• CRISPR-based Rapid Diagnostics for Emerging Antifungal Resistance in Candida auris.
  • Ayda Khatibi,1,*
    1. Department of Biological Sciences, Faculty of Basic Sciences, Institute of Higher Education of Nabi Akram, Tabriz, Iran.


  • Introduction: Invasive fungal infections have become a major public health challenge in the last decade. Among them, Candida auris has attracted special attention as an emerging pathogen. The fungus was first reported in 2009 and has since been identified in more than 40 countries as a cause of hospital infections and deadly pandemics. A distinctive feature of this species is the multiple drug resistance to the main groups of antifungal drugs, including azoles, amphotericin B, and echinocandins. Common diagnostic methods, such as mushroom cultivation or PCR-based tests, although of acceptable accuracy, are not used in many health centers, especially in low-income countries, due to their time-consuming nature, high cost, and need for specialized equipment. So there is an urgent need to develop new and rapid tools to detect drug resistance in C. there is auris. In recent years, CRISPR-Cas technology, especially emerging systems such as SHERLOCK and DETECTR, has been introduced as accurate and cost-effective tools in the field of molecular diagnostics. This technology allows rapid detection of gene mutations associated with antifungal resistance using the proprietary cutting capabilities of nucleic acids.
  • Methods: In this review study, the latest data published in authoritative scientific databases (PubMed, Scopus, Web of Science) were first collected and analyzed by 2025. Then key genes in the formation of antifungal resistance in C. Auris were identified, including ER11 for resistance to azoles, FKS1 for resistance to echinocandins, and genes involved in the ارosterol synthesis pathway. Based on this data, the design of the diagnostic solution was based on CRISPR-Cas12a. The system is programmed to identify specific mutant sequences and produce a traceable fluorescent signal in their presence. To increase sensitivity, isothermal amplification, such as LAMP or RPA, was used alongside CRISPR. Finally, a conceptual model was designed to integrate the technology into Point-of-Care kits that could be used in intensive care units (ICUs) and limited healthcare facilities in terms of facilities.
  • Results: A review of studies showed that CRISPR-Cas technology has been successfully used in recent years to detect viruses (such as SARS-CoV-2) and antibiotic-resistant bacteria. However, its application in the diagnosis of drug-resistant fungal infections is still in its early stages. Data analysis showed that using CRISPR-Cas12a to detect LEG11 gene mutations could provide accurate results with a sensitivity of more than 90% and a specificity of more than 95% in less than 60 Minutes. The proposed model suggests that CRISPR-based kits can detect multiple resistance mutations simultaneously and can be introduced as a quick and inexpensive replacement for classic molecular tests. In addition, it is possible to develop these kits as mobile devices (Portable Devices), which facilitate their clinical use in critical situations.
  • Conclusion: As an emerging and multidrug-resistant pathogen, Candida auris poses a serious threat to the world's public health. The restriction of common diagnostic methods has doubled the need for new and rapid solutions. CRISPR-Cas technology with high precision, high speed, and customization capability provides a new horizon for rapid detection of antifungal resistance in this dangerous species. By examining existing data and designing a conceptual model, the present study shows that integrating CRISPR with isothermal replication methods can lead to the development of point-of-care diagnostic kits. This achievement not only contributes to the timely identification and selection of appropriate treatment but can also dramatically reduce the death rate from hospital infections and medical costs. Finally, it is proposed to conduct more extensive laboratory studies and clinical trials to validate this method to provide the basis for its clinical application globally.
  • Keywords: Candida auris, Antifungal Resistance, CRISPR Cas Diagnostics, Point of Care Testing,Medical Mycology