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. 2020 Sep 8;10:14787. doi: 10.1038/s41598-020-71640-4

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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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The core genome phylogeny based on the Maximum Common Genome. The core genome phylogeny based on the Maximum Common Genome comprising 2,094 orthologous genes present in all isolates show four distinct clusters, whereby the genetic diversity within the clusters is rather low. Furthermore, the isolates metadata show no significant association with the core genome clusters. The 2,003 accessory genes show a distribution pattern that is highly correlated with the core genome clusters (right side), suggesting a lineage-specific gene content. Genes for aureolysin (aur), leucotoxins D and E (lukD, lukE), gamma-haemolysin component A–C (hlgA, hlgB, hlgC) and proteases SpIA or SpIB are present in all isolates. All isolates belonging to ST-1943 as well as some CC130 and CC599 were positive for different variants of the Staphylococcal pathogenicity island (SaPI) harbouring a toxic shock toxin encoding gene (tst), which were variants of tst-bov⁸⁰. Moreover, 48.5% of the mecC-positive isolates harboured staphylococcal enterotoxins (SE). The protease SpIE can just be found in 23/33 isolates and is not associated with any sequence type. The epidermal cell differentiation inhibitor B (edinB) cannot be determined in the isolates of ST-1943, ST-2361, ST-49 and ST-599.