Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry

Bacterial chondronecrosis with osteomyelitis (BCO) impacts animal welfare and productivity in the poultry industry worldwide, yet it has an understudied pathogenesis. While Avian Pathogenic Escherichia coli (APEC) are known to be one of the main causes, there is a lack of whole genome sequence data, with only a few BCO-associated APEC (APEC(BCO)) genomes available in public databases. In this study, we conducted an analysis of 205 APEC(BCO) genome sequences to generate new baseline phylogenomic knowledge regarding the diversity of E. coli sequence types and the presence of virulence associated genes (VAGs). Our findings revealed the following: (i) APEC(BCO) are phylogenetically and genotypically similar to APEC that cause colibacillosis (APEC(colibac)), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APEC(BCO) are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APEC(colibac). Additionally, we performed genomic comparisons, including a genome-wide association study, with a complementary collection of geotemporally-matched genomes of APEC from multiple cases of colibacillosis (APEC(colibac)). Our genome-wide association study found no evidence of novel virulence loci unique to APEC(BCO). Overall, our data indicate that APEC(BCO) and APEC(colibac) are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APEC(BCO) genomes and provides insights for the management and treatment strategies of lameness in poultry.