Draft Genomes of bile duct microbiome strains Klebsiella pneumoniae, Enterococcus faecalis and Enterococcus faecium isolated from bilioenteric catheters from a liver transplantation patient
Whole genome short read sequencing of all three strains was performed on iSeq100 platform with a 300-cycle iSeq reagent kit generating paired-end (2x150bp) raw reads. Here, libraries were prepared using standard protocols for Illumina DNA Prep Kit and NexteraTM CD indexes. A long-read sequencing library was prepared with a one-dimenional ligation sequencing kit SQK-LSK109 (Oxford Nanopore Technologies [ONT]) and NEBNext Companion Module for ONT Ligation Sequencing kit (New England BioLabs, USA) following each manufacturers protocol. Subsequently, the library was loaded into a FLO-MIN106 flow cell (R9.4.1, ONT) on a MinION sequencer (ONT). Base-calling of the fast5 reads were done using MinKNOW (v.19.10.1 (ONT))with Guppy v.3.3.3 in high-accuracy base-calling mode.