A study of resistome of Candidozyma auris from 20 year genomic datasets

To conduct a comprehensive retrospective analysis of antimicrobial resistance (AMR) gene distribution in publicly available Candidozyma auris genomes to characterize global prevalence, temporal trends, geographic distribution patterns, and co-occurrence of resistance determinants over a 20-year period.

A cross-sectional genomic analysis was performed using 538 unique C. auris genome assemblies retrieved from the European Nucleotide Archive (2004-2024). AMR gene detection was conducted using ChroQueTas computational tool with the FungAMR database. Statistical analyses examined resistance gene frequencies, temporal trends, geographic distribution across 32 countries, co-occurrence patterns, and predicted antifungal resistance profiles.

Of 538 genomes analysed, 460 (85.50%) harbored at least one AMR gene. Cyp51 was the most prevalent resistance gene (455 genomes, 84.57%), followed by Tac1 (109 genomes, 20.26%), Erg6 (12 genomes, 2.23%), and Fks (11 genomes, 2.04%). The majority of genomes (61.9%) contained a single resistance gene type, while 23.42% carried two distinct gene types. Temporal analysis revealed increasing detection of Cyp51 and Tac1 from 2019 onwards, peaking in 2022-2023. Geographic hotspots included Pakistan, Turkey, and Hong Kong. The most common gene co-occurrence was Cyp51 and Tac1 (105 genomes). Predicted resistance to fluconazole (85.32%) and voriconazole (83.83%) was most prevalent, with 313 genomes showing predicted pan-drug resistance.

This study confirms high prevalence of AMR determinants in C. auris globally, with increasing temporal trends and significant co-occurrence of multiple resistance mechanisms. The findings emphasize the escalating therapeutic challenge posed by multidrug-resistant C. auris and highlight the critical need for enhanced genomic epidemiology studies.