Saturday, February 21, 2015

EU Suports Development of New Detection Technologies for Bacterial Pathogens

RAPTADIAG is a small or medium-scale focused research project supported by the European Commission under the 7th Framework Programme with Grant agreement no. 304814. It contributes to the programme FP7-HEALTH-2012-INNOVATION-2, topic HEALTH.2012.2.3.0-1: Diagnostics for infectious diseases in humans.

The past two years have seen the consortium turn a novel diagnostic test for bacterial meningitis into what is likely to become a full-blown set of sensor technologies for detecting bacterial pathogens of all kinds.

Whilst the sector has made some giant leaps over the past few years, much contemporary medicine still revolves around symptom-based treatments and costly diagnosis methods. In the case of ‘bacterial meningitis’ (BM), symptoms would usually develop within three to seven days after initial exposure if at all, as some people can carry the bacteria without getting sick. No treatment means a 50 % chance of dying, and the treatment’s effectiveness depends on how soon it is administered.

According to Morten A. Geday, coordinator of the RAPTADIAG (Rapid Aptamer based diagnostics for bacterial meningitis) project and professor, treatment effectiveness is dragged down by the fact that early diagnosis is currently possible only through use of very expensive technologies. Not only are these methods taking too long to give an accurate result, but they are also too complex to be used outside major hospital facilities.

Together with partners from Switzerland and Denmark and thanks to EUR 2.2 million of EU funding, Prof. Geday set out to overcome these obstacles with a fast, easy-to-use and inexpensive diagnostic test for Neisseria meningitides (aka meningococcus) and Streptococcus pneumonia, which are responsible for 80 % of BM cases. He and his team have already developed three groundbreaking technologies, including a microacoustic-resonating sensor and a liquid crystal-based sensor, and are now planning to take their project to the next level.

In this interview, Prof. Geday explains his consortium’s journey since the project started in 2011. He also elaborates on the findings that made them reconsider the project’s raison d’être, from better diagnosis for BM to detection of a much larger spectrum of bacteria, in contexts as varied as food or water borne pathogens entering the food chain, water resources, or even air conditioning units.

What’s so new or innovative about this test? How does it work?

The new diagnostic tests will be faster (minutes rather than hours or days) and cheaper (euros rather than several 10s of euros) than the currently-available technologies. They were intended to address the clinical need for a diagnosis of these diseases with a high degree of morbidity, reducing the possibility of misdiagnosis and abuse of antibiotics.

To enable microorganism recognition, we use novel aptamer receptors rather than conventional antibodies. In a nutshell, aptamers are short single-stranded DNA/RNA molecules which can undertake a three-dimensional structure by intra-strand pairing of the nucleic bases. This structure is then selected based on its high affinity and specificity towards the desired antigen or target.

Three different sensor technologies are being developed in parallel. The first technology is the adaptation of the commercial evanescent biosensor technology (Eva-sensor) using aptamer receptors instead of antibodies. Two more experimental (university-developed) technologies are being employed to develop a rapid test at a significantly lower cost, i.e. a microacoustic-resonating sensor and a liquid crystal-based sensor. The challenge in developing these two sensors was first of all to show that it is possible to develop microacoustic-resonating sensors with the necessary sensitivity, and then that we could develop liquid crystal-based sensors with the potential for single cell detection.

What were the main difficulties you faced and how did you resolve them?

The project has been marred by two problems, one technical and one scientific. Shortly after the kick-off, one of the principal partners went bankrupt. This meant that the project found itself without the possibility of developing the key receptor molecules, i.e. the aptamers. The solution eventually came from one of the partners who took on this responsibility by employing key staff members from the bankrupted partner. The handling of the bankruptcy, the redefinition of responsibilities, and getting the project back up to speed has led to a six-month delay in execution. However, the highly successful development of both the liquid crystal-based sensor and the microacoustic resonators is closely related to the choices we made then.

The second scientific problem is the development of the BM-specific aptamers. As the project is progressing, it is becoming increasingly clear that the necessary affinity and specificity towards the targets will reach the limits of the consortium’s abilities as it stands. To what extent this reflects the limitations of the consortium or the limitations of the aptamer technology is not entirely clear. The workaround is the employment of BM-specific antibodies and existing aptamers targeting alternative pathogens in the testing and validation of the developed technologies.

So you progressively moved away from BM to focus on other types of pathogens. How did that happen?

During the execution of the project, it has become increasingly clear that while the development of cheaper and faster BM detection could impact the detection and subsequent limitation of a BM epidemic in the Third World, the clinical impact in the West would probably be limited.

At the same time, we have realised that the technologies being developed for BM detection have a significant impact on the detection of bacterial pathogens in a large number of contexts, most notably food or water borne pathogens either in the food chain, in water resources or in air conditioning units. Similarly, these technologies may pave the way for novel means of detection of human pathogens in saliva or other bodily fluids.

