PoultryTech Newsletter, Volume 28, Issue 2, Fall, 2016
Whole Genome Sequencing 101

By Dr. John Glisson & Rafael Rivera, U.S. Poultry & Egg Association
Reprinted with permission from Poultry Times


In recent years, we have seen many instances where foodborne illnesses have been traced back to specific products, triggering recalls of products and investigations into production practices. This has affected all segments of the food industry including our own, poultry. Investigations into foodborne illnesses are complex, but one of the standard practices is to try to match the organism which is causing the foodborne illness to an organism in some product eaten by a sick patient.


Various techniques have been used to analyze the DNA sequence of the organisms to see if there is a match. We often call this a DNA fingerprint, with the assumption that if two organisms — for example, two salmonella isolates — have the same DNA fingerprint then they are identical. So, if the salmonella from the sick patient has the same DNA fingerprint as the salmonella from a food product eaten by that patient, the foodborne illness is attributed to that food product.


Attribution of a foodborne illness to a specific food product has become more accurate as the DNA fingerprinting techniques have become more advanced. But, until recently, all of the DNA fingerprinting techniques were only looking at small important sections of the DNA sequence and not taking into account the majority of the organism’s DNA sequence. This provided a level of uncertainty that often made attribution of foodborne illness more difficult.


Today, DNA fingerprinting is rapidly moving toward a technique that provides the sequence of the entire DNA in the organism. The entire DNA of an organism is called its genome. Therefore, when all of the genome is sequenced, the technique is called Whole Genome Sequencing (WGS). The switch to WGS has come about because the cost of the technique has become very reasonable. The cost now of WGS is similar to previous DNA fingerprinting techniques which looked at only a small part of the genome.


WGS has been adopted by the U.S. Food & Drug Administration (FDA), the Centers for Disease Control & Prevention (CDC), and the USDA/Food Safety & Inspection Service (FSIS) to characterize organisms associated with foodborne illness. The data (genomes) are stored in a public database at the National Center for Biotechnology Information (NCBI). Fifty thousand E. coli, salmonella, listeria, and campylobacter genomes have already been stored at NCBI.


The source of these bacterial isolates varies. For example, when FSIS obtains salmonella isolates from a poultry plant, the whole genome sequence of that isolate is stored at NCBI. Likewise, salmonella isolates obtained by CDC from sick patients are sequenced, and the sequences are stored at NCBI. Also, if FDA isolates salmonella from a food product in a store, the whole genome sequence of that organism is stored at NCBI. So, in the case of an outbreak of salmonellosis in people, the isolate from the ill people can be quickly compared to all salmonellas in the NCBI database, potentially facilitating the finding of a “match” and pointing the investigators to the likely food source associated with the outbreak.


In 2011, a network of laboratories, called the GenomeTrakr Network, was established to accelerate the source tracking and tracing of foodborne outbreaks through use of WGS. The network has a partnership with NCBI to store and share the sequence data in the public domain. Today, the network consists of laboratories at FDA, CDC, FSIS, 14 state labs, and nine international labs. When expansion of the network is complete, laboratories from every state will be included.


The relatively rapid adoption of WGS by regulatory agencies has generated much controversy surrounding the security of the data, the interpretation of the data, the use of WGS in foodborne illness investigations, and the actual techniques used to generate the genome sequences. In the NCBI public database, each genome sequence is identified by its source. The source information (metadata) does not include names of companies or people. There is considerable concern from the food industries about the continued anonymity of source identification.


Do two bacteria have to have exactly the same DNA sequence to be considered a match? Regulators and experts disagree on how closely two organisms must match in order to be considered identical. In the past, epidemiology (documentation that the ill patient actually ate the suspected contaminated food) has been a critical part of foodborne illness investigations. FDA, CDC, and FSIS disagree on whether epidemiology will continue to play a key role in foodborne illness investigations or whether WGS can be used alone. There are two major techniques for performing WGS, and the two methods provide differing data sets. The food industries would like the laboratory network to use just one technique and that the technique used be the one that is most accurate and reliable.


The industry also has an opportunity to adopt WGS. WGS can serve as a tool that not only identifies pathogens in your processing facilities, but it can also serve as a way to analyze the overall microbial population of entire production complexes. WGS can provide information to analyze microbial communities during processing stages and can help develop indicator microbial profiles for optimal intervention performance and quality control of microbial testing. It can also identify the changes in bacterial populations in products and help make decisions on how to best handle spoilage and disease causing microorganisms.


Whole Genome Sequencing and the development of the GenomeTrakr Network provide foodborne illness investigators new powerful tools for determining the source of foodborne illness. The food industries need to educate themselves about this technology and these regulatory efforts. In addition, the food industries must interact with FDA, CDC, and FSIS to bring about standardization of the WGS techniques and interpretation of the data, ensure the continued use of epidemiology in investigations, and strengthen the commitment to the security of the metadata in the public NCBI database. The interactions with regulatory agencies must also allow the adoption of this technology by the industry for product improvement, process efficiency, and food safety.





Dr. John Glisson is vice president of research programs for the U.S. Poultry & Egg Association..

Dr. John Glisson is vice president of research programs for the U.S. Poultry & Egg Association.



Rafael Rivera is manager of food safety and production programs for the U.S. Poultry & Egg Association.

Rafael Rivera is manager of food safety and production programs for the U.S. Poultry & Egg Association.