New Technology Enables Simultaneous Testing for Multiple Blood-Borne Pathogens

The emergence of new pathogens like West Nile Virus, Ebola, Dengue, and Zika, threaten human health on a global scale. Identification of these pathogens requires a rapid response from industry to develop new tests and the FDA to assess test safety and efficacy. A report in The Journal of Molecular Diagnostics evaluates the new OpenArray system that offers simultaneous detection of multiple viruses, bacteria, and protozoan pathogens in human blood samples. Investigators determined that this system is a promising tool for flexible, fast, and accurate blood screening.

Some highly virulent pathogens may have a low prevalence rate and/or be restricted seasonally or geographically. However, the impact of transfusion-transmitted infection of such agents can have fatal consequences, particularly in highly vulnerable populations such as newborns, the elderly, or immunocompromised individuals. The cost effectiveness of a multiple agent test means that more testing could be done, resulting in safer blood.

"All blood for transfusion must be tested for infectious agents. The increasing number of agents that may infect blood and the recognition that some of them only pose a risk in certain areas or certain times means that new methods to streamline blood testing must be developed. The major feature of our OpenArray device, the ability to test for multiple infectious agents at the same time, could be an answer to that need," explained Robert Duncan, PhD, an investigator with the Food and Drug Administration's Center for Biologics Evaluation and Research, Silver Spring, MD.

Many "singleplex" tests approved by the FDA are available to measure one specific pathogen. Less commonly available are "multiplex" systems that can detect multiple pathogens. The OpenArray platform (Thermo Fisher Scientific) simultaneously tested 17 viral strains in human plasma samples (e.g., HIV-1, HIV-2, Dengue, influenza, Chikungunya) and 13 types of bacteria (e.g., Escherichia coli, Staphylococcus aureas) and protozoa (e.g., Leishmania donovani, L. infantum, Babesia microti) in human blood samples. The individual tests use real-time PCR, which are spatially separated on the OpenArray device allowing a high level of multiplexing.

"New multiplex PCR-based diagnostic technologies aimed at faster and more accurate pathogen identification are increasingly used for detection of respiratory or gastrointestinal pathogens, yet testing for a multitude of pathogens directly in the blood is still at the research stage. This study demonstrated that new technologies can enable early and accurate detection of pathogens directly in blood samples. The engagement and coordination of a number of stakeholders, including regulatory, clinical practitioner, and the diagnostics industry, are necessary for implementation of such disruptive technologies for patient care," added Elena Grigorenko, PhD, Vice President of Research and Development with Diatherix Laboratories, Eurofins Clinical Diagnostics Division at Huntsville, AL.

To design this device, the first step required choosing regions on each of the pathogen genomes to target and short pieces of DNA to accomplish that targeting. These short pieces, called primers and probes, which achieve the PCR, were loaded into the OpenArray device. The next critical step was laboratory growth of the 30 pathogens and mixing each one of them with normal volunteers' whole blood or plasma to mimic the blood from an infected individual. Once performance of the device was adjusted to maximum ability to detect these infectious agents in the mock clinical samples, it was tested with 92 donor samples obtained from a blood donor testing center with known pathogen content, as determined by FDA-licensed tests. Ninety-five percent of virus-positive samples were correctly identified.

"We need the next generation of superior performance tests that will detect an increasing number of transfusion-transmittable agents in multiplex format with high sensitivity and specificity, robustness, and adaptability to accomplish detection of new pathogens and maintain the safety of blood products," commented Dr. Duncan. "Our goal in this research is to provide a proof of concept that will stimulate device developers to advance new technology for multiple assay testing devices into clinical use."

"In support of this initiative, Phillip Williamson, PhD, VP of Operations and Scientific Affairs, said, "As the largest independent blood donor testing organization in the U.S., Creative Testing Solutions welcomes the opportunity to work with the FDA and others on new research initiatives and clinical trials that will ideally improve blood donor testing and the safety of the U.S. blood supply."

This OpenArray Platform is a research use only device and is not cleared or approved for clinical use.

Reference

Highly Multiplex Real-Time PCR–Based Screening for Blood-Borne Pathogens on an OpenArray Platform. Grigorenko, Elena et al. The Journal of Molecular Diagnostics, Vol. 19, No. 4. 2017.

