DESCRIPTIONS OF MEDICAL FUNGI

Descriptions of Medical Fungi
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PREFACE
Molecular and/or MALDI-TOF MS Identification: The use of PCR-based assays, DNA
sequencing, and other molecular methods, including those incorporating proteomic
approaches such as matrix assisted laser desorption ionization time of flight mass
spectroscopy (MALDI-TOF MS) have shown promising results to aid in accurate species
identification of fungal cultures. These are used mainly to complement conventional
methods since they require standardisation before widespread implementation can be
recommended (Halliday et al. 2015). Molecular-based fungal identification is particularly
helpful for fungi that lack distinguishing morphological features, e.g. Apophysomyces
elegans, or to distinguish between species of the Aspergillus fumigatus complex.
Comparative sequence analysis is now the ‘gold standard’ for identification of fungi.
Methods are referenced where available and in many instances are recommended for
more definitive identifications.
Schematic diagram of the fungal rDNA gene cluster (adapted from CLSI MM18-A
and Halliday et al. 2015). The 18S, 5.8S and 28S rDNA genes are separated by the
two internal transcribed spacers. The 28S and 5S rDNA genes are separated by the
intergenic spacer 1 (IGS1). The intergenic spacer 2 (IGS2) separates the rDNA repeat
units from each other.
Regardless of the genetic locus selected, accurate sequence-based identification is
dependent upon database accuracy and adequate species representation. GenBank
is well known to contain numerous errors in sequences and the species names
attributed to the sequences, which are rarely corrected. Therefore caution must be
used when interpreting sequencing comparisons against this database, and the use of
multiple sequence databases is encouraged. Well-curated databases that are helpful
for species identification include:
1. International Society for Human and Animal Mycoses (ISHAM) ITS database (http://
its.mycologylab.org/).
2. CBS-KNAW Fungal Biodiversity Centre database (http://www.cbs.knaw.nl).