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Alleweldt F, Kara Ş, Best K, Aarestrup FM, Beer M, Bestebroer TM, Campos J, Casadei G, Chinen I, Van Domselaar G, Dominguez C, Everett HE, Fouchier RA, Grant K, Green J, Höper D, Johnston J, Koopmans MP, Oude Munnink BB, Myers R, Nadon C, Patel A, Pohlmann A, Pongolini S, Reimer A, Thiessen S, Wylezich C. Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019. ACTA ACUST UNITED AC 2021; 26. [PMID: 33663647 PMCID: PMC7934224 DOI: 10.2807/1560-7917.es.2021.26.9.1900606] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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.
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Affiliation(s)
| | | | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | | | | | - Gabriele Casadei
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Isabel Chinen
- INEI-ANLIS Dr Carlos G Malbrán, Buenos Aires, Argentina
| | | | | | | | - Ron Am Fouchier
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathie Grant
- Retired.,Public Health England, London, United Kingdom
| | | | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | | | | | | | - Robert Myers
- Maryland Department of Health, Baltimore, United States
| | - Celine Nadon
- Public Health Agency of Canada, Winnipeg, Canada
| | - Ami Patel
- Maryland Department of Health, Baltimore, United States
| | | | - Stefano Pongolini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
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