Fig. 4
Linkage networks for detected alleles of acquired AMR genes in 169 E. coli and 359 Salmonella genomes. Each node represents an allele or a cluster of identically distributed alleles, with a diameter proportional to the allele frequency and a colour indicating the AMR phenotype encoded. Every edge is directed, starting from an explanatory allele and terminating at a response allele, representing a significant association determined using an LMM. The edge width is proportional to \(|\hat {\beta }|\) of the explanatory allele in an LMM. Solid edges represent significant positive associations (\(\hat {\beta } > 0\)) while dashed edges represent significant negative associations (\(\hat {\beta } < 0\)). The edge colour follows a gradient of the distance score sd to indicate the strength of evidence for physical linkage. The shaded area (light green) encircles alleles of known co-transferred AMR genes. AMR classes defined by antimicrobials that bacteria were resistant to: AGly (aminoglycosides), Bla (beta-lactams), Flq (fluoroquinolones), MLS (macrolides, lincosamides, and streptogramins), Phe (phenicols), Sul (sulfonamides), Tet (tetracyclines), Tmt (trimethoprim), and Mix (multiple classes of antimicrobials)