Genetic microevolution of clinical <i>Candida auris</i> with reduced Amphotericin B sensitivity in China

The global rate of Amphotericin B (AmB) resistance in <i>Candida auris</i> has surpassed 12%. However, there is limited data on available clinical treatments and microevolutionary analyses concerning reduced AmB sensitivity. In this study, we collected 18 <i>C. auris</i> isolates from five patients between 2019 and 2022. We employed clinical data mining, genomic, and transcriptomic analyses to identify genetic evolutionary features linked to reduced AmB sensitivity in these isolates during clinical treatment. We identified six isolates with a minimum inhibitory concentration (MIC) of AmB below 0.5 µg/mL (AmB^0.5) and 12 isolates with an AmB-MIC of 1 µg/mL (AmB¹) or ≥ 2 µg/mL (AmB²). All five patients received 24-hour AmB (5 mg/L) bladder irrigation treatment. Evolutionary analyses revealed an <i>ERG3</i> (c923t) mutation in AmB¹ <i>C. auris</i>. Additionally, AmB² <i>C. auris</i> was found to contain a t2831c mutation in the <i>RAD2</i> gene. In the AmB¹ group, membrane lipid-related gene expression (<i>ERG1, ERG2, ERG13,</i> and <i>ERG24</i>) was upregulated, while in the AmB² group, expression of DNA-related genes (e.g. <i>DNA2</i> and <i>PRI1</i>) was up-regulated. In a series of <i>C.auris</i> strains with reduced susceptibility to AmB, five key genes were identified: two upregulated (<i>IFF9</i> and <i>PGA6)</i> and three downregulated (<i>HGT7, HGT13,</i>and <i>PRI32)</i>. In this study, we demonstrate the microevolution of reduced AmB sensitivity in vivo and further elucidate the relationship between reduced AmB sensitivity and low-concentration AmB bladder irrigation. These findings offer new insights into potential antifungal drug targets and clinical markers for the “super fungus”, <i>C. auris</i>.