1
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Kwon HW, Kim SH. Pathological Properties of Cryptococcus pseudolongus on the Mycelia and Fruit Body of Lentinula edodes. MYCOBIOLOGY 2021; 49:173-182. [PMID: 37970187 PMCID: PMC10635231 DOI: 10.1080/12298093.2021.1873486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 11/17/2023]
Abstract
Recently, Cryptococcus pseudolongus has been reported as a new pathogen of shiitake (Lentinula edodes). However, its pathological properties are not much known. To further understand its impact on the mushroom, we investigated the pathogen's interactions with the mycelium of shiitake, histopathological properties, host range, and sensitivity to diverse antifungal agents. The strain C. pseudolongus DUCC 4014 inhibited the mycelial growth of L. edodes strain (cultivar Sanjo 701ho) and caused browning in the mycelia confronted with the yeast on PDA. Spray inoculation of the yeast caused an abnormal browning symptom on the cap and/or gills of three shiitake cultivars grown on sawdust media in vinyl bags. Scanning electron microscopic images of the abnormally browned parts of shiitake fruit body illustrated that mushroom tissues were loosed and dispersed in the middle and edge of the cap and the arrangement of basidiospores borne on basidia in the gills was disturbed compared to those of normal shiitake fruit body. Spray inoculation also led to developing abnormal browning on the harvested fruit body, indicating C. pseudolongus could be a problem during mushroom storage. But the yeast was not able to induce abnormal browning on mushrooms of Pleurotus ferulae, Pleurotus fostreatus, and Agaricus bisporus. But it induced browning only on button mushroom (A. bisporus) when they were inoculated after wounding. Tests with 16 kinds of fungicides revealed that the cell growth of C. pseudolongus could be inhibited by benzalkonium chloride at MIC 7 μg/ml and benomyl at MIC 3 μg/ml.
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Affiliation(s)
- Hyuk Woo Kwon
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju, Korea
| | - Seong Hwan Kim
- Department of Microbiology and Institute of Biodiversity, Dankook University, Cheonan, Korea
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2
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Michael PJ, Jones D, White N, Hane JK, Bunce M, Gibberd M. Crop-Zone Weed Mycobiomes of the South-Western Australian Grain Belt. Front Microbiol 2020; 11:581592. [PMID: 33324368 PMCID: PMC7721668 DOI: 10.3389/fmicb.2020.581592] [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: 07/09/2020] [Accepted: 10/28/2020] [Indexed: 01/16/2023] Open
Abstract
In the absence of a primary crop host, secondary plant hosts may act as a reservoir for fungal plant pathogens of agricultural crops. Secondary hosts may potentially harbor heteroecious biotrophs (e.g., the stripe rust fungus Puccinia striiformis) or other pathogens with broad host ranges. Agricultural grain production tends toward monoculture or a limited number of crop hosts over large regions, and local weeds are a major source of potential secondary hosts. In this study, the fungal phyllospheres of 12 weed species common in the agricultural regions of Western Australia (WA) were compared through high-throughput DNA sequencing. Amplicons of D2 and ITS were sequenced on an Illumina MiSeq system using previously published primers and BLAST outputs analyzed using MEGAN. A heatmap of cumulative presence-absence for fungal taxa was generated, and variance patterns were investigated using principal components analysis (PCA) and canonical correspondence analysis (CCA). We observed the presence of several major international crop pathogens, including basidiomycete rusts of the Puccinia spp., and ascomycete phytopathogens of the Leptosphaeria and Pyrenophora genera. Unrelated to crop production, several endemic pathogen species including those infecting Eucalyptus trees were also observed, which was consistent with local native flora. We also observed that differences in latitude or climate zones appeared to influence the geographic distributions of plant pathogenic species more than the presence of compatible host species, with the exception of Brassicaceae host family. There was an increased proportion of necrotrophic Ascomycete species in warmer and drier regions of central WA, compared to an increased proportion of biotrophic Basidiomycete species in cooler and wetter regions in southern WA.
