2023 FDA Science Forum
Real-time detection of emerging outbreaks using large-scale whole genome sequencing
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Contributing OfficeCenter for Food Safety and Applied Nutrition
Abstract
Background
Whole-genome sequencing (WGS) can detect single base-pair differences between organisms and can be used to identify sources of foodborne bacterial pathogens. Investigators use WGS to find matches between contaminated foods, environments, and sick patients during outbreaks and investigations. Pathogens found during food facility inspections also provide clues about the causes of outbreaks prior to the collection of epidemiologic or traceback evidence and can identify facilities with long-term (resident) contamination. Bioinformatic tools are necessary to streamline this surveillance process.
Purpose
Daily surveillance of WGS data combined with historical data from the database: 1) provides evidence supporting outbreak investigations, 2) detects emerging outbreaks, and 3) identifies resident pathogens.
Methodology
The NCBI Pathogen Detection (PD) system archives all foodborne pathogen WGS data. The NCBI PD Isolates Browser enables users to explore sequence data and identifies groups of closely related sequences and their relationships within that group. NCBI PD Rapid Reports augments the Isolates Browser by providing rapid (< 2hours) results for new data and provides allele distances between newly submitted data and sequences already in the database.
NCBI PD results are processed by software written by the CFSAN/OAO Bioinformatics Team to filter results that meet match criteria. Signals are reviewed with CFSAN’s Coordinated Outbreak Response and Evaluation Network (CORE) and the Office of Compliance for action.
Results
Examples of emerging outbreaks detected:
2021: Three submitted clinical isolates matched previously submitted isolates from imported shrimp. Follow up with CORE resulted in recalls of product and an outbreak investigation.
2022: Submitted clinical isolates matched previous isolates from peanut butter and a food processing facility. Follow up with CORE resulted in recalls of product and an outbreak investigation that confirmed sickened people consumed product from the facility. The data also indicated the likely presence of a resident pathogen.
Conclusion
Surveillance of WGS data is highly effective for preventing illnesses. Tools developed by the CFSAN/OAO Bioinformatics Team, and NCBI’s PD group database are vital to this effort.
