Strain-level typing of Candida albicans and Saccharomyces cerevisiae using Fourier transform infrared spectroscopy and whole-genome sequencing.

Rapid, low-cost strain-level typing is essential for source attribution and microbiological control in clinical and industrial settings. Fourier-transform infrared (FT-IR) spectroscopy using IR Biotyper method was previously optimized to achieve an identification level equivalent to that of whole-genome sequencing (WGS) discrimination of Wickerhamomyces anomalus. However, the species of yeast studied were limited; further, studies that have used the results of WGS as a reference for strain identification in yeast remain limited. Therefore, here, the generalizability of this approach to Candida albicans and Saccharomyces cerevisiae was assessed using publicly available whole-genome datasets as references. Single-nucleotide polymorphisms from 29C. albicans and 27 S. cerevisiae genomes were analyzed to build phylograms and select 5 and 4 mutually distant strains for FT-IR. FT-IR spectra were obtained after a standardized 24-h rotational culture in SD liquid medium, with three independent passages per strain. The same and similar strains clustered tightly, and different strains formed non-overlapping clusters; branches for the same and similar strains were < 0.1 on IR dendrograms, whereas branches for distinct strains were > 0.1. The discriminatory ability of FT-IR fully agreed with the WGS-based same/different classifications. Standardized liquid culture likely reduced cell-state heterogeneity, improving reproducibility. These results extend FT-IR strain typing beyond W. anomalus, providing a rapid, low-cost tool for contamination source attribution.