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Becker P, van den Eynde C, Baert F, D'hooge E, De Pauw R, Normand AC, Piarroux R, Stubbe D. Remarkable fungal biodiversity on northern Belgium bats and hibernacula. Mycologia 2023:1-15. [PMID: 37289484 DOI: 10.1080/00275514.2023.2213138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bats can be affected by fungal pathogens such as Pseudogymnoascus destructans, the causative agent of the white-nose syndrome. Their body surface can also be colonized by fungal commensals or carry transient fungal species and participate in their dispersal. In this study, 114 bat specimens belonging to seven species were sampled from various locations in northern Belgium. Culture-based methods revealed an important mycological diversity, with a total of 209 different taxa out of the 418 isolates. Overall, a mean of 3.7 taxa per bat was recorded, but significant differences were observed between sampling sites and seasons. The mycobiomes were dominated by cosmopolitan and plant-associated species, in particular from the genera Cladosporium, Penicillium, and Aspergillus. Other species known to be related to bats or their environment, such as Apiotrichum otae, were also retrieved. Sampling of hibernacula indicated that diverse fungal species can inhabit these sites, including a yet undescribed Pseudogymnoascus species, distinct from Ps. destructans, namely, Ps. cavicola.
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Affiliation(s)
- Pierre Becker
- BCCM/IHEM Fungi Collection, Mycology and Aerobiology, Sciensano, Brussels 1050, Belgium
| | - Claudia van den Eynde
- Department of Enzootic, Vector-Borne and Bee Diseases, Sciensano, Brussels 1180, Belgium
| | - Frederik Baert
- BCCM/IHEM Fungi Collection, Mycology and Aerobiology, Sciensano, Brussels 1050, Belgium
| | - Elizabet D'hooge
- BCCM/IHEM Fungi Collection, Mycology and Aerobiology, Sciensano, Brussels 1050, Belgium
| | - Robby De Pauw
- Department of Epidemiology and Public Health, Sciensano, Brussels 1070, Belgium
- Department of Rehabilitation Sciences, Ghent University, Ghent 9000, Belgium
| | - Anne-Cécile Normand
- INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Sorbonne Université, Paris 75013, France
| | - Renaud Piarroux
- INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Sorbonne Université, Paris 75013, France
| | - Dirk Stubbe
- BCCM/IHEM Fungi Collection, Mycology and Aerobiology, Sciensano, Brussels 1050, Belgium
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Illner A, Michl C, Sunderkötter C, Uhrlaß S, Krüger C, Baert F, Stubbe D, Nenoff P. Paraphyton mirabile - a rare geophilic dermatophyte - with unclear relation to nail disease. J Eur Acad Dermatol Venereol 2023. [PMID: 36974429 DOI: 10.1111/jdv.19066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Affiliation(s)
- Antje Illner
- Department of Dermatology and Venereology, University Hospital Halle, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120, Halle (Saale), Germany
| | - Christiane Michl
- Department of Dermatology and Venereology, University Hospital Halle, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120, Halle (Saale), Germany
| | - Cord Sunderkötter
- Department of Dermatology and Venereology, University Hospital Halle, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120, Halle (Saale), Germany
| | - Silke Uhrlaß
- Laboratory for Medical Microbiology, Mölbis, Germany
| | | | - Frederik Baert
- Belgian Coordinated Collections of Microorganisms - Fungi Collection: human and animal health (BCCM/IHEM), Sciensano, Section Mycology and Aerobiology, Rue J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Dirk Stubbe
- Belgian Coordinated Collections of Microorganisms - Fungi Collection: human and animal health (BCCM/IHEM), Sciensano, Section Mycology and Aerobiology, Rue J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Pietro Nenoff
- Laboratory for Medical Microbiology, Mölbis, Germany
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van de Peppel LJJ, Aime MC, Læssøe T, Pedersen OS, Coimbra VRM, Kuyper TW, Stubbe D, Aanen DK, Baroni TJ. Four new genera and six new species of lyophylloid agarics (Agaricales, Basidiomycota) from three different continents. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01836-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractFour new genera encompassing six new species are described in the Lyophyllaceae (Agaricales): the monotypic Australocybe from Australia; the monotypic Phaeotephrocybe from Belize; the monotypic Nigrocarnea from Laos containing the novel conidia-producing species N. radicata and Praearthromyces containing two Asian taxa, the conidia-producing P. corneri known from Malaysia and Singapore and P. griseus from Thailand, which lacks conidial production. In addition, we describe Arthromyces glabriceps, which is the first species in the genus Arthromyces that lacks conidial production on the basidiome. Alternative options for a classification of these lyophylloid taxa are discussed and based on morphological, ecological and biogeographical considerations rejected.
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Stubbe D, Becker P, D'hooge E, Debergh H, Packeu A. P500 Validation panel for MALDI-TOF identification of fungi. Med Mycol 2022. [PMCID: PMC9516342 DOI: 10.1093/mmy/myac072.p500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM Sciensano, the Belgian federal scientific institute for public and animal health, houses the BCCM/IHEM Fungi Collection which contains more than 15 000 strains, belonging to over 1 500 different species. The collection is managed according to ISO 9001 standards. Its purpose is to make fungal strains available for academics, clinicians, industry, and education. Fungal pathogens are not as often encountered as bacteria in the clinical laboratory. Additionally, laboratories may not have the knowledge or logistics for the long-term preservation of axenic fungal isolates. Without an array of fungal strains with confirmed identity, it is complicated to implement new protocols and equipment when these need to be validated for the identification of fungi. To short-cut this problem and support laboratories in identifying clinical fungi in routine activities, BCCM/IHEM has developed two validation panels for the identification of fungi via MALDI-TOF mass spectrometry: there is a validation panel with yeasts and a validation panel with filamentous fungi. The selection of strains is based on species that are routinely encountered in a clinical laboratory, and also contains some rarer, but emerging fungal pathogens, like Trichophyton indotineae and Candida auris. The identity and purity of the strains in these panels have been verified according to ISO 17025 accredited protocols. This allows the laboratory to evaluate in a short term the extraction protocol, the MALDI-TOF machine, and the database of reference mass spectra.
