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Somayeh Dolatabadi - One of the best experts on this subject based on the ideXlab platform.
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Supplemental Material for Gryganskyi et al., 2018
2018Co-Authors: Andrii P. Gryganskyi, Somayeh Dolatabadi, Jacob Golan, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-ling LiaoAbstract:Figure S1. Maximum Likelihood phylogeny of the genus Rhizopus based on putative RNA helicase (rnhA), flanking gene that is adjacent to the sex gene within the mating locus of mucoralean fungi. Mucor circinelloides was used as the outgroup (NCBI sequences accession numbers MG97275-98). Figure S2. Maximum Likelihood phylogeny of the genus Rhizopus based on 4-dihydrotrisporin-dehydrogenase (tsp2) of genus Rhizopus, an enzyme of the sex hormone pathway in mucoralean fungi. Mucor mucedo was used as the outgroup (NCBI sequences accession numbers MG97299-324).Table S1. Morphological and ecological characters used for non-molecular phylogenyTable S2. All TE types
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differentiation of clinically relevant mucorales Rhizopus microsporus and r arrhizus by matrix assisted laser desorption ionization time of flight mass spectrometry maldi tof ms
Journal of Medical Microbiology, 2015Co-Authors: Somayeh Dolatabadi, Anna Kolecka, Matthijs Versteeg, Sybren De Hoog, Teun BoekhoutAbstract:This study addresses the usefulness of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS for reliable identification of the two most frequently occurring clinical species of Rhizopus, namely Rhizopus arrhizus with its two varieties, arrhizus and delemar, and Rhizopus microsporus. The test-set comprised 38 isolates of clinical and environmental origin previously identified by internal transcribed spacer (ITS) sequencing of rDNA. Multi-locus sequence data targeting three gene markers (ITS, ACT, TEF ) showed two monophylic clades for Rhizopus arrhizus and Rhizopus microsporus (bootstrap values of 99 %). Cluster analysis confirmed the presence of two distinct clades within Rhizopus arrhizus representing its varieties arrhizus and delemar. The MALDI Biotyper 3.0 Microflex LT platform (Bruker Daltonics) was used to confirm the distinction between Rhizopus arrhizus and Rhizopus microsporus and the presence of two varieties within the species Rhizopus arrhizus. An in-house database of 30 reference main spectra (MSPs) was initially tested for correctness using commercially available databases of Bruker Daltonics. By challenging the database with the same strains of which an in-house database was created, automatic identification runs confirmed that MALDI-TOF MS is able to recognize the strains at the variety level. Based on principal component analysis, two MSP dendrograms were created and showed concordance with the multi-locus tree; thus, MALDI-TOF MS is a useful tool for diagnostics of mucoralean species.
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diversity and delimitation of Rhizopus microsporus
Fungal Diversity, 2014Co-Authors: Somayeh Dolatabadi, Grit Walther, A Gerrits H G Van Den Ende, G S De HoogAbstract:Rhizopus microsporus has been used for centuries in the production of oriental fermented foods, but the species is also known as a toxin producer and from severe human infections. To study the diversity and species delimitation of Rhizopus microsporus, 48 isolates from the reference collection of the CBS-KNAW Fungal Biodiversity Centre, comprising nine environmental, ten clinical, and 23 foodborne strains, in addition to six strains from unknown sources and representing all existing varieties of the species, were examined. Sequence diversity was based on the internal transcribed spacer (ITS), and on a part of the actin (ACT) and translation elongation factor 1-α (TEF) genes. Differences in physiological properties were assessed including temperature relationships. Spore morphology was studied, mating type tests were performed, and MALDI-ToF profiles were generated. Clinical and food-associated strains as well as members of different varieties mated successfully and consequently they belong to a single biological species. Molecular differences did not match with any other parameter investigated. Based on these results the varieties of Rhizopus microsporus are reduced to synonyms.
