WGS of Salmonella isolate from cattle
For each isolate, extracted DNA (1,000 ng) was added to low EDTA TE buffer and made to equal 150 L of total volume. DNA samples were sheared to 8 kbp using g-TUBES (Covaris, Woburn, MA, USA) via centrifugation according to the manufacturers recommended settings of two centrifugations at 7200 rpm for one minute in an Eppendorf 5424 centrifuge (Eppendorf, Hamburg, Germany). The sheared DNA samples were cleaned with AMPure XP beads (Beckman Coulter, Brea, CA, USA) at a ratio of 0.4x and eluted into 14 uL of molecular-grade water. DNA concentrations after bead cleaning were assessed using a NanoDrop Eight device (Thermo Fisher Scientific, Waltham, MA, USA) and fragment sizes were assessed via visualization of the electrophenogram using a Tape Station 4200 device and genomic screentape (Agilent Technologies, Santa Clara, CA, USA). DNA libraries were prepared using the native barcoding kit v14 (SQK-NBD114-24) and sequenced in R10.4.1 flow cells in a MinION Mk1C device (Oxford Nanopore Technologies, Oxford, UK), multiplexing 24 Salmonella isolates per flow cell. Two extraction blanks were also sequenced to assess the presence of background DNA. Isolates that could not be assembled, as well as isolates with poor assembly quality (<100 coverage of the largest contig or >10 contigs in the assembly) were reprocessed.