Fig. 9: AMR-associated genes have been found to impact numerous metabolic pathways in S. enterica, many of them are also considered essential metabolic genes, however, are prevalent across all pathways only in certain serotypes in the S. enterica phylogeny.
a An overview of the metabolic pathways affected by those AMR-associated genes significantly influencing reaction fluxes in S. enterica. All genes annotated were found to have reduced the flux span through the metabolic system when knocked out, six of which were essential genes (i.e. gene knockouts were lethal in rich media). Significance was tested using hypergeometric enrichment tests (two-tailed) with the false discovery rate (FDR) threshold <1%. Genes highlighted in blue were selected in the S. enterica ML models only, genes in red were selected in both the E. coli and S. enterica models, metabolic pathways are labelled in brown. b Heatmap showing, for each S. enterica isolate (columns of the heatmap), whether the isolate contained an AMR-associated gene that if knocked out also significantly affected one or more metabolic pathways. The top part of the heatmap shows the phytogenic relationship between each isolate. The first row of the heatmap indicates the phylogroup to which each isolate belongs. The subsequent rows indicate the metabolic pathways into which the genes were grouped, with only pathways significantly enriched with ML selected genes shown. Pink represents the presence of a mutated gene/accessory gene, blue represent the absence.
