TY - JOUR
T1 - Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019
AU - Alleweldt, Frank
AU - Kara, Şenda
AU - Best, Kris
AU - Aarestrup, Frank M.
AU - Beer, Martin
AU - Bestebroer, Theo M.
AU - Campos, Josefina
AU - Casadei, Gabriele
AU - Chinen, Isabel
AU - Van Domselaar, Gary
AU - Dominguez, Catherine
AU - Everett, Helen E.
AU - Fouchier, Ron Am
AU - Grant, Kathie
AU - Green, Jonathan
AU - Höper, Dirk
AU - Johnston, Jonathan
AU - Koopmans, Marion Pg
AU - Oude Munnink, Bas B.
AU - Myers, Robert
AU - Nadon, Celine
AU - Patel, Ami
AU - Pohlmann, Anne
AU - Pongolini, Stefano
AU - Reimer, Aleisha
AU - Thiessen, Shane
AU - Wylezich, Claudia
N1 - Copyright:
This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of Medicine
PY - 2021/3/4
Y1 - 2021/3/4
N2 - Background Whole 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.
AB - Background Whole 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.
KW - Costs and benefits of pathogen surveillance using WGS
KW - Economic evaluation
KW - Next Generation Sequencing
KW - surveillance systems
KW - Whole Genome Sequencing
KW - ENGLAND
KW - SALMONELLA-ENTERITIDIS
UR - http://www.scopus.com/inward/record.url?scp=85102482222&partnerID=8YFLogxK
U2 - 10.2807/1560-7917.ES.2021.26.9.1900606
DO - 10.2807/1560-7917.ES.2021.26.9.1900606
M3 - Article
C2 - 33663647
AN - SCOPUS:85102482222
SN - 1025-496X
VL - 26
SP - 8
EP - 21
JO - Eurosurveillance
JF - Eurosurveillance
IS - 9
M1 - 1900606
ER -
