Figure 2

Phylogenetic tree presenting Escherichia coli obtained during a non-outbreak period. Midpoint rooted phylogenetic tree based on core genome single-nucleotide polymorphisms (SNPs) of the 77 E. coli isolated from Danish broiler breeder and broiler farms. Farm/progeny origin is indicated on the phylogeny, as is colibacillosis status of the host. Colibacillosis defined as presence of fibrinous-, purulent-, fibrinopurulent or mucopurulent exudate inflammation is presented with black circles, whereas the absence is denoted with open circles. §Single-locus variants are observed within the ST10 cluster (ST7321 (n = 3), ST6665 (n = 3) and ST1141 (n = 1)). The tree is based on 222 391 SNPs detected within a ~3.03 Mbp conserved core genome across the collection. *Depicts E. coli isolate E51 used as reference. Scale bar indicates substitutions per site. Among the 77 isolates, 24 were obtained from the liver, 16 from the salpinx, 22 from the lung, and 12 from the yolk sac. The spleen, umbilical area, and a case of arthritis each contributed with a single isolate. Isolates from birds with an absence of lesions consistent with colibacillosis represented isolation sites: liver, lung, salpinx, yolk sac and joint (n = 6, 11, 2, 4 and 1, respectively).