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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 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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This work is licensed under a Creative Commons Attribution 4.0 International License.
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/content/10.2807/1560-7917.ES.2021.26.9.1900606
2021-03-04
2024-04-18
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2021.26.9.1900606
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Economic evaluation of whole genome sequencing for pathogen identification and surveillance – results of case studies in Europe and the Americas 2016 to 2019
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Frank+Alleweldt&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Alleweldt Frank</a>, <a href="/search?value1=%C5%9Eenda+Kara&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kara Şenda</a>, <a href="/search?value1=Kris+Best&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Best Kris</a>, <a href="/search?value1=Frank+M+Aarestrup&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Aarestrup Frank M</a>, <a href="/search?value1=Martin+Beer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Beer Martin</a>, <a href="/search?value1=Theo+M+Bestebroer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Bestebroer Theo M</a>, <a href="/search?value1=Josefina+Campos&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Campos Josefina</a>, <a href="/search?value1=Gabriele+Casadei&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Casadei Gabriele</a>, <a href="/search?value1=Isabel+Chinen&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Chinen Isabel</a>, <a href="/search?value1=Gary+Van+Domselaar&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Van Domselaar Gary</a>, <a href="/search?value1=Catherine+Dominguez&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Dominguez Catherine</a>, <a href="/search?value1=Helen+E+Everett&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Everett Helen E</a>, <a href="/search?value1=Ron+AM+Fouchier&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Fouchier Ron AM</a>, <a href="/search?value1=Kathie+Grant&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Grant Kathie</a>, <a href="/search?value1=Jonathan+Green&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Green Jonathan</a>, <a href="/search?value1=Dirk+H%C3%B6per&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Höper Dirk</a>, <a href="/search?value1=Jonathan+Johnston&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Johnston Jonathan</a>, <a href="/search?value1=Marion+PG+Koopmans&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Koopmans Marion PG</a>, <a href="/search?value1=Bas+B+Oude+Munnink&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Oude Munnink Bas B</a>, <a href="/search?value1=Robert+Myers&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Myers Robert</a>, <a href="/search?value1=Celine+Nadon&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Nadon Celine</a>, <a href="/search?value1=Ami+Patel&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Patel Ami</a>, <a href="/search?value1=Anne+Pohlmann&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pohlmann Anne</a>, <a href="/search?value1=Stefano+Pongolini&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pongolini Stefano</a>, <a href="/search?value1=Aleisha+Reimer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Reimer Aleisha</a>, <a href="/search?value1=Shane+Thiessen&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Thiessen Shane</a>, <a href="/search?value1=Claudia+Wylezich&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Wylezich Claudia</a></span>. Economic evaluation of whole genome sequencing for pathogen identification and surveillance – results of case studies in Europe and the Americas 2016 to 2019 . <a href="/content/ecdc">Euro Surveill.</a> 2021;26(9):pii=1900606. <a href="https://doi.org/10.2807/1560-7917.ES.2021.26.9.1900606" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2021.26.9.1900606</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 02 Oct 2019;&nbsp;&nbsp; <span class="generated">Accepted</span>: 17 Feb 2020 </span> </p>
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