Use of Genome Scale Metabolic Reconstructions of Avian Pathogenic Escherichia coli (APEC) phylogroups for the identification of lineage-specific metabolic pathways

Avian Pathogenic Escherichia coli (APEC) are a genetically diverse pathotype primarily associated with extra-intestinal infections in birds. APEC lineages are predicted to have unique metabolic capabilities contributing to virulence and survival in the host environment. Here we present a genome-scale metabolic model for the APEC pathotype based on 114 APEC genome sequences, and lineage-specific models for the phylogroups B2, C and G based on a representative isolate for each phylogroup. A total of 1,848 metabolic reactions were predicted in the 114 APEC isolates before gap filling and manual correction. Of these, 89% represented core reactions, whilst the 11% accessory reactions were mostly associated with carbon and nitrogen metabolism. Predictions of auxotrophy were confirmed by inactivation of the conditionally essential lysA and the non-essential potE genes. The APEC metabolic model outperformed the E. coli K-12 iJO1366 model in the Biolog Phenotypic Array platform. Sub-models specific for phylogroups B2, C and G predicted differences in the metabolism of 3-hydroxyphenylacetate (3-HPAA), a phenolic acid derived from the flavonoid quercetin, which is commonly added to poultry feed. Two 3-HPAA associated reactions/genes distinguished APEC phylogroup C from APEC phylogroups B2 and G, and 3-HPAA supported the growth of APEC phylogroup C in minimal media, but not phylogroups B2 and G. In conclusion, we have constructed genome-scale metabolic models for the three major APEC phylogroups B2, C and G, and have identified a metabolic pathway distinguishing phylogroup C APEC. This demonstrates the importance of lineage- and pathotype-specific metabolic models when investigating genetically diverse microbial pathogens. IMPACT STATEMENTAvian Pathogenic Escherichia coli (APEC) are the cause of colibacillosis in poultry, which results in a significant economic burden to the poultry industry, and strongly affects the health and welfare of flocks. APEC isolates show a high level of genetic diversity, which complicates diagnostics, epidemiology and the design of prevention and treatment strategies. In this study we have used genome sequences derived from 114 APEC isolates to investigate their metabolic capabilities, and define the metabolic diversity of APEC within a generalised APEC metabolic model, and lineage-specific metabolic models. These models have been interrogated to find unique pathways that can be targeted for the development of anti-APEC treatments, and one such metabolic pathway was identified as a proof of principle. This approach shows great promise for the design of future strategies to prevent and deal with APEC infections, and can be adapted to other genetically diverse microbial pathogens.