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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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Aghili SR, Alehashemi R, Abastabar M, Niknejad F, Haghani I, Livani F, Kashiri A, Javidnia J, Nosratabadi M. First report of tinea corporis caused by Trichophyton quinckeanum in Iran and its antifungal susceptibility profile. Curr Med Mycol 2022; 8:37-41. [PMID: 37736606 PMCID: PMC10509498 DOI: 10.32598/cmm.2023.1344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/05/2022] [Accepted: 01/03/2023] [Indexed: 09/23/2023] Open
Abstract
Background and Purpose Trichophyton quinckeanum, a known zoophilic dermatophyte responsible for favus form in rodents and camels, is occasionally reported to cause human infections. Case Report This study aimed to report a case of tinea corporis caused by T. quinckeanum that experienced annular erythematous pruritic plaque with abundant purulent secretions. In June 2021, a 15-year-old girl with an erythematous cup shape lesion on the right wrist bigger than 3 cm in diameter was examined for tinea corporis. Since March, 2016 her family has kept several camels at home. Direct examination of skin scraping and purulent exudates revealed branching septal hyaline hyphae and arthrospore. Morphological evaluation of the recovered isolate from the culture and sequencing of ITS1-5.8S rDNA-ITS2 region resulted in the identification of T. quinckeanum. Antifungal susceptibility testing showed that this isolate had low minimum inhibitory concentration (MIC) values for luliconazole, terbinafine, and tolnaftate, but high MICs to itraconazole, fluconazole, posaconazole, miconazole, isavuconazole, ketoconazole, clotrimazole, and griseofulvin. However, the patient was successfully treated with oral terbinafine and topical ketoconazole. Conclusion It can be said that T. quinckeanum is often missed or misidentified due to its morphological similarity to T. mentagrophytes/T. interdigitale or other similar species. This dermatophyte species is first reported as the cause of tinea corporis in Iran. As expected, a few months after our study, T. quinckeanum was detected in other areas of Iran, in a few cases.
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Affiliation(s)
- Seyed Reza Aghili
- Invasive Fungi Research Center, Communicable Diseases Institute/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Raheleh Alehashemi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Abastabar
- Invasive Fungi Research Center, Communicable Diseases Institute/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Farhad Niknejad
- Department of Medical Laboratory Sciences, School of Para Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Iman Haghani
- Invasive Fungi Research Center, Communicable Diseases Institute/Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Livani
- Department of Internal Medicine, Dermatology Group, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Amineh Kashiri
- Department of Internal Medicine, Dermatology Group, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Javad Javidnia
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohsen Nosratabadi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Moskaluk AE, VandeWoude S. Current Topics in Dermatophyte Classification and Clinical Diagnosis. Pathogens 2022; 11:pathogens11090957. [PMID: 36145389 PMCID: PMC9502385 DOI: 10.3390/pathogens11090957] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022] Open
Abstract
Dermatophytes are highly infectious fungi that cause superficial infections in keratinized tissues in humans and animals. This group of fungi is defined by their ability to digest keratin and encompasses a wide range of species. Classification of many of these species has recently changed due to genetic analysis, potentially affecting clinical diagnosis and disease management. In this review, we discuss dermatophyte classification including name changes for medically important species, current and potential diagnostic techniques for detecting dermatophytes, and an in-depth review of Microsporum canis, a prevalent zoonotic dermatophyte. Fungal culture is still considered the “gold standard” for diagnosing dermatophytosis; however, modern molecular assays have overcome the main disadvantages of culture, allowing for tandem use with cultures. Further investigation into novel molecular assays for dermatophytosis is critical, especially for high-density populations where rapid diagnosis is essential for outbreak prevention. A frequently encountered dermatophyte in clinical settings is M. canis, which causes dermatophytosis in humans and cats. M. canis is adapting to its primary host (cats) as one of its mating types (MAT1-2) appears to be going extinct, leading to a loss of sexual reproduction. Investigating M. canis strains around the world can help elucidate the evolutionary trajectory of this fungi.
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Gupta AK, Cooper EA, Summerbell RC, Nakrieko KA. Utility of polymerase chain reaction for assessment of onychomycosis during topical therapy. Int J Dermatol 2022; 61:1385-1389. [PMID: 35535809 DOI: 10.1111/ijd.16241] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/17/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Increased detection of fungi including non-dermatophyte molds (NDMs) using polymerase chain reaction (PCR) methods is well-established. However, the use of PCR to evaluate ongoing onychomycosis treatment outcome has not been investigated. METHODS Nail samples from 28 patients receiving topical efinaconazole were evaluated by both KOH/culture and PCR methods across the study period. Detection of microorganisms by PCR was compared to the culture at baseline and end of study at month 24 (M24). Fungal detection by both methods was evaluated with respect to clinical cure observed as 100% visual clearance of the target toenail. RESULTS By culture, all 28 subjects were dermatophyte-positive at pre-treatment; only 4/28 also exhibited an NDM microorganism. According to PCR, 24/28 subjects were dermatophyte-positive pre-treatment, with 25/28 also exhibiting NDMs. At M24, 18/28 (64.3%) participants had negative KOH/culture results, in contrast to 4/28 (14.3%) negative PCR results. PCR showed higher rates of NDM detection than the culture at baseline as well as M24. Calculations to compare the diagnostic utility of KOH/culture versus PCR found that positive tests with both methods reliably indicate the presence of onychomycosis, but negative PCR correlated better with onychomycosis cure than did KOH/culture. DISCUSSION PCR confirmed a high presence of NDMs pre-treatment, and continued presence of NDMs to M24, with unknown significance requiring further investigation. Though both KOH/culture and PCR have diagnostic limitations, PCR showed better overall utility than culture in predicting onychomycosis topical treatment outcome and should be more strongly considered for evaluation of topical therapies.
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Affiliation(s)
- Aditya K Gupta
- Division of Dermatology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Mediprobe Research Inc., London, ON, Canada
| | | | - Richard C Summerbell
- Sporometrics, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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Dispersal of Aphanoascus keratinophilus by the rook Corvus frugilegus during breeding in East Poland. Sci Rep 2022; 12:2142. [PMID: 35136194 PMCID: PMC8826369 DOI: 10.1038/s41598-022-06227-2] [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: 06/30/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The process of dispersal of the potentially disease-causing, geophilic and keratinolytic fungal strain Aphanoascus keratinophilus (the perfect, sexual stage of Chrysosporium keratinophilum) by the rook Corvus frugilegus was studied. The source of A. keratinophilus strains was pellets of the rook, thus far not considered a carrier of this particular opportunistic pathogen. Pellets collected from breeding colonies of rooks were analysed in terms of the occurrence of keratinolytic fungi with the application of the native keratin bait method. Among the 83 rook pellets analysed, 24 (29%) were infected by keratinophilic fungi. Pure cultures of the fungi were identified to species based on traditional morphological features. Traditional mycological identification was verified by the PCR–RFLP molecular identification method as well as DNA sequencing. The obtained results showed the presence of 90 Aphanoascus keratinophilus strains, 6 Chrysosporium tropicum strains, and 3 Chrysosporium pannicola strains. The PCR melting profile (PCR-MP) method was used to identify intraspecies variations of the 90 analysed A. keratinophilus strains. The dispersal of genotypes and possible pathways of A. keratinophilus dispersal and infection via rook pellets were analysed.
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Faramarzi S, Motamedi M, Rezaei-Matehkolaei A, Aboutalebian S, Ansari S, Didehdar M, Bahadoran M, Mirhendi H. A simple multiplex polymerase chain reaction assay for rapid identification of the common pathogenic dermatophytes: Trichophyton interdigitale, Trichophyton rubrum, and Epidermophyton floccosum. Curr Med Mycol 2022; 7:1-7. [PMID: 35028478 PMCID: PMC8740852 DOI: 10.18502/cmm.7.2.7030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022] Open
Abstract
Background and Purpose: The most common etiological agents of human dermatophytosis in various parts of the world are Trichophyton rubrum, Trichophyton interdigitale, and Epidermophyton floccosum.
The main aim of this study was to design and evaluate a simple and straightforward multiplex polymerase chain reaction (PCR) assay for reliable identification/differentiation of these species
in clinical isolates. Materials and Methods: The reliable sequences of several molecular targets of dermatophytes species were used to design a multiplex PCR for the identification of common pathogenic dermatophytes.
The isolates and clinical specimens examined in this study included seven standard strains of dermatophytes, 101 isolates of dermatophytes and non-dermatophyte molds/yeasts which
had already been identified by sequencing or PCR-restriction fragment length polymorphism (RFLP), and 155 clinical samples from patients suspected of cutaneous mycoses. Results: Species-specific primer pairs for T. rubrum and T. interdigitale/T. mentagrophytes were designed based on the sequence data of the translation elongation factor 1-alpha gene,
and the primers for E. floccosum targeted the specific sequence of the internal transcribed spacer region (ITS). The multiplex PCR successfully
detected T. rubrum, T. interdigitale/T. mentagrophytes, and E. floccosum strains that were identified by sequencing or PCR-RFLP. However, the primer pairs selected
for T. interdigitale/T. mentagrophytes cross-reacted with Trichophyton tonsurans. In testing the PCR system directly for clinical samples, the proportion of positive
multiplex PCR was higher than positive culture (68.1% vs. 55.4%, respectively). Conclusion: The multiplex assay could detect three common agents out of several causal agents of dermatophytosis, namely T. rubrum, T. interdigitale, and E. floccosum. Therefore, by adding
pan-dermatophyte primers it can be used as a comprehensive detection/identification test.
