5 The costs associated with using WGS in an AMR surveillance system

In this section you will cover the costs of introducing and maintaining WGS as part of your AMR surveillance system. You can refer to the course The health and economic burden of AMR [Tip: hold Ctrl and click a link to open it in a new tab. (Hide tip)] for more information on this topic, and the WHO has introduced a genomics costing tool that can serve as a reference for you (WHO, 2024).

While only a few manufacturers dominate the supply of WGS equipment and supplies, costs are variable depending on geography. It is often more expensive to introduce and maintain a WGS system in a low- or middle-income country (LMIC) than in a high-income country owing to the lack of local manufacturing facilities, economies of scale and the cost of transporting materials and equipment – especially items that require a cold chain. Service charges added by local suppliers, national taxes and customs fees can also vary dramatically between countries.

Because of the high costs of conducting WGS, countries might instead consider using regional rather than national or local sequencing laboratories. The WHO report GLASS Whole-genome Sequencing for Surveillance of Antimicrobial Resistance (2020) recommends the creation of regional ‘hub-and-spoke’ surveillance systems where participating countries can send isolates of interest to a regional sequencing centre.

As you think about the costs of WGS, Table 6 can help you to compare the average costs and scale of your current phenotypic surveillance system with a WGS system.