Advanced Software Tool for Salmonella

Salmonella is one of the most prevalent food-borne pathogens in the United States and worldwide. Salmonella serotyping is traditionally determined using a time-consuming laboratory protocol, and it has been the foundation of the national Salmonella surveillance system for over five decades. SeqSero, a publicly available bioinformatics tool developed and launched by a UGA lab with the Center for Food Safety 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 U.S. and other countries. The scientists have now created SeqSero2, an algorithmic transformation and functional update of the original SeqSero software. PulseNet, a national laboratory network that connects food-borne 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 national surveillance. The USDA Food Safety and Inspection Service began using SeqSero2 as of January 2020. The National Antimicrobial Resistance Monitoring System uses SeqSero2 to analyze Salmonella isolates from ill people, retail meats, and food animals. The Food and Drug Administration 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 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.