Genome evolution and the emergence of pathogenicity in avian Escherichia coli

A few years in the making, but we’re finally pleased to see our paper on the emergence of virulence in avian Ecoli (APEC) published in Nature Communications.

University press release [link]

Referenced in Guardian article on Chicken disease [link]
Twitter thread [link]

Chickens are the most common birds on Earth and colibacillosis is 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 single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. 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 functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

Key messages
*Over 26 billion chickens worldwide, with poultry constituting around 70% of all bird biomass on earth.
*Colibacillosis caused by avian pathogenic Escherichia coli (APEC), a type of extraintestinal pathogenic E. coli (ExPEC), is commensal but emerges as a pathogen.
*In some cases mortality can reach 20%, condemning whole flocks, leading to suffering for millions of farmed birds and multimillion pound losses to the worldwide poultry industry.
*APEC emerge from multiple phylogroups and infection-associated elements are found in the core and accessory genome.
*RF model reached an out-of-sample classification accuracy of 76.9% for predicting infection status of E. coli strains (healthy carriage vs. disease).

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