RT Journal Article SR Electronic T1 Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris JF bioRxiv FD Cold Spring Harbor Laboratory SP 201343 DO 10.1101/201343 A1 Johanna Rhodes A1 Alireza Abdolrasouli A1 Rhys A. Farrer A1 Christina A. Cuomo A1 David M. Aanensen A1 Darius Armstrong-James A1 Matthew C. Fisher A1 Silke Schelenz YR 2017 UL http://biorxiv.org/content/early/2017/10/13/201343.abstract AB Background Candida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak of C. auris occurred in a specialised cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak reported worldwide, involving a total of 72 patients.Methods To understand the epidemiology of C. auris infection within this hospital, we sequenced the genomes of outbreak isolates using Oxford Nanopore Technologies and Illumina in order to type antifungal resistance alleles and to explore the outbreak within its local and global context.Findings Phylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin. The outbreak showed similar diversity to that of the entire clade and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations are novel for this pathogen.Interpretation Multiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission as well as implementing outbreak control measures.Funding Antimicrobial Research Collaborative, Imperial College London