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. 2023 Nov 24;14:7715. doi: 10.1038/s41467-023-43345-5

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© The Author(s) 2023

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. 2 — The maximum likelihood phylogeny A shows the S. flexneri 2a isolates South African sub-sampled isolates (indicated by pink dot overlying the terminal node) among Phylogroup 3 representatives. The BAPS clusters for the South African samples are shown in the outer ring according, coloured to the inlaid key. Sub-clusters of polyphyletic Cluster 3 are indicated with ‘a’ (locally circulating) and ‘b’ (possibly imported). B A Maximum Clade Credibility tree from Bayesian analysis shows the population structure of the S. flexneri 2a with branch lengths in time, scaled in years by the concentric rings radiating from the tree MRCA in the centre. BAPS clusters are indicated in the ring immediately adjacent to tree tips, coloured according to top inlaid key) and their MRCA 95% HPDs are indicated by blue bars for BAPS Clusters 1, 2, and 4. The circulating sub-clusters of polyphyletic BAPS Cluster 3 are labelled ‘a’ and ‘b’ and the MRCA 95% HPD of locally circulating ‘a’ indicated at the defining node in orange. Other metadata rings (from inner to outer, coloured according to the inlaid keys) show the: antimicrobial resistance profiles by antimicrobial class (combination of predicted and phenotypic resistance—see methods; blue = resistant and orange = susceptible), breadth of mapping coverage across the SRL (green), the presence of virulence genes capU and traT (black), and where an isolate was derived from a blood sample (rather than stool; red). MRCA most recent common ancestor, HPDs highest posterior density interval, BAPS Bayesian analysis of population structure, SRL Shigella resistance locus. Source data are provided as a Source Data file.