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Costa FDF, Souza RSCD, Voidaleski MF, Gomes RR, Reis GF, Lima BJFDS, Candido GZ, Geraldo MR, Soares JMB, Schneider GX, Trindade EDS, Bini IH, Moreno LF, Bombassaro A, Queiroz-Telles F, Raittz RT, Quan Y, Arruda P, Attili-Angelis D, de Hoog S, Vicente VA. Sugarcane: an unexpected habitat for black yeasts in Chaetothyriales. IMA Fungus 2023; 14:20. [PMID: 37794500 PMCID: PMC10552356 DOI: 10.1186/s43008-023-00124-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
Sugarcane (Saccharum officinarum, Poaceae) is cultivated on a large scale in (sub)tropical regions such as Brazil and has considerable economic value for sugar and biofuel production. The plant is a rich substrate for endo- and epiphytic fungi. Black yeasts in the family Herpotrichiellaceae (Chaetothyriales) are colonizers of human-dominated habitats, particularly those rich in toxins and hydrocarbon pollutants, and may cause severe infections in susceptible human hosts. The present study assessed the diversity of Herpotrichiellaceae associated with sugarcane, using in silico identification and selective isolation. Using metagenomics, we identified 5833 fungal sequences, while 639 black yeast-like isolates were recovered in vitro. In both strategies, the latter fungi were identified as members of the genera Cladophialophora, Exophiala, and Rhinocladiella (Herpotrichiellaceae), Cyphellophora (Cyphellophoraceae), and Knufia (Trichomeriaceae). In addition, we discovered new species of Cladophialophora and Exophiala from sugarcane and its rhizosphere. The first environmental isolation of Cladophialophora bantiana is particularly noteworthy, because this species up to now is exclusively known from the human host where it mostly causes fatal brain disease in otherwise healthy patients.
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Affiliation(s)
- Flávia de F Costa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Rafael S C de Souza
- Molecular Biology and Genetics Engineering Center, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Morgana F Voidaleski
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Guilherme F Reis
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Bruna J F de S Lima
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Giovanna Z Candido
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Marlon R Geraldo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Jade M B Soares
- Biological Sciences Graduation, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Gabriela X Schneider
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | | | - Israel H Bini
- Department of Cell Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Leandro F Moreno
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Flávio Queiroz-Telles
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
- Clinical Hospital of the Federal University of Paraná, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Roberto T Raittz
- Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, Brazil
| | - Yu Quan
- Center of Expertise in Mycology of Radboud, University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Paulo Arruda
- Molecular Biology and Genetics Engineering Center, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Genetics and Evolution Department, Biology Institute, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Derlene Attili-Angelis
- Division of Microbial Resources (DRM/CPQBA), State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Sybren de Hoog
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.
- Center of Expertise in Mycology of Radboud, University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
| | - Vania A Vicente
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil.
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.
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2
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Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology. Sci Rep 2020; 10:14229. [PMID: 32848176 PMCID: PMC7450056 DOI: 10.1038/s41598-020-70915-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
Melanized fungi and black yeasts in the family Herpotrichiellaceae (order Chaetothyriales) are important agents of human and animal infectious diseases such as chromoblastomycosis and phaeohyphomycosis. The oligotrophic nature of these fungi enables them to survive in adverse environments where common saprobes are absent. Due to their slow growth, they lose competition with common saprobes, and therefore isolation studies yielded low frequencies of clinically relevant species in environmental habitats from which humans are thought to be infected. This problem can be solved with metagenomic techniques which allow recognition of microorganisms independent from culture. The present study aimed to identify species of the family Herpotrichiellaceae that are known to occur in Brazil by the use of molecular markers to screen public environmental metagenomic datasets from Brazil available in the Sequence Read Archive (SRA). Species characterization was performed with the BLAST comparison of previously described barcodes and padlock probe sequences. A total of 18,329 sequences was collected comprising the genera Cladophialophora, Exophiala, Fonsecaea, Rhinocladiella and Veronaea, with a focus on species related to the chromoblastomycosis. The data obtained in this study demonstrated presence of these opportunists in the investigated datasets. The used techniques contribute to our understanding of environmental occurrence and epidemiology of black fungi.
