Internet-accessible DNA sequence database for identifying fusaria from human and animal infections.
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.
O'Donnell
Kerry
K
Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL 61604-3999, USA. kerry.odonnell@ars.usda.gov
Sutton
Deanna A
DA
Rinaldi
Michael G
MG
Sarver
Brice A J
BA
Balajee
S Arunmozhi
SA
Schroers
Hans-Josef
HJ
Summerbell
Richard C
RC
Robert
Vincent A R G
VA
Crous
Pedro W
PW
Zhang
Ning
N
Aoki
Takayuki
T
Jung
Kyongyong
K
Park
Jongsun
J
Lee
Yong-Hwan
YH
Kang
Seogchan
S
Park
Bongsoo
B
Geiser
David M
DM
D000818:Animals; D016000:Cluster Analysis; D004271:DNA, Fungal / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D030561:Databases, Nucleic Acid; D005656:Fungal Proteins / Q000235:genetics; D005670:Fusarium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D005838:Genotype; D006801:Humans; D020407:Internet; D009172:Mycology / Q000379:methods*; D009181:Mycoses / Q000175:diagnosis* / Q000382:microbiology / Q000662:veterinary*; D020648:Peptide Elongation Factor 1 / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA
D004271:DNA, Fungal; D005656:Fungal Proteins; D020648:Peptide Elongation Factor 1; D012321:DNA-Directed RNA Polymerases; C113275:RNA polymerase alpha subunit; C105078:RNA polymerase beta subunit