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Mishra A, Forche A, Anderson MZ. Parasexuality of Candida Species. Front Cell Infect Microbiol 2021; 11:796929. [PMID: 34966696 PMCID: PMC8711763 DOI: 10.3389/fcimb.2021.796929] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/19/2021] [Indexed: 12/03/2022] Open
Abstract
While most fungi have the ability to reproduce sexually, multiple independent lineages have lost meiosis and developed parasexual cycles in its place. Emergence of parasexual cycles is particularly prominent in medically relevant fungi from the CUG paraphyletic group of Candida species. Since the discovery of parasex in C. albicans roughly two decades ago, it has served as the model for Candida species. Importantly, parasex in C. albicans retains hallmarks of meiosis including genetic recombination and chromosome segregation, making it a potential driver of genetic diversity. Furthermore, key meiotic genes play similar roles in C. albicans parasex and highlights parallels between these processes. Yet, the evolutionary role of parasex in Candida adaptation and the extent of resulting genotypic and phenotypic diversity remain as key knowledge gaps in this facultative reproductive program. Here, we present our current understanding of parasex, the mechanisms governing its regulation, and its relevance to Candida biology.
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Affiliation(s)
- Abhishek Mishra
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, ME, United States
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
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2
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Chen WC, Chen PY, Yang SC, Yen TY, Lu CY, Chen JM, Lee PI, Chang LY, Chen YC, Huang LM. Comparisons of the clinical and mycological characteristics of pediatric candidemia. J Formos Med Assoc 2021; 121:1668-1679. [PMID: 34876342 DOI: 10.1016/j.jfma.2021.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/17/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND/PURPOSE Invasive candidiasis is a severe infectious disease that could lead to mortality in critically ill children. METHODS We collected data regarding demographics, underlying diseases, predisposing factors, outcomes for pediatric patients with candidemia at a medical centre in Taiwan from 2011 to 2017. RESULTS Fifty-eight patients with 60 candidemia episodes were diagnosed. The 3 most common species were Candida albicans (42%), Candida parapsilosis (25%) and Candida tropicalis (23%). C. parapsilosis predominantly infected infants and neonates (median age: 0.8 years, range: 0.1-14.5). Cases with C. tropicalis had significantly higher rates of multidrug resistance (p = 0.011) and disseminated candidiasis (p = 0.025) compared with other cases. The all-cause mortality rate was 43%, and the candidemia-related mortality rate was 29%. Pediatric sequential organ failure assessment score >8 [adjusted odds ratio (aOR) 66.2, 95% CI 4.03-1088.5] and posaconazole resistance (aOR 33.57, 95% CI 1.61-700.3) were the most significant risk factors associated with candidemia-related mortality, whereas treatment with effective antifungal agents within 48 h (aOR 0.07, 95% CI 0.01-0.9) was the only significant protective factor. CONCLUSIONS Candidemia-related mortality was related to azole resistance; therefore, empirical therapy with echinocandin or amphotericin B is recommended pending species and susceptibility results.
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Affiliation(s)
- Wan-Chen Chen
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Pediatrics, Changhua Christian Children's Hospital, Changhua City, Taiwan
| | - Pao-Yu Chen
- Division of Infectious Disease, Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shun-Chen Yang
- Department of Pediatrics, Changhua Christian Children's Hospital, Changhua City, Taiwan
| | - Ting-Yu Yen
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Yi Lu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jong-Min Chen
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ping-Ing Lee
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Luan-Ying Chang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Yee-Chun Chen
- Division of Infectious Disease, Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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Xu J. Is Natural Population of Candida tropicalis Sexual, Parasexual, and/or Asexual? Front Cell Infect Microbiol 2021; 11:751676. [PMID: 34760719 PMCID: PMC8573272 DOI: 10.3389/fcimb.2021.751676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023] Open
Abstract
Candida tropicalis is one of the most common opportunistic yeast pathogens of humans, especially prevalent in tropical and subtropical regions. This yeast has broad ecological distributions, can be found in both terrestrial and aquatic ecosystems, including being associated with a diversity of trees, animals, and humans. Evolutionary theory predicts that organisms thriving in diverse ecological niches likely have efficient mechanisms to generate genetic diversity in nature. Indeed, abundant genetic variations have been reported in natural populations (both environmental and clinical) of C. tropicalis. However, at present, our understanding on how genetic diversity is generated in natural C. tropicalis population remains controversial. In this paper, I review the current understanding on the potential modes of reproduction in C. tropicalis. I describe expectations of the three modes of reproduction (sexual, parasexual, and asexual) and compare them with the observed genotypic variations in natural populations. Though sexual and parasexual reproduction cannot be excluded, the analyses suggest asexual reproduction alone could explain all the observations reported so far. The results here have implications for understanding the evolution and epidemiology of C. tropicalis and other related human fungal pathogens.