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Affiliation(s)
- Pippa J. Michael
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Darcy Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Nicole White
- TRENDLab, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Michael Bunce
- TRENDLab, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Mark Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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3
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Wang HH, Yin C, Gao J, Tao R, Wang CY, Li YX, Guo LP, Wang Z, Sung CK. Development of a Real-Time TaqMan PCR Method for Absolute Quantification of the Biocontrol Agent Esteya vermicola. PLANT DISEASE 2020; 104:1694-1700. [PMID: 32310719 DOI: 10.1094/pdis-10-19-2076-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Esteya vermicola has been used as an effective biocontrol agent for the management of the pinewood nematode, Bursaphelenchus xylophilus. Tools for monitoring the colonization and parasitism patterns of E. vermicola are required for the development of highly effective biocontrol strategies. Because the TaqMan PCR technique is effective for quantification of species in environmental samples, a real-time PCR-based methodology was developed for absolute quantification of E. vermicola via internal standard addition and extrapolation of DNA quantity to hyphal length. Primers and a probe for the 28S ribosomal RNA gene of E. vermicola were designed, and nested TaqMan real-time PCR-based quantification was performed. In addition, internal standard-based yield measurement was correlated to the absolute quantity of target genomic DNA. Moreover, an extrapolation curve obtained by optical microscopy and image analysis of the mycelia was constructed for the measurement of fungal hyphal length. The absolute quantification method developed in the present study provides a sensitive and accurate technique to quantify fungal density in either wood or other substrate samples and can be used as an effective tool for future studies of biocontrol agents.
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Affiliation(s)
- Hai-Hua Wang
- Department of Food Science and Technology, College of Agriculture and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Can Yin
- Department of Food Science and Technology, College of Agriculture and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Jie Gao
- Department of Food Science and Technology, College of Agriculture and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Ran Tao
- Department of Food Science and Technology, College of Agriculture and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Chun-Yan Wang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yong-Xia Li
- Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China
| | - Lan-Ping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhen Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- College of Pharmacy, Linyi University, Linyi City 276000, Shandong, China
| | - Chang-Keun Sung
- Department of Food Science and Technology, College of Agriculture and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
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4
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Alizadeh M, Kolecka A, Boekhout T, Zarrinfar H, Ghanbari Nahzag MA, Badiee P, Rezaei-Matehkolaei A, Fata A, Dolatabadi S, Najafzadeh MJ. Identification of Candida species isolated from vulvovaginitis using matrix assisted laser desorption ionization-time of flight mass spectrometry. Curr Med Mycol 2017; 3:21-25. [PMID: 29707675 PMCID: PMC5917097 DOI: 10.29252/cmm.3.4.21] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background and Purpose: Vulvovaginal candidiasis (VVC) is a common problem in women. The purpose of this study was to identify Candida isolates by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from women with vulvovaginitis that were referred to Ghaem Hospital, Mashhad, Iran. Materials and Methods: This study was conducted on 65 clinical samples isolated from women that were referred to Ghaem Hospital. All specimens were identified using phenotyping techniques, such as microscopy and culture on Sabouraud dextrose agar and corn meal agar. In addition, all isolates were processed for MALDI-TOF MS identification. Results: Out of the 65 analyzed isolates, 61 (94%) samples were recognized by MALDI-TOF MS. However, the remaining four isolates (6%) had no reliable identification. According to the results, C. albicans (58.5%) was the most frequently isolated species, followed by C. tropicalis (16.9%), C. glabrata (7.7%), C. parapsilosis (7.7%), and guilliermondii (3.1%). Conclusion: As the findings indicated, MALDI TOF MS was successful in the identification of clinical Candida species. C. albicans was identified as the most common Candida species isolated from the women with VVC. Moreover, C. tropicalis was the most common species among the non-albicans Candida species.
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Affiliation(s)
- Majid Alizadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Anna Kolecka
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Hossein Zarrinfar
- Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohamad A Ghanbari Nahzag
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parisa Badiee
- Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Rezaei-Matehkolaei
- Department of Medical Mycology, School of Medicine, Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abdolmajid Fata
- Department of Parasitology and Mycology, Research Center for Cutaneous Leishmaniasis, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Somayeh Dolatabadi
- Faculty of Engineering, Sabzevar University of New Technologies, Sabzevar, Iran
| | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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5
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Das P, Pandey P, Harishankar A, Chandy M, Bhattacharya S. A high yield DNA extraction method for medically important Candida species: A comparison of manual versus QIAcube-based automated system. Indian J Med Microbiol 2016; 34:533-535. [PMID: 27934838 DOI: 10.4103/0255-0857.195360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The prognosis of infected individuals with candidemia depends on rapid and precise diagnosis which enables optimising treatment. Three fungal DNA extraction protocols have been compared in this study for medically important Candida species. The quality and quantity of the DNA extracted by physical, chemical and automated protocols was compared using NanoDrop ND-2000 spectrophotometer. It was found that the yield and purity (260/230) ratio of extracted DNA was significantly high in the physical treatment-based protocol as compared to chemical based or automated protocol. Extracted DNA-based real time-polymerase chain reaction showed an analytical sensitivity of 103 cfu/mL. The result of this study suggests physical treatment is the most successful extraction technique compared to other two protocols.
