Candida auris on Apples: Diversity and Clinical Significance

Abstract

Candida auris is a multidrug-resistant nosocomial fungal pathogen. While the marine environment was recently identified as a natural niche for C. auris, the environment(s) that might have contributed to the development and spread of antifungal resistance in C. auris remains a mystery. Because stored fruits are often treated with fungicides to prevent postharvest spoilage, we hypothesized that stored fruits could serve as a possible selective force for and a transmission reservoir of antifungal-resistant isolates of pathogenic yeasts, including C. auris. To test this hypothesis, we screened fruits to study the diversity of pathogenic yeasts and their antifungal susceptibility profiles. Among the 62 screened apples, the surfaces of 8 were positive for C. auris, and all were stored apples. Whole-genome sequencing (WGS) showed that C. auris strains from apples were genetically diverse and exhibited broad phylogenetic distribution among the subclades within clade I. Interestingly, strains from apples had closely related strains from other sources in India, including from patients, hospitals, and marine environments, and from clinical strains from other parts of the world. A broad range of fungicides, including dimethyl inhibitors (DMIs), were detected in stored apples, and all C. auris isolates exhibited reduced sensitivity to DMIs. Interestingly, C. auris was not isolated from freshly picked apples. Together, the results suggest a potentially complex ecology for C. auris with agriculture fungicide application on stored fruits as a significant selective force for drug resistance in clinics. IMPORTANCE In 2019, the U.S. Centers for Disease Control and Prevention classified the multidrug-resistant Candida auris as one of five pathogens posing the most urgent threats to public health. At present, the environment(s) that might have contributed to the development and spread of antifungal resistance in C. auris is unknown. Here, we tested whether fruits could be a source of multidrug-resistant C. auris. We identified genetically diverse C. auris strains with reduced sensitivity to major triazole dimethyl inhibitors fungicides on the surfaces of stored apples. The successful isolation of C. auris from apples here calls for additional investigations into plants as a reservoir of C. auris. Our findings suggest that C. auris in the natural ecosystem may come in contact with agriculture fungicides and that stored fruits could be a significant niche for the selection of azole resistance in C. auris and other human fungal pathogens.

Keywords: C. auris ecology; agriculture azoles; cross-resistance; dimethyl inhibitors; fungicides; natural environment.

FIG 1

Scatterplot depicting MIC (mg/L) distribution of two DMIs, (A) tebuconazole and (B) flusilazole, against C. auris strains from surfaces of apples (CasSA, n = 16), 25 fluconazole-susceptible clinical strains (MIC, <16 mg/L) and 25 fluconazole-resistant clinical strains (MIC >32 mg/L).

FIG 2

Maximum-likelihood phylogenetic tree of 60 C. auris strains was constructed by using RAxML v8.0.25. Included in the tree are 16 C. auris strains from surfaces of apples (CasSA), 13 environmental strains from Andaman Islands, India, and 30 Indian clinical strains along with reference strain, B8441. The tree was constructed based on the 1,281 shared SNPs among the 59 strains. Branches with bootstrap support over 75% of 100 bootstrap iterations are labeled with red markers. CasSA were highlighted in red and clustered in 5 subclusters (A to E).

FIG 3

Maximum-likelihood phylogenetic tree showing the relationships among 503 clade I Candida auris isolates from around the globe. The isolates’ relationships were inferred based on their whole-genome single nucleotide polymorphisms. Here, based on their branch lengths and bootstrap support values, the 503 isolates were further classified into 7 subclades, including three major subclades (subclade I-1, subclade I-2, and subclade I-3), with subclade I-3 containing five more recently derived ones (subclades I-3a, I-3b, I-3c, I-3d, and I-3e). Isolates within each subclade are highlighted with the same background color over the isolate identifications. The color strip outside the isolate identification indicates the country of origin for each isolate. In addition, isolates from India are highlighted with red squares. Furthermore, the isolates from apples in India are marked with blue stars, placed adjacent to their red square labels. Branch lengths are proportional to the number of SNP differences among strains. Branches in magenta have a bootstrap support above 75%.

FIG 4

Maximum clade credibility phylogenetic tree of 16 CasSA isolated in the present study, and 43 previously published Indian C. auris strains from both clinical and natural marine environments along with clade I reference strain B8441.

FIG 5

Schematic representation of stored apples as a possible reservoir of selection and transmission of azole-resistant C. auris.