Academic Journal
View in EDS

Mobile genetic element diversity across Shiga toxin-producing Escherichia coli lineages in French cattle.

Bibliographic Details
Title: Mobile genetic element diversity across Shiga toxin-producing Escherichia coli lineages in French cattle.
Authors: Vorimore F; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France., Tran ML; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France., Jaudou S; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France.; Present address: Gulliver, CNRS, ESPCI Paris, Université PSL, 10 rue Vauquelin, 75005 Paris, France., Fach P; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France., Delannoy S; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France.
Source: Microbial genomics [Microb Genom] 2026 Jul; Vol. 12 (7).
Publication Type: Journal Article
Language: English
Journal Info: Publisher: Microbiology Society Country of Publication: England NLM ID: 101671820 Publication Model: Print Cited Medium: Internet ISSN: 2057-5858 (Electronic) Linking ISSN: 20575858 NLM ISO Abbreviation: Microb Genom Subsets: MEDLINE
Imprint Name(s): Publication: Oct. 2015- : [London] : Microbiology Society
Original Publication: [London] : Society for General Microbiology, [2015]-
MeSH Terms: Shiga-Toxigenic Escherichia coli*/genetics , Shiga-Toxigenic Escherichia coli*/pathogenicity , Shiga-Toxigenic Escherichia coli*/classification , Shiga-Toxigenic Escherichia coli*/isolation & purification , Escherichia coli Infections*/veterinary , Escherichia coli Infections*/microbiology , Interspersed Repetitive Sequences*, Plasmids/genetics ; Prophages/genetics ; Virulence/genetics ; Animals ; Cattle ; France ; Phylogeny ; Genetic Variation ; Whole Genome Sequencing ; Genome, Bacterial ; Gene Transfer, Horizontal
Abstract: Shiga toxin-producing Escherichia coli (STEC) represent a genetically diverse group of pathogens whose virulence is largely driven by mobile genetic elements (MGEs), including plasmids and bacteriophages. While horizontal gene transfer is central to STEC evolution, the extent to which virulence-associated MGEs circulate within natural reservoirs remains poorly understood. In this study, we investigated the diversity, distribution and lineage associations of MGEs in a collection of 73 E. coli strains isolated from cattle in France, a major reservoir for pathogenic STEC. Using both short-read and long-read whole-genome sequencing, we characterized plasmid content, prophage repertoires and stx-encoding phages and examined their relationships with strain phylogeny. We observed a high diversity of plasmids, with individual strains carrying up to four large plasmids, alongside an even greater diversity of prophages. Despite this diversity, some associations were identified between specific virulence plasmid groups, Stx phage types and defined pathogroups or lineages. These patterns were supported by the congruence between core-genome and accessory-genome phylogenies, suggesting long-term evolutionary coupling rather than frequent exchange of entire MGEs. In contrast, some non-virulence plasmids were broadly distributed, consistent with more general selective advantages. Notably, we identified enterohaemorrhagic E. coli strains (stx- and eae-positive strains) in atypical phylogenetic backgrounds, highlighting the capacity for virulence determinants to emerge in diverse lineages, while underscoring the constraints that limit their stable establishment, as their long-term persistence appears limited to specific genetic backgrounds. Together, our findings indicate that the circulation of virulence-associated MGEs in the bovine reservoir is constrained by ecological and evolutionary factors.
