Aligning in vivo pathogenicity of Escherichia coli in embryos and chickens with genome characteristics

Escherichia coli resides as a gut commensal in healthy chickens but also causes the extraintestinal disease called colibacillosis. Pathotype definition is primarily based on the clinical condition of the host, but it is still not definite due to the lack of genetic traits to differentiate between commensal and harmful isolates, which has led to divided views with regard to the pathogenicity of E. coli in poultry. In this study, embryos and chickens were experimentally infected with E. coli isolates from birds with well-defined clinical history and outcomes were aligned with antimicrobial sensitivity profiles and global genetic traits of isolates revealed by whole genome sequencing. Fifteen isolates (O78:K80) from the femur of broilers with or without femoral head necrosis (Gaußmann et al., 2018) and one from the ovary of a layer with colibacillosis (O1:K1, PA14/17480/5-ovary; Zloch et al., 2018) were selected for the embryo lethality assay. E. coli isolates greatly differed in terms of embryo mortality, which ranged from 33–100%. No correlation was observed among the severity of lesions in the femur, resistance against certain antibiotics and embryo lethality. Subsequently, the pathogenicity of PA14/17480/5 ovary and three broiler isolates (PA15/19103-3, PA15/25396-3-right, PA15/24960-2) that showed the highest embryo mortality rate was tested in two-weeks old chickens. Following infection, clinical signs, macroscopic and microscopic lesions as well as bacterial re-isolation from organs were investigated. Based on these parameters, PA15/19103-3 was the most pathogenic among broiler isolates, similar to PA14/17480/5-ovary. Genetically, all four isolates displayed similarity in the genome length and number of genes contained. PA14/17480/5 ovary and PA15/19103-3 belonged to the phylogroups B2 and C, respectively, whereas the remaining two strains were assigned as phylogroup G. In total, 259 virulence factors were present in at least one of the four E. coli isolates. Out of these, 128 were commonly present in all four strains, which included genes that were previously reported to be associated with avian pathogenic E. coli (APEC). Finally, the PathogenFinder tool predicted the high pathogenic potential of all four isolates in human.
In conclusion, discrepancies were observed in terms of pathogenicity in embryos and chickens among E. coli isolates that contained a similar set of genes. It highlights the importance of the natural host for the determination of the pathogenicity of avian E. coli isolates.