Fig. 3: Multi-drug versus antibiotic-specific resistance mutations.

A Every gene arranged by the number of unique mutations identified in that gene and how much the mutations dispersed throughout the gene. Dispersion was defined as the mean distance between adjacent mutations, divided by the maximum possible distance if all mutations were equally far apart. In other words, low dispersion means that mutations clustered in a specific region of the gene, while higher values indicate mutations were spread across the entire length of the gene. The color shows if the gene was classified as multi-drug, antibiotic-specific, or unclear (those with insufficient mutation occurrences to categorize confidently). Size indicates the proportion of samples where mutations in that gene were observed, out of a maximum of 12 for antibiotic-specific genes or 35 for multi-drug and unclear genes. The bars below summarize each quarter of the plot, with an additional bar on the left representing genes that cannot be displayed on the plot’s axes, as only one unique mutation was observed. B The same plot, with points colored by the average impact type of all mutation occurrences in that gene. High: nonsense and frameshift, Moderate: non-synonymous and in-frame, Low: synonymous. Black indicates a non-coding RNA. Stars indicate that we also detected at least one occurrence of an insertion element mobilization event within the gene. Below is the impact-type distribution of all mutations occurring in MDR vs. ASR genes. C The mean number of mutations associated with MDR vs. ASR in any one sample. Error bars are SEM (multi-drug and unclear: n = 35, CIP and CYC: n = 12, NIT: n = 11). D Proportion of MDR vs. ASR mutations associated with different functional categories. Source data are provided as a Source Data file.