Tuesday, December 10, 2019

Roche Molecular Systems’ cobas vivoDx MRSA Gets FDA Approval

The US Food and Drug Administration (FDA) has granted marketing approval for Roche Molecular Systems’ cobas vivoDx MRSA, a diagnostic test that detects colonisation of Methicillin-resistant Staphylococcus aureus (MRSA) bacteria.

In contrast to conventional culture-based techniques, the cobas vivoDx MRSA diagnostic test uses new technology for rapid detection of bacterial colonisation of MRSA, a common cause of hospital-acquired infections.

FDA’s Center for Devices and Radiological Health Office of In-vitro Diagnostics and Radiological Health director Tim Stenzel said: “Diagnostics that are able to provide accurate results more quickly can offer health care providers an advantage when trying to prevent and contain the spread of resistant bacteria.

“Today’s authorisation adds a new tool in the fight to prevent and control MRSA in high-risk settings. The FDA remains committed to supporting efforts to address antimicrobial resistance in order to better protect patients against this ongoing public health challenge.”

In the US, nearly 5% of hospitalised patients carry the MRSA bacteria, according to the Centres for Disease Control and Prevention (CDC).

CDC considers MRSA as a severe antimicrobial-resistant threat. If infections develop, they can be challenging to treat as they are resistant to conventional antibiotics.

According to the CDC estimates, more than 323,000 MRSA cases in hospitalised patients, as well as 10,000 deaths in the US.

cobas vivoDx MRSA leverages bacteriophage technology based on bioluminescence to evaluate MRSA from nasal swab samples.

The test evaluates the MRSA bacterial colonisation within five hours, compared to two days through the conventional culture method.

Designed to aid in the prevention and control of hospital-acquired MRSA infections, the cobas vivoDx MRSA test will be to identify patients who require enhanced precautions and decolonisation efforts.

The FDA reviewed the test through the de novo premarket review pathway.

QuantuMDx and Ontera Collaborate to Advance Sepsis Diagnosis

QuantuMDx Group Limited and Ontera, Inc have announced a collaboration to create a next-generation solution for blood stream infection and drug resistance detection. The technology will be based on QuantuMDx’s rapid cell/sample preparation technology, Capture-XT® and Ontera’s powerful nanopore biosensor, currently utilized in their SAM and DUO Nano platforms.

The combined technologies should enable clinicians to quickly interrogate blood specimens of those presenting with sepsis signs and symptoms, allowing guided ‘right first time’ care management, at the bedside.

Sepsis affects more than 30 million people worldwide every year leading to an estimated 6 million deaths.¹  If it’s not recognized early and managed promptly with targeted antibiotics, sepsis can lead to septic shock, multiple organ failure and death.

QuantuMDx’s revolutionary Capture-XT® technology captures, concentrates and enriches targeted pathogens from a large sample volume, quickly enabling visual diagnosis and downstream utilization, such as drug-susceptibility analysis, PCR, NGS and now nanopore detection, with this collaboration.

Ontera’s single pore platform provides fast amplification of multiple bacterial targets, differentiation between antibiotic resistant and susceptible strains. The company uses silicon nanopore for in-minutes quantitative measurement of nucleic acids, proteins and small molecules, avoiding time-consuming laboratory procedures that can delay lifesaving, fast and precise treatment.

“Sepsis is one of the hardest diseases to detect. It’s like looking for a needle in a haystack, due to the low concentration of organisms in the blood stream that cause disease,” says Jonathan O’Halloran, Chief Scientific Officer at QuantuMDx. “Our early prototype testing has already shown sensitivity in the range required for this kind of test and performed in minutes from spiked bacteria in whole blood. We haven’t even pushed the technology yet, but it has the potential to become a paradigm-shifting, powerful device. And, by including drug resistance in the assay to enable right first time prescribing, the impact of this partnership could be profound.”

“Today, 30% of patients receive inappropriate antimicrobial therapy. By not only identifying sepsis but also resistance to most common antibiotics in less than 30 minutes, we will transform the sepsis landscape and impact lives,” says Murielle Thinard McLane, CEO of Ontera. “We have set out on a mission to democratize access to molecular information to create a more sustainable planet. This collaboration with QuantuMDx is a major proof point along that mission.”

