TY - JOUR
T1 - Phylogeny and potential virulence of cryptic clade Escherichia coli species complex isolates derived from an arable field trial
AU - MacKenzie, Katrin
AU - Marshall, Jacqueline
AU - Wright, Frank
AU - Gunn, George
AU - Holden, Nicola
N1 - Funding Information:
We thank Leighton Pritchard (Strathclyde university) for useful discussion, and Claus Dieter-Meyer and Glenn Marion (BioSS) for manuscript critique and Mart Achtman for Enterobase discussions. We dedicate this manuscript to the memory of Frank Wright (BioSS) and his contribution to phylogenetics research and teaching. The work done by KMcK, JM, FW, GG, and NH was supported by funding from Scottish Government as part of it's 2016–2021 Environment, Agriculture and Food Strategic Research Programme (project code RD2.2.6).
Publisher Copyright:
© 2021 The Author(s)
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - Cryptic clades
KW - E. marmotae
KW - Naturalised
KW - Pan-genome
KW - Phylogenomics
UR - http://www.scopus.com/inward/record.url?scp=85121580113&partnerID=8YFLogxK
U2 - 10.1016/j.crmicr.2021.100093
DO - 10.1016/j.crmicr.2021.100093
M3 - Article
C2 - 35005658
SN - 2666-5174
VL - 3
JO - Current Research in Microbial Sciences
JF - Current Research in Microbial Sciences
M1 - 100093
ER -
