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Molecular Docking Analysis of Cinnamomum zeylanicum Phytochemicals against Secreted Aspartyl proteinase 4-6 of Candida albicans as Anti-Candidiasis Oral. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating. J Fungi (Basel) 2021; 7:jof7080661. [PMID: 34436200 PMCID: PMC8400180 DOI: 10.3390/jof7080661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
In the study of pathogen evolution, temporal dating of phylogenies provides information on when species and lineages may have diverged in the past. When combined with spatial and epidemiological data in phylodynamic models, these dated phylogenies can also help infer where and when outbreaks occurred, how pathogens may have spread to new geographic locations and/or niches, and how virulence or drug resistance has developed over time. Although widely applied to viruses and, increasingly, to bacterial pathogen outbreaks, phylogenetic dating is yet to be widely used in the study of pathogenic fungi. Fungi are complex organisms with several biological processes that could present issues with appropriate inference of phylogenies, clock rates, and divergence times, including high levels of recombination and slower mutation rates although with potentially high levels of mutation rate variation. Here, we discuss some of the key methodological challenges in accurate phylogeny reconstruction for fungi in the context of the temporal analyses conducted to date and make recommendations for future dating studies to aid development of a best practices roadmap in light of the increasing threat of fungal outbreaks and antifungal drug resistance worldwide.
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Amanloo S, Shams-Ghahfarokhi M, Ghahri M, Razzaghi-Abyaneh M. Genotyping of clinical isolates of Candida glabrata from Iran by multilocus sequence typing and determination of population structure and drug resistance profile. Med Mycol 2018; 56:207-215. [PMID: 28482076 DOI: 10.1093/mmy/myx030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/03/2017] [Indexed: 12/14/2022] Open
Abstract
Candida glabrata is often the second most common causative agent for candidiasis following Candida albicans. Despite the importance of C. glabrata infections, few epidemiological studies have been conducted on this issue. The goal of this study was genotyping of clinical isolates of C. glabrata by multilocus sequence typing (MLST) technique for determination of the endemic prevalent genotypes and any association between isolation source and drug resistance. A total of 50 C. glabrata clinical isolates from Iran were analyzed by MLST and tested for in-vitro susceptibilities to amphotericin-B, caspofungin, fluconazole, and voriconazole according to the Clinical Laboratory Standards Institute (CLSI) M27-A4 document guidelines. Among these isolates, 16 distinct STs were identified, indicating a discriminatory power index of 0.9029. The three major sequence types (STs) were ST-59, ST-74, and ST-7 with 10, 8, and 7 isolates, respectively. Furthermore, a total of 11 new sequences were found, to which no allele numbers were assigned in the MLST database. All the isolates were susceptible to amphotericin B and caspofungin. Fluconazole resistance was shown in four isolates. Also, a sole isolate was voriconazole resistant. This study shows that the population structure of C. glabrata in Iran consists of groups closely related to the global database as well as to some new clonal clusters and STs. Regarding the high prevalence of 11 new sequences found in this study, it can be concluded that, these new alleles are among the endemic genotypes of Iran. The genotypes or STs were independent of drug susceptibility and anatomic sources.
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Affiliation(s)
- Saeid Amanloo
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran
| | | | - Mohammad Ghahri
- Department of Biological Sciences, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran
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Roman F, Iñiguez AM, Yeo M, Jansen AM. Multilocus sequence typing: genetic diversity in Trypanosoma cruzi I (TcI) isolates from Brazilian didelphids. Parasit Vectors 2018; 11:107. [PMID: 29471851 PMCID: PMC5824584 DOI: 10.1186/s13071-018-2696-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi is a protozoan parasite characterized by extensive genetic heterogeneity. There are currently six recognised, genetically distinct, monophyletic clades designated discrete typing units (DTUs). TcI has the broadest geographical range and most genetic diversity evidenced by a wide range of genetic markers applied to isolates spanning a vast geographical range across Latin America. However, little is known of the diversity of TcI that exists within sylvatic mammals across the geographical expanse of Brazil. RESULTS Twenty-nine sylvatic TcI isolates spanning multiple ecologically diverse biomes across Brazil were analyzed by the application of multilocus sequence typing (MLST) using four nuclear housekeeping genes. Results revealed extensive genetic diversity and also incongruence among individual gene trees. There was no association of intralineage genotype with geography or with any particular biome, with the exception of isolates from Caatinga that formed a single cluster. However, haplotypic analyses of METIII and LYT1 constitutive markers provided evidence of recombination events in two isolates derived from Didelphis marsupialis and D. albiventris, respectively. For diversity studies all possible combinations of markers were assessed with the objective of selecting the combination of gene targets that are most resolutive using the minimum number of genes. A panel of just three gene fragments (DHFR-TS, LYT1 and METIII) discriminated 26 out of 35 genotypes. CONCLUSIONS These findings showed geographical association of genotypes clustering in Caatinga but more characteristically TcI genotypes widely distributed without specific association to geographical areas or biomes. Importantly, we detected the signature of recombination events at the nuclear level evidenced by haplotypic analysis and incongruence.
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Affiliation(s)
- Fabiola Roman
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
| | - Alena M Iñiguez
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Matthew Yeo
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ana M Jansen
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How? Clin Microbiol Rev 2017; 30:671-707. [PMID: 28490578 DOI: 10.1128/cmr.00043-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.
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Parasex Generates Phenotypic Diversity de Novo and Impacts Drug Resistance and Virulence in Candida albicans. Genetics 2017; 207:1195-1211. [PMID: 28912344 DOI: 10.1534/genetics.117.300295] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/05/2017] [Indexed: 01/06/2023] Open
Abstract
Candida albicans is a diploid fungus that is a frequent cause of mucosal and systemic infections in humans. This species exhibits an unusual parasexual cycle in which mating produces tetraploid cells that undergo a nonmeiotic program of concerted chromosome loss to return to a diploid or aneuploid state. In this work, we used a multipronged approach to examine the capacity of parasex to generate diversity in C. albicans First, we compared the phenotypic properties of 32 genotyped progeny and observed wide-ranging differences in fitness, filamentation, biofilm formation, and virulence. Strikingly, one parasexual isolate displayed increased virulence relative to parental strains using a Galleria mellonella model of infection, establishing that parasex has the potential to enhance pathogenic traits. Next, we examined parasexual progeny derived from homothallic, same-sex mating events, and reveal that parasex can generate diversity de novo from identical parental strains. Finally, we generated pools of parasexual progeny and examined resistance of these pools to environmental stresses. Parasexual progeny were generally less fit than control strains across most test conditions, but showed an increased ability to grow in the presence of the antifungal drug fluconazole (FL). FL-resistant progeny were aneuploid isolates, often being diploid strains trisomic for both Chr3 and Chr6. Passaging of these aneuploid strains frequently led to loss of the supernumerary chromosomes and a concomitant decrease in drug resistance. These experiments establish that parasex generates extensive phenotypic diversity de novo, and that this process has important consequences for both virulence and drug resistance in C. albicans populations.
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Vanheule A, De Boevre M, Moretti A, Scauflaire J, Munaut F, De Saeger S, Bekaert B, Haesaert G, Waalwijk C, van der Lee T, Audenaert K. Genetic Divergence and Chemotype Diversity in the Fusarium Head Blight Pathogen Fusarium poae. Toxins (Basel) 2017; 9:toxins9090255. [PMID: 28832503 PMCID: PMC5618188 DOI: 10.3390/toxins9090255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/19/2017] [Indexed: 01/02/2023] Open
Abstract
Fusarium head blight is a disease caused by a complex of Fusarium species. F. poae is omnipresent throughout Europe in spite of its low virulence. In this study, we assessed a geographically diverse collection of F. poae isolates for its genetic diversity using AFLP (Amplified Fragment Length Polymorphism). Furthermore, studying the mating type locus and chromosomal insertions, we identified hallmarks of both sexual recombination and clonal spread of successful genotypes in the population. Despite the large genetic variation found, all F. poae isolates possess the nivalenol chemotype based on Tri7 sequence analysis. Nevertheless, Tri gene clusters showed two layers of genetic variability. Firstly, the Tri1 locus was highly variable with mostly synonymous mutations and mutations in introns pointing to a strong purifying selection pressure. Secondly, in a subset of isolates, the main trichothecene gene cluster was invaded by a transposable element between Tri5 and Tri6. To investigate the impact of these variations on the phenotypic chemotype, mycotoxin production was assessed on artificial medium. Complex blends of type A and type B trichothecenes were produced but neither genetic variability in the Tri genes nor variability in the genome or geography accounted for the divergence in trichothecene production. In view of its complex chemotype, it will be of utmost interest to uncover the role of trichothecenes in virulence, spread and survival of F. poae.
