1
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Kabtani J, Ranque S. A Comparative Description of Dermatophyte Genomes: A State-of-the-Art Review. Mycopathologia 2023; 188:1007-1025. [PMID: 37812320 DOI: 10.1007/s11046-023-00802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
The nomenclature and phylogeny of dermatophytes is currently based on the nucleotide sequence polymorphisms of a few genomic regions. However, the limitations of this multilocus sequence-based approach makes dermatophyte species identification difficult. Variation and adaptation are key to the persistence of species. Nevertheless, this heterogeneity poses a genuine problem for the classification and nomenclature of dermatophytes. The relatively high intra-species and low inter-species polymorphisms of this keratinophilic group of fungi hampers both species delineation and identification. Establishing the taxonomic boundaries of dermatophyte species complexes remains controversial. Furthermore, until recently, knowledge of molecular biology, genetics and genomics remained limited. This systematic review highlights the added value of whole genome sequencing and analysis data in dermatophyte classification that might enhance identification and, consequently, the diagnosis and management of dermatophytoses. Our approach consisted in describing and comparing the dermatophyte mitochondrial genomes, secretomes (Adhesins, LysM domains, proteases) and metabolic pathways, with the aim to provide new insights and a better understanding of the phylogeny and evolution of dermatophytes.
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Affiliation(s)
- J Kabtani
- IHU Méditerranée Infection, 13005, Marseille, France
| | - S Ranque
- IHU Méditerranée Infection, 13005, Marseille, France.
- AP-HM, IRD, SSA, VITROME, Aix-Marseille Université, 13005, Marseille, France.
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2
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Koroiva R, Santana DJ. Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae). AN ACAD BRAS CIENC 2022; 94:e20200825. [PMID: 36477987 DOI: 10.1590/0001-3765202220200825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/19/2021] [Indexed: 12/09/2022] Open
Abstract
We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).
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Affiliation(s)
- Ricardo Koroiva
- Universidade Federal da Paraíba, Departamento de Sistemática e Tecnologia, Centro de Ciências Exatas e da Natureza, Laboratório Multiusuário do Programa de Pós-Graduação em Ciências Biológicas/Zoologia, Castelo Branco, Campus Universitário, s/n, 58051900 João Pessoa, PB, Brazil.,Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
| | - Diego José Santana
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
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3
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Abstract
AbstractThe order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.
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4
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Jabet A, Normand AC, Moreno-Sabater A, Guillot J, Risco-Castillo V, Brun S, Demar M, Blaizot R, Nabet C, Packeu A, Piarroux R. Investigations upon the Improvement of Dermatophyte Identification Using an Online Mass Spectrometry Application. J Fungi (Basel) 2022; 8:jof8010073. [PMID: 35050013 PMCID: PMC8780538 DOI: 10.3390/jof8010073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 12/10/2022] Open
Abstract
Online MALDI-TOF mass spectrometry applications, such as MSI-2, have been shown to help identify dermatophytes, but recurrent errors are still observed between phylogenetically close species. The objective of this study was to assess different approaches to reduce the occurrence of such errors by adding new reference spectra to the MSI-2 application. Nine libraries were set up, comprising an increasing number of spectra obtained from reference strains that were submitted to various culture durations on two distinct culture media: Sabouraud gentamicin chloramphenicol medium and IDFP Conidia medium. The final library included spectra from 111 strains of 20 species obtained from cultures on both media collected every three days after the appearance of the colony. The performance of each library was then analyzed using a cross-validation approach. The spectra acquisitions were carried out using a Microflex Bruker spectrometer. Diversifying the references and adding spectra from various culture media and culture durations improved identification performance. The percentage of correct identification at the species level rose from 63.4 to 91.7% when combining all approaches. Nevertheless, residual confusion between close species, such as Trichophyton rubrum, Trichophyton violaceum and Trichophyton soudanense, remained. To distinguish between these species, mass spectrometry identification should take into account basic morphological and/or clinico-epidemiological features.
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Affiliation(s)
- Arnaud Jabet
- AP-HP (Assistance Publique-Hôpitaux de Paris), Service de Parasitologie Mycologie, Hôpital La Pitié-Salpêtrière, 75013 Paris, France; (A.J.); (C.N.); (R.P.)
- AP-HP, Hôpital Saint-Antoine, Service de Parasitologie Mycologie, Sorbonne Université, 75012 Paris, France;
| | - Anne-Cécile Normand
- AP-HP (Assistance Publique-Hôpitaux de Paris), Service de Parasitologie Mycologie, Hôpital La Pitié-Salpêtrière, 75013 Paris, France; (A.J.); (C.N.); (R.P.)
- Correspondence:
| | - Alicia Moreno-Sabater
- AP-HP, Hôpital Saint-Antoine, Service de Parasitologie Mycologie, Sorbonne Université, 75012 Paris, France;
- Inserm, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Jacques Guillot
- Dynamic Research Group, Ecole Nationale Vétérinaire d’Alfort, UPEC, USC ANSES, 94700 Maisons-Alfort, France; (J.G.); (V.R.-C.)
- Department of Parasitology-Mycology, Ecole Nationale Vétérinaire, Agroalimentaire et de L’alimentation, Oniris, 44307 Nantes, France
| | - Veronica Risco-Castillo
- Dynamic Research Group, Ecole Nationale Vétérinaire d’Alfort, UPEC, USC ANSES, 94700 Maisons-Alfort, France; (J.G.); (V.R.-C.)
- Service de Parasitologie-Mycologie, Ecole Nationale Vétérinaire d’Alfort, Biopole Alfort, 94700 Maisons-Alfort, France
- Centre Hospitalier Universitaire Vétérinaire de la Faune Sauvage (Chuv-FS), Ecole nationale vétérinaire d’Alfort, 94700 Maisons-Alfort, France
| | - Sophie Brun
- AP-HP, Hôpital Avicenne, Service de Parasitologie-Mycologie, 93000 Bobigny, France;
| | - Magalie Demar
- EA3593 Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, 97300 Cayenne, French Guiana; (M.D.); (R.B.)