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antifungal susceptibility and phylogeny of opportunistic members of the order mucorales
Journal of Clinical Microbiology, 2012Co-Authors: Roxana G Vitale, Eric Dannaoui, Sybren G De Hoog, Patrick Schwarz, Shuwen Deng, Marie Machouart, Kerstin Voigt, Wendy W J Van De Sande, Somayeh DolatabadiAbstract:The in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the nuclear ribosomal large subunit to reveal taxon-specific susceptibility profiles. The impressive phylogenetic diversity of the Mucorales was reflected in susceptibilities differing at family, genus, and species levels. Amphotericin B was the most active drug, though somewhat less against Rhizopus and Cunninghamella species. Posaconazole was the second most effective antifungal agent but showed reduced activity in Mucor and Cunninghamella strains, while voriconazole lacked in vitro activity for most strains. Genera attributed to the Mucoraceae exhibited a wide range of MICs for posaconazole, itraconazole, and terbinafine and included resistant strains. Cunninghamella also comprised strains resistant to all azoles tested but was fully susceptible to terbinafine. In contrast, the Lichtheimiaceae completely lacked strains with reduced susceptibility for these antifungals. Syncephalastrum species exhibited susceptibility profiles similar to those of the Lichtheimiaceae. Mucor species were more resistant to azoles than Rhizopus species. Species-specific responses were obtained for terbinafine where only Rhizopus arrhizus and Mucor circinelloides were resistant. Complete or vast resistance was observed for 5-fluorocytosine, caspofungin, and micafungin. Intraspecific variability of in vitro susceptibility was found in all genera tested but was especially high in Mucor and Rhizopus for azoles and terbinafine. Accurate molecular identification of etiologic agents is compulsory to predict therapy outcome. For species of critical genera such as Mucor and Rhizopus, exhibiting high intraspecific variation, susceptibility testing before the onset of therapy is recommended.
Teun Boekhout - One of the best experts on this subject based on the ideXlab platform.
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differentiation of clinically relevant mucorales Rhizopus microsporus and r arrhizus by matrix assisted laser desorption ionization time of flight mass spectrometry maldi tof ms
Journal of Medical Microbiology, 2015Co-Authors: Somayeh Dolatabadi, Anna Kolecka, Matthijs Versteeg, Sybren De Hoog, Teun BoekhoutAbstract:This study addresses the usefulness of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS for reliable identification of the two most frequently occurring clinical species of Rhizopus, namely Rhizopus arrhizus with its two varieties, arrhizus and delemar, and Rhizopus microsporus. The test-set comprised 38 isolates of clinical and environmental origin previously identified by internal transcribed spacer (ITS) sequencing of rDNA. Multi-locus sequence data targeting three gene markers (ITS, ACT, TEF ) showed two monophylic clades for Rhizopus arrhizus and Rhizopus microsporus (bootstrap values of 99 %). Cluster analysis confirmed the presence of two distinct clades within Rhizopus arrhizus representing its varieties arrhizus and delemar. The MALDI Biotyper 3.0 Microflex LT platform (Bruker Daltonics) was used to confirm the distinction between Rhizopus arrhizus and Rhizopus microsporus and the presence of two varieties within the species Rhizopus arrhizus. An in-house database of 30 reference main spectra (MSPs) was initially tested for correctness using commercially available databases of Bruker Daltonics. By challenging the database with the same strains of which an in-house database was created, automatic identification runs confirmed that MALDI-TOF MS is able to recognize the strains at the variety level. Based on principal component analysis, two MSP dendrograms were created and showed concordance with the multi-locus tree; thus, MALDI-TOF MS is a useful tool for diagnostics of mucoralean species.
Jinhyeuk Kwon - One of the best experts on this subject based on the ideXlab platform.
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occurrence of Rhizopus soft rot on rubus crataegifolius caused by Rhizopus stolonifer in korea
Research in Plant Disease, 2008Co-Authors: Jinhyeuk KwonAbstract:Rhizopus soft rot caused by Rhizopus stolonifer on June, 2008 occurred on Rubus crataegifolius Bunge in the box at Jinju City Wholesale Market of Agricultural Products at Gyeongnam province in Korea. The infected fruits were rapidly water-soaked, softened, black and eventually rotted. The symptoms occurred after infecting wounds at harvest time. The colony were white to light brown, formed much sporangiospores. The optimum temperature of the fungus on potato dextrose agar was . Sporangiophores were in width. Sporangia were globose or hemispheric, white at first and gradually to black, and in size. Columella were hemispheric, and in size. Sporangiospores were irregular round or oval, brownishblack and in size. On the basis of symptom, mycological characteristics and pathogenicity of the fungus, the causal fungus was identified as Rhizopus stolonifer. This is the first report of Rhizopus soft rot by R. stolonifer on R. crataegifolius in Korea.
