Using next-generation sequencing (NGS) technology, the whole genome sequencing (WGS) of food-borne pathogens provides a much higher level of resolution for typing than conventional typing methods including pulse field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). MiSeq is commonly used for WGS of food-borne pathogens. Among the Vet-LIRN network laboratories, only a few have MiSeq, however, most do not have mainly due to cost. To increase the WGS testing capability of Vet-LIRN network laboratories, this study will propose evaluation of another new less expensive Illumina sequencer MiniSeq for WGS of foodborne pathogens. The cost of MiniSeq is half of MiSeq. If the MiniSeq provides relatively comparable features for WGS of food-borne pathogens, Vet-LIRN network laboratories may purchase and use MiniSeq for case investigations, which eventually increases Vet-LIRN network test capacity.
With the emergence and development of the next generation sequencing technology, whole genome sequencing gradually replaces pulse field gel electrophoresis for outbreak investigation of foodborne pathogens and illness. Through this cooperative agreement, the outcome of this project will help to strengthen the capability and capacity of FDA Vet-LIRN laboratories to utilize the whole genome sequencing for investigation of foodborne pathogens and outbreaks, thus enhancing human and animal food safety.
