title: Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems.
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.
authors: National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
authors: Eelco
authors: E
authors: Franz
authors: Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada.
authors: Pascal
authors: P
authors: Delaquis
authors: National Institute of Health, Rome, Italy.
authors: Stefano
authors: S
authors: Morabito
authors: Federal Institute for Risk Assessment, Berlin, Germany.
authors: Lothar
authors: L
authors: Beutin
authors: CSIRO, Archerfield BC Queensland, Australia.
authors: Kari
authors: K
authors: Gobius
authors: University of MD School of Medicine, Baltimore, USA.
authors: David A
authors: DA
authors: Rasko
authors: USDA/ARS, Clay Centre, NE, USA.
authors: Jim
authors: J
authors: Bono
authors: EpiLab, Infectious Disease Research Centre, Institute of Veterinary Animal and Biomedical Sciences, Massey University, New Zealand.
authors: Nigel
authors: N
authors: French
authors: National Veterinary Research Institute, Pulawy, Poland.
authors: Jacek
authors: J
authors: Osek
authors: Unit of Gene Technology, Akershus University Hospital Lørenskog, Norway.
authors: Bjørn-Arne
authors: BA
authors: Lindstedt
authors: Department of Microbiology, University of Barcelona, Barcelona, Spain.
authors: Maite
authors: M
authors: Muniesa
authors: Microbiology and Molecular Genetics, MI State University, East Lansing, USA.
authors: Shannon
authors: S
authors: Manning
authors: Ohio Agricultural Research and Development Center, Wooster, USA.
authors: Jeff
authors: J
authors: LeJeune
authors: USDA/ARS, College Station, TX, USA.
authors: Todd
authors: T
authors: Callaway
authors: Australian Infectious Disease Research Centre, The University of Queensland, St. Lucia, Australia.
authors: Scott
authors: S
authors: Beatson
authors: Department of Biology, & South Texas Center for Emerging Infectious Diseases (STCEID), The University of Texas at San Antonio, San Antonio, TX, USA.
authors: Mark
authors: M
authors: Eppinger
authors: Health Protection Agency, London, United Kingdom.
authors: Tim
authors: T
authors: Dallman
authors: School of Medicine and Dentistry, The University of Aberdeen, Aberdeen, Scotland, United Kingdom.
authors: Ken J
authors: KJ
authors: Forbes
authors: National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
authors: Henk
authors: H
authors: Aarts
authors: Ontario Veterinary College, University of Guelph, Guelph, Canada.
authors: David L
authors: DL
authors: Pearl
authors: Publ Health Agency Canada, Lab Foodborne Zoonoses, Lethbridge, Canada.
authors: Victor P J
authors: VP
authors: Gannon
authors: Publ Health Agency Canada, Lab Foodborne Zoonoses, Lethbridge, Canada.
authors: Chad R
authors: CR
authors: Laing
authors: School of Biological Sciences, The University of Aberdeen, Aberdeen, Scotland, United Kingdom. Electronic address: n.strachan@abdn.ac.uk.
authors: Norval J C
authors: NJ
authors: Strachan
mesh_terms: D000818:Animals; D030541:Databases, Genetic / Q000592:standards; D005516:Food Microbiology / Q000639:trends*; D005523:Food Supply / Q000592:standards*; D005525:Food-Processing Industry / Q000639:trends*; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D017422:Sequence Analysis, DNA; D054323:Shiga-Toxigenic Escherichia coli / Q000235:genetics*
keywords: E. coli O157; Food chains; Food safety; Public health; Shiga toxin producing E. coli (STEC); Whole genome sequencing