Updated Genomic Epidemiologic Description of Candida (Candidozyma) auris, United States

The multidrug-resistant yeast Candida (Candidozyma) auris has caused several healthcare-associated outbreaks in the United States. We provide a genomic epidemiologic description of 1,535 C. auris isolates collected in the United States during 2013-2022. We identified clades I, II, III, and IV but not clades V or VI. Median pairwise single-nucleotide polymorphism distances indicated lower intraclade relatedness for clades I (91), III (43), and IV (43), compared with clade II (1,455). Phylogenetic analysis showed regional clusters with varying predominant clades. Of 809 isolates that underwent antifungal susceptibility testing, 53 were echinocandin resistant, distributed across 3 clades; 92% (49/53) had FKS1 hotspot mutations, which varied regionally. Our findings corroborate ongoing transmission and clonal expansion of C. auris, likely propagated by multiple introductions within and between geographic regions. Echinocandin resistance in multiple clades highlights the need to increase awareness, improve treatment practices, and engage in rapid public health response.