Determinants of fluconazole resistance and echinocandin tolerance in <i>C. parapsilosis</i> isolates causing a large clonal candidemia outbreak among COVID-19 patients in a Brazilian ICU

Patients presenting with severe COVID-19 are predisposed to acquire secondary fungal infections such as COVID-19-associated candidemia (CAC), which are associated with poor clinical outcomes despite antifungal treatment. The extreme burden imposed on clinical facilities during the COVID-19 pandemic has provided a permissive environment for the emergence of clonal outbreaks of multiple <i>Candida</i> species, including <i>C. auris</i> and <i>C. parapsilosis</i>. Here we report the largest clonal CAC outbreak to date caused by fluconazole resistant (FLZR) and echinocandin tolerant (ECT) <i>C. parapsilosis</i>. Sixty <i>C. parapsilosis</i> strains were obtained from 57 patients at a tertiary care hospital in Brazil, 90% of them were FLZR and ECT. Although only 35.8% of FLZR isolates contained an <i>ERG11</i> mutation, all of them contained the <i>TAC1^L518F</i> mutation and significantly overexpressed <i>CDR1</i>. Introduction of <i>TAC1^L518F</i> into a susceptible background increased the MIC of fluconazole and voriconazole 8-fold and resulted in significant basal overexpression of <i>CDR1</i>. Additionally, FLZR isolates exclusively harboured E1939G outside of Fks1 hotspot-2, which did not confer echinocandin resistance, but significantly increased ECT. Multilocus microsatellite typing showed that 51/60 (85%) of the FLZR isolates belonged to the same cluster, while the susceptible isolates each represented a distinct lineage. Finally, biofilm production in FLZR isolates was significantly lower than in susceptible counterparts Suggesting that it may not be an outbreak determinant. In summary, we show that <i>TAC1^L518F</i> and <i>FKS1^E1393G</i> confer FLZR and ECT, respectively, in CAC-associated <i>C. parapsilosis</i>. Our study underscores the importance of antifungal stewardship and effective infection control strategies to mitigate clonal <i>C. parapsilosis</i> outbreaks.