As a consequence, various proposals aiming to further mature these technologies were presented in the last round of FP7, and a much more ambitious project — which to some extent is building on the experiences gained during RAPTADIAG — is currently being evaluated in a Horizon 2020 Call.

Where do you stand with your objective of delivering at least one commercial product by the end of the project?

The project is well on track. The Eva-sensor can already be purchased, and Davos Diagnostics have proven that their technology is suitable for bacterial detection using aptamer recognition or otherwise. On the other hand, both the microresonators and the liquid crystal sensors are still too immature. These technologies require a strong industrial partner. In the light of the financial situation in Spain, it is unlikely that funding for a spin-off involving the participating scientists can be found, and thus the technology must be transferred to an existing entity. We will, together with the technology transfer office at the University, start looking for potential partners in the near future.

Would you say that the project results meet your expectations?

The project, originally scheduled to finish in June 2015, has already achieved a great number of its objectives. We have proven the use of the aptamers as receptor molecules for bacterial pathogens in the Eva-sensor, resulting in fast and easy pathogen detection (patents pending). At the same time, the microacoustic-resonating biosensor technologies are already approaching the sensibility needed to potentially detect the binding of one microorganism alone, which is the ultimate detection limit, while the liquid crystal sensor is opening the way for an exceedingly simple and inexpensive detection method, with either visual (without the need for any instrumentation!) or simple optoelectronic inspection with miniature readers or even mobile phone cameras. The microacoustic resonators have already been published in various peer-reviewed journals, while a patent has been submitted in order to protect the liquid crystal sensor technology.

Thus from a technological bio-sensor development point of view, the project has vastly exceeded even the participants’ expectations.

When do you think patients and health workers could realistically start benefiting from your findings?

The payback to society will depend to a large extent on the conservatism of the medical sector. It will be immensely difficult even for our finished product, Eva-sensor, to have a significant impact over the next two years, even though Davos Diagnostics, during — and to some extent, thanks to — this project, has become ISO certified. Over the longer term (three to five years), we expect the Eva-sensor to become widespread in hospital wards, providing faster and easier detection of a large number of pathogens and other biological targets. The future of both the liquid crystal and the micro-resonating sensors will entirely depend on the industrial partners that the consortium gets interested in its technologies.

Source: EU Community Research and Development Information Service

WHO Approves Rapid Ebola Test

The United Nations World Health Organization (WHO) today announced that it has approved for use a rapid diagnostic test kit for Ebola that can provide results in 15 minutes and correctly identify 92 percent of patients infected by the disease that has killed more than 9,400 people, mainly in West Africa.

Meanwhile at UN headquarters, Dr. Bruce Aylward, who leads WHO's response on Ebola, and Dr. David Nabarro, the UN Secretary-General's Special Envoy on Ebola, briefed Member States on the need to maintain the robust response to get the number of cases to zero.

“As long as there is even one case of Ebola active in the human population, it's a danger for everybody – it's a problem for West Africa, it's a problem for [wider] Africa and it's a problem for the world, Dr. Nabarro told reporters after their briefing. “We must be fully engaged, all of us, until the last person with Ebola is treated and is cured.”

The two doctors expressed their concerns about the recent slowdown in the pattern of decline in cases over the last four weeks in the three most affected countries of Guinea, Liberia and Sierra Leone.

Referring to a graph showing that the last four weeks has seen more than 120 Ebola cases a week, Dr. Aylward said “this is not what you want to see,” and described the trend as “a very bumpy road” on the wary to zero cases.

They also told reporters that the upcoming rainy season starting in about two months posed as a complicating factor as it could give the virus a chance to get ahead of the response.

Earlier in Geneva, the UN health agency announced that it had “assessed and today listed the ReEBOV Antigen Rapid Test Kit [manufactured by Corgenix Medical Corp of the United States] as eligible for procurement to Ebola affected countries.”

“The test was evaluated under WHO's Emergency Assessment and Use, a procedure established to provide minimum quality, safety and performance assurance for diagnostic products in the context of the Ebola emergency, the announcement said.

The new test, which can provide results within 15 minutes, “is able to correctly identify about 92 per cent of Ebola infected patients and 85 per cent of those not infected with the virus,” according to WHO.

In comparison, Ebola is currently being tested in laboratories largely through the detection of the virus’s nucleic acid (genetic material), using commercial or in-house tests which employ conventional PCR techniques. Nucleic acid tests (NATs) are more accurate but are complex to use and require well-established laboratories and fully trained personnel. In addition, turn-around time can vary between 12 and 24 hours.

WHO Spokesman Tarik Jašareviæ told reporters in Geneva that the new test was a little bit less accurate than the test that WHO was currently using, but it was easy to perform, it did not require electricity and it could be used in lower level health care facilities or in mobile units for patients in remote settings.

The WHO spokesman also said that a number of agencies, such as the Médecins Sans Frontières (MSF), have expressed interest in purchasing it.

The current Ebola outbreak in West Africa has affected more than 23,000 people with over 9,400 deaths, mostly in Guinea, Liberia and Sierra Leone.

