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"We need a clear implementation concept"

In an interview, Jürg Danuser of the FSVO, head of the federal One Health group, talks about the importance of Whole Genome Sequencing for national monitoring.

Whole Genome Sequencing (WGS) swiftly unlocks the entire genetic information of bacteria and other microbes. It provides us with comprehensive insights into pathogens, for instance regarding antibiotic resistance or similarities between bacteria. The new technology makes it possible to monitor the spread of antibiotic resistance more accurately because, among other things, it allows us to compare samples from humans, animals, food and the environment. In an interview, Jürg Danuser of the Federal Offices of Food Safety and Veterinary Affairs (FSVO), who also acts as head of the federal One Health group, talks about the importance of WGS for national monitoring.

Mr Danuser, the FSVO is the first federal office that will adopt WGS technology to monitor resistant pathogens in all of Switzerland. What are your plans?

To start with, WGS will complement the current phenotypic methods to monitor resistance in farm animals and meat, later it will replace those methods. This will affect samples taken from animals before slaughter and from meat on sale.

Why do you prioritise using the new technology in this specific area?

We are looking to use WGS in various other areas. But in this specific area, the European Food Safety Authority has published a transition schedule in early June. The schedule envisages that European countries will contribute WGS data to a European database by 2021. To start with, this would happen on a voluntary basis and only include particular bacteria that are resistant to antibiotics, i.e. ESBL-producing E.coli. As of 2025, WGS will be the standard method for other bacteria too. These rules are binding for us because of the framework agreement in agriculture.

Are you introducing it only because you have to?

No, there are very good reasons to do so. WGS data expose the entire genetic information of a pathogen. If we discover a new gene that causes resistance we can check all the previous samples in the database without having to go back to the lab to find this particular gene sequence. In addition, the comprehensive genetic information of a pathogen allows for other analyses. Maybe we'll want to know more about virulence in a few years time. The same database could provide the necessary data for such a study.

You are head of the federal One Health coordination group. What do you think about the idea of including all genetic data of pathogens from humans, animals, food and the environment in the transition to WGS?

If we were able to do so with consistent data standards, we would gain a much deeper understanding of how resistance spreads. We, as well as everyone involved in the national antibiotic resistance strategy (StAR), are therefore closely following the NRP 72 project in which researchers are developing such an integration platform. We are particularly interested in learning about the pratical solutions that they are testing, from linking data in the background through to the interface which we would ultimately use.

If this platform proves a success and becomes a tool for integrated and detailed monitoring of antibiotic resistance, would you start using it?

This is not a decision for us - the One Health coordination group - to make. To start with, we don't have the necessary resources. I believe that we need to focus on anticipating future developments and that federal and cantonal offices need to look into the topic and approach it in a coordinated manner. On the one hand we need clear national regulations, on the other hand any working system needs to include cantonal chemists, vets and doctors.

What area do you have in mind?

This concerns many areas, one of them is the collection of samples. The analyses in the lab can be done almost everywhere, including in private labs. But collecting samples is mostly a cantonal responsibility. The lay of the land is similar in other areas; for this reason, cantonal and federal authorities work closely together.

You mentioned national regulations. What do we need?

First, we need to contemplate how we could implement joint monitoring in different areas. This touches on food legislation, epizootic legislation and the law governing epidemics. Consequently there are different ways of collaboration between cantonal and federal authorities. Federal offices need to be able to place an order with, for example, reference labs and to pay them accordingly.

What are the next steps in implementing a national one-health monitoring of resistance on the basis of WGS technology?

At this point in time, the NRP 72 project is very important for us. It will be the basis for future discussions. Not only the technology but also the proposed solutions. This project is bringing together data from different cantons including animal, food and human data. We then need a clear implementation concept. It would need to prioritise certain pathogens and clearly link monitoring to fighting resistance. Because, after all, we want to know more about the spread and outbreaks of resistance in order to contain them.