Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids.

Li, D; Elankumaran, P; Kudinha, T; Kidsley, AK; Trott, DJ; Jarocki, VM; Djordjevic, SP

Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids.

Li, D

Elankumaran, P Kudinha, T Kidsley, AK Trott, DJ Jarocki, VM Djordjevic, SP

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Publisher:: Microbiology Society
Publication Type:: Journal Article
Citation:: Microb Genom, 2023, 9, (7)
Issue Date:: 2023-07

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Field	Value	Language
dc.contributor.author	Li, D https://orcid.org/0000-0002-7535-8184
dc.contributor.author	Elankumaran, P
dc.contributor.author	Kudinha, T
dc.contributor.author	Kidsley, AK
dc.contributor.author	Trott, DJ
dc.contributor.author	Jarocki, VM
dc.contributor.author	Djordjevic, SP
dc.date.accessioned	2023-09-29T04:46:07Z
dc.date.available	2023-09-29T04:46:07Z
dc.date.issued	2023-07
dc.identifier.citation	Microb Genom, 2023, 9, (7)
dc.identifier.issn	2057-5858
dc.identifier.issn	2057-5858
dc.identifier.uri	http://hdl.handle.net/10453/172383
dc.description.abstract	Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Most studies of clinical E. coli isolates are selected based on their antimicrobial resistance (AMR) phenotypes; however, this selection bias may not provide an accurate portrayal of which sequence types (STs) cause the most disease. Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. Most isolates (91%) were sourced from patients with UTIs and were not selected based on any AMR phenotypes. No significant differences were observed in AMR and virulence genes profiles across age sex, and uro-clinical syndromes. While 88 STs were identified, ST73, ST95, ST127 and ST131 dominated. F virulence plasmids carrying senB-cjrABC (126/231; 55%) virulence genes were a feature of this collection. These senB-cjrABC+ plasmids were split into two categories: pUTI89-like (F29:A-:B10 and/or >95 % identity to pUTI89) (n=73) and non-pUTI89-like (n=53). Compared to all other plasmid replicons, isolates with pUTI89-like plasmids carried fewer antibiotic resistance genes (ARGs), whilst isolates with senB-cjrABC+/non-pUTI89 plasmids had a significantly higher load of ARGs and class 1 integrons. F plasmids were not detected in 89 genomes, predominantly ST73. Our phylogenomic analyses identified closely related isolates from the same patient associated with different pathologies and evidence of strain-sharing events involving isolates sourced from companion and wild animals.
dc.format	Print
dc.language	eng
dc.publisher	Microbiology Society
dc.relation.ispartof	Microb Genom
dc.relation.isbasedon	10.1099/mgen.0.001068
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0604 Genetics, 0605 Microbiology
dc.subject.classification	3105 Genetics
dc.subject.classification	3107 Microbiology
dc.subject.mesh	Animals
dc.subject.mesh	Escherichia coli
dc.subject.mesh	Virulence
dc.subject.mesh	Anti-Bacterial Agents
dc.subject.mesh	F Factor
dc.subject.mesh	Escherichia coli Infections
dc.subject.mesh	Genotype
dc.subject.mesh	Drug Resistance, Bacterial
dc.subject.mesh	Australia
dc.subject.mesh	Extraintestinal Pathogenic Escherichia coli
dc.subject.mesh	Genomics
dc.subject.mesh	Urinary Tract Infections
dc.subject.mesh	Animals
dc.subject.mesh	Escherichia coli
dc.subject.mesh	Escherichia coli Infections
dc.subject.mesh	Urinary Tract Infections
dc.subject.mesh	Anti-Bacterial Agents
dc.subject.mesh	Genomics
dc.subject.mesh	Drug Resistance, Bacterial
dc.subject.mesh	Virulence
dc.subject.mesh	Genotype
dc.subject.mesh	F Factor
dc.subject.mesh	Australia
dc.subject.mesh	Extraintestinal Pathogenic Escherichia coli
dc.subject.mesh	Animals
dc.subject.mesh	Escherichia coli
dc.subject.mesh	Virulence
dc.subject.mesh	Anti-Bacterial Agents
dc.subject.mesh	F Factor
dc.subject.mesh	Escherichia coli Infections
dc.subject.mesh	Genotype
dc.subject.mesh	Drug Resistance, Bacterial
dc.subject.mesh	Australia
dc.subject.mesh	Extraintestinal Pathogenic Escherichia coli
dc.subject.mesh	Genomics
dc.subject.mesh	Urinary Tract Infections
dc.title	Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids.
dc.type	Journal Article
utslib.citation.volume	9
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 - AIMI - Australian Institute for Microbiology & Infection
utslib.copyright.status	open_access	*
dc.date.updated	2023-09-29T04:45:59Z
pubs.issue	7
pubs.publication-status	Published
pubs.volume	9
utslib.citation.issue	7

Abstract:

Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Most studies of clinical E. coli isolates are selected based on their antimicrobial resistance (AMR) phenotypes; however, this selection bias may not provide an accurate portrayal of which sequence types (STs) cause the most disease. Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. Most isolates (91%) were sourced from patients with UTIs and were not selected based on any AMR phenotypes. No significant differences were observed in AMR and virulence genes profiles across age sex, and uro-clinical syndromes. While 88 STs were identified, ST73, ST95, ST127 and ST131 dominated. F virulence plasmids carrying senB-cjrABC (126/231; 55%) virulence genes were a feature of this collection. These senB-cjrABC+ plasmids were split into two categories: pUTI89-like (F29:A-:B10 and/or >95 % identity to pUTI89) (n=73) and non-pUTI89-like (n=53). Compared to all other plasmid replicons, isolates with pUTI89-like plasmids carried fewer antibiotic resistance genes (ARGs), whilst isolates with senB-cjrABC+/non-pUTI89 plasmids had a significantly higher load of ARGs and class 1 integrons. F plasmids were not detected in 89 genomes, predominantly ST73. Our phylogenomic analyses identified closely related isolates from the same patient associated with different pathologies and evidence of strain-sharing events involving isolates sourced from companion and wild animals.

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http://hdl.handle.net/10453/172383