Difference between revisions of "Team:ETH Zurich/core/human-practices"
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Revision as of 01:35, 22 October 2019
Contents
- 1 Human Practices
- 1.1 Integrated Human Practices
- 1.2 Antibiotic Resistance
- 1.3 Clinical Application
- 1.4 Patient Safety
- 1.5 Biosafety
- 1.6 Regulatory Process
- 1.7 Project Feedback
- 1.8 Public Engagement
Human Practices
Through our human practices work we aimed to ensure the responsibility and benevolence of our work. We identified <a class="a-link" href="#nav-antibiotics-resistance/" onClick="showCorrectTab('nav-antibiotics-resistance/');"> antibiotic resistance</a> as a globally relevant topic and decided to work on phage therapy to offer a potential solution. First, we brainstormed societal concerns that are linked to our project, and we identified <a class="a-link" href="#nav-clinical-application/" onClick="showCorrectTab('nav-clinical-application/');">clinical application</a>, <a class="a-link" href="#nav-patient-safety/" onClick="showCorrectTab('nav-patient-safety/');">patient safety</a>, <a class="a-link" href="#nav-biosafety/" onClick="showCorrectTab('nav-biosafety/');">biosafety</a> and <a class="a-link" href="#nav-regulatory-process/" onClick="showCorrectTab('nav-regulatory-process/');">regulatory process</a> as significant issues to consider.
<img src="" alt="hp-overview-figure" class="responsive-50 center">
The following questions arose among others:
- How could our new method be applied in a clinical setting?
- Is phage therapy safe for the patient and if not, what needs to be done to ensure its safety?
- What happens if our synthetic phages escape into the environment? Do they pose a threat to the ecosystem?
- How is the use of phage therapy regulated today and what would be necessary to obtain a good regulatory framework in the future?
Next, we met with stakeholders from the clinic and experts in safety and regulation to discuss these questions and get some general <a class="a-link" href="#nav-project-feedback/" onClick="showCorrectTab('nav-project-feedback/');"> feedback</a> on our project. Additionally, we were able to use various platforms to <a class="a-link" href="#nav-public-engagement/" onClick="showCorrectTab('nav-public-engagement/');">inform</a> the general public about phage therapy and synthetic biology and in return get some valuable feedback from society. Finally, we <a class="a-link" href="#nav-integrated-human-practices/" onClick="showCorrectTab('nav-integrated-human-practices/');">integrated</a> the gathered knowledge to improve the design of our project.
<img src="" alt="integrated-hp-overview-figure" class="responsive-50 center">
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Integrated Human Practices
Building a fast selection method that is feasible in a clinical setting
Based on discussion with Dr. med Andreas Kronenberg
Input:
Dr. med. Kronenberg pointed out the necessity of developing of a quick selection method for specific phages within our library. This method should be feasible in a clinical setting and would give our project clinical relevance.
Adjustment:
We have designed and built a bioreactor, that can mix the phage library with the novel host and measure the optical density continuously. To learn more about our bioreactor, visit the <a class="a-link-neg-margin" href="https://2019.igem.org/Team:ETH_Zurich/Hardware">hardware page.</a>
Reducing biosafety risk
Based on discussion with Dr. Ursula Jenal
Input:
Dr. Jenal suggested we do a risk assessment to evaluate the potential impact of our phage libraries on the environment.
Adjustment:
You can find our risk assessment here:
<a class="pdf-link" href="https://static.igem.org/mediawiki/2019/5/58/T--ETH_Zurich--RiskAssessment_pdf.pdf"><img src="
" alt="pdf" class="pdf-image">
Risk assessment</a>
We concluded that the risk to impact the ecosystem by generating phages with a broad-host range is low. However, as this risk cannot be neglected, we implemented additional safety measures in the lab once we were working with phage libraries as indicated in the report.
Improving infectious potential through phage training
Based on discussion with Dr. Grégory Resch and Dr. Jean-Paul Pirnay
Input:
Dr. Resch and Dr. Pirnay highlighted that even though the tail fiber protein is very important for host specificity, the infectious potential (the ability of the phage to kill its host) is influenced by the whole genome. Achieving binding but not infection would not be of interest in clinical applications where the main goal is lysis of pathogenic bacteria.
