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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND APPLICATION OF MOLECULAR PHYLOGENETICS OF FUNGI TO ENHANCE FOOD SAFETY AND FOOD SECURITY Title: An Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

item O`donnell, Kerry
item Sutton, Deanna -
item Rinaldi, Michael -
item Sarver, Brice A. -
item Balajee, S. Arunmozhi -
item Schroers, Hans-Josef -
item Summerbell, Richard -
item Robert, Vincent A. R. -
item Crous, Pedro -
item Zhang, Ning -
item Aoki, Takayuki -
item Jung, Kyongyong -
item Park, Jongsun -
item Lee, Yong-Hwan -
item Kang, Seogchan -
item Park, Bongsoo -
item Geiser, David -

Submitted to: Journal of Clinical Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 27, 2010
Publication Date: October 20, 2010
Citation: O Donnell, K., Sutton, D.A., Rinaldi, M.G., Sarver, B.J., Balajee, S., Schroers, H., Summerbell, R.C., Robert, V.G., Crous, P.W., Zhang, N., Aoki, T., Jung, K., Park, J., Lee, Y., Kang, S., Park, B., Geiser, D.M. 2010. An internet-accessible DNA sequence database for identifying Fusaria from human and animal infections. Journal of Clinical Microbiology. 48(10):3708-3718.

Interpretive Summary: In addition to being the single most important group of toxin producing plant pathogens, Fusarium species have emerged over the past three decades as one of the most important genera of filamentous fungi responsible for deeply invasive, opportunistic infections in humans. Infections in immunocompetent patients typically are superficial, or locally invasive such as sinusitis, pneumonia or diabetic cellulitis. In contrast, immunocompromised or immunosuppressed patients may acquire life-threatening fusarial infections associated with a high death rate. The high mortality of immunosuppresed patients is due in part to the broad resistance of most fusaria to the spectrum of antifungals currently available. A series of recent molecular studies have led to the important conceptual advance that morphological data greatly underestimates the diversity of Fusarium species causing infections of humans and other animals. This finding is not too surprising given that methods for identifying fusaria rely on relatively few morphological and cultural characters. Given the importance of fusaria to medicine, veterinary science and agriculture, we constructed an Internet accessible, three-locus database for accurately identifying and placing novel etiologic agents of fusarioses within a precise phylogenetic framework as they are encountered in the clinical microbiology laboratory. This Fusarium database will be incorporated into the web-accessible CBS-KNAW Fungal Biodiversity Center (, and the FUSARIUM-ID ( databases to facilitate global identifications via the Internet and to promote cooperation and coordination in documenting and sharing the diversity and occurrence of clinically relevant fusaria.

Technical 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 1a (EF-1a), 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 dataset 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 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 ( and the CBS-KNAW Fungal Biodiversity Center ( 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 cultures of novel mycosis-associated fusaria in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center), along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.

Last Modified: 12/1/2015
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