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Wellman A, Bazaco M, Blessington T, Pightling A, Dwarka A, Hintz L, Wise ME, Gieraltowski L, Conrad A, Nguyen TA, Hise K, Viazis S, Beal J. An Overview of Foodborne Sample-Initiated Retrospective Outbreak Investigations and Interagency Collaboration in the United States. J Food Prot 2023; 86:100089. [PMID: 37024093 DOI: 10.1016/j.jfp.2023.100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Foodborne outbreak investigations have traditionally included the detection of a cluster of illnesses first, followed by an epidemiologic investigation to identify a food of interest. The increasing use of whole genome sequencing (WGS) subtyping technology for clinical, environmental, and food isolates of foodborne pathogens, and the ability to share and compare the data on public platforms, present new opportunities to identify earlier links between illnesses and their potential sources. We describe a process called sample-initiated retrospective outbreak investigations (SIROI) used by federal public health and regulatory partners in the United States. SIROIs begin with an evaluation of the genomic similarity between bacterial isolates recovered from food or environmental samples and clusters of clinical isolates while subsequent and parallel epidemiologic and traceback investigations are initiated to corroborate their connection. SIROIs allow for earlier hypothesis generation, followed by targeted collection of information about food exposures and the foods and manufacturer of interest, to confirm a link between the illnesses and their source. This often leads to earlier action that could reduce the breadth and burden of foodborne illness outbreaks. We describe two case studies of recent SIROIs and present the benefits and challenges. Benefits include insight into foodborne illness attribution, international collaboration, and opportunities for enhanced food safety efforts in the food industry. Challenges include resource intensiveness, variability of epidemiologic and traceback data, and an increasingly complex food supply chain. SIROIs are valuable in identifying connections among small numbers of illnesses that may span significant time periods; detecting early signals for larger outbreaks or food safety issues associated with manufacturers; improving our understanding of the scope of contamination of foods; and identifying novel pathogen/commodity pairs.
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Affiliation(s)
- Allison Wellman
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland.
| | - Michael Bazaco
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Tyann Blessington
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Asha Dwarka
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Leslie Hintz
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Matthew E Wise
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Amanda Conrad
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thai-An Nguyen
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kelley Hise
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stelios Viazis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Jennifer Beal
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
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Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL, Lauer AC, Pightling A, Jarvis KG, Ottesen A, Ramachandran P, Hintz L, Katz LS, Folster JP, Whichard JM, Trees E, Timme RE, McDERMOTT P, Wolpert B, Bazaco M, Zhao S, Lindley S, Bruce BB, Griffin PM, Brown E, Allard M, Tallent S, Irvin K, Hoffmann M, Wise M, Tauxe R, Gerner-Smidt P, Simmons M, Kissler B, Defibaugh-Chavez S, Klimke W, Agarwala R, Lindsay J, Cook K, Austerman SR, Goldman D, McGARRY S, Hale KR, Dessai U, Musser SM, Braden C. Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States. J Food Prot 2022; 85:755-772. [PMID: 35259246 DOI: 10.4315/jfp-21-437] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) 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 Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety. HIGHLIGHTS
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Affiliation(s)
- Eric L Stevens
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Heather A Carleton
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jennifer Beal
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Glenn E Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Rebecca L Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - A C Lauer
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Arthur Pightling
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Karen G Jarvis
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Andrea Ottesen
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Padmini Ramachandran
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Leslie Hintz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Lee S Katz
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jason P Folster
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jean M Whichard
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eija Trees
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Ruth E Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Patrick McDERMOTT
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Beverly Wolpert
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Michael Bazaco
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Sabina Lindley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Beau B Bruce
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Patricia M Griffin
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eric Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Sandra Tallent
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Kari Irvin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Maria Hoffmann
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Matt Wise
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Robert Tauxe
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Mustafa Simmons
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Bonnie Kissler
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | | | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - James Lindsay
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Kimberly Cook
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Suelee Robbe Austerman
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, Iowa 50010, USA
| | - David Goldman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Sherri McGARRY
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Kis Robertson Hale
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Steven M Musser
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Chris Braden
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
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