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Affiliation(s)
- Sama Faramarzi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Marjan Motamedi
- Department of Medical Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Rezaei-Matehkolaei
- Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shima Aboutalebian
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojtaba Didehdar
- Department of Medical Parasitology and Mycology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Mehran Bahadoran
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Kurokochi H, Yoshitake K, Yonezawa R, Asakawa S. Simultaneous amplicon analysis of multiple soil samples using MinION sequencing. MethodsX 2021; 8:101576. [PMID: 35004210 PMCID: PMC8720897 DOI: 10.1016/j.mex.2021.101576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022] Open
Abstract
The diversity and composition of soil microorganisms needs to be understood as they influence ecosystem processes. MinION is a relatively recent next-generation sequencer, which provides the advantage of sequencing long reads. In this study, two types of soil were prepared experimentally to investigate the possibility of simultaneously analyzing multiple environmental samples using MinION. The MinION sequencing of amplicons was adjusted by the different rounds of PCR performed. Soil fungi and bacteria were compared using ITS and 16S rRNA amplicons, respectively. For ITS, the number of reads available for MinION sequencing were simply increased by performing two PCRs and purification using Agencourt AMPure XP. However, the effect of performing PCR twice was not high for 16S rRNA. Therefore, performing PCR twice appears to be effective for analyzing ITS regions. Regarding the number of reads obtained using MinION sequencing, clustering the same sample was possible if a read of ∼2000 bases or more was obtained in 16S rRNA and ITS. Further, information on 80 samples was obtained by performing only one round of MinION sequencing. Thus, MinION sequencing can be used to analyze a large number of samples simultaneously, providing a strong tool for amplicon sequencing. • Soil microbial composition before and after treatment was compared between 16S rRNA and ITS amplicons using MinION sequencing • One PCR amplification and two PCR amplifications were also compared • Information on 80 samples was obtained by performing only one round of MinION sequencing.
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Affiliation(s)
- Hiroyuki Kurokochi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryo Yonezawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Atter A, Diaz M, Tano-Debrah K, Kunadu APH, Mayer MJ, Colquhoun IJ, Nielsen DS, Baker D, Narbad A, Amoa-Awua W. Microbial Diversity and Metabolite Profile of Fermenting Millet in the Production of Hausa koko, a Ghanaian Fermented Cereal Porridge. Front Microbiol 2021; 12:681983. [PMID: 34421842 PMCID: PMC8371397 DOI: 10.3389/fmicb.2021.681983] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
Hausa koko is an indigenous porridge processed from millet in Ghana. The process involves fermentation stages, giving the characteristic organoleptic properties of the product that is produced largely at a small-scale household level and sold as a street food. Like many other indigenous foods, quality control is problematic and depends on the skills of the processor. In order to improve the quality of the product and standardize the process for large-scale production, we need a deeper understanding of the microbial processes. The aim of this study is to investigate the microbial community involved in the production of this traditional millet porridge and the metabolites produced during processing. High-throughput amplicon sequencing was used to identify the bacterial (16S rRNA V4 hypervariable region) and fungal [Intergenic Transcribed Spacer (ITS)] communities associated with the fermentation, while nuclear magnetic resonance (NMR) was used for metabolite profiling. The bacterial community diversity was reduced during the fermentation processes with an increase and predominance of lactobacilli. Other dominant bacteria in the fermentation included Pediococcus, Weissella, Lactococcus, Streptococcus, Leuconostoc, and Acetobacter. The species Limosilactobacillus fermentum and Ligilactobacillus salivarius accounted for some of the diversities within and between fermentation time points and processors. The fungal community was dominated by the genus Saccharomyces. Other genera such as Pichia, Candida, Kluyveromyces, Nakaseomyces, Torulaspora, and Cyberlindnera were also classified. The species Saccharomyces cerevisiae, Stachybotrys sansevieriae, Malassezia restricta, Cyberlindnera fabianii, and Kluyveromyces marxianus accounted for some of the diversities within some fermentation time points. The species S. sansevieria and M. restricta may have been reported for the first time in cereal fermentation. This is the most diverse microbial community reported in Hausa koko. In this study, we could identify and quantify 33 key different metabolites produced by the interactions of the microbial communities with the millet, composed of organic compounds, sugars, amino acids and intermediary compounds, and other key fermentation compounds. An increase in the concentration of organic acids in parallel with the reduction of sugars occurred during the fermentation process while an initial increase of amino acids followed by a decrease in later fermentation steps was observed.
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Affiliation(s)
- Amy Atter
- Food Microbiology and Mushroom Research Division, CSIR-Food Research Institute, Accra, Ghana
- Department of Nutrition and Food Science, University of Ghana, Accra, Ghana
- Food and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Maria Diaz
- Food and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Kwaku Tano-Debrah
- Department of Nutrition and Food Science, University of Ghana, Accra, Ghana
| | | | - Melinda J. Mayer
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Ian J. Colquhoun
- Analytical Sciences Unit, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Dennis Sandris Nielsen
- Department of Food Science, Section for Food Microbiology and Fermentation, University of Copenhagen, Copenhagen, Denmark
| | - David Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Arjan Narbad
- Food and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Wisdom Amoa-Awua
- Food Microbiology and Mushroom Research Division, CSIR-Food Research Institute, Accra, Ghana
- Department of Agro-Processing Technology and Food Bio-Sciences, CSIR College of Science and Technology, Accra, Ghana
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Yamada S, Anzawa K, Mochizuki T. Molecular epidemiology of Microsporum canis isolated from Japanese cats, dogs and pet owners by multilocus microsatellite typing fragment analysis. Jpn J Infect Dis 2021; 75:105-113. [PMID: 34334533 DOI: 10.7883/yoken.jjid.2020.809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multilocus microsatellite typing (MLMT) was performed on 93 strains of Microsporum canis isolated between 2012 and 2017 from 75 cats, eight dogs and 10 pet owners. These strains were derived from two major reservoirs: commercial breeding facilities and pet shops (PS), and stray cats and pet cats that went outdoors and came in contact with stray cats (Outdoor). Six microsatellite markers were used for genotyping. These 93 strains included 22 genotypes, 11 previously detected in Japan and 11 new genotypes. Strains belonging to the previously reported genotypes P and A were distributed widely throughout Japan. Genotype P was the most frequent, accounting for 37 (39.8%) of the 93 strains, most derived from Outdoor sources. Genotype A was the second most frequent, being present in 11 (11.8%) of the 93 strains, most derived from the PS reservoir. All new genotypes were detected in isolates from cats, with many of these derived from the Outdoor reservoir. The consistency of infection was shown in 18 of 19 familial cases. These findings indicate that genotypes differ in strains derived from PS and Outdoor reservoirs and that genotyping by MLMT is useful for tracking the routes of spread and transmission of M. canis in Japan.
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Affiliation(s)
| | - Kazushi Anzawa
- Department of Dermatology, Kanazawa Medical University, JAPAN
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Checkerboard Analysis To Evaluate Synergistic Combinations of Existing Antifungal Drugs and Propylene Glycol Monocaprylate in Isolates from Recalcitrant Tinea Corporis and Cruris Patients Harboring Squalene Epoxidase Gene Mutation. Antimicrob Agents Chemother 2021; 65:e0032121. [PMID: 34097482 DOI: 10.1128/aac.00321-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recalcitrant dermatophytic infections of the glabrous skin (tinea corporis/cruris/faciei) pose a huge challenge to health care systems. Combinations of oral and topical drugs may potentially improve cure rates, but the same has never been objectively assessed for this condition in laboratory or clinical studies. The present study was undertaken with the aim of identifying synergistic combinations of oral and topical antifungals by testing clinical isolates obtained from patients with recalcitrant tinea corporis/cruris. Forty-two patients with tinea corporis/cruris who had failed oral antifungals or had relapsed within 4 weeks of apparent clinical cure were recruited. Twenty-one isolates were identified by sequencing (all belonging to the Trichophyton mentagrophytes/T. interdigitale species complex) and subjected to antifungal susceptibility testing (AFST) and squalene epoxidase (SQLE) gene mutation analysis. Finally, five isolates, four with underlying SQLE gene mutations and one wild-type strain, were chosen for checkerboard studies using various combinations of antifungal agents. Most isolates (n = 16) showed high MICs of terbinafine (TRB) (0.5 to >16 μg/ml), with SQLE gene mutations being present in all isolates with MICs of ≥0.5 μg/ml. Synergistic interactions were noted with combinations of itraconazole with luliconazole, TRB, and ketoconazole and propylene glycol monocaprylate (PGMC) with luliconazole and with the triple combination of PGMC with luliconazole and ketoconazole. In vitro synergistic interactions provide a sound scientific basis for the possible clinical use of antifungal combinations. Hence, these synergistic combinations may be tested for clinical utility in the wake of rising resistance among dermatophytic infections of the glabrous skin.
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Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species. J Fungi (Basel) 2021; 7:jof7040288. [PMID: 33921243 PMCID: PMC8070597 DOI: 10.3390/jof7040288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022] Open
Abstract
Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.
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Arammehr A, Dehghan P, Chadeganipour M, Katoueezadeh M, Shadzi S. Detection of Dermatophytes from Dermatophytosis-Suspected Cases in Iran, Evaluation of Polymerase Chain Reaction-Sequencing Method. Adv Biomed Res 2021; 9:56. [PMID: 33457339 PMCID: PMC7792868 DOI: 10.4103/abr.abr_21_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/25/2020] [Accepted: 08/05/2020] [Indexed: 11/04/2022] Open
Abstract
Background Dermatophytosis is mostly caused by dermatophytes species, and the diagnosis of disease is very important for early treatment. The aim of this study was to identify the commonly dermatophytes species isolated directly from the clinical samples, using the polymerase chain reaction (PCR) and evaluate both conventional and molecular methods. Materials and Methods This study was performed on 115 clinical samples. Dermatophyte isolates were initially identified by conventional method and confirmed by the sequencing molecular method. In this study, the molecular technique is implemented directly on clinical samples. Statistical analysis of the information was performed by the SPSS software, and the results were statistically analyzed. Results Our findings demonstrated that the most abundant dermatophyte species by PCR-sequencing were Trichophyton mentagrophytes (20%), followed by Trichophyton tonsurans (10%), Trichophyton rubrum (6.7%), T. interdigital (6.7%), Arthroderma otae, and Arthroderma vanbreuseghemii, (3.3%) for each one. Conclusion For medical laboratories, routine procedures are still preferred because of their lower cost, and the results are almost the same as the molecular methods. The sensitivity and specificity values for PCR under our laboratory condition were 60% and 87%, respectively. This study shows that molecular results performed better in nails than other samples, by culture results.
