Difference between revisions of "Template:Team:TU Eindhoven/Application scenarios HTML"

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Our gastrointestinal tract houses billions of gut bacteria, called the microbiome. This microbiome outnumbers our own cells by
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The bacteria which make up our life-sustaining microbiota in our guts secrete small molecules to convince the immune system not to attack them. This communication can be seen as one-way-traffic, but the possibility of making it bilateral is interesting, to say the least. See how our device can assist in enabling us to communicate with our gut bacteria.  
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ten to one. Recently, it has become clearer and clearer that the composition of the microbiome plays a major role for many
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pathologies, such as intestinal cancer, Crohn’s disease and even Alzheimer’s. These observations have sparked an interest
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among the synthetic biology community. We have explored how our system can play a role in sensing and imaging the composition of our gut bacteria, where it can eventually play a role in the accurate and early detection of disease.
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Q fever is a zoological disease which is caused by the extremely infectuous pathogen Coxiella Burnetti. In 2007, the Netherlands
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From 2007-2009, the largest Q Fever outbreak ever recorded took place in The Netherlands. Over 4.000 people became infected with the Q Fever causing pathogen Coxiella Burnetii. Q Fever still remains very hard to diagnose, making prevention easier to accomplish than cure. See how our device can help in detecting Q Fever.
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was hit by a major epidemic of this pathogen and it is still a threat today, with 5 goat farms remaining affected. We dived into the disease to see how our modular membrane sensor could play a role in providing an early and accurate detection of the disease.
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Recent agricultural developments have enabled human civilization to expand to the industrial society as we know it today. These developments, however, have not always been harmless. A particular example of a dangerous agricultural development is the overuse of pesticides. These pesticides are used preventively to protect our crops. In an ideal world, these pesticides would only be present where pathogens are present. As a first step towards this ideal world, we have worked out a future application scenario in which our modular membrane sensor plays a major role.</span>
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Agricultural developments enabled civilization to expand to the industrial society we know today. These developments, however, have not always been harmless. The overuse of pesticides as a prevention to protect our crops is an example of a harmful practice. In an ideal world, pesticides would only be present where pathogens are present. See how our device can be a first step towards this ideal world.
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Revision as of 16:28, 13 September 2015





Application scenarios



Using aptamers as recognition elements for our COMBs enables the COMBs to sense virtually all biomarkers for which aptamers have been generated. These targets include toxins, whole cells, viruses and proteins. To give an overview of the huge impact our membrane sensors might have on society, we sketch three scenarios where our COMBs may be applied. For these scenarios, we have reached out to many stakeholders to gain a clear image of what the problems are that society currently faces and how our membrane sensors can play a role in solving these problems.

The bacteria which make up our life-sustaining microbiota in our guts secrete small molecules to convince the immune system not to attack them. This communication can be seen as one-way-traffic, but the possibility of making it bilateral is interesting, to say the least. See how our device can assist in enabling us to communicate with our gut bacteria.
From 2007-2009, the largest Q Fever outbreak ever recorded took place in The Netherlands. Over 4.000 people became infected with the Q Fever causing pathogen Coxiella Burnetii. Q Fever still remains very hard to diagnose, making prevention easier to accomplish than cure. See how our device can help in detecting Q Fever.
Agricultural developments enabled civilization to expand to the industrial society we know today. These developments, however, have not always been harmless. The overuse of pesticides as a prevention to protect our crops is an example of a harmful practice. In an ideal world, pesticides would only be present where pathogens are present. See how our device can be a first step towards this ideal world.

Q fever



Q fever is a zoonotic disease which is caused by Coxiella Burnetti, a pathogen which usually resides in cattle and ticks and can be transmitted to humans through aerosols and animal products. Q fever is a highly infectious disease, as inhalation of a single pathogen can be enough to infect humans. The high susceptibility of humans for the pathogen was recognized by both the Soviet Union and the United States, who devised to use the organism as a biological weapon [1]. The high infectivity also resulted in numerous transient Q fever outbreaks in animals and humans within the European Union. Concerns were raised, however, in the European Union as the Netherlands was hit with the largest outbreak ever recorded with 4,026 human cases notified between 2007 and 2010 [2].


The primary symptom of affected goats and sheep is abortion and reduced fertility. This abortion results in the release of over a billion C. burnetti bacteria per gram of placenta, providing a major risk for public health. Such abortions were first observed in the Netherlands in 2005 at two dairy goat herds. From 2005 till 2007, fif teen Q fever abortions were diagnosed. Q fever had, however, spread through the Netherlands more transiently, as antibody screening showed that C. burnetti antibodies were detected on 57% of the 344 farms [3].

