Sequence-based identification of Aspergillus, Fusarium
and Mucorales in the clinical mycology laboratory:
Where are we and where should we go from here?
Balajee SA, Borman AM, Brandt ME, Cano J, Cuenca-Estrella M,
Dannaoui E, Guarro J, Haase G, Kibbler CC, Meyer W,
O'Donnell K, Petti CA, Rodriguez-Tudela JL, Sutton D, Velegraki
A, Wickes BL
J Clin Microbiol 2008 Dec 10 [abstract on PubMed]
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Selected by | Susanne Perkhofer and Cornelia Lass-Floerl
Evaluated 16 Jan 2009
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Faculty Comments &
Author Responses
Faculty Member
Comments
Susanne Perkhofer
and
Cornelia LassFloerl
In my opinion, this article is interesting as it highlights the
advantages and limitations of species identification in
Aspergillus, Fusarium and the Mucorales by molecular methods.
The authors provide clear strategies to perform an ideal
identification.
University of Innsbruck,
Austria
Infectious Diseases
New Finding
The authors describe the need of comparative sequence
identification of fungi due to the fact that there is a change of
epidemiology of medically important fungi, a rise of novel
organisms causing diseases, and species-species differences in
antifungal susceptibilities of these fungi. The 'gold standard' to
identify fungal species is the comparative sequence-based
identification (ID). However, the authors state that the
appropriate locus has to be determined very carefully as the
gene target should be orthologous, with a high level of interspecies variation, low levels of intra-specific variation and
should not undergo recombination. The use of nuclear ribosomal
internal transcribed spacer region (ITS) sequencing is
recommended for subgenus/section level identification but
limitations arise for species identification within a given section
(e.g. discrimination of A. fumigatus from A. lentulus, both
section Fumigatus). The authors advise ITS locus sequencebased ID for identification of aspergilli, fusaria and mucorales.
In case of species/strain ID comparative sequence analysis of
protein coding regions should be used. This manuscript
describes the problems and manifoldness of molecular
identification of medically important fungi very clearly, and the
authors point out that many factors affect percent identity
scores including quality and length of query sequence and the
number and accuracy of existing GenBank records for the same
species and locus. In the end, it was a pleasure to have read
such an interesting article as new molecular techniques will be
an important step in making prompt diagnosis of fungal
infections.