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Affiliation(s)
- Akbar Arammehr
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parvin Dehghan
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mostafa Chadeganipour
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Katoueezadeh
- Department of Hematology and Medical Laboratory Science, Faculty of Allied Medicine, Kerman university of Medical Sciences, Kerman, Iran
| | - Shahla Shadzi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Gupta AK, Nakrieko KA. Trichophyton rubrum DNA Strains in Patients with Onychomycosis with Persistent Mixed Infections Involving a Nondermatophyte Mold. J Am Podiatr Med Assoc 2020; 110:442557. [PMID: 32810210 DOI: 10.7547/17-201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Onychomycosis is estimated to occur in approximately 10% of the global population, with most cases caused by Trichophyton rubrum. Some persistent onychomycosis is caused by mixed infections of T rubrum and one or more co-infecting nondermatophyte molds (NDMs). In onychomycosis, T rubrum strain types may naturally switch and may also be triggered to switch in response to antifungal therapy. T rubrum strain types in mixed infections of onychomycosis have not been characterized. METHODS T rubrum DNA strains in mixed infections of onychomycosis containing co-infecting NDMs were compared with a baseline North American population through polymerase chain reaction amplification of ribosomal DNA tandemly repetitive subelements (TRSs) 1 and 2. The baseline DNA strain types were determined from 102 clinical isolates of T rubrum. The T rubrum DNA strain types from mixed infections were determined from 63 repeated toenail samples from 15 patients. RESULTS Two unique TRS-2 types among the clinical isolates contributed to four unique TRS-1 and TRS-2 strain types. Six TRS-1 and TRS-2 strain types represented 92% of the clinical isolates of T rubrum. Four TRS-1 and TRS-2 strain types accounted for 100% of the T rubrum within mixed infections. CONCLUSIONS Four unique North American T rubrum strains were identified. In support of a shared ancestry, the T rubrum DNA strain types found in mixed infections with NDMs were among the most abundant types. A population of T rubrum strains in mixed infections of onychomycosis has been characterized, with more than one strain detected in some nails. The presence of a co-infecting NDM in mixed infections may contribute to failed therapy by stabilizing the T rubrum strain type, possibly preventing the antifungal therapy-induced strain type switching observed with infections caused by T rubrum alone.
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Iwanaga T, Anzawa K, Mochizuki T. Variations in ribosomal DNA copy numbers in a genome of
Trichophyton interdigitale. Mycoses 2020; 63:1133-1140. [PMID: 32783279 PMCID: PMC7607385 DOI: 10.1111/myc.13163] [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: 05/26/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 11/26/2022]
Abstract
Background Ribosomal DNA (rDNA) reportedly has multiple copies in the fungal genome. The internal transcribed spacer (ITS) region in rDNA is useful for investigating relationships between close taxonomic relatives. Thus, ITS has been widely used as a target gene in medical mycology for the detection of pathogenic fungi and identification of fungal species. However, the rDNA copy number in a genome of Trichophyton interdigitale, the pathogen causing dermatophytosis, currently remains unknown. Objective Clarification of the rDNA copy number in a genome of T. interdigitale. Methods rDNA copy numbers in 64 clinical isolates of T. interdigitale were examined using quantitative real‐time PCR (qPCR) with the absolute quantitative method targeting TruMDR2, a single‐copy control gene and the ITS region in rDNA. Results The copy numbers of the rDNA subunit varied among the 64 strains tested, from 24 to 116 copies per genome. The average rDNA copy number ± standard deviation was 59 ± 16. No correlations were observed between the rDNA copy number and colony colour, colony morphology or molecular type of the non‐transcribed spacer region in rDNA. Experiments on rDNA copy numbers obtained from independent colonies of each strain in single‐spore cultures revealed that the copy number was homogeneous within each strain. Conclusion This is the first study to estimate copy numbers of the rDNA subunit in a genome of T. interdigitale. The rDNA copy number of T. interdigitale varied among the strains tested and was homogeneous within each strain.
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Affiliation(s)
- Tomoyuki Iwanaga
- Department of Dermatology Kanazawa Medical University Ishikawa Japan
| | - Kazushi Anzawa
- Department of Dermatology Kanazawa Medical University Ishikawa Japan
| | - Takashi Mochizuki
- Department of Dermatology Kanazawa Medical University Ishikawa Japan
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Gupta AK, Taborda VBA, Taborda PRO, Shemer A, Summerbell RC, Nakrieko KA. High prevalence of mixed infections in global onychomycosis. PLoS One 2020; 15:e0239648. [PMID: 32991597 PMCID: PMC7523972 DOI: 10.1371/journal.pone.0239648] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 09/10/2020] [Indexed: 11/26/2022] Open
Abstract
Onychomycosis is estimated at a prevalence of 10% worldwide with the infecting organism most commonly Trichophyton rubrum (T. rubrum). Traditional culture identification of causative organisms has inherent risks of overestimating dermatophytes, like T. rubrum, by inhibiting the growth of possible nondermatophyte mould (NDM) environmental contaminants which could be causative agents. Recently, molecular methods have revealed that a proportion of onychomycosis cases in North America may be caused by mixed infections of T. rubrum as an agent co-infecting with one or more NDM. Determining the global burden of mixed infections is a necessary step to evaluating the best therapies for this difficult-to-treat disease. To determine the prevalence of mixed infections in a global population, nail samples from onychomycosis patients in Brazil, Canada, and Israel (n = 216) were analyzed by molecular methods for the presence of dermatophytes and five NDMs. If an NDM was detected, repeat sampling was performed to confirm the NDM. T. rubrum was detected in 98% (211/216) of infections with 39% mixed (84/216). The infection type was more likely to be mixed in samples from Brazil, but more likely to be a dermatophyte in samples from Canada and Israel (Χ2 = 16.92, df = 2, P<0.001). The most common cause of onychomycosis was T. rubrum. In all countries (Brazil, Canada and Israel combined) the prevalence of dermatophyte (Χ2 = 211.15, df = 3, P<0.001) and mixed (dermatophyte and NDM; Χ2 = 166.38, df = 3, P<0.001) infection increased with patient age. Our data suggest that mixed infection onychomycosis is more prevalent than previously reported with the aging population being at increased risk for mixed infections.
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Affiliation(s)
- Aditya K. Gupta
- Department of Medicine, the University of Toronto, Toronto, Ontario, Canada
- Mycology Section, Mediprobe Research Inc., London, Ontario, Canada
- * E-mail:
| | | | | | - Avner Shemer
- Sackler School of Medicine, Chaim Sheba Medical Center, the Tel-Aviv University, Tel-Hashomer, Israel
| | - Richard C. Summerbell
- Sporometrics, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Rengasamy M, Shenoy MM, Dogra S, Asokan N, Khurana A, Poojary S, Jayaraman J, Valia AR, Sardana K, Kolalapudi S, Marfatia Y, Rao PN, Bhat RM, Kura M, Pandhi D, Barua S, Kaushal V. Indian Association of Dermatologists, Venereologists and Leprologists (IADVL) Task Force against Recalcitrant Tinea (ITART) Consensus on the Management of Glabrous Tinea (INTACT). Indian Dermatol Online J 2020; 11:502-519. [PMID: 32832435 PMCID: PMC7413465 DOI: 10.4103/idoj.idoj_233_20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/30/2020] [Accepted: 06/22/2020] [Indexed: 01/12/2023] Open
Abstract
Background and Aims: Dermatophytosis has always been a common superficial mycosis in India. However, the past 6-7 years have seen an unprecedented increase in the number of patients affected by recurrent, chronic, recalcitrant and steroid modified dermatophytosis involving the glabrous skin (tinea corporis, tinea cruris and tinea faciei). Importantly, there has been a notable decrease in clinical responsiveness to commonly used antifungals given in conventional doses and durations resulting in difficult-to-treat infections. Considering that scientific data on the management of the current epidemic of dermatophytosis in India are inadequate, the Indian Association of Dermatologists, Venereologists and Leprologists (IADVL) Task force Against Recalcitrant Tinea (ITART) has formulated a consensus statement on the management of dermatophytosis in India. Methods: Seventeen dermatologists with a focussed interest in dermatophytosis participated in a Delphi consensus method, conducted in three rounds. They responded as either “agree” or “disagree” to 132 statements prepared by the lead experts and gave their comments. Consensus was defined as an agreement of 80% or higher concurrence. Statements on which there was no consensus were modified based on the comments and were then recirculated. The results were finally analysed in a face-to-face meeting and the responses were further evaluated. A draft of the consensus was circulated among the participants and modified based on their inputs. Results: Consensus was achieved on 90 of the 132 statements. Direct microscopy using potassium hydroxide mount was recommended in case of diagnostic difficulty on clinical examination. Counselling of patients about strict adherence to general measures and compliance to treatment was strongly recommended as the key to successful management of dermatophytosis. A combination of systemic and topical antifungal drugs was recommended for the treatment of glabrous tinea in the current scenario. Topical corticosteroid use, whether used alone or in combination with other components, was strongly discouraged by all the experts. It was suggested that topical antifungals may be continued for 2 weeks beyond clinical resolution. Itraconazole and terbinafine were recommended to be used as the first line options in systemic therapy, whereas griseofulvin and fluconazole are alternatives. Terbinafine was agreed to be used as a first line systemic agent in treatment naïve and terbinafine naïve patients with glabrous tinea. Regular follow-up of patients to ensure compliance and monitoring of clinical response was recommended by the experts, both during treatment and for at least 4 weeks after apparent clinical cure. Longer duration of treatment was recommended for patients with chronic, recurrent and steroid modified dermatophytosis. Conclusion: Consensus in the management of dermatophytosis is necessary in the face of conventional regimens proving ineffective and dearth of clinical trials re-evaluating the role of available antifungals in the wake of evolving epidemiology of the infection in the country. It needs to be backed by more research to provide the required level of evidence. It is hoped that this consensus statement improves the quality of care for patients with dermatophytosis, which has emerged as a huge public health problem, imposing considerable financial burden on the country.
