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. 2021 Sep 9;9(9):1911. doi: 10.3390/microorganisms9091911

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© 2021 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Phylogenetic relationship between S. Choleraesuis (ST145) wildlife isolates and isolates from food, feed and farm animals. Maximum likelihood phylogenetic tree based on core SNPs in the bacterial chromosome. The chromosome sequence of S. Choleraesuis str. SCSA50 isolate A50 (NZ_CM001062.1) was used as reference. The tree was computed with the snippySnake pipeline with IQ-TREE, visualized in iTOL and manually rooted to the reference. The colour bars (inside to outside) identify the German federal state (f), national country (c), sampling year (y) and matrix (m) of the samples. Isolates carrying antimicrobial resistance genes are highlighted in colour with the type of resistance genes indicated. The scale bar shows the genomic distances of the sequences in substitutions per site.