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Silva Zatti M, Domingos Arantes T, Cordeiro Theodoro R. Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review. Mycoses 2020; 63:1006-1020. [PMID: 32648947 DOI: 10.1111/myc.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fungal infections have increased during the last years due to the AIDS epidemic and immunosuppressive therapies. The available diagnostic methods, such as culture, histopathology and serology, have several drawbacks regarding sensitivity, specificity and time-consuming, while molecular methods are still expensive and dependent on many devices. In order to overcome these challenges, isothermal nucleic acid amplification techniques (INAT) arose as promising diagnostic methods for infectious diseases. OBJECTIVE This review aimed to present and discuss the main contributions of the isothermal nucleic acid amplification techniques applied in medical mycology. METHODS Papers containing terms for each INAT (NASBA, RCA, LAMP, CPA, SDA, HAD or PSR) and the terms 'mycoses' or 'disease, fungal' were obtained from National Center for Biotechnology Information database until August 2019. RESULTS NASBA, RCA, LAMP and PSR are the INAT reported in the literature for detection and identification of pathogenic fungi. Despite the need of a previous conventional PCR, the RCA technique might also be used for genotyping or cryptic species differentiation, which may be important for the treatment of certain mycoses; nevertheless, LAMP is the most used INAT for pathogen detection. CONCLUSION Among all INATs herein reviewed, LAMP seems to be the most appropriate method for fungal detection, since it is affordable, sensitive, specific, user-friendly, rapid, robust, equipment-free and deliverable to end-users, fulfilling all ASSURED criteria of the World Health Organization for an ideal diagnostic method.
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Affiliation(s)
- Matheus Silva Zatti
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Thales Domingos Arantes
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiás, Brazil
| | - Raquel Cordeiro Theodoro
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
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Schneider GX, Gomes RR, Bombassaro A, Zamarchi K, Voidaleski MF, Costa FF, Leão ACR, Lima BJFS, Soley BS, Colombo IR, Cândido GZ, Najafzadeh MJ, Sun J, de Azevedo CMPS, Marques SG, de Hoog GS, Vicente VA. New Molecular Markers Distinguishing Fonsecaea Agents of Chromoblastomycosis. Mycopathologia 2019; 184:493-504. [PMID: 31317385 DOI: 10.1007/s11046-019-00359-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/01/2019] [Indexed: 11/28/2022]
Abstract
The species belonging to the genus Fonsecaea are the main causative agents of chromoblastomycosis. The invasive potential of Fonsecaea differs significantly among its various sibling species. Moreover, the lack of clarity on the virulence and availability of precise markers to distinguish and detect Fonsecaea species is attributed to the different ways of dissemination and pathogenicity. Therefore, the present study aimed to propose new molecular tools to differentiate between sibling species causing chromoblastomycosis. We used an infection model of chromoblastomycosis in BALB/c to study species-specific molecular markers for the in vivo detection of Fonsecaea species in biological samples. Specific primers based on the CBF5 gene were developed for Fonsecaea pedrosoi, Fonsecaea monophora, Fonsecaea nubica, and Fonsecaea pugnacius. In addition, a padlock probe was designed for F. pugnacius based on ITS sequences. We also assessed the specificity of Fonsecaea species using in silico, in vitro, and in vivo assays. The results showed that markers and probes could effectively discriminate the species in both clinical and environmental samples, enabling bioprospecting of agents of chromoblastomycosis, thereby elucidating the infection route of the disease.
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Affiliation(s)
- Gabriela X Schneider
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Kassiely Zamarchi
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Morgana F Voidaleski
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Flávia F Costa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Aniele C R Leão
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna J F S Lima
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna S Soley
- Department of Pharmacology, Federal University of Paraná, Curitiba, Brazil
| | - Israella R Colombo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Giovanna Z Cândido
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jiufeng Sun
- Department of Dermatology, The Second Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Conceição M P S de Azevedo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil.,Department of Medicine, Federal University of Maranhão, São Luis, Brazil
| | - Sirlei G Marques
- University Hospital, Federal University of Maranhão, São Luiz, Brazil.,Cedro Laboratory, São Luiz, Brazil
| | - G Sybren de Hoog
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil. .,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands. .,Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
| | - Vânia A Vicente
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil.
