Title : Functional characterization of multidrug-resistant candida auris waste water isolates from the largest outbreak in the United States
Abstract:
From 2022 to 2023, the United States faced its largest outbreak of Candida auris infections in Las Vegas, Nevada. In response, our multi-disciplinary team, including engineers, geneticists, and epidemiologists, utilized wastewater and public health tools, initially developed during the COVID-19 pandemic, to track the spread of the pathogen across 42 nursing homes and hospitals. We established wastewater sampling protocols and DNA sequencing techniques, enabling the detection and sequencing of C. auris DNA, including drug resistance mutations. This approach identified Clade I and III lineages, uncovering novel mutation patterns across different facilities. We also refined methods to accurately culture C. auris from wastewater, overcoming traditional challenges in distinguishing Candida species. Through these techniques, we analyzed over 500 wastewater isolates using whole genome sequencing and MALDI-TOF mass spectrometry, alongside antibiotic susceptibility testing via the Etest method. Our genome-wide studies revealed significant SNPs in FKS1, ERG11, and other novel sites linked to antifungal resistance. We then cultured 40 distinct sub-lineages of C. auris from Clade I and III in two environments – YPD at 37°C and SSDB with fluconazole at 42°C. RNA sequencing and data-independent acquisition proteomics revealed a perturbation in ribosomal and cell cycle networks. Our study not only sheds light on the dynamics of the C. auris outbreak in Southern Nevada but also illustrates the potential of wastewater monitoring to enhance clinical data, offering deeper insights into pathogen evolution and resistance.