Reference: WHO 2019

Sunday, November 24, 2019

Rutgers University Receives 2019 Edison Award for Rapid Test for Drug Resistant Tuberculosis

A milestone patent for a rapid, automated test for detecting Mycobacterium tuberculosis (TB) and Rifampicin-resistant M. tuberculosis invented by two Rutgers University researchers received the 2019 Edison Patent Award from the Research & Development Council of New Jersey. The annual award commemorates the state’s most prolific inventor, Thomas Alva Edison, and celebrates New Jersey’s exceptional inventors.

The invention receiving the Edison Patent Award in the biotechnology category, “Detection of Drug Resistant Mycobacterium Tuberculosis” (U.S. Patent 9,708,671 B2) consists of a technology that shortens the time it takes to diagnose tuberculosis from around seven weeks to less than two hours. Rutgers inventor David Alland, chief of infectious disease at Rutgers New Jersey Medical School (NJMS) and director of the Center for Emerging Pathogens and Rutgers Regional Biocontainment Laboratory, and Soumitesh Chakravorty, adjunct assistant professor at NJMS and director of R&D at Cepheid Inc., have brought new hope for people at risk of TB or with drug-resistant TB.

“I’m gratified, pleased and honored with this award but also humbled to know that this is just a very small part of a very large mission. Tuberculosis has become more drug resistant. There was a clear need for better diagnostic,” says Alland. “Tuberculosis tests were not sensitive enough to detect TB in patients who had a small amount of TB in their lungs and particularly in patents who are HIV positive. We knew that this test was missing people who had tuberculosis and had to be improved on.”

Alland and Chakravorty developed the tuberculosis detection test: the first near-patient, on-demand diagnostic test for a highly contagious and drug resistant form of M. tuberculosis which has been declared as a global emergency. The assay isolates and then uses a polymerase chain reaction (PCR) to amplify M. tuberculosis directly from sputum specimens enabling detection of M. tuberculosis and multi-drug-resistant tuberculosis in less than two hours in a single hands-free step. Rutgers’ technology has been licensed by Cepheid, a molecular diagnostics company, and is now used on a global scale in Xpert® MTB/RIF Ultra (CE in vitro diagnostic medical device not available in the United States).

“It is extremely gratifying and humbling to have my name associated with Edison whose patents keep lighting up our lives,” says Chakravorty. “This test is faster, more sensitive, more accurate and more definitive. We are getting the same results that were taking over six weeks using conventional diagnostics, in 70 minutes. The patent really revolutionized the diagnostics of drug resistant tuberculosis.”

Xpert® MTB/RIF Ultra has been endorsed and recommended by the World Health Organization (WHO) since 2017. According to the latest WHO Global Tuberculosis Report published in 2019, 10 million people developed TB last year and 1.5 million lost their lives to the disease.

Rutgers University is among over 60 winners of the 2019 Edison Patent Awards, which was in its 40th edition. Co-inventors Alland and Chakravorty accepted the award on November 14th at a ceremony held at Liberty Science Center in Jersey City.

The awards for innovative patent work spanned 15 R&D categories, including: information technology, environmental, enabling technology, medical technology, medical device, energy, industrial process, emerging therapy, pharmaceutical, agriculture, telecommunications, biotechnology, smart grid., medical imaging and telecommunication systems.

Recipients of the 2019 Edison Patent Awards included: Avaya Inc., BASF Corporation, Bristol-Myers Squibb, Celgene Corporation, Ethicon, Inc., a Johnson & Johnson Company, ExxonMobil Research & Engineering Company, Honeywell International, Insmed Incorporated, Merck & Co. Inc., New Jersey Institute of Technology, Nokia Bell Labs, Siemens Corporate Technology, Siemens Healthineers, SubCom and Rutgers.

Immunexpress Announces Grant of U.S. Patent Covering the Differentiation of Gram-Positive and Gram-Negative Sepsis-Causing Bacteria

Immunexpress, Inc. announced the U.S. Patent and Trademark Office (USPTO) has granted Patent No. U.S. 10,364,474 B2, which covers single nucleotide polymorphisms (SNPs) in the ribosomal DNA of bacteria and fungi. Immunexpress plans to use the SNPs to identify and classify sepsis microbes in clinical patient samples.

