1.1 How is WGS relevant to AMR surveillance?

As you may have learned in the course Antimicrobial susceptibility testing [Tip: hold Ctrl and click a link to open it in a new tab. (Hide tip)] , laboratories traditionally use phenotypical testing to determine antimicrobial susceptibility. Laboratories might do additional characterisation of resistance determinants by using, for example, polymerase chain reaction (PCR) for confirmation of specific resistance antimicrobial resistance genes (ARGs). Each additional analysis requires further laboratory procedures. (To dive further into this topic, you might want to visit the course Testing for mechanisms of resistance.)

WGS also offers the ability to conduct many types of analysis from a single sequencing run that enables faster and more comprehensive analysis, which can allow public health systems to respond more rapidly to potential outbreak situations. WGS data can be used to identify genes and mutations present in both chromosomal and plasmid DNAs (Figure 1), allowing you to more easily understand the mechanisms behind AMR. If sequence data is good enough, you can determine the possible origin of the host bacteria and even the transmission networks for AMR during an outbreak situation (WHO, 2020).

Figure 1 Genetic components of a bacterial cell. A bacterial cell containing circular chromosomal DNA (large circle, right) and two plasmids (small circles, left). The zoomed-in section represents DNA (the genetic information) that is read during WGS (Lacy-Roberts, 2025).

Further advantages of using WGS for AMR surveillance are summarised in Table 1.

Table 1 Some of the key advantages of using WGS for AMR surveillance (Rebelo, 2022).
Advantage of WGSHow this helps your AMR surveillance
Single laboratory workflowReduces time and resources needed to characterise isolates; simplifies laboratory consumables and allows automation for increased efficiency (WHO, 2020)
Multiple types of data can be generated from a single sequencing runEnables simultaneous analysis for bacterial typing, reducing the need for multiple assays
Bioinformatic workflowsStandardised workflows increase accuracy, traceability and reproducibility, while reducing human error by minimising manual data-handling and ensuring a consistent and automated analysis pipeline
Broad applicability across pathogensDetection of many types of microbes, including bacteria, viruses, fungi and parasites; allows co-infection detection and distinction between phenotypically similar strains
Easy storage and sharing of dataFacilitates remote collaboration; enables additional analyses without the need to re-culture or transport samples
Retrospective analysesEnable investigation of past outbreaks or re-analysis as new tools/knowledge become available without additional laboratory work
High-resolution dataProvide detailed insights that support more informed decisions for infection control, surveillance and outbreak response

1 What is whole genome sequencing and how can it be used for AMR surveillance?

1.2 What can the data produced by WGS tell you?