New Biological Detection System Predicted to Provide Faster Less Expensive Results for Veterinarians

Veterinarians and agricultural inspectors who seek to detect and contain the spread of animal diseases can now turn to a newer, faster and less expensive biological detection system.

Known as the Axiom Microbiome Array, or AMA, the new biological detection system is the most comprehensive microorganism detection platform built to date and the first high-throughput microarray.

The AMA is the commercialized successor to Lawrence Livermore National Laboratory’s earlier microarray, called the Lawrence Livermore Microbial Detection Array (LLMDA).

The LLMDA was licensed in 2016 to Waltham, Massachusetts-based Thermo Fisher Scientific and went on sale later that year as Applied Biosystems AMA.

In a yearlong evaluation, published earlier this month in the online scientific journal PLOS ONE, a team of researchers from LLNL, Kansas State University and Thermo Fisher Scientific concluded that the microbiome array “is an efficient tool to rapidly analyze large numbers of clinical and environmental samples for the presence of multiple viral and bacterial pathogens.”

“Two of the array’s advantages are that it’s faster and cheaper,” said Raymond “Bob” Rowland, professor of diagnostic medicine and pathobiology at Kansas State’s College of Veterinary Medicine. “I live in the world of veterinary medicine and cost is critical.

“If we were to do a test using the LLMDA, it would have cost us about $250 just for the reagents; now with the AMA we can do the same tests for $40.”

When LLNL biologists and computer scientists first unveiled the versatile LLMDA in 2010, it could analyze samples for nearly 3,000 bacteria and viruses, all within 24 hours. But it could only analyze four samples a day.

With the 96-well AMA, the new detection system can analyze 96 samples in three days. Additionally, each of the 96 wells contain about 1.4 million probes, so samples are analyzed by about 132 million probes.

“One of the most important conclusions of our study is that this is the first high-throughput microarray that has been developed,” said LLNL biologist Crystal Jaing, who heads the LLMDA/AMA efforts. “It increases the throughput by 10- to 20-fold and decreases the cost by five-fold.”

As LLNL and Thermo Fisher Scientific researchers moved to a higher throughput microarray, one of the team’s prime goals has been to maintain a high-resolution and sensitivity of detection.

In their PLOS ONE paper, researchers from the three institutions note that with the new array, they were able to detect both Shigella, a food-borne bacterial pathogen, and Aspergillus, a fungal pathogen, at 100 genome copies, as well as vaccinia virus DNA, a genetic relation to smallpox, at 1,000 genome copies.

In veterinary tests with pigs, the microbiome array detected two viruses – porcine reproductive and respiratory syndrome virus and porcine circovirus type 2 – as well as other common viral and bacterial microbiome species.

During their evaluation, the researchers conducted tests with 14 veterinary samples and 30 environmental samples, finding that the AMA performed at a resolution similar to the LLMDA, according to Jaing.

Because of the microbiome array, veterinarians can now conduct multiple tests on a single animal in Rowland’s view.

“This is a technology that is meant for the veterinary technician to use. It’s the everything test for everything.

“We base our testing on pathology. When we see a change in the tissue of an organ, that’s where your pathogen can usually be found. If we see changes in multiple organs and multiple tissues, now we can sample them all,” Rowland said.

According to the PLOS ONE paper authors, “Rapid detection and characterization of bacterial and viral pathogens is important for clinical microbiological diagnostics, public health, veterinary diagnostics, drug and food safety, environmental monitoring and biodefense.”

The current version of the AMA has the capability to detect more than 12,000 microorganisms and can identify 6,901 bacteria, 4,770 viruses and a combined total of 842 archaea, fungi and protozoa.

The new arrays, which come in 24- and 96-well formats, can analyze a variety of different sample types and can be used for nutrigenomics, agrigenomics, plus animal research and modeling.

