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. 2020 Mar 3;10:3937. doi: 10.1038/s41598-020-61002-5

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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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Phylogenomic relatedness tree constructed based on analysis of single-nucleotide polymorphisms (SNPs) of the core genes of E. faecium genomes (n = 342) isolated from various environments and samples related to beef production and processing systems, environment, and human-related sources. The genomes were compared using E. faecium DO genome (GenBank accession# CP003583.1) as a reference. Phylogenomic analysis of the WGS data was conducted using SNVPhyl⁸⁷ and the resulting newick tree file was visualized in FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/) to obtain phylogenomic dendrogram.