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. and Strachan, Norval J. C. (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, 187 57-72. doi:10.1016/j.ijfoodmicro.2014.07.002


Author 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.
Title Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems
Journal name International Journal of Food Microbiology   Check publisher's open access policy
ISSN 0168-1605
1879-3460
Publication date 2014-09-18
Year available 2014
Sub-type Critical review of research, literature review, critical commentary
DOI 10.1016/j.ijfoodmicro.2014.07.002
Open Access Status
Volume 187
Start page 57
End page 72
Total pages 16
Place of publication Amsterdam, Netherlands
Publisher Elsevier
Collection year 2015
Language eng
Subject 1106 Human Movement and Sports Science
2404 Microbiology
2213 Safety, Risk, Reliability and Quality
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.
Keyword Whole genome sequencing
Shiga toxin producing E. coli (STEC)
Food safety
E. coli O157
Food chains
Public health
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collections: Official 2015 Collection
School of Chemistry and Molecular Biosciences
 
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