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Affiliation(s)
- P Das
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - P Pandey
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - A Harishankar
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - M Chandy
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - S Bhattacharya
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
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6
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Deodato D, Maccari G, De Luca F, Sanfilippo S, Casian A, Martini R, D’Arezzo S, Bonchi C, Bugli F, Posteraro B, Vandeputte P, Sanglard D, Docquier JD, Sanguinetti M, Visca P, Botta M. Biological Characterization and in Vivo Assessment of the Activity of a New Synthetic Macrocyclic Antifungal Compound. J Med Chem 2016; 59:3854-66. [DOI: 10.1021/acs.jmedchem.6b00018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Davide Deodato
- Department
of Biotechnology Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
| | - Giorgio Maccari
- Department
of Biotechnology Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
| | - Filomena De Luca
- Department
of Medical Biotechnology, University of Siena, I-53100 Siena, Italy
| | - Stefania Sanfilippo
- Department
of Biotechnology Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Alexandru Casian
- Department
of Biotechnology Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Riccardo Martini
- Department
of Biotechnology Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Silvia D’Arezzo
- Istituto Nazionale per le Malattie Infettive “Lazzaro Spallanzani”, I-00149 Roma, Italy
| | - Carlo Bonchi
- Dipartimento
di Scienze, Università Roma Tre, I-00154 Roma, Italy
| | - Francesca Bugli
- Institute
of Microbiology, Università Cattolica del Sacro Cuore, I-00168 Roma, Italy
| | - Brunella Posteraro
- Institute
of Public Health, Università Cattolica del Sacro Cuore, I-00168 Roma, Italy
| | - Patrick Vandeputte
- Institute
of Microbiology, University of Lausanne and University Hospital Center, CH-1011 Lausanne, Switzerland
| | - Dominique Sanglard
- Institute
of Microbiology, University of Lausanne and University Hospital Center, CH-1011 Lausanne, Switzerland
| | - Jean-Denis Docquier
- Department
of Medical Biotechnology, University of Siena, I-53100 Siena, Italy
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
| | - Maurizio Sanguinetti
- Institute
of Microbiology, Università Cattolica del Sacro Cuore, I-00168 Roma, Italy
- Institute
of Public Health, Università Cattolica del Sacro Cuore, I-00168 Roma, Italy
| | - Paolo Visca
- Dipartimento
di Scienze, Università Roma Tre, I-00154 Roma, Italy
| | - Maurizio Botta
- Department
of Biotechnology Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Temple University, BioLife
Science Building, Suite 333, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States,
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
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7
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Abstract
Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.
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8
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Musso M, Giannella M, Antonini M, Bordi E, Ettorre GM, Tessitore L, Mariano A, Capone A. Invasive Candidiasis due to Candida Norvegensis in a Liver Transplant Patient: Case Report and Literature Review. Infect Dis Rep 2014; 6:5374. [PMID: 25002960 PMCID: PMC4083299 DOI: 10.4081/idr.2014.5374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 11/23/2022] Open
Abstract
Candida norvegensis is an emerging fluconazole-resistant pathogen isolated in most cases from skin and mucous membranes of immunocompromized patients. Documented invasive candidiasis (IC) due to C. norvegensis has been rarely reported, thus the clinical features of patients at risk for this pathogen are poorly defined. We report a liver transplant patient who developed IC due to C. norvegensis and review other cases of C. norvegensis IC published in the literature.