- Hôpital Andrée Rosemon, Laboratoire Hospitalo-Universitaire de Parasitologie-Mycologie, 97300 Cayenne, French Guiana
| | - Romain Blaizot
- EA3593 Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, 97300 Cayenne, French Guiana; (M.D.); (R.B.)
- Service de Dermatologie, Cayenne Hospital, CEDEX 97300 Cayenne, French Guiana
| | - Cécile Nabet
- AP-HP (Assistance Publique-Hôpitaux de Paris), Service de Parasitologie Mycologie, Hôpital La Pitié-Salpêtrière, 75013 Paris, France; (A.J.); (C.N.); (R.P.)
- Inserm, Institut Pierre Louis d’Epidemiologie et de Santé Publique, Sorbonne Université, 75571 Paris, France
| | - Ann Packeu
- Sciensano, BCCM/IHEM Collection, Mycology and Aerobiology Unit, 1000 Brussels, Belgium;
| | - Renaud Piarroux
- AP-HP (Assistance Publique-Hôpitaux de Paris), Service de Parasitologie Mycologie, Hôpital La Pitié-Salpêtrière, 75013 Paris, France; (A.J.); (C.N.); (R.P.)
- Inserm, Institut Pierre Louis d’Epidemiologie et de Santé Publique, Sorbonne Université, 75571 Paris, France
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5
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Cogliati M, Choappa RC, Vieille Oyarzo P, Noguera M. Trichophyton tonsurans in Chile: genotyping in search of an origin. Med Mycol 2021; 60:6468748. [PMID: 34919706 DOI: 10.1093/mmy/myab077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/17/2021] [Indexed: 11/12/2022] Open
Abstract
Trichophyton tonsurans is a cosmopolitan dermatophyte, highly prevalent in Africa, South America, and endemic in North America, where it is mostly related to cases of tinea capitis. Recently, it was also reported in Chile for the first time in two outbreaks occurred in Santiago. In the present study we sequenced the variable internal repeat (VIR) region of a Chilean isolate and compared its genotype with those of several global T. tonsurans isolates. The results showed that the Chilean isolate presented a new genotype which was strictly correlated with isolates from Europe, USA and Mexico.
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Affiliation(s)
- Massimo Cogliati
- Medical Mycology Laboratory, Dept. Biomedical Sciences for Health, Università degli Studi di Milano, Milano, Italy
| | - Rodrigo Cruz Choappa
- Centro de Diagnóstico e investigación de enfermedades infecciosas. Universidad de Valparaíso, Valparaiso, Chile
| | - Peggy Vieille Oyarzo
- Centro de Diagnóstico e investigación de enfermedades infecciosas. Universidad de Valparaíso, Valparaiso, Chile
| | - Mellisa Noguera
- Centro de Diagnóstico e investigación de enfermedades infecciosas. Universidad de Valparaíso, Valparaiso, Chile
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6
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Clothier KA, Watson KD, Mete A, Giannitti F, Anderson M, Munk B, McMillin S, Clifford DL, Rudd J, Shirkey N, Famini D, Woods L. Generalized dermatophytosis caused by Trichophyton equinum in 8 juvenile black bears in California. J Vet Diagn Invest 2021; 34:279-283. [PMID: 34841977 DOI: 10.1177/10406387211061143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
From 2014-2019, 8 juvenile black bears (Ursus americanus) from different geographic regions were presented to the California Department of Fish and Wildlife because of emaciation, alopecia, and exfoliative dermatitis that resulted in death or euthanasia. Autopsy and histopathology revealed that all 8 bears had generalized hyperkeratotic dermatitis, folliculitis, and furunculosis. Skin structures were heavily colonized by fungal hyphae and arthrospores; fungal cultures of skin from 7 bears yielded Trichophyton equinum, a zoophilic dermatophyte reported only rarely in non-equid species. Additional skin conditions included mites (5), ticks (2), and coagulase-negative Staphylococcus sp. infections (2). No other causes of morbidity or mortality were identified. Molecular comparisons performed at the University of Texas Fungal Reference Laboratory determined that all isolates produced identical banding patterns, potentially representing a clonal population. Dermatophytosis is commonly localized and limited to the stratum corneum of the epidermis and hair follicles. Generalized disease with dermal involvement is rare in immunocompetent individuals; illness, malnutrition, age, or immunosuppression may increase susceptibility. Underlying causes for the severe disease impact in these bears were not evident after physical or postmortem examination. The mechanism by which bears from different geographic locations had severe, T. equinum-associated dermatophytosis from a potentially clonal dermatophyte could not be explained and warrants further investigation.
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Affiliation(s)
- Kristin A Clothier
- California Animal Health and Food Safety Laboratory System, University of California-Davis, CA, USA
| | - Katherine D Watson
- California Animal Health and Food Safety Laboratory System, University of California-Davis, CA, USA
| | - Aslı Mete
- California Animal Health and Food Safety Laboratory System, University of California-Davis, CA, USA
| | - Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, La Estanzuela, Colonia, Uruguay, and Veterinary Population Medicine Department, University of Minnesota, Saint Paul, MN, USA
| | - Mark Anderson
- California Animal Health and Food Safety Laboratory System, University of California-Davis, CA, USA
| | - Brandon Munk
- California Department of Fish and Wildlife, Rancho Cordova, CA, USA
| | - Stella McMillin
- California Department of Fish and Wildlife, Rancho Cordova, CA, USA
| | - Deana L Clifford
- California Department of Fish and Wildlife, Rancho Cordova, CA, USA
| | - Jaime Rudd
- California Department of Fish and Wildlife, Rancho Cordova, CA, USA
| | - Nicholas Shirkey
- California Department of Fish and Wildlife, Rancho Cordova, CA, USA
| | - Dan Famini
- Sonoma County Wildlife Rescue, Petaluma, CA, USA
| | - Leslie Woods
- California Animal Health and Food Safety Laboratory System, University of California-Davis, CA, USA
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7
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Čmoková A, Kolařík M, Dobiáš R, Hoyer LL, Janouškovcová H, Kano R, Kuklová I, Lysková P, Machová L, Maier T, Mallátová N, Man M, Mencl K, Nenoff P, Peano A, Prausová H, Stubbe D, Uhrlaß S, Větrovský T, Wiegand C, Hubka V. Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00465-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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Kandemir H, Dukik K, Hagen F, Ilkit M, Gräser Y, de Hoog GS. Polyphasic Discrimination of Trichophyton tonsurans and T. equinum from Humans and Horses. Mycopathologia 2019; 185:113-122. [PMID: 31278475 DOI: 10.1007/s11046-019-00344-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
The anthropophilic dermatophyte Trichophyton tonsurans and its zoophilic counterpart T. equinum are phylogenetically closely related. The barcoding marker rDNA internal transcribed spacer (ITS) shows limited variation between these two species. In the current study, we combined molecular approaches with phenotypic data to determine the species boundaries between T. tonsurans (n = 52) and T. equinum (n = 15) strains originating from humans (n = 40), horses (n = 26), and a mouse (n = 1). Culture characteristics and physiology on Trichophyton agar media 1 and 5 were evaluated. Multi-locus sequencing involving ITS, partial large rDNA subunit (LSU), β-tubulin (TUB), 60S ribosomal protein (RPB), and translation elongation factor-3 (TEF3) genes, and the mating-type (MAT) locus was performed. Amplified fragment length polymorphism data were added. None of the test results showed complete mutual correspondence. With the exception of strains from New Zealand, strains of equine origin required niacin for growth, whereas most strains from human origin did not show this dependence. It is concluded that T. tonsurans and T. equinum incompletely diverged from a common lineage relatively recently. MAT1-1 and MAT1-2 are the main distinguishing genes between the two species.
