Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups

Bogema, DR; McKinnon, J; Liu, M; Hitchick, N; Miller, N; Venturini, C; Iredell, J; Darling, AE; Roy Chowdury, P; Djordjevic, SP

Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups

Bogema, DR McKinnon, J Liu, M Hitchick, N Miller, N Venturini, C Iredell, J Darling, AE Roy Chowdury, P Djordjevic, SP

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Publication Type:: Journal Article
Citation:: Microbial Genomics, 2020, 6, (1), pp. 428599
Issue Date:: 2020-01

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Field	Value	Language
dc.contributor.author	Bogema, DR
dc.contributor.author	McKinnon, J
dc.contributor.author	Liu, M
dc.contributor.author	Hitchick, N
dc.contributor.author	Miller, N
dc.contributor.author	Venturini, C
dc.contributor.author	Iredell, J
dc.contributor.author	Darling, AE
dc.contributor.author	Roy Chowdury, P
dc.contributor.author	Djordjevic, SP
dc.date.accessioned	2022-04-01T03:35:54Z
dc.date.available	2022-04-01T03:35:54Z
dc.date.issued	2020-01
dc.identifier.citation	Microbial Genomics, 2020, 6, (1), pp. 428599
dc.identifier.uri	http://hdl.handle.net/10453/155863
dc.description.abstract	<jats:title>Abstract</jats:title><jats:p>ST73 has emerged as one of the most frequently isolated extraintestinal pathogenic <jats:italic>E. coli</jats:italic> (ExPEC). To examine the localised diversity of ST73 clonal groups including their mobile genetic elements profile, we sequenced the genomes of 16 multiple drug-resistant ST73 isolates from patients with urinary tract infection from a single hospital in Sydney, Australia between 2009 and 2011. Genome sequences were used to generate a SNP-based phylogenetic tree to determine the relationship of these isolates in a global context with ST73 sequences (n=210) from public databases. There was no evidence of a dominant outbreak strain of ST73 in patients from this hospital, rather we identified at least eight separate groups, several of which reoccur, over a two-year period. The inferred phylogeny of all ST73 strains (n=226) including the ST73 Clone D i2 reference genome shows high bootstrap support and clusters into four major groups which correlate with serotype. The Sydney ST73 strains carry a wide variety of virulence-associated genes but the presence of <jats:italic>iss</jats:italic>, <jats:italic>pic</jats:italic> and several iron acquisition operons was notable.</jats:p><jats:sec><jats:title>Impact</jats:title><jats:p>ST73 is a major clonal lineage of ExPEC that causes urinary tract infections often with uroseptic sequelae but has not garnered substantial scientific interest as the globally disseminated ST131. Isolation of multiple antimicrobial resistant variants of ExPEC ST73 have increased in frequency, but little is known about the carriage of class 1 integrons in this sequence type and the plasmids that are likely to mobilise them. This pilot study examines the ST73 isolates within a single hospital in Sydney Australia and provides the first large-scale core-genome phylogenetic analysis of ST73 utilizing public sequence read datasets. We used this analysis to identify at least 8 sub-groups of ST73 within this single hospital. Mobile genetic elements associated with antibiotic resistance were less diverse and only three class 1 integron structures were identified, all sharing the same basic structure suggesting that the acquisition of drug resistance is a recent event. Genomic epidemiological studies are needed to further characterise established and emerging clonal populations of multiple drug resistant ExPEC to identify sources and aid outbreak investigations.</jats:p></jats:sec>
dc.language	en
dc.relation.ispartof	Microbial Genomics
dc.relation.isbasedon	10.1099/mgen.0.000255
dc.rights	This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0604 Genetics, 0605 Microbiology
dc.title	Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups
dc.type	Journal Article
utslib.citation.volume	6
utslib.for	0604 Genetics
utslib.for	0605 Microbiology
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
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	open_access	*
pubs.consider-herdc	false
dc.date.updated	2022-04-01T03:35:52Z
pubs.issue	1
pubs.publication-status	Published
pubs.volume	6
utslib.citation.issue	1

Abstract:

AbstractST73 has emerged as one of the most frequently isolated extraintestinal pathogenic E. coli (ExPEC). To examine the localised diversity of ST73 clonal groups including their mobile genetic elements profile, we sequenced the genomes of 16 multiple drug-resistant ST73 isolates from patients with urinary tract infection from a single hospital in Sydney, Australia between 2009 and 2011. Genome sequences were used to generate a SNP-based phylogenetic tree to determine the relationship of these isolates in a global context with ST73 sequences (n=210) from public databases. There was no evidence of a dominant outbreak strain of ST73 in patients from this hospital, rather we identified at least eight separate groups, several of which reoccur, over a two-year period. The inferred phylogeny of all ST73 strains (n=226) including the ST73 Clone D i2 reference genome shows high bootstrap support and clusters into four major groups which correlate with serotype. The Sydney ST73 strains carry a wide variety of virulence-associated genes but the presence of iss, pic and several iron acquisition operons was notable.ImpactST73 is a major clonal lineage of ExPEC that causes urinary tract infections often with uroseptic sequelae but has not garnered substantial scientific interest as the globally disseminated ST131. Isolation of multiple antimicrobial resistant variants of ExPEC ST73 have increased in frequency, but little is known about the carriage of class 1 integrons in this sequence type and the plasmids that are likely to mobilise them. This pilot study examines the ST73 isolates within a single hospital in Sydney Australia and provides the first large-scale core-genome phylogenetic analysis of ST73 utilizing public sequence read datasets. We used this analysis to identify at least 8 sub-groups of ST73 within this single hospital. Mobile genetic elements associated with antibiotic resistance were less diverse and only three class 1 integron structures were identified, all sharing the same basic structure suggesting that the acquisition of drug resistance is a recent event. Genomic epidemiological studies are needed to further characterise established and emerging clonal populations of multiple drug resistant ExPEC to identify sources and aid outbreak investigations.

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http://hdl.handle.net/10453/155863