A foresight study on emerging technologies: State of the art of Omics technologies and potential applications in food and feed safety

Abstract

Suggested citation: Pielaat A, Barker GC, Hendriksen P, Peijnenburg A and Kuile BH, 2013. A foresight study on emerging technologies: State of the art of omics technologies and potential applications in food and feed safety. REPORT 1: Review on the state of art of omics technologies in risk assessment related to food and feed safety. EFSA supporting publication 2013:EN-495, 126 pp. ABSTRACTThis report consists of a review of the available scientific evidence on the state of art of omics technologies with a particular focus on applications in the area of food and feed safety. The report gives a description of the different types of omics technologies with respect to recent progresses made on the application of these techniques in chemical and microbiological risk assessment. Hereto, case studies were selected in order to cover different areas under the remit of EFSA. In this review each case study has been investigated with respect to its hazard, experimental methodologies, (statistical) data analysis and its link to food/feed safety risk assessment. Finally, the added value of omics technologies as compared to classical risk assessment and current limitations of omics technologies for their application in chemical and microbiological food safety risk assessment has been discussed. This investigation shows that most of the studies on chemical agents focus on mode of action identification and a search for biomarkers using transcriptomics. As for microbial food safety, omics have not yet been successfully applied often. When applied, they never target the host, but focus on aspects of the pathogen, e.g. in detection or source attribution.

Defining the optimal animal model for translational research using gene set enrichment analysis

“…These set enrichment approaches have been shown to be more robust for comparisons of transcriptomic data between different platforms or with different experimental models or clinical cohorts (Spinelli et al , ). Therefore, these approaches are currently recommended for data analysis for human risk assessment of chemicals and may lead to reductions in animal use in toxicological research (National Research Council (US), ; Pielaat et al , ; European Food Safety Authority, ). Using GSEA, we were able to identify particular mouse models (i.e., Staphylococcus aureus injection and the CLP model) that showed inflammatory pathway regulation profiles that were similar to the human situation; notably, most of these pathways are currently promising clinical targets in several inflammatory disorders.…”

“…If the same sets of experimental data can lead to diametrically opposite conclusions, then the relevance and outcome of genomic (and other “omics”) studies for purposes other than explorative approaches are negligible and strongly require improvement. Thus, better standardization of statistical analyses and data interpretation are urgently needed and should be addressed to improve the use of omics data for regulatory purposes (National Research Council (US), ; Pielaat et al , ; European Food Safety Authority, ).…”

Towards a personalized risk assessment for exposure of humans to toxic substances

“…Such markers may include inborn differences in metabolism, variations in immunoglobulin levels, low organ-reserve capacity, or other identifiable genetically determined or environmentally induced variations in absorption, metabolism, and response to environmental agents 63 . Other factors that may affect individual susceptibilities include nutritional status of the organism, the role of the target site in overall body function, condition of the target tissue (present or prior to disease), and compensation by homeostatic mechanisms during and after exposure 64 . This means that variation in the response to xenobiotics by individuals is closely related to specific genotypes and phenotypes, which is the basis of individual clinical toxicology 65 .…”

First step in using molecular data for microbial food safety risk assessment; hazard identification of Escherichia coli O157:H7 by coupling genomic data with in vitro adherence to human epithelial cells

“…Although the use of molecular data has proved to be a powerful tool in decision making during outbreak investigations ( Dallman et al, 2014; Underwood et al, 2013 ), the application of this data in microbiological risk assessment is currently an unexplored area in the public health domain. In recent years, a number of reviews and opinions have been published exploring the potentials of ‘omics techniques’ for MRA ( Abee et al, 2004; Brul et al, 2012; Carriço et al, 2013; Havelaar et al, 2010; Pielaat et al, 2013a,b ) but, evidence based research, as a first step to convert these heuristic approaches into normative tools for practical use, is still needed.…”