Contributed Indexing: Keywords: France; Shiga toxin-producing Escherichia coli (STEC); Stx phages; cattle; mobile genetic elements; plasmids
Entry Date(s): Date Created: 20260722 Date Completed: 20260722 Latest Revision: 20260722
Update Code: 20260723
DOI: 10.1099/mgen.0.001794
PMID: 42485078
Database: MEDLINE
FullText Text:
  Availability: 0
CustomLinks:
  – Url: https://resolver.ebsco.com/c/fiv2js/result?sid=EBSCO:cmedm&genre=article&issn=20575858&ISBN=&volume=12&issue=7&date=20260701&spage=&pages=&title=Microbial genomics&atitle=Mobile%20genetic%20element%20diversity%20across%20Shiga%20toxin-producing%20Escherichia%20coli%20lineages%20in%20French%20cattle.&aulast=Vorimore%20F&id=DOI:10.1099/mgen.0.001794
    Name: Full Text Finder (for New FTF UI) (ns324271)
    Category: fullText
    Text: Full Text Finder
    MouseOverText: Full Text Finder
Header DbId: cmedm
DbLabel: MEDLINE
An: 42485078
AccessLevel: 3
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Mobile genetic element diversity across Shiga toxin-producing Escherichia coli lineages in French cattle.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AU" term="%22Vorimore+F%22">Vorimore F</searchLink>; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France.<br /><searchLink fieldCode="AU" term="%22Tran+ML%22">Tran ML</searchLink>; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France.<br /><searchLink fieldCode="AU" term="%22Jaudou+S%22">Jaudou S</searchLink>; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France.; Present address: Gulliver, CNRS, ESPCI Paris, Université PSL, 10 rue Vauquelin, 75005 Paris, France.<br /><searchLink fieldCode="AU" term="%22Fach+P%22">Fach P</searchLink>; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France.<br /><searchLink fieldCode="AU" term="%22Delannoy+S%22">Delannoy S</searchLink>; Anses, Laboratory for Food Safety, Pathogenic E. coli Unit & IdentyPath Genomics Platform, 94701 Maisons-Alfort, France.
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22101671820%22">Microbial genomics</searchLink> [Microb Genom] 2026 Jul; Vol. 12 (7).
– Name: TypePub
  Label: Publication Type
  Group: TypPub
  Data: Journal Article
– Name: Language
  Label: Language
  Group: Lang
  Data: English
– Name: TitleSource
  Label: Journal Info
  Group: Src
  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Microbiology+Society%22">Microbiology Society </searchLink><i>Country of Publication: </i>England <i>NLM ID: </i>101671820 <i>Publication Model: </i>Print <i>Cited Medium: </i>Internet <i>ISSN: </i>2057-5858 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2220575858%22">20575858 </searchLink><i>NLM ISO Abbreviation: </i>Microb Genom <i>Subsets: </i>MEDLINE
– Name: PublisherInfo
  Label: Imprint Name(s)
  Group: PubInfo
  Data: <i>Publication</i>: Oct. 2015- : [London] : Microbiology Society<br /><i>Original Publication</i>: [London] : Society for General Microbiology, [2015]-
– Name: SubjectMESH
  Label: MeSH Terms
  Group: Su
  Data: <searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli%22">Shiga-Toxigenic Escherichia coli*</searchLink>/<searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli%22">Shiga-Toxigenic Escherichia coli*</searchLink>/<searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli+pathogenicity%22">pathogenicity</searchLink> <br /><searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli%22">Shiga-Toxigenic Escherichia coli*</searchLink>/<searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli%22">Shiga-Toxigenic Escherichia coli*</searchLink>/<searchLink fieldCode="MM" term="%22Shiga-Toxigenic+Escherichia+coli+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Escherichia+coli+Infections%22">Escherichia coli Infections*</searchLink>/<searchLink fieldCode="MM" term="%22Escherichia+coli+Infections+veterinary%22">veterinary</searchLink> <br /><searchLink fieldCode="MM" term="%22Escherichia+coli+Infections%22">Escherichia coli Infections*</searchLink>/<searchLink fieldCode="MM" term="%22Escherichia+coli+Infections+microbiology%22">microbiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Interspersed+Repetitive+Sequences%22">Interspersed Repetitive Sequences*</searchLink><br /><searchLink fieldCode="MH" term="%22Plasmids%22">Plasmids</searchLink>/<searchLink fieldCode="MH" term="%22Plasmids+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Prophages%22">Prophages</searchLink>/<searchLink fieldCode="MH" term="%22Prophages+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Virulence%22">Virulence</searchLink>/<searchLink fieldCode="MH" term="%22Virulence+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Animals%22">Animals</searchLink> ; <searchLink fieldCode="MH" term="%22Cattle%22">Cattle</searchLink> ; <searchLink fieldCode="MH" term="%22France%22">France</searchLink> ; <searchLink fieldCode="MH" term="%22Phylogeny%22">Phylogeny</searchLink> ; <searchLink fieldCode="MH" term="%22Genetic+Variation%22">Genetic Variation</searchLink> ; <searchLink fieldCode="MH" term="%22Whole+Genome+Sequencing%22">Whole