Team:Heidelberg/Safety


Safety





Safety and Security

Safety is an essential requirement for successful and good work. Throughout the project, it was important to us to ensure the safety of the environment, our fellow human beings and each member of our team.

General laboratory safety

In the context of our work, we have deliberately chosen to work in a biosafety level 1 laboratory. The bacterial strains we used, Escherichia coli and Bacillus Subtilis, are ubiquitous and frequently used model organisms. In addition, we cultivated the Acinetobacter baylyi strain ADP1, which, like the other two, is classified in risk group 1 according to German TRBA. Thus, we worked with strains that, according to current knowledge, are not pathogenic for humans.

Before starting our research in the lab, we received several safety instructions from the BioQuant laboratory team and our Principal Investigator Prof. Dr. Wölfl. In addition, we received special instructions for the use of certain equipment, such as the centrifuges. After the briefings, Prof. Dr. Wölfl and his group members were always available to help us with further problems and questions. When performing our experiments, we made sure to take appropriate protective measures, such as wearing protective clothing. Careless handling of hazardous substances such as ethidium bromide and dinitrosalicylic acid was never an option for us, also with regards to the protection of our environment. For this reason, these substances were separated and disposed of in accordance with regulations.

Corona Safety

This year, due to the Covid 19 pandemic, we had to take special measures to continue working safely and efficiently. We held our meetings exclusively virtually, and safety meetings were held outdoors as if possible. We used a variety of online tools to organize ourselves, such as online to-do lists and messenger services. In addition, to prevent risks, all of our human practice projects ran online. In the lab, regular rapid tests and hygienic work with mandatory masks were the order of the day. We arranged our schedules so that only the necessary number of people worked in the lab at the same time and maintained a safe distance.

Risk Assessment

Thanks to the extensive exchange with the lab facilities at the Heidelberg University our team was introduced to the importance of risk assessment early on in our project. To make our project as risk free as possible as well as to evaluate possible complications that can arise if further research in this direction is continued, we conducted several rounds of brainstorming on possible risk factors as well as organized a risk assessment seminar with other teams.

During these events, we learned some important safety measures that we implemented in our project. The protocol for risk assessment of a study on a laboratory level is standardized. First, possible hazards need to be identified. These could include toxic chemicals that are used during the work or harmful microorganisms. These hazards should then be characterized, meaning what it is, how probable it is for the public to be encountered with it, how dangerous it is, etc. Besides this, it is key to differentiate between exposure routes, in order to set a proper limit for each one of them. After possible risks are identified appropriate safety measures need to be taken and people who could get exposed need to be taught about the risk regulations. Additionally everyone became familiar with the safety databases of the university as well as the important safety contact people.

For many types of studies the mentioned measures are enough. However, our team aims not only to create a good iGEM project, but also to investigate its next steps in case it will be taken up to the clinical level. Prior to that of course all medical safety protocols need to be taken into account. For all medical substances and therapeutic advances there are guidelines which determine the amounts of studies that need to be performed before the product is considered safe for use on humans and market ready. These guidelines are summarized by FDA for the USA and EMA for the European Union. These include all stages of laboratory screenings as well as clinical trials that ensure that the new therapy does not harm and also is better than the already existing ones on the market.

These also include some important design steps that are normally performed already by the end distributor - namely the pharmaceutical companies. These include the optimal delivery and packaging of the therapeutic agent. We decided to put some thoughts into it considering the possible safety risks. Thus, we first considered how our plasmid DNA should be packaged in a way that avoided its malfunction and off-target effect in our design of possible pills, which you can read more about on the proposed implementation site. Besides this, we wanted to make sure that the transformation of natural competent bacteria did not throw the gut microbiota off balance, which could have severe side effects on the patient. Thus, one of the main goals of our project besides the implementation and characterization of natural transformation became the study of bacterial co-cultures as well as the establishment of diet-based selective advantages (summarized in the corresponding section). We also realize that along with the upregulation of the target bacteria strain it’s downregulation might be needed in certain conditions. Therefore further research on selection disadvantages would also be required. These could include toxin-antitoxin systems where the production of antitoxin is activated by specific sugars (like lactose) in the diet. The toxin gene localization on the same plasmid as the target gene would in this case also ensure that the plasmid is not transmitted amongst other bacteria types in the gut, creating unwanted and less controllable clones.

Additionally it is important to state that our proposed implementation lies in the grey area of the currently used GMO regulations in case natural transformation is used. Still, we thought that the general idea of GMO safety regulations that was discussed in seminar was important and we should consider it as well. For example, the fact that GMOs must not harm the environment for them to be accepted was an idea that worried us from the beginning. Because of this, we found it imperative to consider a killswitch, and search for a system that could adapt well to our conditions.

