. Experimental evolution involves the serial passaging of microbial populations under laboratory conditions, such that adaptive mutations can occur and be monitored in real time. This technique plays a key role in investigating the mechanisms of antifungal resistance in C. neoformans, and this can help in developing novel strategies to combat the emergence of resistance. Here, we outline how to make overnight cultures of C. neoformans and how to perform experimental evolution, and we present a spectrophotometric analysis to evaluate the evolution of antifungal resistance. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Growth and sample preparation of Cryptococcus neoformans Basic Protocol 2: Experimental evolution of antifungal resistance Basic Protocol 3: Analyzing the evolution of antifungal resistance Basic Protocol 4: Glycerol stock preparation.
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Affiliation(s)
- Arianne Bermas
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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22
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Candida albicans Genetic Background Influences Mean and Heterogeneity of Drug Responses and Genome Stability during Evolution in Fluconazole. mSphere 2020; 5:5/3/e00480-20. [PMID: 32581072 PMCID: PMC7316494 DOI: 10.1128/msphere.00480-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial resistance is an evolutionary phenomenon with clinical implications. We tested how replicates from diverse strains of Candida albicans, a prevalent human fungal pathogen, evolve in the commonly prescribed antifungal drug fluconazole. Replicates on average increased in fitness in the level of drug they were evolved to, with the least fit parental strains improving the most. Very few replicates increased resistance above the drug level they were evolved in. Notably, many replicates increased in genome size and changed in drug tolerance (a drug response where a subpopulation of cells grow slowly in high levels of drug), and variability among replicates in fitness, tolerance, and genome size was higher in strains that initially were more sensitive to the drug. Genetic background influenced the average degree of adaptation and the evolved variability of many phenotypes, highlighting that different strains from the same species may respond and adapt very differently during adaptation. The importance of within-species diversity in determining the evolutionary potential of a population to evolve drug resistance or tolerance is not well understood, including in eukaryotic pathogens. To examine the influence of genetic background, we evolved replicates of 20 different clinical isolates of Candida albicans, a human fungal pathogen, in fluconazole, the commonly used antifungal drug. The isolates hailed from the major C. albicans clades and had different initial levels of drug resistance and tolerance to the drug. The majority of replicates rapidly increased in fitness in the evolutionary environment, with the degree of improvement inversely correlated with parental strain fitness in the drug. Improvement was largely restricted to up to the evolutionary level of drug: only 4% of the evolved replicates increased resistance (MIC) above the evolutionary level of drug. Prevalent changes were altered levels of drug tolerance (slow growth of a subpopulation of cells at drug concentrations above the MIC) and increased diversity of genome size. The prevalence and predominant direction of these changes differed in a strain-specific manner, but neither correlated directly with parental fitness or improvement in fitness. Rather, low parental strain fitness was correlated with high levels of heterogeneity in fitness, tolerance, and genome size among evolved replicates. Thus, parental strain background is an important determinant in mean improvement to the evolutionary environment as well as the diversity of evolved phenotypes, and the range of possible responses of a pathogen to an antimicrobial drug cannot be captured by in-depth study of a single strain background. IMPORTANCE Antimicrobial resistance is an evolutionary phenomenon with clinical implications. We tested how replicates from diverse strains of Candida albicans, a prevalent human fungal pathogen, evolve in the commonly prescribed antifungal drug fluconazole. Replicates on average increased in fitness in the level of drug they were evolved to, with the least fit parental strains improving the most. Very few replicates increased resistance above the drug level they were evolved in. Notably, many replicates increased in genome size and changed in drug tolerance (a drug response where a subpopulation of cells grow slowly in high levels of drug), and variability among replicates in fitness, tolerance, and genome size was higher in strains that initially were more sensitive to the drug. Genetic background influenced the average degree of adaptation and the evolved variability of many phenotypes, highlighting that different strains from the same species may respond and adapt very differently during adaptation.
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23
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New diphenylphosphane derivatives of ketoconazole are promising antifungal agents. Sci Rep 2019; 9:16214. [PMID: 31700024 PMCID: PMC6838151 DOI: 10.1038/s41598-019-52525-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
Four new derivatives of ketoconazole (Ke) were synthesized: diphenylphosphane (KeP), and phosphane chalcogenides: oxide (KeOP), sulphide (KeSP) and selenide (KeSeP). These compounds proved to be promising antifungal compounds towards Saccharomyces cerevisiae and Candida albicans, especially in synergy with fluconazole. Simulations of docking to the cytochrome P450 14α-demethylase (azoles’ primary molecular target) proved that the new Ke derivatives are capable of inhibiting this enzyme by binding to the active site. Cytotoxicity towards hACSs (human adipose-derived stromal cells) of the individual compounds was studied and the IC50 values were higher than the MIC50 for C. albicans and S. cerevisiae. KeP and KeOP increased the level of the p21 gene transcript but did not change the level of p53 gene transcript, a major regulator of apoptosis, and decreased the mitochondrial membrane potential. Taken together, the results advocate that the new ketoconazole derivatives have a similar mechanism of action and block the lanosterol 14α-demethylase and thus inhibit the production of ergosterol in C. albicans membranes.
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24
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James TY, Michelotti LA, Glasco AD, Clemons RA, Powers RA, James ES, Simmons DR, Bai F, Ge S. Adaptation by Loss of Heterozygosity in Saccharomyces cerevisiae Clones Under Divergent Selection. Genetics 2019; 213:665-683. [PMID: 31371407 PMCID: PMC6781901 DOI: 10.1534/genetics.119.302411] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/29/2019] [Indexed: 01/14/2023] Open
Abstract
Loss of heterozygosity (LOH) is observed during vegetative growth and reproduction of diploid genotypes through mitotic crossovers, aneuploidy caused by nondisjunction, and gene conversion. We aimed to test the role that LOH plays during adaptation of two highly heterozygous Saccharomyces cerevisiae genotypes to multiple environments over a short time span in the laboratory. We hypothesized that adaptation would be observed through parallel LOH events across replicate populations. Using genome resequencing of 70 clones, we found that LOH was widespread with 5.2 LOH events per clone after ∼500 generations. The most common mode of LOH was gene conversion (51%) followed by crossing over consistent with either break-induced replication or double Holliday junction resolution. There was no evidence that LOH involved nondisjunction of whole chromosomes. We observed parallel LOH in both an environment-specific and environment-independent manner. LOH largely involved recombining existing variation between the parental genotypes, but also was observed after de novo, presumably beneficial, mutations occurred in the presence of canavanine, a toxic analog of arginine. One highly parallel LOH event involved the ENA salt efflux pump locus on chromosome IV, which showed repeated LOH to the allele from the European parent, an allele originally derived by introgression from S. paradoxus Using CRISPR-engineered LOH we showed that the fitness advantage provided by this single LOH event was 27%. Overall, we found extensive evidence that LOH could be adaptive and is likely to be a greater source of initial variation than de novo mutation for rapid evolution of diploid genotypes.
