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. 2020 Sep 2;10:14428. doi: 10.1038/s41598-020-71344-9

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Non-metric multidimensional scaling (NMDS) plots of 87 S. Typhimurium genomes constructed using a Jaccard distance metric and presence/absence profiles of (A) orthologous gene clusters output by Roary version 3.11.0 and (B) gene ontology (GO) terms. Points represent isolates, while shaded regions and convex hulls correspond to (1) isolation source (bovine, bovine farm environment, or human clinical) and (2) lineage (I–IV, and “Outliers”, which encompasses the seven human clinical genomes that were not placed into one of the four major NYS S. Typhimurium lineages).