Genomic comparisons of Escherichia coli ST131 from Australia.

Li, D; Wyrsch, ER; Elankumaran, P; Dolejska, M; Marenda, MS; Browning, GF; Bushell, RN; McKinnon, J; Chowdhury, PR; Hitchick, N; Miller, N; Donner, E; Drigo, B; Baker, D; Charles, IG; Kudinha, T; Jarocki, VM; Djordjevic, SP

Genomic comparisons of Escherichia coli ST131 from Australia.

Wyrsch, ER Elankumaran, P Dolejska, M Marenda, MS Browning, GF Bushell, RN McKinnon, J Chowdhury, PR Hitchick, N Miller, N Donner, E Drigo, B Baker, D Charles, IG Kudinha, T Jarocki, VM Djordjevic, SP

Permalink

Publisher:: Microbiology Society
Publication Type:: Journal Article
Citation:: Microb Genom, 2021, 7, (12)
Issue Date:: 2021-12

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download Accepted versionAdobe PDF (8.45 MB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Li, D https://orcid.org/0000-0002-7535-8184
dc.contributor.author	Wyrsch, ER
dc.contributor.author	Elankumaran, P
dc.contributor.author	Dolejska, M
dc.contributor.author	Marenda, MS
dc.contributor.author	Browning, GF
dc.contributor.author	Bushell, RN
dc.contributor.author	McKinnon, J
dc.contributor.author	Chowdhury, PR
dc.contributor.author	Hitchick, N
dc.contributor.author	Miller, N
dc.contributor.author	Donner, E
dc.contributor.author	Drigo, B
dc.contributor.author	Baker, D
dc.contributor.author	Charles, IG
dc.contributor.author	Kudinha, T
dc.contributor.author	Jarocki, VM
dc.contributor.author	Djordjevic, SP
dc.date.accessioned	2022-01-06T07:42:39Z
dc.date.available	2022-01-06T07:42:39Z
dc.date.issued	2021-12
dc.identifier.citation	Microb Genom, 2021, 7, (12)
dc.identifier.issn	2057-5858
dc.identifier.issn	2057-5858
dc.identifier.uri	http://hdl.handle.net/10453/152770
dc.description.abstract	Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.
dc.format	Print
dc.language	eng
dc.publisher	Microbiology Society
dc.relation.ispartof	Microb Genom
dc.relation.isbasedon	10.1099/mgen.0.000721
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0604 Genetics, 0605 Microbiology
dc.title	Genomic comparisons of Escherichia coli ST131 from Australia.
dc.type	Journal Article
utslib.citation.volume	7
utslib.location.activity	England
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	*
dc.date.updated	2022-01-06T07:41:40Z
pubs.issue	12
pubs.publication-status	Published
pubs.volume	7
utslib.citation.issue	12

Abstract:

Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/152770