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Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Alexander D Glasco
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Rebecca A Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Robert A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ellen S James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Fengyan Bai
- Institute of Microbiology, Chinese Academy of Sciences, State Key Laboratory of Mycology, Chaoyang District, Beijing 100101, China
| | - Shuhua Ge
- Technology Development and Transfer Center, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100029, China
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25
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Pais P, Galocha M, Viana R, Cavalheiro M, Pereira D, Teixeira MC. Microevolution of the pathogenic yeasts Candida albicans and Candida glabrata during antifungal therapy and host infection. MICROBIAL CELL 2019; 6:142-159. [PMID: 30854392 PMCID: PMC6402363 DOI: 10.15698/mic2019.03.670] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Infections by the pathogenic yeasts Candida albicans and Candida glabrata are among the most common fungal diseases. The success of these species as human pathogens is contingent on their ability to resist antifungal therapy and thrive within the human host. C. glabrata is especially resilient to azole antifungal treatment, while C. albicans is best known for its wide array of virulence features. The core mechanisms that underlie antifungal resistance and virulence in these pathogens has been continuously addressed, but the investigation on how such mechanisms evolve according to each environment is scarcer. This review aims to explore current knowledge on micro-evolution experiments to several treatment and host-associated conditions in C. albicans and C. glabrata. The analysis of adaptation strategies that evolve over time will allow to better understand the mechanisms by which Candida species are able to achieve stable phenotypes in real-life scenarios, which are the ones that should constitute the most interesting drug targets.
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Affiliation(s)
- Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Mónica Galocha
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Romeu Viana
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Mafalda Cavalheiro
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Diana Pereira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Miguel Cacho Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
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Muthamil S, Balasubramaniam B, Balamurugan K, Pandian SK. Synergistic Effect of Quinic Acid Derived From Syzygium cumini and Undecanoic Acid Against Candida spp. Biofilm and Virulence. Front Microbiol 2018; 9:2835. [PMID: 30534118 PMCID: PMC6275436 DOI: 10.3389/fmicb.2018.02835] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/05/2018] [Indexed: 12/14/2022] Open
Abstract
In recent decades, fungal infections have incredibly increased with Candida genus as the major cause of morbidity and mortality in hospitalized and immunocompromised patients. Most of the Candida species are proficient in biofilm formation on implanted medical devices as well as human tissues. Biofilm related Candida infections are very difficult to treat using common antifungal agents owing to their increased drug resistance. To address these issues, the present study investigated the antibiofilm and antivirulent properties of Syzygium cumini derived quinic acid in combination with known antifungal compound undecanoic acid. Initially, antibiofilm potential of S. cumini leaf extract was assessed and the active principles were identified through gas chromatography and mass spectrometry analysis. Among the compounds identified, quinic acid was one of the major compounds. The interaction between quinic acid and undecanoic acid was found to be synergistic in the Fractional inhibitory concentration index (≤0.5). Results of in vitro assays and gene expression analysis suggested that the synergistic combinations of quinic acid and undecanoic acid significantly inhibited virulence traits of Candida spp. such as the biofilm formation, yeast-to-hyphal transition, extracellular polymeric substances production, filamentation, secreted hydrolases production and ergosterol biosynthesis. In addition, result of in vivo studies using Caenorhabditis elegans demonstrated the non-toxic nature of QA-UDA combination and antivirulence effect against Candida spp. For the first time, synergistic antivirulence ability of quinic acid and undecanoic acid was explored against Candida spp. Thus, results obtained from the present study suggest that combination of phytochemicals might be used an alternate therapeutic strategy for the prevention and treatment of biofilm associated Candida infection.
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Ksiezopolska E, Gabaldón T. Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens. Genes (Basel) 2018; 9:genes9090461. [PMID: 30235884 PMCID: PMC6162425 DOI: 10.3390/genes9090461] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023] Open
Abstract
Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible populations, such as immunocompromised patients or the elderly. Existing treatment options are limited to few antifungal drug families with efficacies that vary depending on the infecting species. In this context, the emergence and spread of resistant Candida isolates are being increasingly reported. Understanding how resistance can evolve within naturally susceptible species is key to developing novel, more effective treatment strategies. However, in contrast to the situation of antibiotic resistance in bacteria, few studies have focused on the evolutionary mechanisms leading to drug resistance in fungal species. In this review, we will survey and discuss current knowledge on the genetic bases of resistance to antifungal drugs in Candida opportunistic pathogens. We will do so from an evolutionary genomics perspective, focusing on the possible evolutionary paths that may lead to the emergence and selection of the resistant phenotype. Finally, we will discuss the potential of future studies enabled by current developments in sequencing technologies, in vitro evolution approaches, and the analysis of serial clinical isolates.
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Affiliation(s)
- Ewa Ksiezopolska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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Abstract
The fungal pathogens Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus have transitioned from a rare curiosity to a leading cause of human mortality. The management of infections caused by these organisms is intimately dependent on the efficacy of antifungal agents; however, fungi that are resistant to these treatments are regularly isolated in the clinic, impeding our ability to control infections. Given the significant impact fungal pathogens have on human health, it is imperative to understand the molecular mechanisms that govern antifungal drug resistance. This review describes our current knowledge of the mechanisms by which antifungal drug resistance evolves in experimental populations and clinical settings. We explore current antifungal treatment options and discuss promising strategies to impede the evolution of drug resistance. By tackling antifungal drug resistance as an evolutionary problem, there is potential to improve the utility of current treatments and accelerate the development of novel therapeutic strategies.
