3.1 Sample collection

As with phenotypic surveillance, the first step in conducting WGS is sample collection.

When you collect a sample for WGS, you will need to ensure that relevant metadata is also collected. Metadata is data that describes the context of your sample and typically includes the location, date and time of collection; species, host and sample source; and type (e.g. faeces, sewage). You may also want to collect demographic, clinical and epidemiological information of relevance.

It is important to collect metadata at the time of sampling, as it will be critical for interpreting your results later and for further analysis. Metadata provides the context needed to interpret WGS data and is key to turning it into meaningful public health or research insights. For more information on the importance of metadata for analysis of AMR patterns and trends you may like to visit the Gender and equity in AMR surveillance course.

Once you have collected your samples, you will need to decide which ones to sequence. Sample selection for WGS can be a complicated topic, as explained below.

• Sequencing is much more costly than typical phenotypic methods, so you may not be able to sequence every isolate.
• You may want to prioritise what you sequence, perhaps by ensuring that you sequence samples from a wide geographic area in your surveillance zone.
• You might want to randomise which isolates are sequenced to understand prevalent genotypes.
• A good sample selection strategy will need to be part of your plan for using WGS in your AMR surveillance.

For more information on this topic, you can watch a webinar produced by the Fleming Fund’s SeqAfrica project, ‘How to decide what to sequence’.