FIGURE 2.

The resistome of 3,377 Salmonella strains. Gene, protein or variant presence were determined using the RGI-CARD (Mcarthur et al., 2013). Of 1,003 unique resistomes, only those present in at least five strains are shown; the histogram at the top represents absolute frequency. Other resistomes are condensed in the “Rare genes” column. AMR genes and variants are grouped by antibiotic family or function. Genes encoding efflux pumps, which are generally conserved, have been removed for figure clarity. Green: perfect match to a gene in the CARD, red: similar to a gene in the CARD, according to curated homology cut-offs, gray: perfect match and/or similar to a gene in the CARD, black: no match in the CARD, ^∗(wildcard) represents multiple forms (exact number between square brackets) of the same gene or protein, ^†specific variants conferring resistance (protein variant models).