An economic evaluation of the Whole Genome Sequencing source tracking program in the U.S.

Abstract

The U.S. Food and Drug Administration (FDA) created the GenomeTrakr Whole Genome Sequencing (WGS) Network in 2013, as a tool to improve food safety. This study presents an analysis of Whole Genome source tracking implementation on potential food contamination and related illnesses through theoretical, empirical, and cost benefit analyses. We conduct empirical tests using data from FDA regulated food commodity outbreaks garnering FDA response from 1999 through 2019 and examine the effect of the National Center for Biotechnology Information (NCBI) Pathogen detection program of source tracking WGS isolates collected in the U.S. on outbreak illnesses for three pilot pathogens (E. coli, Listeria, and Salmonella). Empirical results are consistent with the theoretical model and suggest that each additional 1,000 WGS isolates added to the public NCBI database is associated with a reduction of approximately 6 illnesses per WGS pathogen, per year. Empirical results are connected to existing literature for a Monte Carlo analysis to estimate benefits and costs. By 2019, annual health benefits are estimated at nearly $500 million, compared to an approximately $22 million investment by public health agencies. Even under conservative assumptions, the program likely broke even in its second year of implementation and could produce increasing public health benefits as the GenomeTrakr network matures.

Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking

“…The international agro-food trade specifically plays an increasingly pivotal role in providing food supplies to communities around the globe but can contribute to the dissemination of foodborne pathogens ( 47 , 48 ). Consequently, high-resolution technologies, such as WGS, are being used increasingly to monitor the spread of pathogens along the food supply chain ( 49 , 50 ).…”

“…However, due to a lack of additional publicly available ST2413 B. cereus sensu lato genomes, we were unable to gain additional insights into exactly where this lineage originated. WGS has been shown to improve surveillance and source tracking efforts for numerous foodborne pathogens, including Escherichia coli , Salmonella enterica , and Listeria monocytogenes ( 50 , 59 ). While the amount of publicly available WGS data derived from members of B. cereus sensu lato is increasing ( 34 ), efforts to sequence the genomes of food-associated B. cereus sensu lato strains are lagging relative to other foodborne pathogens.…”

“…Only 2,664 assembled genomes from all B. cereus sensu lato species that met the quality thresholds used in this study were available in NCBI’s RefSeq Assembly database ( 60 , 61 ) during the time this study was conducted (note that the NCBI GenBank Assembly database did not have any large multi-isolate B. cereus sensu lato projects at this time; accessed 20 March 2021). This can be contrasted with other foodborne pathogens for which source tracking and surveillance have proven to be successful ( 50 , 59 ), as the numbers of publicly available genomes from these organisms are orders of magnitude greater than the number of genomes from all B. cereus sensu lato species combined (e.g., Salmonella enterica and Listeria monocytogenes , each single species with more than 100 and 10 times as many publicly available genomes, respectively; NCBI GenBank Assembly database, accessed 25 February 2022). Thus, future B. cereus sensu lato surveillance and WGS initiatives in clinical, industrial, and environmental settings are needed to improve B. cereus sensu lato source tracking and traceback efforts.…”

The Notable Achievements and the Prospects of Bacterial Pathogen Genomics

“…Nowadays, GenomeTrakr is a large network of U.S. federal, state, university, and hospital labs that is utilising WGS in order to detect and analyse outbreaks of food-borne illness caused by pathogens [ 97 ]. Although the annual investment is around USD 22 million, the annual health benefits are estimated to be at nearly USD 500 million [ 98 ]. Furthermore, the European Food Safety Authority (EFSA) has also adopted WGS for the bacterial strain taxonomic identification and characterisation of potential traits of concern [ 99 ].…”

A hybrid sequencing and assembly strategy for generating culture free Giardia genomes

“…Genetic difference between assemblages or strains could also have uses in clinical applications such as drug target determination and vaccine design. Whole genome sequencing of important food borne bacterial pathogens including Escherichia coli, Listeria , and Salmonella has produced significant health and economic benefits, however sequences from thousands of isolates are needed before such benefits can be attained ( Brown et al., 2021 ). Clearly, methods to attain reference quality genomes from primary isolates are needed to bring the benefits of whole genome sequencing to the field of Giardia .…”