New Study Examines Costs, Benefits of FDA’s Whole Genome Sequencing Network

Since 2012, FDA’s GenomeTrakr Whole Genome Sequencing (WGS) Network has compiled a database that contains the genomes of a number of foodborne pathogens, accessible to public and private entities via the National Center for Biotechnology Information Pathogen Detection (NCBI PD) web portal. It is hoped that the network, currently comprising more than 50 national and international laboratories that contribute to the database, will grow to include more public and private laboratories to further speed up the sequencing of pathogens.

“We anticipate that WGS will help us identify the true scope of outbreaks, making clear that some illnesses we now see as sporadic—which research shows is about 95% of foodborne infections—are, in fact, part of an outbreak,” says Brad Brown, PhD, senior scientific advisor for FDA’s Center for Food Safety and Applied Nutrition (CFSAN), adding that the improvements seen with WGS technology can help detect more outbreaks through small clusters, thereby informing both how to respond to an outbreak and how to prevent one.

Data support the improvements already seen with the NCBI PD program and its component, the GenomeTrakr network. A study conducted by Dr. Brown and some of his colleagues at the CFSAN and published in PLOS ONE, performed an economic analysis of the program and concluded that the NCBI PD portal has been successful in reducing the number of total illnesses due to WGS source tracking, and projects the overall cost-effectiveness of the program over time.

A Faster Way to Detect and Stop Foodborne Outbreaks

To examine the benefits and costs of the WGS NCBI PD program to date, Dr. Brown and his team used an economic model to estimate the reduction in foodborne illnesses from three common pathogens (Listeria, Salmonella, and E. coli) by using WGS tracking. Estimates from the model were tested against empirical data. A final analysis was conducted to assess the benefits and costs of implementing the program.

The study estimated that by 2019, the WGS tracking program had effectively helped reduce the number of people who got sick from foodborne illnesses to 210 illnesses annually (13% reduction) for Listeria, the most heavily sequenced pathogen tracked by the program to date, to 19,800 illnesses annually (1.5% reduction) for Salmonella, a relatively less sequenced pathogen; a 6% reduction in E. coli illnesses was also achieved.

According to Dr. Brown, lead author of the study, even accounting for uncertainty in the model used to estimate these numbers, the total burden of illness reduction, or gross estimated benefit of the program, was nearly $150 to $500 million in 2019. This represents between 0.5% and 1.5% of the total burden of illness caused by food regulated by FDA, he says.

“The study provides strong evidence for significant improvement in food safety anywhere WGS source tracking is implemented,” says Marc Allard, PhD, a research microbiologist with CFSAN and coauthor of the study.

Renato Hohl Orsi, PhD, a senior research associate in the department of food science at Cornell University in Ithaca, N.Y., underscored the extreme value of the program and expects that it will generate even better results in the coming years as more isolates are added to the database.

Dr. Orsi also pointed to the range of benefits offered by WSG data, such as specific information on isolates (e.g., the presence of antimicrobial resistance gene, serotypes for some pathogens such as Salmonella, and the presence of certain virulence genes), as well as the ability to better differentiate isolates to identify any that are closely related genetically, which can help to identify the source of an outbreak during an outbreak investigation.