Longitudinal study on the effect of autogenous vaccine application on the sequence type and virulence profiles of Escherichia coli in broiler breeder flocks.

Colibacillosis is one of the most common problems in the poultry industry. Escherichia coli strains on farms are often genetically diverse and therefore commercial vaccines provide little protection to the flocks. Here, we investigated the effect of the autogenous E. coli vaccines on the prevalence of 84 virulence-associated genes in E. coli isolated from four and five consecutive flocks on two broiler breeder farms, respectively. 115 E. coli isolates were sequenced using Illumina technologies, and compared based on both their set of housekeeping genes and their virulence profiles, defined through the composition of virulence genes. Predominantly, phylogenetic analysis showed obvious distinction between the isolates originating from different farms suggesting spatial-dependent transmission of pathogenic strains. We detected 23 sequence types, while 52.58 % of the isolates belonged to two clonal complexes. Analysis of the virulence genes showed highest prevalence (>85 %) of feoB, uspA, uspB, uspG, uspE, fimH, ompA, astA, focA, hlyE, uspC, crl, csgA, ompT and iss, of which 50 % are toxin associated genes, demonstrating the importance of competition in the pathogenesis process. Interestingly, usp genes, which are primarily associated with uropathogenic E. coli strains, were detected in all investigated isolates. The heatmap analysis demonstrated that strains belonging to same phylogenetic groups often share similar virulence profiles, confirming the usefulness of quick tests for phylogenetic typing. However, our results suggest the need to update the list of the minimal predictors used for the identification of avian pathogenic strains. Overall results indicate that continuous application of autogenous vaccines led to lower genetic diversity of E. coli housekeeping genes, but not virulence genes.