After clinical testing was complete, deoxyribonucleic acid (DNA) was extracted from isolates using the Geneaid Presto MinigDNA Bacteria Kit and stored at −80 until sequencing was performed. Whole genome sequencing libraries were prepared as described elsewhere [18 (link)]. Sequencing was performed on the Illumina NextSeq platform using 300 cycle chemistries to a minimum average read depth of at least 20× per isolate. After sequencing, de novo draft genomes were assembled using AbySS v2.0.2 [19 (link)]. To ensure that the conventional microbiological species identification was concordant with the genomic classification, pairwise ANIb analysis was performed against a representative collection of publicly available Klebsiella genomes using the Pyani package (https://github.com/widdowquinn/pyani). Of the 70 total genomes analyzed, 10 matched Klebsiella species that were not K pneumoniae and 2 others evidenced polymicrobial contamination, resulting in a final set of 58 K pneumoniae genomes included in further analysis.