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

Cummins, ML; Li, D; Ahmad, A; Bushell, R; Noormohammadi, AH; Wijesurendra, DS; Stent, A; Marenda, MS; Djordjevic, SP

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

Cummins, ML Li, D

Ahmad, A Bushell, R Noormohammadi, AH Wijesurendra, DS Stent, A Marenda, MS Djordjevic, SP

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Publisher:: MDPI
Publication Type:: Journal Article
Citation:: Microorganisms, 2023, 11, (6), pp. 1513
Issue Date:: 2023-06-06

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Field	Value	Language
dc.contributor.author	Cummins, ML
dc.contributor.author	Li, D https://orcid.org/0000-0002-7535-8184
dc.contributor.author	Ahmad, A
dc.contributor.author	Bushell, R
dc.contributor.author	Noormohammadi, AH
dc.contributor.author	Wijesurendra, DS
dc.contributor.author	Stent, A
dc.contributor.author	Marenda, MS
dc.contributor.author	Djordjevic, SP
dc.date.accessioned	2023-09-29T04:56:27Z
dc.date.available	2023-06-03
dc.date.available	2023-09-29T04:56:27Z
dc.date.issued	2023-06-06
dc.identifier.citation	Microorganisms, 2023, 11, (6), pp. 1513
dc.identifier.issn	2076-2607
dc.identifier.issn	2076-2607
dc.identifier.uri	http://hdl.handle.net/10453/172384
dc.description.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 (APECBCO) genomes available in public databases. In this study, we conducted an analysis of 205 APECBCO 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) APECBCO are phylogenetically and genotypically similar to APEC that cause colibacillosis (APECcolibac), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APECBCO are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APECcolibac. 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 (APECcolibac). Our genome-wide association study found no evidence of novel virulence loci unique to APECBCO. Overall, our data indicate that APECBCO and APECcolibac are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APECBCO genomes and provides insights for the management and treatment strategies of lameness in poultry.
dc.format	Electronic
dc.language	eng
dc.publisher	MDPI
dc.relation.ispartof	Microorganisms
dc.relation.isbasedon	10.3390/microorganisms11061513
dc.rights	info:eu-repo/semantics/openAccess
dc.subject.classification	3107 Microbiology
dc.subject.classification	3207 Medical microbiology
dc.title	Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry.
dc.type	Journal Article
utslib.citation.volume	11
utslib.location.activity	Switzerland
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - AIMI - Australian Institute for Microbiology & Infection
utslib.copyright.status	open_access	*
dc.date.updated	2023-09-29T04:56:20Z
pubs.issue	6
pubs.publication-status	Published online
pubs.volume	11
utslib.citation.issue	6

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 (APECBCO) genomes available in public databases. In this study, we conducted an analysis of 205 APECBCO 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) APECBCO are phylogenetically and genotypically similar to APEC that cause colibacillosis (APECcolibac), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APECBCO are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APECcolibac. 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 (APECcolibac). Our genome-wide association study found no evidence of novel virulence loci unique to APECBCO. Overall, our data indicate that APECBCO and APECcolibac are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APECBCO genomes and provides insights for the management and treatment strategies of lameness in poultry.

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http://hdl.handle.net/10453/172384