WGS of Klebsiella pneumoniae
Isolates were recovered from the MLW sample archive and total nucleic acids were extracted using the MasterPure complete DNA and RNA Purification Kit (Bioresearch Technologies, United Kingdom) according to the manufacturer's instructions. The normalised DNA was used for library preparation using the rapid barcoding kit (SBQ-RBK004, Oxford Nanopore Technologies plc) following the manufacturer's instructions. The prepared library was sequenced on an Oxford Nanopore r9.4.1 flow cell on the MinION Mk1C sequencer (Oxford Nanopore Technologies plc). Data acquisition was done by the MinKNOWTM software (version 20.10.6, Oxford Nanopore Technologies plc). Base calling and demultiplexing using Guppy Basecalling Software, Oxford Nanopore Technologies plc. (version 6.0.7). We used Guppy with the default settings and the dna_r9.4.1_450bps_sup.cfg configuration file for the guppy_barcoder. We used the command line argument --trim_barcodes for the debarcoding step using guppy_barcoder. For guppy_barcoder we passed SQK-RBK004 to the --barcode_kits command line argument.