title: Adult klebsiella pneumoniae cases
design: To prepare for whole genome sequencing (WGS), genomic DNA was extracted directly from stored STGG, using the TANBead Maelstrom 4810 Automated DNA/RNA Purification Platform (Taiwan Advanced Nanotech Inc.) following the manufacturers guidelines. Thirty isolates required an additional pre-lysis step to meet the minimum DNA input requirements, which is further detailed in the supplementary materials. Following DNA extraction, sequencing libraries were prepared using the Nextera XT DNA Kit (Illumina, US) and sequenced on the  Illumina Nextseq 1000 and Illumina Nextseq 2000 platforms to generate short 2 x 150bp paired-end reads (Illumina, San Diego, CA) at the National Institute for Communicable Diseases (NICD), Johannesburg, South Africa. Quality control assessment of raw sequencing reads was performed at Imperial College, London, UK,  with FastQC (version 0.12.1,2023) and MultiQC (version 1.21, 2024) files, generated for raw reads, to assess initial quality metrics. Raw reads were then trimmed, with low quality reads removed using Trimmomatic (version 0.39, 2021). The quality control assessment is further detailed in the supplementary materials.