Whole Genome Sequencing Helps FDA Identify Dangerous Bacteria
Whole genome sequencing is a cutting-edge technology that the Food and Drug Administration (FDA) has put to a novel and health-promoting use: supporting investigations of outbreaks of foodborne illnesses. The technology looks at the DNA fingerprint left behind by disease-causing bacteria, allowing FDA to identify the source of an outbreak with more detail and clarity than ever before.
The extraordinary benefit of this new technology, first adapted to outbreak investigations in the United States by FDA, was recently demonstrated when it was used to help strengthen the agency’s evidence of a strain of Listeria responsible for a multi-state outbreak linked to Hispanic-style cheese products. On March 11, 2014, FDA suspended food production at Roos Foods, Inc. because some of its cheese products tested positive for a strain of Listeria indistinguishable from the one involved in the outbreak investigation. The suspension of the facility made it unlawful for any person to introduce food from the facility into interstate or intrastate commerce in the United States.
The use of genome sequencing provided genetic information that linked outbreak bacteria to those found in the food facility and in samples of the finished cheese product. FDA partnered with the Centers for Disease Control and Prevention (CDC) and state and local partners in the outbreak investigation. At least eight people were infected with the outbreak strain, and one died.
Gene sequences are the ordered chemical building blocks that make up the bacteria's DNA; a genome is an organism’s complete set of DNA, including all of its genes. “This was the first time we used whole genome sequencing to match the environmental and food samples with the CDC’s human biological samples and it helped support the agency in taking regulatory action,” says Eric Brown, Ph.D., director of FDA’s Division of Microbiology. “We were able to suspend food production at a facility to minimize an outbreak.”
How to Build a Program This Big
FDA is coordinating efforts by state, federal and international public health agencies to sequence pathogens (disease-causing bacteria) collected from foodborne outbreaks, contaminated food products and environmental sources. The genome sequences are archived and publically available in a global database called GenomeTrakr that can be used to help pinpoint the contamination sources of current and future outbreaks.
While the GenomeTrakr Network spans continents now, the beginning was much more humble, says Steven Musser, Ph.D., deputy director for scientific operations at FDA’s Center for Food Safety and Applied Nutrition (CFSAN).
It began when Musser’s department first purchased a gene sequencer. At the time, Musser and his team thought the instrument would be useful in screening foods for the presence of harmful bacteria. Soon, however, the group realized that it had the potential to assist in outbreak investigations. Not only could the technology identify harmful bacteria, it could also provide detailed information about the bacteria that could be used to trace them to their source.
In 2012, FDA researchers used the technology as part of an examination of a completed outbreak of Salmonella Bareilly in tuna sushi tied to a plant in Southwest India. The retrospective examination was able to genetically link the Salmonella Bareilly to the area surrounding the source of the outbreak.
In creating the network, the first phase was a collaboration between FDA and the National Center for Biotechnology Information at NIH, which developed the necessary database and associated software tools. Musser says this partnership led to the first global network to sequence foodborne organisms on a real-time basis.
The second phase consisted of a pilot network of six state laboratories and nine FDA field laboratories. “The collaboration with state labs opens up a treasure trove of information from years of investigations,” says Marc Allard, Ph.D., research microbiologist and head of CFSAN’s whole-genome sequencing lab.
Growing the Database
Labs in the GenomeTrakr network have already contributed the genomes of more than 5,000 isolates—the pure form of foodborne Salmonella, Listeria and E. coli—to the public database.
Next-generation sequencing expert, Charlie Wang, prepares a desktop whole genome sequencer for the next batch of Salmonella strains.
The information in the network can also be used to help identify the source of contaminated foods that have not caused illnesses. This information can be used to help enforce compliance with FDA’s food safety rules and remove contaminated food from the food supply before it results in any illness. This is made posssible by collecting samples and cataloging gene sequences from food production facilities.
The current phase of the GenomeTrakr project is expanding the number of participating state, federal and international laboratories. “This is huge. As more laboratories contribute to the database it’s going to be an extraordinary new day in the field of public health and microbiology,” Brown says.
FDA is working with the World Health Organization to build this capacity in food safety laboratories located in other countries. Italian experts have already travelled to CFSAN to train on whole genome sequencing, and FDA is planning a trip to Ireland to work with the agency’s counterpart in that country.
“It’s just been a really exciting project to work on,” Musser says. “It’s a real feather in FDA’s cap to be a true world leader in a public health system that is going to have such a positive impact on American lives.”