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Velasco J, Revankar S. CNS Infections Caused by Brown-Black Fungi. J Fungi (Basel) 2019; 5:jof5030060. [PMID: 31295828 PMCID: PMC6787688 DOI: 10.3390/jof5030060] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 12/20/2022] Open
Abstract
Central nervous system (CNS) infections caused by brown-black or dematiaceous fungi are distinctly rare and represent a small proportion of infections termed phaeohyphomycoses. However, these are becoming more commonly reported. Though many fungi have been implicated in disease, most cases are caused by only a few species, Cladophialophora bantiana being the most common. Most of the fungi described are molds, and often cause infection in immunocompetent individuals, in contrast to infection with other more common molds such as Aspergillus, which is usually seen in highly immunocompromised patients. Diagnosis is challenging, as there are no specific tests for this group of fungi. In addition, these infections are often refractory to standard drug therapies, requiring an aggressive combined surgical and medical approach to improve outcomes, yet mortality remains high. There are no standardized treatments due to a lack of randomized clinical trials, though guidelines have been published based on available data and expert opinion.
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Affiliation(s)
- Jon Velasco
- Detroit Medical Center, Wayne State University, Detroit, MI 48201, USA
| | - Sanjay Revankar
- Division of Infectious Diseases, Department of Medicine, Wayne State University, 3990 John R. Street, 5 Hudson, Detroit, MI 48201, USA.
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Huang TT, Liu SC, Huang CH, Lin CJ, Huang ST. An Integrated Real-time Electrochemical LAMP Device for Pathogenic Bacteria Detection in Food. ELECTROANAL 2018. [DOI: 10.1002/elan.201800382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tsung-Tao Huang
- Department of Chemical Engineering and Biotechnology; National Taipei University of Technology; Taipei 106 Taiwan
- Biomedical Platform and Incubation Services Division; Instrument Technology Research Center, National Applied Research Laboratories; Hsinchu 300 Taiwan
| | - Shao-Chung Liu
- Department of Chemical Engineering and Biotechnology; National Taipei University of Technology; Taipei 106 Taiwan
| | - Chih-Hung Huang
- Department of Chemical Engineering and Biotechnology; National Taipei University of Technology; Taipei 106 Taiwan
| | - Chun-Ju Lin
- Biomedical Platform and Incubation Services Division; Instrument Technology Research Center, National Applied Research Laboratories; Hsinchu 300 Taiwan
| | - Sheng-Tung Huang
- Department of Chemical Engineering and Biotechnology; National Taipei University of Technology; Taipei 106 Taiwan
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7
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Lin H, Jiang X, Yi J, Wang X, Zuo R, Jiang Z, Wang W, Zhou E. Molecular identification of Neofabraea species associated with bull's-eye rot on apple using rolling-circle amplification of partial EF-1α sequence. Can J Microbiol 2017; 64:57-68. [PMID: 29084390 DOI: 10.1139/cjm-2017-0448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A rolling-circle amplification (RCA) method with padlock probes targeted on EF-1α regions was developed for rapid detection of apple bull's-eye rot pathogens, including Neofabraea malicorticis, N. perennans, N. kienholzii, and N. vagabunda (synonym: N. alba). Four padlock probes (PLP-Nm, PLP-Np, PLP-Nk, and PLP-Nv) were designed and tested against 28 samples, including 22 BER pathogen cultures, 4 closely related species, and 2 unrelated species that may cause serious apple decays. The assay successfully identified all the bull's-eye rot pathogenic fungi at the level of species, while no cross-reaction was observed in all target species and no false-positive reaction was observed with all strains used for reference. This study showed that the use of padlock probes and the combination of probe signal amplification by RCA provided an effective and sensitive method for the rapid identification of Neofabraea spp. The method could therefore be a useful tool for monitoring bull's-eye rot pathogens in port quarantine and orchard epidemiological studies.
