Fig. 6

a Phylogenetic SNP-based maximum likelihood tree for E. coli isolates with Novel ST from humans, chickens and poultry farm or market environments. The phylogenetic SNP-based maximum likelihood tree was rooted in a reference isolate E. coli strain NCTC11129. For each isolate, the source and origin: farm (F) or live bird market (LBM) as well as the phylogenetic group is displayed. The phylogenetic tree has several clades with a common ancestor however the red clade has two isolates from the same farm belonging to the same phylogroup and sharing a novel ST. These two isolates from human and poultry farm environments although quite diverse had similar plasmid replicons harbouring AMR genes. b Phylogenetic maximum likelihood tree for E. coli isolates with ST 1638. The SNP-based maximum likelihood tree was rooted in a reference isolate E. coli strain NCTC11129. Two isolates of human and avian origin although not clonally related acquired similar AMR genes