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

Frank Alleweldt, Şenda Kara, Kris Best, Frank Møller Aarestrup, Martin Beer, Theo M. Bestebroer, Josefina Campos, Gabriele Casadei, Isabel Chinen, Gary Van Domselaar, Catherine Dominguez, Helen E. Everett, Ron Am Fouchier, Kathie Grant, Jonathan Green, Dirk Höper, Jonathan Johnston, Marion Pg Koopmans, Bas B. Oude Munnink, Robert MyersCeline Nadon, Ami Patel, Anne Pohlmann, Stefano Pongolini, Aleisha Reimer, Shane Thiessen, Claudia Wylezich

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BackgroundWhole genome sequencing (WGS) is increasingly used for pathogen identification and surveillance.AimWe 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).MethodsThe 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.ResultsOn 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.ConclusionsEven 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.

Original languageEnglish
JournalEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Issue number9
Number of pages14
Publication statusPublished - 2021


  • Costs and benefits of pathogen surveillance using WGS
  • Economic evaluation
  • Next Generation Sequencing
  • surveillance systems
  • Whole Genome Sequencing


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