Genome Sequencing</searchLink> ; <searchLink fieldCode="MH" term="%22Genome%2C+Bacterial%22">Genome, Bacterial</searchLink> ; <searchLink fieldCode="MH" term="%22Gene+Transfer%2C+Horizontal%22">Gene Transfer, Horizontal</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Shiga toxin-producing Escherichia coli (STEC) represent a genetically diverse group of pathogens whose virulence is largely driven by mobile genetic elements (MGEs), including plasmids and bacteriophages. While horizontal gene transfer is central to STEC evolution, the extent to which virulence-associated MGEs circulate within natural reservoirs remains poorly understood. In this study, we investigated the diversity, distribution and lineage associations of MGEs in a collection of 73 E. coli strains isolated from cattle in France, a major reservoir for pathogenic STEC. Using both short-read and long-read whole-genome sequencing, we characterized plasmid content, prophage repertoires and stx-encoding phages and examined their relationships with strain phylogeny. We observed a high diversity of plasmids, with individual strains carrying up to four large plasmids, alongside an even greater diversity of prophages. Despite this diversity, some associations were identified between specific virulence plasmid groups, Stx phage types and defined pathogroups or lineages. These patterns were supported by the congruence between core-genome and accessory-genome phylogenies, suggesting long-term evolutionary coupling rather than frequent exchange of entire MGEs. In contrast, some non-virulence plasmids were broadly distributed, consistent with more general selective advantages. Notably, we identified enterohaemorrhagic E. coli strains (stx- and eae-positive strains) in atypical phylogenetic backgrounds, highlighting the capacity for virulence determinants to emerge in diverse lineages, while underscoring the constraints that limit their stable establishment, as their long-term persistence appears limited to specific genetic backgrounds. Together, our findings indicate that the circulation of virulence-associated MGEs in the bovine reservoir is constrained by ecological and evolutionary factors.
– Name: SubjectMinor
  Label: Contributed Indexing
  Group:
  Data: <i>Keywords: </i>France; Shiga toxin-producing Escherichia coli (STEC); Stx phages; cattle; mobile genetic elements; plasmids
– Name: DateEntry
  Label: Entry Date(s)
  Group: Date
  Data: <i>Date Created: </i>20260722 <i>Date Completed: </i>20260722 <i>Latest Revision: </i>20260722
– Name: DateUpdate
  Label: Update Code
  Group: Date
  Data: 20260723
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.1099/mgen.0.001794
– Name: AN
  Label: PMID
  Group: ID
  Data: 42485078
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=cmedm&AN=42485078
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1099/mgen.0.001794
    Languages:
      – Code: eng
        Text: English
    Subjects:
      – SubjectFull: Plasmids genetics
        Type: general
      – SubjectFull: Prophages genetics
        Type: general
      – SubjectFull: Virulence genetics
        Type: general
      – SubjectFull: Animals
        Type: general
      – SubjectFull: Cattle
        Type: general
      – SubjectFull: France
        Type: general
      – SubjectFull: Phylogeny
        Type: general
      – SubjectFull: Genetic Variation
        Type: general
      – SubjectFull: Whole Genome Sequencing
        Type: general
      – SubjectFull: Genome, Bacterial
        Type: general
      – SubjectFull: Gene Transfer, Horizontal
        Type: general
      – SubjectFull: Shiga-Toxigenic Escherichia coli genetics
        Type: general
      – SubjectFull: Shiga-Toxigenic Escherichia coli pathogenicity
        Type: general
      – SubjectFull: Shiga-Toxigenic Escherichia coli classification
        Type: general
      – SubjectFull: Shiga-Toxigenic Escherichia coli isolation & purification
        Type: general
      – SubjectFull: Escherichia coli Infections veterinary
        Type: general
      – SubjectFull: Escherichia coli Infections microbiology
        Type: general
      – SubjectFull: Interspersed Repetitive Sequences
        Type: general
    Titles:
      – TitleFull: Mobile genetic element diversity across Shiga toxin-producing Escherichia coli lineages in French cattle.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Vorimore F
      – PersonEntity:
          Name:
            NameFull: Tran ML
      – PersonEntity:
          Name:
            NameFull: Jaudou S
      – PersonEntity:
          Name:
            NameFull: Fach P
      – PersonEntity:
          Name:
            NameFull: Delannoy S
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 07
              Text: 2026 Jul
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 2057-5858
          Numbering:
            – Type: volume
              Value: 12
            – Type: issue
              Value: 7
          Titles:
            – TitleFull: Microbial genomics
              Type: main
ResultId 1