Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses
Genomic DNA was sheared to a mean size of 600 bp using a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA). DNA fragments were Ampure (Beckman Coulter Inc., Indianapolis, IN) cleaned and used to prepare dual-indexed sequencing libraries using NEBNext Ultra library prep reagents (New England Biolabs Inc., Ipswich, MA) and barcoding indices synthesized in the CDC Biotechnology Core Facility. Libraries were analyzed for size and concentration, pooled and denatured for loading onto flowcell for cluster generation. Sequencing was performed on an Illumina Miseq using 300x300 cycle paired-end sequencing kit. On completion, sequence reads were filtered for read quality, basecalled and demultiplexed using Casava (v1.8.4).