Progress 10/01/04 to 09/30/09
Outputs
OUTPUTS: The major outcome of this project is the FUSARIUM-ID DNA sequence identification database (http://isolate.fusariumdb.org/index.php). This free resource allows users to identify Fusarium isolates using DNA sequence data by comparing the sequence from an unknown with those of vouchered, publicly available isolates. The database has been updated to include many additional features, including multilocus identification, strain information, downloadable datasets, sequence alignments and phylogenetic trees produced on the fly, and other features. The genotypic data were published in collaborative molecular phylogenetic studies that have clarified the taxonomy and phylogenetic relationships of a broad array of Fusarium species, including plant, human and animal pathogens, and major toxin producers. PARTICIPANTS: David M. Geiser, Professor of Plant Pathology, Penn State; Principal investigator. Jean H. Juba, Research Support Technologist, Penn State, assisted in culture curation and DNA sequence analyses. Seogchan Kang, Professor of Plant Pathology, Penn State, database design and development. Gretchen Kuldau, Associate Professor of Plant Pathology, Penn State, Mycotoxins. Kerry ODonnell and Todd Ward, ARS Scientists, USDA/NRRL, Peoria, IL, collaborator on molecular phylogenetic and population genetics studies on Fusarium; the source of most of the DNA sequence data in FUSARIUM-ID. F.A. Nalim and Dylan Short, Ph.D. students and Michele Mansfield, postdoc, Penn State, contributed data and phylogenetics work. Bob McGovern, University of Florida, Wade Elmer, Connecticut State Experiment Station, collaborator on Fusarium diseases on ornamentals. Mohammed Kahn, Bob Secor, North Dakota State, Linda Hanson, USDA/ARS, East Lansing, MI, collaborator on sugarbeet fusaria. H. J. Schroers, Slovenia, collaborator on F. dimerum. Quirico Migheli and Virgilio Balmas, Department of Plant Protection, University of Sassari, Italy, collaborator on Sardinian soil Fusarium. Sally Miller, Ohio State; Georgina Hakiza, Coffee Research Institute, Uganda; collaborators on coffee wilt disease. Brien David and Pramod Gupta, Bausch & Lomb, Inc. collaborators on indoor environmental Fusarium. John Leslie, Kansas State, Annual Fusarium Laboratory Workshop. Workshop participants are taught DNA identification methods using FUSARIUM-ID. Financial support:USDA/NRI, USDA/CSREES, Bausch & Lomb. Education and training: Geiser is usually an instructor in the annual Fusarium Laboratory workshops covering DNA sequence based identification methods that are the purview of this project. TARGET AUDIENCES: The target audience for this research is anyone who is faced with the task of identifying an unknown Fusarium isolate (plant pathologists, clinical and veterinary pathologists, indoor air specialists, food scientists, industrial microbiologists, biotechnology researchers, APHIS, CDC and other quarantine and epidemiological personnel) anywhere in the world. The underlying molecular phylogenetic work forms an important part of the expanding fabric of knowledge about evolutionary relationships in fungi. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
DNA sequence data are quickly becoming the primary tool for identifying unknown fungi. Major national and international efforts to (Barcode) the fungi are underway, mostly utilizing the internal transcribed spacer (ITS) regions of the ribosomal RNA genes as DNA markers. Because of the advanced state of molecular phylogenetics in the genus Fusarium, we were able to initiate a fairly comprehensive barcoding tool in 2004, utilizing a marker locus with much more resolving power than ITS, elongation factor 1-alpha. Since we made this tool available via the web that year, it has become a key resource for the many clinical pathologists and other scientists faced with the famously daunting task of identifying Fusarium isolates to species. Unlike GenBank, which contains many sequences that are incorrectly annotated and are attached to germplasm that is not available for comparison, all sequences in the FUSARIUM-ID database are attached to cultures that are available to authorized researchers. This has led to FUSARIUM-ID becoming a go-to resource for the molecular identification of unknown Fusarium isolates.
Publications
- Schroers, H.J., K. O'Donnell, S.C. Lamprecht, P.L. Kammemeyer, S. Johnson, D.A. Sutton, M.G. Rinaldi, D.M. Geiser, and R.C. Summerbell. 2009. Taxonomy and phylogeny of the Fusarium dimerum species group. Mycologia 101:44-70.
- Nalim, F.A., W.H. Elmer, R.J. McGovern, and D.M. Geiser. 2009. Multilocus phylogenetic diversity of Fusarium avenaceum pathogenic on lisianthus. Phytopathology 99:462-468.
