100K Genome Project

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Our Approach

Microbiology is embracing high-throughput genomics because many long-standing questions can be quickly addressed and entire microbial communities can be examined quickly. The lack of food-related bacterial genomes is hindering advancements to improve the safety and security of the world food supply. The 100K Foodborne Pathogen Genome Sequencing Project directly addresses the lack of genomic information by sequencing 100,000 foodborne pathogen isolates for the most important worldwide outbreak organisms. To close this knowledge gap and enable worldwide contribution, the genome sequence diversity of the top foodborne pathogens will be produced using NGS with BGI@UCDavis. This new facility will have ~10 HiSeq 2000 instruments for use by this project. A small number of whole genomes will be “finished” to completion for use as reference genomes. The vast majority of isolates will be sequenced and assembled as draft genomes for eventual public release. This approach will enable systematic definition of a biomarker gene sets associated with persistence, serotype diversity, location, antibiotic resistance, pathogenesis, and host association – just to name a few applications.


Production of these genomes will facilitate a new era in food safety by speeding the testing of raw ingredients and finished products, as well as by analyzing samples taken during outbreak investigations with a level of precision and accuracy that has never been seen and cannot be achieved with existing methods. Genomics-enabled diagnostics with molecular tools for surveillance, risk assessment, and diagnosis of foodborne pathogens directly through the global food chain — from farms, slaughterhouses, the transportation chain, processing facilities, to supermarkets will be the direct outcome of this project.

Designed to directly address the lack of genomic information available to tackle new approaches for food security, this project embraces a new era of modernization of food security using cutting edge technology that is a landmark innovation in food microbiology.  

1.     Most notably, it will result in a genetic catalog of some of the most important outbreak organisms that impact human health.  

2.     Access to the genetic database will be public after allowing for an academic publication window by submitting partners.  

3.    A culture bank will be created and maintained at UC Davis within the School of Veterinary Medicine.  

4.     This work will provide the basis of new diagnostic testing methods that leverages the latest in genomics technology to provide time-critical diagnostic assistance that will effectively halt the unfettered expansion of foodborne illness in the United States as well as globally.

5.     The database will provide insights into molecular methods of infection and drug resistance for use in defining new vaccines and therapies.

6.    Isolates provided from world-wide partners, combined with the scale of the project, will provide the beginning of food pathogen forensics for use in a expanding world societies to increase food security.

7.     This project will assist in systematic definition of biomarker gene sets associated with persistence, serotype diversity, location, antibiotic resistance, pathogenesis, and host association.