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Affiliation(s)
- Dirk Stubbe
- Service of Mycology and Aerobiology , Sciensano, Brussels , Belgium
| | - Pierre Becker
- Service of Mycology and Aerobiology , Sciensano, Brussels , Belgium
| | - Elizabet D'hooge
- Service of Mycology and Aerobiology , Sciensano, Brussels , Belgium
| | - Hanne Debergh
- Service of Mycology and Aerobiology , Sciensano, Brussels , Belgium
| | - Ann Packeu
- Service of Mycology and Aerobiology , Sciensano, Brussels , Belgium
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Debergh H, Becker P, Van den Eynde C, Baert F, D'hooge E, De Pauw R, Normand AC, Piarroux R, Stubbe D. P504 Screening of Belgian bats and hibernacula for the description of related fungal microbiomes and the detection of Pseudogymnoascus destructans. Med Mycol 2022. [PMCID: PMC9515947 DOI: 10.1093/mmy/myac072.p504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM
Bats can be affected by fungal pathogens such as Pseudogymnoascus destructans, the causative agent of the white-nose syndrome. Their body surface can also be colonized by fungal commensals or carry transient fungal species and participate in their dispersal. The present study aimed to assess the presence of P. destructans in Northern Belgium, to describe the skin mycobiome of active bats during summer and autumn, and to analyze possible differences in fungal diversity among bat species, sampling sites, and seasons. In total, 114 bat specimens belonging to seven species were sampled from various localities. Culture-based methods revealed an important mycological diversity with 209 different taxa. Overall, a mean of 3.7 taxa per bat was recorded but significant differences were observed between sampling sites and seasons with a higher diversity in autumn as compared to summer. The mycobiomes were dominated by cosmopolitan and plant-associated species, in particular from the genera Cladosporium, Penicillium, and Aspergillus. Other species known to be related to bats or their environment, like Apiotrichum otae, were also retrieved. Although P. destructans was not detected, the sampling of the hibernacula indicated that they can be inhabited by diverse fungal species including a yet undescribed Pseudogymnoascus species, distinct from P. destructans, namely P. cavicola, sp. nov.
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Affiliation(s)
- Hanne Debergh
- BCCM/IHEM fungi collection , Mycology & Aerobiology, Sciensano, Brussels , Belgium
| | - Pierre Becker
- BCCM/IHEM fungi collection , Mycology & Aerobiology, Sciensano, Brussels , Belgium
| | | | - Frederik Baert
- BCCM/IHEM fungi collection , Mycology & Aerobiology, Sciensano, Brussels , Belgium
| | - Elizabet D'hooge
- BCCM/IHEM fungi collection , Mycology & Aerobiology, Sciensano, Brussels , Belgium
| | - Robby De Pauw
- Department of Epidemiology and Public Health , Sciensano, Brussels , Belgium
- Department of Rehabilitation Sciences , Ghent University, Ghent , Belgium
| | - Anne-Cécile Normand
- Sorbonne Université , INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris , France
| | - Renaud Piarroux
- Sorbonne Université , INSERM, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Paris , France
| | - Dirk Stubbe
- BCCM/IHEM fungi collection , Mycology & Aerobiology, Sciensano, Brussels , Belgium
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Abstract
The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.
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Affiliation(s)
- Luc Cornet
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Elizabet D'hooge
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Nicolas Magain
- InBioS, Evolution and Conservation Biology, University of Liège, Liège, Belgium
| | - Dirk Stubbe
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Ann Packeu
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - Denis Baurain
- InBioS, PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Pierre Becker
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
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Baert F, Lefevere P, D’hooge E, Stubbe D, Packeu A. A Polyphasic Approach to Classification and Identification of Species within the Trichophyton benhamiae Complex. J Fungi (Basel) 2021; 7:jof7080602. [PMID: 34436141 PMCID: PMC8397008 DOI: 10.3390/jof7080602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/21/2022] Open
Abstract
In recent years, considerable advances have been made in clearing up the phylogenetic relationships within the Arthrodermataceae family. However, certain closely related taxa still contain poorly resolved species boundaries. Here, we tried to elucidate the species composition of the Trichophyton benhamiae species complex using a combined approach consisting of multi-gene phylogenetic analysis based on internal transcribed spacer (ITS) and beta-tubulin (BT) gene regions, morphological analysis, and spectral comparison using MALDI-ToF. We confirmed the existence of 11 different monophyletic clades within the complex representing either species or genetically distinct groups within species. MALDI-ToF spectrometry analysis revealed that most of these clades were readily distinguishable from one another; however, some closely related sister clades, such as T. europaeum and T. japonicum, were often misidentified as their counterpart. The distinct “yellow” and “white” phenotypes of T. benhamiae do not have a clear genetic basis and should thus be considered as different morphotypes of the same species. Strains traditionally considered T. benhamiae can be divided into three main clades: (i) T. benhamiae, (ii) T. europaeum/T. japonicum, and (iii) the phylogenetically distant T. africanum. While T. europaeum and T. japonicum are distinguishable based on their genotype, spectral and morphological analysis did not provide clear delimiting characteristics.
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Affiliation(s)
- Frederik Baert
- BCCM/IHEM Fungi Collection, Service of Mycology & Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (E.D.); (D.S.); (A.P.)
- Service of Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium;
- Correspondence: ; Tel.: +32-2-642-50-99
| | - Paulien Lefevere
- Service of Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium;
| | - Elizabet D’hooge
- BCCM/IHEM Fungi Collection, Service of Mycology & Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (E.D.); (D.S.); (A.P.)
- Service of Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium;
| | - Dirk Stubbe
- BCCM/IHEM Fungi Collection, Service of Mycology & Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (E.D.); (D.S.); (A.P.)
- Service of Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium;
| | - Ann Packeu
- BCCM/IHEM Fungi Collection, Service of Mycology & Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (E.D.); (D.S.); (A.P.)