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Affiliation(s)
- Madhu Rengasamy
- Department of Dermatology, Venereology and Leprosy, Madras Medical College, Chennai, Tamil Nadu, India
| | - Manjunath M Shenoy
- Department of Dermatology, Venereology and Leprosy, Yenepoya Medical College, Deralakatte, Deralakatte, Mangalore, Karanataka, India
| | - Sunil Dogra
- Department of Dermatology, Venereology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelakandhan Asokan
- Department of Dermatology, Venereology and Leprosy, Government Medical College, Thrissur, Kerala, India
| | - Ananta Khurana
- Department of Dermatology, Venereology and Leprosy, Dr Ram Manohar Lohia Hospital and Postgraduate Institute of Medical Education and Research, New Delhi, India
| | - Shital Poojary
- Department of Dermatology, Venereology and Leprosy, K. J. Somaiya Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Jyothi Jayaraman
- Department of Dermatology, Venereology and Leprosy, Father Muller Medical College, Mangalore, Karnataka, India
| | - Ameet R Valia
- Consultant Dermatologist, Harganga Mahal Annexe, Dadar TT, India
| | - Kabir Sardana
- Department of Dermatology, Venereology and Leprosy, Dr Ram Manohar Lohia Hospital and Postgraduate Institute of Medical Education and Research, New Delhi, India
| | | | - Yogesh Marfatia
- Department of Dermatology, Venereology and Leprosy, SBKS Medical College, Piparia, Vadodara, Gujarat, India
| | - P Narasimha Rao
- Consultant Dermatologist, Masab Tank, Hyderabad, Telangana, India
| | - Ramesh M Bhat
- Department of Dermatology, Venereology and Leprosy, Father Muller Medical College, Mangalore, Karnataka, India
| | - Mahendra Kura
- Department of Dermatology, Venereology and Leprosy, Grant Medical College, Mumbai, Maharashtra, India
| | - Deepika Pandhi
- Department of Dermatology, Venereology and Leprosy, University College of Medical Sciences and GTBH, New Delhi, India
| | - Shyamanta Barua
- Department of Dermatology, Venereology and Leprosy, Assam Medical College and Hospital, Dibrugarh, Assam, India
| | - Vibhor Kaushal
- Consultant Dermatologist, Dr. Kaushal's Skin Clinic, Agra, Uttar Pradesh, India
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Ciesielska A, Stączek P. A new molecular marker for species-specific identification of Microsporum canis. Braz J Microbiol 2020; 51:1505-1508. [PMID: 32696419 PMCID: PMC7688866 DOI: 10.1007/s42770-020-00340-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/15/2020] [Indexed: 11/26/2022] Open
Abstract
Species identification of dermatophytes by conventional mycological methods based on macro- and microscopy analysis is time-consuming and has a lot of limitations such as slow fungal growth or low specificity. Thus, there is a need for the development of molecular methods that would provide reliable and prompt identification of this group of medically important fungi. The are many reports in the literature concerning PCR identification of dermatophyte species, but still, there are not many PCR assays for the separate detection of members of the genera Microsporum, especially Microsporum canis (zoophilic species) and Microsporum audouinii (anthropophilic species). The correct distinction of these species is important to determine the source of infection to implement the appropriate action to eliminate the path of infection transmission. In this paper, we present such a PCR-based method targeting velB gene that uses a set of two primers—Mc-VelB-F (5′-CTTCCCCACCCGCAACATC-3′) and Mc-VelB-R (5′-TGTGGCTGCACCTGAGAGTGG-3′). The amplified fragment is specific due to the presence of (CAGCAC)8 microsatellite sequence only in the velB gene of M. canis. DNA from 153 fungal samples was used in PCR assay followed by electrophoretic analysis. The specificity of the designed set of primers was also confirmed using the online BLAST-Primer tool. The positive results were observed only in the case of M. canis isolates, and no positive results were obtained neither for other dermatophytes and non-dermatophyte fungi nor for other Eukaryotes, including the human genome sequence, as well as the representatives of bacterial and viral taxa. The developed PCR assay using the proposed Mc-VelB-F and Mc-velB-R primers can be included in the algorithm of M. canis detection in animals and humans.
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Affiliation(s)
- Anita Ciesielska
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - Paweł Stączek
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Niu L, Liu X, Ma Z, Yin Y, Sun L, Yang L, Zheng Y. Fungal keratitis: Pathogenesis, diagnosis and prevention. Microb Pathog 2019; 138:103802. [PMID: 31626916 DOI: 10.1016/j.micpath.2019.103802] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/12/2019] [Accepted: 10/12/2019] [Indexed: 02/08/2023]
Abstract
As a kind of serious, potentially sight-threatening corneal infections with poor prognosis, fungal keratitis can bring a heavy economic burden to patients and seriously affect the quality of life, especially those in developing countries where fungal keratitis is more prevalent. Typical clinical features include immune rings, satellite lesions, pseudopods, hypha moss, hypopyon and endothelial plaques. The ideal therapeutic effects could not be achieved by current treatments for many reasons. Therefore, under the current status, understanding the pathogenesis, early diagnosis and prevention strategies might be of great importance. Here, in this review, we discuss the recent progresses that may advance our understanding of pathogenesis, early diagnosis and prevention of fungal keratitis.
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Affiliation(s)
- Lingzhi Niu
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China
| | - Xin Liu
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China
| | - Zhiming Ma
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Yuan Yin
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China
| | - Lixia Sun
- Department of Ophthalmology, Yanbian University Affiliated Hospital, Yanbian University, Yanji, 133000, China
| | - Longfei Yang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetics, The Second Hospital of Jilin University, Changchun 130041, China.
| | - Yajuan Zheng
- Eye Center, The Second Hospital of Jilin University, Changchun 130041, China.
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Salehi Z, Shams-Ghahfarokhi M, Razzaghi-Abyaneh M. Internal Transcribed Spacer rDNA and TEF-1α Gene Sequencing of Pathogenic Dermatophyte Species and Differentiation of Closely Related Species Using PCR-RFLP of The Topoisomerase II. CELL JOURNAL 2019; 22:85-91. [PMID: 31606971 PMCID: PMC6791061 DOI: 10.22074/cellj.2020.6372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/26/2019] [Indexed: 12/04/2022]
Abstract
Objective Precise identification of dermatophyte species significantly improves treatment and controls measures of
dermatophytosis in human and animals. This study was designed to evaluate molecular tools effectiveness of the gene
sequencing and DNA-based fragment polymorphism analysis for accurate identification and differentiation of closely-
related dermatophyte species isolated from clinical cases of dermatophytosis and their antifungal susceptibility to the
current antifungal agents.
Materials and Methods In this experimental study, a total of 95 skin samples were inoculated into mycobiotic agar for
two weeks at 28˚C. Morphological characteristics of the isolated dermatophytes were evaluated. DNA was extracted
from the fungal culture for amplification of topoisomerase II gene fragments and polymerase chain reaction (PCR)
products were digested by Hinf I enzyme. Internal transcribed spacer (ITS) rDNA and TEF-1α regions of the all isolates
were amplified using the primers of ITS1/4 and EF-DermF/EF-DermR, respectively.
Results Based on the morphological criteria, 24, 24, 24 and 23 isolates were identified as T. rubrum, T. interdigitale,
T. tonsurans and E. floccosum, respectively. PCR-restriction fragment length polymorphism (RFLP) results provided
identification pattern of the isolates for T. rubrum (19 isolates), T. tonsurans (28 isolates), T. interdigitale (26 isolates)
and E. floccosum (22 isolates). Concatenated dataset results were similar in PCR-RFLP, except six T. interdigitale
isolates belonging to T. mentagrophytes.
Conclusion Our results clearly indicated that conventional morphology and PCR-RFLP were not able to precisely
identify all dermatophyte species and differentiation of closely related species like T. interdigitale and T. mentagrophytes,
while ITS rDNA and TEF-1α gene sequence analyses provided accurate identification of all isolates at the genus and
species level.
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Affiliation(s)
- Zahra Salehi
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Masoomeh Shams-Ghahfarokhi
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran. Electronic Address:
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Zhang F, Tan C, Xu Y, Yang G. FSH1 regulates the phenotype and pathogenicity of the pathogenic dermatophyte Microsporum canis. Int J Mol Med 2019; 44:2047-2056. [PMID: 31573050 PMCID: PMC6844631 DOI: 10.3892/ijmm.2019.4355] [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: 05/31/2019] [Accepted: 09/03/2019] [Indexed: 11/21/2022] Open
Abstract
Microsporum canis (M. canis) is a common pathogen that causes tinea capitis and is present worldwide. The incidence of M. canis infection, particularly tinea capitis, has been increasing in China. In our previous studies, family of serine hydrolases 1 (FSH1) was identified as a potential virulence factor in tinea capitis infection caused by M. canis. To determine the function of this gene in M. canis, FSH1 was knocked down using double-stranded RNA interference mediated by Agrobacterium tumefaciens. Reverse transcription-quantitative PCR analysis was used to confirm gene knockdown. Loss of FSH1 expression by RNAi resulted in a minor phenotype alteration, but M. canis pathogenicity in guinea pig cutaneous infection was decreased compared with the wild-type strain. To the best of our knowledge, the present study is the first to demonstrate that FSH1 is associated with macroconidia septa formation and is an important contributor to M. canis virulence. These findings may advance the understanding of the function of the FSH1 gene and provide a foundation for future studies on macroconidia septa formation and pathogenicity of M. canis.
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Affiliation(s)
- Furong Zhang
- Department of Dermatology, The First Affiliated Hospital of Dalian Medical University, Chengdu, Sichuan 11736, P.R. China
| | - Can Tan
- Department of Dermatology, The First Affiliated Hospital of Dalian Medical University, Chengdu, Sichuan 11736, P.R. China
| | - Yu Xu
- Department of Dermatology, Hospital of Anjing Town, Chengdu, Sichuan 11736, P.R. China
| | - Guoling Yang
- Department of Dermatology, The First Affiliated Hospital of Dalian Medical University, Chengdu, Sichuan 11736, P.R. China
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Ansari S, Ahmadi B, Norouzi M, Ansari Z, Afsarian MH, Lotfali E, Rezaei-Matehkolaei A. Epidermophyton floccosum: nucleotide sequence analysis and antifungal susceptibility testing of 40 clinical isolates. J Med Microbiol 2019; 68:1655-1663. [PMID: 31573466 DOI: 10.1099/jmm.0.001074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Purpose. Epidermophyton floccosum is an anthropophilic dermatophyte species, which is one of the common causative agents of dermatophytosis in different parts of the world. The aim of the present investigation was to evaluate the genetic diversity of E. floccosum strains isolated from different parts of Iran and to define the in vitro susceptibility profiles of seven antifungal drugs against these clinical isolates.Methodology. Forty clinical strains of E. floccosum isolated from 40 patients with dermatophytosis were subjected to DNA extraction and PCR amplification of the ITS rDNA region using universal primers ITS1 and ITS4. The in vitro activities of griseofulvin, itraconazole, voriconazole, posaconazole, caspofungin, ketoconazole and terbinafine were determined using a broth microdilution method according to the CLSI-M-38A2 protocol.Results. A mean genetic similarity of 99.5 % was found between E. floccosum strains, with intraspecies differences ranging from 0 to 3 nt. The geometric mean (GM) MICs and minimum effective concentrations (MECs) across all isolates were, in increasing order, as follows: terbinafine (GM=0.018 mg l-1), posaconazole (GM=0.022 mg l-1), itraconazole (GM=0.034 mg l-1) and voriconazole (GM=0.045 mg l-1), which had low MICs against all tested strains, whereas caspofungin (GM=0.22 mg l-1), ketoconazole (GM=0.41 mg l-1) and griseofulvin (GM=0.62 mg l-1) demonstrated higher MICs.Conclusion. Our study showed low intraspecies variation within strains of E. floccosum. Furthermore, terbinafine, posaconazole, itraconazole and voriconazole were shown to be the most potent antifungal drugs against E. floccosum strains.
