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. 2023 Jul 12;14:4083. doi: 10.1038/s41467-023-39416-2

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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 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. 4 — The abundance of variants in A genes associated with antibiotic resistance and B all variants as a function of sampling depth (i.e. number of isolates) in single strain (blue) and mixed strain (orange) patients. Each data point represents a unique combination of ST and patient. We modelled the number of variants with a negative binomial regression accounting for the infection type, number of isolates, and a possible interaction between them (n.variants ~ infection type*isolates). The number of isolates per ST was positively associated with increased number of resistance variants (0.13 +/− 0.05 variants per additional isolate; z = 2.57, p = 0.01) and other variants (0.13 +/− 0.03; z = 4.17, p < 0.001). There was no significant difference between STs from single strain and mixed strain patients in terms of A resistance variants or B genetic diversity (Supplementary Table 4a, 4b). We excluded a single strain population with an exceptionally high number of resistance variants (grey data point, see ‘Methods’), although including it did not change this conclusion (Supplementary Table 4c, 4d). The raw data is presented in the source data file.