One thing that we learned from the seminar, is that the risk assessment also requires the consideration of the “bigger picture”, namely the influences the proposed therapy could have on the environment and society. As has been mentioned above, a reliable killswitch presents some considerations for the environmental aspect. The influence on society is more difficult to estimate. During our research we identified several important classes of influences that need to be taken into account:

Data safety

The fact that for the optimal regulation of the natural transformation in the patients microbiome information on its composition is required will lead to microbial screenings of the patients. This in turn leads to the gathering of large amounts of sensitive medical data on the patients. Thus, concise and effective data safety regulations need to be developed in order to on the one hand ensure the optimal treatment of the patient as well as further research progression, but on the other hand avoid leaks of this sensitive data. Although multiple guidelines already exist in the medical field for this issue, some additional measures need to be taken due to the fact that the microbiome data itself can give clues on the origins, the diet and the living place of the people. This leads to additional anonymization strategies that need to be taken to avoid microbiome data based descrimination of people with certain dietary preferences, racial minorities and others when it comes to providing healthcare and insurance.

Treatment and Research accessibility

One risk that is known from the field of medicine is the lack of access to the research data and to the final product for Low- and Middle Income Countries. Publication access and patenting issues inhibit active information exchange that is required for research as well as promote the separation between the high and low income countries. This in turn has a direct influence on patients' health in these countries.

Since the dream goal of our project is to provide a new treatment approach for rare and common microbiome based diseases, provisions on research data results publication as well as later medicine accessibility need to be taken. Thus, we believe that in order to promote fair research, all data on the development of the medicine as well as all the results of clinical trials (successful or not) need to be published in an open access format. For clinical trials in Germany and the EU, this is regulated by the EU Clinical Trials Regulation. However, it is important to note that due to the fact that this regulation is not enforced leads to the failure of multiple universities and pharmaceutical companies to publish their research in an accessible format. This in turn makes this research exclusive and thus inhibits active exchange on it.

When it comes to accessibility of the final product to the general public independent of their origin and place of living, certain regulations must be used early on. One way to achieve this would be to use Global Access Licensing or similar frameworks when filing patents for this type of medical innovations. This format allows for selling licenses to pharmaceutical companies from Low- and Middle Income Countries to promote the production of generica, thus making the medicine accessible to people from these regions.

Reception in the population

As has been seen in the course of the pandemic the general mistrust of the population towards treatments that involve GMO (genetically modified babies from China) or only genetic material (see COVID vaccination crisis) is growing. Although it is important to note the issues and safety problems of any new treatment, it is as well important to balance this to avoid complete research stop and following industry decline for microbiome based treatment as it happened for example to the nuclear power plant research in Germany.

Although our team can not fix all problems including fake-news spread on social media, we have identified some key aspects that could be optimized to avoid the complete shut down at early stages of research.

First, honest communication of results as well as positive and negative effects of the medicine is key along with the strict following of the FDA and EMA guidelines. Second, early education on the topics of biotechnology starting from school might prevent later misunderstandings of the technology (this is what we have tested on our School Workshops with the example on mRNA vaccines). However, information should also be made accessible to everyone, through explanatory youtube videos, newspaper articles and other mass media early before the launch of the technology. Here again the accessibility of the original studies may play a key role.

Another issue is the perception of the children and adults who have been treated by the general public. Here it is especially important to distinguish the technology from gene treatment, which is currently critically viewed by the public. This is especially important, since the association of children with GMO can lead to traumatizing experiences like being mocked at school, or the hindrance to take the medicine due to different beliefs of the children or their parents. Additionally data safety is required to avoid the risk of microbiome information making a change in insurance eligibility.

Biohacking

Since the described microbiome modification technology is simple enough, the danger of unregulated and uncontrolled use by biohackers is present. This can result in lack of safety measures for microbiome control and killswitch loss and contamination of the environment. To avoid this, the possible risks of the described technology need to be clearly communicated early on, as well as optimal safety guidelines in work with natural transformation additionally specified.

Dual use

In the current stage of our project we don’t see a dual use concern of the proposed treatment idea. However, this issue needs to continuously be monitored as the treatment concept becomes more elaborate and research on natural transformation continues.

These are the concepts we found to be important. However, safety assessments of novel technology typically are longer processes which rely on multiple researchers from different fields - from sociology and marketing to robotics. Thus, a more complex assessment for our project needs to be performed.