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Affiliation(s)
- Maria Musso
- Second Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
| | | | - Mario Antonini
- Intensive Care Unit and Anesthesia, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
| | - Eugenio Bordi
- Microbiology Unit, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
| | | | - Loretta Tessitore
- Neurosurgical Intensive Care Unit, S. Camillo-Forlanini Hospital , Rome
| | - Andrea Mariano
- First Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome, Italy
| | - Alessandro Capone
- Second Division of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani , Rome
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9
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Abstract
Parasites are now known to be ubiquitous across biological systems and can play an important role in modulating algal populations. However, there is a lack of extensive information on their role in artificial ecosystems such as algal production ponds and photobioreactors. Parasites have been implicated in the demise of algal blooms. Because individual mass culture systems often tend to be unialgal and a select few algal species are in wide scale application, there is an increased potential for parasites to have a devastating effect on commercial scale monoculture. As commercial algal production continues to expand with a widening variety of applications, including biofuel, food and pharmaceuticals, the parasites associated with algae will become of greater interest and potential economic impact. A number of important algal parasites have been identified in algal mass culture systems in the last few years and this number is sure to grow as the number of commercial algae ventures increases. Here, we review the research that has identified and characterized parasites infecting mass cultivated algae, the techniques being proposed and or developed to control them, and the potential impact of parasites on the future of the algal biomass industry.
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Affiliation(s)
| | - Todd W Lane
- Systems Biology Department, Sandia National Laboratories Livermore, CA, USA
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10
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Potential of MALDI-TOF mass spectrometry as a rapid detection technique in plant pathology: identification of plant-associated microorganisms. Anal Bioanal Chem 2012; 404:1247-55. [DOI: 10.1007/s00216-012-6091-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 11/26/2022]
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11
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Marruchella G, Todisco G, D'Arezzo S, Di Guardo G, Paglia MG. Granulomatous myocarditis caused by Candida albicans in a canary (Serinus canaria). J Avian Med Surg 2012; 25:205-9. [PMID: 22216721 DOI: 10.1647/2010-025.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Candida albicans is among the major agents of mucous membrane mycosis in humans and animals, with systemic and deep infections observed in immunocompromised hosts. We describe a case of fatal granulomatous myocarditis caused by C albicans in a 20-day-old canary (Serinus canaria). The etiologic diagnosis was confirmed by identifying characteristic morphologic features of the organism, combined with histochemical staining, and followed by the use of ad hoc biomolecular analysis.
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Affiliation(s)
- Giuseppe Marruchella
- Department of Comparative Biomedical Sciences, Faculty of Veterinary Medicine, University of Teramo, Piazza Aldo, Moro 45, 64100 Teramo, Italy
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12
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Holmes AR, Chong K, Rodrigues E, Cannon RD, Carpenter E, Ruske DR, Dawes PJD. Yeast Colonization of Voice Prostheses: Pilot Study Investigating Effect of a Bovine Milk Product Containing Anti—Candida Albicans Immunoglobulin A Antibodies on Yeast Colonization and Valve Leakage. Ann Otol Rhinol Laryngol 2012; 121:61-6. [DOI: 10.1177/000348941212100111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objectives: Our goals were to determine whether a bovine milk product containing anti– Candida albicans immunoglobulin A antibodies (“immune milk”) could reduce the adherence of C albicans to voice prosthesis silicone in vitro, and whether administration of the milk could reduce C albicans colonization and voice prosthesis damage in vivo. Methods: An in vitro assay of C albicans attachment to silicone was developed with radiolabeled C albicans. A pilot crossover in vivo trial, over 3 periods of 3 months, was also undertaken for 4 patients with voice prostheses, comparing daily administrations of immune milk and a control milk product. The prosthesis valves were replaced at each change-over and were assessed for wet weight of removable biofilm, yeast numbers in removable biofilm, valve leakage, and valve damage. Results: Immune milk inhibited C albicans adherence to silicone in vitro. However, in a small clinical pilot study, this effect was not replicated. Conclusions: There is scope to further investigate the topical use of immune milk for management of voice prosthesis biofilms.
