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.