Friday, February 13, 2015

Harvard, MIT Researchers Develop Rapid Diagnostic for Virus Detection

Thanks to research by Lee Gehrke, a professor of health sciences and technology, and other researchers at Harvard and MIT, viruses like Ebola may be more rapidly detected and tracked than ever before. The rapid diagnostic, which can detect deadly pathogens in under 30 minutes, is part of an interdisciplinary project supported by the National Institutes of Health.

This invention has grown out years of research at Gehrke’s lab on RNA viruses, viruses that have one-stranded RNA rather than DNA as their genome. Ebola is an example of an RNA virus. The researchers are pairing the rapid diagnostic with a phone application to allow the spread of the viruses to be tracked via real-time maps.


Gehrke said that the goal of the researchers was to develop a rapid diagnostic test that can perform in under 30 minutes and can be used as a point-of-care device to evaluate patients with fevers, which can indicate many different underlying diseases.

“If a patient comes into a clinic and has a fever, you want to be able to rule out some pathogens,” he said. “In West Africa, there are a number of viruses that would present as fever, including Ebola, Lassa, and Marburg, so it is very useful to get a very quick idea of what the patient is suffering from.”

While the Ebola outbreak in West Africa has ascended to international media headlines in recent months, Gehrke warned against ignoring other dangerous viruses.

“Ebola is a terrible disease, but it is not the only one that I think we should be prepared for,” Gehrke added. “There are other emerging viruses that we also need to have a great sense of preparedness for.”

The device is specific for several viruses, including Ebola and dengue fever, and it can detect more than one pathogen at once, according to Gehrke.

“By detecting whether a person’s fever is in fact a symptom of Ebola, the rapid diagnostic can help better quarantine people,” said Kimberly Hamad-Schifferli, MIT professor and senior collaborator on this project.

Gehrke also attested to the value of rapid detection of the virus.

“Being able to detect the virus and identify the people or environments that are contaminated is very important for reducing or stopping the spread. Early detection is important for treatment,” he said.


Unlike other diagnostic tools, the Harvard and MIT-developed device can be operated cheaply by personnel with little training in a variety of settings. Competing approaches, like polymerase chain reaction, require more time and expensive equipment.

“This approach gives much greater flexibility, cost control, and adaptability in responding to outbreaks of different emerging pathogens in different parts of the world,” Gehrke wrote in an email.

Gehrke attributed this flexibility in part to the ability of the device to operate without power or refrigeration. The device does not require specialized chemicals, equipment, or training, researchers said.

“We are interested in making something that can detect disease rapidly and can be operated by an end user, or someone who is not medically trained or a technician,” Hamad-Schifferli said.

The device uses a sample of a body fluid, such as blood, serum, or saliva, to test a patient, Gehrke said. The test operates by diverting the sample in a maze-like structure and making it run into chemicals, said José Gómez-Márquez, director of the Little Devices Lab at MIT and senior collaborator on this research.

According to MIT postdoctoral fellow Justina Tam, who is working on visual markers, or detection agents, for the rapid diagnostic, “the detection agents are agents that have some visible color if they accumulate in a certain area of the test, which means a protein for a specific virus is present in the sample.”

Not only does this visible color indicate whether a patient is infected with a virus, but it also reveals the virus’s specific strain.


According to Gómez-Márquez, aggregating the results of the rapid diagnostic through an accompanying phone app allows researchers to track the spread of viruses in real-time, which he hopes will prevent their spread in the future.

He called the device a crowdsource diagnostic because it relies on many users to send images of their results via the phone app. The diagnostic itself gives a result, but the phone app quantifies it and measures the location of the infectious diseases so that the spread of viruses can be tracked rapidly, Gómez-Márquez said.

“If we can do that for hundreds of patients, then we can get a real-time map of the spread of the disease,” he added.

He said that up to now, maps of the spread of viruses include information of what occurred in the past, based on death records and hospital records that are weeks old. The new technology gives health providers a better understanding of the path viruses could take in the future.

“In public health, we don’t have real-time maps for epidemiology, but that’s important for saving the next lives.The prevailing attitude is looking at the past, which doesn’t allow us to help the future,” he said.

According to Gómez-Márquez, several people are working on the phone app for different platforms, including the Android phone.

According to JN Fang ’16, who is working on an Android version of the app, health workers administering the diagnostic will be able to use the app to read and aggregate the results of the test. The app can determine “if...the change in test strips is enough of a change to indicate that the patient has tested positive for either of the four strains of dengue fever or Ebola,” she said.

After testing the diagnostic in the laboratory, Gehrke said his lab is currently field-testing the device. According to Gehrke, the commercial launch of the device will depend on the regulatory process for approval by the FDA.

This rapid diagnostic will be another tool among “a number of different methods [that] are going to be necessary for detecting and hopefully stopping this virus and other infectious viruses,” Gehrke said.

Source: The Havard Crimson