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Affiliation(s)
- Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Tavia Caplan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
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Novel Zinc-Attenuating Compounds as Potent Broad-Spectrum Antifungal Agents with In Vitro and In Vivo Efficacy. Antimicrob Agents Chemother 2018; 62:AAC.02024-17. [PMID: 29439980 PMCID: PMC5923171 DOI: 10.1128/aac.02024-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/04/2018] [Indexed: 12/23/2022] Open
Abstract
An increase in the incidence of rare but hard-to-treat invasive fungal pathogens as well as resistance to the currently available antifungal drugs calls for new broad-spectrum antifungals with a novel mechanism of action. Here we report the identification and characterization of two novel zinc-attenuating compounds, ZAC307 and ZAC989, which exhibit broad-spectrum in vitro antifungal activity and in vivo efficacy in a fungal kidney burden candidiasis model. The compounds were identified serendipitously as part of a drug discovery process aimed at finding novel inhibitors of the fungal plasma membrane proton ATPase Pma1. Based on their structure, we hypothesized that they might act as zinc chelators. Indeed, both fluorescence-based affinity determination and potentiometric assays revealed these compounds, subsequently termed zinc-attenuating compounds (ZACs), to have strong affinity for zinc, and their growth inhibitory effects on Candida albicans and Aspergillus fumigatus could be inactivated by the addition of exogenous zinc to fungal growth media. We determined the ZACs to be fungistatic, with a low propensity for resistance development. Gene expression analysis suggested that the ZACs interfere negatively with the expression of genes encoding the major components of the A. fumigatus zinc uptake system, thus supporting perturbance of zinc homeostasis as the likely mode of action. With demonstrated in vitro and in vivo antifungal activity, low propensity for resistance development, and a novel mode of action, the ZACs represent a promising new class of antifungal compounds, and their advancement in a drug development program is therefore warranted.
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Genome dynamics and evolution in yeasts: A long-term yeast-bacteria competition experiment. PLoS One 2018; 13:e0194911. [PMID: 29624585 PMCID: PMC5889060 DOI: 10.1371/journal.pone.0194911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/13/2018] [Indexed: 11/29/2022] Open
Abstract
There is an enormous genetic diversity evident in modern yeasts, but our understanding of the ecological basis of such diversifications in nature remains at best fragmented so far. Here we report a long-term experiment mimicking a primordial competitive environment, in which yeast and bacteria co-exist and compete against each other. Eighteen yeasts covering a wide phylogenetic background spanning approximately 250 million years of evolutionary history were used to establish independent evolution lines for at most 130 passages. Our collection of hundreds of modified strains generated through such a rare two-species cross-kingdom competition experiment re-created the appearance of large-scale genomic rearrangements and altered phenotypes important in the diversification history of yeasts. At the same time, the methodology employed in this evolutionary study would also be a non-gene-technological method of reprogramming yeast genomes and then selecting yeast strains with desired traits. Cross-kingdom competition may therefore be a method of significant value to generate industrially useful yeast strains with new metabolic traits.
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Chang M, Sionov E, Khanal Lamichhane A, Kwon-Chung KJ, Chang YC. Roles of Three Cryptococcus neoformans and Cryptococcus gattii Efflux Pump-Coding Genes in Response to Drug Treatment. Antimicrob Agents Chemother 2018; 62:e01751-17. [PMID: 29378705 PMCID: PMC5913978 DOI: 10.1128/aac.01751-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/22/2018] [Indexed: 12/14/2022] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii species complexes are the etiologic agents of cryptococcosis. We have deciphered the roles of three ABC transporters, Afr1, Afr2, and Mdr1, in the representative strains of the two species, C. neoformans H99 and C. gattii R265. Deletion of AFR1 in H99 and R265 drastically reduced the levels of resistance to three xenobiotics and three triazoles, suggesting that Afr1 is the major drug efflux pump in both strains. Fluconazole susceptibility was not affected when AFR2 or MDR1 was deleted in both strains. However, when these genes were deleted in combination with AFR1, a minor additive effect in susceptibility toward several drugs was observed. Deletion of all three genes in both strains caused further increases in susceptibility toward fluconazole and itraconazole, suggesting that Afr2 and Mdr1 augment Afr1 function in pumping these triazoles. Intracellular accumulation of Nile Red significantly increased in afr1Δ mutants of both strains, but rhodamine 6G accumulation increased only in the mdr1Δ mutant of H99. Thus, the three efflux pumps play different roles in the two strains when exposed to different azoles and xenobiotics. AFR1 and AFR2 expression was upregulated in H99 and R265 when treated with fluconazole. However, MDR1 expression was upregulated only in R265 under the same conditions. We screened a library of transcription factor mutants and identified several mutants that manifested either altered fluconazole sensitivity or an increase in the frequency of fluconazole heteroresistance. Gene expression analysis suggests that the three efflux pumps are regulated independently by different transcription factors in response to fluconazole exposure.
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Affiliation(s)
- Miwha Chang
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward Sionov
- Department of Food Quality and Safety, Institute for Postharvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Ami Khanal Lamichhane
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyung J Kwon-Chung
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yun C Chang
- Molecular Microbiology Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Shen T, Huang S. Repositioning the Old Fungicide Ciclopirox for New Medical Uses. Curr Pharm Des 2018; 22:4443-50. [PMID: 27238364 DOI: 10.2174/1381612822666160530151209] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/27/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Ciclopirox (CPX) has been used as an antifungal agent in various formulations to treat superficial fungal infection for decades. Its effectiveness and safety in treatments have been demonstrated by multiple studies. METHODS Here we briefly summarize the pharmacological and toxicological properties of CPX as an antifungal agent, the new medical uses of CPX, as well as the correspondent molecular mechanisms. RESULTS Increasing evidence has demonstrated that CPX is able to inhibit tumor growth, ameliorate diabetes and its complications, prevent human immunodeficiency virus (HIV) infection, and improve age-associated cardiovascular defects. Interestingly, its antifungal activity and all those newly observed effects are more or less related to its capability of chelating iron and interfering with the related signaling pathways. Mechanistically, CPX is capable of modulating the activities of certain enzymes or signaling pathways, such as ribonucleotide reductase (RR), deoxyhypusine hydroxylase (DOHH)/eukaryotic translation initiation factor 5A (eIF5A), Wnt/β-catenin, hypoxia-inducible factor-1α (HIF-1 α)/vascular endothelial growth factor (VEGF), vascular endothelial growth factor receptor 3 (VEGFR-3)/extracellular signal-regulated protein kinases 1/2, mammalian target of rapamycin, and cyclin dependent kinases (CDKs). Most of these activities are related to its chelation of iron. CONCLUSION CPX, as an antifungal agent, may be repositioned for treatment of cancer and other human diseases.
