Economic evaluation of whole genome sequencing for pathogen identification and surveillance – results of case studies in Europe and the Americas 2016 to 2019

Abstract

Background Whole genome sequencing (WGS) is increasingly used for pathogen identification and surveillance. Aim We evaluated costs and benefits of routine WGS through case studies at eight reference laboratories in Europe and the Americas which conduct pathogen surveillance for avian influenza (two laboratories), human influenza (one laboratory) and food-borne pathogens (five laboratories). Methods The evaluation focused on the institutional perspective, i.e. the ‘investment case’ for implementing WGS compared with conventional methods, based on costs and benefits during a defined reference period, mostly covering at least part of 2017. A break-even analysis estimated the number of cases of illness (for the example of Salmonella surveillance) that would need to be avoided through WGS in order to ‘break even’ on costs. Results On a per-sample basis, WGS was between 1.2 and 4.3 times more expensive than routine conventional methods. However, WGS brought major benefits for pathogen identification and surveillance, substantially changing laboratory workflows, analytical processes and outbreaks detection and control. Between 0.2% and 1.1% (on average 0.7%) of reported salmonellosis cases would need to be prevented to break even with respect to the additional costs of WGS. Conclusions Even at cost levels documented here, WGS provides a level of additional information that more than balances the additional costs if used effectively. The substantial cost differences for WGS between reference laboratories were due to economies of scale, degree of automation, sequencing technology used and institutional discounts for equipment and consumables, as well as the extent to which sequencers are used at full capacity.

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

“…Other countries and different geographic regions have different baseline regulatory climates and food safety cultures, so the marginal effect of WGS source tracking may vary from what we observe in US data [ 30 , 31 ], but this study provides strong evidence for a significant improvement in food safety anywhere WGS source tracking is implemented. WGS surveillance technology is transferable to other international food safety agencies and should be a part of capacity building and partnership programs.…”

“…The net benefits presented here, drawn from complete data on only Salmonella outbreaks investigated by FDA from 1999–2019, are more conservative and suggest that the benefits from Salmonella reduction would not approach $90 million dollars until 2019, five years after implementation of the program. Ford et al and Alleweldt et al recently published break-even analyses suggesting that WGS source tracking programs would need to prevent between 0.2% and 2% of illnesses linked to serotyped pathogens in Australia, Europe and the United States [ 30 , 31 ]. Our results suggest this level of prevention is attainable even in the early stages of WGS source tracking implementation.…”

Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020

“…Routine sequencing of the isolates received by the NRC would result in a representative database of circulating strains that enables the estimation of background diversity in the population and a better discrimination of new outbreak isolates [ 6 ]. From an economic perspective, Alleweldt et al [ 21 ] showed that only 0.2–1.1% of reported salmonellosis cases would need to be avoided each year through the use of WGS (e.g. by earlier outbreak detection) in order to make its implementation cost-neutral from a public health perspective.…”

“…by earlier outbreak detection) in order to make its implementation cost-neutral from a public health perspective. In addition, reference laboratories that deal with a high volume of samples achieve a lower per-sample cost than smaller institutions processing a lower amount of samples and the implementation at a central level would alleviate infrastructure investments and staffing requirements [ 21 , 22 ].…”

The economics of improving global infectious disease surveillance

“…New diagnostic tools such as unbiased and targeted next-generation sequencing (NGS) are being explored as options to improve surveillance as these allow to determine causes of unexplained disease outbreaks, trace and link sources of disease transmission, and facilitate a better understanding of how viruses and bacteria pass from animal to humans. With NGS, the same platforms and sometimes even the same protocols can be used for the analysis of viruses, bacteria, genes and parasites with the potential for cost saving through economies of scale (economies of scale occur when the costs per unit decrease when produced quantities increase, as total costs can be divided among more units), improving its affordability also for lower income countries 3 4. As most emerging infectious diseases are zoonotic, further improvements could come from incorporating concepts from ‘One Health’, integrating capacities across human and animal health sectors.…”