Adjustment:
To address this problem, we adapted our selection process to include iterations of phage training. Phage training consists in performing the phage selection procedure multiple times. In practice this is accomplished by isolating the amplified phages and infecting the target host strain again. During each iteration mutations are accumulated across the whole phage genome. In this manner the selected phage has an increased infectivity with respect to the phage isolated during the first selection step. Results can be seen <a class="a-link-neg-margin" href="https://2019.igem.org/Team:ETH_Zurich/Results">here.</a>
Antibiotic Resistance
<img src="https://static.igem.org/mediawiki/2019/b/b5/T--ETH_Zurich--AntibioticsResistance.svg" alt="antibioticsresistance" class="hp-icon"> Antibiotic resistant bacteria affect individuals independent of age, socio-economic status and country of residence and thus pose one of the biggest threats to global health today. The development of resistance mechanisms is an inevitable evolutionary response to the use of antibiotics. Susceptible pathogens are being replaced by more resistant variants by the process of natural selection [2]<a style="color: #ffffff; text-decoration:none;" href="#biblio-antibiotic-resistance">Clinical Impact and relevance of antibiotics resistance, French GL, Advanced Drug Delivery Reviews, 57(10), pp. 1514-1527, 2005</a>. However, despite the fact that this is a natural process, it is greatly accelerated by the misuse of antibiotics in humans and livestock [3] <a style="color: #ffffff; text-decoration:none;" href="#biblio-antibiotic-resistance">Prevalence of Inappropriate Antibiotic Prescriptions Among US Ambulatory Care Visits, 2010-2011, Fleming-Dutra KE et al., JAMA: The Journal of the American Medical Association, 315(17), pp. 1864-1873, 2016</a> [4] <a style="color: #ffffff; text-decoration:none;" href="#biblio-antibiotic-resistance">Antibiotics Overuse in Animal Agriculture: A Call to Action for Health Care Providers, Martin MJ, American Journal for Public Health, 105(12), pp. 2409 - 2410, 2015 </a> . An increasing number of infections such as pneumonia, tuberculosis and food borne diseases are becoming harder to treat as antibiotics become less effective against particular bacterial strains. Standard procedures such as organ transplants, chemotherapy and routine surgeries like caesarean sections will involve more risk in the future if no alternative methods are developed. The length of hospitalizations will increase as a consequence, leading to higher medical costs and potentially increased mortality rates [1] <a style="color: #ffffff; text-decoration:none;" href="#biblio-antibiotic-resistance">Fact sheet on antibiotic resistance,<a class="a-link-neg-margin" href="https://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance">WHO</a>, Accessed: 12.06.2019</a> . For this reason, the treatment of multi-drug resistant bacteria is highly relevant.
Input
Dr. med. Andreas Kronenberg
Member of scientific board at the Swiss Center for Antibiotics Resistance
Group Leader at Institute for Infectious Diseases, University of Bern
- Andreas Kronenberg gave us a broad overview of the current situation in Switzerland, predictions for the future and available resources on this topic
- He sees the importance of our project and names phage therapy as one of many roads to the solution
- Phage therapy faces the challenge of the high specificity of phages for specific pathogens, which makes an empiric therapy and its standardization difficult
- Current phage therapies have the disadvantage that the bacterial strain needs to be identified prior to treatment. This is not always possible in a clinical setting, and when it is, identification takes 24 to 48 hours
- The immune system might degrade phages
<img src="" alt="anresis" class="responsive-50 hp-logo">
Karin Waefler
Technical Officer at World Health Organization
Works on the topic of antimicrobial resistance
- Although the WHO has not published any official guidelines or recommendations regarding phage therapy, they gave us some general information concerning its potential and a statement about its use from the Federal Council of Switzerland
- The WHO provided us with the global list of bacterial strains that should be targeted with priority. The higest priority bacteria are all gram-negative. Therefore, working with E. coli as a host in our project is justifiable.
