5.3 Ongoing costs

Anyone contemplating the introduction of WGS to their AMR surveillance must also consider the maintenance and running costs of the system.

Procuring the necessary reagents can be costly and challenging for many LMICs’ laboratories because of a poor supply chain. Many reagents for WGS have a short shelf-life and/or must be kept cold, so delays owing to customs clearance can be expensive and wasteful. Establishing a network for procurement with other laboratories in your area/country is one solution to be considered prior to starting up WGS. Similarly, establishing a national procurement forecasting plan for reagents can also be a helpful tool (Khoo et al., 2024).

The price of reagents varies according to geography and suppliers. The Fleming Fund SeqAfrica project, for example, saw the price of sequencing a single isolate range from £50 to £140 depending on the country and the throughput of the laboratory. It is worth considering, however, that the cost of testing for all known AMR mechanisms at once using WGS is only marginally higher than testing for only one mechanism, whereas testing all the necessary antimicrobials with phenotypic AST would require more reagents, materials and staff time.

By contrast, phenotypic AST has relatively low and predictable ongoing costs. Reagents such as antibiotic disks or broth media are widely available, have longer shelf lives and do not require cold-chain logistics. Additionally, AST does not require highly specialised staff or computational infrastructure, making it more sustainable for routine surveillance in many low-resource settings. However, while WGS has higher per-sample costs, it can provide broader data from a single test, potentially reducing the need for multiple phenotypic assays.

Beyond ongoing procurement, you should consider the cost of repairs and maintenance of expensive WGS machines. Most suppliers of WGS machines offer a service contract for the first year after the machine is purchased; however, after this runs out, further coverage can be very expensive. For example, in 2024 one laboratory in Senegal was offered a service contract costing $8000 for a one-year contract on a NextSeq 550, while a laboratory in Ghana was quoted $25,000 for a one-year contract on a NextSeq 2000 system. These costs may strain laboratory budgets, but a single repair can cost as much as the service contract, if not more, making the contract a good investment and insurance mechanism.