- Service of Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, B-1050 Brussels, Belgium;
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Čmoková A, Kolařík M, Dobiáš R, Hoyer LL, Janouškovcová H, Kano R, Kuklová I, Lysková P, Machová L, Maier T, Mallátová N, Man M, Mencl K, Nenoff P, Peano A, Prausová H, Stubbe D, Uhrlaß S, Větrovský T, Wiegand C, Hubka V. Resolving the taxonomy of emerging zoonotic pathogens in the Trichophyton benhamiae complex. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00465-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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D'hooge E, Becker P, Stubbe D, Normand AC, Piarroux R, Hendrickx M. Black aspergilli: A remaining challenge in fungal taxonomy? Med Mycol 2020; 57:773-780. [PMID: 30535052 DOI: 10.1093/mmy/myy124] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/18/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022] Open
Abstract
Aspergillus section Nigri is a taxonomically difficult but medically and economically important group. In this study, an update of the taxonomy of A. section Nigri strains within the BCCM/IHEM collection has been conducted. The identification accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was tested and the antifungal susceptibilities of clinical isolates were evaluated. A total of 175 strains were molecularly analyzed. Three regions were amplified (ITS, benA, and caM) and a multi-locus phylogeny of the combined loci was created by using maximum likelihood analysis. The in-house MALDI-TOF MS reference database was extended and an identification data set of 135 strains was run against a reference data set. Antifungal susceptibility was tested for voriconazole, itraconazole, and amphotericin B, using the EUCAST method. Phylogenetic analysis revealed 18 species in our data set. MALDI-TOF MS was able to distinguish between A. brasiliensis, A. brunneoviolaceus, A. neoniger, A. niger, A. tubingensis, and A. welwitschiae of A. sect. Nigri. In the routine clinical lab, isolates of A. sect. Nigri are often identified as A. niger. However, in the clinical isolates of our data set, A. tubingensis (n = 35) and A. welwitschiae (n = 34) are more common than A. niger (n = 9). Decreased antifungal susceptibility to azoles was observed in clinical isolates of the /tubingensis clade. This emphasizes the importance of identification up to species level or at least up to clade level in the clinical lab. Our results indicate that MALDI-TOF MS can be a powerful tool to replace classical morphology.
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Affiliation(s)
- Elizabet D'hooge
- BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Pierre Becker
- BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Dirk Stubbe
- BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Anne-Cécile Normand
- Laboratoire de Parasitologie-Mycologie, Hôpital Pitié-Salpêtrière et Sorbonne Université, Paris, France
| | - Renaud Piarroux
- Laboratoire de Parasitologie-Mycologie, Hôpital Pitié-Salpêtrière et Sorbonne Université, Paris, France
| | - Marijke Hendrickx
- BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
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Baert F, Stubbe D, D’hooge E, Packeu A, Hendrickx M. Updating the Taxonomy of Dermatophytes of the BCCM/IHEM Collection According to the New Standard: A Phylogenetic Approach. Mycopathologia 2019; 185:161-168. [DOI: 10.1007/s11046-019-00338-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/30/2019] [Indexed: 11/30/2022]
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Becker P, Normand AC, Vanantwerpen G, Vanrobaeys M, Haesendonck R, Vercammen F, Stubbe D, Piarroux R, Hendrickx M. Identification of fungal isolates by MALDI-TOF mass spectrometry in veterinary practice: validation of a web application. J Vet Diagn Invest 2019; 31:471-474. [PMID: 30943879 DOI: 10.1177/1040638719835577] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable method to identify fungal isolates. The success of this approach relies on the availability of exhaustive databases, but the latter were built with a focus on human pathogens. We assessed a large in-house database of reference spectra and a dedicated web application for their suitability for use in veterinary laboratories. A panel of 290 mold and yeast isolates representing 69 different fungal species was isolated from various animals (including pets, cattle, and zoo animals) and identified using both MALDI-TOF MS and conventional techniques. The performance of the 2 methods was compared, and identifications were confirmed by DNA sequencing. MALDI-TOF MS allowed distinction between some closely related species and achieved 89% correct identification at the species level. In comparison, only 60% of the isolates were correctly identified with conventional approaches. Using this online application, MALDI-TOF MS thus appears to be a relevant alternative for the identification of fungal isolates encountered by animal health professionals.
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Affiliation(s)
- Pierre Becker
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Anne-Cécile Normand
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Gerty Vanantwerpen
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Mia Vanrobaeys
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Roel Haesendonck
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Francis Vercammen
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Dirk Stubbe
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Renaud Piarroux
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
| | - Marijke Hendrickx
- Belgian Coordinated Collections of Microorganisms (BCCM/IHEM) Fungal Collection, Mycology and Aerobiology, Sciensano, Brussels, Belgium (Becker, Stubbe, Hendrickx).,Animal Health Care Flanders, Torhout, Belgium (Vanantwerpen, Vanrobaeys).,Zoolyx, Aalst, Belgium (Haesendonck).,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium (Vercammen).,Sorbonne University, National Institute for Health and Medical Research, Pierre-Louis Institute of Epidemiology and Public Health (Piarroux).,Public Assistance-Hospitals of Paris, University Hospital Pitie-Salpetriere (Normand, Piarroux), Paris, France
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12
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Imbert S, Normand AC, Gabriel F, Cassaing S, Bonnal C, Costa D, Lachaud L, Hasseine L, Kristensen L, Schuttler C, Raberin H, Brun S, Hendrickx M, Stubbe D, Piarroux R, Fekkar A. Multi-centric evaluation of the online MSI platform for the identification of cryptic and rare species of Aspergillus by MALDI-TOF. Med Mycol 2019; 57:962-968. [DOI: 10.1093/mmy/myz004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
The taxonomy of Aspergillus species has recently been revolutionized with the introduction of cryptic species and section concepts. However, their species-level identification in routine laboratories remains a challenge. The aim of this study was to prospectively assess the identification accuracy of cryptic species of Aspergillus in various laboratories using the mass spectrometry identification (MSI) platform, an independent and freely accessible online mass spectrometry database. Over a 12-month period, when a select set of MSI users identified cryptic species, they were contacted and requested to send the isolates to our laboratory for sequence-based identification. Sequence and MSI identification results were then compared. During the study period, 5108 Aspergillus isolates were identified using MSI including 1477 (28.9%) cryptic species. A total of 245 isolates that corresponded to 56 cryptic species and 13 sections were randomly selected for DNA sequencing confirmation. Agreement between the two methods was 99.6% at the section level and 66.1% at the species level. However, almost all discrepancies (72/83, 86.7%) were misidentifications between closely related cryptic species belonging to the same section. Fifty-one isolates from noncryptic species were also identified, thus yielding 100% and 92.2% agreement at the section and species level, respectively. Although the MSI fungus database is a reliable tool to identify Aspergillus at the section level, the database still requires adjustment to correctly identify rare or cryptic species at the species level. Nevertheless, the application properly differentiated between cryptic and sensu stricto species in the same section, thus alerting on possible specific isolate characteristics.
