Team:Thessaly/Human Practices
INTEGRATED.
As a new team, we were really excited to explore the world of Human Practices in the competition. Soon enough, we realized how important a part this is, not only for iGEM but for science beyond the competition as well. Other teams’ work made us see that incorporating Human Practices into a project equals raising and being able to answer questions concerning the impact it has on society, whether it will actually make the world a better place, comply with ethical principles and public policies, and be safe to implement. That is only the first step to integrating Human Practices into a project though. Besides taking this step through interaction with various experts and stakeholders, we wanted to take another step towards engaging seriously with society and the people directly affected by our project. For this reason, we contacted a simulation of our test in the field to receive feedback on its use. Below, we elaborate on the efforts we made to integrated feedback from our Human Practices and incorporate that into our project.
Our Idea
After our team was created, a long brainstorming session began. During this phase, we had to figure out which of the problems that our society faces these days has the greatest impact, globally as well as in our country. Initially, we were all thrilled by the story of our leader’s friend. Emmanouela Daka was currently a social worker working with the United Nations High Commissioner for Refugees at the Reception and Identification Center (RIC) "Moria" at Lesvos, Greece.
Having that in mind, we also came in touch with professors from our University to examine more ideas. This is when K. Gourgoulianis, pulmonology professor of the Department of Medicine at the University of Thessaly, underlined that tuberculosis is an existing threat, especially for people affected by crises.
During our brainstorming, we had already brought up migration as a defining phenomenon and so, after our discussion with Dr. Gourgoulianis, we started exploring this problem and contacting experts.
While we were studying about Tuberculosis, the organs/systems it affects, how it is transmitted, its symptoms, and the methods used for its diagnosis, we visited hospitals in order to interact with pulmonologists specialized in Tuberculosis.
We first met with Dr. Karayiannis, a pulmonologist at the ICU General Hospital of Larissa, and Dr. Ioannis Kalousis who specializes in tuberculosis. Beyond the information both doctors gave us on the traits of the disease, Dr. Kalousis presented to us significant epidemiological data, while Dr. Karayiannis provided us with information about the commonly used methods for TB detection. A useful input we got from Dr. Karayannis was that TB diagnosis is based on clinical tests meaning that a positive result of our test would indicate the need for the patient to visit a hospital for further examinations.
The greatest difficulty we met at this point was to decide whether it would be the best for our test to detect active and latent tuberculosis rather than only one of the two types. To answer that, we arranged an appointment at the Sotiria Thoracic Diseases Hospital of Athens, the biggest pulmonary center in Greece and among the biggest in Europe. There, we met with Doctors Simona Karampela, Panagiotis Ioannidis and Dimitrios Papavetzis. They helped us figure it out by pointing out that a useful screening tool would detect active tuberculosis since this is the form of the disease that can be transmitted and is more threatening to the patient than latent TB, in which case Mycobacterium tuberculosis stays in the organism at an inactive state.
The first important step in building our test was to choose the biological sample. After studying and meeting with pulmonologists, we found out that the most commonly used sample for tuberculosis detection is sputum. Before moving on with this option, though, we wanted to make sure we are choosing the most suitable input for our in-field test.
To do that, we came in touch with experts from organizations and stakeholders involved in migration health. We initially visited Doctors of the World- Greece, an international non – Governmental, humanitarian organization providing medical care where needed, including refugee reception sites and camps. Doctor Papakonstantinou Sotiris and General Director Evgenia Thanou advised us against using sputum as the biological sample for our test. Judging by their experience, in hotspots sampling and processing sputum are two quite difficult procedures. On top of that, children are unable to produce sputum for tuberculosis testing which is crucial given that the number of unaccompanied minors among arrivals is significantly high.
After that talk, we excluded sputum from our options so we were left with blood and urine. We also met with Ioannis Micropoulos, director of the Migration and Health Program of the World Health Organization. WHO’ s role is mainly consultative when it comes to dealing with the migration challenges faced by policymakers. Ioannis Micropoulos agreed with the opinion about sputum from his own experience and represented WHO’ s position on preferring non-invasive tests for diagnosis of tuberculosis. That way we realized that blood sampling would not be suitable for our test either.
