1.2 What can the data produced by WGS tell you?

As noted in the previous section, WGS can produce detailed genetic information that allows for precise identification of resistance genes and mutations (WHO, 2020).

Beyond the complete DNA sequence of the bacterial genome, you can learn a lot more information about bacteria using WGS.

Some WGS data can help you track, monitor and compare bacterial strains across time, location and sectors to understand how infections spread and evolve. This data includes the stages listed below:

• Outbreak origin: WGS can show whether a strain has been seen before and where; this helps to track outbreaks and for you to understand whether the strains are spreading in hospitals, communities or across regions.
• Detect outbreaks early: By comparing WGS data, you can tell if infections from different places are caused by related bacteria – indicating a possible outbreak.
• Monitor what is circulating: WGS helps you to keep track of which bacteria and resistance mechanisms are present in your location over time.
• Linking data across sectors: WGS can link data from animals, food, the environment and humans; this supports a One Health approach to understanding and tackling AMR (WHO, 2020).
• How your results compare to other laboratories: WGS provides standard typing results that can be easily shared and compared to those from other labs and countries.

WGS data can also help you assess the potential impact of a bacterial strain on public health. This data includes the following benefits:

• Treatability: WGS identifies AMR genes and point mutations (resistance determinants) that can be used to predict which antibiotics are likely to work, or not work, against an infection.
• Transferability: WGS shows where resistance determinants are located in the DNA sequence, which can tell you if the resistance mechanism can be transferred to other bacteria; this helps to determine whether the resistance is likely to spread and whether the strain poses a higher risk.
• Severity: Some bacteria can cause more serious disease than others; WGS data can help you to identify the virulence (disease severity) of bacteria so that you know if it will be more or less harmful to humans or animals.

WGS data can also be used to identify and describe the specific features of the bacteria.

• Prediction of emerging threats: WGS can detect unusual patterns or new combinations of resistance, helping you spot threats before they become widespread.
• Exact type of bacteria: WGS can tell you not just the species, but also the extract type or strain; this helps you to identify who the bacteria might harm and which hosts it could infect (e.g. humans, poultry, cattle) based on how it causes illness.

You have now been introduced to WGS and its applications. In the next section you will learn more details of its use in AMR surveillance programmes and see several real-life examples of its applications.