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Affiliation(s)
- Sébastien Imbert
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, F-75013 Paris, France
- Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, F-75013 Paris, France
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Anne Cécile Normand
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, F-75013 Paris, France
| | - Frédéric Gabriel
- Centre Hospitalier Universitaire de Bordeaux, Service de Parasitologie Mycologie, F-33000, Bordeaux, France
| | - Sophie Cassaing
- Centre Hospitalier Universitaire de Toulouse, Service de Parasitologie Mycologie, F-31059, Toulouse, France
| | - Christine Bonnal
- AP-HP, Hôpital Bichat-Claude Bernard, Service de Parasitologie Mycologie, F-75018 Paris, France
| | - Damien Costa
- Centre Hospitalier Universitaire de Rouen, Service de Parasitologie Mycologie, F-76000, Rouen, France
| | - Laurence Lachaud
- Centre Hospitalier Universitaire de Montpellier, Service de Parasitologie Mycologie, F-34000, Montpellier, France
| | - Lilia Hasseine
- Centre Hospitalier Universitaire de Nice, Service de Parasitologie Mycologie, F-06000, Nice, France
| | - Lise Kristensen
- Aarhus University Hospital, Department of Clinical Microbiology, DK-8200, Aarhus N, Denmark
| | | | - Hélène Raberin
- Centre Hospitalier Universitaire de Saint Etienne, Service de Parasitologie Mycologie, F-42100, Saint Etienne, France
| | - Sophie Brun
- AP-HP, Hôpital Avicenne, Service de Parasitologie Mycologie, F-93000 Bobigny, France
| | - Marijke Hendrickx
- Service of Mycology and Aerobiology, BCCM/IHEM Fungal collection, Scientific Institute of Public Health, B-1050, Brussels, Belgium
| | - Dirk Stubbe
- Service of Mycology and Aerobiology, BCCM/IHEM Fungal collection, Scientific Institute of Public Health, B-1050, Brussels, Belgium
| | - Renaud Piarroux
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, F-75013 Paris, France
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
- Institut Pierre Louis d’Epidémiologie et de Santé Publique, INSERM, F-75013 Paris, France
| | - Arnaud Fekkar
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, F-75013 Paris, France
- Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, F-75013 Paris, France
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
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13
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De Crop E, Hampe F, Wisitrassameewong K, Stubbe D, Nuytinck J, Verbeken A. Novel diversity in Lactifluus section Gerardii from Asia: five new species with pleurotoid or small agaricoid basidiocarps. Mycologia 2018; 110:962-984. [PMID: 30240334 DOI: 10.1080/00275514.2018.1508979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The ectomycorrhizal milkcap genus Lactifluus (Russulaceae) is commonly found in tropical and subtropical forests of Southeast Asia. During several sampling expeditions in Thailand, multiple collections of Lactifluus (Lf.) species with pleurotoid or small agaricoid basidiocarps were found. A molecular study was combined with a morphological study, in which the collections were compared with herbarium material. The molecular study indicated that four Thai collections belonged to undescribed species within Lactifluus section Gerardii, as was also the case for herbarium collections of a pleurotoid species from Nepal. One other collection from Thailand appeared closely related to Lf. uyedae, known only from Japan. Five species are described as new in the genus: Lf. auriculiformis, Lf. gerardiellus, Lf. bhandaryi, Lf. pulchrellus, and Lf. raspei.
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Affiliation(s)
- Eske De Crop
- a Mycology Research Group, Department of Biology , Ghent University , K.L. Ledeganckstraat 35, 9000 Gent , Belgium
| | - Felix Hampe
- a Mycology Research Group, Department of Biology , Ghent University , K.L. Ledeganckstraat 35, 9000 Gent , Belgium
| | - Komsit Wisitrassameewong
- a Mycology Research Group, Department of Biology , Ghent University , K.L. Ledeganckstraat 35, 9000 Gent , Belgium.,b Institute of Excellence in Fungal Research, Mae Fah Luang University , 333 Moo 1, Thasud Sub-district, Muang District, Chiang Rai 57100 , Thailand.,c School of Science, Mae Fah Luang University , 333 Moo 1, Thasud Sub-district, Muang District, Chiang Rai 57100 , Thailand
| | - Dirk Stubbe
- a Mycology Research Group, Department of Biology , Ghent University , K.L. Ledeganckstraat 35, 9000 Gent , Belgium.,d Sciensano, Mycology and Aerobiology Service , Juliette Wytsmanstraat 14, 1050 Brussels , Belgium
| | - Jorinde Nuytinck
- a Mycology Research Group, Department of Biology , Ghent University , K.L. Ledeganckstraat 35, 9000 Gent , Belgium.,e Naturalis Biodiversity Center , P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Annemieke Verbeken
- a Mycology Research Group, Department of Biology , Ghent University , K.L. Ledeganckstraat 35, 9000 Gent , Belgium
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Brun LVC, Roux JJ, Sopoh GE, Aguiar J, Eddyani M, Meyers WM, Stubbe D, Akele Akpo MT, Portaels F, de Jong BC. Subcutaneous Granulomatous Inflammation due to Basidiobolomycosis: Case Reports of 3 Patients in Buruli Ulcer Endemic Areas in Benin. Case Rep Pathol 2018; 2018:1351694. [PMID: 29545962 PMCID: PMC5818906 DOI: 10.1155/2018/1351694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/11/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Basidiobolomycosis is a rare subcutaneous mycosis, which can be mistaken for several other diseases, such as soft tissue tumors, lymphoma, or Buruli ulcer in the preulcerative stage. Microbiological confirmation by PCR for Basidiobolus ranarum and culture yield the most specific diagnosis, yet they are not widely available in endemic areas and with varying sensitivity. A combination of histopathological findings, namely, granulomatous inflammation with giant cells, septate hyphal fragments, and the Splendore-Hoeppli phenomenon, can confirm basidiobolomycosis in patients presenting with painless, hard induration of soft tissue. CASE PRESENTATIONS We report on three patients misdiagnosed as suffering from Buruli ulcer, who did not respond to Buruli treatment. Histopathological review of the tissue sections from these patients suggests basidiobolomycosis. All patients had been lost to follow-up, and none received antifungal therapy. On visiting the patients at their homes, two were reported to have died of unknown causes. The third patient was found alive and well and had experienced local spontaneous healing. CONCLUSION Basidiobolomycosis is a rare subcutaneous fungal disease mimicking preulcerative Buruli ulcer. We stress the importance of the early recognition by clinicians and pathologists of this treatable disease, so patients can timely receive antifungal therapy.
