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. 2021 Jan 20;13:9. doi: 10.1186/s13073-020-00825-3

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© The Author(s) 2021

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Definition of the plasmid types (A–I) observed in the 86 retrieved vanA complete plasmid sequences. a Network representation of the vanA complete plasmid sequences based on Mash distances (k = 21, s = 1000). Nodes (n = 76) in the network correspond to complete plasmid sequences and edges were defined if nodes shared a minimum Mash distance of 0.025. Edges correspond to connections between sequences with a similar k-mer composition. Nodes were colored according to the defined plasmid type assignment. Based on the modularity values and structure of the network components, we identified the plasmid types: A, B, C, D, E, G, H, and I. Twelve complete plasmid sequences (NC_014726.1, AP022823.1, NC_013317.1, NZ_CP012594.1, NC_005054.1, NZ_CP022486.1, NZ_CP014531.1, NZ_CP040238.1, E8172_3, NZ_CP036247.1, NZ_CP018130.1, NZ_CP019973.1) are not present in the network since they did not share any edges connecting to other nodes (singletons). b Heatmap and hierarchical clustering (ward.D2 method) of the pyani pairwise alignment coverage obtained from the 86 vanA complete plasmid sequences. On the left side, the plasmid types (A, B, C, D, E, F, G, H, I) previously defined in the network (panel a) are indicated. The twelve plasmid sequences corresponding to singletons are also included in this analysis