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Affiliation(s)
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA
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Zhang F, Gao J, Wang B, Huo D, Wang Z, Zhang J, Shao Y. Whole-genome sequencing reveals the mechanisms for evolution of streptomycin resistance in Lactobacillus plantarum. J Dairy Sci 2018; 101:2867-2874. [PMID: 29397163 DOI: 10.3168/jds.2017-13323] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/13/2017] [Indexed: 11/19/2022]
Abstract
In this research, we investigated the evolution of streptomycin resistance in Lactobacillus plantarum ATCC14917, which was passaged in medium containing a gradually increasing concentration of streptomycin. After 25 d, the minimum inhibitory concentration (MIC) of L. plantarum ATCC14917 had reached 131,072 µg/mL, which was 8,192-fold higher than the MIC of the original parent isolate. The highly resistant L. plantarum ATCC14917 isolate was then passaged in antibiotic-free medium to determine the stability of resistance. The MIC value of the L. plantarum ATCC14917 isolate decreased to 2,048 µg/mL after 35 d but remained constant thereafter, indicating that resistance was irreversible even in the absence of selection pressure. Whole-genome sequencing of parent isolates, control isolates, and isolates following passage was used to study the resistance mechanism of L. plantarum ATCC14917 to streptomycin and adaptation in the presence and absence of selection pressure. Five mutated genes (single nucleotide polymorphisms and structural variants) were verified in highly resistant L. plantarum ATCC14917 isolates, which were related to ribosomal protein S12, LPXTG-motif cell wall anchor domain protein, LrgA family protein, Ser/Thr phosphatase family protein, and a hypothetical protein that may correlate with resistance to streptomycin. After passage in streptomycin-free medium, only the mutant gene encoding ribosomal protein S12 remained; the other 4 mutant genes had reverted to the wild type as found in the parent isolate. Although the MIC value of L. plantarum ATCC14917 was reduced in the absence of selection pressure, it remained 128-fold higher than the MIC value of the parent isolate, indicating that ribosomal protein S12 may play an important role in streptomycin resistance. Using the mobile elements database, we demonstrated that streptomycin resistance-related genes in L. plantarum ATCC14917 were not located on mobile elements. This research offers a way of combining laboratory evolution techniques and whole-genome sequencing for evaluating antibiotic resistance in probiotics.
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Affiliation(s)
- Fuxin Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Jiayuan Gao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Bini Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Dongxue Huo
- College of Food Science and Technology, Hainan University, Haikou 570228, Hainan, P. R. China
| | - Zhaoxia Wang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, P. R. China
| | - Jiachao Zhang
- College of Food Science and Technology, Hainan University, Haikou 570228, Hainan, P. R. China.
| | - Yuyu Shao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China.
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Targeting Candida spp. to develop antifungal agents. Drug Discov Today 2018; 23:802-814. [PMID: 29353694 DOI: 10.1016/j.drudis.2018.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/09/2017] [Accepted: 01/04/2018] [Indexed: 01/15/2023]
Abstract
Invasive fungal infections are a complex challenge throughout the world because of their high incidence, mainly in critically ill patients, and high mortality rates. The antifungal agents currently available are limited; thus, there is a need for the rapid development of new drugs. In silico methods are a modern strategy to explore interactions between new compounds and specific fungal targets, but they depend on precise genetic information. Here, we discuss the main Candida spp. target genes, including information about null mutants, virulence, cytolocalization, co-regulatory genes, and compounds that are related to protein expression. These data will provide a basis for the future in silico development of antifungal drugs.
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Wertheimer NB, Stone N, Berman J. Ploidy dynamics and evolvability in fungi. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0461. [PMID: 28080987 PMCID: PMC5095540 DOI: 10.1098/rstb.2015.0461] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 12/12/2022] Open
Abstract
Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Noa Blutraich Wertheimer
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
| | - Neil Stone
- Institute of Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
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Hollomon D. Does agricultural use of azole fungicides contribute to resistance in the human pathogen Aspergillus fumigatus? PEST MANAGEMENT SCIENCE 2017; 73:1987-1993. [PMID: 28485100 DOI: 10.1002/ps.4607] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/02/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Azole resistance in human fungal pathogens has increased over the past twenty years, especially in immunocompromised patients. Similarities between medical and agricultural azoles, and extensive azole (14α-demethylase inhibitor, DMI) use in crop protection, prompted speculation that resistance in patients with aspergillosis originated in the environment. Aspergillus species, and especially Aspergillus fumigatus, are the largest cause of patient deaths from fungi. Azole levels in soils following crop spraying, and differences in sensitivity between medical and agricultural azoles (DMIs), indicate weaker selection in cropping systems than in patients receiving azole therapy. Most fungi have just one CYP51 paralogue (isozyme CYP51B), but in Aspergillus sp. mutations conferring azole resistance are largely confined to a second paralogue, CYP51A. Binding within the active centre is similar for medical and agricultural azoles but differences elsewhere between the two paralogues may ensure selection depends on the DMI used on crops. Two imidazoles, imazalil and prochloraz, have been widely used since the early 1970s, yet unlike triazoles they have not been linked to resistance in patients. Evidence that DMIs are the origin, or increase the frequency, of azole resistance in human fungal pathogens is lacking. Limiting DMI use would have serious impacts on disease control in many crops, and remove key tools in anti-resistance strategies. © 2017 Society of Chemical Industry.
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Gutiérrez-Alonso O, Hawkins NJ, Cools HJ, Shaw MW, Fraaije BA. Dose-dependent selection drives lineage replacement during the experimental evolution of SDHI fungicide resistance in Zymoseptoria tritici. Evol Appl 2017; 10:1055-1066. [PMID: 29151860 PMCID: PMC5680630 DOI: 10.1111/eva.12511] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/16/2017] [Indexed: 01/22/2023] Open
Abstract
Fungicide resistance is a constant threat to agricultural production worldwide. Molecular mechanisms of fungicide resistance have been studied extensively in the wheat pathogen Zymoseptoria tritici. However, less is known about the evolutionary processes driving resistance development. In vitro evolutionary studies give the opportunity to investigate this. Here, we examine the adaptation of Z. tritici to fluxapyroxad, a succinate dehydrogenase (Sdh) inhibitor. Replicate populations of Z. tritici derived from the sensitive isolate IPO323 were exposed to increasing concentrations of fluxapyroxad with or without UV mutagenesis. After ten increases in fungicide concentration, sensitivity had decreased dramatically, with replicate populations showing similar phenotypic trajectories. Sequencing the Sdh subunit B, C, and D encoding genes identified seven mutations associated with resistance to fluxapyroxad. Mutation frequency over time was measured with a pyrosequencing assay, revealing sequential lineage replacement in the UV‐mutagenized populations but not in the untreated populations. Repeating selection from set time‐points with different fungicide concentrations revealed that haplotype replacement of Sdh variants was driven by dose‐dependent selection as fungicide concentration changed, and was not mutation‐limited. These findings suggest that fungicide field applications may select for highly insensitive Sdh variants with higher resistance factors if the fungicide concentration is increased to achieve a better disease control. However, in the absence or presence of lower fungicide concentrations, the spread of these strains might be restricted if the underlying Sdh mutations carry fitness penalties.