Read more

Fighting Fire Blight and Detecting Salmonella

ETH Zurich researchers have created an effective weapon against the plant disease fire blight and a new method for detection of Salmonella. Both are based on particular viruses that attack only one species of bacteria.

The plant disease fire blight, caused by the bacterium Erwinia amylovora, is dreaded by fruit growers. It affects apple and pear trees and other plants in the rosacea family, and if a tree becomes affected it usually has to be cleared and burned.

The pathogen that causes fire blight is difficult to control. In exceptional cases, farmers can use the antibiotic streptomycin, but even this cannot prevent the pathogen from disseminating via pollinating insects.

Use the enemy's enemy

A new control strategy has now been presented by researchers led by ETH professor Martin Loessner: they employed a bacterial virus (bacteriophage) designated Y2 that exclusively infects the fire blight pathogen, and equipped it with additional genes. This allowed them to create a highly effective and specific weapon against the Erwinia bacterium.

The native form of Y2 is a natural Erwinia killer, but it is unable to adequately penetrate the thick slime layer that protects the bacterium. Infact, this carbohydrate slime is very tough and clogs the vascular system of plants, causing the flowers and leaves to wither.

Yet, this does not prevent another bacteriophage, named L1, to attack Erwinia. This virus features particular enzymes which can dissolve the mucus efficiently. However, it is not as effective in killing the fire blight pathogen.

Equipping Y2 with mucus-dissolving abilities

By incorporating the gene for this enzyme from L1 into the Y2 phage, the researchers created a genetically modified variant combining the properties of both: it is is able to dissolve its mucus layer efficiently, and highly infective and lethal to the Erwinia bacterium.

As soon as Y2 enters the bacterium, it starts to proliferate on a massive scale. It dissolves the bacterium from the inside out, freeing itself to attack further bacteria. Thus, mucus-dissolving enzymes enter the environment in large quantities, which accelerates the degradation of the mucus layer on further bacteria and thus facilitates their infection. The destructive process then progresses rapidly.

"The optimized bacteriophage proved to be very effective against the fire blight pathogen, not only in the laboratory but also in infected apple blossoms," says Loessner. The tests were conducted with infected plant material in safety-level greenhouses.., Field tests have not been carried out: "Fire blight is one of the worst plant diseases; you cannot experiment in the field," Loessner emphasises.

Turn a virus into a sensor

The researchers not only created a bacterial killer, they also used another gene to produce a second Y2 variant that helps to detect the fire blight pathogen. The gene ensures that the bacteria begin to light up when infected by the bacteriophages. This light can be measured easily and used for specific detection of the pathogen.

This method is not only fast and reliable, it is also very sensitive: "With the help of our sensor phages, a few thousand infected bacteria are sufficient to directly detect fire blight," says Loessner. Previous detection methods were much slower, less sensitive and occasionally providing false results. Because the Y2 sensor phage infects only Erwinia, this is not the case with the new assay.

High specificity as the basis for Salmonella detection

Loessner and his colleagues also made use of the fact that bacteriophages are generally very host-specific in another way: to detect Salmonella. In a second paper, also published in the journal Applied and Environmental Microbiology, they showed how they used synthetically produced bacteriophage components to develop a universal detection method for Salmonella. It means that all 2,500 known sub-types can be detected; previous methods based on antibodies recognised only a fraction of these variants and were also slower.

Loessner's team reproduced a particular component of the Salmonella-specific bacteriophage S16. This component – a virus tail fibre – features a spherical terminal binding protein that can adhere to two specific surface structures of all Salmonella types. The artificial tail fibre, along with the recognition structure, has been attached to the surface of microscopically small magnetic beads.
This allows almost any fluids and samples to be tested for the presence and quantity of Salmonella. As soon as the bacteria binds to the fibres on the magnetic beads, a kind of rusty aggregate forms in the test container, which can be separated easily using an external magnet.

References

Yannick Born et al. Engineering of Bacteriophages Y2::and Y2::for Efficient Control and Rapid Detection of the Fire Blight Pathogen, Erwinia amylovora, Applied and Environmental Microbiology (2017).

Jenna M. Denyes et al. Modified Bacteriophage S16 Long Tail Fiber Proteins for Rapid and Specific Immobilization and Detection of Salmonella Cells, Applied and Environmental Microbiology (2017).