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Affiliation(s)
- Hazal Kandemir
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey.,Centre of Expertise in Mycology, Radboud University Medical Centre/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Karolina Dukik
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey.
| | - Yvonne Gräser
- Institute für Hygiene und Mikrobiologie der Charité, Berlin, Germany
| | - G Sybren de Hoog
- Centre of Expertise in Mycology, Radboud University Medical Centre/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands. .,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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9
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Baert F, Stubbe D, D’hooge E, Packeu A, Hendrickx M. Updating the Taxonomy of Dermatophytes of the BCCM/IHEM Collection According to the New Standard: A Phylogenetic Approach. Mycopathologia 2019; 185:161-168. [DOI: 10.1007/s11046-019-00338-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/30/2019] [Indexed: 11/30/2022]
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10
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Prova A, Akanda AM, Islam S, Hossain MM. Characterization of Sclerotinia sclerotiorum, an Emerging Fungal Pathogen Causing Blight in Hyacinth Bean ( Lablab purpureus). THE PLANT PATHOLOGY JOURNAL 2018; 34:367-380. [PMID: 30369847 PMCID: PMC6200041 DOI: 10.5423/ppj.oa.02.2018.0028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/17/2018] [Accepted: 07/22/2018] [Indexed: 06/08/2023]
Abstract
Stems and pods of hyacinth bean cultivated in a farmer's field in Gazipur District, Bangladesh, were found rotted in nearly 5% hyacinth bean plants. A fungus having fluffy mycelium and large sclerotia was isolated from affected tissues. Combined results of morphological, molecular and pathological analyses identified the fungus as Sclerotinia sclerotiorum (Lib) de Bary. Inoculating the fungus on healthy hyacinth bean plants and pods reproduced the symptoms previously observed in the field. The three isolates obtained from naturally infected plants were cross inoculated in hyacinth bean, okra and African-American marigold and they were pathogenic to these hosts. The optimum temperature and pH for its growth were 20°C and pH 5.0, respectively. Sclerotial development was favored at pH 5.0. Sucrose and mannitol were the best carbon sources to support hyphal growth, while glucose was the most favourable for sclerotial development. The hyacinth bean genotypes, HB-82 (Rupban Sheem) and HB-102 were found highly resistant, while HB-94 (Ashina) was moderate resistant to the fungus. Finally, S. sclerotiorum was sensitive to Bavistin, Dithane M-45 and Rovral fungicides and Ca in the form of CaCl2. This observation could possibly aid in eliminating field loss in hyacinth bean caused by an emerging pathogenic fungus S. sclerotiorum.
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Affiliation(s)
- Ananya Prova
- Department of Plant Pathology, EXIM Bank Agricultural University, Chapainawabganj-6300,
Bangladesh
| | - Abdul Mannan Akanda
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706,
Bangladesh
| | - Shaikhul Islam
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706,
Bangladesh
| | - Md. Motaher Hossain
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706,
Bangladesh
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11
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Álvarez-Mosquera I, Hernáez S, Sánchez J, Suárez MD, Cisterna R. Diagnosis of Superficial Mycoses by a Rapid and Effective PCR Method from Samples of Scales, Nails and Hair. Mycopathologia 2018; 183:777-783. [PMID: 30094709 DOI: 10.1007/s11046-018-0290-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/28/2018] [Indexed: 11/26/2022]
Abstract
Superficial mycoses are the most frequently diagnosed affections of the stratum corneum of the skin, nails and hair. It is generally caused by the presence of yeasts and dermatophytes. Onychomycosis is the most common infection with an incidence of 80-90% in Europe generally produced by Trichophyton rubrum. The aim of this study is to compare the traditional diagnostic techniques of superficial mycoses with a homemade and wide-spectrum fungal polymerase chain reaction (PCR) technique that amplifies a specific region of the 18S ribosomal RNA (rRNA) directly from samples of scales, nails and hair. A total of 626 clinical samples (obtained in the Basurto University Hospital, Bilbao, Spain) were analysed by traditional culture, microscopy and PCR. DNA extraction was carried out by using an extraction buffer and bovine serum, and amplification of samples and performance of the PCR were checked by conventional agarose gel electrophoresis with subsequent sequencing of amplified samples. A total of 211 samples (34%) resulted in positive diagnosis with at least one of the two applied methods: culture (21%) and PCR (22%). Despite the low percentage of identification achieved by the sequencing technique (40%), the value contributed by the amplification of the 18S region of the rRNA was considered important in the identification as it showed a high predictive values for both positive and negative diagnoses (90.9% and 94.6%, respectively). The proposed PCR method has been confirmed as a complementary, rapid, and effective method in the diagnosis of superficial mycoses. Additionally, it reduces the time to obtain satisfactory results from 4 weeks to 7 h.
