Toolbox for Exploring Avian Pathogenic Escherichia coli (APEC) Pathogenesis and Control

Colibacillosis, caused by Avian Pathogenic Escherichia coli (APEC), is a significant disease causing extensive animal and financial losses globally. New colibacillosis control approaches, based on fundamental knowledge of APEC pathogenesis, are needed. To date, limited high-quality, finished APEC genomes are available in the public domain, and are not representative of a diverse group of pathogens.  Here, we describe and compare the genomic sequences of these representative APEC strains that differ in key traits in an effort to generate a community toolbox of strains for studying APEC pathogenesis and control. In particular, we outline a new comparative genomic framework that accurately visualizes all strains showing where they intersect in a ‘core APEC’, drawing attention to analogous conserved regions, while concurrently highlighting aspects of intergenic SNP regions through a heat map across all fully sequenced and annotated genomes.  Moreover, we compare and contrast the sequence, genotypic, and phenotypic traits of APEC O1, O2, O18 and O78, which originate from some of the most common serogroups, phylogenetic groups, virulence genotypes, and syndromes associated with APEC. Ultimately, strains that were consistently virulent in chicks; lay in different but dominant genotype clusters; were assigned to different, but typical, phylogenetic types; and caused different manifestations of colibacillosis, were chosen for sequencing. Consequently, we believe these sequences will underpin vital research long into the future since these strains represent mainstream APEC, while also maximizing the knowledge that can be gleaned from each sequence due to their differences in key traits.