Correlation of Oral Yeast Identification from Swish and Swab Samples

Objective: Cultures to diagnose oropharyngeal candidiasis (OPC) are commonly taken using oral swish and swab samples. Occasionally, swish samples are difficult to obtain from certain patients, yet swab samples may be collected. We compare the effectiveness of DNA isolation between swish and swab samples using a species specific Candida RT-PCR probe assay. Methods: DNA was extracted from a 2mL swish sample and a buccal swab taken from 85 HIV patients with OPC. The swish was pelleted by centrifugation and 500ul of Promega lysis buffer and 50ul of ProteinaseK with beads were added. Swabs were re-suspended in 500ul of buffer and 50ul of ProteinaseK with beads and vortexed for 30s. Both were bead beaten for 30s at maximum speed, and incubated 15min at 56°C. DNA from both supernatants was extracted in a magnetic bead automated system. RT-PCR was performed in an ABI/PRISM 7900 sequence detection system with MGB-probes specific for C.albicans, C.dublinensis, C.tropicalis, C.krusei, C.glabrata, and C.parapsilosis. Results: RT-PCR results of the swish samples showed 84/85 (99%) with C.albicans, 19/85 (22%) were C.dublinensis, 11/85 (13%) were C.glabrata, 6/85 (7%) were C.tropicalis, 2/85 (2%) were C.krusei, and 0/85 were C.parapsilosis. The concordance of swab compared to swish per patient was 71/84 (84%) in the C.albicans assay; 9/19 (47%) in the C.dublinensis, 6/11 (55%) with C.glabrata, 5/6 (83%) with C.tropicalis, 1/2 (50%) with C.krusei and no amplification was detected with C.parapsilosis. Conclusion: We have previously shown a high degree of correlation between RT-PCR identification of orally derived yeasts as compared to standard culture. We show that swabs were successful in isolating and correlating several Candida species, but did not compare favorably overall against the swish. Further studies need to be done in order to optimize the swab DNA extraction technique, swab type and storage conditions. Partial grant support from NIH-NIDCR: R01DE18096.