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

Authors: FRANZ, EELCO - National Institute For Public Health And The Environment (RIVM); DELAQUIS, PASCAL - Agriculture And Agri-Food Canada; STEFANO, MORABITO - Istituto Superiore Di Sanità; BEUTIN, LOTHAR - Federal Institute Of Technology; GOBIUS, KARI - Commonwealth Scientific And Industrial Research Organisation (CSIRO); RASKO, DAVID - University Of Maryland; Bono, James - Jim; FRENCH, NIGEL - Massey University; OSEK, JACEK - Dept Of Hygiene Of Food And Animal Origin; LINDSTEDT, BJORN_ARNE - The Norwegian Institute Of Public Health; MUNIESA, MAITE - University Of Barcelona; MANNING, SHANNON - Michigan State University; LEJEUNE, JEFF - Ohio Agricultural Research & Development Center; Callaway, Todd; BEATSON, SCOTT - University Of Queensland; EPPINGER, MARK - University Of Texas At San Antonio; DALLMAN, TIM - Health Protection Agency; FORBES, KEN - University Of Aberdeen; AARTS, HENK - National Institute For Public Health And The Environment (RIVM); PEARL, DAVID - University Of Aberdeen; STRACHAN, NORVAL - University Of Aberdeen

Submitted to: International Journal of Food Microbiology
Publication Type: Other
Publication Acceptance Date: 7/4/2014
Publication Date: 7/11/2014
Citation: Franz, E., Delaquis, P., Stefano, M., Beutin, L., Gobius, K., Rasko, D., Bono, J.L., French, N., Osek, J., Lindstedt, B., Muniesa, M., Manning, S., LeJeune, J., Callaway, T.R., Beatson, S., Eppinger, M., Dallman, T., Forbes, K., Aarts, H., Pearl, D., Strachan, N.J. 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.

Interpretive Summary: Shiga toxin-encoding Escherichia coli (STEC) are important contributors to foodborne human illness in both the developed and developing worlds. One of the primary challenges in studying STEC is to see that new technologies are effectively utilised to help address the issues associated with these pathogenic organisms. The purpose of this position paper is to investigate the potential benefits and pitfalls of whole genome sequencing of STECs. A number of key recommendations are made to ensure the methods used are valid, data is freely available, software is developed for non-bioinformaticians, and prioritization of funding. Currently the benefits of WGS are being slowly teased out by both government and academic researchers around the world. The next phase will require a coordinated international approach to ensure that its potential to contribute to the challenge of STEC disease can be realized in a cost effective and timely manner.

Technical 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 utilised to help address the issues associated with these pathogenic organisms. 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 (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; prioritisation 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 etc. to ensure take-up of the technology and finally review of progress of implementation of WGS. Currently the benefits of WGS are being slowly teased out by both government and academic researchers around the world. The next phase will require a coordinated international approach to ensure that its potential to contribute to the challenge of STEC disease can be realized in a cost effective and timely manner.