One Health Enteric Package: Expanded and standardized metadata for enteric genomic epidemiology in the US (GenFS Metadata workgroup)

Authors: TIMME, RUTH - Food And Drug Administration(FDA); BALKEY, MARIA - Food And Drug Administration(FDA); GRIM, CHRISTOPHER - Food And Drug Administration(FDA); BATZ, MICHAEL - Food And Drug Administration(FDA); PENNERMAN, KAYLA - Food And Drug Administration(FDA); YANG, ZHIHUI - Food And Drug Administration(FDA); HICKS, JESSICA - Animal And Plant Health Inspection Service (APHIS); Cook, Kimberly - Kim; Van Kessel, Jo Ann; Bono, James - Jim; HARRIS, BETH - Animal And Plant Health Inspection Service (APHIS); FELDGARDEN, MIKE - National Institutes Of Health (NIH); SHUMWAY, MARTIN - National Institutes Of Health (NIH)

Submitted to: Foodborne Pathogens and Disease
Publication Type: Abstract Only
Publication Acceptance Date: 1/28/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Genomics for Food Safety (GenFS) Metadata Workgroup is a cross-agency collaboration comprising members from the United States Department of Agriculture, Centers for Disease Control and Prevention, National Center for Biotechnology Information, and Food and Drug Administration. The primary goal of this workgroup is to expand and standardize the contextual data (metadata) associated with samples collected for enteric surveillance in the US (i.e. where, from what, by whom, and when the sample was collected) moving from a mostly free-text space to one that is machine readable. Our workgroup leveraged two existing metadata packages, the NCBI standard Pathogen metadata package and the draft MIxS Food Environmental Metadata Standard package, to develop a new metadata package for genomic surveillance of enteric pathogens. The “One Health Enteric Package (OHE)” captures the full One Health sample space for enteric pathogens. The OHE package comprises a core suite of attributes describing general sample and isolate features plus four sections covering the major One Health sample spaces: 1) human/animal hosts, 2) food samples, 3) food facilities and the built environment, and 4) environmental samples (farm, water and the natural environment). Each of these sections contain a set of attributes with detailed definitions, guidance, and requirements. Most attributes require standardized input selected from controlled vocabularies or existing ontologies. Curated picklists provide the user easy access to standard terminology for populating the package. Each collaborating agency provided example use cases that new users can follow for different sample types. This effort resulted in a metadata package that will better meet our One Health goals by providing machine readable contextual data enabling more sophisticated data science analyses for investigating links between genomic data and contextual metadata, e.g. machine learning or population-adapted genome wide-association studies (GWAS) to test hypotheses around evolution of virulence, stress tolerance, antimicrobial resistance, risk assessment, and source attribution, among others.