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Affiliation(s)
- Omar Gutiérrez-Alonso
- Biointeractions and Crop Protection Department Rothamsted Research Harpenden Hertfordshir UK
| | - Nichola J Hawkins
- Biointeractions and Crop Protection Department Rothamsted Research Harpenden Hertfordshir UK
| | - Hans J Cools
- Jealott's Hill International Research Centre Syngenta Bracknell Berkshire UK
| | - Michael W Shaw
- School of Agriculture Policy and Development University of Reading Reading Berkshire UK
| | - Bart A Fraaije
- Biointeractions and Crop Protection Department Rothamsted Research Harpenden Hertfordshir UK
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Lo HJ, Tsai SH, Chu WL, Chen YZ, Zhou ZL, Chen HF, Lee CF, Yang YL. Fruits as the vehicle of drug resistant pathogenic yeasts. J Infect 2017. [PMID: 28648496 DOI: 10.1016/j.jinf.2017.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE We investigated the diversity and drug susceptibility of pathogenic yeasts on fruit surfaces. METHOD Fruits were purchased from supermarkets and washed with buffer. The pellets were re-suspended in medium after centrifugation. The cell suspensions were plated onto CHROMagar Candida medium. Yeasts were identified by ribosomal DNA sequencing and their drug susceptibilities were determined by broth microdilution assay. RESULTS Of 184 isolates, comprised of 55 species, from 22 different types of fruits, 29 species, including Candida famata, Candida fermentati, Candida guilliermondii, Candida intermedia, Candida krusei, Candida orthopsilosis, Candida parapsilosis, Candida pelliculosa, Candida tropicalis, and others have been reported to cause diseases in humans. In addition to C. krusei, intrinsically resistant to fluconazole, all Rhodotorula and Rhodosporidium species were resistant to fluconazole. One each of C. tropicalis isolate was belonged to diploid sequence type (DST)149 and DST225, genotypes also detected in isolates from humans. Furthermore, the DST225 isolate was less susceptible to azole drugs. The susceptibilities to azole drugs for clinical and agricultural usage were associated to each other. CONCLUSION It is important to be aware of the existence of pathogenic yeasts, especially drug-resistant ones, on the fruit surfaces, a potential route for pathogenic yeasts to be transmitted to humans.
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Affiliation(s)
- Hsiu-Jung Lo
- Taiwan Mycology Reference Center, National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan; School of Dentistry, China Medical University, Taichung, Taiwan
| | - Sheng-Hua Tsai
- Taiwan Mycology Reference Center, National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen-Li Chu
- Taiwan Mycology Reference Center, National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Yin-Zhi Chen
- Taiwan Mycology Reference Center, National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Zi-Li Zhou
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Hong-Fu Chen
- Department of Applied Science, Nanda Campus, National Tsing Hua University, Hsinchu, Taiwan
| | - Ching-Fu Lee
- Department of Applied Science, Nanda Campus, National Tsing Hua University, Hsinchu, Taiwan
| | - Yun-Liang Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan.
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Horn BW, Dorner JW. Effect of competition and adverse culture conditions on aflatoxin production byAspergillus flavusthrough successive generations. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Joe W. Dorner
- National Peanut Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Dawson, Georgia 31742
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Berman J, Forche A. Haplotyping a Non-meiotic Diploid Fungal Pathogen Using Induced Aneuploidies and SNP/CGH Microarray Analysis. Methods Mol Biol 2017; 1551:131-146. [PMID: 28138844 PMCID: PMC5482211 DOI: 10.1007/978-1-4939-6750-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The generation of haplotype information has recently become very attractive due to its utility for identifying mutations associated with human disease and for the development of personalized medicine. Haplotype information also is crucial for studying recombination mechanisms and genetic diversity, and for analyzing allele-specific gene expression. Classic haplotyping methods require the analysis of hundreds of meiotic progeny. To facilitate haplotyping in the non-meiotic human fungal pathogen Candida albicans, we exploited trisomic heterozygous chromosomes generated via the UAU1 selection strategy. Using this system, we obtained phasing information from allelic biases, detected by SNP/CGH microarray analysis. This strategy has the potential to be applicable to other diploid, asexual Candida species that are important causes of human disease.
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Affiliation(s)
- Judith Berman
- Department of Molecular Microbiology & Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, ME, USA.
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Ayine-Tora DM, Kingsford-Adaboh R, Asomaning WA, Harrison JJEK, Mills-Robertson FC, Bukari Y, Sakyi PO, Kaminta S, Reynisson J. Coumarin Antifungal Lead Compounds from Millettia thonningii and Their Predicted Mechanism of Action. Molecules 2016; 21:molecules21101369. [PMID: 27754464 PMCID: PMC6274499 DOI: 10.3390/molecules21101369] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 11/22/2022] Open
Abstract
Fungal pathogens continue to pose challenges to humans and plants despite efforts to control them. Two coumarins, robustic acid and thonningine-C isolated from Millettia thonningii, show promising activity against the fungus Candida albicans with minimum fungicidal concentration of 1.0 and 0.5 mg/mL, respectively. Molecular modelling against the putative bio-molecular target, lanosterol 14α-demethylase (CYP51), revealed a plausible binding mode for the active compounds, in which the hydroxyl group binds with a methionine backbone carboxylic group blocking access to the iron catalytic site. This binding disrupts the synthesis of several important sterols for the survival of fungi.
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Affiliation(s)
- Daniel M Ayine-Tora
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, 1142 Auckland, New Zealand.