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Affiliation(s)
- Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Department of Biology, McMaster University, Hamilton, ON, Canada
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4
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Canela HMS, Cardoso B, Frazão MR, Falcão JP, Vitali LH, Martinez R, da Silva Ferreira ME. Genetic diversity assessed using PFGE, MLP and MLST in Candida spp. candidemia isolates obtained from a Brazilian hospital. Braz J Microbiol 2021; 52:503-516. [PMID: 33611738 PMCID: PMC8105495 DOI: 10.1007/s42770-021-00446-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/02/2021] [Indexed: 01/12/2023] Open
Abstract
Candida spp. are the main causative agents of invasive fungal infections in immunocompromised patients. Candidemia has attributable mortality rates of 15 to 35% and increases hospitalisation time and costs, thus making this disease a public health concern. This study aimed to use pulsed-field gel electrophoresis (PFGE), microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST) to analyse the genetic relationships among 65 Candida spp. bloodstream isolates, including 35 Candida albicans, 15 Candida glabrata and 15 Candida tropicalis isolates, all of which were obtained from patients in a Brazilian hospital. Moreover, patient clinical data were assessed. All techniques resulted in high discriminatory indexes. C. albicans and C. tropicalis isolates showed high genetic variability, while C. glabrata isolates had relatively low genetic variability. Moreover, a cluster of C. glabrata isolates was identified in a hospital unit. New MLST sequence types, diploid sequence types and alleles are described. Relationships were not observed between the molecular typing results and clinical characteristics. The molecular typing of clinical strains increases our understanding of candidemia epidemiology and promotes the development of strategies that can reduce the incidence of this disease. Moreover, this study is the first to combine these techniques to genotype these three species in Brazil.
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Affiliation(s)
- Heliara Maria Spina Canela
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Bloco S - Térreo - Sala 013A-S, Avenida do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Bárbara Cardoso
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Bloco S - Térreo - Sala 013A-S, Avenida do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Miliane Rodrigues Frazão
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Bloco S - Térreo - Sala 013A-S, Avenida do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Juliana Pfrimer Falcão
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Bloco S - Térreo - Sala 013A-S, Avenida do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Lucia Helena Vitali
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Roberto Martinez
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Márcia Eliana da Silva Ferreira
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Bloco S - Térreo - Sala 013A-S, Avenida do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil.
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Takashima M, Suh SO, Bai FY, Sugita T. Takashi Nakase's last tweet: what is the current direction of microbial taxonomy research? FEMS Yeast Res 2020; 19:5670643. [PMID: 31816016 DOI: 10.1093/femsyr/foz066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022] Open
Abstract
During the last few decades, type strains of most yeast species have been barcoded using the D1/D2 domain of their LSU rRNA gene and internal transcribed spacer (ITS) region. Species identification using DNA sequences regarding conspecificity in yeasts has also been studied. Most yeast species can be identified according to the sequence divergence of their ITS region or a combination of the D1/D2 and ITS regions. Studies that have examined intraspecific diversity have used multilocus sequence analyses, whereas the marker regions used in this analysis vary depending upon taxa. D1/D2 domain and ITS region sequences have been used as barcodes to develop primers suitable for the detection of the biological diversity of environmental DNA and the microbiome. Using these barcode sequences, it is possible to identify relative lineages and infer their gene products and function, and how they adapt to their environment. If barcode sequence was not variable enough to identify a described species, one could investigate the other biological traits of these yeasts, considering geological distance, environmental circumstances and isolation of reproduction. This article is dedicated to late Dr Takashi Nakase (1939-2018).
