Fig. 1

Core genome phylogeny and genomic features of E. coli ST410 isolates. ML phylogeny of 155 Ec ST410 nr genomes built with RAxML [39] based on the 3,937,051-bp core and recombination-free alignment of 3866 SNPs. The Ec ST88 isolate 789 (CP010315.1) was used as an outgroup. Isolates (branch tips) are color-coded according to the geographical origin as indicated in the figure key (left). Genomic features are indicated as indicated in the figure key (right) from left to right: groups according to the phylogeny, including the FQR clade and the OXA-181 subclade, carbapenemases, CTX-M ESBL, mutations in gyrA and parC QRDR region (FQ resistance); mutations in ftsI, ompC, and ompF. SNPs in the dcw cluster compared to the Ec ST410 non-recombined strain ANSES30599 (black arrow) are indicated by small vertical red bars. The upper part, genetic map of the dcw locus, genes are indicated by arrows, ftsI in red. NRC stands for National Reference Centre. Isolates analyzed for β-lactam susceptibility and fitness are indicated by stars (Fig. 7)