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Affiliation(s)
- Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Ahmadi
- Department of Medical Laboratory Sciences, School of Para-Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Norouzi
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Ansari
- Department of Chemistry, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Mohammad Hosein Afsarian
- Department of Medical Mycology and Parasitology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Ensieh Lotfali
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Rezaei-Matehkolaei
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Leal C, Silva G, Silva G, Silva L, Pinheiro Júnior J, Mota R. Padronização de uma PCR para diagnóstico molecular de Microsporum canis em amostras de pelos e crostas de cães e gatos. ARQ BRAS MED VET ZOO 2019. [DOI: 10.1590/1678-4162-9809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO Objetivou-se neste estudo padronizar um protocolo de reação em cadeia da polimerase (PCR) para detecção de Microsporum canis em amostras de pelos e/ou crostas de cães e gatos. Foram selecionadas 48 amostras previamente identificadas por meio de cultura. Destas, 23 foram positivas para dermatófitos no cultivo. Padronizou-se a PCR a partir de primers desenhados para o alvo M. canis. Sessenta e um por cento (14/23) das amostras positivas para dermatófitos foram identificadas como M. canis em cultura. Desse total, 71,4% (10/14) apresentaram um fragmento de 218pb compatível com o esperado para a espécie fúngica alvo dessa reação. Observou-se uma sensibilidade de 71,4% e especificidade de 100% na PCR, além de uma boa concordância entre essas técnicas de diagnóstico (Kappa: 0,78; P<0,0001). O protocolo utilizado neste estudo apresentou alta especificidade na detecção de M. canis diretamente de amostras de pelos e/ou crostas de cães e gatos, viabilizando um diagnóstico mais rápido e específico, podendo esse protocolo ser empregado como um método confirmatório para agilizar a detecção de M. canis.
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Affiliation(s)
- C.A.S. Leal
- Universidade Federal Rural de Pernambuco, Brazil
| | - G.G. Silva
- Universidade Federal Rural de Pernambuco, Brazil
| | - G.M. Silva
- Universidade Federal Rural de Pernambuco, Brazil
| | | | | | - R.A. Mota
- Universidade Federal Rural de Pernambuco, Brazil
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Take a multifaceted approach when treating onychomycosis. DRUGS & THERAPY PERSPECTIVES 2019. [DOI: 10.1007/s40267-019-00640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sangale MK, Shahnawaz M, Ade AB. Potential of fungi isolated from the dumping sites mangrove rhizosphere soil to degrade polythene. Sci Rep 2019; 9:5390. [PMID: 30926843 PMCID: PMC6440974 DOI: 10.1038/s41598-019-41448-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022] Open
Abstract
Polythene is the most widely used plastic around the globe. Among the total plastic waste generated, polythene contributes the maximum share (64%). Various strategies/methods are being utilized to deal with the increasing rate of plastic waste, but among all the methods, bioremediation is regarded as the ecofriendly and widely accepted method. In the current investigation, we have attempted to discover the elite polythene deteriorating fungi (isolated from the rhizosphere soil of Avicennia marina). From 12 different eco-geographical locations along the West Coast of India, total 109 fungal isolates were recorded. The polythene deteriorating fungi were screened at varied pH (3.5, 7 and 9.5) based on changes in weight and tensile strength of the treated polythene at ambient temperature with continuous shaking for 60 days. BAYF5 isolate (pH 7) results in maximum reduction in weight (58.51 ± 8.14) whereas PNPF15 (pH 3.5) recorded highest reduction in tensile strength (94.44 ± 2.40). Surprisingly, we have also reported weight gain, with highest percent weight gain (28.41 ± 6.99) with MANGF13 at pH 9.5. To test the reproducibility of the results, the elite polythene degrading fungal isolates based on weight loss and reduction in tensile strength were only used for repetition experiment and the results based on the reduction in tensile strength were found only reproducible. Polythene biodegradation was further confirmed using Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR) analysis. The most efficient polythene deteriorating fungal isolates were identified as Aspergillus terreus strain MANGF1/WL and Aspergillus sydowii strain PNPF15/TS using both morphological keys and molecular tools.
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Affiliation(s)
- Manisha K Sangale
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India.,Department of Botany, S. M. Joshi College Hadapsar, Malwadi, Hadapsar, Pune, Maharashtra, 411028, India
| | - Mohd Shahnawaz
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India. .,Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road Jammu, Jammu, 180001, Jammu and Kashmir, India.
| | - Avinash B Ade
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India.
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25
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A Practical Guide to Curing Onychomycosis: How to Maximize Cure at the Patient, Organism, Treatment, and Environmental Level. Am J Clin Dermatol 2019; 20:123-133. [PMID: 30456537 DOI: 10.1007/s40257-018-0403-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Onychomycosis is a fungal nail infection caused by dermatophytes, non-dermatophyte molds, and yeasts. Treatment of this infection can be difficult, with relapse likely to occur within 2.5 years of cure. The objective of this article is to review factors that can impact cure and to suggest practical techniques that physicians can use to maximize cure rates. Co-morbidities, as well as disease severity and duration, are among the many patient factors that could influence the efficacy of antifungal therapies. Furthermore, organism, treatment, and environmental factors that may hinder cure include point mutations, biofilms, affinity for non-target enzymes, and exposure to fungal reservoirs. To address patient-related factors, physicians are encouraged to conduct confirmatory testing and treat co-morbidities such as tinea pedis early and completely. To combat organism-focused factors, it is recommended that disruption of biofilms is considered, and drugs with multiple routes of delivery and unique mechanisms of action are prescribed when traditional agents are not effective. Extending follow-up periods, using combination treatments, and considering pulse regimens may also be of benefit. Through these practical techniques, physicians can maximize cure and limit the risk of relapse and re-infection.
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26
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Marizzi C, Florio A, Lee M, Khalfan M, Ghiban C, Nash B, Dorey J, McKenzie S, Mazza C, Cellini F, Baria C, Bepat R, Cosentino L, Dvorak A, Gacevic A, Guzman-Moumtzis C, Heller F, Holt NA, Horenstein J, Joralemon V, Kaur M, Kaur T, Khan A, Kuppan J, Laverty S, Lock C, Pena M, Petrychyn I, Puthenkalam I, Ram D, Ramos A, Scoca N, Sin R, Gonzalez I, Thakur A, Usmanov H, Han K, Wu A, Zhu T, Micklos DA. DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists. PLoS One 2018; 13:e0199015. [PMID: 30020927 PMCID: PMC6051577 DOI: 10.1371/journal.pone.0199015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/30/2018] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.
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Affiliation(s)
- Christine Marizzi
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Antonia Florio
- Department of Herpetology, American Museum of Natural History, New York, New York, United States of America
| | - Melissa Lee
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Mohammed Khalfan
- New York University, New York, New York, United States of America
| | - Cornel Ghiban
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Bruce Nash
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jenna Dorey
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- The New York Botanical Garden, Bronx, New York, United States of America
| | - Sean McKenzie
- The Rockefeller University, New York, New York, United States of America
| | - Christine Mazza
- Genovesi Environmental Study Center, New York City Department of Education, Brooklyn, New York, United States of America
| | - Fabiana Cellini
- Genovesi Environmental Study Center, New York City Department of Education, Brooklyn, New York, United States of America
| | - Carlo Baria
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Ron Bepat
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Lena Cosentino
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Alexander Dvorak
- International High School at Union Square, New York City Department of Education New York, New York, United States of America
| | - Amina Gacevic
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Cristina Guzman-Moumtzis
- Frank McCourt High School, New York City Department of Education, New York, New York, United States of America
| | - Francesca Heller
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Nicholas Alexander Holt
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Jeffrey Horenstein
- Stuyvesant High School, New York City Department of Education, New York, New York, United States of America
| | - Vincent Joralemon
- Frank McCourt High School, New York City Department of Education, New York, New York, United States of America
| | - Manveer Kaur
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Tanveer Kaur
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Armani Khan
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Jessica Kuppan
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Scott Laverty
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Camila Lock
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Marianne Pena
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Ilona Petrychyn
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Indu Puthenkalam
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Daval Ram
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Arlene Ramos
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Noelle Scoca
- Brooklyn International High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Rachel Sin
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Izabel Gonzalez
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Akansha Thakur
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Husan Usmanov
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Karen Han
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Andy Wu
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Tiger Zhu
- Stuyvesant High School, New York City Department of Education, New York, New York, United States of America
| | - David Andrew Micklos
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
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27
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Pecchia S, Da Lio D. Development of a rapid PCR-Nucleic Acid Lateral Flow Immunoassay (PCR-NALFIA) based on rDNA IGS sequence analysis for the detection of Macrophomina phaseolina in soil. J Microbiol Methods 2018; 151:118-128. [PMID: 29959955 DOI: 10.1016/j.mimet.2018.06.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 11/30/2022]
Abstract
The 'Nucleic Acid Lateral Flow Immunoassay' (NALFIA) using a generic 'Lateral Flow Device' (LFD), combined with PCR employing labelled primers (PCR-NALFIA), enables to circumvent the use of electrophoresis, making the diagnostic procedure more rapid and easier. If the specific amplicon is present in the sample, a coloured band, with an intensity proportional to the amplicon concentration, will develop on the LFD strip in addition to the control band. Species-specific primers for M. phaseolina based on the rDNA intergenic spacer (IGS) were developed and their specificity was checked and confirmed using 20 isolates of M. phaseolina and other 16 non-target fungi. A DNA extraction protocol based on a bead-beating technique using silica beads, skimmed milk and PVP was also developed. The M. phaseolina specific primers MP102F/MP102R, 5' labelled with biotin and FITC respectively, were used in the PCR-NALFIA assay to identify the pathogen starting from mycelium or microsclerotia. Microsclerotia of M. phaseolina (1, 10, 100 and 200) were manipulated under a stereomicroscope and their DNA was extracted using microsclerotia alone or mixed with different types of soil. The resulting DNA, used for the PCR-NALFIA assay, provided positive results for all the samples tested. A semi-quantitative grey-scale reference card based on the PCR-NALFIA assay using intervals corresponding to microsclerotia soil number was developed. For this purpose, the normalized pixel grey volumes obtained after a densitometric analysis of the test line intensity generated by the LFD dipsticks were used.