Immunexpress' technology, SeptID™, can identify sepsis-causing bacteria as Gram-positive, Gram-negative or mixed. Treating clinicians use the results of a Gram stain, a technique for the preliminary classification of bacteria, to manage antibiotic treatment regimens for patients suspected of sepsis. However, current methods that rely on microbial growth take approximately 24 hours from blood sample collection to Gram stain results, thereby delaying early and appropriate treatment selection. SeptID™ can accurately determine Gram stain status from a whole blood sample containing a microbe from a sepsis patient in approximately one hour.

Richard Brandon, Ph.D., Chief Scientific Officer of Immunexpress and co-inventor on the patent, said, "For sepsis patients, early and accurate identification of a causative microbe and appropriate antibiotic choice leads to better patient outcomes and reduced hospital costs. The rapid turnaround time of SeptID™ to aid in antibiotic selection means clinicians are better equipped to treat sepsis patients, within a shorter timeframe."

Rolland D. Carlson, Ph.D., Chief Executive Officer of Immunexpress, added, "Our technology lends itself to rapid test development. It is currently formatted for an RT-qPCR machine but is not restricted to a particular technology. Our SeptID™ technology could transform the way clinicians recommend antibiotics for sepsis patients, and we are seeking strategic partners to help us achieve this goal."

About Immunexpress

Immunexpress is a Seattle-based molecular diagnostic company committed to improving outcomes for patients suspected of sepsis. Immunexpress' SeptiCyte™ technology rapidly quantifies, directly from whole blood, specific molecular markers from the patient's own immune system – the 'host response'. SeptiCyte™ LAB, recently cleared by the FDA, is the first of its kind in using the host immune system to differentiate systemic inflammatory response syndrome (SIRS) and sepsis. Detecting the host's response to infection has the potential to differentiate infection earlier, faster and more accurately than finding the invading pathogen because it is independent of whether or not the pathogen is present in the sample. Immunexpress' pipeline includes several sample-to-answer assays for near-patient testing.

Friday, November 01, 2019

Researchers Develop Affordable New Test For Dengue

Researchers have developed a user-friendly dengue test that could help diagnose the growing tropical disease more quickly and efficiently. Every year, nearly 400 million people are infected by dengue, a mosquito-borne disease that continues to spread in tropical climates. While a quarter of those patients will experience flu-like illness, a small fraction could develop severe dengue, a potentially fatal condition.

In a new study, University of Alberta Canada researchers said they have developed an affordable one-step test for dengue that requires just a small blood or plasma sample and a portable tester.

"You could take somebody's blood and run a single test to see what they have," said Ninad Mehta, lead author of the study. "You would know in about two hours what it is." Mehta conducted the study while working in the University of Alberta school of Public Health under Stephanie Yanow, who has spent years working on diagnostic tests for malaria, Medical Xpress reported.

Diagnosis is one of the biggest challenges in treating tropical fevers. Early dengue symptoms resemble malaria, chikungunya, Zika and other diseases. Rapid diagnostic tests can detect antigens or proteins, but they aren't always specific enough and can lead to false positives. More precise diagnosis requires expensive equipment, multiple steps and training. In remote areas where the disease is rampant, it's not always feasible.

Mehta's dengue test would combine the best of both worlds: a highly specific test that's affordable and portable.

It depends on a molecular technique called RT-PCR, which involves finding a stable sequence of viral RNA, translating it into DNA and multiplying the genetic material to the point where it can be detected. It piggybacks on the growing availability of Open PCR machines, a versatile DNA-detection technology that has become cheaper thanks to crowdfunding and open-source technology.

Because there are four distinct variants of the dengue virus, Mehta had to find specific genetic material common to all four but not found in viruses with similar symptoms. He focused on a 253-nucleotide sequence of RNA, which was tested on 126 archived samples from a dengue study in the Philippines. The results were compared with other types of testing.

The test held up well to existing kits, particularly in the first four days of symptoms when the presence of the virus is highest. At under $5 per test, Mehta believes this testing could help public health agencies get better bang for their buck.

"When you start treating one disease, another pops up," Mehta said. "It's a game about shifting resources whenever you can."Mehta hopes his work could help save lives, but he recognizes it still could be years away. Because the new dengue test requires cold chemicals, Yanow's lab is looking at using vacuum-drying to create a powder that could withstand the heat in tropical settings. More work will be needed for field trials.