From 2007 onward, the first human cases of Q fever were reported in the province of Noord-Brabant, taking place aft er visits to dairy goat farms where spontaneous abortions had occurred. The epidemic became apparent aft er general practitioners reported on the occurence of pneumonia within patients not responding to standard antibiotics. The outbreak in 2007 marked the beginning of a course of other outbreaks of Q fever throughout the province of Noord-Brabant (see Figure 1). At the moment, still eight of these companies remain infected [4].

Figure 1: Between 2007 and 2010, the Netherlands was hit with the largest outbreak of Q fever ever recorded with 4,026 human cases notified. Most of these cases were reported in Noord-Brabant, the Dutch province in which our university is located. This image was adapted from RIVM.

Transmission



Coxiella Burnetii’s extreme infectivity stems from its ability to shift from a small cell variant to a large cell variant. In the former state, Coxiella Burnetti is metabolically inactive and extremely resistant within the environment. When the small cell variant enters a cell through phagocytosis, it will shift to its active large cell form which is metabotically active (see Figure 2). This metabotically active form will replicate in the Coxiella Containing Vacuole (CCV). Eventually, the metabotically active large variants will undergo sporogenic differentiation to produce the resistant Small Cell Variants. Upon cell lysis, these are released into the environment where they can survive for longer periods and infect other organisms [5]. Figure 2 - Coxiella Burnetii enters the cell through phagocytosis. The bacterium is internalized in the nascent Coxiella Containing Vacuole (CCV), which rapidly merges with autophagosomes and lysosomes. Normally, the acidification of the phagosome results in degradation of bacteria. Coxiella Burnetti, however, is very resistant to numerous harsh environmental conditions. Acidification therefore does not degrade the bacterium: it even triggers the bacterium to become metabolitically active. As a result, the CCV can grow out to a mature vacuole. This image was adapted from Nature Reviews.

Encountering Coxiella Burnetii is usually very rare. The pathogen is, however, considered a ubiquitous zoonotic contaminant and can reside transiently in numerous hosts. It has, for example, been encountered in cats, dogs, cattle, birds and ticks. Even though outbreaks from much of these hosts have been reported, the most important source of Q fever appears to be goats and sheep. It is thus not surprising that goats and sheep were the primary reservoir of Q fever during the outbreak in the Netherlands.

Transmission of the pathogen to mammals can occur in a number of ways. The most important route of transmission to humans is formed by contaminated aerosols. Important sources of these aerosols are goat feces, contaminated wool and a placenta shed by an infected animal [Veterinary]. Due to Coxiella Burnetii’s high infectivity, inhalation of a single infected particle can be enough to be infected by the pathogen (see Figure 3). Figure 3 - The most important source of Q fever infection during the Q fever outbreak in the Netherlands was goat manure. Goats are a perfect reservoir for Coxiella Burnetti and if they are infected, their manure contains the small cell variant of the pathogen. In windy conditions, aerosols of the manure can form which can infect humans once breathed in.

Pathology



The main challenge of diagnosis of Q fever is its atypicality. Contact with Coxiella Burnetti is followed by a 2-3 week incubation period. Aft er the incubation period symptoms may occur, even though most cases of Q fever remain asymptomatic (60%, Veterinary Microbiology). Even if the patient shows symptoms, these symptoms are oft en very atypical. The infection is characterized by the unpredictability and diversity of its symptoms. Examples of symptoms which may or may not occur within a single patient are fever, headaches, hepatitis and meningoencephalitis. This clinical polymorphism impedes an early and accurate detection of Q fever. This is very problematic, as failure to diagnose Q fever early and accurately can lead to the manifestation of chronic Q fever (see Figure 3). Figure 4 - After contact with Coxiella Burnetti, the pathogen enters the cell. After an incubation period of 2-3 weeks, 40% of the patients begin to show symptoms. These symptoms manifestate in a wide range of forms, but pneumonia is by far the most common. The other 60% of the patients do not show acute symptoms. If the infection goes untreated, it may become chronic. This can lead to multiple complications, including abortion and endocarditis.

