Difference between revisions of "Team:Oxford/Chagas Disease"

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<h1> Safety </h1>
 
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    <h1>Chagas Disease</h1>
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    <h2>Introduction</h2>
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     <p>Chagas disease is a neglected tropical disease named after a Brazilian scientist, Carlos Chagas, who first described the life cycle of the parasite – Trypanosoma cruzi (T.cruzi) that causes the disease.  Chagas is primarily transmitted via the faeces of triatomine bugs, when they take a blood meal. Other forms of transmission include:blood transfusions orally via ingestion of contaminated fluids vertical transmission Chagas is endemic to Latin America but increased migration of infected people has led to it spreading to non-endemic countries, consequently increasing the number of people susceptible to the disease and causing it to be a growing global concern. </p>
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<p>Since the 1990s, strategies to reduce the impact of Chagas in endemic countries have largely focused on preventing transmission through vector control programmes and blood banks. Although these achievements have significantly reduced its incidence, they  are not sufficient to  combat the spread of the disease vertically from a mother to her child. Therefore, congenital Chagas Disease is growing in epidemiological importance, as it is now one of the most persistent form of the transmission among the human population, with prevalence in some rural areas of Bolivia being as high as 70.5%.  <br /> <br /><br /> </p>
  
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<h2 class="text-center">Parasitology</h2>
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<h6>T.cruzi follows the life-cycle shown in the diagram above: </h6>
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<h2>Personal safety is very important in the workplace, we ensured high standards were met. To read more click on each icon below.</h2>
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<div class="collapse indent" id="safety-training">The team attended a safety training session where we learnt about the potential dangers of the different substances and equipment we would be using. We all signed COSHH forms before working in the lab so that we knew the things in the lab that could be dangerous.</div>
 
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We make sure that in all our social media photos that we are adhering this to promote safe practices in all our followers.</div>
 
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<div class="collapse indent" id="protocols">We have protocols for every experiment and method. This allows us to make sure we have good microbial technique. To read our protocols click here. </div>
 
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<div class="collapse indent" id="equipment">We used a UV lamp to visualise and cut agarose gels. We had to ensure we had no exposed skin on our hands/arms and had to wear a visor to protect our faces and eyes. </div>
 
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<div class="collapse indent" id="contamination">To avoid contamination we have 2 areas of workspace: a wet lab bench and dry desk space. These are in different rooms, nothing from the lab is allowed past the door in order to reduce the risk of contamination and increase safety and conversely no food or drink is allowed into the lab</div>
 