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occurrence of Rhizopus soft rot on apple fruit caused by Rhizopus stolonifer in korea
Research in Plant Disease, 2008Co-Authors: Jinhyeuk KwonAbstract:A Rhizopus soft rot caused by Rhizopus stolonifer occurred sporadically on apple fruits (Malus pumila var. dulcissima Koidz.) at a wholesale market of agricultural products in Jinju, Korea in 2006 and 2007. Infected fruits were rapidly water-soaked, softened and rotted. The symptoms were initiated mainly from wounds or cracks occurred at harvest time. Sporangiophores were in length and in width. Sporangia were globose or hemispheric and in size. The color of sporangia was white and cottony at first and gradually turned to brownish black, bearing abundant spores when matured. Columella were hemispheric and in size. Sporangiospores were irregular round or oval, brownish-black streaked and in size. Optimum temperature for mycelial growth of the fungus on PDA was . On the basis of mycological characteristics and pathogenicity to apple the causal fungus was identified as Rhizopus stolonifer (Ehrenb.) Vuill. This is the first report of Rhizopus soft rot by R. stolonifer on Fuji apple in Korea.
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occurrence of Rhizopus soft rot on apple fruit caused by Rhizopus stolonifer in korea
Research in Plant Disease, 2008Co-Authors: Jinhyeuk KwonAbstract:A Rhizopus soft rot caused by Rhizopus stolonifer occurred sporadically on apple fruits (Malus pumila var. dulcissima Koidz.) at a wholesale market of agricultural products in Jinju, Korea in 2006 and 2007. Infected fruits were rapidly water-soaked, softened and rotted. The symptoms were initiated mainly from wounds or cracks occurred at harvest time. Sporangiophores were in length and in width. Sporangia were globose or hemispheric and in size. The color of sporangia was white and cottony at first and gradually turned to brownish black, bearing abundant spores when matured. Columella were hemispheric and in size. Sporangiospores were irregular round or oval, brownish-black streaked and in size. Optimum temperature for mycelial growth of the fungus on PDA was . On the basis of mycological characteristics and pathogenicity to apple the causal fungus was identified as Rhizopus stolonifer (Ehrenb.) Vuill. This is the first report of Rhizopus soft rot by R. stolonifer on Fuji apple in Korea.
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occurrence of Rhizopus soft rot on musa sapientum caused by Rhizopus stolonifer in korea
The Korean Journal of Mycology, 2007Co-Authors: Jinhyeuk KwonAbstract:Rhizopus soft rot caused by Rhizopus stolonifer occurred on banana (Musa sapientum) in the box at Jinju City Wholesale Market of Agricultural Products at Gyeongnam province in Korea. The infected fruits were rapidly water-soaked, softened, blackened and eventually rotted. They were infected from wounds at harvest time. The colony of the isolate from the infected fruit was white to light brown and formed many sporangiospores. The optimum growth temperature of the fungus on potato dextrose agar was . Sporangiophores were in width. Sporangia were globose or hemispheric, white at first and changed gradually to black, and in size. Columella were hemispheric, and in size. Sporangiospores were irregular round or oval, brownish-black and in size. On the basis of symptom, mycological characteristics and pathogenicity to banana, the causal fungus was identified as Rhizopus stolonifer. This is the first report of Rhizopus soft rot by R. stolonifer on banana in Korea.
