Avian pathogenic Escherichia coli (APEC) are a pathotype of extraintestinal pathogenic E. coli (ExPEC) that cause respiratory, soft tissue and systemic infections in poultry, cause significant financial burden and reduce the productivity of poultry operations. APEC have also been implicated as zoonotic agents capable of causing urinary tract infections in mammalian disease models and can carry virulence-associated gene (VAG) combinations that are associated with septicaemia and neonatal meningitis in humans. As APEC are constituents of the normal intestinal microflora of poultry, and common contaminants of poultry products, there is speculation that poultry-associated E. coli may threaten human health. These microbes may also harbor antimicrobial resistance genes (ARGs) which can complicate the treatment of both human and animal disease. Comparative genomic studies of human ExPEC and APEC are required, but genomic epidemiological data on Australian APEC is scarce.
We sequenced ninety-seven APEC genomes from regions across Australia, investigated their phylogenetic relatedness and screened them for ARGs and VAGs. Strains from phylogroups D and B2 predominated, with phylogroups B1 and A comprising the remainder. Thirty-one sequence types (STs) were identified, but ST117-D, ST350-D, ST57-D, ST429-B2, ST95-B2 and ST973-D predominated. Many of these STs have been reported globally as human ExPEC lineages and their VAG profiles resembled those of human ExPEC. SNP analyses and pathogenesis studies are needed to further elucidate these associations. Genotypic multidrug resistance was common, however no genes conferring resistance to critically important antimicrobials were detected. This indicates that tight regulation of these antibiotics in Australia has been efficacious in limiting selection for antimicrobial resistance.
Therefore, APEC sourced from poultry may have zoonotic potential and/or a capacity to augment the pathogenicity of potential human pathogens through disseminating laterally transmissible plasmids carrying VAGs or ARGs.