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. 2020 Dec 21;6(3):327–338. doi: 10.1038/s41564-020-00836-1

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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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Fig. 3 — The combination matrix (bottom) depicts predicted AMR patterns of S. Typhimurium. Isolates collected before 1996 were sampled only sporadically, and thus were excluded from analysis. Within the combination matrix, dark grey circles indicate genome-predicted resistance and the vertical combination of grey circles represents the resistance profile. Total number of isolates with each resistance profile is indicated below the matrix. The combination matrix was created using the UpSetR package⁸⁷. The bubble plot (top) depicts the relative number of isolates (bubble size) with each resistance profile (combination matrix) per year (y axis). Lineage assignments are shown using bubble colour to identify lineage-specific AMR trends. Local Malawi antimicrobial usage policy⁹ is highlighted in background colours overlaid on the timeline in the bubble plot. The bubble plot was created using R ggplot2⁸⁸.