CanID-PCR: A quick and low-cost PCR tool to identify Candida species on gDNA directly extracted from positive blood bottles

Candida bloodstream infection carries a high mortality. Candida species prone to antifungal resistance (e.g. C. auris and C. glabrata) are rising, and delay in species identification might adversely affect patients outcomes. Current workflow by clinical microbiology laboratory requires [~]24 hours for Candida speciation, time to allow for growth of isolates on the agar plates for testing. We established a simple and inexpensive PCR tool, named CanID-PCR, to speciate Candida directly from positive blood bottles. We selected Candida ACT1 gene, which has an intron with varying length that enables the identification of 10 common Candida species. The tool was optimized for gDNA extracted directly from positive blood culture bottles. We showed, by testing positive blood cultures from 64 unique patients, that our tool detects the same species as the microbiology lab in 97% (62/64) of samples. The 2 samples with mismatched results were due to high similarity between Candida metapsilosis and C. parapsilosis, and failure of CanID-PCR to identify C. tropicalis in a patient with C. albicans/C. tropicalis fungemia. On the other hand, CanID-PCR identified a second species (C. fabianii) in a patient with C. parapsilosis fungemia that was missed by the microbiology laboratory. In conclusion, our inexpensive tool was accurate for rapid speciation of Candida directly from blood culture bottles, which could be valuable for clinical and/or research laboratories.