Clinical Aureobasidium Isolates Are More Fungicide Sensitive than Many Agricultural Isolates

Abstract

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. IMPORTANCE 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.

Keywords: Aureobasidium; fungicide resistance.

FIG 1

SNP-based phylogeny of 46 Aureobasidium strains from agricultural and clinical samples. Many clinical Aureobasidium isolates cluster more closely with other Aureobasidium species than with A. pullulans. As references, the analysis included 5 genomes of the 4 Aureobasidium species A. pullulans (NBB 7.2.1 and EXF-150), A. namibiae (EXF-3398), A. melanogenum (CBS 110374), and A. subglaciale (EXF-2481) (7, 15). The x axis represents the relative distances between the taxa. The x axis is discontinuous, as is indicated by the double line to fit the taxa of the genetically distant cluster 1. The numbers of the branches indicate bootstrap values of 100 bootstrap replicates and values <90 are not shown.

FIG 2

Clinical Aureobasidium isolates are more sensitive to captan, cyprodinil, and difenoconazole than many agricultural isolates. Boxplot of the MIC₅₀ values (log₂) for each group of isolates derived from the phylogenetic tree and for the 3 fungicides captan (CAN), cyprodinil (CYP), and difenoconazole (DFN). For 2 isolates that were not controlled at the maximum CYP concentration, 128 μg/mL (the highest concentration tested) was set as the MIC50 value. Different letters indicate statistical significance based on the Dunn’s-Test (P_adj ≤ 0.05).