The intergenic transcribed spacer region 1 as a molecular marker for identification and discrimination of Enterobacteriaceae associated with acute oak decline

James Doonan, Sandra Denman, Christopher Gertler, Justin A. Pachebat, Peter N Golyshin, James McDonald

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Abstract

Aims
We assessed the veracity of intergenic spacer region 1 (ITS1) ribotyping for the rapid, inexpensive and accurate identification ofBrenneria goodwinii and Gibbsiella quercinecans that are associated with Acute Oak Decline (AOD) in the UK.

Methods and Results
Agarose gel electrophoresis and polyacrylamide gel electrophoresis (PAGE) were applied for the typing of ITS1 PCR amplicons from strains of Brenneria goodwinii, Gibbsiella quercinecans and related species (n = 34). The number and lengt
h of ITS1 amplicons varied significantly between strains. ITS1 profiles generated via PAGE were used to differentiate species using a neighbour-joining phylogram. The ITS1 phylogram was compared against DNA gyrase B (gyrB) gene sequences from the same strains, demonstrating that ITS1 ribotyping is as effective as gyrB at resolving G. qurerciecans and B. goodwinii to the species level.

Conclusions
The ITS1 gene has been successfully employed as a novel marker to resolve newly described AOD associated Enterobacteriaceae, Brenneria goodwinii
and Gibbsiella quercinecans, to species level. Significance and Impact of Study
ITS1 ribotyping of Brenneria goodwinii and Gibbsiella quercinecans provides equivalent sensitivity to the current standard method for strain identification
(sequence analysis of the gyrB gene), but with reduced processing time and cost.
Furthermore, the ITS1 gene is widely applicable as a rapid and inexpensive typing system for Enterobacteriaceae.
Original languageEnglish
Pages (from-to)193-201
Number of pages10
JournalJournal of Applied Microbiology
Volume118
Issue number1
Early online date27 Nov 2014
DOIs
Publication statusPublished - Jan 2015

Keywords

  • Plant diseases
  • identification
  • Microbial phylogenetics
  • Rapid methods
  • Genotyping
  • acute oak decline
  • Brenneria goodwinii
  • DNA gyrase B
  • Enterobacteriaceae
  • Gibbsiella quercinecans
  • ITS1

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