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. 2022 Oct 19;17(1):151–162. doi: 10.1038/s41396-022-01329-1

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© The Author(s) 2022

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. 2 — A Relative abundance of gene type. Percentage of antibiotic resistance genes (Abx) compared to metabolic genes (Met). Percentages are calculated from the total of the corresponding bar. “Total” corresponds to all annotated antibiotic resistance and metabolic genes, “Unique” corresponds to all unique gene variants, and “Grouped” refers to those from the “Unique” category further grouped by nucleotide variants (e.g., different variants of the same gene are grouped together). B Average gene type per plasmid. Histogram distributions show the number of genes (antibiotic resistance or metabolism) per total number of genes on each plasmid. Blue indicates frequency of metabolic genes per plasmid (top) and red indicates frequency of antibiotic resistance genes per plasmid (bottom). Black dashed line indicates the average number of gene type per plasmid for comparison. C Proportion of gene types on plasmids. Left and right panels show stacked horizontal bar graphs where the x-axis is the percentage of genes on each plasmid. Blue indicates antibiotic resistance genes, red indicates metabolic genes, and black indicates all other gene types. Plasmids are sorted top to bottom by antibiotic resistance (left) or metabolic (right) gene abundance. Any plasmid with neither an antibiotic resistance nor metabolic gene was removed for visibility. D Proportion of gene types by ST. Stacked bar graphs show percentage of plasmids with the corresponding number of genes belonging to antibiotic resistance or metabolic gene types. Plasmids are divided into the four categories of encoding 0, 1, 2, or 3+ metabolic genes (shades of red from light to dark) and antibiotic resistance genes (shades of blue from light to dark). Data for prevalent STs (131, 11, 73, 95) and other STs are shown separately (left and right panels, respectively). E Percentage of metabolic and antibiotic resistance functions. Red indicates genes belonging to metabolic categories as determined by KEGG (left) and blue indicates known antibiotic classes (right).