‘Omics’ technologies in quantitative microbial risk assessment

‘Omics’ tools are being developed at an ever increasing pace. Collectively, genome sequencing, genome-wide transcriptional analysis (transcriptomics), proteomics, metabolomics, flux analysis (‘fluxomics’) and other applications are captured under the term omics. The data generated using these tools allow researchers to gain an increasingly detailed insight into cellular responses to changes in the environment. For the area of microbiological food safety, these developments mean that mechanistic explanations of the response of microorganisms to food preservation treatments and environmental conditions in the food chain become more attainable. Importantly, the data need to be relevant to real conditions in foods and related environments. Currently, it is still often the case that these data are generated in pure cultures and under very specific conditions albeit that recent years have seen some true in situ analyses. The opportunities offered by the latter in analysing virulence as well as challenges faced in terms of experimental design (including the consideration of strain variability) in efforts to link omics data to phenotypic response and data integration for quantitative microbiological risk assessment in foods are discussed in the current paper. The paper is guided by the output of a workshop organized in May 2011 by the International Life Sciences Institute Europe (ILSI Europe) in which representatives from governmental bodies, industry and academia came together to discuss such challenges and consider how these may be met. In addition, the ILSI Europe workshop identified knowledge gaps where new omics studies can make major contributions.