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Affiliation(s)
- Luc V. C. Brun
- Department of Pathology, School of Medicine, University of Parakou, 03 BP 333 Parakou, Benin
| | - Jean Jacques Roux
- Department of Pathology, Hospital of Chambéry, Place Lucien Biset, 73000 Chambéry, France
| | - Ghislain E. Sopoh
- Buruli Ulcer Treatment Center, Allada, Benin
- Regional Institute of Public Health, Ouidah, Benin
| | - Julia Aguiar
- Nutritional Center of Gbemontin, Zagnanado, Benin
| | - Miriam Eddyani
- Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerpen, Belgium
| | | | - Dirk Stubbe
- BCCM/IHEM Biomedical Fungi and Yeasts Collection, Scientific Institute of Public Health, Brussels, Belgium
| | - Marie T. Akele Akpo
- Department of Pathology, School of Medicine, University of Abomey Calavi, Cotonou, Benin
| | - Françoise Portaels
- Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerpen, Belgium
| | - Bouke C. de Jong
- Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerpen, Belgium
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15
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Nilsson RH, Taylor AFS, Adams RI, Baschien C, Johan Bengtsson-Palme, Cangren P, Coleine C, Heide-Marie Daniel, Glassman SI, Hirooka Y, Irinyi L, Reda Iršėnaitė, Pedro M. Martin-Sanchez, Meyer W, Seung-Yoon Oh, Jose Paulo Sampaio, Seifert KA, Sklenář F, Dirk Stubbe, Suh SO, Summerbell R, Svantesson S, Martin Unterseher, Cobus M. Visagie, Weiss M, Woudenberg JHC, Christian Wurzbacher, den Wyngaert SV, Yilmaz N, Andrey Yurkov, Kõljalg U, Abarenkov K. Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK). MycoKeys 2018; 28:65-82. [PMID: 29559822 PMCID: PMC5804120 DOI: 10.3897/mycokeys.28.20887] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 11/12/2017] [Indexed: 12/22/2022] Open
Abstract
Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
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Affiliation(s)
- R. Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Andy F. S. Taylor
- The James Hutton Institute and University of Aberdeen, Aberdeen, United Kingdom
| | - Rachel I. Adams
- Plant and Microbial Biology, University of California, 94720 Berkeley, California, USA
| | - Christiane Baschien
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
- Department of Plant Pathology & Microbiology and Institute of Integrative Genome Biology, University of California, Riverside, Riverside 92501, CA, USA
| | - Heide-Marie Daniel
- Université catholique de Louvain, Earth and Life Institute, Applied Microbiology, BCCM/MUCL, Louvain-la-Neuve, Belgium
| | - Sydney I. Glassman
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo Japan 184-8584
| | - Laszlo Irinyi
- Sydney Medical School-Westmead Hospital, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney, Australia
- University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Australia
| | - Reda Iršėnaitė
- Institute of Botany, Nature Research Centre, Žaliųjų ežerų Str. 49, 08406 Vilnius, Lithuania
| | - Pedro M. Martin-Sanchez
- Bundesanstalt für Materialforschung und -prüfung (BAM), Department 4. Materials & Environment, Unter den Eichen 87, 12205 Berlin, Germany
| | - Wieland Meyer
- Sydney Medical School-Westmead Hospital, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney, Australia
- University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
- Westmead Institute for Medical Research, Westmead, Australia
| | - Seung-Yoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jose Paulo Sampaio
- UCIBIO-REQUIMTE, DCV, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Keith A. Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
| | - Frantisek Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i, Prague, Czech Republic
| | - Dirk Stubbe
- BCCM/IHEM, Scientific Institute of Public Health WIV-ISP, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Sung-Oui Suh
- ATCC, 10801 University Blvd., Manassas, Virginia 20110, USA
| | - Richard Summerbell
- Sporometrics, 219 Dufferin Street, Suite 20C, Toronto, Ontario Canada, M6K 1Y9
- Dalla Lana School of Public Health, University of Toronto, Health Sciences Building, 155 College Street, 6th floor, Toronto, Ontario Canada, M5T 3M7
| | - Sten Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Martin Unterseher
- Evangelisches Schulzentrum Martinschule, Max-Planck-Str. 7, 17491 Greifswald, Germany
| | - Cobus M. Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
- Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood 0121, Pretoria, South Africa
| | - Michael Weiss
- Steinbeis-Innovationszentrum, Organismische Mykologie und Mikrobiologie, Vor dem Kreuzberg 17, 72070 Tübingen, Germany
| | - Joyce HC Woudenberg
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Silke Van den Wyngaert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775 Stechlin, Germany
| | - Neriman Yilmaz
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
- Department of Biology, University of Ottawa, 30 Marie Curie Ottawa, ON, Canada, K1N 6N5
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
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17
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Stubbe D, Verbeken A. Lactarius subg. Plinthogalus: the European taxa and American varieties of L. lignyotus re-evaluated. Mycologia 2017; 104:1490-501. [DOI: 10.3852/12-039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dirk Stubbe
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium, and Mycology and Aerobiology Service, Belgian Scientific Institute for Public Health, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Annemieke Verbeken
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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18
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Wisitrassameewong K, Looney BP, Le HT, De Crop E, Das K, Van de Putte K, Eberhardt U, Jiayu G, Stubbe D, Hyde KD, Verbeken A, Nuytinck J. Lactarius subgenus Russularia (Basidiomycota, Russulales): novel Asian species, worldwide phylogeny and evolutionary relationships. Fungal Biol 2016; 120:1554-1581. [DOI: 10.1016/j.funbio.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 10/21/2022]
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19
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de Hoog GS, Dukik K, Monod M, Packeu A, Stubbe D, Hendrickx M, Kupsch C, Stielow JB, Freeke J, Göker M, Rezaei-Matehkolaei A, Mirhendi H, Gräser Y. Toward a Novel Multilocus Phylogenetic Taxonomy for the Dermatophytes. Mycopathologia 2016; 182:5-31. [PMID: 27783317 PMCID: PMC5283515 DOI: 10.1007/s11046-016-0073-9] [Citation(s) in RCA: 345] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/28/2016] [Indexed: 12/16/2022]
Abstract
Type and reference strains of members of the onygenalean family Arthrodermataceae have been sequenced for rDNA ITS and partial LSU, the ribosomal 60S protein, and fragments of β-tubulin and translation elongation factor 3. The resulting phylogenetic trees showed a large degree of correspondence, and topologies matched those of earlier published phylogenies demonstrating that the phylogenetic representation of dermatophytes and dermatophyte-like fungi has reached an acceptable level of stability. All trees showed Trichophyton to be polyphyletic. In the present paper, Trichophyton is restricted to mainly the derived clade, resulting in classification of nearly all anthropophilic dermatophytes in Trichophyton and Epidermophyton, along with some zoophilic species that regularly infect humans. Microsporum is restricted to some species around M. canis, while the geophilic species and zoophilic species that are more remote from the human sphere are divided over Arthroderma, Lophophyton and Nannizzia. A new genus Guarromyces is proposed for Keratinomyces ceretanicus. Thirteen new combinations are proposed; in an overview of all described species it is noted that the largest number of novelties was introduced during the decades 1920–1940, when morphological characters were used in addition to clinical features. Species are neo- or epi-typified where necessary, which was the case in Arthroderma curreyi, Epidermophyton floccosum, Lophophyton gallinae, Trichophyton equinum, T. mentagrophytes, T. quinckeanum, T. schoenleinii, T. soudanense, and T. verrucosum. In the newly proposed taxonomy, Trichophyton contains 16 species, Epidermophyton one species, Nannizzia 9 species, Microsporum 3 species, Lophophyton 1 species, Arthroderma 21 species and Ctenomyces 1 species, but more detailed studies remain needed to establish species borderlines. Each species now has a single valid name. Two new genera are introduced: Guarromyces and Paraphyton. The number of genera has increased, but species that are relevant to routine diagnostics now belong to smaller groups, which enhances their identification.