Biomarkers



Currently, diagnostical tools available for Q fever are aimed at a few biomarkers. The first biomarker is the DNA of Coxiella Burnetii. The DNA can approximately be detected until two weeks after contact with the pathogen within blood samples of the patient. After these two weeks, the patient has typically become immune against the pathogen and the DNA of the pathogen can no longer be found within the patient’s blood. The second biomarker is a direct result of this built up immunity: two weeks after the acute infection, two types of antibodies become detectable in the blood. In contrast to Coxiella Burnetii’s DNA, these antibodies remain detectable within the blood for longer periods (see Figure 5). Figure 5 - After first contact with the pathogen, 40% of the patients fall ill. After the patient falls ill, DNA of Coxiella Burnetti becomes detectable in the blood. This DNA remains detectable for approximately 2 weeks. 1.5 weeks after the acute infection, Phase I-antibodies become detectable in the blood. In an acute infection, this is rapidly followed by detectable levels of Phase II-antibodies. In contrast to Coxiella Burnetii’s DNA, serological tests for antibodies remain positive for more than 12 months after the acute infection. Figure 4 - After contact with Coxiella Burnetti, the pathogen enters the cell. After an incubation period of 2-3 weeks, 40% of the patients begin to show symptoms. These symptoms manifestate in a wide range of forms, but pneumonia is by far the most common. The other 60% of the patients do not show acute symptoms. If the infection goes untreated, it may become chronic. This can lead to multiple complications, including abortion and endocarditis.

Diagnostics



The biomarkers available for Q fever have led to a wide range of diagnostical tools. Conventional tools to detect previous Q fever have been serological tests and skin tests. Both tests, however, have major drawbacks. Serological tests suffer from a higher variability and show long return times. Skin tests also suffer from a higher variability and success of skin tests relies on trained personnel [Specific Interferon gamma Detection]. As an alternative to these tests, interferon gamma detection has been developed. In this test, a blood sample from the patient is taken which is incubated with Coxiella Burnetti antigens. Rather than testing for the presence of antibodies, however, the immunity of the patient is tested by interferon gamma detection, a signaling molecule which is secreted by immune cells upon recognition of the pathogen. The developed test shows similar specificity and sensitivity as skin tests and serological tests. Data is, however, available within 24 hours and the test does not depend on training of personnel.

Both serology and the interferon gamma detection test have a major disadvantage, however, as they rely on immunology of the patient. This is a problem because of the lag phase in antibody response: it takes up to two weeks before a patient’s blood gives detectable levels of Phase I-antibodies. Therefore, these tests can only be used to detect previous Q fever rather than acute Q fever. An alternative test which can be used to detect acute Q fever infection is real-time PCR. During this test, part of Coxiella Burnetti’s genome within the patient’s blood is amplified through PCR. The test is highly specific and very sensitive, but only as long as DNA remains detectable within the patient’s blood. This is a disadvantage since DNA is only detectable for approximately two weeks after the acute infection.

The importance of prevention



Numerous serological tests have been developed to target Q fever. Whereas a wide range of tests has become available to detect previous Q fever accurately, these tests can only be used to detect previous Q fever. Therefore, these tests are very important to map Q fever epidemics by assessing whether a person should be vaccinated or not. These tests, however, fail to address acute infections of Q fever.
A test which can detect acute infections of Q fever, the real-time PCR test, can provide an early and accurate diagnosis of Q fever. The problem with this test, however, is that it relies on the presence of Coxiella Burnetii’s DNA in the blood of the patient. Since this DNA can only be detected for about two weeks after the patient falls ill, such a real-time PCR test should be conducted shortly after a patient falls ill. This is problematic as Q fever’s clinical polymorphism impedes doctors to rapidly recognize Q fever. Therefore, prevention of Q fever infection is often easier to accomplish than cure.

Goat vaccination



In 2009 at the peak of the Q fever outbreak, the Dutch government decided to offer risk groups who lived near animal farms vaccines against Q fever [Q fever perception]. In addition to offering vaccines to risk groups, the Dutch government mandated the culling of pregnant goats at farms which were known to be infected, as pregnant goats presented a major threat to public health. All in all, tens of thousands of pregnant goats were killed to stop the Q fever outbreak, even though it was not tested whether the pregnant goats were infected. The decreasing numbers of human cases of Q fever in 2010 might indicate that the measures taken by the Dutch government have been effective at limiting the Q fever epidemic [Roest].

In addition to culling of ten thousands of pregnant goats in 2009, the Dutch government imposed numerous regulations on goat farms to limit the outbreak. These measures include a mandatory vaccination of dairy sheep and dairy goats, mandatory tank milk monitoring for Q fever every 2 weeks and a ban on removing manure from the farm. Many of these regulations are still enforced: dairy goats and sheep have to be vaccinated yearly, there is a report duty for signs of Q fever and every dairy farm is obligated to take part in a biweekly bulk tank milk test for the presence of Coxiella Burnetti as the milk of infected goats contains DNA from the pathogen. Figure 6 - The milk of goats infected with Coxiella Burnetii contains DNA of Coxiella Burnetii. In addition to the DNA of the pathogen, the milk usually contains the Phase I- and Phase II-antibodies which are active against Coxiella Burnetii. The tank milk test, however, consists of a real-time PCR test as the antibodies are present because of the vaccination of goats.