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Affiliation(s)
- Irene Álvarez-Mosquera
- Immunology, Microbiology and Parasitology Department, School of Medicine, University of Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain.
| | - Silvia Hernáez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Juan Sánchez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Maria Dolores Suárez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Ramón Cisterna
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
- Immunology, Microbiology and Parasitology Department, School of Medicine, University of Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain
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12
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Pérez-Laguna V, Rezusta A, Ramos JJ, Ferrer LM, Gené J, Revillo MJ, Gilaberte Y. Daylight photodynamic therapy using methylene blue to treat sheep with dermatophytosis caused by Arthroderma vanbreuseghemii. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Pchelin IM, Zlatogursky VV, Rudneva MV, Chilina GA, Rezaei-Matehkolaei A, Lavnikevich DM, Vasilyeva NV, Taraskina AE. Reconstruction of phylogenetic relationships in dermatomycete genus Trichophyton Malmsten 1848 based on ribosomal internal transcribed spacer region, partial 28S rRNA and beta-tubulin genes sequences. Mycoses 2016; 59:566-75. [PMID: 27071492 DOI: 10.1111/myc.12505] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 02/15/2016] [Accepted: 03/08/2016] [Indexed: 01/21/2023]
Abstract
Trichophyton spp. are important causative agents of superficial mycoses. The phylogeny of the genus and accurate strain identification, based on the ribosomal ITS region sequencing, are still under development. The present work is aimed at (i) inferring the genus phylogeny from partial ITS, LSU and BT2 sequences (ii) description of ribosomal ITS region polymorphism in 15 strains of Trichophyton interdigitale. We performed DNA sequence-based species identification and phylogenetic analysis on 48 strains belonging to the genus Trichophyton. Phylogenetic relationships were inferred by maximum likelihood and Bayesian methods on concatenated ITS, LSU and BT2 sequences. Ribosomal ITS region polymorphisms were assessed directly on the alignment. By phylogenetic reconstruction, we reveal major anthropophilic and zoophilic species clusters in the genus Trichophyton. We describe several sequences of the ITS region of T. interdigitale, which do not fit in the traditional polymorphism scheme and propose emendations in this scheme for discrimination between ITS sequence types in T. interdigitale. The new polymorphism scheme will allow inclusion of a wider spectrum of isolates while retaining its explanatory power. This scheme was also found to be partially congruent with NTS typing technique.
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Affiliation(s)
- Ivan M Pchelin
- Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russia
| | - Vasily V Zlatogursky
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Mariya V Rudneva
- Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russia
| | - Galina A Chilina
- Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russia
| | - Ali Rezaei-Matehkolaei
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Dmitry M Lavnikevich
- Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russia
| | - Natalya V Vasilyeva
- Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russia
| | - Anastasia E Taraskina
- Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russia
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Ahmadi B, Mirhendi H, Makimura K, de Hoog GS, Shidfar MR, Nouripour-Sisakht S, Jalalizand N. Phylogenetic analysis of dermatophyte species using DNA sequence polymorphism in calmodulin gene. Med Mycol 2016; 54:500-14. [PMID: 26868901 DOI: 10.1093/mmy/myw004] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
Use of phylogenetic species concepts based on rDNA internal transcribe spacer (ITS) regions have improved the taxonomy of dermatophyte species; however, confirmation and refinement using other genes are needed. Since the calmodulin gene has not been systematically used in dermatophyte taxonomy, we evaluated its intra- and interspecies sequence variation as well as its application in identification, phylogenetic analysis, and taxonomy of 202 strains of 29 dermatophyte species. A set of primers was designed and optimized to amplify the target followed by bilateral sequencing. Using pairwise nucleotide comparisons, a mean similarity of 81% was observed among 29 dermatophyte species, with inter-species diversity ranging from 0 to 200 nucleotides (nt). Intraspecies nt differences were found within strains of Trichophyton interdigitale, Arthroderma simii, T. rubrum and A. vanbreuseghemii, while T. tonsurans, T. violaceum, Epidermophyton floccosum, Microsporum canis, M. audouinii, M. cookei, M. racemosum, M. gypseum, T. mentagrophytes, T schoenleinii, and A. benhamiae were conserved. Strains of E. floccosum/M. racemosum/M. cookei, A. obtosum/A. gertleri, T. tonsurans/T. equinum and a genotype of T. interdigitale had identical calmodulin sequences. For the majority of the species, tree topology obtained for calmodulin gene showed a congruence with coding and non-coding regions including ITS, BT2, and Tef-1α. Compared with the phylogenetic tree derived from ITS, BT2, and Tef-1α genes, some species such as E. floccosum and A. gertleri took relatively remote positions. Here, characterization and obtained dendrogram of calmodulin gene on a broad range of dermatophyte species provide a basis for further discovery of relationships between species. Studies of other loci are necessary to confirm the results.
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Affiliation(s)
- Bahram Ahmadi
- Department of Microbiology and Parasitology, School of Para-Medicine, Bushehr University of Medical Sciences, Bushehr, Iran Departments of Medical Parasitology & Mycology, School of Public Health; National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Mirhendi
- Departments of Medical Parasitology & Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Koichi Makimura
- Teikyo University Institute of Medical Mycology and Genome Research Center, Tokyo, Japan
| | - G Sybren de Hoog
- Fungal Biodiversity Center, Institute of the Royal Netherlands, Academy of Arts and Sciences, Centraalbureau voor Schimmelcultures-KNAW, Utrecht, The Netherlands
| | - Mohammad Reza Shidfar
- Departments of Medical Parasitology & Mycology, School of Public Health; National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Niloofar Jalalizand
- Departments of Medical Parasitology & Mycology, School of Public Health; National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
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15
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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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16
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Overy DP, Marron-Lopez F, Muckle A, Bourque A, Lund L, MacHattie D, Lopez A. Dermatophytosis in farmed mink (Mustela vison) caused by Trichophyton equinum. J Vet Diagn Invest 2015. [PMID: 26223793 DOI: 10.1177/1040638715596036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This report details 2 outbreaks of dermatophytosis in 2 different mink ranches. On the first farm, only kits were affected, while on the second farm, small numbers of adults were infected. Affected mink were otherwise clinically healthy and in good body condition. Three animals were euthanized and submitted for autopsy. Grossly, mink exhibited locally extensive to coalescing areas of crusting alopecia but no other significant gross lesions in internal organs. Microscopically, skin lesions were characterized by chronic hyperplastic dermatitis with folliculitis, furunculosis, occasional intracorneal pustules, and large numbers of intrafollicular fungal arthrospores and hyphae. The dermatophyte was cultured and identified as Trichophyton equinum based on molecular barcoding of the internal transcribed spacer region of the ribosomal DNA gene.