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Affiliation(s)
- Huijiao Lin
- a Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.,b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Xiang Jiang
- b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Jianping Yi
- c Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200135, China
| | - Xinguo Wang
- b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Ranling Zuo
- b Inspection and Test Center, Huangpu Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510730, China
| | - Zide Jiang
- a Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Weifang Wang
- d Guangdong Key Laboratory of Import and Export Technical Measures of Animal, Plant and Food, Guangdong Inspection and Quarantine Technology Center, Guangzhou 510623, China
| | - Erxun Zhou
- a Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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8
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Rodrigues AM, Najafzadeh MJ, de Hoog GS, de Camargo ZP. Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification. Front Microbiol 2015; 6:1385. [PMID: 26696992 PMCID: PMC4672047 DOI: 10.3389/fmicb.2015.01385] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/20/2015] [Indexed: 01/19/2023] Open
Abstract
Sporothrix infections are emerging as an important human and animal threat among otherwise healthy patients, especially in Brazil and China. Correct identification of sporotrichosis agents is beneficial for epidemiological surveillance, enabling implementation of adequate public-health policies and guiding antifungal therapy. In areas of limited resources where sporotrichosis is endemic, high-throughput detection methods that are specific and sensitive are preferred over phenotypic methods that usually result in misidentification of closely related Sporothrix species. We sought to establish rolling circle amplification (RCA) as a low-cost screening tool for species-specific identification of human-pathogenic Sporothrix. We developed six species-specific padlock probes targeting polymorphisms in the gene encoding calmodulin. BLAST-searches revealed candidate probes that were conserved intraspecifically; no significant homology with sequences from humans, mice, plants or microorganisms outside members of Sporothrix were found. The accuracy of our RCA-based assay was demonstrated through the specificity of probe-template binding to 25 S. brasiliensis, 58 S. schenckii, 5 S. globosa, 1 S. luriei, 4 S. mexicana, and 3 S. pallida samples. No cross reactivity between closely related species was evident in vitro, and padlock probes yielded 100% specificity and sensitivity down to 3 × 106 copies of the target sequence. RCA-based speciation matched identifications via phylogenetic analysis of the gene encoding calmodulin and the rDNA operon (kappa 1.0; 95% confidence interval 1.0-1.0), supporting its use as a reliable alternative to DNA sequencing. This method is a powerful tool for rapid identification and specific detection of medically relevant Sporothrix, and due to its robustness has potential for ecological studies.
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Affiliation(s)
- Anderson M Rodrigues
- Cell Biology Division, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo São Paulo, Brazil
| | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, Ghaem Hospital, School of Medicine, Mashhad University of Medical Sciences Mashhad, Iran
| | - G Sybren de Hoog
- Centraalbureau voor Schimmelcultures, CBS-KNAW Fungal Biodiversity Centre Utrecht, Netherlands
| | - Zoilo P de Camargo
- Cell Biology Division, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo São Paulo, Brazil
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9
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Deng S, Zhou Z, de Hoog GS, Wang X, Abliz P, Sun J, Najafzadeh MJ, Pan W, Lei W, Zhu S, Hasimu H, Zhang P, Guo Y, Deng D, Liao W. Evaluation of two molecular techniques for rapid detection of the main dermatophytic agents of tinea capitis. Br J Dermatol 2015; 173:1494-500. [PMID: 26342174 DOI: 10.1111/bjd.14156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2015] [Indexed: 11/26/2022]
Abstract
BACKGROUND Tinea capitis is very common in Western China, with the most widespread aetiological agent being Trichophyton violaceum, while Microsporum canis is prevalent in the remainder of China. Conventional diagnostics and internal transcribed spacer (ITS) sequencing analyses have proven relatively limited due to the close phylogenetic relationship of anthropophilic dermatophytes. Therefore, alternative molecular tools with sufficient specificity, reproducibility and sensitivity are necessary. OBJECTIVES To evaluate two molecular techniques [multiplex ligation-dependent probe amplification (MLPA) and rolling circle amplification (RCA)] for rapid detection of the aetiological agents of tinea capitis, T. violaceum and M. canis. METHODS Probes of RCA and MLPA were designed with target sequences in the rDNA ITS gene region. Strains tested consist of 31 T. violaceum, 22 M. canis and 24 reference strains of species that are taxonomically close to the target species. RESULTS The specificity and reproducibility of RCA and MLPA in detection of T. violaceum and M. canis were both 100% in both species. Sensitivity testing showed that RCA was positive at concentrations down to 1·68 × 10(6) copies of DNA in the TvioRCA probe, and 2·7 × 10(8) copies of DNA in McRCA. MLPA yielded positive results at concentrations of DNA down to 1·68 × 10(1) copies in the TvioMLPA probe and 2·7 × 10(2) in McMLPA. CONCLUSIONS The two techniques were sufficiently specific and sensitive for discriminating the target DNA of T. violaceum and M. canis from that of closely related dermatophytes. RCA and MLPA are advantageous in their reliability and ease of operation compared with standard polymerase chain reaction and conventional methods.
