Multilocus Sequence Typing of Emerging Azole-Resistant Candida auris Isolates from Critically Ill Patients in a New York City Medical Center

Abstract

Abstract Candida auris has developed into a slow-moving global pandemic since its emergence in 2009, particularly as a source of nosocomial infection amongst immunocompromised and critically-ill patients. According to CDC data, C. auris emergence has accelerated in the US during the COVID-19 pandemic and has garnered particular attention for its high level of resistance to multiple classes of antifungals. C. auris has been categorized into five genetically diverse clades, each with unique antifungal drug resistance patterns. We have observed a sharp increase in cases identified at our tertiary medical center in New York City over the past three years. In this study, we designed a set of C. auris-specific oligonucleotides to determine the clonality of isolates through Multilocus Sequence Typing (MLST) of four genetic loci known to have a high level of divergence amongst Candida species. From 2020 through 2022 we identified 22 patients with C. auris bloodstream infection at our institution by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and performed MLST on isolates that were available from 19 patients. We assessed four genetic loci: ITS1/ITS2, D1/D2, RPB1 and RPB2; ERG11 was included to assess for mutations associated with fluconazole resistance. We found that the number of blood stream infections increased from 2 cases in 2020 to 12 in 2022. Our MLST results showed that all C. auris isolates from blood and body fluids belong to CDC-defined Clade 1c, which carries the ERG11 gene mutation resulting the amino acid substitution K143R in 14-α-Demethylase associated with fluconazole resistance. These isolates also demonstrated fluconazole resistance by in vitro testing (19/19), amphotericin resistance was present in 44% of isolates with available data (7/16), and all isolates were susceptible to micafungin (19/19). Of 19 patients with blood cultures positive for C. auris, 13 (68%) were in a critical care setting at time of collection, 17 (89%) had been in an ICU during the same admission, and 8 (42%) expired within 3 months of C. auris positivity. MLST is considered a relatively fast and inexpensive method of sequence-based strain typing and has recently been applied to assessing the clonality of C. auris isolates. We show that the use of C. auris-specific oligonucleotides for sequencing, rather than those derived from other Candida species, produces high quality data for MLST, as well as the detection of specific mutations involved in antifungal resistance, such as ERG11. Further assessment is needed by the gold standard in sequence typing, Whole Genome Sequencing (WGS), to confirm our analysis of clonality here. MLST may therefore represent a useful tool in understanding the interrelatedness of invasive C. auris infections in hospitalized patients as well as inform clinical decision-making around infection control and empiric antifungal therapy.