Read more

GenMark Receives FDA 510(k) Market Clearance for Its ePlex® Instrument and Respiratory Pathogen Panel

GenMark Diagnostics, Inc., a leading provider of automated, multiplex molecular diagnostic testing systems, today announced that it has received 510(k) market clearance from the U.S. Food and Drug Administration for both its ePlex instrument and Respiratory Pathogen (RP) Panel.

ePlex is a transformational new in vitro diagnostic platform that integrates nucleic acid extraction, amplification, and detection processes into a fully automated, sample-to-answer system. Rapid and highly specific detection is enabled on ePlex by GenMark’s established and proven eSensor® technology, which has been used in more than two million patient tests conducted across multiple FDA-cleared panels on the Company’s XT-8 system. The introduction of ePlex to the U.S. market is expected to enhance the benefits of multiplex molecular testing and make them accessible to many more hospitals and patients across the country.

The ePlex RP Panel detects over 20 viral and bacterial pathogens that commonly cause upper respiratory infections. Combining the comprehensive coverage of the ePlex RP Panel with the true sample-to-answer capabilities of ePlex provides physicians access to rapid, accurate, and actionable test results for high risk patients and helps laboratory directors improve productivity through reduced labor costs, advanced data analytics, and best-in-class customer service and support.

“We are very pleased to announce the 510(k) clearance of ePlex and the Respiratory Pathogen Panel. There is a growing body of evidence that rapid, multiplex molecular testing for respiratory pathogens improves patient outcomes, reduces total cost of care, and enhances key quality metrics,” said Hany Massarany, President and Chief Executive Officer of GenMark. “We believe that ePlex will help laboratories and hospitals realize these benefits as it is the only sample-to-answer molecular platform that integrates the diagnostic process from test order entry, all the way to reporting actionable results,” added Massarany.

“Rapid and accurate diagnosis of respiratory pathogens has been shown to improve outcomes in high risk patients and help hospitals address key priorities such as infection control and antimicrobial stewardship,” said Kimberle C. Chapin, M.D., Professor of Pathology and Medicine at Lifespan Academic Medical Centers and Brown Medical School. “We look forward to having GenMark’s ePlex technology because it is simple enough to be performed any time of day by multiple personnel and can be easily integrated into a patient care algorithm 24/7. It can provide fast, actionable results that will improve cohorting and patient flow through the ED, reduce unnecessary testing, and support appropriate antimicrobial use, particularly during the peak of respiratory season.”

“The Medical Center has relied on GenMark’s first-generation eSensor platform for syndromic infectious disease testing to help optimize patient treatment for the past several years,” noted Wallace H. Greene, PhD, D(ABMM), Director of Diagnostic Virology Laboratory at Penn State Health Milton S. Hershey Medical Center and one of the investigators in GenMark’s RP clinical study. “Our experience has shown that integrating this technology into a sample-to-answer platform like ePlex can further benefit patients with streamlined workflow and a high level of LIS integration to further accelerate the reporting of patient results.”

Read more

T2 Biosystems Presents New T2Sepsis Results at ASM Conference

T2 Biosystems, Inc. announced new data on the company’s T2Sepsis Solution, which includes the T2Bacteria and T2Candida Panels, presented by clinical experts at the ASM Microbe 2017 conference in New Orleans, LA., on June 1-5. The T2Candida Panel is FDA-cleared and the T2Bacteria Panel is currently in clinical trials in the US and performance evaluations in the EU and is currently available for Research Use Only (RUO) in the US.

Dr. Cornelius Clancy, MD, Director of the Mycology Program and Chief of the Infectious Diseases Section at VA Pittsburgh Healthcare System, participated in “Debates in Medical Mycology” featuring the T2Candida Panel. “I was pleased to see that T2Candida has become a standard during any discussion regarding rapid diagnostics and antimicrobial stewardship,” said Dr. Clancy. “I believe that the hospitals using it are seeing strong value for their patients as well as better management of the drugs that lead to high resistance and costs.”

In the Science and Industry Showcase, “Managing Sepsis in the Golden Hour: Controlling Costs and Improving Patient Care through Diagnostic Testing,” Dr. Thomas Kirn, MD, PHD, Rutgers Robert Wood Johnson Medical School, and Dr. Jonathan D. Edwards, Pharm.D., BCPS (AQ-ID), BCGP, Huntsville Hospital, discussed the economic and clinical benefits of the T2Sepsis Solution’s direct-from-whole blood tests at their hospitals.

