Fungicide applications in agriculture and medicine can promote the evolution
of resistant, pathogenic fungi, which is a growing problem for disease management
in both settings. Nonpathogenic mycobiota are also exposed to fungicides, may become
tolerant, and could turn into agricultural or medical problems, for example, due to climate
change or in immunocompromised individuals. However, quantitative data about fungicide
sensitivity of environmental fungi is mostly lacking. Aureobasidium species are widely
distributed and frequently isolated yeast-like fungi. One species, A. pullulans, is used as a
biocontrol agent, but is also encountered in clinical samples, regularly. Here, we compared
16 clinical and 30 agricultural Aureobasidium isolates based on whole-genome data and
by sensitivity testing with the 3 fungicides captan, cyprodinil, and difenoconazole. Our
phylogenetic analyses determined that 7 of the 16 clinical isolates did not belong to
the species A. pullulans. These isolates clustered with other Aureobasidium species, including
A. melanogenum, a recently separated species that expresses virulence traits that are
mostly lacking in A. pullulans. Interestingly, the clinical Aureobasidium isolates were significantly
more fungicide sensitive than many isolates from agricultural samples, which
implies selection for fungicide tolerance of non-target fungi in agricultural ecosystems.
Environmental microbiota are regularly found in clinical samples and
can cause disease, in particular, in immunocompromised individuals. Organisms of the
genus Aureobasidium belonging to this group are highly abundant, and some species
are even described as pathogens. Many A. pullulans isolates from agricultural samples
are tolerant to different fungicides, and it seems inevitable that such strains will eventually
appear in the clinics. Selection for fungicide tolerance would be particularly worrisome for
species A. melanogenum, which is also found in the environment and exhibits virulence
traits. Based on our observation and the strains tested here, clinical Aureobasidium isolates
are still fungicide sensitive. We, therefore, suggest monitoring fungicide sensitivity in species,
such as A. pullulans and A. melanogenum, and to consider the development of fungicide
tolerance in the evaluation process of fungicides.