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. 2021 Feb 4;11:3046. doi: 10.1038/s41598-021-82357-3

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© The Author(s) 2021

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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Maximum likelihood phylogenetic tree based on core genome alignment between the S. uberis isolates identified in this study. S. iniae YSFST01-82 (accession number: GCF_000831485.1) was used as an outgroup and S. uberis 0140J (accession number: AM946015) (MLST ST1, GCC ST5) as an ingroup. Bootstrap values are shown in numbers along branches. Purple labels show Queensland isolates. Yellow labels show Victorian isolates. MLST STs are shown, as well as GCC STs. GCCs are coloured, GCC ST86 coloured red, GCC ST 5 coloured blue, GCC ST143 coloured grey. Core genome alignment was performed in roary (version 3.13.0)¹¹⁵ and maximum likelihood tree was built in RAxML version 8.2.10 (raxmlHPC-PTHREADS-SSE3)¹²⁰ with 1000 replicates. Tree visualised in FigTree version 1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/). For figure clarity, the phylogenetic tree was visualised using a cladogram transformation. Data S1 shows the untransformed tree, along with an isolate-only tree which shows very high bootstrap support at almost every node (~ 100%) due to the increased number of genes in the core genome alignment.