Wednesday, October 16, 2019

Pittsburgh Research Team Uses Rapid Diagnosis Technology to Tackle HIV Testing Problems

As associate medical director of clinical immunopathology at the University of Pittsburgh Medical Center, Sarah Wheeler has received many calls from clinicians about diagnostic testing in the hospital, including those dealing with human immunodeficiency virus.

However, one call made her realize the limits of modern medical technology.

“We received a call from (UPMC) Magee–Womens Hospital that a woman was in active labor with no prior medical history and no baseline infectious disease testing, and we didn’t have any tests that could provide us an accurate result for her HIV status that could be done rapidly,” said Wheeler, who is also an assistant professor of pathology at Pitt.

This isn’t an uncommon scenario, but it was the event that led to Wheeler and other Pitt researchers taking action. She, along with Michael Shurin, a fellow professor of pathology, and Alexander Star, professor of chemistry at Pitt, are creating a testing device that will be able to determine in one minute whether a patient is infected with HIV. Currently, early HIV screening takes 1,440 minutes — an entire day.

Michael Shurin, professor of pathology, is part of the team that created the HIV Detective, a device for giving a rapid diagnosis for HIV infection.
“We thought, ‘We should be able to do something better,’” Shurin said.

Shurin’s tenure in the clinical laboratory took him through the earliest tests for HIV, and he has seen the progress to date in these tests as helpful, but inadequate for the clinical situations he now faces as division director of clinical immunopathology. Building on his decade-long collaboration in cancer research with Star, Shurin started pulling together a team to tackle this problem.

The HIV Detective is the team’s solution to the need for early and rapid diagnosis of HIV. It is a testing platform that would fit in the palm of a hand and allows health care workers to gather a few drops of blood from a patient onto a sensor smaller than Roosevelt’s ear on the dime and provides an HIV screening result in one minute.

This leap forward in testing is possible due to another recent project from the Star laboratory, a working THC breath test.

The THC-detection technology hinges on carbon nanotubes, tiny tubes of carbon 100,000 times smaller than a human hair, which are capable of conducting electricity and monitoring molecular interactions.

“Think of it like wires connected to molecules,” said Star. “The detection is really fast.”

Using the same technology in the HIV Detective means the team members don’t have to wait for the lengthy and insensitive chemical reactions currently used in testing; they can get real-time results from HIV antigen-antibody binding. This allows for a fast and accurate test, as Star’s team has demonstrated with their successful breathalyzer test that also helps in diagnosing and monitoring Type 1 diabetes in patients.

The technology also would allow the team to make the HIV Detective device cost-efficient, which could benefit HIV patients in other countries who cannot afford access to testing. About 34 million people worldwide have the virus.

Patients are most infectious when they first contract HIV, but current rapid tests do not detect HIV in this acute stage — about two to four weeks in. According to the Centers for Disease Control and Prevention, of the 1.1 million people who have HIV in the U.S., about 20% remain unaware they have the virus during this stage because they show no symptoms.

It was this message that helped the HIV Detective team win a $100,000 grand prize from the 2019 Pitt Innovation Challenge (PInCh), hosted by Pitt’s Clinical and Translational Science Institute (CTSI). The prize money will enable the team to create a prototype and use it for clinical trials.

“Our ultimate goal is approval from the Food and Drug Administration, so it can be used across the country,” Wheeler said.

“The PInCh competition provides the opportunity for University teams to identify important medical and public health problems and address those problems with unique solutions,” said CTSI director Steven Reis, who also is associate vice chancellor for clinical research and health sciences, and a professor of medicine at Pitt. “This year’s winners — including HIV Detective — proved, once again, that through creative thinking by diverse research teams, discoveries can be applied to address real world health challenges.”

FDA Allows Marketing of First Rapid Diagnostic Test for Detecting Ebola Virus Antigens

The U.S. Food and Drug Administration allowed marketing of a rapid diagnostic test (RDT) to detect Ebola virus antigens (proteins) in human blood from certain living individuals and samples from certain recently deceased individuals suspected to have died from Ebola (cadaveric oral fluid). The OraQuick Ebola Rapid Antigen Test is the first rapid diagnostic test the FDA has allowed to be marketed in the U.S. for the Ebola Virus Disease (EVD). The test provides a rapid, presumptive diagnosis that must be confirmed.

“Today’s marketing authorization provides another important tool in the effort to fight Ebola, which continues to be a priority of the U.S. Government, especially as we work with our partners, including the World Health Organization, to help address the current Ebola outbreak in the Democratic Republic of Congo (DRC),” said Acting FDA Commissioner Ned Sharpless, M.D. “The current outbreak in the DRC has already killed thousands and the outbreaks in West Africa that began in 2014 tragically killed more than 11,000. Investigational vaccines and therapeutics have shown promising results, but one of the most important tools in stopping these outbreaks is quickly diagnosing patients and supporting safe and dignified burials. This marketing authorization may provide additional assurances to health care professionals seeking to use these types of rapid diagnostics. The ability to use this test to promptly make a presumptive Ebola diagnosis could help providers to more quickly isolate patients and begin treatments that can be potentially life-saving. Additionally, this device could be used to support safe and dignified burials while helping to reduce the risk of transmission during those burials.”

EVD, which is caused by the Ebola virus, is a severe, often fatal disease in humans that can spread through direct contact with blood or body fluids or objects contaminated with body fluids, as well as from the bodies of those who have died from the virus. EVD has led to several large outbreaks in Africa, including the West African Ebola epidemic that began in 2014 and was the largest outbreak of EVD in recorded history, and the ongoing outbreak in the DRC, which is currently the second largest outbreak. Extensive efforts are underway by the Ministry of Health in the DRC to contain the current outbreak with support from the World Health Organization, the U.S. government, and other partners. These measures include campaigns to promote good hygiene, large-scale vaccination campaigns, specialized Ebola treatment centers where those infected or exposed to the virus can receive investigational therapeutics, and comprehensive efforts to trace and prevent the spread of EVD through vaccination campaigns, monitoring for symptoms, diagnostic testing, and implementation of infection prevention and control measures, such as safe and dignified burial procedures.

During the 2014 outbreak, the Secretary of the Department of Health and Human Services declared that circumstances exist justifying the authorization of emergency use of in vitro diagnostics for detection of Ebola virus. At the time, the FDA worked with CDC and test developers to make diagnostic tests, including the OraQuick Ebola Test, available through the Emergency Use Authorization (EUA) pathway. This pathway allows the FDA to temporarily authorize the use of unapproved medical products to address a public health emergency when specific conditions are met, including that there are no adequate, approved and available alternatives to the product for diagnosing, preventing, or treating the disease or condition. The FDA has authorized a number of diagnostic tests for EVD under the EUA pathway to assist with the public health response. Today’s marketing authorization of the first EVD presumptive rapid diagnostic test for Ebola virus antigens through the De Novo review pathway reflects the ongoing collaboration between the U.S. Government and test developers to gather additional data on EUA products.

For the OraQuick Ebola Test submission, the FDA reviewed data from multiple clinical studies of blood samples and cadaveric oral fluid from the 2014 West African outbreak and from a variety of analytical studies. Based on these data, the FDA determined that general and special controls were necessary to provide a reasonable assurance of the safety and effectiveness of the OraQuick Ebola Test when intended to identify antigens associated with Ebola virus in blood from symptomatic patients and oral fluid of cadavers. The amount of Ebola virus when patients have severe symptoms of EVD is usually high; however, the amount of virus in samples taken early after infection when symptoms are not present yet or taken early during the course of EVD when symptoms are mild can be very low. The studies demonstrated the importance of testing only symptomatic individuals so that the amount of virus is high enough to be detectable by this test. Therefore, the OraQuick Ebola Test is intended for use in patients suspected of and with signs or symptoms consistent with EVD, and when the patient meets the CDC’s Ebola virus epidemiological criteria, such as history of residence in or travel to a geographic region with active EVD transmission at the time of travel. The OraQuick Ebola Test is not intended to be used for general Ebola infection screening (e.g., airport screening) or testing of individuals at risk of exposure without observable signs of infection.

The OraQuick Ebola Test may also be used in recently deceased individuals (cadaveric oral fluid) with epidemiological risk factors (including geographic locations with high prevalence of EVD) suspected to have died of EVD to inform decisions on safe handling of cadavers to prevent disease transmission.

Negative results do not rule out Ebola virus infection. The definitive identification of EVD requires additional testing and confirmation procedures (such as by a more sensitive but less rapid polymerase chain reaction test) and in consultation with public health and/or other authorities to whom reporting is required.

The OraQuick Ebola Test was reviewed under the De Novo premarket review pathway, a regulatory pathway for low-to-moderate-risk devices of a new type. Along with this marketing authorization, the FDA is establishing criteria, called special controls, that determine the requirements for demonstrating accuracy, reliability and effectiveness of tests intended to identify Ebola virus antigens. These special controls, when met along with general controls, provide a reasonable assurance of safety and effectiveness for tests of this type. This action also creates a new regulatory classification, which means that subsequent devices of the same type with the same intended use may go through the FDA’s 510(k) pathway, whereby devices can obtain clearance by demonstrating substantial equivalence to a predicate device.