T2 Biosystems’ T2Resistance™ Panel is First Diagnostic to Graduate from CARB-X Portfolio

T2 Biosystems, Inc., a leader in the development and commercialization of innovative medical diagnostic products for critical unmet needs in healthcare, and CARB-X, a global non-profit partnership dedicated to accelerating early development antibacterial R&D to address the rising global threat of drug-resistant bacteria, announced today that the T2Resistance™ Panel is the first diagnostic to graduate from CARB-X’s portfolio. The graduation marks an important milestone on the path toward approval for use on patients in hospitals in the U.S., Europe and elsewhere around the globe.

In 2017, CARB-X awarded T2 Biosystems $2.0 million to support the development of the T2Resistance Panel, designed to detect 13 resistance genes from both gram-positive and gram-negative pathogens directly from a whole-blood specimen, without the need to wait for blood cultures. The panel was granted Breakthrough Device designation by the Food and Drug Administration (FDA) earlier this year and is expected to be available for research use only (RUO) in the US by the end of Q3 2019 and receive CE-Mark for commercial availability in Europe by the end of 2019.

“Addressing the global superbug crisis requires urgent development of innovative diagnostics, like T2’s technology, as well as new drugs and vaccines. This is the first diagnostic to graduate from CARB-X’s portfolio, and we are excited that we could help T2 with funding and support to develop this technology,” said Kevin Outterson, Executive Director of CARB-X, which is based at the Boston University School of Law. “The T2Resistance Panel will provide healthcare professionals with a new rapid test, a first of its kind, to provide timely and accurate detection of drug-resistant infections and inform treatment decisions to ensure patients are given the most appropriate care.”

“We are incredibly grateful to CARB-X for the funding and support they provided to our team in the development of the T2Resistance Panel over the past year and a half,” said John McDonough, chairman and chief executive officer of T2 Biosystems. “Rapid identification of the genes and species associated with antibiotic resistance can help enable the reduction of unnecessary antibiotic use, which is the primary cause of resistance. Being the first diagnostic to graduate from CARB-X’s portfolio is a significant milestone in the development of technology that has such capabilities.”

The T2Resistance Panel identifies 13 of the most serious superbugs and resistance genes on the antibiotic-resistance threat list published by the Centers for Disease Control and Prevention (CDC), including genes indicating resistance to common empiric antibiotic therapies such as carbapenems, vancomycin, penicillin and more.

Diagnosing infections faster means saving lives and fighting the spread of superbugs

Bacterial bloodstream infections can be deadly even at low concentrations. If bacterial infections are identified quickly, patients can be placed on effective antibiotic therapy faster. T2MR technology enables rapid identification of bacterial pathogens and resistance markers directly in whole blood within three to five hours. Existing diagnostics rely primarily on blood cultures conducted in laboratories, which can take days, and do not always produce reliable results. As a result, physicians are often unable to treat infections quickly with the appropriate antibiotics, leading to higher mortality and use of unnecessary antibiotics.

T2 Biosystems is the company behind the T2Bacteria Panel, which was the first in-vitro diagnostic test to receive approval for a New Technology Add-on Payment (NTAP) by the United States Centers for Medicare & Medicaid Services (CMS). The panel is the only FDA-cleared test to identify sepsis-causing bacterial pathogens directly from whole blood without the need to wait for blood culture, and its counterpart for fungal bloodstream infections is the T2Candida Panel, the first and only FDA-cleared direct-from-whole blood diagnostic for detection of fungal pathogens that are associated with sepsis. Both panels provide results in three to five hours instead of days. The products are two of several panels that are approved or in development that are run on the Company’s T2Dx® Instrument, which is powered by miniaturized magnetic resonance (T2MR®) technology.

The CARB-X graduation news follows the recent announcement that T2 Biosystems has been awarded a milestone-based contract of initial value of $6 million with a potential value of up to $69 million, if all contract options are exercised, from the Biomedical Advanced Research and Development Authority (BARDA), within the Office of the Assistant Secretary for Preparedness and Response (ASPR) at the US Department of Health and Human Services’ (HHS). BARDA is also the main US founder and funder of CARB-X.