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Affiliation(s)
- Adriaan Vanheule
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
- Laboratory of Applied Mycology and Phenomics, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Marthe De Boevre
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
| | - Antonio Moretti
- Institute of Sciences of Food Production, National Research Council, 70126 Bari, Italy.
| | - Jonathan Scauflaire
- Applied Microbiology, Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium.
| | - Françoise Munaut
- Applied Microbiology, Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium.
| | - Sarah De Saeger
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
| | - Boris Bekaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
- Laboratory of Applied Mycology and Phenomics, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Geert Haesaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Cees Waalwijk
- Wageningen University and Research Centre, 6708PB Wageningen, The Netherlands.
| | - Theo van der Lee
- Wageningen University and Research Centre, 6708PB Wageningen, The Netherlands.
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
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Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, De Saeger S, Haesaert G, Waalwijk C, van der Lee T. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genomics 2016; 17:670. [PMID: 27552804 PMCID: PMC4994206 DOI: 10.1186/s12864-016-2941-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/14/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. RESULTS Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. CONCLUSIONS For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
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Affiliation(s)
- Adriaan Vanheule
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Wageningen UR, Wageningen, The Netherlands
| | - Kris Audenaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sarah De Saeger
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Geert Haesaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Schmid J, Magee PT, Holland BR, Zhang N, Cannon RD, Magee BB. Last hope for the doomed? Thoughts on the importance of a parasexual cycle for the yeast Candida albicans. Curr Genet 2015; 62:81-5. [DOI: 10.1007/s00294-015-0516-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 08/21/2015] [Accepted: 08/22/2015] [Indexed: 12/16/2022]
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Scaduto CM, Bennett RJ. Candida albicans the chameleon: transitions and interactions between multiple phenotypic states confer phenotypic plasticity. Curr Opin Microbiol 2015; 26:102-8. [PMID: 26189047 DOI: 10.1016/j.mib.2015.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 06/12/2015] [Accepted: 06/30/2015] [Indexed: 11/29/2022]
Abstract
The ability of microbial cells to exist in multiple states is a ubiquitous property that promotes adaptation and survival. This phenomenon has been extensively studied in the opportunistic pathogen Candida albicans, which can transition between multiple phenotypic states in response to environmental signals. C. albicans normally exists as a commensal in the human body, but can also cause debilitating mucosal infections or life-threatening systemic infections. The ability to switch between cellular forms contributes to C. albicans' capacity to infect different host niches, and strictly regulates the program of sexual mating. We review the unique properties associated with different phenotypic states, as well as how interactions between cells in different states can further augment microbial behavior.
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Affiliation(s)
| | - Richard J Bennett
- Brown University, 171 Meeting St, Providence, RI 02912, United States.
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Selective Advantages of a Parasexual Cycle for the Yeast Candida albicans. Genetics 2015; 200:1117-32. [PMID: 26063661 DOI: 10.1534/genetics.115.177170] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/08/2015] [Indexed: 11/18/2022] Open
Abstract
The yeast Candida albicans can mate. However, in the natural environment mating may generate progeny (fusants) fitter than clonal lineages too rarely to render mating biologically significant: C. albicans has never been observed to mate in its natural environment, the human host, and the population structure of the species is largely clonal. It seems incapable of meiosis, and most isolates are diploid and carry both mating-type-like (MTL) locus alleles, preventing mating. Only chromosome loss or localized loss of heterozygosity can generate mating-competent cells, and recombination of parental alleles is limited. To determine if mating is a biologically significant process, we investigated if mating is under selection. The ratio of nonsynonymous to synonymous mutations in mating genes and the frequency of mutations abolishing mating indicated that mating is under selection. The MTL locus is located on chromosome 5, and when we induced chromosome 5 loss in 10 clinical isolates, most of the resulting MTL-homozygotes could mate with each other, producing fusants. In laboratory culture, a novel environment favoring novel genotypes, some fusants grew faster than their parents, in which loss of heterozygosity had reduced growth rates, and also faster than their MTL-heterozygous ancestors-albeit often only after serial propagation. In a small number of experiments in which co-inoculation of an oral colonization model with MTL-homozygotes yielded small numbers of fusants, their numbers declined over time relative to those of the parents. Overall, our results indicate that mating generates genotypes superior to existing MTL-heterozygotes often enough to be under selection.
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Parasexual Ploidy Reduction Drives Population Heterogeneity Through Random and Transient Aneuploidy in Candida albicans. Genetics 2015; 200:781-94. [PMID: 25991822 PMCID: PMC4512543 DOI: 10.1534/genetics.115.178020] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/16/2015] [Indexed: 11/19/2022] Open
Abstract
The opportunistic pathogen Candida albicans has a large repertoire of mechanisms to generate genetic and phenotypic diversity despite the lack of meiosis in its life cycle. Its parasexual cycle enables shifts in ploidy, which in turn facilitate recombination, aneuploidy, and homozygosis of whole chromosomes to fuel rapid adaptation. Here we show that the tetraploid state potentiates ploidy variation and drives population heterogeneity. In tetraploids, the rate of losing a single heterozygous marker [loss of heterozygosity (LOH)] is elevated ∼30-fold higher than the rate in diploid cells. Furthermore, isolates recovered after selection for LOH of one, two, or three markers were highly aneuploid, with a broad range of karyotypes including strains with a combination of di-, tri-, and tetrasomic chromosomes. We followed the ploidy trajectories for these tetraploid- and aneuploid-derived isolates, using a combination of flow cytometry and double-digestion restriction-site-associated DNA analyzed with next-generation sequencing. Isolates derived from either tetraploid or aneuploid isolates predominately resolved to a stable euploid state. The majority of isolates reduced to the conventional diploid state; however, stable triploid and tetraploid states were observed in ∼30% of the isolates. Notably, aneuploid isolates were more transient than tetraploid isolates, resolving to a euploid state within a few passages. Furthermore, the likelihood that a particular isolate will resolve to the same ploidy state in replicate evolution experiments is only ∼50%, supporting the idea that the chromosome loss process of the parasexual cycle is random and does not follow trajectories involving specific combinations of chromosomes. Together, our results indicate that tetraploid progenitors can produce populations of progeny cells with a high degree of genomic diversity, from altered ploidy to homozygosis, providing an excellent source of genetic variation upon which selection can act.
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Yurkov A, Guerreiro MA, Sharma L, Carvalho C, Fonseca Á. Multigene assessment of the species boundaries and sexual status of the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales). PLoS One 2015; 10:e0120400. [PMID: 25811603 PMCID: PMC4374795 DOI: 10.1371/journal.pone.0120400] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/21/2015] [Indexed: 02/06/2023] Open
Abstract
Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful.
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Affiliation(s)
- Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- * E-mail:
| | - Marco A. Guerreiro
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Lav Sharma
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Cláudia Carvalho
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Álvaro Fonseca
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Merseguel KB, Nishikaku AS, Rodrigues AM, Padovan AC, e Ferreira RC, de Azevedo Melo AS, Briones MRDS, Colombo AL. Genetic diversity of medically important and emerging Candida species causing invasive infection. BMC Infect Dis 2015; 15:57. [PMID: 25887032 PMCID: PMC4339437 DOI: 10.1186/s12879-015-0793-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/30/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis. METHODS We selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis. RESULTS Among 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp. CONCLUSIONS Molecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.
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Affiliation(s)
- Karina Bellinghausen Merseguel
- Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil.
| | - Angela Satie Nishikaku
- Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil.
| | - Anderson Messias Rodrigues
- Departamento de Microbiologia, Imunologia e Parasitologia, Disciplina de Biologia Celular, Universidade Federal de São Paulo, São Paulo, Brazil.
| | - Ana Carolina Padovan
- Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil.
- Departamento de Microbiologia e Imunologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG, Brazil.
| | - Renata Carmona e Ferreira
- Laboratório de Genômica Evolutiva e Biocomplexidade, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil.
| | - Analy Salles de Azevedo Melo
- Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil.
| | - Marcelo Ribeiro da Silva Briones
- Laboratório de Genômica Evolutiva e Biocomplexidade, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil.
| | - Arnaldo Lopes Colombo
- Laboratório Especial de Micologia (LEMI), Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, Rua Pedro de Toledo, 669, quinto andar, Edifício de Pesquisas II, Zipcode 04039-032, São Paulo, SP, Brazil.