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13
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Slechta ES, Hohmann SL, Simmon K, Hanson KE. Internal transcribed spacer region sequence analysis using SmartGene IDNS software for the identification of unusual clinical yeast isolates. Med Mycol 2011; 50:458-66. [PMID: 22103344 DOI: 10.3109/13693786.2011.630683] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rapid and accurate identification of clinically important yeasts is essential given their inherent differences in antifungal susceptibility. We implemented nucleic acid sequencing for those species that could not be identified by phenotypic methods. Internal Transcribed Spacer region 1 and 2 (ITS1 and ITS2) sequences were investigated using SmartGene IDNS software, an rDNA sequence database and analysis program for microbial identification (ID). Over a 2.5-year period, 2,938 specimens were evaluated. Most (94%) isolates were fully identified by conventional methods, with Candida species accounting for the majority of them. Of the 169 organisms that required molecular analysis, 79% were identified to species level, 19% to genus and 2% remained unresolved. Sequenced isolates encompassed 33 unique species of which approximately half (52%) were common pathogens with atypical biochemical profiles and the remainder were rarer yeast species. A significant proportion (33%) of sequenced organisms displayed elevated MICs to fluconazole. Our experience supports the use of molecular techniques as an adjunct to conventional methods for the identification of medically important yeasts. Susceptibility testing alone may provide valuable treatment information in situations where phenotypic assessments are inconclusive and molecular or proteomic testing is not readily available.
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Affiliation(s)
- E Susan Slechta
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
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14
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Spencer J, Rawling S, Stratford M, Steels H, Novodvorska M, Archer DB, Chandra S. Yeast identification: reassessment of assimilation tests as sole universal identifiers. Lett Appl Microbiol 2011; 53:503-8. [PMID: 21801184 DOI: 10.1111/j.1472-765x.2011.03130.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To assess whether assimilation tests in isolation remain a valid method of identification of yeasts, when applied to a wide range of environmental and spoilage isolates. METHODS AND RESULTS Seventy-one yeast strains were isolated from a soft drinks factory. These were identified using assimilation tests and by D1/D2 rDNA sequencing. When compared to sequencing, assimilation test identifications (MicroLog™) were 18·3% correct, a further 14·1% correct within the genus and 67·6% were incorrectly identified. The majority of the latter could be attributed to the rise in newly reported yeast species. CONCLUSIONS Assimilation tests alone are unreliable as a universal means of yeast identification, because of numerous new species, variability of strains and increasing coincidence of assimilation profiles. Assimilation tests still have a useful role in the identification of common species, such as the majority of clinical isolates. SIGNIFICANCE AND IMPACT OF THE STUDY It is probable, based on these results, that many yeast identifications reported in older literature are incorrect. This emphasizes the crucial need for accurate identification in present and future publications.
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Affiliation(s)
- J Spencer
- GSK GlaxoSmithKline, Nutritional Healthcare R&D, Royal Forest Factory, Coleford, Gloucestershire, UK
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15
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Herendael BH, Bruynseels P, Bensaid M, Boekhout T, Baere T, Surmont I, Mertens AH. Validation of a modified algorithm for the identification of yeast isolates using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Eur J Clin Microbiol Infect Dis 2011; 31:841-8. [DOI: 10.1007/s10096-011-1383-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/03/2011] [Indexed: 11/28/2022]
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16
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Pannanusorn S, Elings MA, Römling U, Fernandez V. Pyrosequencing of a hypervariable region in the internal transcribed spacer 2 to identify clinical yeast isolates. Mycoses 2011; 55:172-80. [PMID: 21736632 DOI: 10.1111/j.1439-0507.2011.02064.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The incidence of invasive fungal infection has increased significantly. A majority of the infections is caused by yeast. Clinically important yeast show species-specific differences in susceptibility to antifungal agents therefore rapid and accurate identification of the pathogen is essential. We aimed to validate pyrosequencing of 40 nucleotides in the internal transcribed spacer 2 (ITS2) for species identification of yeast. Amplification of ITS2 and pyrosequencing of targeted region were performed in 940 clinical isolates of yeast. A local database containing the 40 nucleotide ITS2 sequences of 33 species of medically important yeast was generated using published sequences of type strains. The sequencing results were searched against the local database using the BLAST algorithm to identify the species of yeast. The length of sequences obtained from pyrosequencing averaged between 40-61 nucleotides. Pyrosequencing identified 940 clinical isolates of yeast down to 14 species level, whereby 931 isolates belonged to genus Candida (11 species), four of Saccharomyces cerevisiae, three of Malassezia pachydermatis and two of Rhodotorula mucilaginosa. In addition, intraspecies specific sequence variations in Candida albicans and Candida glabrata were detected. Pyrosequencing of 40 nucleotides in ITS2 is reliable for species identification of yeast. This methodology can contribute to the high quality management of patients with fungal infections.