Supporting innovation in the race against drug-resistant bacteria

Drug-resistant infections are responsible for an estimated 700,000 deaths worldwide each year, according to the World Health Organization (WHO).

The CARB-X portfolio is the world’s largest early development portfolio addressing drug-resistant bacteria, with 31 active projects. In the three years since its launch, CARB-X has funded and supported 48 innovative projects, for a total obligation of over $139.4 million with the potential of additional funds if project milestones are met. These funds are in addition to investments made by the companies themselves. The CARB-X pipeline will continuously evolve, as projects progress and graduate from CARB-X and others fail for a variety of reasons. The current portfolio supports 13 new classes of antibiotics, 15 new molecular targets, 12 non-traditional approaches including microbiome-based therapeutics, four diagnostics and three vaccines.

CARB-X is investing up to $500 million in antibacterial R&D between 2016-2021. The goal is to support projects in the early phases of development, so that they will attract additional private or public support for further clinical development and approval for use in patients. CARB-X funding is restricted to projects that target drug-resistant bacteria highlighted on the CDC’s 2013 Antibiotic Resistant Threats list, or the Priority Bacterial Pathogens list published by the WHO in 2017.

CARB-X is led by Boston University and funding is provided by BARDA, the Wellcome Trust, Germany’s Federal Ministry of Education and Research (BMBF), the UK Department of Health and Social Care’s Global Antimicrobial Resistance Innovation Fund (UK GAMRIF), the Bill & Melinda Gates Foundation, and with in-kind support from National Institute of Allergy and Infectious Diseases (NIAID).

Portable DNA Sequencer Quickly and Accurately Diagnoses Wheat Viruses

A group of scientists in Kansas, based at The Agricultural Research Service of the US Department of Agriculture (USDA-ARS) and Kansas State University, have developed a new technology that makes it possible to rapidly identify viruses in wheat fields with a higher level of accuracy.

It is said that blast, a disease that results from a fungus that infects the wheat spikes in the field, turning the grain to inedible chaff, cause significant loses in wheat crops. Recently, Bangladesh was devastated by an invasion of South American races of wheat blast fungus, which occurred for the first time in the country in 2016. The disease spread to an estimated 15,000 hectares (16 percent of cultivated wheat area in the country) and resulted in yield losses as high as 100 percent.

Diagnosis of crop disease is considered crucial but traditional methods rely on the expertise of pathologists, who in turn rely on the physical appearance of disease symptoms, which can be similar to damage caused by other factors, such as nutrient deficiencies or environmental elements. Pathologists also experience difficulty detecting coinfections and pathogens that do not infect aerial parts of the plant.

Rapid detection is also considered a key issue for identifying unknown pathogens during an outbreak, as was made clear during the wheat blast fungus outbreak in Bangladesh.

The Kansas scientists collected four wheat samples from western Kansas and used a new “harmonica-sized” DNA sequencer and a computer programme to quickly detect three different viruses in the samples. The results suggested that the samples contained a new virus strain.

The scientists are now working on improving the technique so that it can be used in field applications. Their research, described in ‘Wheat Virus Identification Within Infected Tissue Using Nanopore Sequencing Technology,’ published in the September 2019 issue of Plant Disease, is the first report of using the new portable DNA sequencing technology for wheat virus identification. These results hope to have broad application to plant and animal disease identification and field diagnostics technology in the near future.

Faster Identification of Bacterial Infections Using Raman Spectroscopy Could Save Lives

Utilizing a Renishaw Raman spectroscopy system, a team of researchers from the Czech Academy of Sciences have been testing a novel way to identify Staphylococcal bacteria, paving the way for faster diagnosis and treatment of infectious diseases.

Staphylococci are a type of bacteria commonly found on the skin and hair of humans and mammals. They are usually harmless, however some strains, such as Staphylococcus aureus (S. aureus), can cause more serious infections if they are able to enter the body. The management of patients with bacterial infections relies on the early detection and identification of pathogens, as it enables the appropriate administration of antibiotics which saves lives. In the case of more serious conditions, such as sepsis, treatment should be started within an hour of the diagnosis. Unfortunately, current tests often take days to complete, putting lives at risk.