- Department of Chemistry, University of Ghana, LG 56, Legon-Accra, Ghana.
| | | | | | | | - Felix C Mills-Robertson
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Yahaya Bukari
- Botany Department, University of Ghana, LG 55, Legon-Accra, Ghana.
| | - Patrick O Sakyi
- Department of Chemistry, University of Ghana, LG 56, Legon-Accra, Ghana.
| | | | - Jóhannes Reynisson
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, 1142 Auckland, New Zealand.
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42
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Fisher KJ, Lang GI. Experimental evolution in fungi: An untapped resource. Fungal Genet Biol 2016; 94:88-94. [PMID: 27375178 DOI: 10.1016/j.fgb.2016.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 10/21/2022]
Abstract
Historically, evolutionary biology has been considered an observational science. Examining populations and inferring evolutionary histories mold evolutionary theories. In contrast, laboratory evolution experiments make use of the amenability of traditional model organisms to study fundamental processes underlying evolution in real time in simple, but well-controlled, environments. With advances in high-throughput biology and next generation sequencing, it is now possible to propagate hundreds of parallel populations over thousands of generations and to quantify precisely the frequencies of various mutations over time. Experimental evolution combines the ability to simultaneously monitor replicate populations with the power to vary individual parameters to test specific evolutionary hypotheses, something that is impractical or infeasible in natural populations. Many labs are now conducting laboratory evolution experiments in nearly all model systems including viruses, bacteria, yeast, nematodes, and fruit flies. Among these systems, fungi occupy a unique niche: with a short generation time, small compact genomes, and sexual cycles, fungi are a particularly valuable and largely untapped resource for propelling future growth in the field of experimental evolution. Here, we describe the current state of fungal experimental evolution and why fungi are uniquely positioned to answer many of the outstanding questions in the field. We also review which fungal species are most well suited for experimental evolution.
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Affiliation(s)
- Kaitlin J Fisher
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
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Gerstein AC, Rosenberg A, Hecht I, Berman J. diskImageR: quantification of resistance and tolerance to antimicrobial drugs using disk diffusion assays. MICROBIOLOGY-SGM 2016; 162:1059-1068. [PMID: 27126388 DOI: 10.1099/mic.0.000295] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microbial pathogens represent an increasing threat to human health. Although many infections can be successfully treated and cleared, drug resistance is a widespread problem. The existence of subpopulations of 'tolerant' cells (where a fraction of the population is able to grow above the population resistance level) may increase the rate of treatment failure; yet, existing methods to measure subpopulation effects are cumbersome. Here we describe diskImageR, a computational pipeline that analyses photographs of disk diffusion assays to determine the degree of drug susceptibility [the radius of inhibition, (RAD)], and two aspects of subpopulation growth [the fraction of growth (FoG) within the zone of inhibition, (ZOI), and the rate of change in growth from no drug to inhibitory drug concentrations, (SLOPE)]. diskImageR was used to examine the response of the human fungal pathogen Candida albicans to the antifungal drug fluconazole across different strain backgrounds and growth conditions. Disk diffusion assays performed under Clinical and Laboratory Standards Institute (CLSI) conditions led to more susceptibility and less tolerance than assays performed using rich medium conditions. We also used diskImageR to quantify the effects of three drugs in combination with fluconazole, finding that all three combinations affected tolerance, with the effect of one drug (doxycycline) being very strain dependent. The three drugs had different effects on susceptibility, with doxycycline generally having no effect, chloroquine generally increasing susceptibility and pyrvinium pamoate generally reducing susceptibility. The ability to simultaneously quantitate different aspects of microbial drug responses will facilitate the study of mechanisms of subpopulation responses in the presence of antimicrobial drugs.
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Affiliation(s)
- Aleeza C Gerstein
- Department of Microbiology & Immunology, Medical School, University of Minnesota, MN, USA.,Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, MN, USA.,Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Alexander Rosenberg
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Inbal Hecht
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Judith Berman
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, MN, USA.,Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Department of Microbiology & Immunology, Medical School, University of Minnesota, MN, USA
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Rossi SA, Trevijano-Contador N, Scorzoni L, Mesa-Arango AC, de Oliveira HC, Werther K, de Freitas Raso T, Mendes-Giannini MJS, Zaragoza O, Fusco-Almeida AM. Impact of Resistance to Fluconazole on Virulence and Morphological Aspects of Cryptococcus neoformans and Cryptococcus gattii Isolates. Front Microbiol 2016; 7:153. [PMID: 26909069 PMCID: PMC4754443 DOI: 10.3389/fmicb.2016.00153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 01/12/2023] Open
Abstract
Cryptococcus sp. are responsible for around 1 million cases of meningitis every year. Fluconazole (FLU) is commonly used in the treatment of cryptococcosis, mainly in immunocompromised patients and the resistance is usually reported after long periods of treatment. In this study, the morphological characterization and virulence profile of FLU-susceptible and FLU-resistant clinical and environmental isolates of C. neoformans and C. gattii were performed both in vitro and in vivo using the Galleria mellonella model. FLU-susceptible isolates from C. neoformans were significantly more virulent than the FLU-resistant isolates. FLU-susceptible C. gattii isolates showed a different virulence profile from C. neoformans isolates where only the environmental isolate, CL, was more virulent compared with the resistant isolates. Cell morphology and capsule size were analyzed and the FLU-resistant isolates did not change significantly compared with the most sensitive isolates. Growth at 37°C was also evaluated and in both species, the resistant isolates showed a reduced growth at this temperature, indicating that FLU resistance can affect their growth. Based on the results obtained is possible suggest that FLU resistance can influence the morphology of the isolates and consequently changed the virulence profiles. The most evident results were observed for C. neoformans showing that the adaptation of isolates to antifungal selective pressure influenced the loss of virulence.