In addition to Rowland and Jaing, the paper’s lead author, other paper co-authors are LLNL biologists James Thissen and Nicholas Be, LLNL bioinformaticists Kevin McLoughlin and Shea Gardner (deceased), retired LLNL computer scientist Tom Slezak and Thermo Fisher Scientific biologists Paul Rack and Michael Shapero.

Texas State Researcher Develops a Simple Test to Diagnose Deadly Global Illnesses

Here is a glimpse into the future of global public health: a credit-card sized piece of paper is dunked into a liquid sample at a health clinic in a developing nation, quickly telling a doctor or nurse whether a malnourished child with diarrhea is infected with a virus, a bacteria, or a parasitic protozoan.

Gastrointestinal ailments may sound like a small matter in the industrialized world, but in millions of remote villages in developing nations, food, and waterborne illnesses are potentially deadly matters. According to the World Health Organization, diarrheal diseases are among the top 10 causes of death; and they are the second biggest killer of children under the age of 5.

Rapid diagnosis can mean fast, appropriate treatment. This is the quest of Shannon Weigum, an associate professor of biology at Texas State University. Her laboratory is merging principles of biochemistry and materials science to create a miniature, highly portable, rapid-detection tool for diarrheal illnesses. Her hope is that this tool could someday make a major impact on global health.

“In healthy people, diarrheal illnesses often resolve themselves without treatment,” she said. “When a person is malnourished, immune compromised, or suffering from chronic illness, the consequences can become very serious. This is especially true in malnourished children.”

Weigum’s first diagnostic targets are noroviruses, which cause more than half of the foodborne illnesses in the United States. Health data show that noroviruses are the most common cause of diarrhea in adults and the second most common cause in children. The tests have been expanded to detect bacteria and protozoan parasites.

The overall goal is to make diagnostic testing available where it previously was not. To be practical for remote clinics in undeveloped areas, though, laboratory tools have to be inexpensive as well as highly portable. Poor countries lack medical infrastructure and skilled personnel to operate the sophisticated diagnostic tools found in large urban medical centers.

Imbued with nanoparticles and using microfluidics, the paper cards interact with specific bacteria or viruses to quickly, accurately identify diseases. A faster diagnosis means healthcare workers can move beyond treating symptoms and attack the disease.

“We’ve teamed up with Paratus Diagnostics, a biotech startup company located in Texas

State’s Science, Technology and Advanced Research (STAR) Park. By working and teaming up with a biotech company, we are able to progress the technology to the point of commercial viability,” Weigum said.

Additional funding for the project has come from the U.S. Department of Defense and a Small Business Innovation Research (SBIR) grant. “We had a successfully funded phase one and phase two. SBIR supports research and development and potential commercialization,” she said.

The ‘sample to answer’ test provides results in about 20 minutes. It utilizes smartphone technology as an analytical instrument. Now, instead of reading the sample with the naked eye the phone acts as an optical instrument to read the light-based signal. “We can detect signals from many different pathogens at the same time. Our goal is to detect six to eight pathogens that most commonly cause illnesses.”

Weigum began her science career as a high school teacher in San Antonio, and then returned to the classroom as a student to pursue advanced degrees at The University of Texas at Austin. After earning master’s and doctoral degrees in biochemistry, she moved to a postdoctoral fellowship in bioengineering at Rice University, where her love of biology began to merge with materials science and opened the door to cutting-edge engineering innovations in developing diagnostics.

Next up is pre-clinical and clinical testing. Working with Dell Children’s Medical Center in Austin, Weigum expects pre-clinical trials to begin in six months to one year.

“The whole process is moving from the lab to the marketplace so that eventually it can get into the hands of medical personnel in the field.”

Source: Texas State University

Bluejay Diagnostics, Inc. and U.S. Navy Enter Co-Operative Research and Development Agreement to Develop Non-Invasive Point-of-Care Tests for Lyme Disease

Bluejay Diagnostics, Inc. (Bluejay) is pleased to announce a new Cooperative Research & Development Agreement (CRADA) with the U.S. Naval Medical Research Center (NMRC), Silver Spring, Md. The project, which will take place in Maryland, will investigate and develop a non-invasive point-of-care test for Lyme disease with the goal of improving detection of Lyme disease at an early stage.

