375 MinION Nanopore Sequencing of Candida Pathogens for Identification and Antifungal Resistance Detection: Proof of Concept

Introduction/Objective Candida species are significant fungal pathogens associated with high morbidity, mortality, and rising antifungal resistance. Traditional diagnostic methods remain slow and labor-intensive. This study evaluates the clinical utility of Nanopore MinION sequencing (Oxford Nanopore Technologies. Oxford, United Kingdom) for identifying drug-resistant Candida species and detecting relevant resistance mutations. Methods/Case Report Clinical isolates from Candida albicans, Nakaseomyces glabratus, and Candida parapsilosis were selected. A multiplex PCR amplified four antifungal resistance genes (ERG3, ERG11, FKS1, FKS2). Amplicons were sequenced using Nanopore MinION and Sanger platforms. Psychometric analysis assessed reliability and validity using ICC, Kappa, Bland-Altman plots, and diagnostic accuracy metrics. Results Nanopore sequencing identified isolates to species level with 100% accuracy. While ICC revealed poor quantitative agreement (ICC = 0.31), Kappa showed good categorical agreement (κ = 0.78). Bland-Altman analysis indicated no significant bias, except at low-quality scores. Sensitivity, specificity, and diagnostic accuracy of Nanopore were 96.3%, 100%, and 96.6%, respectively. Variant detection in target regions achieved perfect classification (AUC = 1.00, P < 0.001). Conclusion Nanopore sequencing demonstrated diagnostic performance comparable to Sanger sequencing and successfully identified antifungal resistance markers. These findings support its potential integration into molecular clinical laboratories and open the door for larger-scale studies investigating its role in detecting drug-resistant Candida species.