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Affiliation(s)
- S Deng
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Department of Dermatology, First Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Z Zhou
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Department of Dermatology, Puyang Oilfield General Hospital, Puyang, Henan, China
| | - G S de Hoog
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, the Netherlands
- Basic Pathology Department, Federal University of Paraná State, Curitiba, Paraná, Brazil
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - X Wang
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, the Netherlands
| | - P Abliz
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, the Netherlands
| | - J Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, China
| | - M J Najafzadeh
- Department of Parasitology and Mycology & Cancer Molecular Pathology Research Center, School of Medicine, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - W Pan
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - W Lei
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - S Zhu
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - H Hasimu
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, the Netherlands
| | - P Zhang
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Y Guo
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - D Deng
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - W Liao
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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10
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Zakeri H, Shokohi T, Badali H, Mayahi S, Didehdar M. Use of Padlock Probes and Rolling Circle Amplification (RCA) for Rapid Identification of Trichophyton Species, Related to Human and Animal Disorder. Jundishapur J Microbiol 2015; 8:e19107. [PMID: 26421127 PMCID: PMC4584133 DOI: 10.5812/jjm.19107v2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 08/07/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022] Open
Abstract
Background: The high degree of phenotypic similarity among Trichophyton species makes their identification difficult. Objectives: The current study aims to establish the use of rolling circle amplification (RCA) based on internal transcribed spacer ribosomal DNA (ITS rDNA) as a powerful, simple, and rapid procedure for distinguishing closely related organisms, and specifically to identify Trichophyton species, which cause human and animal disorders. Materials and Methods: A total of sixty-one isolates belonging to three species of Trichophyton were identified to the species level based on microscopic and macroscopic examinations and their ITS rDNA regions were sequenced. Three specific circular oligonucleotide probes targeting the ITS1 and ITS2 regions were designed to differentiate Trichophyton rubrum, T. mentagrophytes, and T. tonsurans. Results: Of the 61 putative Trichophyton clinical isolates, 52 were identified to the species level. The most common species was T. mentagrophytes var. interdigitale (31 isolates), followed by T. rubrum (11 isolates), T. tonsurans (9 isolates), and T. violaceum (1 isolates); moreover, 9 isolates were identified as non-Trichophyton species. The RCA method correctly identified four Trichophyton species and was 100% specific for each species. Neither cross-reaction between the examined species of Trichophyton nor false positive or false negative results were observed. Conclusions: Species identification of Trichophyton is crucially important for epidemiological and phylogenetic purposes and for genotype delineation. RCA based on ITS polymorphisms can be used to generate identification barcodes and as an alternative to DNA sequencing; it is a very fast, specific, and economical tool for species identification.
