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

Max L Cummins; Dmitriy Li; Aeman Ahmad; Rhys Bushell; Amir H Noormohammadi; Dinidu S Wijesurendra; Andrew Stent; Marc S Marenda; Steven P Djordjevic

doi:10.3390/microorganisms11061513

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

Microorganisms. 2023 Jun 6;11(6):1513. doi: 10.3390/microorganisms11061513.

Authors

Max L Cummins^{1

2}, Dmitriy Li^{1

2}, Aeman Ahmad^{1

2}, Rhys Bushell³, Amir H Noormohammadi³, Dinidu S Wijesurendra³, Andrew Stent⁴, Marc S Marenda³, Steven P Djordjevic^{1

2}

Affiliations

¹ Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia.
² The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia.
³ Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia.
⁴ Gribbles Veterinary Pathology, Clayton, VIC 3168, Australia.

Abstract

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.

Keywords: ST117; ST57; ST69; ST95; avian pathogenic E. coli (APEC); bacterial chondronecrosis; bacterial osteomyelitis; lameness; microbial genomics; poultry production.

Grants and funding

1.5.8/Poultry Cooperative Research Centre