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Affiliation(s)
- Srisuda Pannanusorn
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
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Pan W, Liao W, Hagen F, Theelen B, Shi W, Meis JF, Boekhout T. Meningitis caused by Filobasidium uniguttulatum: case report and overview of the literature. Mycoses 2011; 55:105-9. [PMID: 21729175 DOI: 10.1111/j.1439-0507.2011.02054.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cryptococcal meningitis is mainly caused by Cryptococcus neoformans and Cryptococcus gattii, but occasionally other Cryptococcus species and phylogenetically related species are involved. Herein, we present a case of cryptococcal meningitis from China, which was caused by an azole and flucytosine resistant Filobasidium uniguttulatum. In addition, we present an overview of the literature of meningitis caused by Cryptococcus species other than C. neoformans and C. gattii. Eight cases were related to infections of the central nervous system. Leukaemia and cancer were important risk factors in HIV-negative patients. Molecular identification and susceptibility testing are important for proper management of patients because the species involved may differ in susceptibility to antifungal drugs.
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Affiliation(s)
- Weihua Pan
- National Laboratory of Cryptococcus neoformans, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China.
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Sequence‐Based Fungal Identification and Classification. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cornet M, Sendid B, Fradin C, Gaillardin C, Poulain D, Nguyen HV. Molecular identification of closely related Candida species using two ribosomal intergenic spacer fingerprinting methods. J Mol Diagn 2010; 13:12-22. [PMID: 21227390 DOI: 10.1016/j.jmoldx.2010.11.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2010] [Indexed: 12/24/2022] Open
Abstract
Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic.
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Affiliation(s)
- Muriel Cornet
- Laboratoire de Microbiologie, Hôtel-Dieu, AP-HP, Université Paris Descartes, Paris, France
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Putignani L, Del Chierico F, Onori M, Mancinelli L, Argentieri M, Bernaschi P, Coltella L, Lucignano B, Pansani L, Ranno S, Russo C, Urbani A, Federici G, Menichella D. MALDI-TOF mass spectrometry proteomic phenotyping of clinically relevant fungi. MOLECULAR BIOSYSTEMS 2010; 7:620-9. [PMID: 20967323 DOI: 10.1039/c0mb00138d] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteomics is particularly suitable for characterising human pathogens with high life cycle complexity, such as fungi. Protein content and expression levels may be affected by growth states and life cycle morphs and correlate to species and strain variation. Identification and typing of fungi by conventional methods are often difficult, time-consuming and frequently, for unusual species, inconclusive. Proteomic phenotypes from MALDI-TOF MS were employed as analytical and typing expression profiling of yeast, yeast-like species and strain variants in order to achieve a microbial proteomics population study. Spectra from 303 clinical isolates were generated and processed by standard pattern matching with a MALDI-TOF Biotyper (MT). Identifications (IDs) were compared to a reference biochemical-based system (Vitek-2) and, when discordant, MT IDs were verified with genotyping IDs, obtained by sequencing the 25-28S rRNA hypervariable D2 region. Spectra were converted into virtual gel-like formats, and hierarchical clustering analysis was performed for 274 Candida profiles to investigate species and strain typing correlation. MT provided 257/303 IDs consistent with Vitek-2 ones. However, amongst 26/303 discordant MT IDs, only 5 appeared "true". No MT identification was achieved for 20/303 isolates for incompleteness of database species variants. Candida spectra clustering agreed with identified species and topology of Candida albicans and Candida parapsilosis specific dendrograms. MT IDs show a high analytical performance and profiling heterogeneity which seems to complement or even outclass existing typing tools. This variability reflects the high biological complexity of yeasts and may be properly exploited to provide epidemiological tracing and infection dispersion patterns.
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Affiliation(s)
- Lorenza Putignani
- Microbiology Unit, Children's Hospital and Research Institute Bambino Gesù, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
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Diagnosis of invasive fungal infections by a real-time panfungal PCR assay in immunocompromised pediatric patients. Leukemia 2010; 24:2032-8. [DOI: 10.1038/leu.2010.209] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species. J Clin Microbiol 2010; 48:3482-6. [PMID: 20668126 DOI: 10.1128/jcm.00687-09] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid identification of yeast species. Using Bruker Daltonics MALDI BioTyper software, we created a spectral database library with m/z ratios of 2,000 to 20,000 Da for 109 type and reference strains of yeast (44 species in 8 genera). The database was tested for accuracy by use of 194 clinical isolates (23 species in 6 genera). A total of 192 (99.0%) of the clinical isolates were identified accurately by MALDI-TOF MS. The MALDI-TOF MS-based method was found to be reproducible and accurate, with low consumable costs and minimal preparation time.
