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. 2020 Aug 3;14(8):e0008440. doi: 10.1371/journal.pntd.0008440

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© 2020 Kariuki et al

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Fig 2 — Maximum likelihood phylogenetic tree based on the 130 S. Typhimurium genome sequences from this study. Sequencing reads were mapped to S. Typhimurium ST313 lineage II reference strain D23580, and S. Typhi 10040_15 was added as an outgroup to root the tree. The tree is based on 61161 chromosomal SNPs. Patient state (case/control) and the source (blood/stool) is visualized as indicated in the legend. Presence of multidrug resistance markers (MDR; bla, dfrA, sul, cat), blaCTX-M/blaOXA antimicrobial resistance markers and SNPs in gyr are annotated. Branch lengths represent numbers of SNPs as indicated in the scale bar.