Team:Pasteur Paris/Human Practices
Education
Law
Events
Design
Results
Entrepreneurship
Demonstrate
Chalenges
Improve
Collaborations
Attributions
Results Attributions
Integrated Human Practices
Since our first brainstorming sessions, we took an interest in the biggest health problems of our century. Aware that iGEM could allow us to embrace a project and take it to another level, we had the ambition to tackle infectious diseases. We started to develop DIANE, a new generation of diagnostic device to fight the 40% of the total 50 million annual estimated worldwide deaths due to these infections. From its beginning to now, we truly wanted to incorporate human practices into all aspects of our project, making it evolve according to the feedback we received.
Why is our project responsible and good for the world?
Thanks to our interactions with professionals, scientists and the public, we have succeeded in creating a project as close as possible to their need and feelings. First, our device will drastically reduce the diagnosis time for a patient with sepsis, and in a few minutes, the practitioner will be able to give an adequate treatment. This will have a direct impact on the patient’s state of health and will help to fight antibiotic resistance by avoiding the use of large-spectrum antibiotics. Indeed, international health organizations launched a call to develop both new treatments and rapid diagnosis methods in order to face this threat. This willingness is also present in the medical community, as we have noticed it during our conversations.
Moreover, we created a small, easy-to-use, automated and portable device meeting as much as possible the user’s expectations. Our diagnostic method can be used in hospitals and intensive care units, close to the patients. But it can also be transported in more uneven places, such as during humanitarian missions. It will provide the most health disadvantaged-countries, where infectious diseases are often devastating, with access to rapid and effective diagnosis methods. This could have an impact on equality of diagnosis systems around the world.
We built an iterative process around our project. In terms of science, we solved issues by discussing with scientists and professionals and collecting their precious feedback. We attended conferences on intellectual property and protection. To complement entrepreneurship with human practices activities, we collaborated with Guillaume Berteloot from DeepTech Founders on market analysis and business model elements. We finally collaborated with SMC, a global leader of industrial automation to validate the feasibility of our prototype and adapt it to the needs identified on the field.
➔Click to know more about our collaborations and events integrating Human Practices.
One of our main objectives was to engage with communities. IGEM is a wonderful excuse to reach out to the public, whether young or old. Public’s feedback has been an important source of complementation to our project. We hope that we succeeded in gathering people around biology, and that we sparked vocations.
➔Click to know more about our public education and engagement.
As previously mentioned, Human Practices have shaped our project at every stage of its construction. We want to demonstrate, through all the encounters and interviews professionals have granted us, the process that we conducted to integrate the investigated issues into the execution of our project, and to always improve ourselves.
We met professionals from different fields in order to adapt our device (design, design, detection method, market) as well as possible. Each exchange was significant and truly helped us to refine our project. On this page, you will find a summary of discussions we had with them.
We wanted scientific expertise on DNA and aptamer synthesis and chemical modification from a Head of Structure at Pasteur
Dr. Marcel. Hollenstein
Head of Structure and researcher at the Institut Pasteur
24/04/2019
Marcel Hollenstein is our scientific expert for aptamers. He is head of the junior group of bioorganic chemistry of nucleic acids at the Institut Pasteur, and a member of the department of structural biology and chemistry. He accompanied us as we established protocols for the SELEX method.
He advised us to start the selection of the aptamers with a library of single-stand DNA that are between 80 and 100 nucleotides long. In the middle of the sequence, 40 nucleotides would be random to produce a large quantity of different aptamers. According to his experience, 12 selections should be enough, which should take between 3 weeks and 6 months. DNA is preferable to RNA for its stability and lower synthesis price.
The sequences are very stable and only require storage in the fridge, however, creating a storage buffer to avoid breakdown by nuclease activity was advised.
Concerning the linking to carbon nanotube electrodes, M. Hollenstein warned us against the conduction of electricity through the guanine in the DNA, which will indubitably cause damage over time if we measure a current. However, we only measure a potential difference, so this wearing down of the aptamers isn’t an issue. It was moreover pointed out that to avoid the adsorption of the aptamers on the electrode, we should ensure that the link is long enough.
We thank Marcel Hollenstein for his expertise and relevant advice, without which we couldn’t have produced a successful protocol for our SELEX method. His enthusiasm and insight the project was also greatly appreciated, and this interview helped us point out problems we hadn’t considered before.
We wished to expose our project to the Ministry of Health and gain insight from a member of the government used to the conditions we want to work with
Dr. Sylvie Renard-Dubois
Health Care Delivery Branch - Ministry of Health
11/07/2019
Dr. Sylvie Renard-Dubois has a very diverse professional background, offering us objective insight on the potential uses of our diagnostic device. She started as a hospital doctor working on infectious diseases in France, and left for Africa in the late 1980s to fight against the rise of HIV in these areas. After this fieldwork, she worked 12 years for Sanofi, a large french biopharmaceutical company, to develop antibiotics before leaving for the Ministry of Health, where she is health officer in the military hospital of Begin.
