Rapid Identification and Source Tracing of a Typhimurium Outbreak in China by Metagenomic and Whole-Genome Sequencing.

spp. are among the most prevalent foodborne pathogens. Rapid identification of etiologic agents during foodborne outbreaks is of great importance. In this study, we report a traceback investigation of a outbreak in China. Metagenomic sequencing of suspected food samples was performed on MinION and MiSeq platforms. Real-time nanopore sequencing analysis identified reads belonging to the family. MiSeq sequencing identified 63 reads specifically mapped to . Conventional methods including quantitative-PCR and culture-based isolation confirmed as serovar Typhimurium. The foodborne outbreak of Typhimurium was further recognized by whole-genome sequencing and pulsed-field gel electrophoresis analysis. Our study demonstrates the ability of metagenomic sequencing to rapidly identify enteric pathogens directly from food samples. These results highlight the capacity of metagenomic sequencing to deliver actionable information rapidly and to expedite the tracing and identification of etiologic agents during foodborne outbreaks.