Diagnostic Challenges in the Identification of Candida auris: A Comprehensive Review and Practical Workflow for Routine Clinical Microbiology Laboratories

Background: Candida auris has emerged as one of the most important multidrug-resistant fungal pathogens worldwide and represents a major challenge for clinical microbiology laboratories and healthcare systems. Since its first identification in ۲۰۰۹, this opportunistic yeast has spread rapidly across multiple continents and has become a leading cause of healthcare-associated outbreaks. Its ability to survive on environmental surfaces for prolonged periods, colonize patients, resist routine disinfectants, and develop resistance to several classes of antifungal agents distinguishes it from most other Candida species. Delayed or inaccurate laboratory identification often results in inappropriate antifungal therapy, delayed implementation of infection prevention measures, prolonged hospitalization, increased healthcare costs, and higher mortality, particularly among critically ill and immunocompromised patients. Consequently, rapid and accurate identification of C. auris has become a global public health priority.Objective: This review summarizes the major diagnostic challenges associated with the identification of Candida auris in routine clinical microbiology laboratories. It critically evaluates the advantages and limitations of conventional phenotypic methods, biochemical identification systems, chromogenic media, MALDI-TOF mass spectrometry, molecular diagnostic techniques, and emerging genomic technologies. In addition, an evidence-based diagnostic workflow is proposed to facilitate accurate laboratory recognition of C. auris in settings with varying levels of technical expertise and laboratory resources.Main Findings: One of the greatest challenges in identifying C. auris is its frequent misidentification by conventional biochemical identification systems. Commercial platforms based on phenotypic and biochemical characteristics may incorrectly identify the organism as members of the Candida haemulonii species complex, Candida famata, Rhodotorula species, or other closely related yeasts, particularly when outdated reference databases are used. Such errors may delay appropriate patient management and increase the risk of unnoticed healthcare-associated transmission. Therefore, laboratories should maintain a high level of suspicion whenever uncommon yeast species are isolated from high-risk patients or when unexpected identification results are obtained. Current recommendations emphasize confirmatory testing whenever C. auris is suspected, especially during outbreaks or in regions where the pathogen has already been reported.Recent advances in laboratory diagnostics have significantly improved the identification of C. auris. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently regarded as one of the most reliable methods for species-level identification when supported by updated and validated reference databases. Compared with conventional biochemical systems, MALDI-TOF MS provides higher diagnostic accuracy, shorter turnaround times, and lower long-term operating costs. Emerging evidence also suggests that this technology may contribute to the rapid prediction of antifungal susceptibility patterns, although additional clinical validation is still required.Chromogenic media have become valuable tools for screening and surveillance. Among them, CHROMagar Candida Plus has demonstrated improved performance by producing characteristic colony morphology that facilitates the presumptive recognition of C. auris. Nevertheless, colony appearance may vary according to incubation conditions and mixed cultures; therefore, chromogenic media should be considered screening tools rather than definitive identification methods. Confirmation using proteomic or molecular techniques remains essential for reliable diagnosis.Molecular diagnostic methods currently provide the highest level of diagnostic accuracy. Conventional PCR, real-time PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP), DNA sequencing, and whole-genome sequencing have demonstrated excellent sensitivity and specificity for both direct detection and confirmation of clinical isolates. Whole-genome sequencing additionally offers valuable information regarding genetic relatedness, antifungal resistance mechanisms, and transmission dynamics during healthcare-associated outbreaks. More recently, metagenomic next-generation sequencing has emerged as a promising culture-independent approach capable of detecting fungal pathogens directly from clinical specimens, although its widespread implementation remains limited by cost, technical complexity, and bioinformatics requirements.Because no single diagnostic method fulfills all clinical and laboratory needs, an integrated diagnostic strategy is recommended. A practical workflow should begin with appropriate clinical suspicion, proper specimen collection, routine culture, and preliminary laboratory identification. Isolates showing unusual biochemical profiles or suspected misidentification should undergo confirmation by MALDI-TOF MS whenever available. Laboratories without access to proteomic technologies should refer suspicious isolates to regional reference laboratories for molecular confirmation. Antifungal susceptibility testing should be performed according to current CLSI or EUCAST recommendations to guide treatment and monitor emerging resistance. During suspected outbreaks, rapid laboratory confirmation should be combined with patient isolation, contact screening, environmental surveillance, and strict infection prevention measures to reduce ongoing transmission.Conclusion: Accurate identification of Candida auris remains one of the greatest challenges facing contemporary clinical microbiology laboratories. The unique biological characteristics of this emerging pathogen and the limitations of conventional diagnostic methods highlight the need for reliable and standardized laboratory approaches. An evidence-based diagnostic workflow integrating phenotypic, proteomic, and molecular methods according to available laboratory resources can substantially improve diagnostic accuracy, reduce turnaround time, support timely antifungal therapy, strengthen infection prevention programs, and ultimately improve patient outcomes. Continued investment in diagnostic innovation, laboratory capacity, and international surveillance will be essential to address the expanding global threat posed by Candida auris

کلیدواژه ها:

Candida auris ، Clinical microbiology ، Laboratory diagnosis ، MALDI-TOF MS ، Molecular diagnostics ، CHROMagar Candida Plus ، Diagnostic workflow ، Antifungal resistance