The OraQuick Ebola Test was granted Breakthrough Device designation, meaning the FDA provided intensive interaction and guidance to the company on efficient device development, to expedite evidence generation and the agency’s review of the device. To qualify for such designation, a device must provide for more effective treatment or diagnosis of a life-threatening or irreversibly debilitating disease or condition, and meet one of the following criteria: the device must represent a breakthrough technology; there must be no approved or cleared alternatives; the device must offer significant advantages over existing approved or cleared alternatives; or the availability of the device is in the best interest of patients.

The FDA granted marketing authorization of the OraQuick Ebola Test to OraSure Technologies, Inc.

Microfluidic Device for Rapid Lyme Disease Diagnosis

Researchers at Columbia University have developed a microfluidic device that can diagnose Lyme disease in as little as 15 minutes. The device is particularly accurate in identifying antibody biomarkers that are present during early stage Lyme disease, raising hopes that it could be useful in detecting cases of early infection in a doctor’s office, leading to timely treatment.

Lyme disease, which is spread by infected ticks, is incredibly common. Approximately 300,000 Americans are diagnosed with the disease each year, and if left untreated it can result in serious neurological and cardiac symptoms. The disease is difficult to spot, as many of the early symptoms are similar to those found with other conditions.

Diagnosing and treating the disease early is important in achieving good patient outcomes, but the current diagnostic tests require both an ELISA and a western blot, which are cumbersome, take a while to perform, and require trained laboratory specialists. Moreover, the accuracy of these tests in identifying early cases of Lyme disease is quite poor.

Zoomed photo of fluid moving through a small channel in the new microfluidic chip.
To address these issues, the Columbia researchers developed a point-of-care microfluidic test for Lyme disease, which a doctor could use in their office, and which can provide a diagnosis within just 15 minutes.

“Our findings are the first to demonstrate that Lyme disease diagnosis can be carried out in a microfluidic format that can provide rapid quantitative results,” said Sam Sia, a researcher involved in the study. “This means that our test could easily be used directly in a doctor’s office, obviating having to send the samples out to a laboratory that needs at least a couple of hours, if not days, to get test results.”

The new assay detects three biomarkers of Lyme disease in patient samples, and demonstrates greater sensitivity than traditional Lyme detection assays. Excitingly, the device also appears to be better at detecting early stage Lyme disease and can detect antibodies that are present in the blood in the first few weeks after someone contracts Lyme disease.

“While the assay will require more refinement and testing before it can be approved for widespread use as a test for Lyme disease, our results are very exciting,” said Siddarth Arumugam, another researcher involved in the study. “It will help so many people if we can develop a single, rapid, multiplexed diagnostic test to identify Lyme disease stage that can be used in doctors’ offices.”

Reference: A Multiplexed Serologic Test for Diagnosis of Lyme Disease for Point-of-Care Use

Wednesday, August 07, 2019

Researchers Use Electrical Signalling to Detect Bacteria

Researchers at the University of Warwick have found bacteria can be detected in minutes by zapping them with electricity.

Scientists at the university in the United Kingdom discovered healthy bacteria cells and those inhibited by antibiotics or UV light show different electric reactions. When zapped with an electrical field, live bacteria absorb dye molecules causing the cells to light up so they can be counted. Bacillus subtilis and E. coli were used as model organisms.

Testing commercial products for bacterial contamination can take days. During this time, they can cause significant numbers of illnesses and infections can become life threatening if not identified and treated appropriately.

The researchers’ findings, published in Proceedings of the National Academy of Sciences of the United States of America, could lead to development of medical devices that can rapidly detect live bacterial cells, evaluate the effects of antibiotics on growing bacteria colonies, or identify different types of bacteria and reveal antibiotic-resistant bacteria. One target is quality control in the water, pharmaceutical, food, and beverage industries.

James Stratford, from the School of Life Sciences and spinout company Cytecom, said “the system we have created can produce results which are similar to the plate counts used in medical and industrial testing but about 20 times faster. This could save many people’s lives and also benefit the economy by detecting contamination in manufacturing processes.”

Scientists showed bioelectrical signals from bacteria can be used to determine if they are alive or dead. The approach uses membrane-potential dynamics and electrical stimulation to differentiate between incapacitated and viable cells.

The team developed an experimental tool to study the relation of bacterial electrical signaling. Using it combined with time-lapse microscopy, they showed live and inhibited cells respond to electrical stimulation in opposite directions. A 2.5-second electrical stimulation caused hyperpolarization in unperturbed cells while inducing depolarization in inhibited cells.

Findings offer an approach for rapid detection of proliferative bacteria without observation of actual proliferation or time-consuming calibrations for bacterial species. It can detect proliferative cells within a minute after electrical stimulation.

Researchers founded a start-up company called Cytecom. The firm has been awarded a grant from Innovate UK, a national funding agency, which means devices could be available to researchers and businesses shortly.

The team combined biological experiments, engineering and mathematical modelling.

“This work demonstrates that bacterial electricity can lead to societally important technology, while at the same time gaining fundamental insights into our basic understanding of cells. The tool we developed can offer more opportunities by allowing experiments which were not possible to perform before,” said Munehiro Asally, assistant professor at the University of Warwick.

NC State Developing New Technology that will Help Farmers Detect Plant Pathogens

The fresh food in your grocery stores could eventually get cheaper thanks in part to new technology being developed at NC State that’ll help farmers protect their crops better and apply just the right amount of chemicals to prevent disease.

When a crop gets diseased, it can spread really quickly in a field, so it’s essential for farmers to detect problems fast.

But, traditional methods of disease detection can take weeks. Now a team of NC State researchers have come up with something that’s much quicker and portable.

The device literally smells disease.

Currently, it’s being tested in a lab run by assistant professor Qingshan Wei of the Emerging Plant Disease & Global Food Security Cluster at NC State.

They’ve detailed their results in a paper published by the Journal Nature.

Here’s how it works in laymen’s terms.

When a plant is diseased, it will actually give off gasses.

To test their proof of concept, Wei’s team puts part of a tomato plant leaf in a sealed glass tube.

The wait about 15 minutes as the air in the sealed vial becomes saturated with volatiles from the plant.

Once enough gas is collected, a device attached to the back of a cell phone is used to suck the air from the vial into a chamber where it’s analyzed.

The gas reacts with a tiny paper strip that’s coated with chemical dots.

The dots change color based on the disease affecting the plant.

The cell phone user then takes a magnified picture of the strip to be used by them as a reference on what chemical treatments need to be applied to the crops to stop the spread of disease.

“You want to know if it’s a bacterial infection or a fungal infection or other type of infection and guide your treatment steps,” said Wei.

Right now, the sniffer device only works on potato leaves and tomato leaves, but Wei’s team is developing sensors which will work with other crops.

The idea for the sensor was built on previous discoveries by other researchers who found out diseased plants gave off certain gasses.

“The leaf is breathing,” said Wei. “It’s exchanging molecules with the air.”

Right now, a farmers only options for figuring out what’s plaguing a crop is either guesswork or sending a sample to as clinical lab where it can take weeks to figure out the pathogen affecting the plants.

By the time the results are sent back to the farmer, the disease could have ruined an entire field of crops.

Once this lab porotype is fully developed, farmers will be able to use it in their fields to get instant results and can minimize the amount of chemical they apply.

“You want to have a rapid decision if you want to apply a fungicide or not,” said Wei.

Deciding how much and what chemical to apply is important because the less that’s applied is better for the environment.

And, saving a crop early will end up keeping prices lower because farmers won’t lose as much in the field.

Actual use of the sniffer is still about a year or so away because as it still needs a little more testing.

Mesa Biotech to Present Comparative Flu & RSV Detection Analysis with Other FDA-Cleared Molecular Assays at AACC

Mesa Biotech Inc. is a privately-held, molecular diagnostic company that has developed the Accula™ System, an affordable, sample-to-answer, CLIA-waived PCR (polymerase chain reaction) testing platform designed specifically for point-of-care (POC) infectious disease diagnosis. Today, Mesa Biotech announced it will present performance comparisons of its visually read PCR testing platform with other FDA-cleared molecular tests for influenza A/B and respiratory syncytial virus (RSV) assays. The lecture will take place on August 6, 2019 at 1:00 pm in theater 3 of the exhibit hall at the 71st American Association of Clinical Chemistry (AACC) Annual Meeting and Clinical Lab Expo in Anaheim, CA. Additionally, the Accula System's RSV and Flu A/Flu B molecular tests will be on exhibit in Booth 3902 at AACC.

"Antiviral drug treatments are becoming increasingly popular and more widely used. The antivirals work best when taken within 48 hours of symptom onset, therefore highly accurate, POC testing is crucial for healthcare professionals to achieve rapid and accurate confirmation of the infection to enable the best patient outcome," said Hong Cai, Co-founder and Chief Executive Officer, Mesa Biotech, Inc.

Stephen Young, PH.D., Director of Research and Clinical Trials at TriCore Reference Laboratory will present the session titled 'Sample-to-answer, CLIA-waived PCR System with Visually Read Results for POC: Comparative Flu and RSV Detection Analysis with Other FDA-cleared Molecular POC Assays'. The presentation will provide a technology overview and performance characteristics of the visually interpreted, CLIA-waived Accula System that possesses the simplicity, convenience and procedural familiarity of traditional POC rapid immunoassays. Additionally, Dr. Young will provide insight on the user experience with the Accula System.