After studying a lot, we decided to use urine as our test’s input since studies have shown that once Mycobacterium tuberculosis dies in a patient's lung, it releases fragments of nucleic acids (cell-free DNA) into the blood as it breaks down. cfDNA’ s small size allows for it to cross the kidney barrier and appear in the urine [1].
With our purpose being to detect the IS6110 gene, the first step of our test should be the amplification of this target. Considering that our goal was to develop a test designed to be applied in refugee reception centers, we searched a lot for the best option of an amplification method. Initially, we were between LAMP, NASBA, and RPA. At a point where we almost hit a dead end, we met with Dr. Tilemachos Dimitriou.
Dr. Dimitriou is a Lecturer and researcher in the Department of Biochemistry and Biotechnology of the University of Thessaly, and Supervisor of the Molecular Virology-Molecular Bacteriology lab.
Our conversation with him was enlightening as he gave us important insight into the methods’ advantages and disadvantages regarding the implementation of our test.
Starting with NASBA (Nucleic acid sequence based amplification), the issue we met concerned time. This method takes about 90 minutes which of course would not be ideal for a screening tool that needs to be time-saving. When it comes to LAMP (Loop-mediated isothermal amplification method), the limitations lay on the primers it requires to work as a method. Specifically, it requires 4 types of primers that consist of 6 regions. Therefore, it would be difficult to amplify just a small region as the target we chose for our test. Our choice was based on the fact that cell-free DNA is found in patients' urine in the form of fragments so, to enhance the sensitivity of our kit we had to amplify just a small region that would appear in as many fragments as possible.
We finally, concluded that RPA was our best option as using the RPA allows our test to be conducted on a variety of temperatures 25 – 42oC without the need for specialized equipment and it gives us the chance to amplify regions that consist of a small number of bps.
The first thing that crossed our minds concerning the visualization of the detection, was the use of a fluorescent protein as a report. We got very important feedback on that from Doctors of the World as well as from Doctors Without Borders, an international, medical humanitarian organization that delivers emergency aid to people affected by crises and exclusion of healthcare.
Doctor Apostolos Veizis has worked for the Doctors Without Borders during the period that Doctors Without Borders was the primary coordinating organization in the country concerning migration health. Our discussion with him had a great impact on our project design as he made us understand that our test would be the most helpful with the least possible equipment requirements.
Taking that into consideration, we figured out that the result of our test should be able to be seen with the naked eye. For this reason, we decided to use a colorimetric method based on an enzymatic reaction to visualize the detection. So, our reporter gene encodes for β- lactamase which hydrolyzes nitrocefin, a chromogenic cephalosporin, which then turns from yellow to red.
Dr. Veizis was also the one who sparked our interest in proposing a new Healthcare Model, underlying the current challenges and needs in health services.
During our Human Practices activities for communicating our project, we often met Kostas Vavitsas, Biotechnology/Synthetic Biology Researcher and currently Senior Research Associate at the University of Athens and Nikolaos Balatsos, Assistant Professor, Biochemistry at the Department of Biochemistry and Biotechnology, University of Thessaly.
We discussed with them our design and they both pointed out the significance of positive and negative control selection for a detection method like ours. A suitable control would eliminate the possibilities of false positive or negative results. More specifically, Professor N. Balatsos advised us that we should use as a positive control a gene from the human genome that is found in urine; this way it will always give a positive result.
After these observations, we chose to use the cox3 gene, deriving from the human mitochondrial DNA, as a positive control.
Our talk with Doctor Veizis from the Doctors Without Borders was basically around the issue of current needs and challenges in reception and identification centers in Greece. When we let him know of our idea to develop a test detecting Tuberculosis in refugee camps, he immediately stated that the most needed tool in field is a kit containing diagnostic tests not only for TB but for other diseases commonly appeared as well.
We gave that some thought and decided that, instead of developing different detection methods for each disease, we could build a universal tool able to detect several diseases. To incorporate this thought into our test, we designed the primers used for the amplification accordingly. Briefly, we incorporated universal overhangs in front of the annealing sequences that activate a downstream colorimetric readout module. Thus, by changing the annealing region of the primer, the downstream detection is unaffected.