- Rivera, V., J. Rengifo, M. Khan, D.M. Geiser, M. Mansfield, and G. Secor. 2008. First report of a novel Fusarium species causing yellowing decline of sugar beet in Minnesota. Plant Disease 92:1589-1589.
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Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: New steps were taken toward our goal to create a comprehensive multilocus DNA sequence database for Fusarium. Our current database, FUSARIUM-ID, consists of translation elongation factor 1-alpha sequences from vouchered cultures that can be used for identification purposes. A comprehensive database of sequences from the RNA polymerase II subunit RPB2 for Fusarium now exists, that will be added to the database in late 2008. A new database platform derived from the Phytophthora database (phytophthoradb.org) has been established and the identification database will be solely housed there. Efforts were contributed to the establishment of a sequence database of over 2000 isolates of Fusarium Head Blight species, leading to the discovery of an adaptive shift in populations across Canada. PARTICIPANTS: David Geiser: Directed research performed. Jean Juba: Research Technologist. Cultured fungi, performed morphological and molecular identifications. Collaborators: Kerry O'Donnell, USDA/ARS (shared molecular data for database), Seogchan Kang, Penn State (developed database structure). TARGET AUDIENCES: Plant disease diagnosticians, plant quarantine pathogen identifiers, medical and veterinary clinical diagnosticians, plant pathologists, molecular ecologists PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The use of DNA sequence tools to identify Fusarium species is now in the mainstream, and a standard of good science. The FUSARIUM-ID database is in high demand as an identification tool, because unlike GenBank, all of the sequences within it are attached to expertly identified cultures. It is important, however, to expand the database and to add new features, including data from more isolates within species, more loci, and additional analytical tools. Our work in the last year has been focused on these new features, which will lead to a more user-friendly and practical research tool.
Publications
- O'Donnell, K., D.A. Sutton, A. Fothergill, D. McCarthy, M.G. Rinaldi, M.E. Brandt, N. Zhang, and D.M. Geiser. 2008. Molecular phylogenetic diversity, multilocus haplotype nomenclature and in vitro antifungal resistance within the Fusarium solani species complex. J. Clin. Microbiol. 46:2477-2490.
- Ward, T.J., R.M. Clear, A.J. Rooney, K. O'Donnell, D. Gaba, S. Patrick, D.E. Starkey, J. Gilbert, D.M. Geiser, and T. Nowicki. 2007. An adaptive evolutionary shift in Fusarium head blight pathogen populations is driving the rapid spread of more toxigenic Fusarium graminearum in North America. Fungal Genetics and Biology. 45:473-484.
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: A major, long-term goal is to create a comprehensive multilocus DNA sequence database for the genus Fusarium, which will be useful for the identification of known pathogenic species, the discovery of new pathogens, and surveillance of the global dynamics of pathogens. Efforts were contributed to the establishment of a sequence database of over 2000 isolates of Fusarium Head Blight species, leading to the discovery of new species with novel toxin chemotypes. On the clinical front, contributions were made toward a DNA sequence database of isolates from clinical infections. Current translation elongation factor 1-alpha DNA sequence databases serve as tools for identification, and aided in the discovery of Fusarium oxysporum on roselle in the United States.
PARTICIPANTS: David Geiser (project leader), Dylan Short (grad student), Michele Mansfield (postdoc), Jean Juba (Research Technologist III).
TARGET AUDIENCES: Government, Industry and Academic Researchers.
Impacts
With a comprehensive database of over 2000 isolates of Fusarium species associated with head blight having been released [1], it is now possible to monitor the dynamics of Fusarium species globally, to identify novel pathogens as they arise and to characterize the population dynamics of known species. Fusarium infections of humans are an increasing problem, particularly in immunosuppressed patients undergoing transplant therapies. We now have comprehensive sequence databases of most species associated with human infections [2]. As we continually utilize DNA sequence tools to identify isolates associated with plant and human diseases and toxicoses [3], more and more data are being added.
Publications
- Starkey, D.E., et al. 2007. Global molecular surveillance reveals novel Fusarium head blight species and trichothecene toxin diversity. Fungal Genetics and Biology 44(11):1191-1204.
- O'Donnell, K., et al. 2007. Phylogenetic diversity and microsphere array-based genotyping of human pathogenic fusaria, including isolates from the multistate contact lens - Associated US Keratitis outbreaks of 2005 and 2006. Journal of Clinical Microbiology 45(7):2235-2248.
- Ploetz, R.C., et al. 2007. First report of Fusarium wilt caused by Fusarium oxysporum on roselle in the United States. Plant Disease 91(5):639-639.
