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

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.

Developing a framework to assess the costeffectiveness of COMPARE - a global platform for the exchange of sequence-based pathogen data

Analysing the genomic data of pathogens with the help of next-generation sequencing (NGS) is an increasingly important part of disease outbreak investigations and helps guide responses. While this technology has already been successfully employed to elucidate and control disease outbreaks, wider implementation of NGS also depends on its cost-effectiveness. COMPARE - short for 'Collaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks' - is a major project, funded by the European Union, to develop a global platform for sharing and analysing NGS data and thereby improve the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks. This article introduces the project and presents the results of a review of the literature, composed of previous relevant cost-benefit and cost-effectiveness analyses. The authors also outline the implications for a methodological framework to assess the costeffectiveness of COMPARE and similar systems.

The cost of national prevention systems for animal diseases and zoonoses in developing and transition countries

This study, published in October 2009 by the World Organisation for Animal Health (OIE), aimed to estimate the essential costs of veterinary prevention systems in sample countries and to develop economic indicators for the veterinary performance evaluation provided by the OIE Tool for the Evaluation of Performance of Veterinary Services (PVS Tool). Full sets of data were collected from seven developing and transition countries. The sources used were literature review, a questionnaire survey and country visits by the core expert team. The total costs of national prevention systems (NPS), net of donor programmes, ranged from 10 million international dollars in Kyrgyzstan to 167 million international dollars in Turkey. These costs are associated with the size of the livestock sector, in veterinary livestock units (VLUs), and national income. It was concluded that NPS cost per VLU provides a meaningful comparative measure of the cost of service provision, varying from 1.92 international dollars in Uganda to 9.40 international dollars in Turkey. The relationship with national income provides estimated indicators of expected NPS costs for other countries. Introduction of quantitative measures to PVS Evaluations would help when assessing the degree of compliance with OIE standards.