Endometrial pathogenic E. coli (EnPEC) isolates are involved in endometrial infections in animals and humans. Besides the high aggressiveness of the endometrial infections, the EnPEC virulence profile and pathogenesis are still little known. In this study, we have sequenced and analyzed an EnPEC strain from canine pyometra (E. coli_LBV005/17), following a molecular characterization of the virulence profile and phylogenetic evolution of an EnPEC collection from canines and felines (45 strains). Most of the strains belonged to phylo-group B2, and display a high virulence profile. In particular we highlight the classification of the E. coli_LBV005/17 as sequence type 131 (ST131), in addition to other five strains, as observed by gyrB phylogenetic analysis. Also, the phylogenetic position of EnPEC strains from pyometra in companion animals suggests that their origins are from both extraintestinal and commensal E. coli strains. Accordingly to Principal Coordinates Analysis (PCoA) and phylogenetic analysis we can propose that EnPEC strains have neither the same genetic profile, nor a unique common ancestral. In summary, the present work characterize an EnPEC genome from bitch pyometra and the genetic profile of 45 EnPEC strains from companion animals pyometra, being the commonest virulence pattern: fimA, papC, hlyA, hlyE, cnf1, entB, iroN, irp1, bssS, bssR, and hmsP. These data improving the background knowledge of this E. coli pathotype related to pyometra in companion animals and may support new methods to prevent the disease evolution. •An EnPEC isolated from canine pyometra had its genome described and classified as ST131.•EnPEC strains isolated from canines and felines have a high virulent potential.•Most of EnPEC strains isolates in companion animals pyometra cases were classified as B2 phylo-group.•The phylogenetic evolution of companion animals EnPECs seems to be from ancestral both intestinal and extraintestinal E. coli.