Then, we started thinking of the next disease on which we could prove that our tool was universal. Despite TB being the most commonly screened disease among newly arrived refugees, the Hepatitis B virus (HBV) is high on the list as well. It is a major global health problem and, in highly endemic areas, is spread from mother to child at birth, or through horizontal transmission. DNA fragments derived from HBV have been reported to appear in patients’ urine.
To prove the universality of our detection method, we tested our system in a small DNA fragment of a sequence that encodes for a DNA polymerase of the virus. By changing the set of primers and making them specific for the HBV sequence, we managed to get a detection result for Hepatitis B. Therefore, we successfully proved that our system is able to detect several diseases, by only adjusting the template specific regions of the primer set, depending on the pathogenic agent targeted.
Stelios Psarras is a Staff Research Scientist, Associate Professor Level at the Histochemistry Core Facility of Biomedical Research Foundation Academy of Athens, Greece.
On April 3, we conducted a project presentation at the BRFAA which was attended by many important scientists from various scientific fields. After getting familiar with our design, S. Psarras made a significant point about the issue of antibiotic resistance that arises, since our reporter protein β- lactamase can hydrolise β- lactam antibiotics such as penicillins, cephalosporins, cephamycins, and carbapenems.
Since there is no possible way to control antibiotic concentration in urine, we decided to include in our test’s manual the need for prevention of antibiotic consumption before undergoing it.
To face the challenges posed by large influxes, the States need to call upon the assistance and support of the international community. This international support is delivered by organizations with mandates and experience in this field, most notably International Organization for Migration (IOM), European Asylum Support Office (EASO) and Doctors of the World.
Eirini Gerogli, Coordinator of the Migration Health Division at IOM, together with Xristina Zarogianni, Legal Rapporteur at EASO thought that our test would be most useful if implemented in Reception and Identification Centres (RIC); hotspot facilities to which migrants and asylum seekers arrive by boat. Both Ms. Eirini and Xristina talked us through the policy and procedures followed at the Greek Islands’ hotspots.
In addition to that, Doctor Papakonstantinou and General Director Evgenia Thanou from Doctors of the World- Greece, suggested that our test would also be useful and time-saving if applied in the organization’s Open Polyclinics. Six Open Polyclinics are operating in Greece with the main objective of provision of primary healthcare services, pharmaceutical coverage and psychosocial counseling to persons with limited or no access to the National Healthcare System.
From those discussions we understood that the point on which our test would have the greater impact is at the RIC of our country, as well as worldwide; when new arrivals are detained for registration purposes, after having been identified.
In June, we planned a meeting with Eleni Mpletsa, Associate Protection Expert at the United Nations High Commissioner for Refugees (UNHCR) and Andromachi Sereti, field coordinator of the temporary accommodation centre “Koutsoxero”, Thessaly with the National Public Health Organization (NPHO). Our purpose was to discuss with the representatives of these important organizations our thoughts and identify needs that we might have not taken into account.
They helped us understand the demands that emerge in Reception Identification Centres (RICs). A challenge that both those experts pointed out was that there is a significant lack of interpreters at hotspots, which makes the communication between the personnel and the migrants extremely hard, leading also to a lack of trust.
So, in our effort to address this challenge, we decided to provide workers in the field with a simplified produt guide for our test. Taking a step towards removing the barriers in communication and enabling migrants to have full knowledge on the health services provided to them, we asked Ms. Andromachi from NPHO which languages are the most commonly spoken in hotspots according to their data on arrivals' origins. So, we collaboratedwith our fellow iGEMers from iGEM AFCM Egypt, iGEM Montpellier, and iGEM Lacas BioBots who helped us make it possible for the steps of our test to be also available in Arabic, French, and Urdu.
Throughout our whole project, we tried to deeply understand every stakeholder’s viewpoint and incorporate their feedback into our design. Soon enough we came up with our prototype “2 tubes philosophy”. Our goal was to ultimately test it on-site and get comments, appreciations, suggestions, and improvements on its use.