This collaboration will focus on the study of antigens from various pathogens, and successful identification of the most immunoreactive antigen. This information will then be used to develop a rapid test for the efficient detection of pathogen-antigens in biofluids (such as serum, urine or other biofluids) using Bluejay’s FDA-Cleared platform technology, which combines immunochromatography and laminar flow using proprietary materials and design.

“We are confident this collaboration will allow the Navy and Bluejay to pursue not only the development of Lyme disease tests, but also for other infectious diseases,” said Neil Dey, Chief Executive Officer for Bluejay Diagnostics. “We look forward to working with the Navy on this project.

The two-year agreement between the Navy and Bluejay Diagnostics will be completed in four phases to identify the most pertinent antigen, confirm sensitivity and specificity, generate specific high-efficient antibodies, and provide a proof-of-concept test on the platform technology.

About Bluejay Diagnostics, Inc.

Bluejay Diagnostics, Inc. develops, manufactures and markets easy-to-use, point-of-care medical diagnostics tests. The company offers multiple FDA-Cleared non-invasive, affordable products, including the Allereye® Tear Total IgE Test used to aid in the diagnosis of allergic conjunctivitis, and a urine-based HIV-1 screening test and a HIV-1 confirmatory test. Bluejay, headquartered in Acton, Massachusetts, continues to leverage its innovate, proprietary platform to develop new products for underserved diagnostic markets.

Specific Diagnostics Begins Clinical Demonstrations and Testing of the Reveal AST System

Specific Diagnostics today announced clinical demonstrations of the Reveal AST system will be conducted at a clinical laboratory in Amsterdam during the ECCMID conference April 13-16. The Reveal AST system delivers phenotypic AST in an average of 4 hours, directly from positive blood culture or isolate dilutions. The system provides minimum inhibitory concentration (MIC) with wide antimicrobial coverage for bacteria species responsible for bloodstream and other acute infections.

Current methodologies require 2 days to determine the effective antibiotic while Specific's Reveal AST solution provides antibiotic susceptibility results in hours, allowing same-shift impact. The demonstrations conducted during ECCMID for leading European clinical laboratory directors and partners will demonstrate this rapid AST performance with both spiked and clinical blood culture samples. The simple and rapid sample preparation workflow, just a 2- minute simple dilution of a positive blood culture fluid, will be demonstrated as well as the intuitive and elegant touch screen controller of the Reveal system. The demonstrations will allow customers to directly assess the simplicity and capability of the Reveal system in advance of its availability for adoption in Europe upon issuance of CE-IVD registration, expected in Q4 2019.

Bloodstream infection leading to sepsis is responsible for more than half of all deaths in hospitals and is the most expensive condition treated in hospitals. Mortality rate increases at more than 6% every hour from onset. Therefore, the same-shift susceptibility determination provided by Reveal can and will save lives.

“We are looking forward to demonstrating the clinical performance of the Reveal AST instrument and consumable assays during this year’s ECCMID conference. This is another major step towards commercial deployment. We consistently hear from clinical lab and infectious disease doctors that rapid, affordable AST is vital to patient outcome and of their desire to include this transformative solution in their labs. The world needs affordable, rapid susceptibility testing to treat time critical, acute infections and to combat growing antimicrobial resistance." said Ray Martino, Specific COO.

About Specific Diagnostics

Specific Diagnostics has developed in vitro diagnostic systems for the detection and identification of microorganisms while they grow in culture. The company’s unique patented technology leverages a low-cost printed chemical sensor array, enabling diagnostic products that simplify workflow and speed time-to-answer at low cost. During growth in culture, bacteria emit organism-specific small molecule metabolite mixtures. Specific’s products utilize inexpensive printed sensor arrays to obtain a profile of such mixtures, enabling detection of growth, determination of antibiotic efficacy, and microorganism ID with simple, automated, low-cost instruments and disposables. Specific and its founders have written almost 60 peer-reviewed publications, detailing the successful demonstration of the SMS array technology. The Company itself has independently authored over 20 scientific publications and conference abstracts detailing the SMS array powered detection, identification and antibiotic susceptibility testing.

