Food safety poses a continuous challenge for growers, manufacturers, market sectors, and consumers. According to the Centers for Disease Control and Prevention (CDC), about one in six Americans get sick from a foodborne illness each year; as a result, 128,000 individuals are hospitalized and 3,000 die. Costs associated with these illnesses exceeded $15.5 billion.

The route from farm to fork is long and complex, with many vulnerable points where pathogens can enter our food systems. Changes in food production and supply—such as centralizing processes and year-round food importing—further intensify food safety issues.

Pathogens must be detected quickly and accurately, especially as multistate outbreaks increase. People across geographic areas are at risk and are being affected in shorter amount of time.

Combating food safety risks requires quick identification of contaminants. That’s why producers and agencies must be equipped with technology that can streamline the identification process. By using whole genome sequencing (WGS), genetic information can be deciphered down to each individual nucleotide in the DNA, thus providing higher discrimination of an organism’s identity to below the species level to track sources and conduct epidemiological studies.

Noblis is using WGS as a tool to solve food safety challenges. With our expertise and tools, you will be able to manage and analyze data, track contaminants, compare and monitor samples, and create a dataset of known organisms for your baseline testing.


In 2016, in conjunction with the Grocery Manufacturer’s Association (GMA), Noblis conducted a pilot project to introduce WGS technology to the food industry and demonstrate its efficacy as a rapid identification tool. The process of this study is outlined below:

Tree of Life Study


  • Four partners from food industries, a testing laboratory, and an academic institute
  • A total of 430 samples were submitted to a third party to conduct WGS; data generated were sent to Noblis and analyzed using the BioVelocity pipeline
  • All samples were successfully identified to the species level
    • Salmonella and Listeria constituted the predominant organisms submitted
    • Six additional bacterial genera relevant to food safety were also included
  • Results were communicated with partners; overall, they were enthusiastic about this technology and its potential

At the conclusion of the pilot study, Noblis presented Developing Tools for Rapid and Accurate Post-Sequencing Analysis of Foodborne Pathogens at the 2016 International Food Technologist (IFT) annual conference to a standing-room-only audience.

pathogen mixed with dna


Environmental monitoring is a challenge for food manufacturing and distribution. A comprehensive monitoring program is costly, labor-intensive, and time-consuming. The large amount of data generated is difficult to interpret and manage. The Noblis approach customizes the results and protects data privacy by:

  • Collecting, managing and analyzing a private data repository
  • Identifying organisms found within each environment throughout the facility and noting certain trends
  • Providing analytics about your system over time and determining potential weak points within your processes
  • Enabling preventive measures to be implemented to minimize contamination or adulteration of products
Factory production, process, industry testing


Tracking a contamination requires data to cross reference and map out the potential causes. When contamination occurs, the food sector faces many questions: What is causing the contamination? Where was it introduced? How far has it progressed? How do we effectively control it? What are the preventive measures?

Using multiple bioinformatic capabilities, Noblis helps identify, track, and predict contaminations through the entire food process from field to table. Using the metagenomic analysis capabilities of our BioVelocity tool, we can:

  • Rapidly identify the contaminant in food products, ingredients, or environmental samples
  • Reveal specific genetic traits to aid in tracking and determining the route of travel
  • Discriminate to the species level for more precise tracking and monitoring
  • Trace where contaminations occur to identify the source
  • Enable courses of actions to prevent future occurrence

fork covered in bacteria

Data Privacy

Data privacy is a concern for many industries, especially if there might be legal-implications or intellectual property potential downstream. Noblis recognizes this challenge and will work with companies to ensure that data generated using our tools is not deposited into a public database or shared without explicit consent. We put this to practice during the Food Safety Pilot Study.

We have a multitude of tools and experience to handle data requirements:

  • Anonymize submitted samples before any data is generated and analyzed
  • Ensure no data is shared with third parties or presented in conferences without explicit consent; this includes metadata associated with samples (identifier, locations, etc.)
  • Adhere to request to properly store, transfer, or delete data at the end of the study

data privacy


Traditional bacterial identification has relied heavily on phenotypic traits; this includes visually observing organisms under a microscope for cell morphology and testing for metabolic capabilities. Among the food pathogens, certain serotypes cause more serious illnesses; these serotypes should be rapidly distinguished from other less virulent but highly related strains. The current serotyping methods are labor-intensive and expensive; for example, over 2,000 Salmonella serotypes have been discovered and tested over the years.

Among the feedback received from our food community partners, the ability to identify serotypes accurately and quickly is one of the most pressing needs. Noblis conducted preliminary research to identify Salmonella serotypes by their WGS data and demonstrated the feasibility of this approach. We continue to refine and expand our testing to other food pathogens, enabling food industries to:

  • Identify the causative agent of outbreak or contaminant below the species level (serotype)
  • Conduct surveillance and routine monitoring to ensure safe products for the consumers
  • Track serotypes over the years to detect trends for process improvement
  • Use advanced genome analysis to augment traditional phenotypic testing

bacteria microscopic view


FDA initiative: GenomeTrakr: Using Genomics to Identify Food Contamination