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Affiliation(s)
- Suélen A Rossi
- Faculdade de Ciências Farmacêuticas, UNESP - Universidade Estadual Paulista, Campus Araraquara, Departamento de Análises Clíncas São Paulo, Brazil
| | - Nuria Trevijano-Contador
- Centro Nacional de Microbiologia, Unidad de Micologia, Instituto de Salud Carlos III, Majadahonda Madrid, Spain
| | - Liliana Scorzoni
- Faculdade de Ciências Farmacêuticas, UNESP - Universidade Estadual Paulista, Campus Araraquara, Departamento de Análises Clíncas São Paulo, Brazil
| | | | - Haroldo C de Oliveira
- Faculdade de Ciências Farmacêuticas, UNESP - Universidade Estadual Paulista, Campus Araraquara, Departamento de Análises Clíncas São Paulo, Brazil
| | - Karin Werther
- Faculdade de Medicina Veterinária e Zootecnia, USP - Universidade de São Paulo, Departamento de Patologia São Paulo, Brazil
| | - Tânia de Freitas Raso
- Faculdade de Medicina Veterinária e Zootecnia, USP - Universidade de São Paulo, Departamento de Patologia São Paulo, Brazil
| | - Maria J S Mendes-Giannini
- Faculdade de Ciências Farmacêuticas, UNESP - Universidade Estadual Paulista, Campus Araraquara, Departamento de Análises Clíncas São Paulo, Brazil
| | - Oscar Zaragoza
- Centro Nacional de Microbiologia, Unidad de Micologia, Instituto de Salud Carlos III, Majadahonda Madrid, Spain
| | - Ana M Fusco-Almeida
- Faculdade de Ciências Farmacêuticas, UNESP - Universidade Estadual Paulista, Campus Araraquara, Departamento de Análises Clíncas São Paulo, Brazil
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Ou TY, Chang FM, Cheng WN, Lara A, Chou ML, Lee WF, Lee KC, Lin CT, Lee WS, Yu FL, Su CH. Fluconazole induces rapid high-frequency MTL homozygosis with microbiological polymorphism in Candida albicans. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2016; 50:899-904. [PMID: 26928371 DOI: 10.1016/j.jmii.2015.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/15/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Candida albicans, a common fungal pathogen that can cause opportunistic infections, is regarded as an apparently asexual, diploid fungus. A parasexual cycle was previously found between homozygotes with opposite mating type-like loci (MTLa/α). Fluconazole-resistant strains had a higher proportion of MTL homozygotes, whereas MTL homozygous C. albicans was found in only about 3.2% of clinical strains. MTL heterozygotes had a low frequency (1.4 × 10-4) of white-opaque switching to MTL homozygotes in nature. METHODS Here, a reference C. albicans strain (SC5314) was used in a fluconazole-induced assay to obtain standard opaque MTL homozygous strains and first-generation daughter strains from the fluconazole inhibition zone. Further separation methods were employed to produce second- and third-generation daughter strains. Polymerase chain reaction analysis based on MTL genes was used to define MTL genotypes, and microscopic observations, a flow-cytometric assay, and an antifungal E-test were used to compare microbiological characteristics. RESULTS MTL homozygotes were found at a high frequency (17 of 35; 48.6%) in fluconazole-induced first-generation daughter strains, as were morphological polymorphisms, decreased DNA content, and modified antifungal drug susceptibility. High-frequency MTL homozygosity was identified inside the fluconazole inhibition zone within 24 hours. The DNA content of fluconazole-induced daughter strains was reduced compared with their progenitor SC5314 and standard MTL homozygous strains. CONCLUSION Treatment with fluconazole, commonly used to treat invasive candidiasis, inhibited the growth of C. albicans and altered its microbiological characteristics. Our results suggest that fluconazole treatment induces the high frequency of loss of heterozygosity and microbiological polymorphism in C. albicans.
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Affiliation(s)
- Tsong-Yih Ou
- Division of Infectious Disease, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Fang-Mo Chang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Ning Cheng
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan
| | - Adela Lara
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ming-Li Chou
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
| | - Wei-Fang Lee
- School of Dental Technology, Taipei Medical University, Taipei, Taiwan
| | - Kai-Cheng Lee
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
| | - Che-Tong Lin
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wen-Sen Lee
- Division of Infectious Disease, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Fang-Lan Yu
- Division of Microbiology, Department of Clinical Laboratory, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ching-Hua Su
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan.
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46
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ERG11 mutations and expression of resistance genes in fluconazole-resistant Candida albicans isolates. Arch Microbiol 2015; 197:1087-93. [DOI: 10.1007/s00203-015-1146-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 08/05/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022]
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47
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Pierce CG, Chaturvedi AK, Lazzell AL, Powell AT, Saville SP, McHardy SF, Lopez-Ribot JL. A Novel Small Molecule Inhibitor of Candida albicans Biofilm Formation, Filamentation and Virulence with Low Potential for the Development of Resistance. NPJ Biofilms Microbiomes 2015; 1. [PMID: 26691764 PMCID: PMC4681527 DOI: 10.1038/npjbiofilms.2015.12] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND/OBJECTIVES Candida albicans is the principal causative agent of candidiasis, the most common fungal infection in humans. Candidiasis represents the third-to-fourth most frequent nosocomial infection worldwide, as this normal commensal of humans causes opportunistic infections in an expanding population of immune- and medically-compromised patients. These infections are frequently associated with biofilm formation, which complicates treatment and contributes to unacceptably high mortality rates. METHODS To address the pressing need for new antifungals we have performed a high content screen of 20,000 small molecules in a chemical library (NOVACore™) to identify compounds that inhibit C. albicans biofilm formation, and conducted a series of follow-up studies to examine the in vitro and in vivo activity of the identified compounds. RESULTS The screen identified a novel series of diazaspiro-decane structural analogs which were largely represented among the bioactive compounds. Characterization of the leading compound from this series indicated that it inhibits processes associated with C. albicans virulence, most notably biofilm formation and filamentation, without having an effect on overall growth or eliciting resistance. This compound demonstrated in vivo activity in clinically-relevant murine models of both invasive and oral candidiasis and as such represents a promising lead for antifungal drug development. Furthermore, these results provide proof of concept for the implementation of anti-virulence approaches against C. albicans and other fungal infections that would be less likely to foster the emergence of resistance.