About Mesa Biotech Inc.

Mesa Biotech designs, develops, manufactures and commercializes next generation molecular diagnostic tests, bringing the superior diagnostic performance of nucleic acid PCR amplification to the point-of-care (POC). Mesa Biotech's Accula™ System consists of a portable, palm-sized dock and single-use, assay-specific test cassettes. This patented system enables healthcare professionals to access actionable, laboratory-quality results at the POC with greater sensitivity and specificity than current infectious disease rapid immunoassay tests. The Accula Flu A/Flu B and the Accula RSV tests have obtained CE Mark in the EU and 510(k) clearance and Clinical Laboratory Improvements Amendments (CLIA) waiver from the U.S. Food and Drug Administration (FDA). Both products are distributed in the US by Sekisui Diagnostics under the Silaris™ brand. Mesa Biotech has also secured a number of strategic agreements for distribution in Europe and Asia.

Using Quantum Dots and a Smartphone to Rapidly Detect Bacterial Pathogens

A combination of off-the-shelf quantum dot nanotechnology and a smartphone camera soon could allow doctors to identify antibiotic-resistant bacteria in just 40 minutes, potentially saving patient lives.

Staphylococcus aureus (golden staph), is a common form of bacterium that causes serious and sometimes fatal conditions such as pneumonia and heart valve infections. Of particular concern is a strain that does not respond to methicillin, the antibiotic of first resort, and is known as methicillin-resistant S. aureus, or MRSA.

Recent reports estimate that 700,000 deaths globally could be attributed to antimicrobial resistance, such as methicillin-resistance. Rapid identification of MRSA is essential for effective treatment, but current methods make it a challenging process, even within well-equipped hospitals.

Soon, however, that may change, using nothing except existing technology.

Researchers from Macquarie University and the University of New South Wales, both in Australia, have demonstrated a proof-of-concept device that uses bacterial DNA to identify the presence of Staphylococcus aureus positively in a patient sample -- and to determine if it will respond to frontline antibiotics.

In a paper published in the international peer-reviewed journal Sensors and Actuators B: Chemical the Macquarie University team of Dr Vinoth Kumar Rajendran, Professor Peter Bergquist and Associate Professor Anwar Sunna with Dr Padmavathy Bakthavathsalam (UNSW) reveal a new way to confirm the presence of the bacterium, using a mobile phone and some ultra-tiny semiconductor particles known as quantum dots.

"Our team is using Synthetic Biology and NanoBiotechnology to address biomedical challenges. Rapid and simple ways of identifying the cause of infections and starting appropriate treatments are critical for treating patients effectively," says Associate Professor Anwar Sunna, head of the Sunna Lab at Macquarie University.

"This is true in routine clinical situations, but also in the emerging field of personalised medicine."

The researchers' approach identifies the specific strain of golden staph by using a method called convective polymerase chain reaction (or cPCR). This is a derivative of a widely -employed technique in which a small segment of DNA is copied thousands of times, creating multiple samples suitable for testing.

Vinoth Kumar and colleagues then subject the DNA copies to a process known as lateral flow immunoassay -- a paper-based diagnostic tool used to confirm the presence or absence of a target biomarker. The researchers use probes fitted with quantum dots to detect two unique genes, that confirms the presence of methicillin resistance in golden staph

A chemical added at the PCR stage to the DNA tested makes the sample fluoresce when the genes are detected by the quantum dots -- a reaction that can be captured easily using the camera on a mobile phone.

The result is a simple and rapid method of detecting the presence of the bacterium, while simultaneously ruling first-line treatment in or out.

Although currently at proof-of-concept stage, the researchers say their system which is powered by a simple battery is suitable for rapid detection in different settings.

"We can see this being used easily not only in hospitals, but also in GP clinics and at patient bedsides," says lead author, Macquarie's Vinoth Kumar Rajendran.

Reference:

Vinoth Kumar Rajendran, Padmavathy Bakthavathsalam, Peter L. Bergquist, Anwar Sunna. Smartphone detection of antibiotic resistance using convective PCR and a lateral flow assay. Sensors and Actuators B: Chemical, 2019; 298: 126849

IIT Guwahati Researchers Develop Tri-Layer Dielectric Organic Field Effect Transistor to Rapidly Detect Bacteria

Indian Institute of Technology Guwahati Researchers have developed a low-cost, hand-held device to detect bacteria. This Research by IIT Guwahati will enable rapid detection of bacteria, which is important not only in healthcare, but also in anti-bioterrorism measures and environmental monitoring applications.

Bacterial infection is a common cause of morbidity and mortality worldwide and despite development of a range of antibiotics, the challenge continues to lie in detecting and diagnosing bacterial infection early on, as present detection techniques tend to be time-consuming.

The research team led by Prof Parameswar K Iyer, Department of Chemistry, and Prof Siddhartha S Ghosh, Department of Biosciences and Bioengineering, IIT Guwahati, has developed this novel, low-cost, bio-compatible sensor that can detect bacteria almost instantaneously without the need for cell culture and microbiological assays. The Organic Field Effect Transistor (OFET)-based bacterial diagnostic device has been shown to have the ability to detect 103 cfu mL-1 of bacteria and distinguish between Gram positive and Gram negative types.

Their work has been patented as well as published in the July 2019 issue of the reputed peer-reviewed Journal of Materials Chemistry A of the Royal Society of Chemistry.

At present, the detection of bacteria in body fluids is done in laboratories. The cells that are derived from the patient are initially cultured or grown so that enough of the bacterial cells are available for microbiological analysis.

Explaining the need to develop faster and easier methods to detect bacteria, Prof. Iyer says, “Current diagnostic processes are frustratingly time-consuming, especially when time is of the essence in administering treatment.” While newly developed techniques such as real time qPCR can detect bacteria faster than conventional assay-based methods, they are restricted by the need for expensive apparatuses and trained personnel. What would be useful are hand-held rapid detection kits like those used for blood sugar monitoring and pregnancy detection.”

The IIT Guwahati team consisting of Dr Anamika Dey, Dr Ashish Singh, Dr Deepanjalee Dutta (all three former PhD scholars from Center for Nanotechnology, IITG), Prof Siddhartha Sankar Ghosh and Prof Parameswar Krishnan Iyer, brings portable bacterial detection kits closer to reality. The sensor detects the charges on the cell walls of bacteria.

Highlighting the functionality of the device, Prof Ghosh said, “It is known that Gram positive bacteria such as S pneumoniae, have different cell wall compositions than Gram negative bacteria such as the common E coli. Such asymmetric cell wall organisations could alter flow of electrons at the channel of OFETs during their detection”.

The important breakthrough by the team was in developing and using an Organic Field Effect Transistor (OFET) to detect this surface charge. The OFET is an electronic device that works on the principle that charges in the vicinity of the channels of certain semiconductors can induce a current in them. Thus, the charges on the surface of the bacterium, induces a current in the OFET, which is registered and read.

The OFET devices developed by the team consists of a unique and hybrid tri-layer dielectric system built on simple glass and flexible PET (a kind of plastic) substrates, and can operate at ultra-low operating voltages. The team has shown that this OFET sensor can not only detect bacteria, but also differentiate between Gram positive and Gram negative bacteria.

“Not only have we shown the sensing capabilities of this portable OFET device, but we have also shown the mechanism by which sensing occurs and elucidated the role of bacterial wall in distinguishing various bacterial types”, added Prof. Iyer on the significance of this latest interdisciplinary research work.

The OFET-based ready-to-use diagnostic tool will facilitate rapid detection and diagnosis at the point of care. The current device is particularly useful for the detection of bacteria primarily for water-borne diseases. These sensors will also be useful in instantaneous detection of time-critical illnesses such as meningitis.

Wednesday, July 03, 2019

Luminex Submits ARIES MRSA Assay for FDA Clearance

Luminex Corporation announced that the company submitted the ARIES® MRSA Assay to the U.S. Food and Drug Administration (FDA) for clearance on Friday, June 28, 2019. The assay is a real-time, quantitative polymerase chain reaction (qPCR)-based, in vitro diagnostic test for the direct detection of methicillin-resistant Staphylococcus aureus (MRSA) DNA from nasal swabs in patients at risk for nasal colonization.

"This submission demonstrates our continued dedication to expanding the menu of clinically relevant and high-value tests that support patient care throughout the world on our sample to answer platforms," said Homi Shamir, President and CEO of Luminex. "Our VERIGENE® II GI Flex and RSP Flex submissions, as well as the commercialization of our new SENSIPLEX™ instrument, remain on track with our previously communicated timelines."

According to the U.S. Centers for Disease Control and Prevention, in 2016, there was approximately one case of MRSA for every 30 people in the U.S. This works out to around 10 million cases of MRSA in the U.S. each year.1,2 Rapid molecular tests for organisms such as MRSA have the potential to aid physicians in reigning in the spread of antimicrobial resistance and the associated negative outcomes for both patients and healthcare facilities by reducing the unnecessary use of antimicrobial therapies, thus allowing for more effective patient management.

The Luminex ARIES® System is a sample to answer, real-time system designed to increase laboratory efficiency, ensure result accuracy, and fit seamlessly into the modern laboratory. The system already offers six FDA and seven CE-IVD cleared assays, as well as the ability to run laboratory developed tests. "This assay will add another foundational test to the ARIES® System, increasing its value for customers and patients," said Shamir.

