100K Genome Project By: Amanda Crichton and Laura Henkel

FDA Launches Genome Project for Food Pathogens

What is the 100K Genome Project?  “U.S. Food and Drug Administration (FDA) is launching a 5-year collaboration with public and private partners to create a public database of the gene sequences of 100,000 bacteria that have been responsible for outbreaks of foodborne illnesses around the world.”

A collaboration of private and public sectors:  This initiative is a collaboration between FDA, the University of California/Davis, and Agilent Technologies Inc.  FDA is providing hundreds of genetic sequences its scientists have already drafted, thousands of actual food pathogens for additional sequencing, and other technical support  The genomic sequencing will be done at a new facility at UC Davis  Agilent —a company that manufactures equipment for electronic and bio-analytical measurement—is supplying expertise, instrumentation and funding

CDC and the U.S. Department of Agriculture's Food Safety and Inspection Service (FSIS) have both joined the initiative

The new database containing the genetic codes of food pathogens will:  Enable scientists in both the public and private sectors to develop tests that can identify the bacteria present in a sample within days or even hours  Help investigators discover the likely source of an outbreak  And greatly expand the pool of researchers able to develop software for the diagnosis and analysis of potential hazards that could lead to new methods of preventing and controlling outbreaks.

An Example  “A cluster of Salmonella illnesses is detected using current testing procedures but the contaminated food is not easily identified. A test would reveal what bacteria is present in the person's body and the genome database could indicate where that strain or one like it came from the last time it was detected. That would point investigators in the direction of a specific food or region.” htm

The endeavor is also a reflection of FDA's focus on regulatory science  As it relates to food safety, regulatory science involves the development of tools, standards and approaches to assess the safety of the foods consumed by people and animals in this country

The Genomic Controversy  Some fear that encoding the genomes of humans may lead to manipulating the natural process of genetics.  This fear can be related to altering the sequence of food genomes  The availability to construct and trace genes could fall into the wrong hands and be a possibility for bioterrorism  Fear of altering nature

Who should have the ability to choose genes?

The Genomic Controversy (cont’d)  Genetic treatment may also be equated with eugenics in the future. Eugenics is "the use of genetic knowledge to improve the human race" The term has a negative connotation because it implies some people or traits are better than others are.  The same technology manipulation can be used to alter the genes in our food 

 " This initiative shows great promise as we look to improve our ability to identify and track down potential sources of foodborne outbreaks," said USDA Under Secretary for Food Safety Elisabeth Hagen, M.D. "FSIS intends to submit important bacterial strains from our regulatory testing program for sequencing at UC Davis, and we look forward to the benefits this public database could provide federal, state and local public health agencies. "  htm

Some Stats:  One in six Americans is sickened by foodborne illness each year, leading to an estimated 128,000 hospitalizations and 3,000 deaths  Many food outbreak events are never linked definitively to a food source or agent.

 E. coli Outbreak ( November 10, 2012)- outbreak/  Salmonella Peanut Butter Outbreak Hits 41( November 8, 2012)- outbreak-hits-41/  E. coli Cases in Northwest Michigan Linked to Unpasteurized Cider ( November 8, 2012)- to-apple-cider /

States vary widely in reporting foodborne illnesses “ Inconsistent reporting of foodborne illnesses such as listeria, salmonella and E. coli leaves large portions of the country vulnerable to the spread of potentially deadly outbreaks before health officials can identify their causes and recall contaminated foods”-before health officials can identify their causes alth-science/states-vary-widely-in-reporting- foodborne- illnesses/2011/08/22/gIQAwFeFWL_story.html Her father died Aug. 31 of the same listeria strain as the nationwide outbreak traced to Colorado cantaloupe

References:  ates/round5/fda-100k-genome.html ates/round5/fda-100k-genome.html  12/07/fda-launches-genome-project-for-food- pathogens.aspx 12/07/fda-launches-genome-project-for-food- pathogens.aspx  Updates/ucm htm Updates/ucm htm  alth-science/states-vary-widely-in-reporting- foodborne- illnesses/2011/08/22/gIQAwFeFWL_story.html alth-science/states-vary-widely-in-reporting- foodborne- illnesses/2011/08/22/gIQAwFeFWL_story.html