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Affiliation(s)
- Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan.,Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Sung-Oui Suh
- Manufacturing Science and Technology, American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA
| | - Feng-Yan Bai
- Institute of Microbiology, State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing 100101, China
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
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6
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Mancera E, Frazer C, Porman AM, Ruiz-Castro S, Johnson AD, Bennett RJ. Genetic Modification of Closely Related Candida Species. Front Microbiol 2019; 10:357. [PMID: 30941104 PMCID: PMC6433835 DOI: 10.3389/fmicb.2019.00357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 02/11/2019] [Indexed: 11/25/2022] Open
Abstract
Species from the genus Candida are among the most important human fungal pathogens. Several of them are frequent commensals of the human microbiota but are also able to cause a variety of opportunistic infections, especially when the human host becomes immunocompromised. By far, most of the research to understand the molecular underpinnings of the pathogenesis of these species has focused on Candida albicans, the most virulent member of the genus. However, epidemiological data indicates that related Candida species are also clinically important. Here, we describe the generation of a set of strains and plasmids to genetically modify C. dubliniensis and C. tropicalis, the two pathogenic species most closely related to C. albicans. C. dubliniensis is an ideal model to understand C. albicans pathogenesis since it is the closest species to C. albicans but considerably less virulent. On the other hand, C. tropicalis is ranked among the four most common causes of infections by Candida species. Given that C. dubliniensis and C. tropicalis are obligate diploids with no known conventional sexual cycle, we generated strains that are auxotrophic for at least two amino acids which allows the tandem deletion of both alleles of a gene by complementing the two auxotrophies. The strains were generated in two different genetic backgrounds for each species — one for which the genomic sequence is available and a second clinically important one. In addition, we have adapted plasmids developed to delete genes and epitope/fluorophore tag proteins in C. albicans so that they can be employed in C. tropicalis. The tools generated here allow for efficient genetic modification of C. dubliniensis and C. tropicalis, and thus facilitate the study of the molecular basis of pathogenesis in these medically relevant fungi.
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Affiliation(s)
- Eugenio Mancera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato, Mexico.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Corey Frazer
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, United States
| | - Allison M Porman
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, United States
| | - Susana Ruiz-Castro
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato, Mexico
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, United States
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7
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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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Benedetti VP, Savi DC, Aluizio R, Adamoski D, Kava-Cordeiro V, Galli-Terasawa LV, Glienke C. Analysis of the genetic diversity of Candida isolates obtained from diabetic patients and kidney transplant recipients. Mem Inst Oswaldo Cruz 2017; 0:0. [PMID: 27276363 PMCID: PMC4957493 DOI: 10.1590/0074-02760160042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/16/2016] [Indexed: 11/22/2022] Open
Abstract
Yeasts of the genus Candida have high genetic variability and are the most common opportunistic pathogenic fungi in humans. In this study, we evaluated the genetic diversity among 120 isolates of Candida spp. obtained from diabetic patients, kidney transplant recipients and patients without any immune deficiencies from Paraná state, Brazil. The analysis was performed using the ITS1-5.8S-ITS2 region and a partial sequence of 28S rDNA. In the phylogenetic analysis, we observed a consistent separation of the species C. albicans, C. dubliniensis, C. glabrata, C. tropicalis, C. parapsilosis, C. metapsilosis and C. orthopsilosis, however with low intraspecific variability. In the analysis of the C. albicans species, two clades were formed. Clade A included the largest number of isolates (91.2%) and the majority of isolates from GenBank (71.4%). The phylogenetic analysis showed low intraspecific genetic diversity, and the genetic polymorphisms between C. albicans isolates were similar to genetic divergence found in other studies performed with isolates from Brazil. This low genetic diversity of isolates can be explained by the geographic proximity of the patients evaluated. It was observed that yeast colonisation was highest in renal transplant recipients and diabetic patients and that C. albicans was the species most frequently isolated.
