Applications of single-cell RNA sequencing in fungal infections

Fungal infection elicits markedly different cellular responses depending on the pathogen, tissue involved, host immune status, and stage of disease. Bulk measurements capture broad changes but can obscure the cell populations associated with fungal control, persistence, or tissue injury. Single-cell RNA sequencing (scRNA-seq) offers a way to resolve this heterogeneity, although fungal infection studies remain uneven in both technical feasibility and disease coverage. We review evidence from cutaneous, mucosal, pulmonary, central nervous system, and systemic infections, with attention to tissue context, experimental design, and the strength of supporting validation. Across these studies, myeloid, lymphoid, epithelial, and stromal compartments show substantial remodeling, yet similarly named cell states do not necessarily have equivalent functions in different tissues or infections. Direct fungal single-cell studies are fewer, but they reveal variation in developmental stage, morphogenesis, stress responses, and responses to antifungal exposure. Most evidence still centers on Candida, whereas studies of Aspergillus, Cryptococcus, Pneumocystis, Coccidioides, and chronic cutaneous mycoses remain restricted to particular models or sample types. Interpretation is complicated by dissociation-related bias, unequal cell recovery, sparse fungal RNA, cross-species mapping, and small human cohorts. Spatial and functional validation are therefore important for distinguishing transcriptional associations from mechanisms. At present, single-cell approaches are most useful for defining context-dependent states and generating mechanistic questions; broader clinical application will require standardized sampling, independent validation, and scalable assays.