Phylogeny and potential virulence of cryptic clade Escherichia coli species complex isolates derived from an arable field trial

Katrin MacKenzie, Jacqueline Marshall, Frank Wright, George Gunn, Nicola Holden

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2 Citations (Scopus)
162 Downloads (Pure)


Analysis of Escherichia coli taxonomy has expanded into a species-complex with the identification of divergent cryptic clades. A key question is the evolutionary trajectory of these clades and their relationship to isolates of clinical or veterinary importance. Since they have some environmental association, we screened a collection of E. coli isolated from a long-term spring barley field trial for their presence. While most isolates clustered into the enteric-clade, four of them clustered into Clade-V, and one in Clade-IV. The Clade -V isolates shared >96% intra-clade average nucleotide sequence identity but <91% with other clades. Although pan-genomics analysis confirmed their taxonomy as Clade -V (E. marmotae), retrospective phylogroup PCR did not discriminate them correctly. Differences in metabolic and adherence gene alleles occurred in the Clade -V isolates compared to E. coli sensu scricto. They also encoded the bacteriophage phage-associated cyto-lethal distending toxin (CDT) and antimicrobial resistance (AMR) genes, including an ESBL, blaOXA-453. Thus, the isolate collection encompassed a genetic diversity, and included cryptic clade isolates that encode potential virulence factors. The analysis has determined the phylogenetic relationship of cryptic clade isolates with E. coli sensu scricto and indicates a potential for horizontal transfer of virulence factors.

Original languageEnglish
Article number100093
Number of pages11
JournalCurrent Research in Microbial Sciences
Early online date20 Dec 2021
Publication statusPublished - 2022


  • Cryptic clades
  • E. marmotae
  • Naturalised
  • Pan-genome
  • Phylogenomics

ASJC Scopus subject areas

  • Microbiology
  • Immunology and Microbiology (miscellaneous)
  • Infectious Diseases
  • Microbiology (medical)


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