NDLI: Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections ▿

Content Provider	PubMed Central
Author	O'donnell, Kerry Sutton, Deanna A. Rinaldi, Michael G. Sarver, Brice A. J. Balajee, S. Arunmozhi Schroers, Hans-josef Summerbell, Richard C. Robert, Vincent A. R. G. Crous, Pedro W. Zhang, Ning Aoki, Takayuki Jung, Kyongyong Park, Jongsun Lee, Yong-hwan Kang, Seogchan Park, Bongsoo Geiser, David M.
Copyright Year	2010
Abstract	Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.
Related Links	http://dx.doi.org/10.1128/jcm.00989-10
Ending Page	3718
Page Count	11
Starting Page	3708
File Format	PDF
ISSN	00951137
e-ISSN	1098660X
Journal	Journal of Clinical Microbiology
Issue Number	10
Volume Number	48
Language	English
Publisher	American Society for Microbiology (ASM)
Publisher Date	2010-10-01
Access Restriction	Open
Rights Holder	American Society for Microbiology (ASM)
Subject Keyword	Microbiology (medical) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Microbiology (medical)

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