100K Pathogen Genome Project

Microbiology is embracing high-throughput genomics because many long-standing questions can be addressed, and entire microbial communities can be examined at unprecedented resolution. With the increase in production of whole genome sequence and release into the public domain, every it is creating the need ever increasing computational capabilities. The 100K Pathogen Genome Sequencing Project directly producing and analyzing genomic information that is important worldwide for pathogens from agriculture, public health, and the environment.

With the observation that bacterial genome sequence diversity is extremely large and new genes are being found with every new sequence, we can examine the genotype with increasing resolution to define the global location, disease association, virulence potential and create new diagnostics to accompany control strategies.

This project is using 2^nd and 3^rd generation sequencing technologies to produce draft and closed genomes. Independently, and in cooperation with groups around the world, we have sequenced over 35,000 genomes to date with more on the way. 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 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.

Outcomes

Production of these genomes will facilitate a new era in microbial genomics by increasing the speed of genome production to near real-time directly from test materials 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 pathogen diagnostics directly from sample to genome result in hours rather than days. For example, samples from farms, processing facilities, the transportation chain, and supermarkets are the direct outcome of this project. Additionally, coupling this approach to culture-independent methods using capture/concentration methods provides a near real-time answer that is anchored in the DNA and RNA contained in an organism residing in the sample.

Designed to directly address the lack of genomic information available to tackle new approaches for public health, this project embraces a new era of modernization of microbiology into a forensic tool using cutting-edge technology that is a landmark innovation 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 leverage 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 worldwide partners, combined with the scale of the project, will provide the beginning of food pathogen forensics for use in an expanding world trade stage.
7. This project is assisting in creating a systematic definition of a genome-anchored phylogeny, biomarker gene sets associated with persistence, serotype diversity, location, antibiotic resistance, pathogenesis, and host association.