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Affiliation(s)
- David P Overy
- Departments of Pathology and Microbiology (Overy, Marron-Lopez, Muckle, Bourque, Lopez) and Chemistry (Overy), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaDiagnostic Services (Muckle, Bourque, Lund), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaNautilus Biosciences Canada Inc., Duffy Research Center, Charlottetown, Prince Edward Island, Canada (Overy)Middleton Veterinary Services, Middleton, Nova Scotia, Canada (MacHattie)
| | - Fany Marron-Lopez
- Departments of Pathology and Microbiology (Overy, Marron-Lopez, Muckle, Bourque, Lopez) and Chemistry (Overy), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaDiagnostic Services (Muckle, Bourque, Lund), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaNautilus Biosciences Canada Inc., Duffy Research Center, Charlottetown, Prince Edward Island, Canada (Overy)Middleton Veterinary Services, Middleton, Nova Scotia, Canada (MacHattie)
| | - Anne Muckle
- Departments of Pathology and Microbiology (Overy, Marron-Lopez, Muckle, Bourque, Lopez) and Chemistry (Overy), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaDiagnostic Services (Muckle, Bourque, Lund), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaNautilus Biosciences Canada Inc., Duffy Research Center, Charlottetown, Prince Edward Island, Canada (Overy)Middleton Veterinary Services, Middleton, Nova Scotia, Canada (MacHattie)
| | - Andrea Bourque
- Departments of Pathology and Microbiology (Overy, Marron-Lopez, Muckle, Bourque, Lopez) and Chemistry (Overy), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaDiagnostic Services (Muckle, Bourque, Lund), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaNautilus Biosciences Canada Inc., Duffy Research Center, Charlottetown, Prince Edward Island, Canada (Overy)Middleton Veterinary Services, Middleton, Nova Scotia, Canada (MacHattie)
| | - Lorraine Lund
- Departments of Pathology and Microbiology (Overy, Marron-Lopez, Muckle, Bourque, Lopez) and Chemistry (Overy), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaDiagnostic Services (Muckle, Bourque, Lund), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaNautilus Biosciences Canada Inc., Duffy Research Center, Charlottetown, Prince Edward Island, Canada (Overy)Middleton Veterinary Services, Middleton, Nova Scotia, Canada (MacHattie)
| | - David MacHattie
- Departments of Pathology and Microbiology (Overy, Marron-Lopez, Muckle, Bourque, Lopez) and Chemistry (Overy), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaDiagnostic Services (Muckle, Bourque, Lund), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaNautilus Biosciences Canada Inc., Duffy Research Center, Charlottetown, Prince Edward Island, Canada (Overy)Middleton Veterinary Services, Middleton, Nova Scotia, Canada (MacHattie)
| | - Alfonso Lopez
- Departments of Pathology and Microbiology (Overy, Marron-Lopez, Muckle, Bourque, Lopez) and Chemistry (Overy), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaDiagnostic Services (Muckle, Bourque, Lund), Atlantic Veterinary College, University of Prince Edward Island, Prince Edward Island, CanadaNautilus Biosciences Canada Inc., Duffy Research Center, Charlottetown, Prince Edward Island, Canada (Overy)Middleton Veterinary Services, Middleton, Nova Scotia, Canada (MacHattie)
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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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18
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Mohammadi R, Abastabar M, Mirhendi H, Badali H, Shadzi S, Chadeganipour M, Pourfathi P, Jalalizand N, Haghani I. Use of Restriction Fragment Length Polymorphism to Rapidly Identify Dermatophyte Species Related to Dermatophytosis. Jundishapur J Microbiol 2015; 8:e17296. [PMID: 26301058 PMCID: PMC4541063 DOI: 10.5812/jjm.8(5)2015.17296] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/30/2014] [Accepted: 04/08/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Dermatophytes are a group of keratinophilic fungi worldwide, which can infect the skin, hair and nails of humans and animals. This genus includes several species that present different features of dermatophytosis. Although, laboratory diagnosis of dermatophytes is based on direct microscopy, biochemical tests and culture, these manners are expensive, time consuming and need skilled staff. Therefore, molecular methods like PCR-RFLP are the beneficial tools for identification, which are rapid and sensitive. Thus, dermatophyte species are able to generate characteristic band patterns on agarose gel electrophoresis using PCR-RFLP technique, which leads to successful identification at the species level within a 5-hour period. OBJECTIVES The purpose of this study was to study inter- and intraspecific genomic variations for identification of clinically important dermatophyte species obtained from clinical specimens in Isfahan, Iran using PCR-RFLP. MATERIALS AND METHODS From March 2011 to August 2012, 135 clinical isolates were collected from infected patients at Isfahan, Iran. ITS1-5.8S-ITS2 region of rDNA was amplified using universal fungal primers. Subsequently, amplified products were digested by the MvaI restriction enzyme. Using discriminating band profiles on agarose gel, dermatophyte species were identified. However, DNA sequencing was used for unidentifiable strains. RESULTS The specimens were obtained from skin scrapings (70.3%), nail (24.4%) and hair (5.1%) clippings. Most patients were between 21 - 30 years and the ratio of male to female was 93/42. Trichophyton interdigitale was the commonest isolate (52.5%) in our findings, followed by Epidermophyton floccosum (24.4%), T. rubrum (16.2%), Microsporum canis (2.2%), T. erinacei (1.4%), T. violaceum (1.4%), T. tonsurans (0.7%) and M. gypseum (0.7%) based on PCR-RFLP. CONCLUSIONS Combination of traditional methods and molecular techniques considerably improves identification of dermatophytes in the species level in clinical laboratories, which can lead to properly antifungal therapy and successful management of infections. However, restriction and specificity and sensitivity should be lowered and increased, respectively, to be useful for a wide variety of clinical applications.