- According to the WHO, phage therapy is not as useful to second and third world countries because their infrastructure is often poorly developed and during shipping both the phages and the patients’ bacteria could evolve multiple times
<img src="" alt="who" class="responsive-50 hp-logo">
[1] Fact sheet on antibiotic resistance, WHO, https://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance, Accessed: 12.06.2019
[2] Clinical Impact and relevance of antibiotics resistance, French GL, Advanced Drug Delivery Reviews, 57(10), pp. 1514-1527, 2005
[3] Prevalence of Inappropriate Antibiotic Prescriptions Among US Ambulatory Care Visits, 2010-2011, Fleming-Dutra KE et al., JAMA: The Journal of the American Medical Association, 315(17), pp. 1864-1873, 2016
[4] Antibiotics Overuse in Animal Agriculture: A Call to Action for Health Care Providers, Martin MJ, American Journal for Public Health, 105(12), pp. 2409 - 2410, 2015
Clinical Application
<img src="https://static.igem.org/mediawiki/2019/f/f7/T--ETH_Zurich--ClinicalApplication.svg" alt="clinicalapplication" class="hp-icon">
For the use of phages in the clinic, the following considerations are important:
Product availability, or more simply having bacteriophages available for treatment, requires having access to phages that are both biologically active against the patient’s pathogen and that satisfy the regulatory requirements. To date there are no registered phage products in western medicine, this is a deficiency which we aim to address with our project. To facilitate exchange, it would be desirable to have an organized phage bank that links phages to susceptible bacterial strains.
Secondly, produced phages need to be of the highest level of purity for clinical use. Phage preparations are considered medicinal products and as such they are subject to Good Manufacturing Practice (GMP) compliance. However, the stability and consistency of phages is harder to guarantee and control than that of a chemical, which puts a strain on the clinical development of phage therapy.
The administration and dosage of treatment must be considered carefully for optimal treatment because circulating phages are sequestered by the reticuloendothelial system in the spleen and liver. The presence of bacterial targets also influences the pharmacokinetics, for this reason it is hard to estimate pharmacokinetics in a patient.
Finally, therapeutic evaluation is necessary to improve the therapy further [1]
<a style="color: #ffffff; text-decoration:none;" href="#biblio-clinical-application">Clinical Indications and Compassionate Use of Phage Therapy: Personal Experience and Literature Review with a Focus on Osteoarticular Infections. Patey O. McCallin S. Mazure H. Liddle M. Smithyman A. Dublanchet A. Viruses, Vol. 11, No. 18, 2019</a>
.
<img src="" alt="clinicalapplication-overview" class="responsive">
Input
Prof. Dr. med. Jürg Hafner
Department of Dermatology, University Hospital Zurich
Has experience with resistant bacteria through his work with patients who are having chronic wounds.
- Chronic wounds are very common: 1% of the population is expected to deal with a chronic wound in his or her lifetime. They are mainly caused by diabetes and insufficient blood flow in arteries and veins. Roughly 80% of these wounds are populated by bacteria, and in a third of these cases pathogens like Methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes and Pseudomonas aeruginosa are found, which are not part of the natural microbiome.
- From literature it is hard to verify the influence of bacteria on wound healing as no randomized clinical trials have been carried out to study this phenomenon yet. However, empirical data suggests, that bacteria can form biofilms on wounds, which presumably influence wound healing in a negative way. Thus, it is likely that bacterial infections are relevant for wound healing and for this reason should be studied more extensively.
- The current treatment of chronic wounds includes periodical debridement of the biofilm and topical disinfection using octenilin for example. Additionally, treatment to remove the cause of the disease is prescribed including the decrease of venous congestion, the release of water from the leg and the use of catheters to improve blood flow. In case of non-healing wounds, surgical procedures are necessary. The application of antibiotics is not desirable as it poses the risk to select for antibiotic resistant bacteria.
- Currently phages are not being used to treat chronic wounds. However, phage therapy would be a promising strategy to fight bacterial infections as it would remove the need for antibiotics. For various other conditions the systemic administration of phage therapy could be used.
Désirée Schwendimann
Assistant doctor in anesthesia, Inselspital Bern
Has come in contact with patients that are infected by multi-resistant bacteria.
- Ms. Schwendimann gave us an insight into how antibiotic resistance affects her work as an anesthetist.
- Thorough cleaning is necessary whenever a hospital has a patient with resistant bacteria and various safety measures have to be followed.
- In case of a surgery, the whole operation room has to be deep cleaned, before it can be used again.
- She mentions that hospitals in the Netherlands have a system that limits the occurrence of antibiotic resistances. Nurses have less patients, which leads to fewer mistakes with cleaning hands between patients, surgeries are performed less frequently on elderly people and they always have immunologists in their teams that check for the presence of bacteria.