Thanks to her experience, Mme Sylvie Renard-Dubois was able to give us her thoughts on three important points of our project: the sampling types, the special care required for the analysis, and fight against antibiotic resistance.
1. Sampling types
For many general practitioners (GPs), the most common patient
samples taken are urine samples. It is possible to take skin
swabs and blood samples for blood cultures, but these remain
rare as not all doctors’ offices are equipped for taking these
samples. These other sampling methods must usually be done in
hospitals. However, high quality laboratories are becoming more
and more common in GP practices, which allow for finer analysis
of samples from nearby hospitals and private clinics.
It is possible for our diagnostic device to be integrated in such laboratories, providing the size is compatible with the available space. In terms of security, the biological waste is the responsibility of the laboratory, as well as the disinfection of the device.
2. Special care for analysis -
maybe change to “Potential Pitfalls due to Sample Type”
The potential for false positives due to the sample types must
be addressed. For urine samples, the problem can be avoided with
proper sampling and handling. This problem is more relevant for
pulmonary sputum, as one must ensure the number of epithelial
cells is high enough to guarantee the sample was taken from the
respiratory system and not just the mouth. Finally, concerning
blood tests, at least 3 blood cultures must be done to avoid the
confusion between an infection of the patient and the
contamination of a petri dish.
3. Antibiotic resistance
93% of antibiotic consumption occurs outside of the hospital,
which means our efforts must be focused on general
practitioners. Nursing homes are also relevant for the usage of
our device. Each resident is allowed to keep their own referring
physician, which multiplies the medical opinions, and often
multiplies the amount of medications. Using DIANE could
therefore greatly facilitate physician coordination.
This interview gave us the insight of the Ministry of Health which was particularly applicable as we built our diagnostic device, as they are actively working towards solutions for antibiotic resistance and patient care. For instance, usage by a general practitioner wasn’t initially considered in the project, collecting this information helped us extend the impact of DIANE.
Getting advice from a field doctor
Dr. David Lebeaux
Doctor for infectious diseases PhD student at the Institut Pasteur (2013)
18/06/2019
Doctor Lebeaux is a Physician working in infectious diseases in Georges Pompidou European Hospital. In addition, he completed PhD in 2013 at the Institut Pasteur in a biofilm lab. As a field doctor, he gave us insight on the practicality of our device in such conditions.
1. Necessary characteristics of DIANE
a. Targeted pathogens
Concerning the pathogens, it was important to know whether we would target only bacteria or also viruses and fungi, as the causes of diseases aren’t always the same depending on the country. The afflicted population may also differ. In our case, we target immunocompromised patients, which is a wide spectrum: bacterial or viral infection, fungi, parasites... Field doctors usually can’t tell and must rely on lots of tests. For Dr. Lebeaux, a test like ours could be very useful to detect a broad range of pathogens.
According to Dr. Lebeaux, most of sick children with diarrhea in developing countries get a systematic treatment against parasites and bacteria, which may favor the spread of antibiotic resistance . We would truly be useful if we could target the situations where making the difference between bacteria and non bacteria is difficult.
b. Size
One of the major points for the conception of DIANE was its portability, but we were told it wasn’t the most vital characteristic. Field doctors sometimes work with large devices (one meter high) and it isn’t a problem, at least in western countries. However, it must allow for delocalised analysis, meaning that it mustn’t require a lab. Power supply is also an important aspect that needs to be taken into account.
c. Analysis
The problem of false positives was of course discussed. We want DIANE to be reusable, but must make sure that it doesn’t induce false results. Dr. Lebeaux therefore proposed a closed and automatic washing system to keep the device decontaminated.
It was pointed out that when taking blood cultures, there is a risk that respiratory and digestive diseases go undetected, which is very problematic as it is the most deadly to children across the world. It was advised to quickly extend our samples to urine and lung samples to avoid missing most pathogens. However, it would be best to keep away from topical infections at least for our proof of concept, as they are quite complicated.
2. Patient care
When a patient is sick, several factors need to be taken into account to diagnose the illness. First is the source of the infection: if signs like respiratory or digestive distress point towards a septic shock, a treatment that covers more than 90% of possible pathogens is given. The state of the patient and whether he is immunocompromised or not is important to adapt the treatment. Finally, the geographic zone is studied, as is can help narrow down the type of pathogens.
This interview with a field doctor was greatly appreciated to give us insight on the reality of the humanitarian context, which is a key component of the use of DIANE.
