Genotypic and phenotypic characterisation of a nosocomial outbreak of Candida auris in Spain during 5 years.

OBJECTIVES: The investigation of Candida auris outbreaks is needed to provide insights into its population structure and transmission dynamics. We genotypically and phenotypically characterised a C. auris nosocomial outbreak occurred in Consorcio Hospital General Universitario de Valencia (CHGUV), Spain. METHODS: Data and isolates were collected from CHGUV from September 2017 (first case) until September 2021. Thirty-five isolates, including one from an environmental source, were randomly selected for whole genome sequencing (WGS), and the genomes were analysed along with a database 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 three publicly available genomes from a hospital from where the first patient was transferred, being the probable origin. The mutation VF125AL in the ERG11 gene, conferring resistance to fluconazole, was present in all the isolates and one isolate also carried the mutation S639Y in the FKS1 gene. All the isolates had a non-aggregating phenotype (potentially more virulent). 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.

Uso de las tecnologías de secuenciación masiva para el diagnóstico y epidemiología de enfermedades infecciosas / Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases

Por primera vez, la tecnología de secuenciación masiva permite acceder a la información genómica a un precio y a una escala tales, que se está implementado en la práctica clínica y epidemiológica rutinaria. Los obstáculos para dicha implementación son todavía muchos. Sin embargo, ya existen muchos ejemplos de las grandes ventajas que supone en comparación con métodos anteriores. Esto es, sobre todo, porque con una sola determinación podemos obtener simultáneamente información epidemiológica del microorganismo causante, así como de su perfil de resistencias, si bien estas ventajas están más o menos desarrolladas según el patógeno considerado. En esta revisión se repasan varios ejemplos del uso clínico y epidemiológico de la secuenciación masiva aplicada a genomas completos y microbiomas, y se reflexiona sobre su futuro en la práctica clínica

For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice