Most Fusarium species are soil fungi and have a worldwide distribution. Some are plant pathogens, causing root and stem rot, vascular wilt or fruit rot. Several species have emerged as important opportunistic pathogens in humans causing hyalohyphomycosis (especially in burn victims and bone marrow transplant patients), mycotic keratitis and onychomycosis (Guarro 2013). Other species cause storage rot and are important mycotoxin producers.
Multi-locus sequence analysis of EF-1α, β-tubulin, calmodulin, and RPB2 have revealed the presence of multiple cryptic species within each “morphospecies” of medically important fusaria (Balajee et al. 2009). For instance, Fusarium solani represents a complex (i.e. F. solani complex) of over 45 phylogenetically distinct species of which at least 20 are associated with human infections. Similarly, members of the Fusarium oxysporum complex are phylogenetically diverse, as are members of the Fusarium incarnatum-equiseti complex and Fusarium chlamydosporum complex (Balajee et al. 2009, Tortorano et al. 2014, Salah et al. 2015).
Currently the genus Fusarium comprises at least 300 phylogenetically distinct species, 20 species complexes and nine monotypic lineages (Balajee et al. 2009, O’Donnell et al. 2015). Most of the identified opportunistic Fusarium pathogens belong to the F. solani complex, F. oxysporum complex and F. fujikuroi complex. Less frequently encountered are members of the F. incarnatum-equiseti, F. dimerum and F. chlamydosporum complexes, or species such as F. sporotrichioides (O’Donnell et al. 2015, van Diepeningen et al. 2015).
Morphological Description: Colonies are usually fast growing, pale or bright-coloured (depending on the species) with or without a cottony aerial mycelium. The colour of the thallus varies from whitish to yellow, pink, red or purple shades. Species of Fusarium typically produce both macro- and microconidia from slender phialides. Macroconidia are hyaline, two to several-celled, fusiform to sickle-shaped, mostly with an elongated apical cell and pedicellate basal cell. Microconidia are one or two-celled, hyaline, smaller than macroconidia, pyriform, fusiform to ovoid, straight or curved. Chlamydospores may be present or absent.
Cultures of F. oxysporum showing purple pigmentation and F. subglutinans showing pink pigmentation.
- Fusarium chlamydosporum complex
- Fusarium dimerum complex
- Fusarium fujikuroi complex
- Fusarium incarnatum-equiseti complex
- Fusarium oxysporum complex
- Fusarium solani complex
Identification of Fusarium species is often difficult due to the variability between isolates (e.g. in shape and size of conidia and colony colour) and because not all features required are always well developed (e.g. the absence of macroconidia in some isolates after subculture). Note: Sporulation may need to be induced in some isolates and a good slide culture is essential. The important characters used in the identification of Fusarium species are as follows.
1. Colony growth diameters on potato dextrose agar and/or potato sucrose agar after incubation in the dark for four days at 25C.
2. Culture pigmentation on potato dextrose agar and/or potato sucrose agar after incubation for 10-14 days with daily exposure to light.
3. Microscopic morphology including shape of the macroconidia; presence or absence of microconidia; shape and mode of formation of microconidia; nature of the conidiogenous cell bearing microconidia; and presence or absence of chlamydospores.
Molecular Identification: Current species identification is on the basis of multilocus sequence data (Guarro 2013, O’Donnell et al. 2015, van Diepeningen et al. 2015). Internet-accessible validated databases dedicated to the identification of fusaria via nucleotide BLAST queries are available at FUSARIUM-ID at Pennsylvania State University (http://www.fusariumdb.org) and Fusarium MLST at the CBS-KNAW Fungal Biodiversity Centre (http://www.cbs.knaw.nl/Fusarium/).
For sequence-based identification of Fusarium species (O’Donnell et al. 2015).
1. Use EF-1α, RPB1 and/or RPB2. Use of at least two independent loci will increase the accuracy of identification.
2. Fusarium MLST or FUSARIUM-ID are the recommended sequence databases, rather than GenBank.
3. Ensure sequences are carefully edited and free of ambiguities.
4. Ensure the species names associated with the top BLASTn matches are the same. If multiple species names have similar scores it may be necessary to sequence additional loci.
Note: ITS and D1/D2 sequences are too conserved to resolve species limits of most fusaria. O’Donnell et al. (2015) recommend avoiding ITS or D1/D2 sequences from an unknown isolate to query GenBank, because >50% of the sequences from Fusarium species are misidentified in this database.
Identifications based on morphology and/or ITS and D1/D2 sequences should be reported as species complexes. Sequencing of EF-1α, RPB1 and/or RPB2 is required for accurate species identification.
MALDI-TOF MS: A comprehensive ‘in-house’ database of reference spectra allows accurate identification of Fusarium species complexes (Lau et al. 2013).
References: Booth (1971, 1977), Domsch et al. (1980), McGinnis (1980), Burgess and Liddell (1983), Rippon (1988), Samson et al. (1995), de Hoog et al. (2000, 2015), O’Donnell et al. (2008, 2009a, 2009b, 2015), Balajee et al. (2009), Guarro (2013), Geiser et al. (2013), van Diepeningen et al. (2015), Salah et al. (2015), Tortorano et al. (2014).