We met with Iraklis Telidis, Senior Accommodation Supervisor, INTERSOS Hellas. INTERSOS is one of the implementation partners of UNHCR under the program E.S.T.I.A., and operates with the structure, ‘’Agia Eleni’’, which is specialized in the assistance of the most vulnerable.
Iraklis initially visited us at our campus to follow up with our work. There, we talked about conducting a simulation of our test at the "Agia Eleni" facility, intending to find out if it is truly easy and safe to use.
Once we developed our product and 3D printed it, we visited the facility. There, the Hygiene Specialist Nikola Skoula was waiting for us. She started by showing us around the structure and the polyclinic located in it, ran by the National Public Health Organization (NPHO).
The facility’s personnel including social workers, biologists, along with the doctors from the polyclinic were there to participate in our product presentation. Iraklis who performed the test and does not belong to the healthcare workforce confirmed that the design of our product ensures a safe, simple and fast implementation.
The doctors from the NPHO commented that our “2 tubes philosophy” seems to have great potential as they believe that healthcare services would invest in an easy to use, timesaving tool for screening of high-risk diseases for people affected by crises.
After we presented ODYSSEE, Nikola made a really important point concerning vaccinations against tuberculosis and the risk of them affecting the result of our test (false positive). She advised us to find out which strain is contained in the vaccine and maybe use it as a positive control.
After that conversation, we looked that up and found the BCG vaccine. Bacillus Calmette-Guerin (BCG) vaccine is a live vaccine that gives variable protection against TB disease. BCG vaccine should ideally be given 3 months prior to travel to a high TB incidence country. Protection against TB will only start 6-8 weeks after the vaccination has been given and lasts for about 10 years [2].
So, it is most likely that if someone has been vaccinated with the BCG before undertaking our test, macrophages will have not been produced yet, meaning that the bacillus’ cfDNA wouldn’t be found in urine. Its cfDNA will not appear until a period of 2 months has passed; the time at which the immune system will attack. The question that arises is for how long the cfDNA of the bacillus can be found in urine.
Ines Labugger et al [3], have shown with PCR that after treatment, cfDNA fell to undetectable levels after 12 weeks. We assume that BCG from the vaccine will not have the same bacterial load as MTB, meaning its cfDNA would appear for fewer weeks in urine.
Beyond the medical aspect, the social workers that were present during the implementation stated that it was very thoughtful of us to provide a product guide translated in different languages, in terms of contributing to the communication and trust issues met at refugee camps.
We chose to work on our project ODYSSEE, aspiring to play our part, as future scientists, in achieving a better and more sustainable future for all. We understood, though, that intention and purpose weren’t enough to ensure that ethics are integrated into our work.
So, we started raising ethical questions to ourselves and to the stakeholders we contacted throughout our Human Practices. We were, and still are, aware that because ODYSSEE affects real people directly, we needed to be extremely cautious. Our interaction with humanitarian organizations and governmental authorities was based, beyond everything else on the directions we could adjust our project design in a way that would impact vulnerable groups’ experiences for better.
Ethics on design
Our decisions on the design came after our interaction with big humanitarian organizations with a great experience in refugee camps and Reception and Identification Centres; WHO, IOM, UNHCR, MSF, MDM. According to these stakeholders, among other difficulties, trust and communication are challenges faced by the arriving population. This is why the workforce in refugee camps in Greece includes cultural mediators, who are trying to bridge those gaps.
The way we tried to cover these issues when it comes to our project design, is by choosing a biological sample non- invasive and easily accessible, avoiding any unnecessary force to collect it and panic the people that have just crossed the borders seeking a secure situation. In our effort to allow, as much as possible, the people undertaken our test to understand the health services and treatment provided to them, we designed the result of the detection to be seen with a naked eye. Adding to that, we created a product guide accompanying our kit and containing the steps in a simplified way. We also got the guide translated into the three most commonly spoken languages in hotspots in Greece, according to the National Public Health Organization (NPHO), which are; Arabic, French and Urdu.