[1] Clinical Indications and Compassionate Use of Phage Therapy: Personal Experience and Literature Review with a Focus on Osteoarticular Infections. Patey O. McCallin S. Mazure H. Liddle M. Smithyman A. Dublanchet A. Viruses, Vol. 11, No. 18, 2019
Biosafety
<img src="https://static.igem.org/mediawiki/2019/0/01/T--ETH_Zurich--Biosafety.svg" alt="biosafety" class="hp-icon">
After injecting their DNA into a host, phages either multiply and induce lysis of the host cell or they are stabilized as prophages either integrated into the host chromosome (temperate phages) or as a free plasmid molecule. Temperate phages can mediate horizontal gene transfer that occurs in bacteria through transduction. Transduction is a mechanism by which a segment of the bacterial genome is inserted in a newly formed viral particle instead of the viral genome and can therefore be transferred to other bacteria and can recombine with the host’s genome by homologous recombination. From a biosafety point of view, the introduction of new genetic material from a recombinant viral particle into the bacterial gene pool may have positive, negative or neutral outcomes depending on the genetic marker introduced [1]
<a style="color: #ffffff; text-decoration:none;" href="#biblio-biosafety">Contained Use of Bacteriophages: Risk Assessment and Biosafety Recommendations. Verheust C. Pauwels K. Mahillon J. Helsinki DR. Herman P. Applied Biosafety, Vol. 15, No. 1, pp. 32 – 44, 2010</a>
.
The survival of bacteriophages outside a host depends on the nature of the phage itself and is further influenced by the environmental conditions. Even if free phages can survive a rather long time in the environment, they need to infect susceptible bacterial hosts to replicate and propagate. Many phages are known to be highly specific for bacterial receptors and are therefore characterized by a narrow host range. However, some phages that are able to infect a large range of bacterial species have also been identified. These broad-host-range phages may promote genetic diversity and genetic exchange among a wider range of bacterial populations. Determination of the host range, virulence, resistance to environmental factors or the potential for gene transfer of the manipulated bacteriophage is therefore an important step in the risk assessment process to evaluate the probability of the phage’s propagation in a particular environment and its potential role in global gene transfer [1]
<a style="color: #ffffff; text-decoration:none;" href="#biblio-biosafety">Contained Use of Bacteriophages: Risk Assessment and Biosafety Recommendations. Verheust C. Pauwels K. Mahillon J. Helsinki DR. Herman P. Applied Biosafety, Vol. 15, No. 1, pp. 32 – 44, 2010</a>
.
Input
Dr. Ursula Jenal
Jenal & Partners Biosafety Consulting
- T7 phage is categorized as BSL-1. Its narrow host range among bacterial strains, incapability to infect eukaryotic cells and decreased efficiency of DNA packaging under UV light reduces its capacity to survive in nature and disbalance the ecosystem in case of an accidental release from the laboratory.
- If we randomize the tail fiber protein of T7 however, the situation has to be analyzed anew, as no laws are in place that regulate this case. Therefore, a risk assessment is necessary. We conducted one that you can find <a class="a-link" href="https://static.igem.org/mediawiki/2019/5/58/T--ETH_Zurich--RiskAssessment_pdf.pdf">here.</a>
<img src="" alt="jenal" class="responsive-50 hp-logo">
Dr. Grégory Resch
Department of Fundamental Microbiology (DMF), University of Lausanne
Expert in the field of phage research
- Infectious phages from our library most probably already exist in nature, but haven't been found and characterized yet. Therefore, they should not be considered to be GMO and most likely do not affect the environment.
- If a phage is created, that can infect and lyse many bacterial strains, it can only be used in a highly controlled environment to prevent destabilization of the ecosystem.
[1] Contained Use of Bacteriophages: Risk Assessment and Biosafety Recommendations. Verheust C. Pauwels K. Mahillon J. Helsinki DR. Herman P. Applied Biosafety, Vol. 15, No. 1, pp. 32 – 44, 2010
Regulatory Process
<img src="https://static.igem.org/mediawiki/2019/8/80/T--ETH_Zurich--RegulatoryProcess.svg" alt="regulatoryprocess" class="hp-icon"> Phages are currently classified as Medicinal Products (MP) under European Union (EU) legislation and as a drug by the Food and Drug Administration (FDA) in the United States, which necessitates that phages must be produced under Good Manufacturing Practice (GMP) guidelines and require clinical trials. The few formal experimental clinical trials that have been completed to date have produced inconclusive results on the efficacy of phage therapy, which contradicts the many successful treatment outcomes observed in recent individual case reports. Therefore, phages continue to lack any market approval in western medicine as a recognized drug but are nevertheless increasingly used as an experimental therapy for the compassionate treatment of patients experiencing antibiotic failure [1] <a style="color: #ffffff; text-decoration:none;" href="#biblio-regulatory-process">Clinical Indications and Compassionate Use of Phage Therapy: Personal Experience and Literature Review with a Focus on Osteoarticular Infections. Patey O. McCallin S. Mazure H. Liddle M. Smithyman A. Dublanchet A. Viruses, Vol. 11, No. 18, 2019</a> .