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Affiliation(s)
- Susanna Pecchia
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy.
| | - Daniele Da Lio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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28
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da Cunha KC, Riat A, Normand AC, Bosshard PP, de Almeida MTG, Piarroux R, Schrenzel J, Fontao L. Fast identification of dermatophytes by MALDI-TOF/MS using direct transfer of fungal cells on ground steel target plates. Mycoses 2018; 61:691-697. [PMID: 29762871 DOI: 10.1111/myc.12793] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/01/2018] [Accepted: 05/08/2018] [Indexed: 11/30/2022]
Abstract
Dermatophytes cause human infections limited to keratinised tissues. We showed that the direct transfer method allows reliable identification of non-dermatophytes mould and yeast by MALDI-TOF/MS. We aimed at assessing whether the direct transfer method can be used for dermatophytes and whether an own mass spectra library would be superior to the Bruker library. We used the Bruker Biotyper to build a dermatophyte mass spectra library and assessed its performance by 1/testing a panel of mass spectrum produced with strains genotypically identified and, 2/comparing MALDI-TOF/MS identification to morphology-based methods. Identification of dermatophytes using the Bruker library is poor. Our library provided 97% concordance between ITS sequencing and MALDI-TOF/MS analysis with a panel of 1104 spectra corresponding to 276 strains. Direct transfer method using unpolished target plates allowed proper identification of 85% of dermatophytes clinical isolates most of which were common dermatophytes. A homemade dermatophyte MSP library is a prerequisite for accurate identification of species absent in the Bruker library but it also improves identification of species already listed in the database. The direct deposit method can be used to identify the most commonly found dermatophytes such as T. rubrum and T. interdigitale/mentagrophytes by MALDI-TOF/MS.
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Affiliation(s)
- Keith C da Cunha
- Dermatology Laboratory, Division of Laboratory Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Arnaud Riat
- Bacteriology Laboratory, Division of Laboratory Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Anne-Cecile Normand
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université d'Aix-Marseille, Marseille, France
| | - Philipp P Bosshard
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland.,Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Margarete T G de Almeida
- Department of Infectious and Parasitic Diseases, Faculty of Medicine of São José do Rio Preto, São Paulo, Brazil
| | - Renaud Piarroux
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université d'Aix-Marseille, Marseille, France
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Lionel Fontao
- Dermatology Laboratory, Division of Laboratory Medicine, University Hospital of Geneva, Geneva, Switzerland
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29
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DNA Barcoding for Identification of Consumer-Relevant Fungi Sold in New York: A Powerful Tool for Citizen Scientists? Foods 2018; 7:foods7060087. [PMID: 29890621 PMCID: PMC6025134 DOI: 10.3390/foods7060087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Although significant progress has been made in our understanding of fungal diversity, identification based on phenotype can be difficult, even for trained experts. Fungi typically have a cryptic nature and can have a similar appearance to distantly related species. Moreover, the appearance of industrially processed mushrooms complicates species identification, as they are often sold sliced and dried. Here we present a small-scale citizen science project, wherein the participants generated and analyzed DNA sequences from fruiting bodies of dried and fresh fungi that were sold for commercial use in New York City supermarkets. We report positive outcomes and the limitations of a youth citizen scientist, aiming to identify dried mushrooms, using established DNA barcoding protocols and exclusively open-access data analysis tools for species identification. Our results indicate that the single-locus nuclear ribosomal internal transcribed spacer (ITS) DNA barcoding approach allowed for identification of only a subset of all of the samples at the species level, although the generated high-quality DNA barcodes were submitted to three different databases. Our results highlight the need for a curated, centralized, and open access ITS reference database that allows rapid third-party annotations for the benefit of both traditional research as well as the emerging citizen science community.
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30
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Farokhipor S, Ghiasian SA, Nazeri H, Kord M, Didehdar M. Characterizing the clinical isolates of dermatophytes in Hamadan city, Central west of Iran, using PCR-RLFP method. J Mycol Med 2018; 28:101-105. [PMID: 29439839 DOI: 10.1016/j.mycmed.2017.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 11/27/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Dermatophytosis is one of the most common mycotic infections, which considered as a public health problem in the major of countries. This study evaluated the molecular epidemiology of dermatophytosis in patients referred to Farshchian hospital in Hamadan city with PCR-RFLP method. MATERIALS AND METHODS Four hundred and five specimens from clinically suspected patients of dermatophytosis were collected and analyzed by direct microscopic and culture. The isolates were identified by PCR-RFLP method using the MvaI restriction enzyme. RESULTS Of the 405 specimens, 88 specimens were positive in direct examination and culture. Among the patients, 64.8% were males and35.2% females. Tinea pedis (31.8%) was the most common type of dermatophytosis followed by tinea corporis (22.7%), tinea cruris (20.5%), tinea capitis (10.2%), tinea manuum (5.7%), tinea faciei (4.6%) and tinea unguium (4.6%). Trichophyton interdigitale (36.4%) was the most common isolate followed by Trichophyton rubrum (27.3%), Epidermophyton floccosum (17%), Trichophyton tonsurans (11.4%), Microsporum canis (4.5%), Microsporum gypseum (2.3%) and Trichophyton benhamiae (1.1%). CONCLUSION Our finding showed that the anthropophilic dermatophyte species causing dermatophytosis are increasing, and molecular methods are reliable assays for accurse identification of dermatophyte species in epidemiological studies.
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Affiliation(s)
- S Farokhipor
- Department of Microbiology, Islamic Azad University, Arak Branch, Arak, Iran
| | - S A Ghiasian
- Medical Parasitology and Mycology Department, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Psoriasis Research Center, Department of Dermatology, Farshchian Hospital, Hamadan University of Medical Sciences, Hamadan, Iran
| | - H Nazeri
- Mycology Laboratory, Farshchian Hospital, Hamadan University of Medical Sciences, Hamadan, Iran
| | - M Kord
- Department of Medical Parasitology and Mycology, Tehran University of Medical Sciences, Tehran, Iran
| | - M Didehdar
- Infectious Diseases Research Center (IDRC), Department of Medical Parasitology and Mycology, Arak University of Medical Sciences, Arak, Iran.
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31
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Gupta AK, Nakrieko KA. Onychomycosis Infections Do Polymerase Chain Reaction and Culture Reports Agree?. J Am Podiatr Med Assoc 2017; 107:280-286. [PMID: 28880601 DOI: 10.7547/15-136] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Mycological culture is the traditional method for identifying infecting agents of onychomycosis despite high false-negative results, slower processing, and complications surrounding nondermatophyte mold (NDM) infections. Molecular polymerase chain reaction (PCR) methods are faster and suited for ascertaining NDM infections. METHODS To measure agreement between culture and PCR methods for identification of infecting species of suspected onychomycosis, single toenail samples from 167 patients and repeated serial samples from 43 patients with suspected onychomycosis were processed by culture and PCR for identification of 16 dermatophytes and five NDMs. Agreement between methods was quantified using the kappa statistic (κ). RESULTS The methods exhibited fair agreement for the identification of all infecting organisms (single samples: κ = 0.32; repeated samples: κ = 0.38). For dermatophytes, agreement was moderate (single samples: κ = 0.44; repeated samples: κ = 0.42). For NDMs, agreement was poor with single samples (κ = 0.16) but fair with repeated samples (κ = 0.25). Excluding false-negative reports from analyses improved agreement between methods in all cases except the identification of NDMs from single samples. CONCLUSIONS Culture was three or four times more likely to report a false-negative result compared with PCR. The increased agreement between methods observed by excluding false-negative reports statistically clarifies and highlights the major discord caused by false-negative cultures. The increased agreement of NDM identification from poor to fair with repeated sampling along with their poor agreement in the single samples, with and without false-negatives, affirms the complications of NDM identification and supports the recommendation that serial samples help confirm the diagnosis of NDM infections.
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Affiliation(s)
- Aditya K. Gupta
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Mycology Section, Mediprobe Research Inc, London, Ontario, Canada
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32
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Watanabe J, Anzawa K, Mochizuki T. Molecular Epidemiology of Japanese Isolates of Microsporum canis Based on Multilocus Microsatellite Typing Fragment Analysis. Jpn J Infect Dis 2017; 70:544-548. [DOI: 10.7883/yoken.jjid.2016.424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Verant ML, Bohuski EA, Lorch JM, Blehert DS. Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples. J Vet Diagn Invest 2016; 28:110-8. [PMID: 26965231 DOI: 10.1177/1040638715626963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid from P. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer-based qPCR test for P. destructans to refine quantification capabilities of this assay.
