Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples
D'Andreano, Sara (Universitat Autònoma de Barcelona. Vetgenomics)
Cuscó, Anna (Universitat Autònoma de Barcelona. Vetgenomics)
Francino, Olga (Universitat Autònoma de Barcelona. Servei Veterinari de Genètica Molecular (SVGM))

Data:	2020
Resum:	The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5. 8S-ITS2-28S) and to improve the taxonomy assignment of the communities up to species level and in real-time. We assess the applicability for taxonomic assignment of amplicons targeting a 3. 5 Kb region (V3 18S-ITS1-5. 8S-ITS2-28S D2) and a 6 Kb region (V1 18S-ITS1-5. 8S-ITS2-28S D12) with the What's in my pot (WIMP) classifier. We used the ZymoBIOMICS TM mock community and different microbiological fungal cultures as positive controls. Long amplicon sequencing correctly identified Saccharomyces cerevisiae and Cryptococcus neoformans from the mock community and Malassezia pachydermatis, Microsporum canis and Aspergillus fumigatus from the microbiological cultures. Besides, we identified Rhodotorula graminis in a culture mislabelled as Candida spp. We applied the same approach to external otitis in dogs. Malassezia was the dominant fungal genus in dogs' ear skin, whereas Ma. pachydermatis was the main species in the healthy sample. Conversely, we identified a higher representation of Ma. globosa and Ma. sympodialis in otitis affected samples. We demonstrate the suitability of long ribosomal amplicons to characterize the fungal community of complex samples, either healthy or with clinical signs of infection.
Nota:	Ajuts: Generalitat de Catalunya 2015DI044 i Vetgenomics.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Fungi ; Nanopore ; Ribosomal operon ; Malassezia ; Otitis ; Dog
Publicat a:	Biology Methods & Protocols, Vol. 6 (december 2020) , ISSN 2396-8923

DOI: 10.1093/biomethods/bpaa026
PMID: 33506108

6 p, 282.5 KB

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