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Affiliation(s)
- G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands. .,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands. .,Basic Pathology Department, Federal University of Paraná State, Curitiba, Paraná, Brazil. .,Peking University Health Science Center, Research Center for Medical Mycology, Beijing, China. .,Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China. .,Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Karolina Dukik
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Michel Monod
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Ann Packeu
- Mycology and Aerobiology, Scientific Institute of Public Health, Brussels, Belgium
| | - Dirk Stubbe
- Mycology and Aerobiology, Scientific Institute of Public Health, Brussels, Belgium
| | - Marijke Hendrickx
- Mycology and Aerobiology, Scientific Institute of Public Health, Brussels, Belgium
| | - Christiane Kupsch
- Institute of Microbiology and Hygiene, University Medicine Berlin - Charité, Berlin, Germany
| | - J Benjamin Stielow
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Thermo Fisher Scientific, Landsmeer, The Netherlands
| | - Joanna Freeke
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Thermo Fisher Scientific, Landsmeer, The Netherlands
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Ali Rezaei-Matehkolaei
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Yvonne Gräser
- Institute of Microbiology and Hygiene, University Medicine Berlin - Charité, Berlin, Germany.
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Becker PT, Stubbe D, Claessens J, Roesems S, Bastin Y, Planard C, Cassagne C, Piarroux R, Hendrickx M. Quality control in culture collections: Confirming identity of filamentous fungi by MALDI-TOF MS. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2014.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Irinyi L, Serena C, Garcia-Hermoso D, Arabatzis M, Desnos-Ollivier M, Vu D, Cardinali G, Arthur I, Normand AC, Giraldo A, da Cunha KC, Sandoval-Denis M, Hendrickx M, Nishikaku AS, de Azevedo Melo AS, Merseguel KB, Khan A, Parente Rocha JA, Sampaio P, da Silva Briones MR, e Ferreira RC, de Medeiros Muniz M, Castañón-Olivares LR, Estrada-Barcenas D, Cassagne C, Mary C, Duan SY, Kong F, Sun AY, Zeng X, Zhao Z, Gantois N, Botterel F, Robbertse B, Schoch C, Gams W, Ellis D, Halliday C, Chen S, Sorrell TC, Piarroux R, Colombo AL, Pais C, de Hoog S, Zancopé-Oliveira RM, Taylor ML, Toriello C, de Almeida Soares CM, Delhaes L, Stubbe D, Dromer F, Ranque S, Guarro J, Cano-Lira JF, Robert V, Velegraki A, Meyer W. International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Med Mycol 2015; 53:313-37. [PMID: 25802363 DOI: 10.1093/mmy/myv008] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 01/19/2015] [Indexed: 12/13/2022] Open
Abstract
Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Carolina Serena
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia Unitat de Recerca, Hospital Joan XXIII, Institut de Investigacio Sanitaria Rovira I Virgili (IISPV), Universitat Rovira i Virgili, Tarragona, Spain
| | - Dea Garcia-Hermoso
- Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France
| | - Michael Arabatzis
- Mycology Research Laboratory, Department of Microbiology, Medical School, the University of Athens Hellenic Collection of Pathogenic Fungi (UOA/HCPF), National and Kapodistrian University of Athens, Athens, Greece
| | - Marie Desnos-Ollivier
- Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France
| | - Duong Vu
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences-Università degli Studi di Perugia, Perugia, Italy
| | - Ian Arthur
- Mycology Laboratory, Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Anne-Cécile Normand
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Alejandra Giraldo
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Keith Cassia da Cunha
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Marcelo Sandoval-Denis
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Marijke Hendrickx
- BCCM/IHEM, Biomedical fungi and yeasts collection, Scientific Institute of Public Health, Brussels, Belgium
| | - Angela Satie Nishikaku
- Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Analy Salles de Azevedo Melo
- Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Aziza Khan
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Juliana Alves Parente Rocha
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Laboratório de Biologia Molecular, Goiânia, Goiás, Brazil
| | - Paula Sampaio
- Centre of Molecular and Environmental Biology (CBMA), Biology Department, School of Sciences, University of Minho, Braga, Portugal
| | - Marcelo Ribeiro da Silva Briones
- Laboratório de Genômica e Biocomplexidade Evolutiva, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renata Carmona e Ferreira
- Laboratório de Genômica e Biocomplexidade Evolutiva, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mauro de Medeiros Muniz
- Instituto de Pesquisa Clínica Evandro Chagas (IPEC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Laura Rosio Castañón-Olivares
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Daniel Estrada-Barcenas
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carole Cassagne
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Charles Mary
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Shu Yao Duan
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Annie Ying Sun
- School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA, Australia; Robinson Institute, University of Adelaide, Adelaide, SA, Australia
| | - Xianyu Zeng
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Zuotao Zhao
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Nausicaa Gantois
- BDEEP-EA4547, CIIL, Institut Pasteur de Lille, CHU de Lille, Université de Lille2, Lille, France
| | - Françoise Botterel
- Unité de Parasitologie - Mycologie, Dynamyc Team, CHU Henri Mondor, AP-HP, Créteil, France
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Conrad Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Walter Gams
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - David Ellis
- Mycology and Infectious Diseases, SA Pathology, University of Adelaide, Adelaide, SA, Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Sharon Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Tania C Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Renaud Piarroux
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Arnaldo L Colombo
- Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Célia Pais
- Centre of Molecular and Environmental Biology (CBMA), Biology Department, School of Sciences, University of Minho, Braga, Portugal
| | - Sybren de Hoog
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | | | - Maria Lucia Taylor
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Conchita Toriello
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Célia Maria de Almeida Soares
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Laboratório de Biologia Molecular, Goiânia, Goiás, Brazil