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Molecular identification of veterinary yeast isolates by use of sequence-based analysis of the D1/D2 region of the large ribosomal subunit. J Clin Microbiol 2010; 48:2140-6. [PMID: 20392917 DOI: 10.1128/jcm.02306-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conventional methods of yeast identification are often time-consuming and difficult; however, recent studies of sequence-based identification methods have shown promise. Additionally, little is known about the diversity of yeasts identified from various animal species in veterinary diagnostic laboratories. Therefore, in this study, we examined three methods of identification by using 109 yeast samples isolated during a 1-year period from veterinary clinical samples. Comparison of the three methods-traditional substrate assimilation, fatty acid profile analysis, and sequence-based analysis of the region spanning the D1 and D2 regions (D1/D2) of the large ribosomal subunit-showed that sequence analysis provided the highest percent identification among the three. Sequence analysis identified 87% of isolates to the species level, whereas substrate assimilation and fatty acid profile analysis identified only 54% and 47%, respectively. Less-stringent criteria for identification increased the percentage of isolates identified to 98% for sequence analysis, 62% for substrate assimilation, and 55% for fatty acid profile analysis. We also found that sequence analysis of the internal transcribed spacer 2 (ITS2) region provided further identification for 36% of yeast not identified to the species level by D1/D2 sequence analysis. Additionally, we identified a large variety of yeast from animal sources, with at least 30 different species among the isolates tested, and with the majority not belonging to the common Candida spp., such as C. albicans, C. glabrata, C. tropicalis, and the C. parapsilosis group. Thus, we determined that sequence analysis of the D1/D2 region was the best method for identification of the variety of yeasts found in a veterinary population.
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Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology. J Clin Microbiol 2009; 47:1063-73. [PMID: 19244466 DOI: 10.1128/jcm.01558-08] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In immunocompromised patients suffering from invasive fungal infection, rapid identification of the fungal species is a prerequisite for selection of the most appropriate antifungal treatment. We present an assay permitting reliable identification of a wide range of clinically relevant fungal pathogens based on the high-throughput Luminex microbead hybridization technology. The internal transcribed spacer (ITS2) region, which is highly variable among genomes of individual fungal species, was used to generate oligonucleotide hybridization probes for specific identification. The spectrum of pathogenic fungi covered by the assay includes the most commonly occurring species of the genera Aspergillus and Candida and a number of important emerging fungi, such as Cryptococcus, Fusarium, Trichosporon, Mucor, Rhizopus, Penicillium, Absidia, and Acremonium. Up to three different probes are employed for the detection of each fungal species. The redundancy in the design of the assay should ensure unambiguous fungus identification even in the presence of mutations in individual target regions. The current set of hybridization oligonucleotides includes 75 species- and genus-specific probes which had been carefully tested for specificity by repeated analysis of multiple reference strains. To provide adequate sensitivity for clinical application, the assay includes amplification of the ITS2 region by a seminested PCR approach prior to hybridization of the amplicons to the probe panel using the Luminex technology. A variety of fungal pathogens were successfully identified in clinical specimens that included peripheral blood, samples from biopsies of pulmonary infiltrations, and bronchotracheal secretions derived from patients with documented invasive fungal infections. Our observations demonstrate that the Luminex-based technology presented permits rapid and reliable identification of fungal species and may therefore be instrumental in routine clinical diagnostics.
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The β-tubulin gene as a molecular phylogenetic marker for classification and discrimination of the Saccharomyces sensu stricto complex. Antonie van Leeuwenhoek 2008; 95:135-42. [DOI: 10.1007/s10482-008-9296-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/02/2008] [Indexed: 11/26/2022]
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Identification of fungal species by fragment length analysis of the internally transcribed spacer 2 region. Eur J Clin Microbiol Infect Dis 2008; 28:613-22. [DOI: 10.1007/s10096-008-0683-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 11/29/2008] [Indexed: 11/26/2022]
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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