Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene

Cummins, ML; Reid, CJ; Chowdhury, PR; Bushell, RN; Esbert, N; Tivendale, KA; Noormohammadi, AH; Islam, S; Marenda, MS; Browning, GF; Markham, PF; Djordjevic, SP

Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene

Cummins, ML Reid, CJ

Chowdhury, PR

Bushell, RN Esbert, N Tivendale, KA Noormohammadi, AH Islam, S Marenda, MS Browning, GF Markham, PF Djordjevic, SP

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Publication Type:: Journal Article
Citation:: Microbial Genomics, 2019, 5 (2)
Issue Date:: 2019-02-01

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Field	Value	Language
dc.contributor.author	Cummins, ML	en_US
dc.contributor.author	Reid, CJ https://orcid.org/0000-0001-6872-330X	en_US
dc.contributor.author	Chowdhury, PR https://orcid.org/0000-0003-4352-603X	en_US
dc.contributor.author	Bushell, RN	en_US
dc.contributor.author	Esbert, N	en_US
dc.contributor.author	Tivendale, KA	en_US
dc.contributor.author	Noormohammadi, AH	en_US
dc.contributor.author	Islam, S	en_US
dc.contributor.author	Marenda, MS	en_US
dc.contributor.author	Browning, GF	en_US
dc.contributor.author	Markham, PF	en_US
dc.contributor.author	Djordjevic, SP https://orcid.org/0000-0001-9301-5372	en_US
dc.date.issued	2019-02-01	en_US
dc.identifier.citation	Microbial Genomics, 2019, 5 (2)	en_US
dc.identifier.uri	http://hdl.handle.net/10453/129833
dc.description.abstract	© 2019 The Authors. Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum b-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes bla TEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids.	en_US
dc.relation.ispartof	Microbial Genomics	en_US
dc.relation.isbasedon	10.1099/mgen.0.000250	en_US
dc.subject.mesh	Animals	en_US
dc.subject.mesh	Escherichia coli	en_US
dc.subject.mesh	Escherichia coli Infections	en_US
dc.subject.mesh	Poultry Diseases	en_US
dc.subject.mesh	Integrases	en_US
dc.subject.mesh	Escherichia coli Proteins	en_US
dc.subject.mesh	DNA, Bacterial	en_US
dc.subject.mesh	DNA Transposable Elements	en_US
dc.subject.mesh	Bacterial Toxins	en_US
dc.subject.mesh	Virulence Factors	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Drug Resistance, Multiple, Bacterial	en_US
dc.subject.mesh	Virulence	en_US
dc.subject.mesh	Genome, Bacterial	en_US
dc.subject.mesh	Plasmids	en_US
dc.subject.mesh	Australia	en_US
dc.subject.mesh	Whole Genome Sequencing	en_US
dc.title	Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene	en_US
dc.type	Journal Article
utslib.citation.volume	2	en_US
utslib.citation.volume	5	en_US
utslib.for	0604 Genetics	en_US
utslib.for	0605 Microbiology	en_US
pubs.embargo.period	Not known	en_US
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 - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access
pubs.issue	2	en_US
pubs.publication-status	Published	en_US
pubs.volume	5	en_US

Abstract:

© 2019 The Authors. Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum b-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes bla TEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids.

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http://hdl.handle.net/10453/129833