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Affiliation(s)
- Rasoul Mohammadi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Mahdi Abastabar
- Department of Medical Mycology and Parasitology, Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Hamid Badali
- Department of Medical Mycology and Parasitology, Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
| | - Shahla Shadzi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Mustafa Chadeganipour
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Parinaz Pourfathi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Niloufar Jalalizand
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Iman Haghani
- Department of Medical Mycology and Parasitology, Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
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19
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Mirhendi H, Makimura K, de Hoog GS, Rezaei-Matehkolaei A, Najafzadeh MJ, Umeda Y, Ahmadi B. Translation elongation factor 1-α gene as a potential taxonomic and identification marker in dermatophytes. Med Mycol 2014; 53:215-24. [PMID: 25550390 DOI: 10.1093/mmy/myu088] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Intra- and interspecies variations of the translation elongation factor 1-α (Tef-1α) gene were evaluated as a new identification marker in a wide range of dermatophytes, which included 167 strains of 30 species. An optimized pan-dermatophyte primer pair was designed, and the target was sequenced. Consensus sequences were used for multiple alignment and phylogenetic tree analysis and the levels of intra- and interspecific nucleotide polymorphism were assessed. Between species, the analyzed part of the Tef-1α gene varied in length from 709 to 769 nucleotides. Significant numbers of species including Trichophyton rubrum, T. tonsurans, T. schoenleinii, T. concentricum, T. violaceum, Epidermophyton floccosum, Microsporum ferrugineum, M. canis, M. audouinii, T. equinum, T. eriotrephon, and T. erinacei were invariant in Tef-1α and had sufficient barcoding distance with neighboring species. Although overall consistency was found between ITS phylogeny as the current molecular marker of dermatophytes and Tef-1α, a higher discriminatory power of Tef-1α appeared particularly useful in some clades of closely related species such as the A. vanbreuseghemii, T. rubrum, A. benhamiae, and A. otae complexes. Nevertheless, we stress that a single gene can not specify species borderlines among dermatophytes and multiple lines of evidence based on a multilocus inquiry may ascertain an incontrovertible evaluation of kinship.
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Affiliation(s)
- Hossein Mirhendi
- Departments of Medical Parasitology & Mycology, School of Public Health; National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Koichi Makimura
- Teikyo University, Institute of Medical Mycology and Genome Research Center, Tokyo, Japan
| | | | - Ali Rezaei-Matehkolaei
- Department of Medical Mycology, School of Medicine; Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology, Ghaem Hospital, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yoshiko Umeda
- Teikyo University, Institute of Medical Mycology and Genome Research Center, Tokyo, Japan
| | - Bahram Ahmadi
- Departments of Medical Parasitology & Mycology, School of Public Health; National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
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Cafarchia C, Iatta R, Latrofa MS, Gräser Y, Otranto D. Molecular epidemiology, phylogeny and evolution of dermatophytes. INFECTION GENETICS AND EVOLUTION 2013; 20:336-51. [PMID: 24060735 DOI: 10.1016/j.meegid.2013.09.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 11/16/2022]
Abstract
Dermatophytes are fungi that invade and propagate in the keratinized skin of mammals, including humans, often causing contagious infections. The species of medical concern belong to the genera Microsporum, Trichophyton, Epidermophyton (in their anamorphic state) and Arthroderma (in their telomorphic state), which were traditionally identified based on their morphology and biochemical characters. Nonetheless, limitations linked to the differentiation of closely related agents at species and strains level have been recently overcome by molecular studies. Indeed, an accurate identification of dermatophytes is pivotal for the establishment of effective control and prevention programs as well as for determining the most appropriate and effective antifungal therapies to be applied. This article reviews the DNA techniques and the molecular markers used to identify and to characterize dermatophyte species, as well as aspects of their phylogeny and evolution. The applications of typing molecular strain to both basic and applied research (e.g., taxonomy, ecology, typing of infection, antifungal susceptibility) have also been discussed.
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Affiliation(s)
- Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università di Bari, Str. prov. le per Casamassima Km 3, 70010 Valenzano, Bari, Italy.
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21
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Roe AD, Rice AV, Bromilow SE, Cooke JEK, Sperling FAH. Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle. Mol Ecol Resour 2013; 10:946-59. [PMID: 21565104 DOI: 10.1111/j.1755-0998.2010.02844.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is strong community-wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single-locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.
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Affiliation(s)
- Amanda D Roe
- CW 405 - Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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22
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Rezaei-Matehkolaei A, Makimura K, De Hoog GS, Shidfar MR, Satoh K, Najafzadeh MJ, Mirhendi H. Discrimination ofTrichophyton tonsuransandTrichophyton equinumby PCR-RFLP and by β-tubulin and Translation Elongation Factor 1-α sequencing. Med Mycol 2012; 50:760-4. [DOI: 10.3109/13693786.2012.661885] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Giudice MC, Reis-Menezes AA, Rittner GMG, Mota AJ, Gambale W. Isolation of Microsporum gypseum in soil samples from different geographical regions of brazil, evaluation of the extracellular proteolytic enzymes activities (keratinase and elastase) and molecular sequencing of selected strains. Braz J Microbiol 2012; 43:895-902. [PMID: 24031904 PMCID: PMC3768881 DOI: 10.1590/s1517-83822012000300007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 06/07/2012] [Indexed: 11/22/2022] Open
Abstract
A survey of Microsporum gypseum was conducted in soil samples in different geographical regions of Brazil. The isolation of dermatophyte from soil samples was performed by hair baiting technique and the species were identified by morphology studies. We analyzed 692 soil samples and the recuperating rate was 19.2%. The activities of keratinase and elastase were quantitatively performed in 138 samples. The sequencing of the ITS region of rDNA was performed in representatives samples. M. gypseum isolates showed significant quantitative differences in the expression of both keratinase and elastase, but no significant correlation was observed between these enzymes. The sequencing of the representative samples revealed the presence of two teleomorphic species of M. gypseum (Arthroderma gypseum and A. incurvatum). The enzymatic activities may play an important role in the pathogenicity and a probable adaptation of this fungus to the animal parasitism. Using the phenotypical and molecular analysis, the Microsporum identification and their teleomorphic states will provide a useful and reliable identification system.