Chemiluminescence Probes for the Rapid and Sensitive Detection of Salmonella and Listeria

Salmonella and listeria are among the most widely distributed and deadliest causes of foodborne infections. Their rapid and reliable detection on food and industrial food processing equipment is very important. In the journal Angewandte Chemie, scientists have introduced a new, ultrasensitive, chemiluminescence-based method for the direct detection of Salmonella and Listeria monocytogenes. Because of the simplicity and sensitivity, this test is significantly faster than conventional methods and can be carried out in the field.

It is estimated that about a million people per year are infected with salmonella infections in the USA alone. Of these, 380 die. Infections with listeria can also often be fatal. Current testing methods usually require the growth of bacterial cultures in a containment laboratory. A conclusive result based on standard diagnostic techniques generally takes two to six days.

Researchers working with Urs Spitz and Doron Shabat at the University of Tel Aviv, Nemis Technologies AG (Zurich, Switzerland), Zurich University of Applied Sciences, and Biosynth AG (Staad, Switzerland) have now introduced a new and efficient method for the ultrasensitive and significantly faster detection of Salmonella and Listeria. The method is based on chemiluminescence -- the emission of light resulting from a chemical process. The simplicity of the tests allows for both enrichment of the bacteria and their detection in a test tube, with no further sample preparation, so no containment laboratory is required. The chemiluminescence probes have proven to be about 600 times more sensitive than conventional fluorescence probes.

The success of this technique is due to two specially developed probe molecules made by combining a luminescent substance (a phenoxy-dioxetane) with a "trigger." In this form the probe does not light up. The trigger is tailored to the bacteria to be detected: it is recognized by a specific enzyme produced by the pathogen -- a special esterase in the case of Salmonella and a special phospholipase C for Listeria -- that splits it from the luminescent part. This initiates a chemical reaction that causes the luminescent molecule to split off more pieces. The energy released by the reaction is emitted in the form of a very intense green glow. Tests with various bacteria demonstrated that the probe tailored to Listeria test only reacts to Listeria monocytogenes, not to other, non-pathogenic, strains of listeria. The intensity of the glow can be used to quantify the concentration of bacteria. The tests are so sensitive that, for example, a count of ten salmonella can be detected within six hours of enrichment. Even dried bacteria can be swabbed from surfaces and detected.

The researchers are confident that their new method can be used more broadly to develop specific chemiluminescence probes for other bacteria.

Reference

Michal Roth-Konforti, Ori Green, Mario Hupfeld, Lars Fieseler, Nadine Heinrich, Julian Ihssen, Raffael Vorberg, Lukas Wick, Urs Spitz, Doron Shabat. Ultrasensitive Detection of Salmonella and Listeria monocytogenes by Small-Molecule Chemiluminescence Probes. Angewandte Chemie International Edition, 2019; DOI: 10.1002/anie.201904719

Thursday, June 27, 2019

LamdaGen and Arisan Therapeutics Receive a $2 Million NIH SBIR Phase II Grant to Develop a Dual Rapid Point-of-Care Test for Acute Dengue and Zika Viral Infections

LamdaGen Corporation and Arisan Therapeutics announced today they will share a $2 million Phase II Small Business Innovation Research (SBIR) grant from the National Institute of Allergy and Infectious Diseases, a division of the National Institutes of Health (NIH), to develop a high-sensitivity point-of-care (POC) dual diagnostic to detect both acute dengue and Zika viral infections in a single rapid test on LamdaGen's L'AuRa digital diagnostic platform.

The L'AuRa platform enables robust diagnostic testing that is simple, compact and cost-effective with no moving parts. L'AuRa technology can be integrated into designs ranging from miniaturized handhelds to small desktops to lab-based throughput systems, each providing powerful on-the-spot performance of high-sensitivity, rapid and quantitative diagnostic assays.

Global incidence of dengue has grown dramatically in recent decades with half of the world's population now at risk. In fact, incidence of both dengue and Zika are escalating and prone to unpredictable outbreaks due to climate shifts and proliferation of carriers such as mosquitoes and ticks. Currently, an estimated 390 million dengue infections occur annually. Of these, approximately 500,000 cases develop into life-threatening dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS), severe forms of the disease which result in over 25,000 deaths globally each year.

"Early diagnosis of patients with dengue, in particular, is critical for timely clinical intervention and disease control," commented Randolph Storer, CEO of LamdaGen. "Dengue and Zika are closely related and currently there is no FDA-approved multiplex POC test that can differentiate between the two during the acute phases of infection. Our collaborators at Arisan have identified highly specific antibodies for each test, which we are integrating into the development on the L'AuRa platform."

In addition to enabling differentiation between the two viruses, this highly sensitive and quantitative POC assay will have the potential to act as a prognostic for identifying patients at risk of developing severe forms of dengue including DHF and DSS based on concentration of viral antigen found in blood. Early identification of at-risk patients may help reduce mortality and morbidity by enabling immediate monitoring and medical care.

Speaking of the importance of this NIH grant, Ken McCormack, president of Arisan, added, "We are very appreciative of NIH's support and excited to move forward in our collaboration with LamdaGen to develop these potentially life-saving solutions."

About LamdaGen Corporation

Based in Menlo Park, California, LamdaGen is a developer of nano-based plasmonic biosensors and robust diagnostic systems. The company is increasing access to healthcare with its L'AuRa diagnostic platform, a game-changing technology. L'AuRa is an immuno-based platform that combines the high sensitivity and precision of ELISA with the simplicity and speed of lateral flow to enable quantitative and rapid detection of diseases, pathogens and contaminants. LamdaGen licenses its L'AuRa technology to companies in the human diagnostic, companion animal and food safety industries.

About Arisan Therapeutics Inc.

A privately held life science company based in San Diego, California, Arisan was founded to develop therapeutics for neglected and emerging viral diseases, focusing on infectious diseases with the potential for significant impact on public health and those classified as priority biodefense-related pathogens. The company's mission is to identify unmet medical needs and provide appropriate solutions through development, collaboration and partnerships to benefit patients with life-threatening infectious diseases.

Wednesday, June 26, 2019

New Rapid Test Significantly More Effective for TB-diagnosis in People with HIV

A new study has shown a new point-of-care (POC) device to diagnose tuberculosis (TB) in people living with HIV to be substantially (28%) more effective at identifying TB-positive patients than the only POC TB diagnostic device currently available, Alere Determine TB LAM Ag (AlereLAM).

The new Fujifilm SILVAMP TB LAM (FujiLAM) device was shown to be more sensitive than the current POC TB test, at 70.4% compared to 42.3%. This means that FujiLAM has the potential to reduce the number of false negative test results (where someone who has TB incorrectly tests negative). The specificity of the two tests, which measures the likelihood of a test returning a false negative result, was comparable at 90.8% for FujiLAM and 95% for AlereLAM.

There is an urgent need for more rapid, point-of-care diagnostic devises for TB. The challenge is especially important for people living with HIV, because sputum-based tests (which detect TB in saliva and mucous) have consistently demonstrated suboptimal results for immunocompromised individuals.

People living with HIV often have extrapulmonary TB, where the infection has affected parts of the body other than the lungs. This is difficult to diagnose with sputum alone, and severely immunocompromised individuals may have trouble producing the sputum needed for a sample.

Instead of using sputum, both FujiLAM and AlereLAM test for TB in samples of urine, detecting lipoarabinomannan a component of a bacterium found in urine and indicative of TB infection. This present study was conducted to assess the diagnostic accuracy of FujiLAM for the detection of active tuberculosis compared with AlereLAM in hospital patients with HIV.

968 patients from three separate cohorts of hospital in-patients living with HIV in South Africa were included in the final analysis. 62% of the patients were later defined as having active TB, 9% were defined as unknown, and 29% were defined as non-TB.

The median patient age was 35, and the median CD4 count was 113 cells per copy in cohort 1, 153 cells per copy in cohort 2 and 59 cells per copy in cohort 3. Just under half (45%) had a previous history of TB. Cohort 3, which had more people with advanced HIV disease than other cohorts, had the highest sensitivity result at 81% compared to the microbiological reference standard.

Among all patients with a CD4 count less than 100 cells per copy, FujiLAM had a sensitivity of 84.2% compared with 57.3% for AlereLAM. Among patients with CD4 counts over 200 cells per copy, sensitivity was 44% and 12.2% respectively.

The findings are backed up by a previous systematic review carried out by the World Health Organization, which found similar sensitivity and specificity results for the AlereLAM device. The authors conclude that the FujiLAM point-of-care assay could save lives by enabling earlier diagnosis of HIV-associated TB in more inpatients than AlereLAM. But before it can be implemented into clinical practice, further research is warranted and outside of a research laboratory setting.

Authors of the present study led by Tobias Broger and Bianca Sossen, comment, “since AlereLAM has demonstrated survival benefit, FujiLAM might potentially further reduce tuberculosis-related mortality in people with HIV.”

“These findings will inform a WHO policy review for lipoarabinomannan-based diagnostic tests of active tuberculosis. Further research, including prospective and operational studies on the FujiLAM assay in settings of intended use and in additional patient populations, including outpatients with HIV, populations without HIV, and paediatric populations, are needed.”

