Fig. 2: High-level ampicillin resistance is achieved by increased expression of AmpC through promoter mutations and increasingly focusing gene amplifications.

a Promoter sequence of ampC gene, indicating all mutated loci observed in isolates from Experiments A and B (red letters). Each observed change, of either a single or multiple nucleotides, is indicated by a unique symbol. For combinations, a symbol indicates a change in all loci connected to it by black lines, e.g., the hexagram symbol indicates a concomitant change in three loci: two G > A transitions marked by sideways-pointing triangles and a single C > A transversion. b The normalised nucleotide copy number across the genome of the same isolates appearing in Fig. 1. Inset shows a zoom-in on the region around the ampC gene (grey box). Black scale bar represents 1000 bp. c The MIC and the copy number of the ampC locus are shown for each isolate (Exp A, n = 148, Grey; Exp B, n = 89; Pink). Shapes indicate the promoter mutation (as defined in a). Circle represents no ampC-associated mutation. Vertical lines denote antibiotic concentrations beyond which the ampC gene is always either amplified or carries a promoter mutation (orange) or is highly amplified in all isolates (green). d, e Normalised gene copy number of the region surrounding the ampC locus (150 genes from each side). Isolates ordered by the copy number of the ampC locus itself, for MEGA-plate Experiments A (d) and B (e). Source data are provided as a Source Data file.