Nanopore sequencing of a pathogenic fungi outbreak in a UK hospital

Johanna Rhodes, Imperial College London, gives a plenary talk at Nanopore Community Meeting 2016

Candida auris is a globally emerging multidrug resistant fungal pathogen causing nosocomial transmission. After the initial infection in April 2015 in a London cardio-thoracic center, we are now currently seeing the largest global outbreak of C. auris in an intensive care unit. As such, a rapid response is required. We investigated this outbreak by nanopore sequencing technology using the MinION from Oxford Nanopore Technologies to generate a reference genome; these data were integrated with whole-genome sequences, to place the outbreak into a global context, and identify the origin of this outbreak. Nanopore sequencing also allowed rapid species identification and the acquisition of clinically relevant information within a short time frame, reducing the current hospital workflow by days. The rapid availability of reliable clinical data in the C. auris outbreak enabled the identification of drug resistance mutations and transmission.