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Short DPG, O'Donnell K, Geiser DM. Clonality, recombination, and hybridization in the plumbing-inhabiting human pathogen Fusarium keratoplasticum inferred from multilocus sequence typing. BMC Evol Biol 2014; 14:91. [PMID: 24766947 PMCID: PMC4026394 DOI: 10.1186/1471-2148-14-91] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/16/2014] [Indexed: 01/05/2023] Open
Abstract
Background Recent work has shown that Fusarium species and genotypes most commonly associated with human infections, particularly of the cornea (mycotic keratitis), are the same as those most commonly isolated from plumbing systems. The species most dominant in plumbing biofilms is Fusarium keratoplasticum, a cosmopolitan fungus known almost exclusively from animal infections and biofilms. To better understand its diversity and population dynamics, we developed and utilized a nine-locus sequence-based typing system to make inferences about clonality, recombination, population structure, species boundaries and hybridization. Results High levels of genetic diversity and evidence for recombination and clonality were detected among 75 clinical and 156 environmental isolates of Fusarium keratoplasticum. The multilocus sequence typing system (MLST) resolved 111 unique nine-locus sequence types (STs). The single locus bifactorial determinants of mating compatibility (mating types MAT1-1 and MAT1-2), were found in a ratio of 70:30. All but one of the 49 isolates of the most common ST (FSSC 2d-2) came from human infections, mostly of the cornea, and from biofilms associated with contact lenses and plumbing surfaces. Significant levels of phylogenetic incongruence were found among loci. Putative clonal relationships among genotypes were estimated, showing a mixture of large clonal complexes and unrelated singletons. Discordance between the nuclear ribosomal rRNA and other gene genealogies is consistent with introgression of ribosomal RNA alleles of phylogenetic species FSSC 9 into F. keratoplasticum. No significant population subdivision based on clinical versus non-clinical sources was found. Conclusions Incongruent phylogenetic trees and the presence of both mating types within otherwise identical STs were observed, providing evidence for sexuality in F. keratoplasticum. Cryptic speciation suggested in a published three-locus MLST system was not supported with the addition of new loci, but evidence of introgression of ribosomal RNA genes from another strongly supported phylogenetic species (FSSC 9), also known from plumbing systems and human infections, was detected in two isolates. Overall, F. keratoplasticum is a diverse and geographically unstructured species with a mixed clonal and recombinant life history.
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Affiliation(s)
- Dylan P G Short
- Department of Plant Pathology, University of California, Davis, 1636 E Alisal St,, Salinas, CA 93905, USA.
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Molecular epidemiology, phylogeny and evolution of Candida albicans. INFECTION GENETICS AND EVOLUTION 2013; 21:166-78. [PMID: 24269341 DOI: 10.1016/j.meegid.2013.11.008] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 11/21/2022]
Abstract
A small number of Candida species form part of the normal microbial flora of mucosal surfaces in humans and may give rise to opportunistic infections when host defences are impaired. Candida albicans is by far the most prevalent commensal and pathogenic Candida species. Several different molecular typing approaches including multilocus sequence typing, multilocus microsatellite typing and DNA fingerprinting using C. albicans-specific repetitive sequence-containing DNA probes have yielded a wealth of information regarding the epidemiology and population structure of this species. Such studies revealed that the C. albicans population structure consists of multiple major and minor clades, some of which exhibit geographical or phenotypic enrichment and that C. albicans reproduction is predominantly clonal. Despite this, losses of heterozygosity by recombination, the existence of a parasexual cycle, toleration of a wide range of aneuploidies and the recent description of viable haploid strains have all demonstrated the extensive plasticity of the C. albicans genome. Recombination and gross chromosomal rearrangements are more common under stressful environmental conditions, and have played a significant role in the evolution of this opportunistic pathogen. Surprisingly, Candida dubliniensis, the closest relative of C. albicans exhibits more karyotype variability than C. albicans, but is significantly less adaptable to unfavourable environments. This disparity most likely reflects the evolutionary processes that occurred during or soon after the divergence of both species from their common ancestor. Whilst C. dubliniensis underwent significant gene loss and pseudogenisation, C. albicans expanded gene families considered to be important in virulence. It is likely that technological developments in whole genome sequencing and data analysis in coming years will facilitate its routine use for population structure, epidemiological investigations, and phylogenetic analyses of Candida species. These are likely to reveal more minor C. albicans clades and to enhance our understanding of the population biology of this versatile organism.
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Gong YB, Zheng JL, Jin B, Zhuo DX, Huang ZQ, Qi H, Zhang W, Duan W, Fu JT, Wang CJ, Mao ZB. Particular Candida albicans strains in the digestive tract of dyspeptic patients, identified by multilocus sequence typing. PLoS One 2012; 7:e35311. [PMID: 22536371 PMCID: PMC3335024 DOI: 10.1371/journal.pone.0035311] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/13/2012] [Indexed: 12/12/2022] Open
Abstract
Background Candida albicans is a human commensal that is also responsible for chronic gastritis and peptic ulcerous disease. Little is known about the genetic profiles of the C. albicans strains in the digestive tract of dyspeptic patients. The aim of this study was to evaluate the prevalence, diversity, and genetic profiles among C. albicans isolates recovered from natural colonization of the digestive tract in the dyspeptic patients. Methods and Findings Oral swab samples (n = 111) and gastric mucosa samples (n = 102) were obtained from a group of patients who presented dyspeptic symptoms or ulcer complaints. Oral swab samples (n = 162) were also obtained from healthy volunteers. C. albicans isolates were characterized and analyzed by multilocus sequence typing. The prevalence of Candida spp. in the oral samples was not significantly different between the dyspeptic group and the healthy group (36.0%, 40/111 vs. 29.6%, 48/162; P > 0.05). However, there were significant differences between the groups in the distribution of species isolated and the genotypes of the C. albicans isolates. C. albicans was isolated from 97.8% of the Candida-positive subjects in the dyspeptic group, but from only 56.3% in the healthy group (P < 0.001). DST1593 was the dominant C. albicans genotype from the digestive tract of the dyspeptic group (60%, 27/45), but not the healthy group (14.8%, 4/27) (P < 0.001). Conclusions Our data suggest a possible link between particular C. albicans strain genotypes and the host microenvironment. Positivity for particular C. albicans genotypes could signify susceptibility to dyspepsia.
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Affiliation(s)
- Yan-Bing Gong
- Laboratory of Ze-Bin Mao, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- * E-mail: (YBG); (JLZ); (ZBM)
| | - Jian-Ling Zheng
- Department of Microbiology, Medical Sciences Institute of Liaoning, Shenyang, China
- * E-mail: (YBG); (JLZ); (ZBM)
| | - Bo Jin
- Laboratory of Ze-Bin Mao, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - De-Xiang Zhuo
- Laboratory of Ze-Bin Mao, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhu-Qing Huang
- Department of Microbiology, Medical Sciences Institute of Liaoning, Shenyang, China
| | - He Qi
- Department of Microbiology, Medical Sciences Institute of Liaoning, Shenyang, China
| | - Wei Zhang
- Department of Microbiology, Medical Sciences Institute of Liaoning, Shenyang, China
| | - Wei Duan
- Department of Microbiology, Medical Sciences Institute of Liaoning, Shenyang, China
| | - Ji-Ting Fu
- Division of Gastroenterology, The First Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Chui-Jie Wang
- Division of Gastroenterology, The First Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Ze-Bin Mao
- Laboratory of Ze-Bin Mao, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- * E-mail: (YBG); (JLZ); (ZBM)
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Yeo M, Mauricio IL, Messenger LA, Lewis MD, Llewellyn MS, Acosta N, Bhattacharyya T, Diosque P, Carrasco HJ, Miles MA. Multilocus sequence typing (MLST) for lineage assignment and high resolution diversity studies in Trypanosoma cruzi. PLoS Negl Trop Dis 2011; 5:e1049. [PMID: 21713026 PMCID: PMC3119646 DOI: 10.1371/journal.pntd.0001049] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 05/23/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Multilocus sequence typing (MLST) is a powerful and highly discriminatory method for analysing pathogen population structure and epidemiology. Trypanosoma cruzi, the protozoan agent of American trypanosomiasis (Chagas disease), has remarkable genetic and ecological diversity. A standardised MLST protocol that is suitable for assignment of T. cruzi isolates to genetic lineage and for higher resolution diversity studies has not been developed. METHODOLOGY/PRINCIPAL FINDINGS We have sequenced and diplotyped nine single copy housekeeping genes and assessed their value as part of a systematic MLST scheme for T. cruzi. A minimum panel of four MLST targets (Met-III, RB19, TcGPXII, and DHFR-TS) was shown to provide unambiguous assignment of isolates to the six known T. cruzi lineages (Discrete Typing Units, DTUs TcI-TcVI). In addition, we recommend six MLST targets (Met-II, Met-III, RB19, TcMPX, DHFR-TS, and TR) for more in depth diversity studies on the basis that diploid sequence typing (DST) with this expanded panel distinguished 38 out of 39 reference isolates. Phylogenetic analysis implies a subdivision between North and South American TcIV isolates. Single Nucleotide Polymorphism (SNP) data revealed high levels of heterozygosity among DTUs TcI, TcIII, TcIV and, for three targets, putative corresponding homozygous and heterozygous loci within DTUs TcI and TcIII. Furthermore, individual gene trees gave incongruent topologies at inter- and intra-DTU levels, inconsistent with a model of strict clonality. CONCLUSIONS/SIGNIFICANCE We demonstrate the value of systematic MLST diplotyping for describing inter-DTU relationships and for higher resolution diversity studies of T. cruzi, including presence of recombination events. The high levels of heterozygosity will facilitate future population genetics analysis based on MLST haplotypes.