Our discussion mainly with Doctors of the World and the NPHO led to important decisions regarding our design. Doctors of the World are operating in refugee camps basically voluntarily, while NPHO is the coordinating organization of migration health in our country, as appointed by the government.
Simplicity and safety are two of the pillars on which we built our product. Our design is based on the need for use of as less equipment as possible in the field. Also, the way that ODYSSEE is developed, allows for it to be conducted by not specialized personnel, as well. All these are key components ensuring that misusage of our test by actors on the field can be avoided as well as misinformation on the steps that need to be taken. Together with the fact that the time needed for the detection result to be visible is about 3 hours, we eventually have managed to contribute to the arrival country’s preparedness to large influxes taking up minimum resources.
Ethical questions that need to be answered
Given the amount of impact our project would have on potentially vulnerable populations, we wanted to discuss the ethical aspect with an expert on societal sciences. So, we met with the Vice Rector of Research and Lifelong Learning of the University of Thessaly, Ioanna Laliotou. She is a professor at the Department of History, Archaeology and Social Anthropology and her research interests include cultural history, subjectivity, mobility, migration, and visions of future and utopia in contemporary society. Our conversation resulted mainly in asking questions that we couldn’t practically answer, but make us aware as scientists. She summarized it to 3 basic questions;
-How do we set parameters when it comes to citizen status in biopolitics? What is the factor that diversifies a citizen from an arriving migrant when it comes to public provisions?
-Whether a newly arrived person chooses to undertake our test, what effect would that choice have during their stay in our country?
-Is our test a practice that would make a migrant’s world better?
These are questions raised throughout the history of migration. For the majority of refugees in Europe integration is the most relevant durable solution and European Union (EU) Member States have placed integration high on the policy and political agenda particularly since the mid-1990s [4]. Tuberculosis screening provides migrants with data they are obliged to possess for asylum procedures to move forward. Therefore, ODYSSEE it's a tool that would facilitate immigrant integration and naturalization.
During our discussion with the Vice Rector, we also talked about our upcoming visit to the facility "Agia Eleni" for conducting a simulation of our test.
Our electronic platform complying with GDPR
We built an electronic platform determining the health status of the person of interest, to improve healthcare provision for migrants and achieve their integration into national healthcare systems. Our platform contains personal data, medical history, previous examinations, and current treatments.
We discussed our idea with Eirini Gerogli, Medical Anthropologist and Project Coordinator at International Organization of Migration (IOM), and understood that personal data should be processed in a manner that ensures appropriate security of the personal data, including protection against unauthorized or unlawful processing and accidental loss, destruction or damage, using appropriate technical or organizational measures.
The principles of, and rules on the protection of natural persons with regard to the processing of their personal data should, whatever their nationality or residence, respect their fundamental rights and freedoms, in particular their right to the protection of personal data [5].To comply with GDPR, we decided that the platform will be designed in a way that it would be accessible by only the caring doctor, revised by the Ministry of Health and Social Solidarity.
References
1. Fernández-Carballo, B. L., Broger, T., Wyss, R., Banaei, N., & Denkinger, C. M. (2018). Toward the development of a circulating free DNA-Based in vitro diagnostic test for infectious diseases: A review of evidence for tuberculosis. Journal of Clinical Microbiology, 57(4), 1–9
2. Goverment of Western Australia, Tuberculosis BCG vaccination, [Online] Available: https://healthywa.wa.gov.au/Articles/S_T/Tuberculosis-BCG-Vaccination [Accessed 20/10/2019]
3. Labugger I, Heyckendorf J, Dees S, Häussinger E, Herzmann C, Kohl T A, Richter E, Milla E R, Lange C. Detection of transrenal DNA for the diagnosis of pulmonary tuberculosis and treatment monitoring, Infection (2016). doi:10.1007/s15010-016-0955-2
4. United Nations High Commissioner for Refugees (UNHCR). (1948). a New Beginning: refugee integration. The Ecumenical Review, 1(1), 4–10. https://doi.org/10.1111/j.1758-6623.1948.tb00689.x
5. REGULATION (EU) 2016/679 OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation), Official Journal of the European Union]
