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


Whole genome sequencing (WGS) is transforming the work of microbiological reference laboratories across the globe. Complete genomic sequences from an isolate or sample have the potential to improve infectious disease surveillance programmes and strengthen epidemiological investigations. Examples include the potential to identify outbreaks earlier through the added value of genome-based cluster detection, the tracking of strains with specific markers relevant for health (for instance antigenicity, virulence, transmissibility, resistance markers) and the monitoring of effectiveness of control measures (for instance vaccination, elimination programmes) [1]. Development of pathogen genomics and the tools, infrastructure and necessary analytics for WGS can be used across sectors (public health, veterinary health or food safety) and pathogen types (viruses, bacteria or parasites), providing potential for further integration of surveillance activities and thus for economies of scale [1,2].

However, in practice, a model currently favoured involves the introduction of WGS into individual pathogen-focused programmes, where the costs of implementing WGS in routine diagnostics and surveillance remain high in comparison to the mainly phenotypic testing currently in use [2]. To better understand the cost differential between conventional methods and WGS in the context of pathogen identification and surveillance, and to identify the main factors affecting the costs and benefits of WGS-based surveillance systems, we conducted an economic evaluation in eight reference laboratories in seven countries (Argentina, Canada, Germany, Italy, the Netherlands, the United States (US) and two institutes from the United Kingdom (UK)). In a second step, we wanted to understand whether the benefits derived from the additional information obtained through the sequencing of pathogens is likely to balance out the additional cost of WGS. For this purpose, we estimated for the example of salmonellosis the number of cases of illness that would need to be prevented each year through the use of WGS in order to ‘break even’ on costs, i.e. in order to make the use of WGS cost-neutral.

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