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Affiliation(s)
- Christopher G Pierce
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Ashok K Chaturvedi
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Anna L Lazzell
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Alexander T Powell
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Stephen P Saville
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Stanton F McHardy
- Department of Chemistry and Center for Innovation in Drug Discovery, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
| | - Jose L Lopez-Ribot
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX 78249, United States of America
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Yousefimanesh H, Amin M, Robati M, Goodarzi H, Otoufi M. Comparison of the Antibacterial Properties of Three Mouthwashes Containing Chlorhexidine Against Oral Microbial Plaques: An in vitro Study. Jundishapur J Microbiol 2015; 8:e17341. [PMID: 25825646 PMCID: PMC4362091 DOI: 10.5812/jjm.17341] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 11/16/2022] Open
Abstract
Background: The mouth provides an environment that allows the colonization and growth of a wide variety of microorganisms, especially bacteria. One of the most effective ways to reduce oral microorganisms is using mouthwashes. Objectives: The aim of this study was to investigate the antibacterial effects of chlorhexidine mouthwashes (manufacture by Livar, Behsa, Boht) on common oral microorganisms. Materials and Methods: In this in vitro study, isolated colonies of four bacteria, including Streptococcus mutans, S. sanguinis, S. salivarius and Lactobacillus casei, were prepared for an antimicrobial mouth rinse test. The tube dilution method was used for determining the minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC). Results: The MICs for Kin gingival, Behsa and Boht mouthwashes were 0.14, 0.48 and 1000 micrograms/mL using the tube method for S. mutans, respectively. The MBCs for the mentioned mouthwashes were 0.23, 1.9 and 2000 micrograms/mL for S. mutans, respectively. The MICs for Kin gingival, Behsa and Boht mouthwashes were 0.073, 0.48 and 250 micrograms/mL using the tube method for S. sanguinis, respectively. The MBCs for the mentioned mouthwashes were 0.14, 1.9 and 1000 micrograms/mL for S. sanguinis, respectively. Conclusions: The Kin Gingival chlorhexidine mouthwash has a greater effect than Behsa and Boht mouthwashes on oral microorganisms and is recommended to be used for plaque chemical inhibition.
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Affiliation(s)
- Hojatollah Yousefimanesh
- Department of Periodontology, School of Dentistry, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Mansour Amin
- Health Research Institute, Infectious and Tropical Diseases Research Center Ahvaz, Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Corresponding author: Mansour Amin, Health Research Institute, Infectious and Tropical Diseases Research Center, Jundishapur University of Medical Sciences, Ahvaz, IR Iran. Tel: +989166711679, E-mail:
| | - Maryam Robati
- Department of Oral Medicine, School of Dentistry, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Hamed Goodarzi
- Infectious and Tropical Diseases Research Center, Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Masumeh Otoufi
- Department of Periodontology, School of Dentistry, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
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Basso LR, Gast CE, Bruzual I, Wong B. Identification and properties of plasma membrane azole efflux pumps from the pathogenic fungi Cryptococcus gattii and Cryptococcus neoformans. J Antimicrob Chemother 2015; 70:1396-407. [PMID: 25630649 DOI: 10.1093/jac/dku554] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 12/11/2014] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Cryptococcus gattii from the North American Northwest (NW) have higher azole MICs than do non-NW C. gattii or Cryptococcus neoformans. Since mechanisms of azole resistance in C. gattii are not known, we identified C. gattii and C. neoformans plasma membrane azole efflux pumps and characterized their properties. METHODS The C. gattii R265 genome was searched for orthologues of known fungal azole efflux genes, expression of candidate genes was assessed by RT-PCR and the expressed genes' cDNAs were cloned and expressed in Saccharomyces cerevisiae. Azole MICs and intracellular [(3)H]fluconazole were measured in C. gattii and C. neoformans and in S. cerevisiae expressing each cDNA of interest, as was [(3)H]fluconazole uptake by post-Golgi vesicles (PGVs) isolated from S. cerevisiae sec6-4 mutants expressing each cDNA of interest. RESULTS Intracellular [(3)H]fluconazole concentrations were inversely correlated with fluconazole MICs only in 25 NW C. gattii strains. S. cerevisiae expressing three C. gattii cDNAs (encoded by orthologues of C. neoformans AFR1 and MDR1 and the previously unstudied gene AFR2) and their C. neoformans counterparts had higher azole MICs and lower intracellular [(3)H]fluconazole concentrations than did empty-vector controls. PGVs from S. cerevisiae expressing all six Cryptococcus cDNAs also accumulated more [(3)H]fluconazole than did controls, and [(3)H]fluconazole transport by all six transporters of interest was ATP dependent and was inhibited by excess unlabelled fluconazole, voriconazole, itraconazole and posaconazole. CONCLUSIONS We conclude that C. gattii and C. neoformans AFR1, MDR1 and AFR2 encode ABC transporters that pump multiple azoles out of S. cerevisiae cells, thereby causing azole resistance.
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Affiliation(s)
- Luiz R Basso
- Infectious Diseases Division, Department of Medicine, Oregon Health & Science University, Portland, OR, USA Department of Cellular and Molecular Biology and Pathogenic Bioagents, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Charles E Gast
- Infectious Diseases Division, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Igor Bruzual
- Infectious Diseases Division, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian Wong
- Infectious Diseases Division, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
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50
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Lucas JA, Hawkins NJ, Fraaije BA. The evolution of fungicide resistance. ADVANCES IN APPLIED MICROBIOLOGY 2014; 90:29-92. [PMID: 25596029 DOI: 10.1016/bs.aambs.2014.09.001] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fungicides are widely used in developed agricultural systems to control disease and safeguard crop yield and quality. Over time, however, resistance to many of the most effective fungicides has emerged and spread in pathogen populations, compromising disease control. This review describes the development of resistance using case histories based on four important diseases of temperate cereal crops: eyespot (Oculimacula yallundae and Oculimacula acuformis), Septoria tritici blotch (Zymoseptoria tritici), powdery mildew (Blumeria graminis), and Fusarium ear blight (a complex of Fusarium and Microdochium spp). The sequential emergence of variant genotypes of these pathogens with reduced sensitivity to the most active single-site fungicides, methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, and succinate dehydrogenase inhibitors illustrates an ongoing evolutionary process in response to the introduction and use of different chemical classes. Analysis of the molecular mechanisms and genetic basis of resistance has provided more rapid and precise methods for detecting and monitoring the incidence of resistance in field populations, but when or where resistance will occur remains difficult to predict. The extent to which the predictability of resistance evolution can be improved by laboratory mutagenesis studies and fitness measurements, comparison between pathogens, and reconstruction of evolutionary pathways is discussed. Risk models based on fungal life cycles, fungicide properties, and exposure to the fungicide are now being refined to take account of additional traits associated with the rate of pathogen evolution. Experimental data on the selection of specific mutations or resistant genotypes in pathogen populations in response to fungicide treatments can be used in models evaluating the most effective strategies for reducing or preventing resistance. Resistance management based on robust scientific evidence is vital to prolong the effective life of fungicides and safeguard their future use in crop protection.
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Affiliation(s)
- John A Lucas
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Nichola J Hawkins
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Bart A Fraaije
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
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