Whole-Genome Sequencing of HCAI Isolates

DNA was extracted from 30 of the 31 isolates with an UltraClean microbial DNA isolation kit (Mo-Bio) as previously described (48 (link)). One of the HCAI outbreak isolates (MBT16-008) failed to grow and therefore could not be analyzed by WGS. Total DNA concentration was estimated using a Qubit fluorometer and a double-stranded DNA (dsDNA) high-sensitivity (HS) assay kit (both ThermoFisher). Fifty nanograms of DNA was prepared using the NEBNext Ultra II FS DNA library prep kit for Illumina (New England Biolabs), and post-PCR cleanup was carried out using AMPure XP beads (Beckman). Library size was validated at approximately 300 bp using the Agilent 2200 TapeStation with an Agilent D1000 ScreenTape system (Willoughby, Australia), and 75-bp paired-end reads were sequenced on a NextSeq 550 system (Illumina).