Microbial Genome Analysis of Food Products

Objectives

The objectives of the second phase of the “food safety” Noblis Sponsored Research (NSR) project were focused on addressing specific needs learned from our industry partners so that our capability can be impactful to the community as a whole. In the process, we worked on broadening and augmenting the capability of BioVelocity to develop a minimum viable product for industry customer usage. This is especially crucial as the Food and Drug Administration (FDA) plans to fully implement whole genome sequencing (WGS) technology in all of their facilities by 2018; eventually compelling the industry to follow suit. Our building of trust with food professionals during our fiscal year (FY) 2016 and FY 2017 pilots, by demonstrating and providing genomic solutions, will play a role in assisting the food industry in this transition.

Background

The food industry continuously faces food safety is-sues that result in outbreaks, illnesses, and product recalls. Because the route from farm to fork is often long and complex, there are ample vulnerable points for pathogens and contaminants to gain entry into our food system. In FY 2016, we completed the first phase of our pilot study by introducing WGS as a potential method to rapidly identify foodborne pathogens. Interacting with partners, we gained a better understanding of the challenges and immediate needs from the industries.

Approach

Due to the complex nature of the requirements for this NSR, we divided the tasking into three individual facets:

BioVelocity minimum viable product (MVP). This facet of the project included development of remaining times from FY 2016.

Polymerase chain reaction (PCR) primer and assay design. Using a fail-fast approach, determine the viability of PCR primer and assay design in the current food safety market space. Utilize the PCR Signature Erosion Tool (PSET) and BioVelocity signature/conserved sequence detection for initial assay region detection and erosion detection of common organisms that cause foodborne illnesses.

Phase 1: Determine viability

  • Using the regions identified by BioVelocity’s signature sequence detection pipeline, test open source tools to create PCR primers.
  • Test the validity and erosion factor of the newly designed primers using PSET and BLAST.

Phase 2: In-depth development

  • Create a fully autonomous pipeline that creates primers for food safety organisms and also tests the erosion factor.
  • Create a database to store assay information (in-
    silico vs. a lab tested, date of last erosion test, etc.).
  • Create a web portal to view, manage, and submit primers.
  • Potential for development of an online store.
  • Research wet-lab testing of new primers.

Food safety research and development. Develop new features for our bioinformatics capability based on industry need.

Features

  • Serovar detection
  • Adopt SeroSeq approach but limit our focus
    on Salmonella strains initially. Determine if
    BioVelocity can replace BLAST for antigen comparison.
  • Direct strain to strain comparison
  • Compare BioVelocity output variant call format (VCF) files for similar SNPs to determine relatedness between two strains. We currently have developed a comparison script that gives a simple score to determine relatedness, but we’ll need to dive much deeper to satisfy the industry need.
  • Quality assurance analysis (samples containing multiple organisms)
  • Determine if a product contains a desired list
    of strains/organisms. Run samples through
    BioVelocity using a custom index file which contains all desired organisms.

Accomplishments

  • Successfully validated the PCR primer and assay design pipeline capability.
  • Created new PCR primers, including the erosion factor, for the majority of Salmonella strains.
  • Made further development on the BioVelocity MVP in conjunction with the human DNA (hDNA) NSR, and Critical Reagents Program (CRP) client projects.
  • Presented the Bloom Cipher capability at the SFAF conference along with the Primer Design and Portable Genome Classifer posters in May 2017.
  • In conjunction with our partners at the GMA, Noblis presented the “WGS of Food Isolates Pilot” presentation at the Institute for Food Safety and Health WGS Symposium in May 2017.
  • Noblis also sat on the panel representing the “food industry” point of view representing subject matter experts along with GMA.

Advancements

The advancements that can be credited to this project are:

  • Contributed funds and researchers toward the development of the Noblis Bioportal. Bioportal was conceived as the central hub for life sciences at Noblis. Bioportal allows new and current clients to explore Noblis’ capabilities within this space, including BioVelocity, PSET, ASSET, etc. Bioportal is live and can be viewed at https://bioportal.noblis.org/.

Inquires

Noblis Sponsored Research projects are conceptualized and developed with federal agencies and the public interest at top of mind. We don’t believe in a “one size fits all” approach, and can work with your agency to determine how to best tailor our solutions and expertise to your unique needs.

To learn more about this project and how it could contribute to your mission, contact us here.

To learn more about the Noblis Sponsored Research program, visit Noblis Research & Development.