Dual colored phenotypic switching and interaction-driven heterogeneity in clonal Candida auris clinical isolates.

Candida auris is an emerging multidrug-resistant pathogen designated by the World Health Organization as a critical priority due to its persistence, transmissibility, and association with healthcare outbreaks. Despite its clinical significance, the contribution of phenotypic heterogeneity to pathogenicity and treatment response remains poorly understood. In this study, we identified dual white (W) and pink (P) morphotypes in seven of 278 clinical isolates screened on CHROMagar™ Candida Plus and characterized their genetic relatedness, antifungal susceptibility, and phenotypic switching behavior. Whole-genome sequencing and internal transcribed spacer (ITS) analyses confirmed that paired morphotypes were clonally related (0-57 SNPs divergence) and belonged to Clade I, indicating within-host diversification rather than co-infection with distinct strains. All isolates carried identical ERG11 Y132F mutations and wild-type FKS1 sequences across both morphotypes, demonstrating that morphotype variation occurs independently of primary antifungal resistance determinants. Phenotypic profiling demonstrated comparable resistance profiles and aggregation capacity between paired morphotypes, with pseudohyphal formation as the principal differential trait. Systematic switching analysis across CHROMagar, yeast peptone dextrose (YPD), and sabouraud dextrose agar (SDA) under multiple temperature and population conditions identified three principal patterns: interaction-dependent switching, in which mixed subpopulations generated enhanced or novel phenotypes not reproduced in pure cultures; morphotype-driven switching, dominated by a single subpopulation; and intrinsic switching capacity retained independently by both morphotypes. Switching dynamics were strongly modulated by temperature, growth medium, and incubation duration. These findings establish phenotypic switching in C. auris as a dynamic, environmentally modulated process driven in part by intercellular interactions within clonal populations. This plasticity may contribute to persistence and virulence without altering antifungal resistance profiles, underscoring the need to recognize and separately evaluate distinct C. auris morphotypes for antifungal susceptibility, particularly in persistent or treatment-refractory infections.