Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Johanna Rhodes (Corresponding Author), Alireza Abdolrasouli (Corresponding Author), Rhys A Farrer, Christina A Cuomo, David M Aanensen, Darius Armstrong-James, Matthew C Fisher, Silke Schelenz

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Abstract

Candida auris was first described in 2009, and it has since caused nosocomial outbreaks, invasive infections, and fungaemia across at least 19 countries on five continents. An outbreak of C. auris occurred in a specialized cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak in the UK, involving a total of 72 patients. To understand the genetic epidemiology of C. auris infection both within this hospital and within a global context, we sequenced the outbreak isolate genomes using Oxford Nanopore Technologies and Illumina platforms to detect antifungal resistance alleles and reannotate the C. auris genome. Phylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin; the outbreak showed similar genetic 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 add to a growing body of research on multiple antifungal drug targets in this organism. 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 and implement outbreak control measures.

Original languageEnglish
Article number43
JournalEmerging Microbes and Infections
Volume7
DOIs
Publication statusPublished - 29 Mar 2018

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Candida
Disease Outbreaks
Epidemiology
Nanopores
Genome
Echinocandins
Fungemia
Flucytosine
Molecular Epidemiology
Isoleucine
Pakistan
Amino Acid Substitution
Infection
Phenylalanine
Serine
Genes
Cluster Analysis
Tyrosine
India
Alleles

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Rhodes, J., Abdolrasouli, A., Farrer, R. A., Cuomo, C. A., Aanensen, D. M., Armstrong-James, D., ... Schelenz, S. (2018). Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris. Emerging Microbes and Infections, 7, [43]. https://doi.org/10.1038/s41426-018-0045-x

Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris. / Rhodes, Johanna (Corresponding Author); Abdolrasouli, Alireza (Corresponding Author); Farrer, Rhys A; Cuomo, Christina A; Aanensen, David M; Armstrong-James, Darius; Fisher, Matthew C; Schelenz, Silke.

In: Emerging Microbes and Infections, Vol. 7, 43, 29.03.2018.

Research output: Contribution to journalArticle

Rhodes, J, Abdolrasouli, A, Farrer, RA, Cuomo, CA, Aanensen, DM, Armstrong-James, D, Fisher, MC & Schelenz, S 2018, 'Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris', Emerging Microbes and Infections, vol. 7, 43. https://doi.org/10.1038/s41426-018-0045-x
Rhodes, Johanna ; Abdolrasouli, Alireza ; Farrer, Rhys A ; Cuomo, Christina A ; Aanensen, David M ; Armstrong-James, Darius ; Fisher, Matthew C ; Schelenz, Silke. / Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris. In: Emerging Microbes and Infections. 2018 ; Vol. 7.
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