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<p>All life stages of T.cruzi secrete a specific protease, known as cruzipain, which allow the presence of the trypomastigotes to be detected by our biosensor. However, the levels of trypomastigotes in the human blood falls with time after infection, as shown in figure 2. </p>
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<h6>Figure 2. Scheme of evolution of T.cruzi trypomastigotes in the blood of a human host </h6>
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<h2>Safe Project Design</h2>
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<p>Within 4-8 weeks of being bitten, adults move from the acute phase of Chagas disease to the chronic phase if untreated. </p>
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<p>During the chronic phase, cruzipain levels are very low in the blood and cost effective diagnosis of adults focuses on detecting antibodies specific to T.cruzi. However, antibody based diagnosis is unsuitable for newborns who lack a fully developed immune system. Newborns infected with congenital Chagas disease remain in the acute phase for up to 9 months, during which period there is no current cost-effective diagnostic available. We hope to fill this gap in the ability to diagnose congenital Chagas disease in newborns, using synthetic biology to create a specific protease detection system. </p>
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            <p>The use of genetically modified organisms (GMOs) in the field of healthcare</p>
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          <li>Evaluation:</li>
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            <p>There is a fear factor to consider when thinking about using GMOs in health care. GMOs have had bad media coverage and so you have to consider the acceptance of the new technology with its target user.</p>
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            <p>(Another issue we may have is that biosafety, biosecurity and dual usage are all the same word in spanish (bioseguridad) so we will have to be careful when discussing this with our target audience.)</p>
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            <p>Our system will be cell free so there will be no GMO’s present in our final device. In terms of regulation there are less barriers to this technology. However in some areas anything that is labelled as synthetic biology may be seen as the same thing as GMOs, so we must be careful in how we market our device so that patients are not put off.</p>
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            <p>The use of cruzipain to test our system in a proof-of-concept</p>
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            <p>Cruzipain is a pathogenic protein so it would be dangerous to use in the lab. It is also hard to obtain.</p>
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          <li>Solution:</li>
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            <p> We will be using TEV instead for proof of concept, in order to best ensure our safety as well as get meaningful data. TEV has the added benefit of being a well characterised and widely used protein (so could be more reliable?). </p>
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        <li>Problem:</li>
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            <p>The distribution of needles in our initial kit could be problematic due to the chances of reuse which can lead to the transmission of diseases. Also the misuse of/inability to use needles if this were to be a home kit.</p>
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        <li>Evaluation:</li>
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            <p>If a fairly large sample of blood were needed it would require the test to be done by a trained medical professional. This would mean that the distribution of the kit to more rural areas would be limited as not all places have access to doctors or nurses. If only a finger prick were needed then it could be done by the patients themselves and distributed to villages. </p>
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        <li>Solution:</li>
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            <p>We have decided to move away from the home kit idea and since our test now focuses on congenital Chagas disease  it will be done in a hospital or maternity clinic with  a medical professional present. This would ensure that any blood needed would be taken in a safe way. . </p>
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        <li>Evidence:</li>
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            <p>‘FIND’s goal is to support intensified global control efforts through the following specific objectives: To reduce the burden of congenital Chagas disease through improved diagnostic solutions’ -  (https://www.finddx.org/wp-content/uploads/2016/02/NTD_Strategy_WEB.pdf)</p>
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          <li>Problem:</li> 
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            <p>Medical infrastructure in the places worst affected by Chagas disease face complex challenges so the chance for follow ups or distributing results is not perfect. . </p>
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          <li>Evaluation:</li>
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            <p>a point of care diagnostic would be better</p>
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          <li>Solution:</li>
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            <p>We will try to make our diagnostic one that is at the point of care at birth. This would enable a diagnosis to be give straight away and treatment plans set up as soon as possible. Through modelling we have found that our test takes  [INSERT TIME HERE]  to work This would also help with the distribution of our test as hospitals are more accessible  with supplies.</p>
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          <li>Evidence:</li>
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            <p> ‘For congenital Chagas disease, the best time for parasitological or molecular diagnosis is during the first few weeks after birth when parasitaemia is often high. This is difficult, however, due to limitations in infrastructure and resources. As a result, children born from infected mothers have to wait for up to ten months after birth before they can be tested by serology (serological tests are only useful after maternal antibodies have waned). Many children are thus lost to follow-up during this waiting period. A point-of-care test for congenital Chagas disease to enable testing of neonates at the place of birth would ensure early detection and safer treatment.’  -  FIND Strategy for neglected tropical diseases 2015-2020 (https://www.finddx.org/wp-content/uploads/2016/02/NTD_Strategy_WEB.pdf)</p>
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          <p>The more sensitive our system is the more likely we are to get false positives due to the amplification system we have. </p>
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        <li>Evaluation:</li>
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          <p> False positives could have an impact on the mental wellbeing of patients, and can also lead to administering expensive drugs and treatments when they are not needed and could lead to uncomfortable side effects for the patients. </p>
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        <li>Solution:</li>
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          <p>Our device will only be for screening, and will be integrated into  our recommended plan of action to diagnose and treat congenital Chagas disease. This can be viewed by clicking here. </p>
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<p>Please visit <a href="https://2017.igem.org/Safety">the main Safety page</a> to find this year's safety requirements & deadlines, and to learn about safe & responsible research in iGEM.</p>
