Fig. 5

SNP-based phylogeny of MDR E. coli isolates from humans, chickens, and poultry environments in Abuja, 2019. SNP-based maximum likelihood phylogeny of E. coli isolates visualized in iterative Tree of life tool (iTol). The tree was rooted in a reference isolate E. coli strain NCTC11129. Clustering of isolates was found to be following the core genome and SNP-based phylogenies. The clustering of isolates belonging to the same phylogenetic group and sequence type was consistent. Shown for each isolate is the source/origin: farm (F) or live bird market (LBM) and phylogroup. AMR genes cluster for 110 E. coli strains are displayed on the phylogenetic tree. The presence (orange) and absence (white) of 12 AMR genes that were most prevalent are represented in the image while the presence (gray) and absence (white) of 10 prevalent plasmid replicons are also represented in the image