Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States

Abstract

This multi-agency report developed under the Interagency Collaboration for Genomics for Food and Feed Safety (Gen-FS) provides an overview of the use of and transition to Whole-Genome Sequencing (WGS) technology to detect and characterize pathogens transmitted commonly by food and identify their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among federal agencies, including the National Institutes of Health (NIH); the Department of Health and Human Services’ Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA); and the U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS), Agricultural Research Service (ARS), and Animal and Plant Health Inspection Service (APHIS). We describe single nucleotide polymorphism (SNP), core-genome (cg) and whole-genome multi-locus sequence typing (wgMLST) data analysis methods as used in CDC’s PulseNet and FDA’s GenomeTrakr networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Gen-FS agency partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles), source attribution efforts, and increasing transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information (NCBI). Finally, we highlight the impact of current trends in the use of culture-independent diagnostics tests (CIDT) for human diagnostic testing on analytical approaches related to food safety. Lastly, we highlight what is next for WGS in food safety.

Genomic characteristics and comparative genomics analysis of Salmonella enterica subsp. enterica serovar Thompson isolated from an outbreak in South Korea

“…2 b). The presence of 20 or fewer SNPs indicates that bacteria are genetically very similar and recently originated from the same source 24 , 25 . Therefore, the chocolate cake-related outbreak S. Thompson strains are distant from other isolates in South Korea.…”

“…Thompson strains isolated from a multistate chocolate cake-related outbreak in 2018 had low genetic relevance to previously reported S . Thompson strains 24 , 25 . In addition, comparative genomic analysis provides comprehensive information on the disease potential of the outbreak strains.…”

Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017–2020

“…The use of the first two options is limited by strict institutional requirements and availability of appropriate operating systems. Intersectoral collaboration between public health and food safety authorities (e.g., GenomeTrackr) will also strengthen bioinformatics analyses and investigations of outbreaks and surveillance activities of foodborne pathogens [ 17 ]. Here, we show that collaborations with universities and academic research laboratories can also be an effective approach to supporting state public health laboratories by providing computing power, bioinformatics expertise, and software.…”

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

“…In the United States, CDC, FDA and USDA FSIS work together with state agencies to protect public health and food safety. To this end, agencies work to identify and implement cost-effective advances in technology, such as HTS and its Whole Genome Sequencing (WGS) application, to rapidly detect and investigate foodborne outbreaks of domestic and international origin 23 . The decreasing cost of WGS ( https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost ) coupled with its superior discriminatory power compared to previous generations of “gold standard” methods such as Pulsed-Field Gel Electrophoresis (PFGE) has resulted in a transition to WGS across regulatory agencies in the United States and several other countries.…”