Dr. Ota Samek heads a Biophotonics and Optofluidics group at the Institute of Scientific Instruments within the Czech Academy of Sciences. The group has been using Raman spectroscopy to speed up the identification of bacterial infections and are hoping to introduce this method to hospitals as a tool for clinical diagnosis.

The team’s initial study focused on using Raman spectroscopy to identify staphylococci strains from bacterial colonies grown on an agar plate. Using a Renishaw inVia™ Raman microscope, the researchers acquired Raman spectra for 277 different staphylococcal strains and were able to differentiate between 16 species of staphylococci with almost 100% accuracy. This led to further research on the two most common infection-causing species of staphylococci – S. aureus and S. epidermidis. The team found that Raman spectroscopy techniques enabled them to rapidly and reliably distinguish between the strains.

The group’s success in identifying strains of staphylococci using Raman spectroscopy inspired further studies into whether the technique could also be used to investigate bacterial biofilms. Biofilms provide microorganisms with their own microenvironment that helps them survive within a host organism. They can be found on objects such as catheters, cannulas, artificial heart valves and even contact lenses. In this study, the team selected bacterium Staphylococcus epidermis and yeast Candida parapsilosis and used the inVia Raman microscope to distinguish between biofilm-positive- and biofilm-negative-strains directly from colonies grown on agar plates.

Dr. Samek has been using Renishaw Raman instruments to study staphylococci since 2007 when he spent two years at Swansea University, sponsored by a Marie-Curie Intra-European Fellowship. He noted the strong relationships between Renishaw and Swansea University and this encouraged him to connect with Renishaw on his return to the Czech Republic.

Published Papers on the Research

  • K. Rebrosova, M. Siler, O. Samek, F. Ruzicka, S. Bernatova, V. Hola, J. Jezek, P. Zemanek, J. Sokolova, P. Petras: Rapid identification of staphylococci by Raman spectroscopy, Scientific Reports 7, 14846, 2017.
  • K. Rebrosovsa, M. Siler, O. Samek, F. Ruzicka, S. Bernatova, J. Jezek, P. Zemanek, V. Hola: Differentiation between Staphylococcus aureus and Staphylococcus epidermidis strains using Raman spectroscopy, Future Microbiology 12, 881-890, 2017.
  • K. Rebrošová, M. Šiler, O. Samek, F. Růžička, S. Bernatová, J. Ježek, P. Zemánek,  V. Holá,  Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy. Future Microbiology 14,  509–518, 2019

IIT Delhi Researchers Developing Technology for Rapid Diagnosis by Reducing Antibacterial Resistance

Researchers at IIT Delhi are working on a technology to devise diagnostic solutions for combating the problem of antimicrobial resistance to enable rapid diagnosis of bacterial infection and guide clinical decision making.
According to the team at IIT, the research will greatly reduce the unnecessary use of antimicrobials in diagnostic tests and minimise the development of resistance as currently there is a big knowledge gap in microbial resistance biology and the availability of biomarkers and technology for rapid diagnostics.

"Antibacterial resistance is now widely recognised as the biggest healthcare problem of this century. Due to limitations in the current microbiological methods, it is estimated that more than two-thirds of antibiotic prescriptions are unnecessary and are empirical in nature. This practice is a major cause of the emergence of AMR and its rapid spread in the last decade," said IIT professor Vivekanandan Perumal, who is the Principal Investigator (PI) of the project.

"Although the requirement of rapid pathogen identification and methods for antimicrobial susceptibility testing (AST) are well recognized, major limitations include the knowledge gaps in understanding the genomic signatures and their correlation with Antimicrobial Resistance (AMR)," he added.

The research team will focus on 4 major pathogens (Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumanii, Pseudomonas aeruginosa) that are often resistant to antibiotics in Indian clinical settings.

The main objectives of the research project include -- characterization of AMR among Indian isolates using whole-genome sequencing of clinical isolates and optical genome mapping for pathogen identification using a unique genome-based signature for microbial typing with the optical mapping of DNA fragments.

"The research will also look into development of methods for rapid antimicrobial susceptibility testing by carrying out the pH measurements inside spherical microgels microreactors with embedded pH-sensitive carbon dot nanosensors and identification of bacteria species and spread of AMR using clothes worn by HCWs (healthcare workers) with a rapid culture-independent method based on bacterial 16s RNA," Perumal said.

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.