Abstract
Globalization of food networks increases opportunities for the spread of foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping of pathogens promises to vastly improve our ability to track and control foodborne disease, but to do so it must be combined with epidemiological, clinical, laboratory and other health care data (called “contextual data”) to be meaningfully interpreted for regulatory and health interventions, outbreak investigation, and risk assessment. However, current multi-jurisdictional pathogen surveillance and investigation efforts are complicated by time-consuming data re-entry, curation and integration of contextual information owing to a lack of interoperable standards and inconsistent reporting. A solution to these challenges is the use of ‘ontologies’ - hierarchies of well-defined and standardized vocabularies interconnected by logical relationships. Terms are specified by universal IDs enabling integration into highly regulated areas and multi-sector sharing (e.g., food and water microbiology with the veterinary sector). Institution-specific terms can be mapped to a given standard at different levels of granularity, maximizing comparability of contextual information according to jurisdictional policies. Fit-for-purpose ontologies provide contextual information with the auditability required for food safety laboratory accreditation. Our research efforts include the development of a Genomic Epidemiology Ontology (GenEpiO), and Food Ontology (FoodOn) that harmonize important laboratory, clinical and epidemiological data fields, as well as existing food resources. These efforts are supported by a global consortium of researchers and stakeholders worldwide. Since foodborne diseases do not respect international borders, uptake of such vocabularies will be crucial for multi-jurisdictional interpretation of WGS results and data sharing.
Highlights
THE IMPORTANCE OF METADATA AND CONTEXTUAL INFORMATION IN FOODBORNE SAFETY AND SURVEILLANCEFoodborne pathogens impact global health and can cost economies millions of dollars in lost productivity (Flynn, 2014; Minor et al, 2015; World Health Organization, 2015)
We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes
With the international nature of food distribution and food safety concerns, the most effective semantic resources must be open source, interoperable and collaboratively developed in order to best represent the needs of the international community
Summary
THE IMPORTANCE OF METADATA AND CONTEXTUAL INFORMATION IN FOODBORNE SAFETY AND SURVEILLANCEFoodborne pathogens impact global health and can cost economies millions of dollars in lost productivity (Flynn, 2014; Minor et al, 2015; World Health Organization, 2015). Contextual information in genomic epidemiology investigations includes critical knowledge about sequencing pipelines and sequence quality, sources of exposure and risk, clinical phenotypes, susceptible populations, geographical distribution and more. Clinical information about the host, and epidemiological information about possible exposures (high-risk food types), are all useful to establish at-risk populations and hypothesize about likely sources of contamination (World Health Organization, 2008). This information is used to establish the geographic distribution of pathogenic strains, as well as among populations, which is critical for determining transmission patterns (Moura et al, 2016; Njamkepo et al, 2016). Risk analysis in particular requires precise data on pathogen hazards in food to be systematically linked to epidemiological data, in order to make assessments, implement interventions and monitor outcomes (Lammerding and Fazil, 2000; Hoornstra et al, 2001; Food and Agriculture Organization of the United Nations [FAO], 2005)
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