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Affiliation(s)
- Volmir Pitt Benedetti
- Universidade Paranaense, Universidade Paranaense, Departamento de Microbiologia, Francisco Beltrão PR , Brasil, Universidade Paranaense, Departamento de Microbiologia, Francisco Beltrão, PR, Brasil.,Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba, PR, Brasil
| | - Daiani Cristina Savi
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Rodrigo Aluizio
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Douglas Adamoski
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Vanessa Kava-Cordeiro
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Lygia V Galli-Terasawa
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
| | - Chirlei Glienke
- Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Patologia Básica, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Universidade Federal do Paraná, Departamento de Genética, Curitiba PR , Brasil, Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brasil
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Wu Y, Zhou HJ, Che J, Li WG, Bian FN, Yu SB, Zhang LJ, Lu J. Multilocus microsatellite markers for molecular typing of Candida tropicalis isolates. BMC Microbiol 2014; 14:245. [PMID: 25410579 PMCID: PMC4247128 DOI: 10.1186/s12866-014-0245-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/10/2014] [Indexed: 01/08/2023] Open
Abstract
Background Candida tropicalis is considered to be the leading pathogen causing nosocomial fungemia and hepatosplenic fungal infections in patients with cancer, particularly those with leukemia. Microsatellite-based typing methods using sets of genetic markers have been developed and reported for population structure analysis of C. albicans, C. glabrata, and C. parapsilosis, but no studies have been published for genetic analysis of C. tropicalis. The objective of this study was to develop new microsatellite loci that have the ability to distinguish among C. tropicalis isolates. Results DNA sequences containing over 10 bi- or tri-nucleotide repeats were selected from the C. tropicalis genome database. Thirty PCR primers sets specific for the microsatellite loci were designed and tested using eight clinically independent isolates. According to the amplification efficiency, specificity, and observed polymorphisms, eight markers were selected for further population structure analysis and molecular typing. Sixty-five independent C. tropicalis isolates were genotyped using these 8 markers. Based on these analyses, six microsatellite loci were confirmed, although two loci were found to be with unstable flanking areas. The six polymorphic loci displayed 4–22 alleles and 7–27 genotypes. The discriminatory power of the six loci ranged from 0.70 to 0.95. Genotyping results obtained by microsatellite analysis were compared to PCR-fingerprinting and multi-locus sequence typing (MLST). The comparisons showed that microsatellite analysis and MLST had the similar discriminatory power for C. tropicalis, which were more powerful than PCR-fingerprinting. Conclusions This is the first attempt to develop new microsatellite loci for C. tropicalis. These newly developed markers will be a valuable resource for the differentiation of C. tropicalis isolates. More C. tropicalis isolates will need to be sequenced and analyzed in order to fully show the potential of these newly developed microsatellite markers.
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Affiliation(s)
- Yuan Wu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China.
| | - Hai-jian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China.
| | - Jie Che
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China.
| | - Wen-ge Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China.
| | - Fu-ning Bian
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China.
| | - Shuan-bao Yu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China.
| | - Li-juan Zhang
- Department of Gynecology and Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China.
| | - Jinxing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang bai Road 155, Chang ping District, Beijing, China.
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Molecular fingerprints to identify Candida species. BIOMED RESEARCH INTERNATIONAL 2013; 2013:923742. [PMID: 23844370 PMCID: PMC3703398 DOI: 10.1155/2013/923742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/30/2013] [Accepted: 06/06/2013] [Indexed: 11/17/2022]
Abstract
A wide range of molecular techniques have been developed for genotyping Candida species. Among them, multilocus sequence typing (MLST) and microsatellite length polymorphisms (MLP) analysis have recently emerged. MLST relies on DNA sequences of internal regions of various independent housekeeping genes, while MLP identifies microsatellite instability. Both methods generate unambiguous and highly reproducible data. Here, we review the results achieved by using these two techniques and also provide a brief overview of a new method based on high-resolution DNA melting (HRM). This method identifies sequence differences by subtle deviations in sample melting profiles in the presence of saturating fluorescent DNA binding dyes.
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Wu Y, Zhou H, Wang J, Li L, Li W, Cui Z, Chen X, Cen R, Lu J, Cheng Y. Analysis of the clonality of Candida tropicalis strains from a general hospital in Beijing using multilocus sequence typing. PLoS One 2012; 7:e47767. [PMID: 23152759 PMCID: PMC3494695 DOI: 10.1371/journal.pone.0047767] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/19/2012] [Indexed: 11/29/2022] Open
Abstract
Multilocus sequence typing (MLST) based on six loci was used to analyze the relationship of 58 Candida tropicalis isolates from individual patients in a general hospital in Beijing, China. A total of 52 diploid sequence types (DSTs) were generated by the MLST, all of which were new to the central database. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrograms were constructed, which showed that the 58 isolates were distributed robustly and 6 main groups were clustered regardless of the specimen source and medical department. The minimum spanning tree (MST) of the 58 isolates (52 DSTs) and all 401 isolates (268 DSTs) in the C. tropicalis central database (http://pubmlst.org/ctropicalis/) indicated that the isolates in this study clustered in three relative pure clonal complexes, and 2 clustered with isolates from Taiwan, Belgium, Brazil, and the US. This study presents the first MLST analysis of C. tropicalis isolates from Mainland China, which may be useful for further studies on the similarity, genetic relationship, and molecular epidemiology of C. tropicalis strains worldwide.