Expertise on carbon nanotube electrodes
Dr. Sophie Griveau
Associate Professor at Chimie ParisTech
14/06/2019
Mme Sophie Griveau is a professor and researcher at the school of chemistry Chimie Paristech. Three student of our team study in said school, and Mme Griveau agreed to give us advice about making carbon nanotube electrodes for the detection of pathogens in DIANE.
Our goal was to deposit carbon nanotubes on a supporting electrode. Vitreous carbon was advised for this support, as it is the top-notch solution, however, it is quite expensive. Alternative solutions that were proposed were PVC or carbon graphite, both of which are cheaper, but require more tests beforehand.
As for the fixation, it should be done in several passes, to avoid undesirable agglomerates. While we suggested spraying the nanotubes on, Mme Griveau preferred an electrochemical approach, so as to deposit only on the working electrode. It was confirmed that nanotubes aren't soluble in water and therefore quite durable.
Mme Griveau recommended to us the Dropsens electrodes, which we ended up using, as they are quite cheap and comes in packages of 50-100 electrodes. She was also able to introduce us to a PhD student who works on electrode fictionalization and who gave us advice about linking aptamers to the carbon nanotubes.
Mme Sophie Griveau, as an expert in the field of analytical chemistry, therefore helped us apprehend the electrochemical part of DIANE, as well as recommended several protocols and materials for the experimental part.
We discussed with a humanitarian field doctor to learn from his experience of harsh working conditions
Dr. Pedro Clauteaux
Researcher at the Translational Research Center at the Institut Pasteur
29/05/2019
Dr. Pedro Clauteaux is a researcher at the Institut Pasteur. He has worked in South America, in a critical zone with little equipment. We have asked him about the relevance of a rapid-diagnostic device in such cases.
Because of his experience, Dr. Clauteaux gave us advice of the practicality of the device, if it is to be used in a humanitarian context. It must be completely resistant to rain and water, as well at impervious to oxidation in the case of the electrodes. It also must be as lightweight as possible, because the machines used in these areas must be easy to carry around. We were advised to buy a glucometer to see how it is constructed. For the battery, using solar energy is a real plus. It could also power an automatic thermometer to avoid wide gaps in temperature that could affect the measures.
In a more classical hospital context, our device could also be useful given a few modifications. The common factor is that the detection of pathogens must be adapted to the zone, even within Europe. In ICUs, the real value our device could bring is the fact that a lab isn’t required, which spares time and effort. Keeping the device small isn’t a necessity but would be appreciated, as well as a completely automated system.
This interview with a humanitarian doctor helped us apprehend the reality of field work, and adapt DIANE to the rigorous environment it will be subjected to.
Expertise in antibiotic resistance
P. Patrice Courvalin
Expert in antibiotic resistance Antibacterial Agents Unit, Pasteur Institut
14/08/2019
Patrice Courvalin, M.D., is Emeritus Professor at the Institut Pasteur in the Department of Microbiology. He is internationally recognized as an expert in the genetics and biochemistry of antibiotic resistance. His work is reported in more than 340 publications in international scientific journals (H index 92, citations ca. 28,000).
Our discussion with him cleared out the difference between a POCT (Point Of Care Tests) and a rapid diagnostic device. POCT are meant to be portable enough and easy to use so that it can be used as much in patient bedside as in remote areas. It has a lot of requirements to meet but at the same time, it must be cheap. Thus, POCT are not developed so much because of their lack of financial incentive. A rapid diagnostic device doesn’t have this financial restriction and can also be used in hospitals and laboratories as long as it provides results in a short amount of time. Therefore, there is no competition between a POCT and a rapid diagnosis because their use and performances are not the same.
The essential cause of antibiotic resistance emergence is the abuse of animal and human antibiotic use. That’s why he confirmed that a rapid diagnosis could allow a treatment which is appropriate and thus avoid the misuse of antibiotics. It could also allow an antibiotic de-escalation which is crucial to preserve the last-resort antibiotics. Although he pointed out that a device which could also give rapidly the resistance of the pathogen would be revolutionary, he confirmed us that a device which could quickly show which pathogen is responsible of the infection (a virus, a bacterium, which bacteria…) could already be a great asset to treat patients in a more effective way, helping in the fight against antibiotic resistance.
We also discussed of the possibility for our device to detect the resistance and the mechanism of resistance of the bacteria. Several obstacles were outlined. We have to distinguish the mechanisms of resistance which can be detected on the surface of the bacteria or inside the bacteria. If it’s related to a protein at the surface our device could directly detect it, and if it’s inside the bacteria we could lyse the bacteria to detect the proteins. However, sometimes it’s not the presence or the absence of a protein which is responsible for a resistance, but its quantity (over or under-expression of a protein). In this case, we should think of a more complex method using our device to detect the resistance of the bacteria (determining accurately the quantity of the responsible protein present in each bacterium).