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

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dc.contributor.authorLi, D.
dc.contributor.authorElankumaran, P.
dc.contributor.authorKudinha, T.
dc.contributor.authorKidsley, A.K.
dc.contributor.authorTrott, D.J.
dc.contributor.authorJarocki, V.M.
dc.contributor.authorDjordjevic, S.P.
dc.date.issued2023
dc.description.abstractExtraintestinal 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.description.statementofresponsibilityDmitriy Li, Paarthiphan Elankumaran, Timothy Kudinha, Amanda K. Kidsley, Darren J. Trott, Veronica Maria Jarocki, and Steven Philip Djordjevic
dc.identifier.citationMicrobial Genomics, 2023; 9(7):1-18
dc.identifier.doi10.1099/mgen.0.001068
dc.identifier.issn2057-5858
dc.identifier.issn2057-5858
dc.identifier.orcidTrott, D.J. [0000-0002-8297-5770]
dc.identifier.urihttps://hdl.handle.net/2440/139793
dc.language.isoen
dc.publisherMicrobiology Society
dc.relation.granthttp://purl.org/au-research/grants/arc/LP130100736
dc.rights© 2023 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License
dc.source.urihttps://doi.org/10.1099/mgen.0.001068
dc.subjectUTIs; ExPEC; F plasmids; pUTI89; senB; antimicrobial resistance
dc.subject.meshAnimals
dc.subject.meshEscherichia coli
dc.subject.meshEscherichia coli Infections
dc.subject.meshUrinary Tract Infections
dc.subject.meshAnti-Bacterial Agents
dc.subject.meshGenomics
dc.subject.meshDrug Resistance, Bacterial
dc.subject.meshVirulence
dc.subject.meshGenotype
dc.subject.meshF Factor
dc.subject.meshAustralia
dc.subject.meshExtraintestinal Pathogenic Escherichia coli
dc.titleDominance 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.typeJournal article
pubs.publication-statusPublished

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