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Affiliation(s)
- Mauro Cintra Giudice
- Instituto de Ciências Biomédicas, Departamento de Microbiologia, Universidade de São Paulo , SP , Brasil ; Laboratório de Bacteriologia, Laboratório de Investigação Médica/54, Hospital das Clínicas, Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo , São Paulo, SP , Brasil
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Stockinger H, Krüger M, Schüßler A. DNA barcoding of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2010; 187:461-474. [PMID: 20456046 DOI: 10.1111/j.1469-8137.2010.03262.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
*Currently, no official DNA barcode region is defined for the Fungi. The COX1 gene DNA barcode is difficult to apply. The internal transcribed spacer (ITS) region has been suggested as a primary barcode candidate, but for arbuscular mycorrhizal fungi (AMF; Glomeromycota) the region is exceptionably variable and does not resolve closely related species. *DNA barcoding analyses were performed with datasets from several phylogenetic lineages of the Glomeromycota. We tested a c. 1500 bp fragment spanning small subunit (SSU), ITS region, and large subunit (LSU) nuclear ribosomal DNA for species resolving power. Subfragments covering the complete ITS region, c. 800 bp of the LSU rDNA, and three c. 400 bp fragments spanning the ITS2, the LSU-D1 or LSU-D2 domains were also analysed. *Barcode gap analyses did not resolve all species, but neighbour joining analyses, using Kimura two-parameter (K2P) distances, resolved all species when based on the 1500 bp fragment. The shorter fragments failed to separate closely related species. *We recommend the complete 1500 bp fragment as a basis for AMF DNA barcoding. This will also allow future identification of AMF at species level based on 400 or 1000 bp amplicons in deep sequencing approaches.
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Affiliation(s)
- Herbert Stockinger
- LMU Munich, Department of Biology, Genetics, Grosshaderner Strasse 4, D-82152 Martinsried, Germany
| | - Manuela Krüger
- LMU Munich, Department of Biology, Genetics, Grosshaderner Strasse 4, D-82152 Martinsried, Germany
| | - Arthur Schüßler
- LMU Munich, Department of Biology, Genetics, Grosshaderner Strasse 4, D-82152 Martinsried, Germany
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Del-Prado R, Cubas P, Lumbsch HT, Divakar PK, Blanco O, de Paz GA, Molina MC, Crespo A. Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation. Mol Phylogenet Evol 2010; 56:125-33. [DOI: 10.1016/j.ympev.2010.04.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 04/08/2010] [Accepted: 04/09/2010] [Indexed: 11/17/2022]
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Aveskamp M, de Gruyter J, Woudenberg J, Verkley G, Crous P. Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera. Stud Mycol 2010; 65:1-60. [PMID: 20502538 PMCID: PMC2836210 DOI: 10.3114/sim.2010.65.01] [Citation(s) in RCA: 277] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the beta-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa.
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Affiliation(s)
- M.M. Aveskamp
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of
Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The
Netherlands
| | - J. de Gruyter
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
- Dutch Plant Protection Service (PD), Geertjesweg 15, 6706 EA Wageningen,
The Netherlands
| | - J.H.C. Woudenberg
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
| | - G.J.M. Verkley
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The
Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of
Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The
Netherlands
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De Baere T, Summerbell R, Theelen B, Boekhout T, Vaneechoutte M. Evaluation of internal transcribed spacer 2-RFLP analysis for the identification of dermatophytes. J Med Microbiol 2010; 59:48-54. [DOI: 10.1099/jmm.0.013870-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 95 isolates, belonging to 33 species of five dermatophyte genera, i.e. Arthroderma (15 species), Chrysosporium (two), Epidermophyton (one), Microsporum (three) and Trichophyton (12), were studied using internal transcribed spacer 2 (ITS2)-PCR-RFLP analysis (ITS2-RFLP), consisting of amplification of the ITS2 region, restriction digestion with BstUI (CG/CG) and restriction fragment length determination by capillary electrophoresis. ITS2-RFLP analysis proved to be most useful for identification of species of the genera Arthroderma, Chrysosporium and Epidermophyton, but could not distinguish between several Trichophyton species. The identification results are in agreement with established and recent taxonomical insights into the dermatophytes; for example, highly related species also had closely related and sometimes difficult-to-discriminate ITS2-RFLP patterns. In some cases, several ITS2-RFLP groups could be distinguished within species, again mostly in agreement with the taxonomic delineations of subspecies and/or genomovars, confirming the relevance of ITS2-RFLP analysis as an identification technique and as a useful taxonomic approach.
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Affiliation(s)
- Thierry De Baere
- Laboratory for Bacteriology Research, University of Ghent, B-9000 Ghent, Belgium
| | - Richard Summerbell
- CBS Fungal Diversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bart Theelen
- CBS Fungal Diversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Teun Boekhout
- Division of Acute Medicine and Infectious Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
- CBS Fungal Diversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research, University of Ghent, B-9000 Ghent, Belgium
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Porter TM, Skillman JE, Moncalvo JM. Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Mol Ecol 2008; 17:3037-50. [PMID: 18494767 DOI: 10.1111/j.1365-294x.2008.03813.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
This is the first study to assess the diversity and community structure of the Agaricomycotina in an ectotrophic forest using above-ground fruiting body surveys as well as soil rDNA sampling. We recovered 132 molecular operational taxonomic units, or 'species', from fruiting bodies and 66 from soil, with little overlap. Fruiting body sampling primarily recovered fungi from the Agaricales, Russulales, Boletales and Cantharellales. Many of these species are ectomycorrhizal and form large fruiting bodies. Soil rDNA sampling recovered fungi from these groups in addition to taxa overlooked during the fruiting body survey from the Atheliales, Trechisporales and Sebacinales. Species from these groups form inconspicuous, resupinate and corticioid fruiting bodies. Soil sampling also detected fungi from the Hysterangiales that form fruiting bodies underground. Generally, fruiting body and soil rDNA samples recover a largely different assemblage of fungi at the species level; however, both methods identify the same dominant fungi at the genus-order level and ectomycorrhizal fungi as the prevailing type. Richness, abundance, and phylogenetic diversity (PD) identify the Agaricales as the dominant fungal group above- and below-ground; however, we find that molecularly highly divergent lineages may account for a greater proportion of total diversity using the PD measure compared with richness and abundance. Unless an exhaustive inventory is required, the rapidity and versatility of DNA-based sampling may be sufficient for a first assessment of the dominant taxonomic and ecological groups of fungi in forest soil.
