Fig. 4

Heatmap indicating presence or absence of virulence factors. Each row of the binary matrix indicates the presence or absence of a virulence-associated gene (a BLASTP+ hit). VF classes are indicated at the side in black and grey. Strain names are color-coded for MAEC (red) or commensal (green) pathotype affiliation, columns for strain phylogroup affiliation (green: A, blue: B1, orange: B2, red: E). The clustering dendrogram attached to the heatmaps is based upon the whole binary dataset (not for each heatmap separately) of a best scoring ML tree with 1000 bootstrap resamplings (a more detailed representation of the cladogram can be found in Additional file 3: Figure S2C). Bootstrap support values are arbitrarily indicated at the bifurcations of the cladogram. Statistically significant pathotype-enriched VF genes are indicated for MAEC and commensal isolates by cows in red or green, respectively. Only the aerobactin biosynthesis cluster (Aer) plus transport protein ShiF is significantly commensal-enriched and not associated with a phylogroup (indicated by a black-rimmed and opaque green cow). All other pathotype-enriched virulence-associated genes also have a significant phylogroup association. The genes of well-known and important E. coli VFs are highlighted in alternating red and brown squares: Curli = curli fibres, AFA-VIII = aggregative adherence fimbriae AFA-VIII, Auf = fimbrial adhesin, CS31A = CS31A capsule-like antigen (K88 family adhesin), Lpf = long polar fimbriae, F17b = F17b fimbriae, Pap = P/Pap pilus, Pix = Pix fimbriae, Flag-1 = E. coli peritrichous flagella 1 gene cluster, Flk = alternative flk flagellin islet, Flag-2 = E. coli lateral flagella 2 gene cluster, Heme = chu heme transport system, Enterobactin = enterobactin biosynthesis/transport gene cluster, Fec = ferric iron(III)-dicitrate uptake system, Fit = ferrichrome iron transport system, Aer = aerobactin biosynthesis cluster with iutA receptor, Ybt = yersiniabactin iron transport system, G4C = group 4 capsule, K5 = K5 capsule, T2SS-1 = gsp general secretion pathway 1, ETT2 = E. coli type three secretion system 2, T6SS/1_ECC-1470 = MAEC ECC-1470 subtype i1 T6SS/1, T6SS/2_536 = UPEC 536 subtype i2 T6SS 2, AAI/SCI-II = EAEC 042 subtype i4b T6SS 3, SCI-I = EAEC 042 subtype i2 T6SS 2, Cdt = cytolethal distending toxins, Hly = alpha-hemolysin, Mch_H47 = microcin H47. Clustering of the strains according to virulence-associated gene presence/absence also follows mostly the phylogenetic history of the strains, no clustering of pathotypes was detected. Both MAEC and commensal isolates are distinguished by the lack of classical pathogenic E. coli VFs. The same heatmap, but including gene names/locus tags, can be found in Additional file 3: Figure S6