Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems

Eelco Franz, Pascal Delaquis, Stefano Morabito, Lothar Beutin, Kari Gobius, David A Rasko, Jim Bono, Nigel French, Jacek Osek, Bjørn-Arne Lindstedt, Maite Muniesa, Shannon Manning, Jeff LeJeune, Todd Callaway, Scott Beatson, Mark Eppinger, Tim Dallman, Ken J Forbes, Henk Aarts, David L PearlVictor P J Gannon, Chad R Laing, Norval J C Strachan

Research output: Contribution to journalArticlepeer-review

62 Citations (Scopus)


The rates of foodborne disease caused by gastrointestinal pathogens continue to be a concern in both the developed and developing worlds. The growing world population, the increasing complexity of agri-food networks and the wide range of foods now associated with STEC are potential drivers for increased risk of human disease. It is vital that new developments in technology, such as whole genome sequencing (WGS), are effectively utilized to help address the issues associated with these pathogenic microorganisms. This position paper, arising from an OECD funded workshop, provides a brief overview of next generation sequencing technologies and software. It then uses the agent-host-environment paradigm as a basis to investigate the potential benefits and pitfalls of WGS in the examination of (1) the evolution and virulence of STEC, (2) epidemiology from bedside diagnostics to investigations of outbreaks and sporadic cases and (3) food protection from routine analysis of foodstuffs to global food networks. A number of key recommendations are made that include: validation and standardization of acquisition, processing and storage of sequence data including the development of an open access "WGSNET"; building up of sequence databases from both prospective and retrospective isolates; development of a suite of open-access software specific for STEC accessible to non-bioinformaticians that promotes understanding of both the computational and biological aspects of the problems at hand; prioritization of research funding to both produce and integrate genotypic and phenotypic information suitable for risk assessment; training to develop a supply of individuals working in bioinformatics/software development; training for clinicians, epidemiologists, the food industry and other stakeholders to ensure uptake of the technology and finally review of progress of implementation of WGS. Currently the benefits of WGS are being slowly teased out by academic, government, and industry or private sector researchers around the world. The next phase will require a coordinated international approach to ensure that it's potential to contribute to the challenge of STEC disease can be realized in a cost effective and timely manner.

Original languageEnglish
Pages (from-to)57-72
Number of pages16
JournalInternational Journal of Food Microbiology
Early online date11 Jul 2014
Publication statusPublished - 18 Sept 2014

Bibliographical note

Copyright © 2014. Published by Elsevier B.V.
The OECD for both sponsoring the STEC genomics workshop held in Charlotte, North Carolina, July 2013 and the open access journal fees.


  • Animals
  • Databases, Genetic
  • Food Microbiology
  • Food Supply
  • Food-Processing Industry
  • Genome, Bacterial
  • Humans
  • Sequence Analysis, DNA
  • Shiga-Toxigenic Escherichia coli
  • Whole genome sequencing
  • Shiga toxin producing E. coli (STEC)
  • Food Safety
  • E. coli O157
  • Food Chains
  • Public Health


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