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Affiliation(s)
- Hamideh Zakeri
- Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
| | - Tahereh Shokohi
- Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, IR Iran
- Department of Medical Mycology and Parasitology, Mazandaran University of Medical Sciences, Sari, IR Iran
- Corresponding author: Tahereh Shokohi, Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, IR Iran. Tel: +98-1133543781, Fax: 98-1513543248, E-mail:
| | - Hamid Badali
- Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, IR Iran
- Department of Medical Mycology and Parasitology, Mazandaran University of Medical Sciences, Sari, IR Iran
| | - Saba Mayahi
- Department of Medical Mycology and Parasitology, Mazandaran University of Medical Sciences, Sari, IR Iran
| | - Mojtaba Didehdar
- Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
- Arak Medical Faculty, Arak University of Medical Sciences, Arak, IR Iran
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Rapid identification of black grain eumycetoma causative agents using rolling circle amplification. PLoS Negl Trop Dis 2014; 8:e3368. [PMID: 25474355 PMCID: PMC4256478 DOI: 10.1371/journal.pntd.0003368] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/22/2014] [Indexed: 11/19/2022] Open
Abstract
Accurate identification of mycetoma causative agent is a priority for treatment. However, current identification tools are far from being satisfactory for both reliable diagnosis and epidemiological investigations. A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Rolling Circle Amplification (RCA) uses species-specific padlock probes and isothermal DNA amplification. The tests were based on ITS sequences and developed for Falciformispora senegalensis, F. tompkinsii, Madurella fahalii, M. mycetomatis, M. pseudomycetomatis, M. tropicana, Medicopsis romeroi, and Trematosphaeria grisea. With the isothermal RCA assay, 62 isolates were successfully identified with 100% specificity and no cross reactivity or false results. The main advantage of this technique is the low-cost, high specificity, and simplicity. In addition, it is highly reproducible and can be performed within a single day. Treatment of eumycetoma largely depends on the causative pathogen. Identification of mycetoma agent with phenotypic features is too limited, and physiological and biochemical techniques are laborious, time-consuming and nonspecific, whereas the currently available molecular methods based on DNA sequencing are specific but extremely expensive. We describe rolling circle amplification method for identification of black grain eumycetoma using species-specific padlock probes. Eight probes were designed and successfully used for species identification and the results were easily visualized in 1% agarose gel. RCA provides a simple, reproducible, and cost-effective method for rapid identification of mycetoma agent that can be used in low-resource clinical settings.
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Detection and identification of opportunistic Exophiala species using the rolling circle amplification of ribosomal internal transcribed spacers. J Microbiol Methods 2013; 94:338-42. [PMID: 23872449 DOI: 10.1016/j.mimet.2013.06.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 06/25/2013] [Accepted: 06/26/2013] [Indexed: 11/23/2022]
Abstract
Deep infections by melanized fungi deserve special attention because of a potentially fatal, cerebral or disseminated course of disease in otherwise healthy patients. Timely diagnostics are a major problem with these infections. Rolling circle amplification (RCA) is a sensitive, specific and reproducible isothermal DNA amplification technique for rapid molecular identification of microorganisms. RCA-based diagnostics are characterized by good reproducibility, with few amplification errors compared to PCR. The method is applied here to species of Exophiala known to cause systemic infections in humans. The ITS rDNA region of five Exophiala species (E. dermatitidis, E. oligosperma, E. spinifera, E. xenobiotica, and E. jeanselmei) was sequenced and aligned in view of designing specific padlock probes to be used for the detection of single nucleotide polymorphisms (SNPs) of the Exophiala species concerned. The assay proved to successfully amplify DNA of the target fungi at the level of species; while no cross-reactivity was observed. Amplification products were visualized on 1% agarose gels to verify the specificity of probe-template binding. Amounts of reagents were minimized to avoid the generation of false positive results. The sensitivity of RCA may help to improve early diagnostics of these difficult to diagnose infections.
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The bright future of darkness--the rising power of black fungi: black yeasts, microcolonial fungi, and their relatives. Mycopathologia 2013; 175:365-8. [PMID: 23715632 DOI: 10.1007/s11046-013-9666-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 05/10/2013] [Indexed: 10/26/2022]
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Severe Disseminated Phaeohyphomycosis in an Immunocompetent Patient Caused by Veronaea botryosa. Mycopathologia 2013; 175:497-503. [DOI: 10.1007/s11046-013-9632-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/21/2013] [Indexed: 10/27/2022]
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15
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Veronaea botryosa: Molecular Identification with Amplified Fragment Length Polymorphism (AFLP) and In vitro Antifungal Susceptibility. Mycopathologia 2013; 175:505-13. [DOI: 10.1007/s11046-013-9631-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/21/2013] [Indexed: 10/27/2022]
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