Metagenomic Sequencing Improves Diagnosis of Neurologic Infections

Metagenomic next-generation sequencing, or NGS, of cerebrospinal fluid can improve the diagnosis of neurologic infections in patients with encephalitis or meningitis, according to findings from a 1-year, multicenter, prospective study published in The New England Journal of Medicine.

During the study, metagenomic NGS identified some infections that clinical testing missed, leading to adjusted treatment in some cases, researchers reported.

“A new clinical metagenomic sequencing test of cerebrospinal fluid is able to diagnose mysterious neurological illnesses in patients that are missed by conventional approaches,” Charles Chiu, MD, PhD, director of University of California, San Francisco’s Abbott Viral Diagnostics and Discovery Center, told Infectious Disease News.

“The metagenomic next-generation sequencing test is a comprehensive test that looks for nucleic acid (DNA and RNA) from all potential pathogens — bacteria, viruses, fungi and parasites. It may be particularly useful for diagnosing neurological infections from organisms that do not grow or grow poorly in culture (eg, viruses, fungi, atypical bacteria such as Nocardia) or rare organisms that are not commonly considered in the differential diagnosis (eg, parasites such as Angiostrongylus cantonensis and Balamuthia mandrillaris, viruses such as St. Louis encephalitis virus and hepatitis E virus).”

According to Chiu and colleagues, the traditional approach to diagnosing neuroinflammatory diseases presents difficulties because of overlapping clinical manifestations of infectious and noninfectious causes, the limited availability and volume of central nervous system samples obtained through invasive procedures and a lack of diagnostic tests for rare pathogens. Because of these challenges, a cause is not identified in half of acute meningoencephalitis cases, they said.

To address this diagnostic need, the researchers enrolled 204 adult and pediatric patients from eight hospitals who presented with idiopathic meningitis with or without encephalitis or myelitis, or both. According to Chiu and colleagues, many patients were severely ill, with 48.5% having been admitted to the ICU. Patients in the study had a 30-day mortality rate of 11.3%, they reported.

Physicians diagnosed 58 infections of the nervous system in 57 patients (27.9%). According to the study, metagenomic NGS identified 13 (22%) infections that were not identified by clinical testing at the source hospital. Out of these 13 diagnoses, eight had a “likely clinical effect,” and seven resulted in treatment adjustments by physicians, the researchers found.

“The highest diagnostic yield resulted from a combination of metagenomic NGS of [cerebrospinal fluid] and conventional testing, including serologic testing and testing of sample types other than [cerebrospinal fluid],” Chiu and colleagues wrote.

T2Candida Diagnostic Test for ICU Patients at Risk for Invasive Candidiasis

Although the diagnostic performance for all tests were modest in regards to the detection of invasive candidiasis in patients in a high-risk intensive care unit (ICU), the combination of the new test T2Candida and blood culture seemed to have the best performance, according to a study published in Open Forum Infectious Diseases.

Blood culture is the gold standard test for invasive candidiasis, comprising candidemia and deep-seated candidiasis, but the sensitivity of this test is low. The average time to blood culture positivity is approximately 2 days, and some studies have associated a 2-day antifungal therapy delay with a more than doubled mortality rate. There is, therefore, a need for rapid diagnostic testing in invasive candidiasis.

Researchers investigated the performance of T2Candida, a new diagnostic test recently approved by the Food and Drug Administration, compared with Candida mannan antigen (MAg), and blood culture for the detection of invasive candidiasis in a study cohort of 126 ICU patients at high risk for invasive candidiasis. Despite 3 days of broad-spectrum antibiotics, the patients still had sepsis. Paired sets of T2Candida, MAg, and blood culture were obtained 2 times per week for a total of 334 sets. Based on a review of patient records, patients were classified into categories of unlikely, possible, likely, or proven invasive candidiasis.

At the time of enrollment, 77% (n=92) of patients were already receiving antifungal therapy (primarily fluconazole 66%). Fifteen patients (11.9%) tested positive by T2Candida (n=11), MAg (n=10), or blood culture (n=4). At inclusion, the T2Candida species distribution was supported by the identification of colonizing isolates or blood culture in 10 of 11 cases (Candida albicans/Candida tropicalis: 8/11 [72.3%] and Candida glabrata/Candida krusei: 3/11 [27.3%]). Patients were classified as unlikely (n=98), possible (n=11), likely (n=6), and proven (n=11).

In patients in the category of proven invasive candidiasis, sensitivity was found as 55%, 45%, and 36% for T2Candida, blood culture, and MAg tests, respectively. In patients with proven or likely invasive candidiasis, the sensitivities increased to 59%, 29%, and 41% for T2Candida, blood culture, and Mag test, respectively. The sensitivity increased to 64%-65% when T2 Candida was combined with one of the other tests; whereas when T2Candida was not included, sensitivity decreased to 53%-55%. The negative predictive value for proven vs others, and proven/likely vs others was similar across all tests (94% to 96% and 90% to 95%, respectively). The positive predictive value for T2Candida in proven cases of invasive candidiasis was 50% compared with 36% for MAg testing. Positive predictive value for these tests respectively to 83% compared with 64%, in patients with either proven or likely invasive candidiasis.

Researchers concluded, “T2Candida was the biomarker that contributed the most to improving the diagnostic sensitivity while retaining a good specificity and [negative predictive value]. This makes it a promising addition to the diagnostic armamentarium. However, our study also suggests that maximal benefit of diagnostic efforts may require that sampling is initiated as early as possible, preferably before initiation of antifungal therapy, when the sensitivity and [negative predictive value] of T2Candida and [blood culture] testing are maximal and probably sufficient for excluding [invasive candidiasis].”

This work was supported in part (test kits were provided, and part of the hourly fee for the ICU doctors spent on patient record review was reimbursed to the ICU departments) by T2Biosystems.

Reference

Arendrup MC, Andersen JS, Holten MK, et al. Diagnostic performance of T2Candida among ICU patients with risk factors for invasive candidiasis [published online March 25, 2019]. Open Forum Infect Dis. doi: 10.1093/ofid/ofz136

New Data Shows That Karius Blood Test Can Non-Invasively Detect Pathogens In Deep Infections

Karius, a life sciences company that delivers genomic insights for infectious diseases, announced new findings that show the potential clinical utility of its Karius® Test to detect pathogens causing serious infections using a simple blood draw. This includes pathogens that are otherwise difficult to culture or identify without an invasive biopsy.

The Karius Test is a non-invasive blood test based on next-generation sequencing of microbial cell-free DNA. It can identify and quantify over 1,000 clinically relevant pathogens including bacteria, DNA viruses, fungi, and parasites.

Applications include complicated pneumonia, immunocompromised patients, and endocarditis.

During an acute infection, pathogens leave microbial cell-free DNA (mcfDNA) in the blood. Even when an infection is localized, mcfDNA from the infection can be detected.

A sample workflow is illustrated below:



"Rigorous clinical studies of the Karius Test continue to show its ability to identify and quantify pathogens from a single blood test," said Karius Co-founder and CEO, Dr. Mickey Kertesz. "In some of the studies, this was the first time that a non-invasive method was able to identify pathogens that were previously only detectable with invasive biopsies."

Below are the five studies Karius presented at ASM Microbe 2019.

1.    Detection of Bartonella species in Culture-Negative Endocarditis using the
       Karius Test, a Plasma Next-Generation Sequencing test for Pathogen Detection

Bartonella species are fastidious, gram-negative bacteria that can cause culture-negative endocarditis (CNE), lymphadenitis, visceral abscesses, and fever of unknown origin. Diagnosis frequently requires sampling of infected tissue. Dr. Asim Ahmed, Karius Medical Director, will present the Karius Test's ability to identify Bartonella species in culture-negative endocarditis and will discuss how the quantitative aspect of the test may offer a means to monitor patient response to therapy.

2.    Next-generation Sequencing of Pathogen Cell-free DNA in Plasma (Karius Test)
       Reveals Nocardia Species Diversity in Clinical Infections

Nocardia can cause pulmonary, brain, skin, or disseminated infections in immunocompromised and immunocompetent patients. Nocardia is difficult to culture and often requires invasive methods for diagnosis. Dr. Asim Ahmed, Karius Medical Director, will present new findings that highlight the Karius Test's ability to uncover new insights on genus complexity of Nocardia species, which can potentially help inform treatment decisions.

3.    Sequencing of Plasma Cell-Free DNA for Pathogen Detection in Prosthetic
       Joint Infections

Currently, identification of pathogens causing prosthetic joint infections typically requires testing tissue directly from the site. In an evaluation of the Karius Test's ability to detect pathogens in prosthetic joint infections, David Danko of Weill Cornell Medicine will present how the Karius Test was able to identify pathogens in prosthetic joint infection cases. These findings highlight the potential of the Karius Test to serve as a non-invasive alternative to detect deep infections.

4.    Evaluation of Karius Plasma Next Generation Sequencing of Cell-free Pathogen
       DNA to Detect and Quantitate Cytomegalovirus, Epstein-Barr Virus, and BK
       polyomavirus

Dr. Tim Blauwkamp, Karius Chief Scientific Officer, will present new findings that show a high correlation between the Karius Test and industry-standard quantitative PCRs for Cytomegalovirus (CMV), Epstein-Barr Virus (EBV), and BK polyomavirus (BKV). These viruses can cause serious complications for immunocompromised patients. The findings highlight the Karius Test's ability to simultaneously detect and quantify CMV, EBV, and BKV.

