Fig. 2: Overview of the population structure, metadata, antimicrobial resistance genes and plasmid replicon types of S. Concord super-lineage A. | Nature Communications

Fig. 2: Overview of the population structure, metadata, antimicrobial resistance genes and plasmid replicon types of S. Concord super-lineage A.

From: A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Fig. 2

Maximum likelihood phylogeny for 245 S. Concord isolates belonging to super-lineage A and based on 7148 non-recombinant core SNPs. The tree was rooted on a closely related S. enterica serovar Potsdam isolate that was also part of super-lineage A. Lineage names are indicated in each coloured square (e.g. Lineage 1 = L1). Tips highlighted with a coloured dot were selected for long-read sequencing. Ggtree v2.2.4 was used to plot the tree. Metadata is shown at the right side of the tree together with a summary of commonly occurring AMR genotypes and the presence- (blue cells) or absence (white cells) of common AMR genes and replicon types. The scale bar indicates the number of substitutions per site. ComplexHeatmap v2.8.0 was used to for plotting. Abbreviations: AMR = antimicrobial resistance, MDR = multidrug resistance, ESBL = extended-spectrum beta-lactamase, XDR = extensive drug resistance, PDR = pandrug resistance, sus = susceptible, 3GC = third-generation cephalosporin, AZ = azithromycin.

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