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. 2019 Apr 2;10:542. doi: 10.3389/fmicb.2019.00542

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Copyright © 2019 Roe, Vazquez, Esposito, Zarrilli and Sahl.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Maximum-likelihood phylogeny of the Klebsiella pneumoniae ST101 lineage. The tree is based on 4,077 SNPs using the K3P+ASC+G4 nucleotide substitution model and includes 45 genomes that collectively cover 85.95% of the reference genome. The PHI test found statistically significant evidence for recombination in this dataset (P = 0.00e+00). All samples were screened for antibiotic resistance using ResFinder. The percent identity for each resistance gene was plotted using shinyheatmap alongside the phylogenetic tree. Gene lists are in Supplementary Table S6. MLS includes genes that confer resistance to macrolides-lincosamides-streptogramin B.