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Affiliation(s)
- Yuan Wu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jing Wang
- China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Lianqing Li
- Shanxi Center for Clinical Laboratories, TaiYuan, Shanxi, People's Republic of China
| | - Wenge Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhigang Cui
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xia Chen
- Department of Critical Care Medicine, Fu Xing Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Ruiqi Cen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jinxing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- * E-mail: (JL); (YC)
| | - Ying Cheng
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- * E-mail: (JL); (YC)
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Discovery of a phenotypic switch regulating sexual mating in the opportunistic fungal pathogen Candida tropicalis. Proc Natl Acad Sci U S A 2011; 108:21158-63. [PMID: 22158989 DOI: 10.1073/pnas.1112076109] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sexual reproduction can promote genetic diversity in eukaryotes, and yet many pathogenic fungi have been labeled as obligate asexual species. It is becoming increasingly clear, however, that cryptic sexual programs may exist in some species, and that efficient mating requires the necessary developmental switch to be triggered. In this study we investigate Candida tropicalis, an important human fungal pathogen that has been reported to be asexual. Significantly, we demonstrate that C. tropicalis uses a phenotypic switch to regulate a cryptic program of sexual mating. Thus, diploid a and α cells must undergo a developmental transition to the mating-competent form, and only then does efficient cell-cell conjugation take place resulting in the formation of stable a/α tetraploids. We show that both the phenotypic switch and sexual mating depend on the conserved transcriptional regulator Wor1, which is regulated by temperature in other fungal species. In contrast, C. tropicalis mating occurs efficiently at both 25 °C and 37 °C, suggesting that it could occur in the mammalian host and have direct consequences for the outcome of an infection. Transcriptional profiling further reveals that ≈ 400 genes are differentially expressed between the two phenotypic states, including the regulatory factor Wor1. Taken together, our results demonstrate that C. tropicalis has a unique sexual program, and that entry to this program is controlled via a Wor1-mediated, metastable switch. These observations have direct implications for the regulation and evolution of cryptic sexual programs in related fungal pathogens.
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Chen YN, Lo HJ, Wu CC, Ko HC, Chang TP, Yang YL. Loss of heterozygosity of FCY2 leading to the development of flucytosine resistance in Candida tropicalis. Antimicrob Agents Chemother 2011; 55:2506-14. [PMID: 21422221 PMCID: PMC3101439 DOI: 10.1128/aac.01777-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 01/28/2011] [Accepted: 03/03/2011] [Indexed: 11/20/2022] Open
Abstract
As fluconazole resistance becomes an emerging issue for treating infections caused by Candida tropicalis, searching for alternative becomes a prominent task. In the present study, 97 clinical isolates of C. tropicalis were tested for the susceptibilities to flucytosine (5FC) with the Etest method. Although only one isolate was resistant to 5FC, 30 susceptible isolates could produce resistant progeny after exposure to the drug. Interestingly, 22 of these 30 clinical isolates had a heterozygous G/T at the 145th position on FCY2, encoding purine-cytosine permease, whereas their progeny recovered from within the inhibitory ellipses had homozygous T/T, resulting in null alleles for both copies of the gene and produced only truncated proteins, effecting the 5FC resistance. Furthermore, we found that two major fluconazole-resistant clinical clones, diploid sequence type 98 (DST98) and DST140, had a homozygous G/G at the 145th position, and neither was able to produce 5FC-resistant progeny within the inhibitory ellipses. Hence, strains of C. tropicalis containing heterozygous alleles may develop 5FC resistance readily, whereas those with homozygous G/G wild-type alleles can be treated with 5FC. Subsequently, a combination of 5FC and another antifungal drug is applicable for treating infections of C. tropicalis.
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Affiliation(s)
- Yen-Ning Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu
| | - Hsiu-Jung Lo
- Division of Infectious Diseases, National Health Research Institutes, Miaoli
| | - Chia-Chen Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hui-Ching Ko
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Te-Pin Chang
- Division of Infectious Diseases, National Health Research Institutes, Miaoli
| | - Yun-Liang Yang
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
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Alby K, Bennett RJ. Sexual reproduction in the Candida clade: cryptic cycles, diverse mechanisms, and alternative functions. Cell Mol Life Sci 2010; 67:3275-85. [PMID: 20552251 DOI: 10.1007/s00018-010-0421-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 05/18/2010] [Accepted: 05/25/2010] [Indexed: 12/16/2022]
Abstract
To have sex, or not to have sex, is a question posed by many microorganisms. In favor of a sexual lifestyle is the associated rearrangement of genetic material that confers potential fitness advantages, including resistance to antimicrobial agents. The asexual lifestyle also has benefits, as it preserves complex combinations of genes that may be optimal for pathogenesis. For this reason, it was thought that several pathogenic fungi favored strictly asexual modes of reproduction. Recent approaches using genome sequencing, population analysis, and experimental techniques have now revised this simplistic picture. It is now apparent that many pathogenic fungi have retained the ability to undergo sexual reproduction, although reproduction is primarily clonal in origin. In this review, we highlight the current understanding of sexual programs in the Candida clade of species. We also examine evidence that sexual-related processes can be used for functions in addition to mating and recombination in these organisms.
