cgMLST typing reveals allelic differences between genomes utilizing different basecaller models and sequencing kits. The minimum spanning tree pictures four K. pneumoniae samples based on 2358 genes for pairwise comparison of allelic variations. Missing values were ignored. Nodes (samples) are connected by lines depicting the distance by numbers of allelic differences. Loci are considered different if one or more bases change between the samples. Loci without allelic differences are described as being the same. Samples with allelic differences of 15 or fewer are considered as part of the cluster. All isolates were prepared with Kit 14 and Kit 12 and basecalled with each respective Guppy “superaccurate” basecalling model (see subsection “Basecalling and assembly” in the Methods). We basecalled all Kit 14–prepared samples with Dorado using the default and a modification-aware model (see subsection “Basecalling and assembly” in the Methods).
