Short and long read sequencing of whole genome and plasmid extractions of multiple bacterial species for the development of a NGS-based workflow.

This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localisation, i.e. chromosomal or on a plasmid. MiSeq and Nanopore sequencing were performed on whole genome and plasmid extractions of several bacterial species. Then assemblies with each technology separately and combined (hybrid) were performed. Furthermore, the added value of conjugation of a plasmid to a known host was evaluated.