5.    Improving the Clinical Specificity of the Unbiased Karius Test via Literature Mining

Dr. Lily Blair, Investigative Computational Biologist at Karius, will present the benefits of applying artificial intelligence methods to increase the utility of diagnostic tests for infectious diseases. Using machine learning algorithms, the Karius team processed more than 27 million abstracts from PubMed to compute how likely a microbe was to cause sepsis. Significant clinical specificity improvements are demonstrated by applying this method to the SEP-SEQ study, a study that validated the performance of the Karius Test in 350 patients with suspected sepsis recently published in Nature Microbiology.

A Forgotten Disease': the Diagnostic Test Which Could Revive the Battle to Eradicate Yaws

A rapid diagnostic test to identify yaws, a debilitating skin disease which affects thousands of the world’s poorest children, could reinvigorate efforts to eradicate the illness, experts say.

The molecular test, which detects yaws within 30 minutes, could allow on-the-spot diagnosis in remote regions – eliminating the need to transfer disease samples for hours or even days to high-tech laboratories for expensive tests.

Yaws is a bacterial disease (caused by the bacterium Treponema pertenue) which spreads through skin-to-skin contact and causes skin lesions and ulcers all over the body. Though easily treated with a single dose of antibiotics, yaws still impacts more than 46,000 people globally—75 to 80 percent of whom are children under the age of 15 years old.

It is not fatal but if left untreated, the illness leads to chronic disfigurement and disability.

“Yaws affects children living in very rural, hard to reach communities – there is a saying that where the road ends, that is where yaws begins,” said Laud Anthony Basing, biomedical engineering research graduate at Purdue University in the US, and creator of the rapid test.

“It eats into the skin, into the bones, into the cartilage, and if you do not treat it the child will grow up with deformities or disabilities,” he added.

More than 80,000 suspected cases of yaws were reported to the World Health Organization in 2018, but the real number of infections is likely to be much higher.

Just 15 countries known to be endemic with the disease record cases, but more than 70 other nations which previously saw high rates of yaws no longer track infections.

While most people today have never heard of yaws, it was once the subject of an ambitious eradication campaign.

Between 1952 and 1964, Unicef and the WHO screened some 300 million people for the illness, in a coordinated programme which treated more than 50 million cases. Yaws was on the brink of being wiped out and reports of the disease dropped by 95 per cent.

But eradication efforts were a victim of their own success. Yaws-specific programmes were dismantled and existing health care systems were left to tackle the ‘final cases’. Resources and attention disappeared as other illnesses took priority – yaws and attempts to eradicate it were largely forgotten.

That was until 2012, when a team led by Oriol Mitjà in Papua New Guinea found that a single dose of the antibiotic azithromycin cures yaws within four weeks. The drug is safer and easier to administer than previous treatment Рa penicillin injection in the buttocks.

The discovery led the WHO to renew its strategy to wipe out yaws, setting an audacious goal to eradicate the illness by 2020 – though this target is likely to be pushed back to 2030.

“The question is, did these countries [which no longer report cases] get rid of yaws in the 1950s and 1960s, or do they still have cases in isolated, poor populations where we are not looking?” said Dr Michael Marks, assistant professor and yaws expert at the London School of Hygiene and Tropical Medicine.

“Because there's currently no good estimates in much of the world, it's plausible that numbers [of cases] will actually go up as surveillance improves, before they go down,” he added.

But as the world moves closer to reaching eradication accurate and portable diagnostics are needed to confirm cases.

Currently DNA samples are either taken to laboratories and tested using a complicated technique called polymerase chain reaction (PCR), or rapid syphilis tests are used – the disease has an almost identical genetic makeup to yaws.

But to certify the illness as eliminated and paint a better picture of the global prevalence, a portable but accurate DNA test is required.

“This work is extremely important,” said Dr Kingsley Asiedu, from the WHO’s department of control of neglected tropical diseases. “We will need a molecular test that is deployable in the field soon so we can move from reference labs in cities to tests that can be used to absolutely confirm cases in remote areas.”

“We don’t want to wait until the final cases – the yaws endgame – to have these tests in use,” he added. “I would like to see Anthony’s molecular test developed and used as soon as possible.”

The new rapid yaws-specific diagnostic, which tests a swab of saliva, costs $2 per use and has yielded “impressive results” in small trials, said Dr Basing.

He was one of 30 finalists of the WHO Innovation Challenge – which saw more than 2,400 entries – and showcased the rapid test at the Africa Health Forum in Cape Verde earlier this year.

“Going forward we would like to do larger scale testing with a lot more samples,” Dr Basing said.

“But I think that by the year 2020, we can actually start the yaws eradication process with mass drug administration and with diagnosis and treatment at the same time. If we do this, within a few years we can eradicate yaws,” Dr Basing added.

But not everyone is certain the test is the answer.

“We will probably continue to use PCR in labs as we get to the final cases,” said Dr Marks. “I think this [test] is a valuable contribution and will be useful in many settings, but currently is probably not going to replace PCR.”

New Rapid Test Diagnoses Pneumonia and Other Lower Respiratory Infections

Scientists at UEA and the Quadram Institute have developed a new, rapid way of diagnosing lower respiratory tract infections that could improve patient care and control the spread of antimicrobial resistance.

Lower respiratory infections, such as pneumonia, account for around 3 million deaths worldwide each year, and can be caused by a variety of different microbes.

Current diagnostic methods rely on growing bacteria from patient samples, but this takes two to three days and may still not identify the cause. During this time, patients are given broad spectrum antibiotics, which may not work if the infection is caused by a resistant pathogen and could trigger side-effects. This can also drive the development of antimicrobial resistance.

Dr. Justin O"Grady from UEA's Norwich Medical School and his team at the Quadram Institute have successfully developed a clinical metagenomics test to precisely identify the bacterial causes of lower respiratory infections.

Clinical metagenomics uses modern sequencing technology to study all the genetic material in a patient sample and identify the pathogens present. It can also identify genes that make the pathogens resistant to particular antibiotics.

The new method, developed with colleagues at the Norfolk and Norwich University Hospital and the Earlham Institute, reduces the time to diagnose the precise causes of infection to just six hours.

This allows rapid treatment with targeted antibiotics, resulting in improved patient outcomes whilst reducing the use of broad-spectrum antibiotics and helping in the fight against antimicrobial resistance.

Dr. O"Grady said: "Clinical metagenomics has the promise to revolutionise the diagnosis of infectious diseases, and our study describes the first rapid affordable and accurate clinical metagenomic test that could readily be used on a routine basis in a clinical setting."

The study, published in the journal Nature Biotechnology, overcomes some of the hurdles that have to date held back the widespread deployment of clinical metagenomics.

The method incorporates a step that rapidly and efficiently removes human genetic material from the sample provided by the patient, thereby leaving mainly pathogen DNA for sequencing. Funding for the study came from the Biotechnology and Biological Sciences Research Council, the Medical Research Council and the National Institute for Health Research.

Themoula Charalampous, from UEA's Norwich Medical School, said: "Respiratory samples are difficult to work with because they are mainly comprised of human genetic material. Removing this makes detecting the pathogens easier and reduces the sequencing cost and time."

The researchers worked with Oxford Nanopore Technologies, using their portable MinION sequencing device that facilitated real-time sequencing data generation and analysis. This reduces time-to-result from days to hours.

The pilot method was tested on 40 samples from patients with suspected lower respiratory infections. The team then refined the test to improve its sensitivity and reduce the time from sample to result to six hours and tested on a further 41 respiratory samples.

Dr. Gemma Kay, from UEA's Norwich Medical School, said: "The pipeline that we've developed in this study produces data that can be used not only for clinical diagnostics but for public health applications such as outbreak detection and hospital infection control."

The protocol is now being assessed in a larger multi-site clinical trial to evaluate its performance for the diagnosis of hospital acquired pneumonia.

Tuesday, June 04, 2019

Loyola Research Paves Way for Simple Test for Ebola Virus

Existing tests for the deadly virus are inaccurate, expensive and can be challenging to administer, but new research from Loyola University Chicago could lead to a simple filter paper test that changes color if Ebola is present.

The breakthrough is possible thanks to the discovery of two antibodies to the deadly virus and the related Marburg virus by Loyola University Chicago professors Ravi Durvasula and Adinarayana Kunamneni.

Ebola and Marburg viruses can cause severe bleeding and organ failure, with fatality rates reaching as high as 90% in some outbreaks, according to researchers. Major Ebola outbreaks in West Africa from 2013 to 2016 resulted in more than 28,600 cases and 11,325 deaths, according to the U.S. Centers for Disease Control and Prevention. There is no cure or vaccine to treat the diseases.

Both viruses spread through direct contact with bodily fluids of an infected person, monkey, gorilla, chimpanzee or bat. Early symptoms of the diseases mimic that of common diseases, including fever, headache and diarrhea, making the need for a rapid diagnostic test critical, say researchers. Such a test could help curb outbreaks by quickly quarantining infected individuals, but current diagnostic tests are either inaccurate or expensive and require extensive training to administer, according to researchers who say antibodies could be the key to diagnosis.

