Whole genome sequencing (WGS) provides insight into the genetic fingerprint of a pathogen by sequencing the chemical building blocks that make up its DNA and is increasingly being employed in food safety efforts.  Since 2012, the U.S. Food and Drug Administration (FDA) has regularly turned to WGS to better understand foodborne pathogens, including identifying the nature and source of microbes that contaminate food and cause outbreaks of foodborne illness. In 2012, FDA launched GenomeTrakr.  GenomeTrakr is an international network of laboratories that sequences microbial foodborne pathogens and uploads the data to a common public database in real time.

At a recent Codex Alimentarius Commission meeting in Geneva, FDA scientists explained that WGS has fundamentally changed the way microbiological food hazards in the U.S. are detected and noted that the most effective use of WGS in foodborne disease surveillance requires coordination and collaboration.

The FDA hopes that other countries currently using WGS will share their data with GenomeTrakr. FDA is aiming to include developing countries as they are able to join. As it stands, GenomeTrakr consists of 13 federal labs, 25 state health and university labs, one U.S. hospital lab, two other labs located in the U.S., 20 labs located outside of the U.S., and collaborations with independent academic researchers.

To date, GenomeTrakr has collected more than 142,000 sequenced strains.  Proponents of WGS proffer that greater availability and coordination of WGS data could go a long way towards helping to identify the source and extent of outbreaks more quickly so fewer people get sick from preventable foodborne illnesses.