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Affiliation(s)
- Michelle L Verant
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI (Verant)U.S. Geological Survey-National Wildlife Health Center, Madison, WI (Bohuski, Lorch, Blehert)
| | - Elizabeth A Bohuski
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI (Verant)U.S. Geological Survey-National Wildlife Health Center, Madison, WI (Bohuski, Lorch, Blehert)
| | - Jeffery M Lorch
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI (Verant)U.S. Geological Survey-National Wildlife Health Center, Madison, WI (Bohuski, Lorch, Blehert)
| | - David S Blehert
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI (Verant)U.S. Geological Survey-National Wildlife Health Center, Madison, WI (Bohuski, Lorch, Blehert)
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Tartor YH, El Damaty HM, Mahmmod YS. Diagnostic performance of molecular and conventional methods for identification of dermatophyte species from clinically infected Arabian horses in Egypt. Vet Dermatol 2016; 27:401-e102. [PMID: 27549079 DOI: 10.1111/vde.12372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 11/27/2022]
Abstract
BACKGROUND Rapid and accurate identification of dermatophytes is crucial for the effective control of disease outbreaks. Current methods based on culture and microscopic characteristics may require weeks before positive identification is made. OBJECTIVES To (i) identify the most common pathogenic dermatophytes affecting Arabian horses; (ii) compare the performance of direct microscopy (DM), culture, PCR using hair samples (PCRhair ) and PCR based on culture isolates (PCRculture ) for the diagnosis of dermatophytosis. METHODS Samples of hair and crusts of skin lesions from Arabian horses were collected on a monthly basis by scraping skin of affected horses. Samples were divided into three portions: the first portion was used for microscopic examination, the second for culture and the third portion for PCR amplification of intergenic spacer (ITS) regions. RESULTS Out of 200 horses examined, 70 (35%) showed cutaneous lesions characteristic of dermatophytosis. DM revealed that 70.4% were positive for fungal elements and 85.7% were culture positive. The identified species were Microsporum canis, Trichophyton verrucosum, T. mentagrophytes var. mentagrophytes and M. equinum. Among 25 selected samples, 64, 92, 91.3 and 52% were positive for dermatophytes, as determined by DM, culture, PCRculture and PCRhair , respectively. CONCLUSIONS The dermatophytes M. canis, T. verrucosum, T. mentagrophytes var. mentagrophytes and M. equinum were the most common cause of dermatophytosis in Arabian horses. Although the number of samples was small, the ITS-based PCR may be a useful diagnostic tool when combined with culture.
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Affiliation(s)
- Yasmine H Tartor
- Departments of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Zagazig University, 44511, Zagazig, Sharkia Province, Egypt
| | - Hend M El Damaty
- Departments of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, 44511, Zagazig, Sharkia Province, Egypt
| | - Yasser S Mahmmod
- Departments of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, 44511, Zagazig, Sharkia Province, Egypt. ,
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35
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Mochizuki T, Takeda K, Anzawa K. Molecular Markers Useful for Intraspecies Subtyping and Strain Differentiation of Dermatophytes. Mycopathologia 2016; 182:57-65. [PMID: 27456819 DOI: 10.1007/s11046-016-0041-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 07/07/2016] [Indexed: 02/04/2023]
Abstract
Dermatophytosis is a very common skin disorder and the most frequent infection encountered by practicing dermatologists. The identification, pathogenicity, biology, and epidemiology of dermatophytes, the causative agents of dermatophytosis, are of interest for both dermatologists and medical mycologists. Recent advances in molecular methods have provided new techniques for identifying dermatophytes, including intraspecies variations. Intraspecies subtyping and strain differentiation have made possible the tracking of infections, the identification of common sources of infections, recurrence or reinfection after treatment, and analysis of strain virulence and drug resistance. This review describes molecular methods of intraspecies subtyping and strain differentiation, including analyses of mitochondrial DNA and non-transcribed spacer regions of ribosomal RNA genes, random amplification of polymorphic DNA, and microsatellite markers, along with their advantages and limitations.
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Affiliation(s)
- Takashi Mochizuki
- Department of Dermatology, Kanazawa Medical University, Daigaku 1-1, Uchinada, Ishikawa, 920-0293, Japan.
| | - Kiminobu Takeda
- Department of Dermatology, Kanazawa Medical University, Daigaku 1-1, Uchinada, Ishikawa, 920-0293, Japan
| | - Kazushi Anzawa
- Department of Dermatology, Kanazawa Medical University, Daigaku 1-1, Uchinada, Ishikawa, 920-0293, Japan
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Neji S, Trabelsi H, Hadrich I, Cheikhrouhou F, Sellami H, Makni F, Ayadi A. Molecular characterization of strains of theTrichophyton verrucosumcomplex from Tunisia. Med Mycol 2016; 54:787-93. [DOI: 10.1093/mmy/myw036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/10/2016] [Indexed: 11/13/2022] Open
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Chadeganipour M, Mohammadi R. Causative Agents of Onychomycosis: A 7-Year Study. J Clin Lab Anal 2016; 30:1013-1020. [PMID: 27790797 DOI: 10.1002/jcla.21973] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 12/15/2015] [Accepted: 01/11/2016] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Onychomycosis is principally caused by dermatophyte species, but nondermatophyte molds and yeasts have also been involved, causing different clinical manifestations. The aim of this investigation is to determine the clinicomycological and epidemiological profile of the etiologic agents of onychomycosis. METHODS The study population included 9,785 suspected cases of onychomycosis referred to the Medical Mycology Reference Laboratory in Isfahan, Iran, during 2007-2014. Nail clipping was collected in sterile Petri dishes for direct microscopic examination and culture. Clinical isolates were identified by using phenotypic tests and molecular techniques. RESULTS Of total 9,785 cases with clinical suspicion of onychomycosis comprised in the present study, 1,284 patients (13.1%) were positive by direct microscopy. Age range of patients was between 1 and 82 years. Housewives were the commonest infected population. Candida albicans was the most prevalent species isolated from patients in this study (34.9%) followed by Trichophyton interdigitale (11.7%) and Aspergillus flavus (9.1%). CONCLUSION The pattern of causative agents and clinical signs of onychomycosis is altering region to region, so repeated epidemiological surveys of onychomycosis seems to be fundamental. The present study provides novel and appropriate epidemiologic data of onychomycosis for the better prevention and treatment of this fungal infection.
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Affiliation(s)
- Mostafa Chadeganipour
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Mohammadi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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Mirhendi H, Motamedi M, Makimura K, Satoh K. Development a diagnostic pan-dermatophyte TaqMan probe real-time PCR assay based on beta tubulin gene. Mycoses 2016; 59:520-7. [PMID: 27071371 DOI: 10.1111/myc.12502] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/30/2016] [Accepted: 03/05/2016] [Indexed: 11/28/2022]
Abstract
Early differentiation of dermatophytosis from other cutaneous mycoses is essential to avoid inaccurate therapy. DNA-based techniques including real-time PCR have increasingly been considered for detection of fungal elements in clinical specimens. In this study, after partial sequence analysis of beta tubulin (BT2) gene in 13 common and rare pathogenic dermatophyte species, a pan-dermatophyte primer and probe set was designed in a TaqMan probe-based PCR format. The sensitivity and specificity of the system was tested with 22 reference strains of dermatophytes, 234 positive clinical specimens, 32 DNA samples extracted from normal nails, several fungi other than dermatophytes and human DNAs. Analytical detection limit of the designed PCR on serially diluted DNAs of prepared recombinant plasmid indicated that only five molecules per sample are the minimum number for reliable detection by the assay. A total of 226 out of 234 (96.5%) DNAs extracted from clinical samples, but none of the 32 nail samples, from healthy volunteers were positive in PCR. The real-time PCR targeted beta tubulin gene established in this study could be a sensitive diagnostic tool which is significantly faster than the conventional culture method and should be useful in the clinical settings, in large-scale epidemiological studies and in clinical trials of antifungal therapy.
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Affiliation(s)
- Hossein Mirhendi
- Departments of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Departments of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Motamedi
- 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, Tokyo, Japan
| | - Kazuo Satoh
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
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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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Hayette MP, Sacheli R. Dermatophytosis, Trends in Epidemiology and Diagnostic Approach. CURRENT FUNGAL INFECTION REPORTS 2015. [DOI: 10.1007/s12281-015-0231-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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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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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Mochizuki T, Takeda K, Anzawa K. Molecular markers useful for epidemiology of dermatophytoses. J Dermatol 2015; 42:232-5. [DOI: 10.1111/1346-8138.12813] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Takashi Mochizuki
- Department of Dermatology; Research Institute of Medical Science; Kanazawa Medical University; Uchinada Ishikawa Japan
- Division of Dermatomycology; Research Institute of Medical Science; Kanazawa Medical University; Uchinada Ishikawa Japan
| | - Kiminobu Takeda
- Department of Dermatology; Research Institute of Medical Science; Kanazawa Medical University; Uchinada Ishikawa Japan
| | - Kazushi Anzawa
- Department of Dermatology; Research Institute of Medical Science; Kanazawa Medical University; Uchinada Ishikawa Japan
- Division of Dermatomycology; Research Institute of Medical Science; Kanazawa Medical University; Uchinada Ishikawa Japan
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Ziółkowska G, Nowakiewicz A, Gnat S, Trościańczyk A, Zięba P, Dziedzic BM. Molecular identification and classification of Trichophyton mentagrophytes complex strains isolated from humans and selected animal species. Mycoses 2015; 58:119-26. [PMID: 25643744 DOI: 10.1111/myc.12284] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/24/2014] [Accepted: 11/20/2014] [Indexed: 11/30/2022]
Abstract
Species differentiation within Trichophyton mentagrophytes complex group currently poses a major diagnostic challenge, with molecular methods increasingly supplementing classical identification based on the morphological and physiological properties of the fungi. Diagnostic and epidemiological research aimed at determining the source and means of transmission of dermatophytoses in both humans and animals requires not only species differentiation of isolates but also differentiation within species. The study was conducted on 24 isolates originating in humans and various animal species with clinical symptoms of dermatophytosis. The analysis included phenotypical identification methods and molecular methods: internal transcribed spacer sequencing and ITS-restriction fragment length polymorphism (RFLP) with multi-enzyme restriction. ITS sequence analysis identified the isolates to species - Trichophyton interdigitale, Arthroderma benhamiae and A. vanbreuseghemii, and ITS-RFLP detected six different genotypes. Genotypes I, II and III characterised strains belonging to A. benhamiae, genotype IV characterised the A. vanbreuseghemii strain, and genotypes V and VI occurred only within the species T. interdigitale. Strains isolated from guinea pigs were dominant within genotype I, while genotype II was found mainly in strains from foxes. Multi-enzyme restriction analysis of this region enables intraspecific differentiation, which may be useful in epidemiological research, particularly in determining the source of infections.
