WGS of E. faecalis isolates from Poultry farm samples
Genomic DNA was extracted from overnight freshly grown culture of the isolate using the HiPurA bacterial genomic DNA isolation kit (HiMedia, India), following the manufacturer's instructions. The extracted genomic DNA was quantified using a NanoDrop spectrophotometer (ThermoFisher, USA) and a Qubit assay (ThermoFisher, USA). The sample with intact DNA bands and concentrations of 50 ng passed quality control. Paired-end sequencing with a read length of 2  150 base pairs was performed on the NovaSeq6000 platform (Illumina, USA) by MedGenome Laboratories (Bangalore, India). The raw sequences obtained from the sequencing run underwent quality checks, including a Phred score >30, Q30% >89%, and GC content >38%. The high-quality trimmed sequences were then aligned to the reference genome (E. faecalis EnGen0336), and consensus sequences were generated using Samtools version 1.17. The genome annotation was performed using Prokka version 1.14.6 to identify and annotate genes and functional elements. Additionally, sequence coverage and depth were determined using BEDtools (Browser Extensible Data) version 2.30.0.