Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny

Reid, CJ; De Maere, MZ; Djordjevic, SP

Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny

Reid, CJ

De Maere, MZ Djordjevic, SP

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Publication Type:: Journal Article
Citation:: Microbial Genomics, 2019, 5 (3)
Issue Date:: 2019-03-01

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Field	Value	Language
dc.contributor.author	Reid, CJ https://orcid.org/0000-0001-6872-330X	en_US
dc.contributor.author	De Maere, MZ	en_US
dc.contributor.author	Djordjevic, SP https://orcid.org/0000-0001-9301-5372	en_US
dc.date.issued	2019-03-01	en_US
dc.identifier.citation	Microbial Genomics, 2019, 5 (3)	en_US
dc.identifier.uri	http://hdl.handle.net/10453/128248
dc.description.abstract	© 2019 The Authors. We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reportedas human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonizationevents. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenicE. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessorygene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion ofCC10 is not a recent event and may be associated with faecal carriage in humans.	en_US
dc.relation	http://purl.org/au-research/grants/arc/LP150100912
dc.relation.ispartof	Microbial Genomics	en_US
dc.relation.isbasedon	10.1099/mgen.0.000225	en_US
dc.title	Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny	en_US
dc.type	Journal Article
utslib.citation.volume	3	en_US
utslib.citation.volume	5	en_US
utslib.for	0605 Microbiology	en_US
utslib.for	0604 Genetics	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	3	en_US
pubs.publication-status	Published	en_US
pubs.volume	5	en_US

Abstract:

© 2019 The Authors. We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reportedas human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonizationevents. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenicE. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessorygene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion ofCC10 is not a recent event and may be associated with faecal carriage in humans.

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http://hdl.handle.net/10453/128248