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Affiliation(s)
- Grażyna Ziółkowska
- Sub-Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Institute of Biological Bases of Animal Diseases, University of Life Sciences, Lublin, Poland
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Gupta A, Nakrieko KA. Trichophyton rubrumDNA strain switching increases in patients with onychomycosis failing antifungal treatments. Br J Dermatol 2014; 172:74-80. [DOI: 10.1111/bjd.13165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2014] [Indexed: 11/26/2022]
Affiliation(s)
- A.K. Gupta
- Division of Dermatology; Department of Medicine; University of Toronto; Toronto ON Canada
- Mycology Section; Mediprobe Research Inc.; 645 Windermere Road London ON N5X 2P1 Canada
| | - K.-A. Nakrieko
- Mycology Section; Mediprobe Research Inc.; 645 Windermere Road London ON N5X 2P1 Canada
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Ahmadi B, Mirhendi H, Shidfar MR, Nouripour-Sisakht S, Jalalizand N, Geramishoar M, Shokoohi GR. A comparative study on morphological versus molecular identification of dermatophyte isolates. J Mycol Med 2014; 25:29-35. [PMID: 25533610 DOI: 10.1016/j.mycmed.2014.10.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/04/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Dermatophytes are taxonomically classified in the genera Trichophyton, Microsporum, and Epidermophyton. Pleomorphism, cultural variability, slow growth and sporulation, and the need for additional physiological tests make dermatophytes notoriously difficult to identify. The present study aimed to compare the results of morphological and molecular identification of certain groups of clinical isolates of dermatophytes with a view to evaluating the accuracy of molecular methods. PATIENTS AND METHODS For each sample, the ITS1-5.8S-ITS2 rDNA region was amplified using the primers ITS1 and ITS4. PCR products were subjected to restriction fragment length polymorphism (RFLP) analysis using the enzyme MvaI and isolate identification was performed by comparing the electrophoretic RFLP patterns with reference profiles obtained previously. Finally, paired comparative analyses of molecular and conventional methods were performed. RESULTS While morphology results from routine daily reports of the laboratories indicated that 18 (6.8%) and 136 (52.10%) of the isolates were T. rubrum and T. interdigitale, respectively, PCR-RFLP results suggested that T. rubrum was the most common etiological agent of ringworm accounting for 94 (36.01%), followed by T. interdigitale accounting for 71 (27.20%). Interestingly, 80.8% out of the 94 isolates identified as T. rubrum by molecular testing had been identified by morphological examination as belonging to different species, such as T. interdigitale (75.5%), E. floccosum (2.1%) and M. canis, T. verrucosum, and T. tonsurans (each 1.06%). Ten strains out of 261 (T. interdigitale, n=8; E. floccosum, n=2) had been defined as unknown species by morphological tests. CONCLUSION An unexpected high percent of isolates identified as T. interdigitale by conventional methods were in effect T. rubrum shown by PCR-RFLP, and regarding the necessity of correct identification of dermatophytes recovered from different clinical forms of the infection, we highly recommend ITS-sequencing or ITS-RFLP of the isolates, particularly for epidemiological research studies.
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Affiliation(s)
- B Ahmadi
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - H Mirhendi
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran.
| | - M R Shidfar
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - S Nouripour-Sisakht
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - N Jalalizand
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - M Geramishoar
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - G R Shokoohi
- Department of Medical Parasitology and Mycology, School of Public Health, National Institute of Health Research, Tehran University of Medical Sciences, Tehran, Iran
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Mochizuki T, Kawasaki M, Tanabe H, Ishizaki H. A Nail Drilling Method Suitable for the Diagnosis of Onychomycosis. J Dermatol 2014; 32:108-13. [PMID: 15906540 DOI: 10.1111/j.1346-8138.2005.tb00726.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We describe a nail drilling method suitable for the diagnosis of onychomycosis. Thirty-three patients with onychomycosis in which the big toenail had a white band or spike were enrolled in this study. We drilled a hole about 3-mm-wide in the most proximal part of the white band or spike using a ball-shaped metal file and then, through the hole, sampled the underlying nail material softened by fungi after removing the superficial hard nail plate. Fungi in 32 (97.0%) of the nail samples were detected by direct KOH examination. When incubated on Sabouraud's dextrose agar slant with chloramphenicol and cycloheximide, fungal cultures were obtained from 27 (81.8%) of the 33 nail samples. Fourteen of the fungal isolates were identified as T. rubrum, 11 as T. mentagrophytes, and 2 as Acremonium sp. The nail drilling method is suitable for diagnosing onychomycosis with a white band or spike, because it gives a high isolation rate and leaves the patients' nail relatively more intact compared with other methods.
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Affiliation(s)
- Takashi Mochizuki
- Department of Dermatology, Kanazawa Medical University, Daigaku 1-1, Uchinada, Ishikawa 920-0293, Japan
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Gupta AK, Nakrieko KA. Molecular determination of mixed infections of dermatophytes and nondermatophyte molds in individuals with onychomycosis. J Am Podiatr Med Assoc 2014; 104:330-6. [PMID: 25076075 DOI: 10.7547/0003-0538-104.4.330] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Reports of mixed infections with nondermatophyte molds (NDMs) and dermatophytes in onychomycosis are rare, possibly owing to the inhibition of NDM growth during traditional culture. We sought to determine the prevalence of mixed infections in onychomycosis using molecular identification. METHODS Molecular analyses were used to identify infecting organisms directly from at least two serial great toenail samples from each of the 44 patients. RESULTS Mixed infections were present in 41% of the patients (18 of 44). A single coinfecting NDM was the most common mixed infection and was detected in 34% of patients with onychomycosis (15 of 44), with Fusarium oxysporum present in 14% (6 of 44), Scopulariopsis brevicaulis in 9% (4 of 44), Acremonium spp in 2% (1 of 44), Aspergillus spp in 4.5% (2 of 44), and Scytalidium spp in 4.5% (2 of 44). Mixed infections with two NDMs were found in 7% of patients (3 of 44). CONCLUSIONS Mixed onychomycosis infections may be more prevalent than previously reported.
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Affiliation(s)
- Aditya K. Gupta
- Division of Dermatology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Mycology and Molecular Biology Sections, Mediprobe Research Inc, London, ON, Canada
| | - Kerry-Ann Nakrieko
- Mycology and Molecular Biology Sections, Mediprobe Research Inc, London, ON, Canada
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Liu G, He C, Zhang H. Identification and characterization of dermatophyte species and strains with PCR amplification. Exp Ther Med 2014; 8:545-550. [PMID: 25009617 PMCID: PMC4079408 DOI: 10.3892/etm.2014.1785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 05/13/2014] [Indexed: 11/17/2022] Open
Abstract
The aim of the present study was to use two polymerase chain reaction (PCR) methods, with (GACA)4 and non-transcribed spacer (NTS) as primers, to identify and characterize dermatophyte isolates from dogs and cats to a species and strain level. A total of 45 isolates from nine dermatophyte species were collected from pet dogs and cats and subjected to PCR amplification with the microsatellite primer (GACA)4. Dermatophyte strains of three of the same species collected from four cities were subjected to PCR amplification with the NTS primer set. These two PCR methods were applied to identify and characterize the dermatophyte isolates to a species and strain level. Regional differences among the strain specificities were also examined. The results from PCR with (GACA)4 demonstrated that strains from the same species produced similar PCR product band patterns. In addition, these patterns differed among species, indicating that (GACA)4 primer-based PCR was able to distinguish between the various dermatophyte species. By contrast, dermatophyte isolates and/or strains within the same species revealed various band patterns with NTS-based PCR. In addition, the results indicated that regional differences contributed to the variations in PCR product band patterns. Therefore, the results of the present study indicate that the NTS-based PCR method is efficient in distinguishing dermatophytes to the strain level, while a combination of (GACA)4 and NTS primer-based PCR methods is able to clarify dermatophyte isolates to a species and strain level. The present study provides information concerning the identification of pathogenic fungi and the epidemiological characteristics of fungal skin diseases.
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Affiliation(s)
- Guofang Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China ; Department of Animal Husbandry and Veterinary Medicine, Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang, Jiangsu 212400, P.R. China
| | - Chenghua He
- Department of Animal Husbandry and Veterinary Medicine, Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang, Jiangsu 212400, P.R. China
| | - Haibin Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
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Jung HJ, Kim SY, Jung JW, Park HJ, Lee YW, Choe YB, Ahn KJ. Identification of dermatophytes by polymerase chain reaction-restriction fragment length polymorphism analysis of metalloproteinase-1. Ann Dermatol 2014; 26:338-42. [PMID: 24966633 PMCID: PMC4069644 DOI: 10.5021/ad.2014.26.3.338] [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: 11/15/2012] [Revised: 06/13/2013] [Accepted: 07/09/2013] [Indexed: 11/16/2022] Open
Abstract
Background Transgenic research on metalloproteinase-1 is an emerging field in the area of plant molecular biology. The new method reported here can similarly be applied in fungal molecular biology to identify different dermatophytes. Our method is more accurate than traditional methods such as molecular analyses. Objective To identify Trichophyton rubrum, T. mentagrophytes var. mentagrophytes, T. tonsurans, T. mentagrophytes var. interdigitale, Microsporum canis and M. gypseum, by using the restriction fragment length polymorphism (RFLP) analysis and polymerase chain reaction (PCR) to detect polymorphisms in the metalloproteinase-1 gene (MEP1). Methods From each fungal strain, we isolated genomic DNA and performed PCR to amplify the region coding for metalloproteinase-1. Primers for the metalloproteinase-1 gene were designed based on the sequence in NCBI GenBank. Subsequently, we purified the amplified PCR product and performed RFLP analysis. After restriction enzyme digestion, BsrDI (NEB, England), the samples were subjected to electrophoresis. Four different patterns of DNA fragments were observed among 6 fungal species. Results The DNA fragments for T. mentagrophytes var. mentagrophytes, T. mentagrophytes var. interdigitale and T. tonsurans showed similar patterns on electrophoresis and were not distinguishable, whereas T. rubrum, M. canis, and M. gypseum showed different patterns. Conclusion To our knowledge, it is the first study to introduce the analysis of the nucleotide sequence of metalloproteinase-1 enzyme to study differentiation in dermatophytes. Based on our results, more accurate differentiation and subtyping of T. rubrum and T. mentagrophytes var. interdigitale might be possible. This might contribute to better understanding of the epidemiology and pathogenesis of dermatophyte.
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Affiliation(s)
- Ho Jung Jung
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Soo Young Kim
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Jae Wook Jung
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Hyun Jung Park
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Yang Won Lee
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea. ; Research Institute of Medical Science, Konkuk University, Seoul, Korea
| | - Yong Beom Choe
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea. ; Research Institute of Medical Science, Konkuk University, Seoul, Korea
| | - Kyu Joong Ahn
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea. ; Research Institute of Medical Science, Konkuk University, Seoul, Korea
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