An antibody is a Y-shaped protein made by the immune system that destroys viruses or pathogens when they invade the body. Using a technology called cell-free ribosome display, researchers generated two synthetic antibodies that bind to all four known types of Ebola and two known types of Marburg viruses, according to a Loyola press release.

Actual viruses were not used in the study, so there was no risk of infection to researchers or the public. Instead, researchers used nonhazardous proteins that sit on the surface of Ebola and Marburg viruses, according to a press release.

Researchers say further study is needed to validate the antibodies’ diagnostic potential. Kunamneni and Durvasula published their findings in the “American Journal of Tropical Medicine & Hygiene,” with co-authors Elizabeth Clarke, Chunyan Ye and Steven Bradfute of the University of New Mexico.

Cepheid Receives FDA Clearance for Same-Day Extragenital Testing for Chlamydia and Gonorrhea

Cepheid announced today that it has received U.S. Food and Drug Administration (FDA) 510(k) clearance for testing throat and rectal specimens with its Xpert® CT/NG test. The test provides fast and accurate molecular detection of chlamydia and gonorrhea, making same-day consultation and treatment possible.

Xpert CT/NG test is an automated in vitro diagnostic test for qualitative detection and differentiation of DNA from Chlamydia trachomatis and/or Neisseria gonorrhoeae. In addition to the new extragenital specimens, Xpert CT/NG is indicated for use with urine, vaginal, and endocervical specimens from symptomatic and asymptomatic patients.

"Xpert CT/NG is the most sophisticated test in its class, yet it can be performed on-demand by virtually any laboratory to maximize the medical impact of the results. Adding throat and rectal sample types addresses a critical unmet need allowing for more complete patient screening," said David H. Persing, M.D., Ph.D., Cepheid's Chief Medical and Technology Officer. "Considering the increasing rates of chlamydial and gonorrheal infection, this is particularly important for public health screening programs, to capture patients who previously would have gone undiagnosed if only genital specimens were tested. [1, 2] It is not uncommon for patients to have an infection only in their throat or rectum, which may be asymptomatic. Same day consultation and treatment is critical for patient management so patients are not lost to follow up."

Detection of patients with extragenital gonorrheal and chlamydial infections is critical for optimal treatment of disease and can prevent development of antibiotic resistance in strains due to inadequate treatment regimens that do not cover extragenital sites. [3, 4] This is particularly important for men who have sex with men, where disease may be limited to the pharynx or rectum. Such infections will go undetected if only genital sites are tested. [5] Extragenital disease has also been reported in women. [6]

The clinical study used to validate the new claims was led by Drs. Jeffrey Klausner of University of California Los Angeles and Sarah Doernberg of University of California, San Francisco, and coordinated by the Antibacterial Resistance Leadership Group (ARLG), which is funded and supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number UM1AI104681.*

"Over the last decade, cases of chlamydia and gonorrhea have continued to increase sharply both in the Unites States and abroad necessitating better diagnostics and treatment regimens," said Dr. Jeffrey Klausner, professor of medicine and public health at the University of California, Los Angeles, and lead researcher on the study. "Screening for both genital and extragenital disease with fast turn-around times is critical for optimizing therapy for both male and female populations to reduce the spread of infection."

The Xpert CT/NG test is performed on the Cepheid GeneXpert® Systems. The test's capability to detect DNA from organisms in both genital and extragenital specimens allows for improved screening and detection in patients to ensure infections can be treated in the same day.

About Cepheid

Based in Sunnyvale, Calif., Cepheid is a leading molecular diagnostics company that is dedicated to improving healthcare by developing, manufacturing, and marketing accurate yet easy-to-use molecular systems and tests. By automating highly complex and time-consuming manual procedures, the company's solutions deliver a better way for institutions of any size to perform sophisticated genetic testing for organisms and genetic-based diseases. Through its strong molecular biology capabilities, the company is focusing on those applications where accurate, rapid, and actionable test results are needed most, such as managing infectious diseases and cancer.

*The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

References
  1. CDC. Sexually Transmitted Disease Surveillance 2017. Accessed Mar 2019. https://www.cdc.gov/std/stats17/infographic.htm
  2. Patton ME, et al. Extragenital gonorrhea and chlamydia testing and infection among men who have sex with men – STD Surveillance Network, United States, 2010-2012. Clin Infect Dis. 2014 Jun;58(11):1564-70.
  3. Deguchi T, Yasuda M, Ito S. 2012. Management of pharyngeal gonorrhea is crucial to prevent the emergence and spread of antibiotic-resistant Neisseria gonorrhoeae. Antimicrob Agents Chemother. 56: 4039-4040.
  4. Dukers-Muijrers NHTM, Schachter J, van Liere GAFS, et al. 2015. What is needed to guide testing for anorectal and pharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae in women and men? Evidence and opinion. BMC Infectious Diseases. 15;533:1-13.
  5. Tao G, Hoover KW, Nye MB, et. al. 2016. Rectal infection with Neisseria gonorrhoeae and Chlamydia trachomatis in men in the United States. Clin Infect Dis. 63(10):1325-1331.
  6. Cosentino LA, Danby CS, Rabe LK, et.al. 2017. Use of nucleic acid amplification testing for diagnosis of extragenital sexually transmitted infections. J Clin Microbiol. 55(9):2801-2807.

Lumos Diagnostics and RPS Diagnostics Merge to Support International Commercialization of the FebriDx Rapid Pathogen Test

Lumos Diagnostics, a California-based full-service point-of-care (POC) diagnostic development company and previous spinoff from Australia-based Planet Innovation and RPS Diagnostics, a Florida-based commercial diagnostic developer, manufacturer, and marketer of POC diagnostic tests, announced today that they have merged. The combined company will be called Lumos Diagnostics.

Lumos Diagnostics’ initial focus is on the international launch of the FebriDx® test, a rapid, in-office POC test that incorporates a built-in safety lancet to obtain a fingerstick blood sample, rotating blood collection and transfer system, and integrated push-button buffer activation, to provide clinicians with a rapid assessment of the body’s immune response to an acute respiratory infection (ARI). The single use test identifies patients within 10 minutes that have a clinically significant underlying infection and aids in the differentiation of viral and bacterial ARIs through the simultaneous detection of both Myxovirus resistance protein A (MxA) and C-reactive protein (CRP) directly from peripheral whole blood. MxA is an intracellular protein that becomes elevated in the presence of acute viral infection and CRP is an acute-phase inflammatory protein that is elevated in the presence of clinically significant infection.

Sam Lanyon, chairman of the board for Lumos Diagnostics states, “We have evaluated many technologies over the years, and believe that combining RPS Diagnostics’ novel biomarker technology and commercial experience together with Lumos Diagnostics’ reader-based platform results in a highly strategic and synergistic union that will support a robust pipeline and commercial success.”

ARI are often highly contagious and result in more than half of all antibiotics that are prescribed for outpatient primary and urgent care visits. ARIs may be associated with nonspecific flu-like symptoms, including fever, sore throat, cough, nasal congestion, and fatigue. Bacterial infections pose the highest risk of morbidity and are the only infections that benefit from antibiotic treatment. Diagnostic uncertainty from overlapping ARI symptoms and signs combined with patient or parent pressures for antibiotic prescriptions lead to more than 50% of all unnecessary antibiotic prescriptions. Rapid single pathogen tests, such as for Strep A and Influenza, cannot differentiate colonization from true infection and are indicated for only specific respiratory conditions, accounting for about 15% and 25% of patient visits, respectively; whereas the majority of the patients have other viral infections, bacterial infections, or a microbiologically unconfirmed respiratory illness.

Clinical performance from two prospective multi-center U.S. clinical trials demonstrate the FebriDx test’s high accuracy and 97-99% negative predictive value to exclude a bacterial infection. Moreover, in a small United Kingdom outcome study, FebriDx was shown to alter clinical management decisions in 48% of patients tested and reduced unnecessary antibiotic prescriptions by 80%. By enabling a rapid diagnosis at the initial office visit, the FebriDx test may help to limit the amount of unnecessary antibiotic prescriptions that can lead to avoidable adverse reactions and antibiotic resistance, resulting in lower costs.

Robert Sambursky, MD, the president and chief executive officer of RPS Diagnostics, who will continue in the same role for the joint Lumos Diagnostics entity states, “Using FebriDx to help triage outpatient ARI is a game changer because successful antibiotic stewardship requires the clinician to first rule out a clinically significant bacterial infection. In addition, access to novel Lumos Diagnostics reader technology will facilitate next generation digital enhancements which will accelerate speed to results, allow for quantitation, and enhance objectivity of our branded product lines.”

About Lumos Diagnostics

Lumos Diagnostics provides rapid, cost effective, and complete point-of-care (POC) diagnostic test solutions that utilize proprietary digital reader platforms to help healthcare professionals more accurately diagnose and manage diseases and medical conditions. Lumos provides assay development and manufacturing services for customized POC tests as well as directly develops, manufactures, and will commercialize a suite of Lumos-branded POC tests. Conditions targeted by Lumos tests include infectious and inflammatory diseases with unmet diagnostic needs, including fever, biological threats, and infectious disease, resulting in less unnecessary treatments with associated adverse events, reduced spread of disease, and more effective antibiotic stewardship initiatives.