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Affiliation(s)
- Matthew Yeo
- London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Self-induction of a/a or alpha/alpha biofilms in Candida albicans is a pheromone-based paracrine system requiring switching. EUKARYOTIC CELL 2011; 10:753-60. [PMID: 21498642 DOI: 10.1128/ec.05055-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Like MTL-heterozygous (a/α) cells, white MTL-homozygous (a/a or α/α) cells of Candida albicans, to which a minority of opaque cells of opposite mating type have been added, form thick, robust biofilms. The latter biofilms are uniquely stimulated by the pheromone released by opaque cells and are regulated by the mitogen-activated protein kinase signal transduction pathway. However, white MTL-homozygous cells, to which opaque cells of opposite mating type have not been added, form thinner biofilms. Mutant analyses reveal that these latter biofilms are self-induced. Self-induction of a/a biofilms requires expression of the α-receptor gene STE2 and the α-pheromone gene MFα, and self-induction of α/α biofilms requires expression of the a-receptor gene STE3 and the a-pheromone gene MFa. In both cases, deletion of WOR1, the master switch gene, blocks cells in the white phenotype and biofilm formation, indicating that self-induction depends upon low frequency switching from the white to opaque phenotype. These results suggest a self-induction scenario in which minority opaque a/a cells formed by switching secrete, in a mating-type-nonspecific fashion, α-pheromone, which stimulates biofilm formation through activation of the α-pheromone receptor of majority white a/a cells. A similar scenario is suggested for a white α/α cell population, in which minority opaque α/α cells secrete a-pheromone. This represents a paracrine system in which one cell type (opaque) signals a second highly related cell type (white) to undergo a complex response, in this case the formation of a unisexual white cell biofilm.
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Abbes S, Amouri I, Sellami H, Sellami A, Makni F, Ayadi A. A review of molecular techniques to type Candida glabrata isolates. Mycoses 2011; 53:463-7. [PMID: 19638001 DOI: 10.1111/j.1439-0507.2009.01753.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Candida glabrata has emerged as a common cause of fungal infection causing mucosal and systemic infections. This yeast is of concern because of its reduced antifungal susceptibility to azole antifungals such as fluconazole. A clear understanding of the epidemiology of Candida infection and colonisation required a reliable typing system for the evaluation of strain relatedness. In this study, we discuss the different molecular approaches for typing C. glabrata isolates. Recent advances in the use of molecular biology-based techniques have enabled investigators to develop typing systems with greater sensitivities. Several molecular genotypic approaches have been developed for fast and accurate identification of C. glabrata in vitro. These techniques have been widely used to study diverse aspects such as nosocomial transmission. Molecular typing of C. glabrata could also provide information on strain variation, such as microvariation and microevolution.
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Affiliation(s)
- S Abbes
- Laboratoire de biologie moléculaire parasitaire et fongique, faculté de médecine, Sfax, Tunisia
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21
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Evolution of a new signal transduction pathway in Candida albicans. Trends Microbiol 2010; 19:8-13. [PMID: 21036616 DOI: 10.1016/j.tim.2010.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 09/02/2010] [Accepted: 10/04/2010] [Indexed: 11/22/2022]
Abstract
The evolution of new signal transductions pathways is poorly understood. Here I present a rare glimpse into the evolution of one such pathway, namely the white-cell pheromone response pathway in Candida albicans. In this pathway, the upper portion has been derived intact from the ancestral pathway for mating, the targeted transcription factor from an ancestral filamentation or biofilm pathway, and the upregulated genes from an ancestral biofilm pathway. Each component of this pathway, therefore, has been derived from a conserved pathway. I suggest that the evolution of this new pathway provides one possible paradigm for the evolution of other signal transduction pathways in new cell types.
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Lyon JP, Moraes KCM, Moreira LM, Aimbire F, de Resende MA. Candida albicans: genotyping methods and clade related phenotypic characteristics. Braz J Microbiol 2010; 41:841-9. [PMID: 24031564 PMCID: PMC3769759 DOI: 10.1590/s1517-83822010000400003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 02/26/2010] [Accepted: 04/26/2010] [Indexed: 11/22/2022] Open
Abstract
Several molecular methods, such as Southern blotting hybridization, Multilocus Sequence Typing, and DNA microsatellite analysis, have been employed to genotype Candida albicans. The genotype analysis allows to group strains in clades, that is, a group composed of one ancestor and its descendants. These genotype studies demonstrate that clades distribution is influenced by geographic area as well as that antifungal resistance is associated with particular clades. These findings suggested that C. albicans reproduces mainly in a clonal manner, with certain degree of DNA microevolution. Additionally, virulence factors and site of isolation have also been associated with clade specificity. The present article is a brief review about the methods used for Candida genotyping and the correlated clade systems established. Special emphasis is given to Ca3 hybridization, MLST, and Microsatellites. The present work is also focused on the phenotypic and physiological traits associated with Candida clades.
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Affiliation(s)
- Juliana P Lyon
- Universidade Federal de São João Del Rei , São João Del-Rei, MG , Brasil ; Universidade do Vale do Paraíba , São José dos Campos, SP , Brasil
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Abstract
Human fungal pathogens are associated with diseases ranging from dandruff and skin colonization to invasive bloodstream infections. The major human pathogens belong to the Candida, Aspergillus, and Cryptococcus clades, and infections have high and increasing morbidity and mortality. Many human fungal pathogens were originally assumed to be asexual. However, recent advances in genome sequencing, which revealed that many species have retained the genes required for the sexual machinery, have dramatically influenced our understanding of the biology of these organisms. Predictions of a rare or cryptic sexual cycle have been supported experimentally for some species. Here, I examine the evidence that human pathogens reproduce sexually. The evolution of the mating-type locus in ascomycetes (including Candida and Aspergillus species) and basidiomycetes (Malassezia and Cryptococcus) is discussed. I provide an overview of how sex is suppressed in different species and discuss the potential associations with pathogenesis.
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Abstract
Candida albicans, a diploid yeast commensal and opportunist pathogen, has evolved unusual mechanisms for maintenance of genetic diversity in the absence of a complete sexual cycle. These include chromosomal polymorphisms, mitotic recombination events, and gains and losses of heterozygosity, superimposed on a fundamentally clonal mode of reproduction. Molecular typing of C. albicans strains shows geographical evolutionary associations but these have become partially blurred, probably as a result of extensive human travel. Individual patients usually carry a single C. albicans strain type, but this may undergo microvariation leading to detection of mixtures of closely related types. Associations have been found between clade 1, the most common multilocus sequence typing cluster of related C. albicans strains, and resistance to flucytosine and terbinafine. There are also clade-related associations with lengths of tandem repeats in some cell-surface proteins, but not with virulence or type of infection.
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Affiliation(s)
- Frank C Odds
- Aberdeen Fungal Group, Institute of Medical Sciences, Aberdeen AB25 2ZD, UK.
