Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance

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.

INNUENDO: A cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens

“…One is to create a decentralized, shared digital computer system and database allowing secure communication between all stakeholders in an outbreak setting, with implemented functions for submission of samples, outbreak notification and reporting. Currently, communication between laboratories and other national and local stakeholders is usually done by Email (at least in two of the studies countries), which is badly suited to preserve patient privacy security and IT-security (van Panhuis et al, 2014;Griffiths et al, 2017). A digital communication system would aid in the harmonization and storing of contextual information, using controlled vocabulary and defined ontology.…”

“…Sufficient and well-defined metadata and an efficient and accurate communication between public health, food and veterinary authorities, laboratories, medical practitioners, food industries, media and the public are important when solving an outbreak. For WGS subtyping to be a valuable tool in genomic epidemiology, it must be combined with epidemiological, clinical, laboratory, genomic and other health care data ("contextual data") (Griffiths et al, 2017). Availability of such data increase the utility of genomic information in outbreak investigations, but barriers of legal, political and technical nature challenge the sharing of data and integration between agencies, especially during multi-states outbreaks (van Panhuis et al, 2014).…”

“…Therefore, WGS-based typing is replacing traditional analyses for certain microbial pathogens in several countries, revolutionizing outbreak detection and investigation, and gradually becoming a relevant tool for control-oriented surveillance (van Panhuis et al, 2014). Genomics also introduces new opportunities for more efficient use of isolate information, defined as contextual data (Griffiths et al, 2017), especially when combining high-resolution typing with the epidemiological and clinical data (such as exposures or clinical symptoms and outcomes) in real-time.…”

“…The value of WGS data extends well beyond a single laboratory or laboratory network, since WGS data is useful for answering various scientific questions with the ultimate aim of reducing the burden of disease worldwide. However, this is only possible if molecular typing data is shared, which facilitates immediate public health actions, strengthens long-term studies and has a strong impact on applied research (van Panhuis et al, 2014;Griffiths et al, 2017). However, there are country-specific legal barriers as well as several technical issues and diffuse political and ethical skepticism concerning sharing sensitive data from human or food products (van Panhuis et al, 2014).…”

Establishment of a prototypic Quantitative Microbial Risk Assessment (QMRA) food and feed safety model repository

“…The original model metadata schema and the controlled vocabularies were proposed from the Risk Assessment Knowledge Integration Platform (RAKIP) community. Ontologies encode standardized terminologies, contextual information and interrelationships of metadata concepts (Griffiths et al, 2017). FSK-ML and bestpractice annotation guidelines were designed such that they can serve as a bridge between different software tools, data and model repositories.…”