| | - Laurence Delhaes
- BDEEP-EA4547, CIIL, Institut Pasteur de Lille, CHU de Lille, Université de Lille2, Lille, France
| | - Dirk Stubbe
- BCCM/IHEM, Biomedical fungi and yeasts collection, Scientific Institute of Public Health, Brussels, Belgium
| | - Françoise Dromer
- Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France
| | - Stéphane Ranque
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Josep Guarro
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Jose F Cano-Lira
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Vincent Robert
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Aristea Velegraki
- Mycology Research Laboratory, Department of Microbiology, Medical School, the University of Athens Hellenic Collection of Pathogenic Fungi (UOA/HCPF), National and Kapodistrian University of Athens, Athens, Greece
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
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Triest D, Stubbe D, De Cremer K, Piérard D, Detandt M, Hendrickx M. Banana infecting fungus, Fusarium musae, is also an opportunistic human pathogen: are bananas potential carriers and source of fusariosis? Mycologia 2014; 107:46-53. [PMID: 25361833 DOI: 10.3852/14-174] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
During re-identification of Fusarium strains in the BCCM™/IHEM fungal collection by multilocus sequence-analysis we observed that five strains, previously identified as Fusarium verticillioides, were Fusarium musae, a species described in 2011 from banana fruits. Four strains were isolated from blood samples or biopsies of immune-suppressed patients and one was isolated from the clinical environment, all originating from different hospitals in Belgium or France, 2001-2008. The F. musae identity of our isolates was confirmed by phylogenetic analysis using reference sequences of type material. Absence of the gene cluster necessary for fumonisin biosynthesis, characteristic to F. musae, was also the case for our isolates. In vitro antifungal susceptibility testing revealed no important differences in their susceptibility compared to clinical F. verticillioides strains and terbinafine was the most effective drug. Additional clinical F. musae strains were searched by performing BLAST queries in GenBank. Eight strains were found, of which six were keratitis cases from the U.S. multistate contact lens-associated outbreak in 2005 and 2006. The two other strains were also from the U.S., causing either a skin infection or sinusitis. This report is the first to describe F. musae as causative agent of superficial and opportunistic, disseminated infections in humans. Imported bananas might act as carriers of F. musae spores and be a potential source of infection with F. musae in humans. An alternative hypothesis is that the natural distribution of F. musae is geographically a lot broader than originally suspected and F. musae is present on different plant hosts.
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Affiliation(s)
- David Triest
- Scientific Institute of Public Health, Department of Mycology and Aerobiology, BCCM™/IHEM fungal collection, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Dirk Stubbe
- Scientific Institute of Public Health, Department of Mycology and Aerobiology, BCCM™/IHEM fungal collection, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Koen De Cremer
- Scientific Institute of Public Health, Department of Biomonitoring, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Denis Piérard
- Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Department of Microbiology and Infection Control, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Monique Detandt
- Scientific Institute of Public Health, Department of Mycology and Aerobiology, BCCM™/IHEM fungal collection, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Marijke Hendrickx
- Scientific Institute of Public Health, Department of Mycology and Aerobiology, BCCM™/IHEM fungal collection, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
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Savini V, Hendrickx M, Sisti M, Masciarelli G, Favaro M, Fontana C, Pitzurra L, Arzeni D, Astolfi D, Catavitello C, Polilli E, Farina C, Fazii P, D'Antonio D, Stubbe D. An atypical, pigment-producing Metschnikowia strain from a leukaemia patient. Med Mycol 2012; 51:438-43. [PMID: 23170963 DOI: 10.3109/13693786.2012.733429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A yeast strain was isolated from the sputum sample of a leukaemia patient in the Spirito Santo Hospital of Pescara, Italy. The fungus produced a pigment that formed a reddish halo around colonies, and was identified and deposited as a Metschnikowia spp. (accession number IHEM 25107-GenBank accession number JQ921016) in the BCCM/IHEM collection of biomedical fungi and yeasts (Bruxelles, Belgium). Although the physiology of the strain was close to that of Metschnikowia sinensis, the D1/D2 sequence did not correspond to any previously described Metschnikowia species. Phylogeny of the genus Metschnikowia is complex and requires far more analysis. We present the first non-M. pulcherrima Metschnikowia spp. isolate recovered from a human, and emphasize the role of man as a transient carrier of environmental yeasts, the pathogenicity of which still needs to be defined.
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Affiliation(s)
- Vincenzo Savini
- Clinical Microbiology and Virology, Spirito Santo Hospital, Pescara, PE, Italy.
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Beguin H, Pyck N, Hendrickx M, Planard C, Stubbe D, Detandt M. The taxonomic status ofTrichophyton quinckeanumandT. interdigitalerevisited: a multigene phylogenetic approach. Med Mycol 2012; 50:871-82. [DOI: 10.3109/13693786.2012.684153] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wang XH, Stubbe D, Verbeken A. Lactifluus parvigerardiisp. nov., a New Link Towards the Pleurotoid Habit inLactifluusSubgen.Gerardii(Russulaceae, Russulales). CRYPTOGAMIE MYCOL 2012. [DOI: 10.7872/crym.v33.iss2.2012.181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Montoya L, Bandala VM, Haug I, Stubbe D. A new species of Lactarius (subgenus Gerardii) from two relict Fagus grandifolia var. mexicana populations in Mexican montane cloud forests. Mycologia 2011; 104:175-81. [PMID: 21914830 DOI: 10.3852/11-051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new milkcap species, Lactarius fuscomarginatus, was found in the subtropical region of central Veracruz (eastern Mexico) associated with two relict populations of Fagus grandifolia var. mexicana. The species is characterized macroscopically by its dark pileus and stipe and by its distant and whitish lamellae with blackish to blackish brown edges. A molecular phylogenetic analyses based on ITS and LSU nucDNA sequences confirms the delimitation of this new taxon and places L. fuscomarginatus in subgenus Gerardii. A detailed morphological comparison is given with similar species.