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<p>On this page of your wiki, you should write about how you are addressing any safety issues in your project. The wiki is a place where you can <strong>go beyond the questions on the safety forms</strong>, and write about whatever safety topics are most interesting in your project. (You do not need to copy your safety forms onto this wiki page.)</p>
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<h5>Safe Project Design</h5>
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<p>Does your project include any safety features? Have you made certain decisions about the design to reduce risks? Write about them here! For example:</p>
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<li>Choosing a non-pathogenic chassis</li>
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<li>Choosing parts that will not harm humans / animals / plants</li>
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<li>Substituting safer materials for dangerous materials in a proof-of-concept experiment</li>
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<h2>Symptoms and current diagnosis</h2>
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<p>Diagnosis of Chagas disease is difficult, as the disease is mostly asymptomatic in the acute phase and for the majority of the chronic phase. However, prolong onset of the chronic phase leads to 30% of patients develop cardiac disorders and up to 10% develop digestive, neurological or mixed alterations that cause 1200 deaths per year.
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The main diagnostic methods currently used to diagnose Chagas are summarised in the table below:</p>
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<h5>Safe Lab Work</h5>
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        <th>Test</th>
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        <th>How it works</th>
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        <th>Benefits</th>
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        <th>Limitations</th>
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        <th>Suitable for newborns</th>
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        <td>Whole parasite microscopy</td>
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        <ul>
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        <li>Preparation of Giesma blood smears</li>
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        <li>Visualised using light microscopy</li>
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        <li>Established method</li>
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        <li>Carried out by already trained professionals</li>
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        <li>Not suitable for the when there is little T.cruzi  in the blood</li>
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        <li>Not always possible to differentiate between T.cruzi from T.rangeli, which does not cause disease in humans.</li>
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        <td>Yes</td>
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    <td>Polymerase Chain Reaction (PCR)</td>
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    <li>Molecular detection of T. cruzi DNA is performed using a combination of three real-time PCR assays.</li>
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    <li>Acceptable specimen types are EDTA blood, heart biopsy tissue or cerebrospinal fluid.</li>
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    <li>Allows high sensitivity in the acute phase</li>
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    <li>Allows the presence of T.cruzi to be accurately distinguished from T.rangeli</li>
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    <li>Allows direct detection of infection and easy interpretation of results</li>
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    <li>High variation in accuracy and lack of international quality controls</li>
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    <li>High cost and complexity means it is not practical to use in a clinical practice</li>
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    <li>Further validation is needed to prove whether PCR is suitable to diagnose the  chronic phase of Chagas</li>
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    <td>Yes</td>
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      <td>Serological tests</td>
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      <li>Detection of antibodies against T.cruzi</li>
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      <li>Includes techniques such as indirect fluorescent antibody (IFA) test, a commercial enzyme immunoassay (EIA) and immunochromatographic tests</li>
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      <li>Can be used for acute phase and chronic phase</li>
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      <li>High specificity and sensitivity</li>
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      <li>Commercialised and approved for use by WHO</li>
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      <li>Low-cost formats are available</li>
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      <li>Cross reactivity can occur with diseases, such as leishmaniasis and schistosomiasis </li>
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      <li>Performance of these tests is lower than reported by their manufacturer, especially against specific strains of T. cruzi</li>
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      <li>Not suitable for immunocompromised patients and newborns</li>
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      </ul>
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      <td>No</td>
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  <p>The table highlights the lack of a rapid and feasible diagnostic for congenital Chagas disease. Moreover, in June 2016 the WHO and experts on Chagas disease based in Latin America regarded a point of care diagnostic for congenital Chagas as their top priority in terms of the diagnostic needs for Chagas disease. The diagnostic needs were ranked following considerations of existing diagnostic tools and the expected clinical and epidemiological scenario of Chagas disease in the next five years. </p>
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  <h2>Treatment</h2>
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  <p>An 8 week course of benznidazole or nifurtimox can be used to kill the parasite and treat Chagas disease. The younger the patient and the closer to acquisition of the infection, the higher the probability of parasitologic cure. Therefore, newborns with congenital Chagas disease have the greatest chance for cure, with data from Argentina indicating that the cure rate is higher than 90% if treatment is given within the first year of life. In most cases the potential benefits of medication in curing, preventing or delaying the Chagas is balanced against the possible adverse reactions that occurring in up to 40% of treated patients. However, newborns are least affected by side effects of  benznidazole or nifurtimox, due to the lower weight-accounted dosage, making treatment a very viable option. If the chronic phase is left untreated, additional specific treatment for cardiac or digestive manifestations may be required.</p>
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  <h2>References</h2>
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  <p>http://www.who.int/chagas/strategy/en/ <br/> https://www.hindawi.com/journals/bmri/2014/401864/ <br/> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618875/ <br/>
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552304/ <br/> https://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&doptcmdl=Citation&defaultField=Title%20Word&term=Marin-Neto%5Bauthor%5D%20AND%20Pathogenesis%20of%20chronic%20Chagas%20heart%20disease
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<br/> http://emedicine.medscape.com/article/214581-treatment?pa=8NzeMcIsf2L2NYDeJvy4ZoO1LWEPOwX7vVdtvcVUJoOYwMyg61ZQ3PAOKQ1pIwNHbOMFnZcMllAKcR9rY0RREHf7Bj2Gvk6BKC47oRZ1BB8%3D </p>
  
