Development of SeqSero2, an advanced software tool for Salmonella characterization that contributes to public health surveillance and regulatory implementation nationally and globally

Summary

Center for Food Safety researchers developed SeqSero2, an advanced software tool for Salmonella characterization that contributes to public health surveillance and regulatory implementation nationally and globally

Situation

Every year foodborne pathogens sicken 1 in 6 Americans and impose an economic burden of over $15.6 billion in the United States. Salmonella is one of the most prevalent foodborne pathogens in the United States and worldwide. Salmonella serotyping is traditionally determined using a time-consuming laboratory protocol, and it is the foundation of the US national Salmonella surveillance system for over five decades. SeqSero, a publicly available bioinformatics tool developed and launched by Dr. Xiangyu Deng’s lab in 2015, provided a faster alternative and has been used worldwide for Salmonella serotype prediction from whole genome sequencing data, which has helped transform Salmonella surveillance in the US and other countries.

Response

Funded by an FDA Broad Agency Announcement award, Dr. Xiangyu Deng’s lab created SeqSero2, an algorithmic transformation and functional update of the original SeqSero software launched by the lab in 2015.

Impact

PulseNet, a national laboratory network that connects foodborne illness cases to detect outbreaks, has adopted SeqSero2 since 2019. Under PulseNet, SeqSero2 is used by every state public health laboratory to characterize every Salmonella isolate from the US national surveillance. The USDA Food Safety and Inspection Service began using SeqSero2 as of January 2020 for high-throughput characterization of ~10,000 regulatory isolates annually. The National Antimicrobial Resistance Monitoring System uses SeqSero2 to analyze Salmonella isolates from ill people, retail meats, and food animals. FDA has completed single-lab and multi-lab validation of SeqSero2 as well as agency-wide implementation and testing. Full regulatory implementation of SeqSero2 by FDA is expected by January 31, 2021. GenFS, an interagency standards group by NCBI, CDC, FDA and USDA for next-generation sequencing of bacterial pathogens, has established a subcommittee dedicated to harmonizing Salmonella serotyping based on SeqSero2. Internationally, SeqSero2 has been integrated into EnteroBase, a global genome database for enteric bacteria. SeqSero2 is also being incorporated to the NCBI Pathogen Detection system, a centralized system that integrates sequence data for bacterial pathogens.

State Issue

Food Safety and Quality

Details

  • Year: 2020
  • Geographic Scope: International
  • County: Spalding
  • Location: Georgia Station, Griffin
  • Program Areas:
    • Agriculture & Natural Resources

Author

    Deng, Xiangyu

Collaborator(s)

CAES Collaborator(s)

  • Den Bakker, Hendrik C

Non-CAES Collaborator(s)

  • Ana Lauer
  • Blake Dinsmore
  • Patti Fields
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Research Impact