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Lewis MD, Ma J, Yeo M, Carrasco HJ, Llewellyn MS, Miles MA. Genotyping of Trypanosoma cruzi: systematic selection of assays allowing rapid and accurate discrimination of all known lineages. Am J Trop Med Hyg 2010; 81:1041-9. [PMID: 19996435 DOI: 10.4269/ajtmh.2009.09-0305] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Trypanosoma cruzi, the agent of Chagas disease, can be subdivided into six discrete typing units (DTUs), TcI, TcIIa, TcIIb, TcIIc, TcIId or TcIIe, each having distinct epidemiologically important features. Dozens of genetic markers are available to determine the DTU to which a T. cruzi isolate belongs, but there is no consensus on which should be used. We selected five assays: three polymerase chain reaction (PCR)-restriction fragment length polymorphisms based on single nucleotide polymorphisms (SNPs) in the HSP60, Histone H1, and GPI loci, and PCR product size polymorphism of the LSU rDNA and mini-exon loci. Each assay was tested for its capacity to differentiate between DTUs using a panel of 48 genetically diverse T. cruzi clones. Some markers allowed unequivocal identification of individual DTUs, however, only by using a combination of multiple markers could all six DTUs be resolved. Based upon the results we recommend a triple-assay comprising the LSU rDNA, HSP60 and GPI markers for reliable, rapid, low-cost DTU assignment.
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Affiliation(s)
- Michael D Lewis
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Ben Abdeljelil J, Ben Saida N, Saghrouni F, Fathallah A, Boukadida J, Sboui H, Ben Said M. Systemic neonatal candidosis: the karyotyping of Candida albicans strains isolated from neonates and health-workers. Mycoses 2010; 53:72-7. [DOI: 10.1111/j.1439-0507.2008.01664.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Parra-Ortega B, Cruz-Torres H, Villa-Tanaca L, Hernández-Rodríguez C. Phylogeny and evolution of the aspartyl protease family from clinically relevant Candida species. Mem Inst Oswaldo Cruz 2009; 104:505-12. [DOI: 10.1590/s0074-02762009000300018] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 03/23/2009] [Indexed: 11/21/2022] Open
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Cubillos FA, Vásquez C, Faugeron S, Ganga A, Martínez C. Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations. FEMS Microbiol Ecol 2008; 67:162-70. [PMID: 19016866 DOI: 10.1111/j.1574-6941.2008.00600.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Saccharomyces cerevisiae is a model eukaryotic organism for classical genetics and genomics, and yet its ecology is still largely unknown. In this work, a population genetic analysis was performed on five yeast populations isolated from wine-making areas with different enological practices using simple sequence repeats and restriction fragment length polymorphism of mitochondrial DNA as molecular markers on 292 strains. In accordance with other studies, genome size estimation suggests that native S. cerevisiae strains are mainly homothallic and diploids. Analysis of mtDNA data showed that yeast populations from nonindustrial areas have 40% higher genetic diversity than populations isolated from industrial areas, demonstrating that industrial enological practices are likely to affect native yeast populations negatively by reducing its biodiversity. On the other hand, genetic differentiation analysis based on their microsatellite showed no correlation between genetic and geographic distance and a nonsignificant value when a Mantel test was applied. Finally, in the five populations studied, positive inbreeding (F(is)) values from 0.4 to 0.75, a low but significant level of linkage disequilibrium and a high number of multilocus genotypes were detected. These results strongly advocate that sexual reproduction is frequent enough to erase clonal signature in natural populations and that self-fertilization is the main mating system.
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Affiliation(s)
- Francisco A Cubillos
- Departamento de Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Estación Central, Santiago, Chile
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Jacobsen MD, Boekhout T, Odds FC. Multilocus sequence typing confirms synonymy but highlights differences between Candida albicans and Candida stellatoidea. FEMS Yeast Res 2008; 8:764-70. [PMID: 18547330 DOI: 10.1111/j.1567-1364.2008.00392.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We used multi-locus sequence typing (MLST) to investigate 35 yeast isolates representing the two genome-sequenced strains plus the type strain of Candida albicans, four isolates originally identified as Candida stellatoidea type I and 28 representing type strains of other species now regarded as synonymous with C. albicans. DNA from all 32 C. albicans synonyms readily formed PCR products with the C. albicans MLST primer sets. Their sequences placed all of them within the existing C. albicans clade structure, represented by 1516 isolates. One isolate, originally received as Mycotorula sinensis, was resistant to flucytosine, but no other unusual susceptibilities were found to polyene, azole or echinocandin antifungal agents. The four isolates of C. stellatoidea type I coclustered with two other sucrose-negative isolates, originally identified as examples of Candida africana, in a group of strains highly distinct from the majority of C. albicans. Our results not only confirm the synonymity of all the isolates with C. albicans but also confirm an obvious genotypic difference in the case of C. stellatoidea type I.
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Affiliation(s)
- Mette D Jacobsen
- Aberdeen Fungal Group, Institute of Medical Sciences, Aberdeen, UK
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Cliff PR, Sandoe JAT, Heritage J, Barton RC. Use of multilocus sequence typing for the investigation of colonisation by Candida albicans in intensive care unit patients. J Hosp Infect 2008; 69:24-32. [PMID: 18396349 DOI: 10.1016/j.jhin.2008.02.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 02/06/2008] [Indexed: 11/30/2022]
Abstract
A prospective study was performed to determine the prevalence of candidal colonisation on the general intensive care unit at a large teaching hospital. Colonisation with Candida spp. was found to be common, occurring in 79% of patients on the unit. C. albicans was the commonest species, colonising 64% of patients, followed by C. glabrata (18%) and C. parapsilosis (14%). Most of the members of staff tested carried Candida spp. at some point, although carriage appeared to be transient. C. parapsilosis was the most commonly isolated species from staff hands, whereas C. albicans was the most commonly isolated species from the mouth. The molecular epidemiology of C. albicans was investigated using Ca3 typing and multilocus sequence typing (MLST). MLST proved to be a reproducible typing method and a useful tool for the investigation of the molecular epidemiology of C. albicans. The results of the molecular typing provided evidence for the presence of an endemic strain on the unit, which was isolated repeatedly from patients and staff. This finding suggests horizontal transmission of C. albicans on the unit though it may also reflect the relative frequency of C. albicans strain types colonising patients on admission. This study has important implications for the epidemiology of systemic candidal infections.
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Affiliation(s)
- P R Cliff
- Mycology Reference Centre, The General Infirmary at Leeds, Leeds, UK
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Barada G, Basma R, Khalaf RA. Microsatellite DNA Identification and Genotyping of Candida albicans from Lebanese Clinical Isolates. Mycopathologia 2008; 165:115-25. [DOI: 10.1007/s11046-008-9089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 01/07/2008] [Indexed: 11/30/2022]
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Jacobsen MD, Rattray AMJ, Gow NAR, Odds FC, Shaw DJ. Mitochondrial haplotypes and recombination inCandida albicans. Med Mycol 2008; 46:647-54. [DOI: 10.1080/13693780801986631] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Mating is rare within as well as between clades of the human pathogen Candida albicans. Fungal Genet Biol 2007; 45:221-31. [PMID: 18063395 DOI: 10.1016/j.fgb.2007.10.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 10/12/2007] [Accepted: 10/16/2007] [Indexed: 11/20/2022]
Abstract
Candida albicans is a diploid yeast that can undergo mating and a parasexual cycle, but is apparently unable to undergo meiosis. Characterization of the population structure of C. albicans has shown that reproduction is largely clonal and that mating, if it occurs, is rare or limited to genetically related isolates. Because molecular typing has delineated distinct clades in C. albicans, we have tested whether recombination was common within clades, but rare between clades. Two hundred and three C. albicans isolates have been subjected to multilocus sequence typing (MLST) and the haplotypes at heterozygous MLST genotypes characterized. The C. albicans isolates were distributed among nine clades, of which five corresponded to those previously identified by Ca3 fingerprinting. In each of these clades with more than 10 isolates, polymorphic nucleotide positions located on between 3 and 4 of the six loci were in Hardy-Weinberg disequilibrium. Moreover, each of these polymorphic sites contained excess heterozygotes. This was confirmed by an expanded analysis performed on a recently published MLST dataset for 1044 isolates. On average, 66% of polymorphic positions in the individual clades were in significant excess of heterozygotes over the five clades. These data indicate that mating within clades as well as self-fertilization are both limited and that C. albicans clades do not represent a collection of cryptic species. The study of haplotypes at heterozygous loci performed on our dataset indicates that loss of heterozygosity events due to mitotic recombination is moderately common in natural populations of C. albicans. The maintenance of substantial heterozygosity despite relatively frequent loss of heterozygosity could result from a selective advantage conferred by heterozygosity.
