Case studies 2016-2019: the economics of whole-genome sequencing for pathogen identification and surveillance

The work of microbiological reference laboratories throughout the world is being transformed by whole genome sequencing (WGS). Complete genomic sequences from an isolate or sample have the potential to boost epidemiological research and improve infectious disease surveillance programs. Examples include the possibility to identify outbreaks at an earlier date through added value of genome-based cluster detection, tracking germs with specific health-related markers (e.g. antigenicity, pathogenicity, transmissibility, resistance markers) and monitoring of control measures efficacy (for instance vaccination, elimination programmes).  

Nevertheless, in reality, WGSs are now utilized in individual pathogen-focused programs, where cost of adopting WGS in regular diagnosis and monitoring is still expensive compared to already in use phenotypic testing. Through the study an economic assessment in eight reference laboratories in seven countries ((Argentina, Canada, Germany, Italy, the Netherlands, the United States and two institutes from the United Kingdom) has been conducted, to better understand the cost difference among conventional methods and WGS in pathogen identification and monitoring, and to identify key factors that impact on costs and advantages of WGS-based surveillance systems.  

The study showed that in all of the reference laboratories studied, the overall per-sample costs of WGS were higher than the costs of traditional techniques, with the exception of one that used a non-routine approach. Other than that, the cost disparity was between EUR 15 and EUR 727 per sample and the use of WGS was between 1.1 and 4.3 times more expensive than the usage of conventional techniques. With WGS analysis, there was a general trend of rising returns to scale, with average per-sample costs of WGS decreasing as sample volume and batch size increased. As a result, reference laboratories that handle a large volume of samples are more likely to have cheaper per-sample costs than smaller institutions that handle fewer samples. Regarding the effects on sampling, the majority of reference laboratories found no differences in sampling and sampling techniques. However, one of the food-borne pathogen monitoring reference laboratories stated that the adoption of WGS had resulted in a shift in sampling, from sampling of products to environmental sampling, such as swabbing surfaces in production sites for instance. Moreover, the study concluded that WGS had a significant beneficial impact on the quality of the findings obtained in terms of detail, accuracy, specificity, and sensitivity in the majority of the reference laboratories. WGS research, for example, gave insights into how bacterial strains evolve through time, allowing strains to be recognized as connected when they would have been thought unrelated using earlier approaches. Lastly, when the effects on outbreak detection and response were tested, WGS had a demonstrated beneficial effect on all laboratories in terms of enhanced identification of outbreaks and increased information on outbreak epidemiology.