Extraction and WGS of Salmonella genomic DNA
We extracted genomic DNA from overnight cultured Salmonella spp. using the MagAttract®kit (Qiagen GmbH, Hilden, Germany) as described by the manufacturer. The purity and concentration of the extracted DNA were measured with the NanoDropTMspectrophotometer (Thermo Fisher Scientific) and the QuantusTM fluorometer (Promega, Madison, WI, USA), respectively. A library was prepared for sequencing using the Native barcoding genomic DNA kits and WGS sequencing was performed using the MinION system (Oxford Nanopore Technologies Ltd., Oxford, UK) as described by the respective manufacturers. The library was loaded onto FLO-MIN106 R9.4.1 Flow Cells and sequenced for 48 h. Data were base-called using the Albacore (Oxford Nanopore Technologies Ltd). A library prepared using the TrueSeq Nano DNA (Illumina, San Diego, CA, USA) was also sequenced using the HiSeq4000 system (Illumina, San Diego, CA, USA) for error correction of the nanopore sequencing results.