5.1 Set-up costs

The costs of setting up WGS in a laboratory will depend on many factors, including the considerations below.

• What infrastructure is currently in the laboratory? Laboratories that already conduct molecular methods, for example, will see lower conversion costs to WGS.
• How many isolates will be sequenced on a regular basis? This will determine whether you need a large, high-throughput machine or can use a smaller one.
• Is the laboratory currently limited to phenotypic methods such as AST? Laboratories without existing molecular workflows may face steeper initial investments in equipment, staff training and bioinformatics capacity. However, leveraging existing AST data to prioritise isolates for sequencing can help to maximise the value of early WGS efforts and support a phased implementation approach.

As you think about the costs of setting up a system, don’t forget about broadband internet connections, generators and uninterruptible power supplies.

For laboratories currently using only phenotypic AST, it is important to recognise that these methods will continue to play a role in AMR surveillance; WGS is a complementary tool that enhances the resolution and scope of surveillance, rather than a replacement for existing phenotypic systems.