Input
Pia Stadelmann
Swissmedic
- Swissmedic explained us the legal framework for the use of bacteriophages.
- Phages are considered to be medicinal products and therefore the provisions of the Therapeutic Product Act (HMG) apply.
- They must have a production authorization granted by Swissmedic and comply with Good Manufacturing Practice (GMP).
- For clinical trials, a license from the ethics commission and Swissmedic is required.
- The use of the product under a temporary license (“compassionate use”) is only possible if the product is already in clinical trials.
<img src="" alt="swissmedic" class="responsive-50 hp-logo">
Dr. Jean-Paul Pirnay
Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital Brussels
Expert in the field of phage research
- Regulatory issues include the declaration of phages as medicinal products, which require Good Manufacturing Practice, preclinical studies, phase I, II and III clinical trials and centralized marketing authorization. This is too expensive as phages are biological entities that cannot be patented. Moreover, this process is also not feasible for an evolving therapy.
- In Belgium phages were used earlier under the WMA declaration of Helsinki, Article 37, which enables their use for desperate cases without the need to perform clinical trials and work under GMP conditions. While demonstration of the efficiency of phage therapy is not feasible from compassionate use cases only, the generated data suggests that phage therapy is safe, as no adverse effects were detected. The main problem with this approach is however, that too much time is lost in case of critically ill patients.
- The Dedicated PT framework is a new concept elaborated by scientists in cooperation with Belgian Authorities. It includes the characterization of phages, their storage in a banking system, the production of a single phage (active pharmaceutical ingredient) using a suitable host according to a monograph and external quality testing by a "Belgian Approved Laboratory". Then approved phages can be bought in a pharmacy upon prescription as magistral preparations.
Dr. Grégory Resch
Department of Fundamental Microbiology (DMF), University of Lausanne
Expert in the field of phage research
- The phage from which the library is derived needs to be well characterized and has to undergo a clinical trial.
- The evolved phages don't have to undergo this procedure again, as they underwent only an accelerated natural selection process. Instead they only have to be sequenced to exclude the existence of dangerous sequences.
- A physician with no other treatment option can contact Swissmedic via a special demand form. Phages that were authorized in another country with similar medical standards can be used in this case.
[1] Clinical Indications and Compassionate Use of Phage Therapy: Personal Experience and Literature Review with a Focus on Osteoarticular Infections. Patey O. McCallin S. Mazure H. Liddle M. Smithyman A. Dublanchet A. Viruses, Vol. 11, No. 18, 2019
Public Engagement
Scientifica
Scientifica is a fair that aims to educate the broad public about the most recent scientific achievements. It includes special activities for children as well as a specific program for politicians and economists. Scientists have the opportunity to explain their projects, raise enthusiasm for science and get valuable feedback from a very diverse audience. We shared the iGEM booth with last year’s team, AROMA, and had the opportunity to present our project and explain the principles of synthetic biology in general.
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<img style="width: 33%; float: right;" src="
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- The project was received well by the public and visitors were open to the idea of using phages to treat bacterial infections.
- The concerns that were raised more often were the price of phage therapy, a comparison of modified phages to naturally occurring phages, biosafety issues and the efficacy of treatment.
<img src="" alt="Scientifica" class="responsive-50 hp-logo">
Presentation at the Intra-Departmental Seminar
The Seminar is a series of talks that takes place during the semester at the Department of Biosystems Science and Engineering (D-BSSE) of ETH. The talks are great for interaction and the sharing of expertise with scientists from different backgrounds. We were given the opportunity to present our project during the seminar on the 4th of October. During the discussion some good questions were raised that helped to direct our work in the last weeks before the Jamboree.
<img src="" alt="VMB" class="responsive-50 hp-logo">
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