Candida auris Direct Detection from Surveillance Swabs, Blood, and Urine Using a Laboratory-Developed PCR Method

Abstract

Candida auris is an emerging fungal pathogen with cases reported in countries around the world and in 19 states within the United States as of August 2020. The CDC has recommended that hospitals perform active surveillance upon admission for patients with the appropriate risk factors. Currently, active surveillance requires that local hospitals send surveillance swabs to a public health laboratory for analysis. In this work, a real-time PCR assay was developed for the specific detection of C. auris from surveillance swabs, blood, and urine to enable rapid detection of this pathogen. The assay uses commercially available primers and reporter probes and it was verified on the LightCycler 480 PCR platform. Contrived specimens and prospectively collected composite groin/axilla surveillance swabs were used to validate the assay. The performance of the PCR assay on surveillance swabs was also compared to a second PCR assay targeting C. auris that was performed at the Minnesota Department of Health-Public Health Laboratory (MDH-PHL). Our PCR assay is able to detect and differentiate C. auris from closely related Candida species such as C. duobushaemulonii, C. haemulonii, and C. pseudohaemulonii on the basis of melting curve temperature differences.

Keywords: Candida auris; PCR; identification; surveillance; yeast.

Figure 1

(a) Sequence alignment of the C. auris internal transcribed spacer (ITS) target region with the PCR assay primers (green arrows) and probes (red arrows). (b) Sequence alignment of the Phocine herpesvirus type 1 internal control target region with the PCR assay primers (green and yellow arrows) and probes (red and yellow arrows).

Figure 2

PCR melting curves for C. auris and closely related Candida species.

Figure 3

Sequence alignment of C. auris ITS target region with 8 closely related Candida species. Green arrows indicate the position of the PCR assay primers. Red arrows indicate the position of the PCR assay reporter probes.