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Affiliation(s)
- Leticia Montoya
- Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, México.
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Stubbe D, Le HT, Wang XH, Nuytinck J, Van de Putte K, Verbeken A. The Australasian species of Lactarius subgenus Gerardii (Russulales). FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0111-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Leroux O, Bagniewska-Zadworna A, Rambe SK, Knox JP, Marcus SE, Bellefroid E, Stubbe D, Chabbert B, Habrant A, Claeys M, Viane RLL. Non-lignified helical cell wall thickenings in root cortical cells of Aspleniaceae (Polypodiales): histology and taxonomical significance. Ann Bot 2011; 107:195-207. [PMID: 21118842 PMCID: PMC3025727 DOI: 10.1093/aob/mcq225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Extraxylary helical cell wall thickenings in vascular plants are not well documented, except for those in orchid velamen tissues which have been studied extensively. Reports on their occurrence in ferns exist, but detailed information is missing. The aim of this study is to focus on the broad patterns of structure and composition and to study the taxonomic occurrence of helical cell wall thickenings in the fern family Aspleniaceae. METHODS Structural and compositional aspects of roots have been examined by means of light, electron, epifluorescence and laser scanning confocal microscopy. To assess the taxonomical distribution of helical cell wall thickenings a molecular phylogenetic analysis based on rbcL sequences of 64 taxa was performed. KEY RESULTS The helical cell wall thickenings of all examined species showed considerable uniformity of design. The pattern consists of helical, regularly bifurcating and anastomosing strands. Compositionally, the cell wall thickenings were found to be rich in homogalacturonan, cellulose, mannan and xyloglucan. Thioacidolysis confirmed our negative phloroglucinol staining tests, demonstrating the absence of lignins in the root cortex. All taxa with helical cell wall thickenings formed a monophyletic group supported by a 100 % bootstrap value and composed of mainly epiphytic species. CONCLUSIONS This is the first report of non-lignified pectin-rich secondary cell walls in ferns. Based on our molecular analysis, we reject the hypothesis of parallel evolution of helical cell wall thickenings in Aspleniaceae. Helical cell wall thickenings can mechanically stabilize the cortex tissue, allowing maximal uptake of water and nutrients during rainfall events. In addition, it can also act as a boundary layer increasing the diffusive pathway towards the atmosphere, preventing desiccation of the stele of epiphytic growing species.
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Affiliation(s)
- O. Leroux
- Pteridology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - A. Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - S. K. Rambe
- NSSE–Biology, National Institute of Education, Nanyang Technological University, Nanyang Walk 1, 637616, Singapore
| | - J. P. Knox
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - S. E. Marcus
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - E. Bellefroid
- Pteridology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - D. Stubbe
- Research Group Mycology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - B. Chabbert
- URCA, UMR Fractionnement Agroressources & Environment 614, F-51686 Reims, France
| | - A. Habrant
- URCA, UMR Fractionnement Agroressources & Environment 614, F-51686 Reims, France
| | - M. Claeys
- Nematology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - R. L. L. Viane
- Pteridology, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- For correspondence. E-mail
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Stubbe D, Nuytinck J, Verbeken A. Critical assessment of the Lactarius gerardii species complex (Russulales). Fungal Biol 2010; 114:271-83. [PMID: 20943137 DOI: 10.1016/j.funbio.2010.01.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 12/21/2009] [Accepted: 01/11/2010] [Indexed: 11/18/2022]
Abstract
This paper investigates species delimitation within the Lactarius gerardii species complex and explores its taxonomic and geographical extent. A combined molecular phylogeny based on ITS, LSU and rpb2 gene sequences is constructed and morphological characters are evaluated. While L. gerardii was originally described from North America, it has later been reported from all over Asia. Therefore a worldwide sampling range was aimed at, including species exhibiting morphological affinities with L. gerardii. The phylogenetic analyses indicate that intercontinental conspecificity in L. gerardii is absent. Thirty strongly supported clades are retrieved of which 18 are morphologically identifiable species. The group is elevated to Lactarius subg. Gerardii stat. nov. It includes, apart from L. gerardii s.l., L. atrovelutinus, L. bicolor, L. ochrogalactus, L. petersenii, L. reticulatovenosus, L. sepiaceus, L. subgerardii and L. wirrabara, as well as the pleurotoid L. uyedae. The paraphyletic nature of the genus Lactarius is confirmed. Lactarius subg. Gerardii appears not affiliated with L. subg. Plinthogalus and this can be substantiated morphologically. No representatives are known from Europe, Africa or South America. The high frequency of intercontinental sister relationships observed between America, Asia and the Australian region, suggests multiple migration and speciation events have occurred across continents.
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Affiliation(s)
- Dirk Stubbe
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
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Abstract
Today, the question of the physiological cause of phase transition, the transition from the solitary to the gregarious phase, in locusts remains unanswered. We hereby present a novel approach by which we have attempted to determine whether different phases express or release different peptides in similar physiological conditions. For this purpose, a peptidomic analysis of the corpora cardiaca and hemolymph of crowded and isolated locusts of Schistocerca gregaria was performed using high performance liquid chromatography and matrix-assisted laser desorption ionisation time of flight mass spectrometry. A comparison between the two conditions reveals differences in the number and amount of peptides present in the corpora cardiaca and the hemolymph. Further research will have to identify these phase specific differences and their role in locust phase polymorphism.
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Affiliation(s)
- Elke Clynen
- Laboratory for Developmental Physiology and Molecular Biology, K.U. Leuven, Leuven, Belgium.
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32
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Jansen P, Maene N, Raedt WD, Naten S, Stubbe D, Schoenmaker W, Van Rossum M, De Meyer K. AlGaAs/GaAs: High electron mobility transistor simulations with PRISM. ACTA ACUST UNITED AC 1990. [DOI: 10.1002/ett.4460010411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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