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. 2024 May 29;15:4555. doi: 10.1038/s41467-024-48352-8

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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 An illustration of our workflow for detecting resistance islands in plasmid genomes. Arrow boxes correspond to genes. (1) Protein-coding genes in bacterial genomes were clustered into gene families. ARGs and SSR genes were identified. (2) Significant cooccurrence tests for ARG pairs were conducted per replicon type in each genus. (3) Collinear syntenic blocks (CSBs) including coARGs were identified across genomes and (4) further compared to previously recognized transposable elements by sequence similarity (see Methods for additional clarifications). (B) Cumulative Distribution Function (CDF) plots show that the distance between ARGs is shorter than the distance between a control group of randomly sampled genes in plasmids (left), but not in chromosomes (right). Intergenic distances were calculated by counting the number of protein-coding genes between two, and up to ten, adjacent ARGs. Source data are provided as a Source Data file.