Whole genome sequencing of Vancomycin resistant Enteroccus faecium: human sample
E. faecium DNA was extracted using the automated BD Max system (Becton Dickinson) from inoculated tryptic soy broth cultures grown for 18-24 hours at 37C. Sample libraries were prepared from 100-500ng of DNA using the Illumina DNA Prep kit and barcoded using the Illumina DNA/RNA UD Indexes Set A kit per manufacturer instructions. Library concentrations and fragment sizes were assessed with Qubit and Agilent 5300 fragment analyzer instruments, respectively. Sample libraries were normalized by diluting to a concentration of 4nM, pooled, and denatured in 0.2N NaOH. The pooled denatured libraries were diluted to a final loading concentration of 20pM. PhiX run control (Illumina, FC-110-3001) was diluted, denatured, and loaded as described for the sample libraries. Up to 18 sample libraries were run on an Illumina MiSeq System using the MiSeq Reagent Kit v3 150 Cycle Cartridge (MS-102-3001) with paired end reads.