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. 2019 Nov 22;9:17394. doi: 10.1038/s41598-019-54004-5

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© The Author(s) 2019

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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The distribution of core (π, x-axis) and accessory pairwise genome distances (a, y-axis) with blue dots indicating isolate pairs and the contours indicating dot density (higher in yellow). Top left: All 4,071 assemblies displayed pairwise differences such that the contours indicated the three main clades: Clade A at π = 0.0038, a = 0.15; Clade B at π = 0.0014, a = 0.18; Clade C at both π = 0.0005, a = 0.08 and π = 0.0001, a = 0.09. Top right: 1,113 subclade C1_6 assemblies had a peaks mainly at π ≤ 0.001, a = 0.06. Bottom left: 386 subclade C2_4 assemblies had peaks at π = 0.0006, a = 0.045 and π = 0.0001, a = 0.040. Bottom right: 1,651 subclade C2_9 assemblies had peaks at π = 0.0007, a = 0.065 and π = 0.0, a = 0.090. Results for 2,416 bla_CTX-M-positive Clade C assemblies and 52 subclade C0 assemblies were similar. Within subclades C1_6, C2_4, C2_9, isolates had more diverse accessory genomes compared to their core ones.