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A single SNP, G929T (Gly310Val), determines the presence of a functional and a non-functional allele of HIS4 in Candida albicans SC5314: detection of the non-functional allele in laboratory strains. Fungal Genet Biol 2007; 45:527-41. [PMID: 17964203 DOI: 10.1016/j.fgb.2007.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 08/24/2007] [Accepted: 08/26/2007] [Indexed: 11/20/2022]
Abstract
Candida albicans is a diploid organism that exhibits high levels of heterozygosity. Although the precise manner by which this heterozygosity provides advantage for the commensal/pathogenic life styles of C. albicans is not known, heterozygous markers are themselves useful for studying genomic rearrangements, which occur frequently in C. albicans. Treatment of CAI-4 with UV light yielded histidine auxotrophs which could be complemented by HIS4, suggesting that strain CAI-4 is heterozygous for HIS4. These auxotrophs appeared to have undergone mitotic recombination and/or chromosome loss. As expected from a heterozygote, disruption of the functional allele of HIS4 resulted in a his4::hisG-URA3-hisG strain that is auxotrophic for histidine. Sequencing of random clones of the HIS4 ORF from CAI-4 and its precursor SC5314 revealed the presence of 11 SNPs, seven synonymous and four non-synonymous. Site-directed mutagenesis indicates that only one of those SNPs, T929G (Gly310Val), is responsible for the non-functionality of the encoded enzyme. HIS4 analysis of five commonly used laboratory strains is reported. This study provides a new, easily measured nutritional marker that can be used in future genetic studies in C. albicans.
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Conde-Ferráez L. El locus MAT (mating-type) de los ascomicetos: su evolución, estructura y regulación. Rev Iberoam Micol 2007; 24:95-9. [PMID: 17604425 DOI: 10.1016/s1130-1406(07)70021-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Invasive fungal infections of the respiratory tract are a major cause of serious morbidity and mortality especially in immunocompromised patients due to neutropenia, corticosteroids, or hematologic malignancy. The role of imaging is very important in the management of patients with fungal infections and chest x-ray is still the most used exploration. Nevertheless, new approaches recommend the systematic use of computed tomography scan for early documentation of invasive fungal infection. Combination of clinical setting with recognition of radiological pattern is the best approach to pulmonary fungal diseases. The following is a review of the imaging features of different invasive fungal infections we can face in our daily practice.
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Affiliation(s)
- Laura Conde-Ferráez
- Centro de Investigación Científica de Yucatán, No. 130 Chuburná de Hidalgo, Mérida, Yucatán, México.
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38
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Odds FC, Bougnoux ME, Shaw DJ, Bain JM, Davidson AD, Diogo D, Jacobsen MD, Lecomte M, Li SY, Tavanti A, Maiden MCJ, Gow NAR, d'Enfert C. Molecular phylogenetics of Candida albicans. EUKARYOTIC CELL 2007; 6:1041-52. [PMID: 17416899 PMCID: PMC1951527 DOI: 10.1128/ec.00041-07] [Citation(s) in RCA: 237] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then alpha/alpha types and was lowest for heterozygous a/alpha types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.
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Affiliation(s)
- Frank C Odds
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
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Andaluz E, Gómez-Raja J, Hermosa B, Ciudad T, Rustchenko E, Calderone R, Larriba G. Loss and fragmentation of chromosome 5 are major events linked to the adaptation of rad52-DeltaDelta strains of Candida albicans to sorbose. Fungal Genet Biol 2007; 44:789-98. [PMID: 17300968 PMCID: PMC2000335 DOI: 10.1016/j.fgb.2007.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 12/30/2006] [Accepted: 01/05/2007] [Indexed: 12/27/2022]
Abstract
Candida albicans can adapt and grow on sorbose plates by losing one copy of Chr5. Since rad52 mutants of Saccharomyces cerevisiae lose chromosomes at a high rate, we have investigated the ability of C. albicans rad52 to adapt to sorbose. Carad52-DeltaDelta mutants generate Sou(+) strains earlier than wild-type but the final yield is lower, probably because they die at a higher rate in sorbose. As other strains of C. albicans, CAF2 and rad52-DeltaDelta derivatives generate Sou(+) strains by a loss of one copy of Chr5 about 75% of the time. In addition, rad52 strains were able to produce Sou(+) strains by a fragmentation/deletion event in one copy of Chr5, consisting of loss of a region adjacent to the right telomere. Finally, both CAF2 and rad52-DeltaDelta produced Sou(+) strains with two apparent full copies of Chr5, suggesting that additional genomic changes may also regulate adaptation to sorbose.
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Affiliation(s)
- Encarnación Andaluz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain
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40
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Odds FC, Davidson AD, Jacobsen MD, Tavanti A, Whyte JA, Kibbler CC, Ellis DH, Maiden MCJ, Shaw DJ, Gow NAR. Candida albicans strain maintenance, replacement, and microvariation demonstrated by multilocus sequence typing. J Clin Microbiol 2006; 44:3647-58. [PMID: 17021093 PMCID: PMC1594753 DOI: 10.1128/jcm.00934-06] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 05/18/2006] [Accepted: 07/24/2006] [Indexed: 11/20/2022] Open
Abstract
We typed 165 Candida albicans isolates from 44 different sources by multilocus sequence typing (MLST) and ABC typing of rRNA genes and determined their homozygosity or heterozygosity at the mating-type-like locus (MTL). The isolates represented pairs or larger sets from individual sources, which allowed the determination of strain diversity within patients. A comparison of replicate sequence data determined a reproducibility threshold for regarding isolates as MLST indistinguishable. For 36 isolate sets, MLST and ABC typing showed indistinguishable or highly related strain types among isolates from different sites or from the same site at different times from each patient. This observation included 11 sets with at least one isolate from a blood culture and a nonsterile site from the same patient. For one patient, strain replacement was evidenced in the form of two sets of isolates from different hospital admissions where the strain types within each set were nearly identical but where the two sets differed both by MLST and ABC typing. MLST therefore confirms the existing view of C. albicans strain carriage. Microvariation, evidenced as small differences between MLST types, resulted in most instances from a loss of heterozygosity at one or more of the sequenced loci. Among isolate sets that showed major strain type differences, some isolates could be excluded as likely examples of handling errors during storage. However, for a minority of isolates, intermittent differences in ABC type for tightly clustered MLST types and intermittent appearances of MTL homozygosity lead us to propose that some C. albicans isolates, or all isolates under yet-to-be-determined conditions, maintain a high level of genetic diversity by mechanisms such as recombination, gene conversion, or chromosomal ploidy change.
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Affiliation(s)
- F C Odds
- Aberdeen Fungal Group, Institute of Medical Sciences, Aberdeen AB25 2ZD, United Kingdom.
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41
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Holmes AR, Tsao S, Ong SW, Lamping E, Niimi K, Monk BC, Niimi M, Kaneko A, Holland BR, Schmid J, Cannon RD. Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2. Mol Microbiol 2006; 62:170-86. [PMID: 16942600 DOI: 10.1111/j.1365-2958.2006.05357.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Elevated expression of the plasma membrane drug efflux pump proteins Cdr1p and Cdr2p was shown to accompany decreased azole susceptibility in Candida albicans clinical isolates. DNA sequence analysis revealed extensive allelic heterozygosity, particularly of CDR2. Cdr2p alleles showed different abilities to transport azoles when individually expressed in Saccharomyces cerevisiae. Loss of heterozygosity, however, did not accompany decreased azole sensitivity in isogenic clinical isolates. Two adjacent non-synonymous single nucleotide polymorphisms (NS-SNPs), G1473A and I1474V in the putative transmembrane (TM) helix 12 of CDR2, were found to be present in six strains including two isogenic pairs. Site-directed mutagenesis showed that the TM-12 NS-SNPs, and principally the G1473A NS-SNP, contributed to functional differences between the proteins encoded by the two Cdr2p alleles in a single strain. Allele-specific PCR revealed that both alleles were equally frequent among 69 clinical isolates and that the majority of isolates (81%) were heterozygous at the G1473A/I1474V locus, a significant (P < 0.001) deviation from the Hardy-Weinberg equilibrium. Phylogenetic analysis by maximum likelihood (Paml) identified 33 codons in CDR2 in which amino acid allelic changes showed a high probability of being selectively advantageous. In contrast, all codons in CDR1 were under purifying selection. Collectively, these results indicate that possession of two functionally different CDR2 alleles in individual strains may confer a selective advantage, but that this is not necessarily due to azole resistance.
