The single nucleotide polymorphism calling pipeline and additional bioinformatic pipelines were described previously (18 (link)). Strains from Holt et al. were downloaded from European Nucleic Acid Archive (accession number ERP000165). BLAST was performed using the NCBI BLAST toolkit as well as CLC Genomics Workbench v.10.1. Visualization of SNP distribution was performed using CLC Genomics Workbench v.10.1. FASTQ files were assembled into contigs using Spades v3.9.0, and contigs were annotated using Prokka v1.12 (43 (link), 44 (link)). Gene content analysis was performed using Roary v3.6.1 (45 (link)). The 12 strains of ESBL-producing K. pneumoniae included for pangenome comparison are KPN1, KPN2, KPN9, KPN11, KPN12, KPN17, KPN18, KPN133, KPN1998, KPN2000, KPN2108, and KPN2129 (18 (link)). Assembly of SNPs into phylogenetic trees was accomplished with the scripts prephix v3.3.0, phrecon v4.6.0, and FastTreeMP v2.1 (46 (link)). Prephix and phrecon are available from GitHub (https://github.com/codinghedgehog).
Long S.W., Linson S.E., Ojeda Saavedra M., Cantu C., Davis J.J., Brettin T, & Olsen R.J. (2017). Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. mSphere, 2(4), e00290-17.
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