In 2014-2016 the broiler production in most of North European countries was severely challenged by infections due to Escherichia coli. During this period, the mortality in broilers and, to a lesser extent, in broiler breeders increased dramatically. The genotypic analysis identified one particular virulent clone of Escherichia coli (ST117 O78:H4) to be highly associated with the increased mortality. In Denmark, introduction of an autogenously vaccine based on two E. coli strains (ST117 O78:H4 and ST95 O2:H5) in broiler breeders began late 2016. Mortality has subsequently decreased but it was unknown whether the birds remained to carry E. coli strains similar to the two strains included in the autogenous vaccine in their intestinal tract. In the present study cloacal samples were investigated for the presence of the two strains used for the autogenous vaccine. Cloacal samples from 170 broiler breeders and 190 broilers were obtained and plated on selective media. A total of 360 confirmed E. coli isolates were analyzed by an ST95- and an ST117 O78:H4 specific PCR. Subsequently, isolates identified as E. coli ST95 (n=6) were whole-genome sequenced (WGS). E. coli ST117 O78:H4 was not detected in any of the fecal samples. WGS data obtained from Enterobase showed that E. coli ST117 078:H4 and E. coli ST95 are still associated with disease in broilers and breeders both outside and inside Denmark.
In conclusion, despite application of an autogenous vaccine based on the outbreak strains from 2014-2016 E. coli ST117 and ST95 remains to cause mortality in the broiler production in and outside Denmark, however, at a much lower rate than in 2014-2016. While E. coli ST95 may have a reservoir in the intestine of apparently healthy carries, the same could not be documented for E. coli ST117 O78:H4.