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. 2024 May 7;2:14. doi: 10.1038/s44259-024-00032-9

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© The Author(s) 2024

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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Fig. 1 — a Midpoint-rooted maximum likelihood tree showing the phylogenetic relationships of 852 S. aureus genomes. The tree was built using 105,706 SNPs of aligned sequences of 2128 core genes. The tree scale represents the number of nucleotide substitutions per site. Support for phylogenetic nodes was estimated using 100 bootstrap replicates. For visual clarity, only the bootstrap values for major internal nodes are shown. For details of the bootstrapping analysis, the tree file is included in Supplementary Table 7. Colored lines extending out of the branches in the tree represent the 16 sequence clusters inferred by the program BAPS. The three outer rings represent the sequence type (ST) and phenotypic results of cefoxitin or oxacillin phenotypic screenings. Clonal complexes (CC) are shown in parentheses next to the STs in the color legend. b Yearly distribution of the proportion of major STs across the entire population throughout the study period. The number of isolates per year is shown at the top of the plot. c Linear regression model of the maximum number of different STs per year. d Yearly distribution of the number of isolates identified as methicillin-resistant based on in vitro testing as a proportion of the total number of isolates of each ST throughout the study period. The black dashed line shows the overall percentage of methicillin-resistant isolates over the years. For visual clarity, in panels a, b, d, only the seven most common STs are labeled, and less common STs were grouped together as Other STs.