Accuracies of minimum inhibitory concentration (MIC) determination meet those of gold standard broth microdilution methods, but with results obtained within four hours of a positive blood culture, directly from a diluted positive blood sample. The system will streamline lab workflow, reduce costs, and substantially shorten the time from sample arrival to selection of effective therapy, saving patients faced with fast-moving and deadly drug-resistant blood infections.

FDA Classifies IVDs for Bacillus Detection

In vitro diagnostic (IVD) devices for the detection of the Bacillus species were assigned to class II on Friday, following the release of a US Food and Drug Administration (FDA) final rule.

The IVDs are prescription devices and indicated to aid in the diagnosis of diseases caused by the Bacillus species, including anthrax. They are intended for the detection and differentiation of the bacteria, such as Bacillus anthracis, and had been unclassified devices prior to FDA’s final classification regulation.

The final rule comes as the awareness of the anthrax bioterrorism threat has been raised since the 11 September 2001 events in the US and the anthrax letters. "Anthrax is a bioterrorism threat because the spores are resistant to destruction and can be spread by release in the air,” FDA Commissioner Scott Gottlieb said on Friday. “Exposure to anthrax can and has caused serious injury or death.”

Gottlieb noted device manufacturers have inquired about how the agency reviews tests that can detect Bacillus anthracis, citing the important role such devices play in a public health response to an anthrax attack. The final rule is the culmination of FDA’s “effort to provide a clear and predictable review pathway for these specific test developers” as it helps “understand the requirements, including testing criteria and how to address potential safety risks for lab workers using the devices,” Gottlieb added.

The decision to finalize the class II regulation resulted from recommendations made by the Microbiology Devices Advisory Panel in 2002. Rather than that of de novo classification requests, most unclassified devices have been classified under device classification panel procedures. The procedures involved a 2016 comment period, though the proposed rule for the IVDs did not receive any relevant comments.

The final rule will come into effect 30 days from its publication in the Federal Register. FDA clarified that manufacturers are not required to submit a 510(k) for IVDs legally marketed prior to the publication of the final rule. For such devices, the agency does not intend to enforce compliance with the special controls in sections VI, VII and IX of a new FDA guideline issued in conjunction with the final rule. Yet the final rule established a one-year grace period for such devices to comply with the labeling special controls set forth in section VIII of the guideline, after which FDA intends to consider taking enforcement actions.

The implementation strategy differs, however, for manufacturers required to submit a new 510(k) for devices undergoing significant changes or modifications. In addition to those that have not been legally marketed prior to the final rule, modified devices must comply with the new set of special controls.

The new class II special controls guideline on IVD devices for Bacillus species detection is partly based on the feedback from the device classification panel. Special controls identified in the guideline relate to device description requirements, performance studies and labeling, among other specific IVD requirements.

The requirements that will eventually apply to all devices, including those that are currently legally marketed, fall under labeling. Labeling special controls in the new guideline address IVD intended use, directions for use, precautions, performance characteristics as well as interpretation and reporting of assay results.

The final rule also restricts the use and distribution of IVDs for Bacillus species detection to laboratories that follow public health guidelines.

The class II assignment follows on the heels of the new Tri-Agency Task Force for Emergency Diagnostics’ launch to facility the rapid development and deployment of IVDs during public health emergencies.

Five winners selected to receive $80,000 in Pathogen Monitoring Prize Competition from the Bureau of Reclamation

To optimize the design and operations of advanced water treatment facilities the Bureau of Reclamation completed a prize competition and has selected five submissions to share $80,000 in prizes in the Pathogen Monitoring Stage 1 Challenge, with half of the prize purse contributed by Xylem, Inc. The team of Hannah Safford and Heather Bischel, both of Davis, California, was selected to receive the top prize of $40,000 in this competition.

