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Fig. 3 | BMC Genomics

Fig. 3

From: GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

Fig. 3

Comparative 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 fill colour indicating the AMR phenotype encoded. The yellow node border denotes an allele or allele cluster detected in one genome. The edge width is proportional to the strength of a significant association (\(|\hat {\beta }|\)) determined using an LMM. Edge colours indicate significant associations from LMMs or PLMs or both. Solid and dashed edges represent significant positive (\(\hat {\beta } > 0\)) and significant negative associations (\(\hat {\beta } < 0\)), respectively, identified using models indicated by edge colours. The Venn diagram of each panel counts edges under each colour. 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)

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