Poultry of skin swabs
Bacterial DNA was extracted using Illumina TG TruSeq Nano DNA HT Sample Preparation Kit, following the manufacturers instructions. DNA concentrations were measured using the Qubit Fluorometer, while DNA purities were determined using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientifc, Waltham, MA, USA). Library preparation and sequencing were performed using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, USA) and the MiSeq platform (Illumina) providing 2  300 bp paired-end reads. Reads were filtered, quality trimmed and subsequently assembled using SPAdes v3.13 software.