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Affiliation(s)
- Kevin Alby
- Department of Molecular Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI 02912, USA
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15
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Li SY, Yang YL, Lin YH, Ko HC, Wang AH, Chen KW, Wang CW, Chi H, Lo HJ. Two closely related fluconazole-resistant Candida tropicalis clones circulating in Taiwan from 1999 to 2006. Microb Drug Resist 2009; 15:205-10. [PMID: 19728779 DOI: 10.1089/mdr.2009.0915] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, we reported that diploid sequence type (DST) 140 was a predominant type of Candida tropicalis among isolates with fluconazole minimum inhibitory concentrations (MICs) >or=64 microg/ml collected in the Taiwan Surveillance of Antimicrobial Resistance of Yeasts (TSARY) in 1999. To determine if DST140 persists in Taiwan, we have used multilocus sequence typing to characterize the genetic profiles of 31 resistant isolates (MICs >or=64 microg/ml), together with 19 susceptible isolates (MICs <or=16 microg/ml) collected in TSARY 2006. Among the 50 isolates, 33 distinct DSTs were detected. Of the 31 resistant isolates, 11 (35.5%) belonged to two closely related DSTs (140 and 98), whereas none of the 19 susceptible isolates did (p = 0.004). The isolates belonging to DST140 and 98 were from different geographic regions instead of a restricted area. Thus, our data show temporal and spatial transmission of C. tropicalis clones with high fluconazole MICs in Taiwan from 1999 to 2006.
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Affiliation(s)
- Shu-Ying Li
- 1 Mycotic Diseases Laboratory, Research and Diagnostic Center, Centers for Disease Control , Taipei, Taiwan
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Trtkova J, Pavlicek P, Ruskova L, Hamal P, Koukalova D, Raclavsky V. Performance of optimized McRAPD in identification of 9 yeast species frequently isolated from patient samples: potential for automation. BMC Microbiol 2009; 9:234. [PMID: 19903328 PMCID: PMC2779194 DOI: 10.1186/1471-2180-9-234] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 11/10/2009] [Indexed: 05/25/2023] Open
Abstract
Background Rapid, easy, economical and accurate species identification of yeasts isolated from clinical samples remains an important challenge for routine microbiological laboratories, because susceptibility to antifungal agents, probability to develop resistance and ability to cause disease vary in different species. To overcome the drawbacks of the currently available techniques we have recently proposed an innovative approach to yeast species identification based on RAPD genotyping and termed McRAPD (Melting curve of RAPD). Here we have evaluated its performance on a broader spectrum of clinically relevant yeast species and also examined the potential of automated and semi-automated interpretation of McRAPD data for yeast species identification. Results A simple fully automated algorithm based on normalized melting data identified 80% of the isolates correctly. When this algorithm was supplemented by semi-automated matching of decisive peaks in first derivative plots, 87% of the isolates were identified correctly. However, a computer-aided visual matching of derivative plots showed the best performance with average 98.3% of the accurately identified isolates, almost matching the 99.4% performance of traditional RAPD fingerprinting. Conclusion Since McRAPD technique omits gel electrophoresis and can be performed in a rapid, economical and convenient way, we believe that it can find its place in routine identification of medically important yeasts in advanced diagnostic laboratories that are able to adopt this technique. It can also serve as a broad-range high-throughput technique for epidemiological surveillance.
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Affiliation(s)
- Jitka Trtkova
- Department of Microbiology, Palacky University and University Hospital Olomouc, Czech Republic.
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The β-tubulin gene as a molecular phylogenetic marker for classification and discrimination of the Saccharomyces sensu stricto complex. Antonie van Leeuwenhoek 2008; 95:135-42. [DOI: 10.1007/s10482-008-9296-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/02/2008] [Indexed: 11/26/2022]
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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