One health enteric package v1.0: Expanded and standardized metadata package for the US’s genomic epidemiology network for enteric surveillance

Authors: TIMME, RUTH - Us Food & Drug Administration (FDA); BALKEY, MARIA - Us Food & Drug Administration (FDA); GRIM, CHRISTOPHER - Us Food & Drug Administration (FDA); BATZ, MICHAEL - Us Food & Drug Administration (FDA); HICKS, JESSICA - Animal And Plant Health Inspection Service (APHIS); COOK, KIMBERLY - US Department Of Agriculture (USDA); Van Kessel, Jo Ann; BONO, JIM - US Department Of Agriculture (USDA); HARRIS, BETH - Animal And Plant Health Inspection Service (APHIS); FULLERTON, KATHLEEN - Centers For Disease Control And Prevention (CDC) - United States; KATZ, LEE - Centers For Disease Control And Prevention (CDC) - United States; ADAMS, JENNIFER - Centers For Disease Control And Prevention (CDC) - United States; STROIKA, STEVEN - Centers For Disease Control And Prevention (CDC) - United States; JOSEPH, LAVIN - Centers For Disease Control And Prevention (CDC) - United States

Submitted to: International Association for Food Protection
Publication Type: Abstract Only
Publication Acceptance Date: 1/19/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Introduction: Genomic data is intrinsically standard across all life on earth, making these data an incredibly useful tool for food safety surveillance and outbreak investigations; however, the contextual data associated with these genomes (where, from what, by whom, and when the sample was collected), are generally not inherently standard, requiring preset, controlled vocabularies before they can be logically compared. An early global standard was key in establishing basic interoperability for cluster detection, but, more sophisticated analyses to tackle risk, root cause, source attribution, and others require richer, more structured contextual data, or metadata, to accompany each genome. Purpose: We propose an expanded, standardized, metadata package to be used for all US contributors across our open genomic epidemiology network for enteric surveillance. Methods: The Genomics for Food Safety (GenFS) metadata working group reviewed the existing metadata standard, National Center for Biotechnology Information (NCBI) pathogen metadata package, identifying a set of core attributes to retain and flagging ones that were not utilized or relevant to our mission. In addition, a new set of attributes were developed to standardize and expand upon existing free-text fields, like isolation source, providing machine-readable, ontologically structured metadata describing samples taken from across the One Health arena. Results: The One Health Enteric Package v1.0 marks the first major update to the NCBI pathogen metadata template for use in genomic foodborne pathogen surveillance. This release includes the same core set of fields utilized in the NCBI pathogen package plus a set of custom fields specific to our community. Significance: Improved metadata resulting from this project will enable sophisticated data science-type analyses into investigating links between genomic data and source data, e.g. machine learning or population-adapted genome-wide association studies (GWAS) to test hypotheses around evolution of virulence, stress tolerance, and AMR, risk assessment, source attribution, among others.