The demand for water is growing throughout the western United States and one of the ways the demand is being met is through water reuse, a method where wastewater is treated to be used again by the community. While advanced water treatment technologies exist to produce high quality, potable water from wastewater, improved pathogen detection and monitoring is needed.

Safford and Bischel’s idea used novel computational tools for quantifying waterborne viruses detected through flow cytometry. Their concept incorporates advanced data processing techniques to assist in the underlying signal to noise ratio problems that have prevented the use of this technology in the identification of viruses to this point. The proposed computational tool will use cluster analysis and diffusion mapping to facilitate rapid quantification of viruses in raw or treated wastewater.

In addition to the winning solution, another solver received a $10,000 prize for an idea that adapts an approach that is used clinically to identify pathogens in human patient specimens to detect viruses in wastewater.

Other winners in the prize competition each received $10,000.

• James Vickers of Separation Processes Inc., Carlsbad, California, for his idea use of automated conductivity profiles to verify reverse osmosis unit integrity in full-scale recycled water treatment facilities.
• John Newport, Chadds Ford, Pennsylvania, for his idea using microcapsules with external antibodies and internal nanomagnets and reporter molecules to quantify viruses in wastewater.
• David Wick, Stevensville, Montana, for his idea of identifying and quantifying viruses in raw and treated wastewater by sorting viruses by mass/charge ratio and quantifying them according to size.

The Bureau of Reclamation in partnership with Xylem, Inc., a global water technology provider and leader in digital water, The Water Research Foundation, and the Environmental Protection Agency sought ideas for the development of a rapid, accurate and preferably online/onsite monitoring techniques for various pathogens at advanced water treatment facilities.

To learn more about this and other prize competitions at Reclamation, please visit Reclamation's Water Prize Competition Center at: http://www.usbr.gov/research/challenges.

IIT Develops AI-based Detector for TB

Very soon cost effective, time saving equipment to diagnose tuberculosis (TB) caused by the mycobacterium, malaria, intestinal parasite, and cervical cancer would be available as the researchers from Indian institute of Technology (IIT-D), Delhi have developed a low costing 'Artificial Intelligence (AI)-based low-power electronic hardware system', a device which is estimated to bring down the detection time of the deadly disease from two days to few milliseconds.

The device has been designed by the students of Department of Electrical Engineering: Khushal Sethi, Narayani Bhatia, Vivek and Shridu Verma. The team was headed by the Professor Manan Suri of the same department.

With detecting the disease in a few seconds, the device can also be used for healthcare access in resource-constrained areas with limited access to human specialists.

"While several software AI models exist for healthcare and diagnostic related applications, need of the hour is to efficiently map these models on portable dedicated low-power, low-cost hardware to enable edge-AI systems accessible to all in low resource environment," said professor Suri.

The researcher says that TB is one of the top10 causes of death worldwide and 39 percents of the population is at risk of malaria. "Rapid screening of TB is possible, but the service accessibility is still poor in rural areas and require specialized equipment that is not readily available," said Puri.

Further as per the data shared by the team, cervical cancer is the fourth most common cancer in women, and seventh overall, with an estimated 528,000 new cases and 266,000 reported deaths worldwide.

 Intestinal parasites infect the gastrointestinal tract of humans. They have a consistent external and internal morphology throughout the different stages of development that is egg, larva and adult stages.

The professor added that microscopy is particularly well adapted to low-resource, high disease burden areas, being both simple and versatile; even for diagnostic tasks for which newer technologies are available the cost of specialized equipment may render it impractical in such places.

"Such diagnosis requires skilled persons and there is a critical shortage of skilled technicians in our country. Thus, diagnoses are often made on the basis of clinical signs and symptoms alone, which are error-prone and lead to higher mortality, drug resistance, and the economic burden of buying unnecessary drugs. Hence, such alternatives will provide an access to quality diagnosis that is currently unavailable," said the professor.