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 articlepeer-review

811 Citations (Scopus)


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
Issue number1
Publication statusPublished - 7 Jan 2016


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


Dive into the research topics of 'Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens'. Together they form a unique fingerprint.

Cite this