Team:TUDelft/HP/Gold Integrated

Integrated Human

The key role of Integrated Human Practices in our project

Because our project was focused on tackling a problem extremely relevant to our society, it was essential that we looked at the impact our project would have and how we could adapt our design according to the acquired information from stakeholder dialogues. Only then would our project have the desired value to be able to contribute to the issue of antibiotic resistance. Developing a detection method in the lab is one challenge, but developing a detection method that could be used in the real world is another, more complex, challenge. The complexity of the challenge in the antibiotic field made it hard to find the niche in which we could apply and validate our detection method. By meeting with experts and stakeholders, we were able to shape our design to fit everyone's wishes as best possible, and make our design relevant and responsible. The timeline of our integrated human practices process is illustrated to give an impression on how our project evolved over time due to interviews with stakeholders, and those we collaborated with.

For example, we collaborated with farmer Paul Oosthoek and did experiments on his cow’s milk samples. Additionally, we performed experiments with the isolates gained from the experts Dik Mevius and Fimme van der Wal. Also, veterinarians gave us insights in their documents to gain more knowledge about the treatment procedures. Futhermore, multiple stakeholders participated in our project How can iGEM teams best include Relevance and Responsibility in their Design?

In the last section, we summarise the most crucial insights and how stakeholders interactions lead to impressive changes in our experiments and design.

Project Timeline

In this timeline, we take you on a journey through the evolution of our design. In this tree-like interactive element on this page, you can hover over different icons, that depict important developments in the project. Each icon will fold-out to show the insights and changes we gained together with further relevant information about people/institutions involved. Additionally, our timeline is featured in the second video of our video project!

  • Our interactive timeline

    Click on the icons in the timeline, and find out about all the insights we gained from our stakeholders and how the dialogues shaped our project.

Integration in our project

There were several interactions with stakeholders that heavily impacted the direction of our design. Integrated Human Practices was extremely valuable in shaping our project. In response to dialogues with the public, risk assessors, and potential users, we changed our design from a GMO-based lab tool to a safe and reliable end product. Key points that we took from discussions with stakeholders were that the method needs to combine a simplified sample preparation, a fast, easy readout and the possibility for on-site use. We integrated all these in our project, by designing a cell-free method that can be stored for up to two weeks and produces a visible readout.

We started by finding a relevant case in which our device could make a contribution. Through a conversation with a veterinarian, we were advised to narrow our scope to mastitis, an udder infection affecting dairy cows.

Every milk farmer faces mastitis, a challenging udder disease affecting dairy cows.Bouwe Gall Frank (veterinarian)

This infection is not easy to get rid of; udders are exposed to the open environment, making the infection a common re-occurrence. All dairy farmers we spoke to in the Netherlands have had to deal with mastitis. Farmers want to have fast administration of antibiotics when treating this disease, as time is of the essence. Our tool makes sure that fast treatment of mastitis can be done in a responsible way, without misusing antibiotics, thereby helping to prevent the evolution of antibiotic resistant bacteria. Looking to mastitis, we adapted our tool to detect relevant resistance genes in the common pathogen, Staphylococcus Aureus (SAU), causing this disease.

It is relevant to be able to detect SAU pathogens. As there is a huge difference in sensitivity for antibiotics considering MRSA, it would be added value to have a conclusive result on the sensitivity.Maaike van den Berg (veterinarian)

After talking to experts with expertise in mastitis from the Wageningen Bioveterinary Research Center in Lelystad, we found that detecting the mecA and blaZ genes was the way to go.

MecA can be used to detect resistance against all β-lactam antibiotics.Fimme van der Wal (agricultural researcher)
Detection of blaZ is a conclusive result to exclude commonly used penicillin treatment.Dik Mevius (agricultural researcher)

For further information about these genes check out our applied design and demonstrate page.

After defining our end-users and detection goal, we looked at how we could make our device as user-friendly as possible. From the start of our project, we wanted to integrate the use of tardigrade intrinsically disordered proteins (TDPs) which are able to maintain the functionality of other proteins upon desiccation. This fitted perfectly in our design with respect to our end-users, as our TDPs enable the transportation and storage of our detection tool at room temperature. Normally, protein function can be maintained when stored at -80 degrees celsius, something that is not always available at your local dairy farm! We also envisioned that this improved storage method will be advantageous for shipping our versatile RNA-detection tool for broader applications. For further information on our TDPs, check out our TDP design page.

Adding to the storability, we realised that our tool needed to give a readout visible to the naked eye. At a farm, there are no fancy lasers or microscopes, so we had to get creative! We started by designing a microfluidics paper chip with GMOs with a kill switch to detect resistance genes, but gained crucial feedback on this.

Even if GMO kill switches were reliable, there is no public acceptance to use GMOs in the environment. If it will be accepted in the future, it will take years from now to legislate this principle. Innovation based on this gets stuck.Cecile van der Vlugt (Risk Assessor GMO)

This led us to come up with a new application: CINDY-Seq. This method allows for a simple yes or no answer to the question: is the pathogen causing mastitis in my cow resistant to penicillins, or even all β-lactamases depending on the design of Cas13a, in a matter of hours, without the use of GMOs in the environment. For more information on how CINDY-Seq works, please visit our coacervation design page.

Now that we completed the design of our detection tool, we needed to look at how we could make the sample preparation as simple as possible for a farmer, as farmers like to do most things themselves.

We try to do most things by ourselves to prevent high bills from the veterinarian.Tjerkje Poppinga (dairy farmer)

In the case of mastitis, the pathogen is present in the milk of the infected cow. By hitting the books and optimising existing protocols, we came up with an easy method to prepare a fresh milk sample for the detection tool. To know more about which methods we came up with, look at our sample prep design page where we describe this extensively.

Finally, our integrated human practices strategy helped us to think a step further about our design, regarding, for example, the costs involved in our device and what it should actually look like; what kind of ‘kit’ will it be and what will it contain? We also looked at the feasibility of our device in the context of whether or not farmers would actually be allowed to use such a device and what needs to be done considering legislation to make this possible.

Only veterinarians can prescribe or change antibiotic treatments.Engeline van Duijkeren (veterinarian)

Stakeholder interactions shaped our final design and made it feasible to transform our detection method into an application, resulting in a toolbox with which the farmers can perform the resistance test themselves on-site, instead of being dependent on slow lab processes. Simple, cheap and safe methods - for example the hand-powered centrifuge and boiling method during sample preparation, together with an optimized readout - make our device applicable for rapid frontline diagnostics. We developed our toolbox to detect the most relevant multiple antibiotic resistance genes, expanding the impact of our product to achieve better animal and human treatment strategies, see our applied design page for more info!