4.1 Existing capacity

Genomic surveillance has many of the same requirements as phenotypic surveillance. Therefore, a key requirement for building a genomic AMR surveillance system is usually the existence of a functioning phenotypic AMR surveillance system. To conduct AMR surveillance you will need a referral system through which samples are collected and sent to a national reference laboratory (NRL) for analysis. The referral sites should collect the needed metadata related to each sample.

In most cases, the NRL should be endorsed by the national authorities for its surveillance role to lend the laboratory legitimacy and remit. The referral system and NRL will need sufficient resources such as capacity, staff and funding to perform their roles within the system. The referral system should be as comprehensive as possible in both demographic and geographic scope. The timeliness of your referral system is also important: the turnaround time from sample collection and sequencing is vital to ensuring that your system can inform public health action.

The NRL should have the required and competent staff to analyse and use the data resulting from WGS. These specialists must work closely together to achieve their collective surveillance goals. At a minimum this staff should include the specialists listed below:

• Bioinformatician: Responsible for ensuring sequencing data quality is suited for analysis. They will also employ tools for sequencing data analysis. They should be able to use a variety of bioinformatic tools for both analysis and quality control. They should ideally have strong knowledge of genomics and how to work with genomic data because they will interpret what the data shows for the other team members.
• Microbiologist: Responsible for interpreting bacterial typing results. Their job is to determine what is important about a specific bacterium within a specific context. The microbiologist will work closely with the bioinformatician to help them determine what markers to look for in the data; they will also work closely with the epidemiologist to provide an interpretation of the biological data for action.
• Epidemiologist: Responsible for examining and interpreting epidemiological data, resistance trends and changing epidemiology. They will identify possible sources of outbreaks, and record and report outbreak signals to determine what action should be taken to protect public health. The epidemiologist will work closely with the bioinformatician to determine what type of analysis should be conducted.