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Rhizopus soft rot on pear pyrus serotina caused by Rhizopus stolonifer in korea
Mycobiology, 2006Co-Authors: Jinhyeuk KwonAbstract:Rhizopus soft rot caused by Rhizopus stolonifer occurred on pears (Pyrus serotina) in the Jinju City Agricultural Products Wholesale Market in Korea from 2004 to 2005. The infection usually started from wounds due to cracking at harvest time. The lesions started as water-soaked, rapidly softened, then gradually expanded. The mycelia grew vigorously on the surface of the fruits and formed stolons. Colonies on potato dextrose agar at 25℃ were white cottony to brownish black. Sporangia were globose, black and 90~120 µm in size. Sporangiophores were light brown and 480~2600 × 12~18 µm in size. Sporangiospores were globose to oval, brownish, streaked, and 8~14 × 6~10 µm in size. Columella were light brownish gray, hemispherical and 70~80 µm in size. On the basis of these symptoms, mycological characteristics and pathogenicity tests on host plants, the fungus was identified as Rhizopus stolonifer (Ehrenb.) Vuill. This is the first report of Rhizopus soft rot on pear (P. serotina) caused by R. stolonifer in Korea.
Matthijs Versteeg - One of the best experts on this subject based on the ideXlab platform.
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differentiation of clinically relevant mucorales Rhizopus microsporus and r arrhizus by matrix assisted laser desorption ionization time of flight mass spectrometry maldi tof ms
Journal of Medical Microbiology, 2015Co-Authors: Somayeh Dolatabadi, Anna Kolecka, Matthijs Versteeg, Sybren De Hoog, Teun BoekhoutAbstract:This study addresses the usefulness of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS for reliable identification of the two most frequently occurring clinical species of Rhizopus, namely Rhizopus arrhizus with its two varieties, arrhizus and delemar, and Rhizopus microsporus. The test-set comprised 38 isolates of clinical and environmental origin previously identified by internal transcribed spacer (ITS) sequencing of rDNA. Multi-locus sequence data targeting three gene markers (ITS, ACT, TEF ) showed two monophylic clades for Rhizopus arrhizus and Rhizopus microsporus (bootstrap values of 99 %). Cluster analysis confirmed the presence of two distinct clades within Rhizopus arrhizus representing its varieties arrhizus and delemar. The MALDI Biotyper 3.0 Microflex LT platform (Bruker Daltonics) was used to confirm the distinction between Rhizopus arrhizus and Rhizopus microsporus and the presence of two varieties within the species Rhizopus arrhizus. An in-house database of 30 reference main spectra (MSPs) was initially tested for correctness using commercially available databases of Bruker Daltonics. By challenging the database with the same strains of which an in-house database was created, automatic identification runs confirmed that MALDI-TOF MS is able to recognize the strains at the variety level. Based on principal component analysis, two MSP dendrograms were created and showed concordance with the multi-locus tree; thus, MALDI-TOF MS is a useful tool for diagnostics of mucoralean species.
Sybren De Hoog - One of the best experts on this subject based on the ideXlab platform.
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differentiation of clinically relevant mucorales Rhizopus microsporus and r arrhizus by matrix assisted laser desorption ionization time of flight mass spectrometry maldi tof ms
Journal of Medical Microbiology, 2015Co-Authors: Somayeh Dolatabadi, Anna Kolecka, Matthijs Versteeg, Sybren De Hoog, Teun BoekhoutAbstract:This study addresses the usefulness of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS for reliable identification of the two most frequently occurring clinical species of Rhizopus, namely Rhizopus arrhizus with its two varieties, arrhizus and delemar, and Rhizopus microsporus. The test-set comprised 38 isolates of clinical and environmental origin previously identified by internal transcribed spacer (ITS) sequencing of rDNA. Multi-locus sequence data targeting three gene markers (ITS, ACT, TEF ) showed two monophylic clades for Rhizopus arrhizus and Rhizopus microsporus (bootstrap values of 99 %). Cluster analysis confirmed the presence of two distinct clades within Rhizopus arrhizus representing its varieties arrhizus and delemar. The MALDI Biotyper 3.0 Microflex LT platform (Bruker Daltonics) was used to confirm the distinction between Rhizopus arrhizus and Rhizopus microsporus and the presence of two varieties within the species Rhizopus arrhizus. An in-house database of 30 reference main spectra (MSPs) was initially tested for correctness using commercially available databases of Bruker Daltonics. By challenging the database with the same strains of which an in-house database was created, automatic identification runs confirmed that MALDI-TOF MS is able to recognize the strains at the variety level. Based on principal component analysis, two MSP dendrograms were created and showed concordance with the multi-locus tree; thus, MALDI-TOF MS is a useful tool for diagnostics of mucoralean species.