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Affiliation(s)
- Teresita M Porter
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada.
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The New Species Concept in Dermatophytes—a Polyphasic Approach. Mycopathologia 2008; 166:239-56. [DOI: 10.1007/s11046-008-9099-y] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 01/15/2008] [Accepted: 01/30/2008] [Indexed: 11/25/2022]
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Li HC, Bouchara JP, Hsu MML, Barton R, Su S, Chang TC. Identification of dermatophytes by sequence analysis of the rRNA gene internal transcribed spacer regions. J Med Microbiol 2008; 57:592-600. [DOI: 10.1099/jmm.0.47607-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Identification of dermatophytes using the traditional method is sometimes problematic because of atypical microscopic or macroscopic morphology. The aim of this study was to evaluate the feasibility of using sequencing of the ribosomal internal transcribed spacer (ITS)1 and ITS2 regions for identification of 17 dermatophyte species. The ITS regions of 188 strains (62 reference strains and 126 clinical isolates) were amplified by PCR and sequenced. Species identification was made by sequence comparison with an in-house database comprising ITS sequences of type or neotype strains or by blast searches for homologous sequences in public databases. Strains producing discrepant results between conventional methods and ITS sequence analysis were analysed further by sequencing the D1–D2 domain of the large-subunit rRNA gene for species clarification. The identification rates by ITS1 and ITS2 sequencing were higher than 97 %. Based on reference sequences of type or neotype strains, it was noted that most strains of Trichophyton mentagrophytes were misidentifications of Trichophyton interdigitale. In addition, barcode sequences were present in species of the Microsporum canis complex and Trichophyton rubrum complex. These barcode sequences are useful for species delineation when the results of ITS sequencing are ambiguous. In conclusion, ITS sequencing provides a very accurate and useful method for the identification of dermatophytes.
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Affiliation(s)
- Hsin Chieh Li
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Jean-Philippe Bouchara
- Laboratory of Parasitology and Mycology, University Hospital, Angers, France
- Host-Pathogen-Interaction Study Group, UPRES-EA 3142, Angers University, Angers, France
| | - Mark Ming-Long Hsu
- Department of Dermatology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Richard Barton
- Institute of Molecular and Cellular Biology, School of Biochemistry and Microbiology, University of Leeds, Leeds, UK
| | - Shuli Su
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Tsung Chain Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
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Rapid identification and differentiation of Trichophyton species, based on sequence polymorphisms of the ribosomal internal transcribed spacer regions, by rolling-circle amplification. J Clin Microbiol 2008; 46:1192-9. [PMID: 18234865 DOI: 10.1128/jcm.02235-07] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA sequencing analyses have demonstrated relatively limited polymorphisms within the fungal internal transcribed spacer (ITS) regions among Trichophyton spp. We sequenced the ITS region (ITS1, 5.8S, and ITS2) for 42 dermatophytes belonging to seven species (Trichophyton rubrum, T. mentagrophytes, T. soudanense, T. tonsurans, Epidermophyton floccosum, Microsporum canis, and M. gypseum) and developed a novel padlock probe and rolling-circle amplification (RCA)-based method for identification of single nucleotide polymorphisms (SNPs) that could be exploited to differentiate between Trichophyton spp. Sequencing results demonstrated intraspecies genetic variation for T. tonsurans, T. mentagrophytes, and T. soudanense but not T. rubrum. Signature sets of SNPs between T. rubrum and T. soudanense (4-bp difference) and T. violaceum and T. soudanense (3-bp difference) were identified. The RCA assay correctly identified five Trichophyton species. Although the use of two "group-specific" probes targeting both the ITS1 and the ITS2 regions were required to identify T. soudanense, the other species were identified by single ITS1- or ITS2-targeted species-specific probes. There was good agreement between ITS sequencing and the RCA assay. Despite limited genetic variation between Trichophyton spp., the sensitive, specific RCA-based SNP detection assay showed potential as a simple, reproducible method for the rapid (2-h) identification of Trichophyton spp.
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Geiser DM, Klich MA, Frisvad JC, Peterson SW, Varga J, Samson RA. The current status of species recognition and identification in Aspergillus. Stud Mycol 2007; 59:1-10. [PMID: 18490947 PMCID: PMC2275194 DOI: 10.3114/sim.2007.59.01] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The species recognition and identification of aspergilli and their teleomorphs is discussed. A historical overview of the taxonomic concepts starting with the monograph of Raper & Fennell (1965) is given. A list of taxa described since 2000 is provided. Physiological characters, particularly growth rates and the production of extrolites, often show differences that reflect phylogenetic species boundaries and greater emphasis should be placed on extrolite profiles and growth characteristics in species descriptions. Multilocus sequence-based phylogenetic analyses have emerged as the primary tool for inferring phylogenetic species boundaries and relationships within subgenera and sections. A four locus DNA sequence study covering all major lineages in Aspergillus using genealogical concordance theory resulted in a species recognition system that agrees in part with phenotypic studies and reveals the presence of many undescribed species not resolved by phenotype. The use of as much data from as many sources as possible in making taxonomic decisions is advocated. For species identification, DNA barcoding uses a short genetic marker in an organism"s DNA to quickly and easily identify it to a particular species. Partial cytochrome oxidase subunit 1 sequences, which are used for barcoding animal species, were found to have limited value for species identification among black aspergilli. The various possibilities are discussed and at present partial beta-tubulin or calmodulin are the most promising loci for Aspergillus identification. For characterising Aspergillus species one application would be to produce a multilocus phylogeny, with the goal of having a firm understanding of the evolutionary relationships among species across the entire genus. DNA chip technologies are discussed as possibilities for an accurate multilocus barcoding tool for the genus Aspergillus.
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Affiliation(s)
- D M Geiser
- Department of Plant Pathology, Pennsylvania State University, University Park 16802, U.S.A
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