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 Pearl & 3 others Victor P J Gannon, Chad R Laing, Norval J C Strachan

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

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
Volume187
Early online date11 Jul 2014
DOIs
Publication statusPublished - 18 Sep 2014

Fingerprint

Shiga-Toxigenic Escherichia coli
Shiga toxin-producing Escherichia coli
Explosions
explosions
food production
production technology
Genome
Food
genome
Software
Technology
outbreak investigation
Foodborne Diseases
research support
Private Sector
prioritization
private sector
Information Storage and Retrieval
Food Industry
foodborne illness

Keywords

  • 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

Cite this

Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems. / Franz, Eelco; Delaquis, Pascal; Morabito, Stefano; Beutin, Lothar; Gobius, Kari; Rasko, David A; Bono, Jim; French, Nigel; Osek, Jacek; Lindstedt, Bjørn-Arne; Muniesa, Maite; Manning, Shannon; LeJeune, Jeff; Callaway, Todd; Beatson, Scott; Eppinger, Mark; Dallman, Tim; Forbes, Ken J; Aarts, Henk; Pearl, David L; Gannon, Victor P J; Laing, Chad R; Strachan, Norval J C.

In: International Journal of Food Microbiology, Vol. 187, 18.09.2014, p. 57-72.

Research output: Contribution to journalArticle

Franz, E, Delaquis, P, Morabito, S, Beutin, L, Gobius, K, Rasko, DA, Bono, J, French, N, Osek, J, Lindstedt, B-A, Muniesa, M, Manning, S, LeJeune, J, Callaway, T, Beatson, S, Eppinger, M, Dallman, T, Forbes, KJ, Aarts, H, Pearl, DL, Gannon, VPJ, Laing, CR & Strachan, NJC 2014, 'Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems', International Journal of Food Microbiology, vol. 187, pp. 57-72. https://doi.org/10.1016/j.ijfoodmicro.2014.07.002
Franz, Eelco ; Delaquis, Pascal ; Morabito, Stefano ; Beutin, Lothar ; Gobius, Kari ; Rasko, David A ; Bono, Jim ; French, Nigel ; Osek, Jacek ; Lindstedt, Bjørn-Arne ; Muniesa, Maite ; Manning, Shannon ; LeJeune, Jeff ; Callaway, Todd ; Beatson, Scott ; Eppinger, Mark ; Dallman, Tim ; Forbes, Ken J ; Aarts, Henk ; Pearl, David L ; Gannon, Victor P J ; Laing, Chad R ; Strachan, Norval J C. / Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems. In: International Journal of Food Microbiology. 2014 ; Vol. 187. pp. 57-72.
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AU - Beutin, Lothar

AU - Gobius, Kari

AU - Rasko, David A

AU - Bono, Jim

AU - French, Nigel

AU - Osek, Jacek

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AU - Pearl, David L

AU - Gannon, Victor P J

AU - Laing, Chad R

AU - Strachan, Norval J C

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KW - Databases, Genetic

KW - Food Microbiology

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KW - Food-Processing Industry

KW - Genome, Bacterial

KW - Humans

KW - Sequence Analysis, DNA

KW - Shiga-Toxigenic Escherichia coli

KW - Whole genome sequencing

KW - Shiga toxin producing E. coli (STEC)

KW - Food Safety

KW - E. coli O157

KW - Food Chains

KW - Public Health

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