Genotypic and phenotypic characterization of a nosocomial outbreak of Candida auris in Spain during five years

Objectives: The investigation of Candida auris outbreaks is needed to provide insights into its population structure and transmission dynamics. We genotypically and phenotypically characterized a C. auris nosocomial outbreak occurred at the Consorcio Hospital General Universitario de Valencia (CHGUV), Spain. Methods: Data and isolates were collected at CHGUV from September 2017 (first case) until September 2021. Thirty-five isolates, one from an environmental source, were selected for whole genome sequencing (WGS), and the genomes were analyzed along with 335 publicly available genomes, assigning them to one of the five major clades. In order to identify polymorphisms associated with drug resistance, we used the fully susceptible GCA_003014415.1 strain as reference sequence. Known mutations in genes erg11 and fks1 conferring resistance to fluconazole and echinocandins, respectively, were investigated. Isolates were classified into aggregating or non-aggregating. Results: All isolates belonged to clade III and were from an outbreak with a single origin. They clustered close to 3 publicly available genomes from a hospital from where the first patient was transferred, being the probable origin. The mutation VF125AL in the ERG11 protein, conferring resistance to fluconazole, was present in all the isolates and one isolate also carried the mutation S639Y in the FKS1 protein. All the isolates had a non-aggregating phenotype. Conclusions: Isolates are genotypically related and phenotypically identical but one with resistance to echinocandins, which seems to indicate that they all belong to an outbreak originated from a single isolate, remaining largely invariable over the years. This result stresses the importance of implementing infection control practices as soon as the first case is detected or when a patient is transferred from a setting with known cases.