3 What is needed to conduct WGS of AMR in your laboratory?

Based on what you have learnt in the previous sections about the advantages of WGS for AMR surveillance, you might be considering introducing WGS for your country or region’s AMR surveillance.

Activity 5: Reflection

Timing: Allow 10 minutes

You reflected on the current approaches to testing used in your area after studying Table 2. Now take a few minutes to reflect on your own plans for introducing or building WGS capacity in your context. Are you considering using WGS? If so, what motivates you? Think about a specific challenge or issue you are facing in your institution or country. How would WGS help you deal with this challenge? You may want to use the space below for your notes.

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Discussion

You’ve made a thoughtful start by reflecting on your plans for introducing or building WGS capacity. As you continue the course, keep thinking about how to align your motivations with practical steps for implementation, especially in light of any constraints on resources or infrastructure that you may face. If you have doubts about what is possible in your context, now might be a good time to discuss this question with colleagues.

Introducing WGS can be a complicated process; you must consider various factors. This section will help you consider how you might apply WGS in your own work. It starts by reviewing the process of conducting WGS, including the equipment and tools needed, from DNA extraction to data analysis. By the end of this section, you should understand the essential components required to establish an AMR WGS surveillance facility.

An overview of the four main stages of WGS is shown in Figure 5.

Described image
Figure 5 The four stages of WGS for AMR surveillance (Nilsson, 2025).
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Stage 1 – sample collection: biological or environmental samples are collected from humans, animals, food or the environment as part of One Health surveillance. Stage 2 – DNA isolation and library preparation: DNA is extracted from the samples and prepared into sequencing libraries. Stage 3 – sequencing: DNA is sequenced using sequencing machines, such as Illumina or Oxford Nanopore’s MinION. Stage 4 – data analysis: sequencing data is analysed to identify antimicrobial resistance genes, bacterial species or strains, and potential epidemiological links.

Figure 5 The four stages of WGS for AMR surveillance (Nilsson, 2025).

Each of the four stages is discussed in more detail in the following sections. Data sharing and infrastructure considerations are also discussed. The specific steps in each stage are tailored to whether you are conducting short or long read sequencing. Important aspects that need to be considered in planning are noted in the next sections.

2.4 Linking data to action

3.1 Sample collection