Pathogenic Budding Yeasts Isolated outside of Clinical Settings

Abstract

9Budding yeasts are distributed across a wide range of habitats, including as human 10 commensals. However, under some conditions, these commensals can cause superficial, 11 invasive, and even lethal infections. Despite their importance to human health, little is known 12 about the ecology of these opportunistic pathogens, aside from their associations with 13 mammals and clinical environments. During a survey of approximately 1000 non-clinical 14 samples across the United States of America, we isolated 54 strains of budding yeast species 15 considered opportunistic pathogens, including Candida albicans and Candida (Nakaseomyces) 16glabrata. We found that, as a group, pathogenic yeasts were positively associated with fruits 17 and soil environments, while the species Pichia kudriavzevii (syn. Candida krusei syn. 18 Issatchenkia orientalis) had a significant association with plants. These results suggest that 19 pathogenic yeast ecology is more complex and diverse than is currently appreciated and raises 20 the possibility that these additional environments could be a point of contact for human 21 infections. 127 We thank the following citizen scientists or lab members for collecting samples or 128 generating preliminary results:

Diverse Lineages ofCandida albicansLive on Old Oaks

“…For example, three surveys of trees did not discover C. albicans but reported the isolation of other Candida species, and therefore could have detected C. albicans if it were present (Maganti et al 2011; Charron et al 2014; Sylvester et al 2015). More recently, a larger survey did yield several C. albicans strains on fruit, soil, and plant matter in northern North America (Opulente et al . 2018), so the lack of C. albicans environmental isolates could be due to a lack of past sampling effort.…”

Signatures of optimal codon usage predict metabolic ecology in budding yeasts

“…Only two species were found in human-associated niches and not insectassociated niches, Debaryomyces subglobosus and Cephaloascus fragrans; thus, we combined the human-associated species with the human-and insect-associated species into one group for subsequent analyses. Recent work has shown that many opportunistically pathogenic budding yeasts are likely to be associated with both environmental and human niches [94]. The 13 CUG-Ser1 species isolated from humans with genome-wide evidence of selection on codon usage had a mean optimization of 0.74, 0.76, and 0.69 for GAL1, GAL10, and GAL7, respectively.…”

“…This observation is particularly interesting given the hypothesis that some features of saprophytic fungi, such as Aspergillus fumigatus and Cryptococcus spp., enable or predispose them to colonize human hosts [103,104]. Moreover, some pathogenic budding yeasts, including C. albicans and C. tropicalis, have recently been associated with soil [94]. Figure 3 -Codon optimization in the GAL pathway is correlated with specific ecological niches in two different major clades of budding yeasts.…”