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Journal of Clinical Microbiology, August 2008, p. 2477-2490, Vol. 46, No. 8
0095-1137/08/$08.00+0     doi:10.1128/JCM.02371-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Molecular Phylogenetic Diversity, Multilocus Haplotype Nomenclature, and In Vitro Antifungal Resistance within the Fusarium solani Species Complex{triangledown}

Kerry O'Donnell,1* Deanna A. Sutton,2 Annette Fothergill,2 Dora McCarthy,2 Michael G. Rinaldi,2 Mary E. Brandt,3 Ning Zhang,4 and David M. Geiser5

Microbial Genomics and Bioprocessing Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois,1 Department of Pathology, University of Texas Health Science Center, San Antonio, Texas,2 Centers for Disease Control and Prevention, Atlanta, Georgia,3 Department of Plant Pathology, Cornell University, Geneva, New York,4 Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania5

Received 10 December 2007/ Returned for modification 17 April 2008/ Accepted 24 May 2008

Members of the species-rich Fusarium solani species complex (FSSC) are responsible for approximately two-thirds all fusarioses of humans and other animals. In addition, many economically important phytopathogenic species are nested within this complex. Due to their increasing clinical relevance and because most of the human pathogenic and plant pathogenic FSSC lack Latin binomials, we have extended the multilocus haplotype nomenclatural system introduced in a previous study (D. C. Chang, G. B. Grant, K. O'Donnell, K. A. Wannemuehler, J. Noble-Wang, C. Y. Rao, L. M. Jacobson, C. S. Crowell, R. S. Sneed, F. M. T. Lewis, J. K. Schaffzin, M. A. Kainer, C. A. Genese, E. C. Alfonso, D. B. Jones, A. Srinivasan, S. K. Fridkin, and B. J. Park, JAMA 296:953-963, 2006) to all 34 species within the medically important FSSC clade 3 to facilitate global epidemiological studies. The typing scheme is based on polymorphisms in portions of the following three genes: the internal transcribed spacer region and domains D1 plus D2 of the nuclear large-subunit rRNA, the translation elongation factor 1 alpha gene (EF-1{alpha}), and the second largest subunit of RNA polymerase II gene (RPB2). Of the 251 isolates subjected to multilocus DNA sequence typing, 191 sequence types were differentiated, and these were distributed among three strongly supported clades designated 1, 2, and 3. All of the mycosis-associated isolates were restricted to FSSC clade 3, as previously reported (N. Zhang, K. O'Donnell, D. A. Sutton, F. A Nalim, R. C. Summerbell, A. A. Padhye, and D. M. Geiser, J. Clin. Microbiol. 44:2186-2190, 2006), and these represent at least 20 phylogenetically distinct species. Analyses of the combined DNA sequence data by use of two separate phylogenetic methods yielded the most robust hypothesis of evolutionary relationships and genetic diversity within the FSSC to date. The in vitro activities of 10 antifungals tested against 19 isolates representing 18 species that span the breadth of the FSSC phylogeny show that members of this complex are broadly resistant to these drugs.

* Corresponding author. Mailing address: Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604-3999. Phone: (309) 681-6383. Fax: (309) 681-6672. E-mail: kerry.odonnell{at}ars.usda.gov

{triangledown} Published ahead of print on 4 June 2008.

Journal of Clinical Microbiology, August 2008, p. 2477-2490, Vol. 46, No. 8
0095-1137/08/$08.00+0     doi:10.1128/JCM.02371-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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