Bacterial genomic DNA was extracted using the Fastprep beadbeater (MPBio) and the QIAamp UCP Pathogen mini kit (Qiagen) following manufacturers instructions. a genomic DNA library was prepared by multiplexing 100 ng of end-prepped, barcoded genomic DNA (SQK-LSK109 and EXP-NBD104 kits). Sequencing was performed on MinION using FLO-MIN106 (v9.4.1) flowcells. Basecalling and demultiplexing were performed using MinKNOW (v21.06.0).