Purpose: Currently, it takes weeks to identify an organism, such as those listed in Table 1, using serotyping methods, a challenge during a foodborne pathogen outbreak. Robust molecular identification methods cannot be developed to industry standards with available sequences.
Methods: The genome sequence diversity of the top 5 foodborne pathogens will be produced using next generation sequencing (NGS) with BGI@UCDavis). The facility at Davis will have ~10 HiSeq 2000 instruments for use by this project. Isolate priority list includes Salmonella, Campylobacter, Escherichia coli, Vibrio, Listeria, then Yersinia, Shigella, Clostridium, Enterococcus, Cronobacter, followed by toxigenic bacilli, norovirus, hepatitis A & E, rotavirus and enteroviruses. A small number of whole genomes will be “finished” to completion. The majority of isolates will be used to produce draft genomes and assembled using genomes in the public domain. This approach will enable a systematic analysis of the minimal set of genes associated with persistence, serotype diversity, location, antibiotic resistance, pathogenesis, and host association. Isolates will be grown, serotyped, banked, sequenced, and then metadata will be stored with the genomic sequences, either in finished or in draft form.
Results: This extraordinary collaboration is resulting in the public availability of matched genomic sequences and isolates. As the food network is increasingly global, faster approaches for use in surveillance and outbreak investigation are imperative.
Significance: This microbial ecology-based information will lead to the use of new molecular methods for diagnostic development.