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Affiliation(s)
- Ann R Holmes
- Department of Oral Sciences, School of Dentistry, University of Otago, Dunedin, New Zealand
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42
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Bougnoux ME, Diogo D, François N, Sendid B, Veirmeire S, Colombel JF, Bouchier C, Van Kruiningen H, d'Enfert C, Poulain D. Multilocus sequence typing reveals intrafamilial transmission and microevolutions of Candida albicans isolates from the human digestive tract. J Clin Microbiol 2006; 44:1810-20. [PMID: 16672411 PMCID: PMC1479199 DOI: 10.1128/jcm.44.5.1810-1820.2006] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is a human commensal that is also responsible for superficial and systemic infections. Little is known about the carriage of C. albicans in the digestive tract and the genome dynamics that occur during commensalisms of this diploid species. The aim of this study was to evaluate the prevalence, diversity, and genetic relationships among C. albicans isolates recovered during natural colonization of the digestive tract of humans, with emphasis on Crohn's disease patients who produce anti-yeast antibodies and may have altered Candida sp. carriage. Candida sp. isolates were recovered from 234 subjects within 25 families with multiple cases of Crohn's disease and 10 control families, sampled at the oral and fecal sites. Prevalences of Candida sp. and C. albicans carriage were 53.4% and 46.5%, respectively, indicating frequent commensal carriage. No differences in prevalence of carriage could be observed between Crohn's disease patients and healthy subjects. Multilocus sequence typing (MLST) of C. albicans isolates revealed frequent colonization of a subject or several members of the same family by genetically indistinguishable or genetically close isolates. These latter isolates differed by loss-of-heterozygosity events at one or several of the MLST loci. These loss-of-heterozygosity events could be due to either chromosome loss followed by duplication or large mitotic recombination events between complementary chromosomes. This study was the first to jointly assess commensal carriage of C. albicans, intrafamilial transmission, and microevolution. The high frequency of each of these events suggests that the digestive tract provides an important and natural niche for microevolutions of diploid C. albicans through the loss of heterozygosity.
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Affiliation(s)
- M-E Bougnoux
- Unité Postulante Biologie et Pathogénicité Fongiques, INRA USC 2019, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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43
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Nébavi F, Ayala FJ, Renaud F, Bertout S, Eholié S, Moussa K, Mallié M, de Meeûs T. Clonal population structure and genetic diversity of Candida albicans in AIDS patients from Abidjan (Côte d'Ivoire). Proc Natl Acad Sci U S A 2006; 103:3663-8. [PMID: 16501044 PMCID: PMC1450139 DOI: 10.1073/pnas.0511328103] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have investigated the genotype at 14 enzyme-encoding loci in 275 isolates of the pathogenic yeast Candida albicans sampled from 42 HIV-positive patients (all but one with AIDS) from Abidjan (Côte d'Ivoire). We separately analyzed the following variables: patient, residence, age, gender, T cell count, hospitalization (yes or no), drug treatment, date of sampling, multilocus genotype, and serotype. The most important factors contributing to the genetic variability of C. albicans are individual patient and gender. Our data manifest that the population size of the parasite is relatively small within each patient, although larger in women than in men, and that, at least for the patients involved in the study, the transmission rate of C. albicans between human adults is very low. Most important is the inference that the prevailing mode of reproduction of C. albicans in natural populations is clonal, so that sexual reproduction is extremely rare, if it occurs at all.
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Affiliation(s)
- François Nébavi
- *Laboratoire de Parasitologie et Mycologie Médicale, EA 2413, Faculté de Pharmacie, 34060 Montpellier Cedex 1, France
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - François Renaud
- Génétique et Evolution des Maladies Infectieuses, Equipe Evolution des Systèmes Symbiotiques, Unité Mixte de Recherche 2724, Institute de Recherche pour le Développement, Centre National de la Recherche Scientifique, BP 64501, 34394 Montpellier Cedex 5, France
| | - Sébastien Bertout
- *Laboratoire de Parasitologie et Mycologie Médicale, EA 2413, Faculté de Pharmacie, 34060 Montpellier Cedex 1, France
| | - Serge Eholié
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Treichville, 01 BP V 3 Abidjan, Côte d’Ivoire
| | - Koné Moussa
- Laboratoire de Parasitologie Mycologie, Institut Pasteur de Côte d’Ivoire, BP V 116 Abidjan, Côte d’Ivoire; and
| | - Michèle Mallié
- *Laboratoire de Parasitologie et Mycologie Médicale, EA 2413, Faculté de Pharmacie, 34060 Montpellier Cedex 1, France
| | - Thierry de Meeûs
- Génétique et Evolution des Maladies Infectieuses, Equipe Evolution des Systèmes Symbiotiques, Unité Mixte de Recherche 2724, Institute de Recherche pour le Développement, Centre National de la Recherche Scientifique, BP 64501, 34394 Montpellier Cedex 5, France
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44
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Chauhan N, Ciudad T, Rodríguez-Alejandre A, Larriba G, Calderone R, Andaluz E. Virulence and karyotype analyses of rad52 mutants of Candida albicans: regeneration of a truncated chromosome of a reintegrant strain (rad52/RAD52) in the host. Infect Immun 2006; 73:8069-78. [PMID: 16299301 PMCID: PMC1307084 DOI: 10.1128/iai.73.12.8069-8078.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The virulence of Candida albicans mutants lacking one or both copies of RAD52, a gene involved in homologous recombination (HR), was evaluated in a murine model of hematogenously disseminated candidiasis. In this study, the virulence of the rad52Delta mutant was dependent upon the inoculum concentration. Mice survived at a cell inoculum of 1 x 10(6), but there was a decrease in survival time at dosages of 1.5 x 10(6) and especially at 3 x 10(6) cells per animal. The heterozygote RAD52/rad52 behaved like wild type, whereas a reintegrant strain was intermediate in its ability to cause death compared to these strains and to the avirulent rad52/rad52 null at inocula of 1 x 10(6) and 1.5 x 10(6) cells. A double mutant, lig4/lig4/rad52/rad52, was avirulent at all inocula used. PCR analysis of the RAD52 and/or LIG4 loci showed that all strains recovered from animals matched the genotype of the inoculated strains. Analysis of the electrophoretical karyotypes indicated that the inoculated, reintegrant strain carried a large deletion in one copy of chromosome 6 (the shortest homologue, or Chr6b). Interestingly, truncated Chr6b was regenerated in all the strains recovered from moribund animals using the homologue as a template. Further, regeneration of Chr6b was paralleled by an increase in virulence that was still lower than that of wild type, likely because of the persistent loss of heterozygosity in the regenerated region. Overall, our results indicate that systemic candidiasis can develop in the absence of HR, but simultaneous elimination of both recombination pathways, HR and nonhomologous end-joining, suppresses virulence even at very high inocula.
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Affiliation(s)
- Neeraj Chauhan
- Georgetown University Medical Center, Department of Microbiology & Immunology, Washington, DC, USA
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45
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Tavanti A, Davidson AD, Johnson EM, Maiden MCJ, Shaw DJ, Gow NAR, Odds FC. Multilocus sequence typing for differentiation of strains of Candida tropicalis. J Clin Microbiol 2005; 43:5593-600. [PMID: 16272492 PMCID: PMC1287820 DOI: 10.1128/jcm.43.11.5593-5600.2005] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 07/20/2005] [Accepted: 08/27/2005] [Indexed: 11/20/2022] Open
Abstract
A system is described for typing isolates of the pathogenic fungus Candida tropicalis, based on sequence polymorphisms in fragments of six genes: ICL1, MDR1, SAPT2, SAPT4, XYR1, and ZWF1a. The system differentiated 87 diploid sequence types (DSTs) among a total of 106 isolates tested or 80 DSTs among 88 isolates from unique sources. Replicate isolates from the same source clustered together with high statistical similarity, with the exception of one isolate. However, a clade of very closely related isolates included replicate isolates from three different patients, as well as single isolates from eight other patients. This clade, provisionally designated clade 1, was one of three clusters of isolates with high statistical similarity. Five of six isolates in one cluster that may acquire clade status were resistant to flucytosine. This study adds C. tropicalis to Candida albicans and Candida glabrata as Candida species for which a multilocus sequence typing (MLST) system has been set up. The C. tropicalis MLST database can be accessed at http://pubmlst.org/ctropicalis/.
