Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

Leighton Pritchard, Rachel H. Glover, Sonia Humphris, John G. Elphinstone, Ian K. Toth

Research output: Contribution to journalReview article

155 Citations (Scopus)

Abstract

Soft rot Enterobacteriaceae (SRE) are bacterial plant pathogens that cause blackleg, wilt and soft rot diseases on a broad range of important crop and ornamental plants worldwide. These organisms (spanning the genera Erwinia, Pectobacterium, Dickeya, and Pantoea) cause significant economic and yield losses in the field, and in storage. They are transmissible through surface water, by trade and other movement of plant material and soil, and in some cases are subject to international legislative and quarantine restrictions. Effective detection and diagnosis in support of food security legislation and epidemiology is dependent on the ability to classify pathogenic isolates precisely. Diagnostics and classification are made more difficult by the influence of horizontal gene transfer on phenotype, and historically complex and sometimes inaccurate nomenclatural and taxonomic assignments that persist in strain collections and online sequence databases. Here, we briefly discuss the relationship between taxonomy, genotype and phenotype in the SRE, and their implications for diagnostic testing and legislation. We present novel whole-genome classifications of the SRE, illustrating inconsistencies between the established taxonomies and evidence from completely sequenced isolates. We conclude with a perspective on the future impact of widespread whole-genome sequencing and classification methods on detection and identification of bacterial plant pathogens in support of legislative and policy efforts in food security.

Original languageEnglish
Pages (from-to)12-24
Number of pages13
JournalAnalytical Methods
Volume8
Issue number1
DOIs
Publication statusPublished - 7 Jan 2016

Keywords

  • food microbiology
  • classification (of information)
  • diagnosis
  • food supply
  • gene transfer
  • genes
  • laws and legislation
  • surface waters
  • taxonomies
  • classification methods
  • detection and diagnosis

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  • Research Output

    • 155 Citations
    • 1 Poster
    • 1 Software

    pyani v0.2.8: average nucleotide identity (ANI) and related measures for whole genome comparisons

    Pritchard, L., Cock, P. & Esen, Ö., 5 Mar 2019

    Research output: Non-textual formSoftware

    Open Access
  • 1 Downloads (Pure)

    Activities

    • 1 Key-note speaker and plenary lectures at conferences
    • 1 Invited talk

    Computational design of Pectobacterium diagnostics

    Leighton Pritchard (Speaker)

    16 Nov 2018

    Activity: Talk or presentation typesInvited talk

    Focused Meeting 2018: Microbiomes Underpinning Agriculture

    Leighton Pritchard (Speaker)

    2 Oct 2018

    Activity: Participating in or organising an event typesKey-note speaker and plenary lectures at conferences

    Cite this