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<p>What safety procedures do you use every day in the lab? Did you perform any unusual experiments, or face any unusual safety issues? Write about them here!</p>
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Revision as of 17:51, 28 October 2017


Chagas Disease

Introduction

Chagas disease is a neglected tropical disease named after a Brazilian scientist, Carlos Chagas, who first described the life cycle of the parasite – Trypanosoma cruzi (T.cruzi) that causes the disease. Chagas is primarily transmitted via the faeces of triatomine bugs, when they take a blood meal. Other forms of transmission include:blood transfusions orally via ingestion of contaminated fluids vertical transmission Chagas is endemic to Latin America but increased migration of infected people has led to it spreading to non-endemic countries, consequently increasing the number of people susceptible to the disease and causing it to be a growing global concern.

Since the 1990s, strategies to reduce the impact of Chagas in endemic countries have largely focused on preventing transmission through vector control programmes and blood banks. Although these achievements have significantly reduced its incidence, they are not sufficient to combat the spread of the disease vertically from a mother to her child. Therefore, congenital Chagas Disease is growing in epidemiological importance, as it is now one of the most persistent form of the transmission among the human population, with prevalence in some rural areas of Bolivia being as high as 70.5%.


Parasitology

T.cruzi follows the life-cycle shown in the diagram above:

All life stages of T.cruzi secrete a specific protease, known as cruzipain, which allow the presence of the trypomastigotes to be detected by our biosensor. However, the levels of trypomastigotes in the human blood falls with time after infection, as shown in figure 2.

Figure 2. Scheme of evolution of T.cruzi trypomastigotes in the blood of a human host

Within 4-8 weeks of being bitten, adults move from the acute phase of Chagas disease to the chronic phase if untreated.

During the chronic phase, cruzipain levels are very low in the blood and cost effective diagnosis of adults focuses on detecting antibodies specific to T.cruzi. However, antibody based diagnosis is unsuitable for newborns who lack a fully developed immune system. Newborns infected with congenital Chagas disease remain in the acute phase for up to 9 months, during which period there is no current cost-effective diagnostic available. We hope to fill this gap in the ability to diagnose congenital Chagas disease in newborns, using synthetic biology to create a specific protease detection system.

Symptoms and current diagnosis

Diagnosis of Chagas disease is difficult, as the disease is mostly asymptomatic in the acute phase and for the majority of the chronic phase. However, prolong onset of the chronic phase leads to 30% of patients develop cardiac disorders and up to 10% develop digestive, neurological or mixed alterations that cause 1200 deaths per year. The main diagnostic methods currently used to diagnose Chagas are summarised in the table below:

Test How it works Benefits Limitations Suitable for newborns
Whole parasite microscopy
  • Preparation of Giesma blood smears
  • Visualised using light microscopy
  • Established method
  • Carried out by already trained professionals
  • Not suitable for the when there is little T.cruzi in the blood
  • Not always possible to differentiate between T.cruzi from T.rangeli, which does not cause disease in humans.
 Yes
Polymerase Chain Reaction (PCR)
  • Molecular detection of T. cruzi DNA is performed using a combination of three real-time PCR assays.
  • Acceptable specimen types are EDTA blood, heart biopsy tissue or cerebrospinal fluid.
  • Allows high sensitivity in the acute phase
  • Allows the presence of T.cruzi to be accurately distinguished from T.rangeli
  • Allows direct detection of infection and easy interpretation of results
  • High variation in accuracy and lack of international quality controls
  • High cost and complexity means it is not practical to use in a clinical practice
  • Further validation is needed to prove whether PCR is suitable to diagnose the chronic phase of Chagas
 Yes
Serological tests
  • Detection of antibodies against T.cruzi
  • Includes techniques such as indirect fluorescent antibody (IFA) test, a commercial enzyme immunoassay (EIA) and immunochromatographic tests
  • Can be used for acute phase and chronic phase
  • High specificity and sensitivity
  • Commercialised and approved for use by WHO
  • Low-cost formats are available
  • Cross reactivity can occur with diseases, such as leishmaniasis and schistosomiasis
  • Performance of these tests is lower than reported by their manufacturer, especially against specific strains of T. cruzi
  • Not suitable for immunocompromised patients and newborns
 No

The table highlights the lack of a rapid and feasible diagnostic for congenital Chagas disease. Moreover, in June 2016 the WHO and experts on Chagas disease based in Latin America regarded a point of care diagnostic for congenital Chagas as their top priority in terms of the diagnostic needs for Chagas disease. The diagnostic needs were ranked following considerations of existing diagnostic tools and the expected clinical and epidemiological scenario of Chagas disease in the next five years.

Treatment

An 8 week course of benznidazole or nifurtimox can be used to kill the parasite and treat Chagas disease. The younger the patient and the closer to acquisition of the infection, the higher the probability of parasitologic cure. Therefore, newborns with congenital Chagas disease have the greatest chance for cure, with data from Argentina indicating that the cure rate is higher than 90% if treatment is given within the first year of life. In most cases the potential benefits of medication in curing, preventing or delaying the Chagas is balanced against the possible adverse reactions that occurring in up to 40% of treated patients. However, newborns are least affected by side effects of benznidazole or nifurtimox, due to the lower weight-accounted dosage, making treatment a very viable option. If the chronic phase is left untreated, additional specific treatment for cardiac or digestive manifestations may be required.

References

http://www.who.int/chagas/strategy/en/
https://www.hindawi.com/journals/bmri/2014/401864/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618875/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552304/
https://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&doptcmdl=Citation&defaultField=Title%20Word&term=Marin-Neto%5Bauthor%5D%20AND%20Pathogenesis%20of%20chronic%20Chagas%20heart%20disease
http://emedicine.medscape.com/article/214581-treatment?pa=8NzeMcIsf2L2NYDeJvy4ZoO1LWEPOwX7vVdtvcVUJoOYwMyg61ZQ3PAOKQ1pIwNHbOMFnZcMllAKcR9rY0RREHf7Bj2Gvk6BKC47oRZ1BB8%3D