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Progress 01/01/06 to 12/31/06
Outputs
Members of the Fusarium solani species complex (FSSC) are increasingly implicated as the causative agents of human mycoses, particularly in the expanding immunocompromised and immunosuppressed patient populations. Best known as ubiquitous plant pathogens and saprotrophs, the FSSC comprises over 45 phylogenetically distinct species distributed among three major clades. To identify which species are associated with human infections, we generated multilocus haplotypes based on four partial gene sequences from 471 isolates. Of these, 278 were from human patients, 21 from hospital environments, and 172 from non-clinical sources. Phylogenetic trees inferred from an ergosterol biosynthesis gene (erg-3) were highly discordant with those inferred from the three other partial gene sequences; therefore, this partition was analyzed separately. Multilocus analysis showed that isolates from humans were restricted to but spread throughout clade 3 of the FSSC phylogeny, comprising at
least 18 phylogenetically distinct species. The majority (74.5%) of the clinical isolates, however, were associated with four major lineages designated Groups 1-4. Groups 1 and 2 were strongly supported as phylogenetic species, whereas Groups 3 and 4 were not. Although isolates from ocular infections were found in all four groups, they had a significant tendency to belong to Group 3 (P<0.001). Human clinical isolates shared identical multilocus haplotypes with isolates from plants, other animals, and from hospital environments, suggesting potential nosocomiality. The major finding of this study is that FSSC-associated mycoses of humans and other animals have origins in a broad phylogenetic spectrum, indicating widespread ability to cause infection in this diverse species complex.
Impacts
Fusarium infections of humans are an increasing problem, particularly in immunosuppressed patients undergoing transplant therapies. In this work we identified and characterized the spectrum of fungi in the F. solani complex associated with infections. The results strongly indicated a connection between isolates involved in human infection and isolates common in the environment. The DNA sequence database compiled in this work allowed for the quick and accurate identification of pathogens associated with the 2006 outbreak of Fusarium corneal infections, and played a key role in the development of an infection model.
Publications
- Zhang, N., ODonnell, K., Sutton, D.A., Nalim, F.A., Summerbell, R.C., Padhye, A.A., and Geiser, D.M. 2006. Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment. J. Clin. Microbiol. 44: 2186-2190.
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Progress 01/01/05 to 12/31/05
Outputs
Tracheomycosis or coffee wilt has emerged as a major disease of robusta coffee in Uganda in the last ten years. Coffee wilt historically has been associated with Fusarium xylarioides Steyaert (teleomorph Gibberella xylarioides Heim and Sacc.), a species that has been classified as a member of Fusarium section Lateritium. We investigated the molecular phylogenetics of fusarial coffee wilt isolates by generating partial DNA sequences from two protein coding regions, translation elongation factor 1-alpha (tef) and beta-tubulin (benA), in 36 isolates previously identified as F. xylarioides and related fusaria from coffee and other woody hosts, as well as from twelve isolates associated with a current coffee wilt outbreak in Uganda. These isolates fell into two morphologically and phylogenetically distinct groups. The first group was found to represent previously unidentified members of the Gibberella fujikuroi species complex (GFC), a clade that replaces the artificial
Fusarium section Liseola. This group of isolates fits the original description of F. xylarioides, thus connecting it to the GFC. The second group, which was diverse in its morphology and DNA sequences, comprised four distinct lineages related to Fusarium lateritium. One of F. xylarioides' close relatives within the GFC, F. udum, also causes vascular wilt diseases of woody hosts. Our finding of unrelated species associated with coffee wilt disease has important implications regarding its epidemiology, etiology and control.
Impacts
We used phylogenetics to clear up decades of confused systematics of this fungus, which is causing devastating damage to coffee production in East Africa. Knowledge that the true pathogen is a member of the GFC opens up the possibility of comparing it to other pathogens in that group, including F. verticillioides, F. proliferatum and F. circinatum, and potentially utilizing genomics tools from these well-studied fungi to develop F. xylarioides as a genetic system. In addition, it clarifies the role of Lateritium clade isolates in the disease as probably secondary invaders, rather than as the primary pathogens in this complex disease.
Publications
- Geiser, D. M., Lewis Ivey, M. L., Hakiza, G., Juba, J. H. and Miller, S. A. 2005. Gibberella xylarioides (anamorph: Fusarium xylarioides), a causative agent of coffee wilt disease in Africa, is a previously unrecognized member of the G. fujikuroi species complex. Mycologia 97:191-201.
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