Profound cell wall remodeling in <i>Candida parapsilosis</i> during systemic infection confers simultaneous tolerance to echinocandins and host immunity

Antifungal tolerance can promote the emergence of resistance yet often incurs fitness costs for fungal pathogens. How tolerant populations compensate for these deficits and how they may be therapeutically targeted remain poorly understood. Here, we investigate four sequential <i>Candida parapsilosis</i> isolates recovered from a patient with persistent candidemia and failure of micafungin therapy. The infection was ultimately cleared with liposomal amphotericin B (LAMB). Whole-genome sequencing (WGS) confirmed clonal relatedness and the absence of known resistance mutations. Later isolates displayed marked cell wall remodeling (CWR), characterized by increased mannan and reduced β-glucan content, as revealed by microscopy and solid-state nuclear magnetic resonance. These isolates formed thicker biofilms and displayed enhanced echinocandin tolerance but paradoxically showed increased susceptibility to amphotericin B (AMB) <i>in vitro</i> and during systemic infection in mice. Despite a complex mutational landscape, transcriptomic profiling across planktonic and biofilm growth showed minimal divergence from the earliest isolate. Functionally, evolved isolates suppressed M1 macrophage polarization, dampened proinflammatory cytokine production, survived better during neutrophil interactions, and transiently increased fungal burden <i>in vivo</i>. These findings show that host-driven CWR could promote echinocandin tolerance while simultaneously sensitizing <i>C. parapsilosis</i> to AMB. Our results suggest that alternating echinocandin and LAMB therapy may effectively eliminate echinocandin-tolerant fungal populations.IMPORTANCEAntifungal tolerance is increasingly recognized as a precursor to resistance, yet its clinical and biological consequences remain poorly defined. By analyzing sequential <i>Candida parapsilosis</i> isolates from a case of persistent candidemia, we show that cell wall remodeling is associated with echinocandin tolerance, alters host immune interactions, and increases susceptibility to amphotericin B (AMB). These findings reveal how tolerance-associated adaptations shape pathogen fitness during infection and highlight the therapeutic potential of alternating echinocandin and AMB therapy. This work advances our understanding of antifungal tolerance and suggests that exploiting opposing drug susceptibilities may improve treatment outcomes for challenging-to-treat <i>Candida</i> infections.