pntd.0008991.g001.tif (859.75 kB)
A maximum likelihood single-nucleotide polymorphism (SNP)–based phylogeny of S. Typhimurium isolates from Kenya between 2000 and 2011 associated with invasive disease.
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posted on 2021-02-01, 18:32 authored by Jessica Z. Kubicek-Sutherland, Gary Xie, Migun Shakya, Priya K. Dighe, Lindsey L. Jacobs, Hajnalka Daligault, Karen Davenport, Loreen R. Stromberg, Zachary R. Stromberg, Qiuying Cheng, Prakasha Kempaiah, John Michael Ong’echa, Vincent Otieno, Evans Raballah, Samuel Anyona, Collins Ouma, Patrick S. G. Chain, Douglas J. Perkins, Harshini Mukundan, Benjamin H. McMahon, Norman A. DoggettThe strains that were sequenced as part of this study are represented as UGA followed by a number, and all other strains were previously reported by the publications indicated in the “Reference” column. Names of genomes from this study are colored in pink, isolates from lineage 1 and lineage 2 identified previously by Okoro et al. [24] are colored in cyan and purple respectively, and all other genomes are colored in gray. The tree was rooted using the midpoint method in iTOL. The scale bar indicates number of substitutions per site. Bootstrap support are labeled on branches with black dots whose size correspond to bootstrap support values.