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Affiliation(s)
- Arianna Tavanti
- Institute of Medical Sciences, Aberdeen, AB25 2ZD, United Kingdom
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46
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Paoletti M, Rydholm C, Schwier EU, Anderson MJ, Szakacs G, Lutzoni F, Debeaupuis JP, Latgé JP, Denning DW, Dyer PS. Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus. Curr Biol 2005; 15:1242-8. [PMID: 16005299 DOI: 10.1016/j.cub.2005.05.045] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 05/13/2005] [Accepted: 05/16/2005] [Indexed: 10/25/2022]
Abstract
Aspergillus fumigatus is a medically important opportunistic pathogen and a major cause of respiratory allergy. The species has long been considered an asexual organism. However, genome analysis has revealed the presence of genes associated with sexual reproduction, including a MAT-2 high-mobility group mating-type gene and genes for pheromone production and detection (Galagan et al., personal communication; Nierman et al., personal communication). We now demonstrate that A. fumigatus has other key characteristics of a sexual species. We reveal the existence of isolates containing a complementary MAT-1 alpha box mating-type gene and show that the MAT locus has an idiomorph structure characteristic of heterothallic (obligate sexual outbreeding) fungi. Analysis of 290 worldwide clinical and environmental isolates with a multiplex-PCR assay revealed the presence of MAT1-1 and MAT1-2 genotypes in similar proportions (43% and 57%, respectively). Further population genetic analyses provided evidence of recombination across a global sampling and within North American and European subpopulations. We also show that mating-type, pheromone-precursor, and pheromone-receptor genes are expressed during mycelial growth. These results indicate that A. fumigatus has a recent evolutionary history of sexual recombination and might have the potential for sexual reproduction. The possible presence of a sexual cycle is highly significant for the population biology and disease management of the species.
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Affiliation(s)
- Mathieu Paoletti
- School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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47
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Sampaio P, Gusmão L, Correia A, Alves C, Rodrigues AG, Pina-Vaz C, Amorim A, Pais C. New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes. J Clin Microbiol 2005; 43:3869-76. [PMID: 16081924 PMCID: PMC1233915 DOI: 10.1128/jcm.43.8.3869-3876.2005] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five new microsatellite loci were described and characterized for use as molecular markers for the identification and genetic differentiation of Candida albicans strains. Following the typing of 72 unrelated clinical isolates, the analysis revealed that they were all polymorphic, presenting from 5 to 30 alleles and 8 to 46 different genotypes. The discriminatory power obtained by combining the information generated by three microsatellites used in a multiplex PCR amplification strategy was 0.99, the highest ever reported. The multiplex PCR was later used to test a total of 114 C. albicans strains, including multiple isolates from the same patient collected from different body locations and along episodes of vulvovaginal infections. Three different scenarios for strain relatedness were identified: (i) different isolates that were revealed to be the same strain, (ii) isolates that were the same strain but that apparently underwent a process of microevolution, and (iii) isolates that corresponded to different strains. Analysis of the microevolutionary changes between isolates from recurrent infections indicated that the genotype alterations observed could be the result of events that lead to the loss of heterozygosity (LOH). In one case of recurrent infection, LOH was observed at the CAI locus, and this could have been related to exposure to fluconazole, since such strains were exposed to this antifungal during treatment. The analysis of microsatellites by a multiplex PCR strategy was found to be a highly efficient tool for the rapid and accurate differentiation of C. albicans strains and adequate for the identification of fine microevolutionary events that could be related to strain microevolution in response to environmental stress conditions.
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Affiliation(s)
- Paula Sampaio
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Leonor Gusmão
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Alexandra Correia
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Cíntia Alves
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Acácio G. Rodrigues
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Cidália Pina-Vaz
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - António Amorim
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Célia Pais
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
- Corresponding author. Mailing address: Departamento de Biologia, Centro de Biologia da Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal. Phone: (351)253604312. Fax: (351)253678980. E-mail:
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48
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Pringle A, Baker DM, Platt JL, Wares JP, Latgé JP, Taylor JW. CRYPTIC SPECIATION IN THE COSMOPOLITAN AND CLONAL HUMAN PATHOGENIC FUNGUS ASPERGILLUS FUMIGATUS. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb01059.x] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Forche A, May G, Magee PT. Demonstration of loss of heterozygosity by single-nucleotide polymorphism microarray analysis and alterations in strain morphology in Candida albicans strains during infection. EUKARYOTIC CELL 2005; 4:156-65. [PMID: 15643071 PMCID: PMC544165 DOI: 10.1128/ec.4.1.156-165.2005] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Candida albicans is a diploid yeast with a predominantly clonal mode of reproduction, and no complete sexual cycle is known. As a commensal organism, it inhabits a variety of niches in humans. It becomes an opportunistic pathogen in immunocompromised patients and can cause both superficial and disseminated infections. It has been demonstrated that genome rearrangement and genetic variation in isolates of C. albicans are quite common. One possible mechanism for generating genome-level variation among individuals of this primarily clonal fungus is mutation and mitotic recombination leading to loss of heterozygosity (LOH). Taking advantage of a recently published genome-wide single-nucleotide polymorphism (SNP) map (A. Forche, P. T. Magee, B. B. Magee, and G. May, Eukaryot. Cell 3:705-714, 2004), an SNP microarray was developed for 23 SNP loci residing on chromosomes 5, 6, and 7. It was used to examine 21 strains previously shown to have undergone mitotic recombination at the GAL1 locus on chromosome 1 during infection in mice. In addition, karyotypes and morphological properties of these strains were evaluated. Our results show that during in vivo passaging, LOH events occur at observable frequencies, that such mitotic recombination events occur independently in different loci across the genome, and that changes in karyotypes and alterations of phenotypic characteristics can be observed alone, in combination, or together with LOH.
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Affiliation(s)
- Anja Forche
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St. SE, Minneapolis, MN 55455, USA
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50
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Chen KW, Lo HJ, Lin YH, Li SY. Comparison of four molecular typing methods to assess genetic relatedness of Candida albicans clinical isolates in Taiwan. J Med Microbiol 2005; 54:249-258. [PMID: 15713608 DOI: 10.1099/jmm.0.45829-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This report describes the investigation of the genetic profiles of 53 Candida albicans isolates collected from 18 hospitals in Taiwan using three PFGE-based typing methods (PFGE karyotyping, and PFGE of SfiI and BssHII restriction fragments) and one repetitive-sequence-PCR (rep-PCR) method. All four methods were able to identify clonal related isolates from the same patients. PFGE-BssHII exhibited the highest discriminatory power by discriminating 40 genotypes, followed by PFGE-SfiI (35 genotypes) and then by rep-PCR (31 genotypes), while PFGE karyotyping exhibited the lowest discriminatory power (19 genotypes). High discriminatory power can also be achieved by combining typing methods with different typing mechanisms, such as rep-PCR and PFGE-based typing methods. The results also showed that the genotype of each isolate was patient-specific and not associated with the source of the isolation, geographic origin or antifungal resistance.
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Affiliation(s)
- Kuo-Wei Chen
- Laboratory for Mycopathogens, Chlamydia and Mycoplasma, Division of Laboratory Research and Development, Center for Disease Control, 161 Kun-Yang Street, Nan-Kang District, Taipei 115, Taiwan 2Division of Clinical Research, National Health Research Institutes, Taipei, Taiwan
| | - Hsiu-Jung Lo
- Laboratory for Mycopathogens, Chlamydia and Mycoplasma, Division of Laboratory Research and Development, Center for Disease Control, 161 Kun-Yang Street, Nan-Kang District, Taipei 115, Taiwan 2Division of Clinical Research, National Health Research Institutes, Taipei, Taiwan
| | - Yu-Hui Lin
- Laboratory for Mycopathogens, Chlamydia and Mycoplasma, Division of Laboratory Research and Development, Center for Disease Control, 161 Kun-Yang Street, Nan-Kang District, Taipei 115, Taiwan 2Division of Clinical Research, National Health Research Institutes, Taipei, Taiwan
| | - Shu-Ying Li
- Laboratory for Mycopathogens, Chlamydia and Mycoplasma, Division of Laboratory Research and Development, Center for Disease Control, 161 Kun-Yang Street, Nan-Kang District, Taipei 115, Taiwan 2Division of Clinical Research, National Health Research Institutes, Taipei, Taiwan
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