Diagnostic Approaches for Candida auris: A Comprehensive Review of Screening, Identification, and Susceptibility Testing

Abstract

Candida auris (C. auris) is an emerging multidrug-resistant fungal pathogen recognized by the World Health Organization (WHO) as a critical global health threat. Its rapid transmission, high mortality rate, and frequent misidentification in clinical laboratories present significant challenges for diagnosis and infection control. This review provides a comprehensive overview of current and emerging diagnostic methods for C. auris detection, including culture-based techniques, biochemical assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and molecular diagnostics such as PCR and loop-mediated isothermal amplification (LAMP). We evaluate each method's sensitivity, specificity, turnaround time, and feasibility in clinical and surveillance settings. While culture remains the diagnostic gold standard, it is limited by slow turnaround and phenotypic overlap with related species. Updated biochemical platforms and MALDI-TOF MS with expanded databases have improved identification accuracy. Molecular assays offer rapid, culture-independent detection. Antifungal susceptibility testing (AFST), primarily using broth microdilution, is essential for guiding treatment, although standardized breakpoints remain lacking. This review proposes an integrated diagnostic workflow and discusses key innovations and gaps in current practice. Our findings aim to support clinicians, microbiologists, and public health professionals in improving early detection, containment, and management of C. auris infections.

Keywords: Candida auris; diagnostic methods; matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

Figure 1

Workflow Algorithm for Detection in Clinical and Surveillance Samples. Clinical and surveillance samples are detected using culture-based methods, with colonies confirmed by MALDI-TOF and biochemical tests (e.g., VITEK 2). Biochemical tests risk misidentification and require CDC algorithm interpretation (Table 2). Alternative screening includes DNA-based confirmatory tests and chromogenic agar for presumptive identification. WGS aids outbreak and epidemiological investigations. Red lines indicate confirmatory tests. Abbreviations: AFST, antifungal susceptibility testing; BDG, beta-D-glucan; CDC, Centers for Disease Control and Prevention; MALDI-TOF MS, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; PCR, polymerase chain reaction; VITEK 2, VITEK 2 Biochemical Identification System; WGS, whole genome sequencing.

Figure 2

Recommended Sample Collection Sites for Screening. Swab the bilateral axillae and groins 3–5 times with the soft end of the collection swab. Recent studies suggest including nasal swabs to improve sensitivity.

Figure 3

Workflow of Surveillance Sample Testing Using Chromogenic Agar. 10 µL of surveillance sample was streaked onto the culture media in a Z-pattern for optimal isolation. Plates were incubated at 37 °C for 48 to 72 h, with presumptive C. auris appearing with green colonies on the media (per manufacturer’s recommendation). Plates with no growth or colonies of other colors (e.g., white, pink, or purple) are considered negative.

Figure 4

General workflow of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS)-based identification analysis. (1) C. auris colonies are cultivated on solid agar, followed by sample preparation via tube-based protein extraction or direct smear methods. (2) Prepared samples are transferred onto a MALDI-TOF MS target plate and overlaid with a suitable matrix solution. (3) Samples are analyzed using MALDI-TOF MS to generate mass spectra. (4) Experimental mass spectra are matched against a database of reference strain spectra to achieve species-level identification, the colors represent different sample groups for comparison.