Short Read Illumina WGS of Enterococcus faecalis from A New Arsenal Against E. faecalis: identification of novel Phages Combatting Multidrug Resistant clinical isolates
Short-read sequencing was conducted on the Illumina platform, using the Illumina NextSeq 550 (Illumina Inc, San Diego, USA) and NextSeq 500/550 Mid-Output kit v2.5 (Illumina Inc., FC-131-1024) at SA Pathology (Adelaide, SA, Australia). To prepare for short-read sequencing, the genomic DNA was isolated using the DNeasy blood & tissue kit (Qiagen, Hilden, Germany) according to manufacturers instructions. The sequencing libraries were prepared using a modified protocol for the Nextera XT DNA library preparation kit (Illumina Inc. FC-131-1024). The genomic DNA was fragmented, after which a low-cycle PCR reaction was used to amplify the Nextera XT indices to the DNA fragments. Sequencing yielded one hundred fifty bp paired end reads.