The FebriDx test has received Health Canada approval, Saudi FDA clearance, Singapore Health Sciences Authority registration, and is CE marked for sale in Europe. At this time, the FebriDx test has not received U.S. Food and Drug Administration (FDA) clearance and is not commercially available in the United States.

PATH, Quansys Bio Develop New Diagnostic Tool for Malaria

PATH and Quansys Biosciences, Inc. have announced the launch of a new diagnostic tool designed to help researchers develop more sensitive and reliable malaria rapid diagnostic tests (RDTs) and to support public health surveillance. The Q-Plex™ Human Malaria Array (5-Plex) is a quantitative immunoassay that simultaneously measures multiple malaria antigens.

With almost half of the world’s population at risk for malaria and more than 200 million cases annually, the disease is a public health priority. Accurate diagnostics are critical to both disease management and public health surveillance. RDTs are a critical tool in malaria case management, particularly in remote settings, providing access to prompt diagnosis.

Many current RDTs function by detecting the histidine rich protein 2 (HRP2) to identify P. falciparum malaria and the Plasmodium lactate dehydrogenase (pLDH) antigen to diagnose P. vivax malaria and all other human malaria species. As RDTs improve in quality, there is a need to understand how these antigens behave in a malaria exposed population so that the performance of these RDTs and their potential to support malaria elimination can be fully assessed.

With a single sample, the Q-Plex™ Human Malaria Array can measure HRP2 and pLDH at low concentrations, as well as quantify P. vivax- and P. falciparum-specific LDH epitopes to distinguish between malaria species and C-reactive protein (CRP) as an indicator of inflammation.

Researchers can use the Q-Plex™ Human Malaria Array (5-Plex) as a reference test to evaluate RDTs in the development pipeline that detect malaria infections with low parasite concentrations and address the challenge of diagnosing P. falciparum malaria parasite strains that do not produce HRP2 and therefore are not detected by RDTs designed to identify the antigen.

“Quansys is excited to continue our partnership with PATH in bringing the power of multiplexing to such important world health issues,” said Chris Lyman, Director of R&D at Quansys Biosciences, “It aligns perfectly with Quansys’ goal to cure the world of communicable diseases by supporting front-line researchers with the most powerful and efficient tools possible.”

“It is important to equip researchers and the public health community with tools like the new Q-Plex™ Human Malaria Array, which has high sensitivity, requires a single sample, and may support higher throughput,” said Tala de Los Santos, PATH’s Global Program Leader, Diagnostics. “These features will assist with the development of improved diagnostics and support use for epidemiologic surveillance.”

The Q-Plex™ Human Malaria Array (5-Plex) is available and can be ordered directly from Quansys Biosciences.

This project is supported by a grant from the Bill & Melinda Gates Foundation.

About PATH

PATH is a global organization that works to accelerate health equity by bringing together public institutions, businesses, social enterprises, and investors to solve the world’s most pressing health challenges. With expertise in science, health, economics, technology, advocacy, and dozens of other specialties, PATH develops and scales solutions—including vaccines, drugs, devices, diagnostics, and innovative approaches to strengthening health systems worldwide.

About Quansys Biosciences, Inc.

At Quansys Biosciences, our teams build and develop customizable multiplex and singleplex protein assay technologies that allow pharmaceutical companies, clinical laboratories, government institutions, universities, and researchers around the world access to large amounts of quantitative data quickly and efficiently. Q-Plex Array Technology has been aiding researchers to better understand disease and improve their biological sample testing since 2005.

Thermo Scientific SureTect Real-Time PCR Pathogen Detection System Extended Validation for Food Pathogens

Thermo Scientific SureTect PCR Assays are now validated to run on the Applied Biosystems SimpliAmp Thermal Cycler and Applied Biosystems QuantStudio 5 Food Safety System, which means a streamlined workflow that requires fewer touchpoints. Laboratories can now work more efficiently and release products quickly and confidently when helping to safeguard the world's food. AOAC PTM and NF VALIDATION certification covers SureTect Assay workflows for the detection of Salmonella species, Listeria species, Listeria monocytogenes, Escherichia coli O157:H7 and Cronobacter species (NF VALIDATION certification only) in a variety of foods and production environment samples.

Heating steps for the SureTect Assay sample preparation process are now fully automated using the SimpliAmp Thermal Cycler, taking just 25 minutes to prepare sample lysates ready for PCR. The SimpliAmp touchscreen interface makes it easy to set up and save the parameters required for SureTect Assays and other applications. When needed, the required program can be recalled and ready to use in seconds.

The Applied Biosystems QuantStudio 5 Food Safety Instrument is a high-performance benchtop platform that gives users greater control of data and combines out-of-the box installation, ease-of-use and system connectivity with powerful options to enable maximum control. The 6-channel, 96-well, cloud-enabled open platform is suitable for running the full range of PCR solutions for food safety, authenticity and quality testing. Combining the QuantStudio 5 Food Safety Instrument with user-friendly Thermo Scientific RapidFinder Analysis software makes SureTect test set-up, running and automatic result interpretation simple and helps avoid errors and subjective result determination.

"This year we are not only extending the validation scope with simplified workflows and access to powerful new instruments, but also expanding the range of SureTect Assays with new kits for additional foodborne pathogen targets important to our customers," said Bernd Hofmann, vice president, marketing, Thermo Fisher Scientific. "We continue to invest in our mission to enable our customers to make the world safer by simplifying food pathogen testing to deliver speed, accuracy and reliability of results. We expect the new SureTect Assays to launch in the second half of the year."

Validation studies to certify the SureTect Assays with the new instrumentation will match the current scope of AOAC-RI and NF VALIDATION certified workflows with the Applied Biosystems 7500 Fast Food Safety System covering an extensive range of food and production environment sample types. In addition, a 375 g milk powders and ingredients category will be added to the SureTect Salmonella species Assay range of NF VALIDATION claims as well as adding the fruits and vegetables category to the SureTect E coli O157:H7 Assay claims.

The new SureTect Assay workflows will follow the same parameters of those already available, including:
  • Single enrichment protocols for faster time-to-result and streamlined workflow
  • Pre-dispensed reagents, reducing handling steps and risk of operational error
  • Universal PCR protocols for detecting multiple targets in the same run
  • User-friendly RapidFinder Analysis software for simple set-up and avoidance of subjective interpretation

Sunday, May 05, 2019

DNA-based PCR Test Accurately Predicts Antibiotic Resistance

A rapid high-throughput PCR test developed by OpGen “accurately and reliably” predicted antibiotic resistance in common bacteria at a rate of 90% or higher, researchers reported.

According to a study published in Antimicrobial Agents and Chemotherapy, the researchers evaluated more than 7,500 highly antibiotic-resistant clinical isolates of Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa for antibiotic-resistance genes and compared them with phenotypic resistance across penicillins, cephalosporins, carbapenems, aminoglycosides, trimethoprim-sulfamethoxazole, fluoroquinolones and macrolides.

“In the most comprehensive study of its kind, OpGen’s informatics technology (Acuitas Lighthouse) rapidly predicted antibiotic resistance to 15 antibiotics accurately and reliably, with an average positive predictive value of 90%,” G. Terrance Walker, PhD, senior vice president of research and development at OpGen, told Infectious Disease News. “On a larger scale, the paper supports a potential breakthrough in the global effort to speed up the rapid detection of antimicrobial resistance.

“Today, phenotypic methods based on bacterial growth are the standard of care. It can take days to provide results to patients. However, DNA testing can be completed in just hours and represents an attractive potential solution. Showing that DNA testing can be used to accurately predict antibiotic resistance has been a critical challenge that scientists have been working on for many years. This paper demonstrates that a well-defined set of DNA markers can potentially be used to perform rapid, accurate antibiotic resistance detection in key pathogens.”

Walker and colleagues reported testing 2,919 E. coli isolates, 1,974 K. pneumoniae isolates, 1,150 P. mirabilis isolates and 1,484 P. aeruginosa isolates, of which 34% originated in hospitals in North America, 23% in Europe, 13% in Asia, 12% in South America, 7% in Africa and 1% in Oceania, according to the study. Another 9% of tested isolates were of unknown origin.

According to the study, they “developed statistical methods to predict phenotypic resistance from resistance genes for 49 antibiotic-organism combinations, including gentamicin, tobramycin, ciprofloxacin, levofloxacin, trimethoprim-sulfamethoxazole, ertapenem, imipenem, cefazolin, cefepime, cefotaxime, ceftazidime, ceftriaxone, ampicillin, and aztreonam.”

The findings revealed that the test’s average positive predictive value for genotypic prediction of phenotypic resistance was 91% for E. coli, 93% for K. pneumoniae, 87% for P. mirabilis and 92% for P. aeruginosa, according to the study.

OpGen expects the first FDA clearances for the test this year, Walker noted.

“In high-risk patients needing urgent care and patients with complicated urinary tract infections, the faster determination of appropriate antibiotic therapy translates to improved health outcomes, lower hospital costs and better antibiotic stewardship,” Walker said. “OpGen’s technology is the application of precision medicine to infectious disease management, which has become more complex with the proliferation of antimicrobial resistance.”