Population genomics and evolution of Avian Pathogenic E. coli

Chickens are the most common birds on earth and colibacillosis in among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no one virulence gene present in all pathogenic isolates. Here we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse predicted functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. Horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenicity elements in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification emergent APEC in healthy flocks.