“With the T2Sepsis Solution, our hospital is not only reducing the use of antifungal therapy, we’re also identifying far more infected patients than was possible with blood culture,” said Dr. Edwards.

Dr. Edwards reported the following findings from Huntsville Hospital:

• T2Candida detects more Candida infections, days faster than blood culture.
• T2Candida provides superior sensitivity as compared to blood culture (94.4% vs. 28% sensitivity). Blood culture missed 26 confirmed Candida infections.
• Negative T2Candida results led to cessation or no initiation of antifungal therapy in 64% of patients.
• T2Candida improves hospital economics through de-escalation/non-initiation of unnecessary antifungals. T2Candida negative results decreased duration of micafungin by 2.1 days.

Dr. Thomas Kirn reported that Robert Wood Johnson Medical School is including the T2Candida Panel as a standard order in their sepsis protocol. Dr. Kirn reported that:

• Negative T2Candida results led to cessation or no initiation of antifungal therapy in 67% of patients.
• T2Candida would be most effective in standard, automated ordering practices.

Dr. Kirn also presented preliminary information about Robert Wood Johnson Medical School’s experience as part of the T2Bacteria pivotal trial. Dr. Kirn reported that initial data generated at their institution suggest that the T2Bacteria Panel may be identifying patients that would likely be missed by blood culture due to its insensitivity.

In the Science and Industry Showcase, “Application of Rapid, Blood Culture-Free Diagnostics in the Emergency Department: Improving the Signal to Noise Ratio,” Dr. Mitchell J. Cohen, M.D., Director of Surgery at the Denver Health and the University of Colorado School of Medicine, discussed the important role the T2Sepsis Solution may play in the emergency department.

“In the emergency department, rapid and precise results are critical to triage, treat, and make admission decisions in the best interest of the patient,” said Dr. Cohen. “The T2Sepsis Solution has the potential to provide the rapid results and high sensitivity necessary to make it a valuable tool for the management of infections that lead to sepsis in the ED.”

Dr. Cohen reported that T2Bacteria can be easily integrated in the emergency department setting due to its rapid turnaround time, while blood culture-reliant tests cannot.

“There was excitement and high quality, inbound interest from our target market during ASM Microbe 2017 Conference,” said John McDonough, president and chief executive officer. “There is growing evidence of improved patient care and hospital savings with T2Candida and market enthusiasm about T2Bacteria.”

Read more

bioMérieux receives FDA Clearance for BioFire’s FilmArray® Respiratory Panel 2 (RP2)

bioMérieux, a world leader in the field of in vitro diagnostics, announced that BioFire Diagnostics, its molecular biology affiliate, has received 510(k) clearance from the FDA for the FilmArray® Respiratory Panel 2 (RP2). The FilmArray® RP2 tests for 21 pathogens (17 viruses and 4 bacteria) responsible for respiratory tract infections and will be commercially available by mid-June 2017. This follows the announcement in April that the FilmArray® Respiratory Panel 2 plus (RP2plus) is CE marked. The FilmArray® RP2plus contains one more pathogen than FilmArray® RP2 - the Middle East Respiratory Syndrome coronavirus (MERS-CoV). The FilmArray® RP2plus has been submitted as a de novo application to the US FDA.

The FilmArray® RP2 advances the existing FilmArray® Respiratory Panel (RP) by reducing the assay time from about an hour to less than 45 minutes, while also improving overall sensitivity and enhancing several assays. FilmArray® RP2 also includes an additional pathogen, Bordetella parapertussis. B. parapertussis represents a significant cause of whooping cough and is often missed because of a clinical presentation largely indistinguishable from other viral infections and a lack of reliable diagnostic tests.

Randy Rasmussen, bioMérieux Corporate Vice President of Molecular Biology and CEO of BioFire Diagnostics, said: “A growing body of evidence strongly supports the added medical value of rapid syndromic infectious disease testing enabled by BioFire’s market leading technology. Reducing the turnaround time of FilmArray® Respiratory Panel 2 demonstrates bioMérieux’s continued commitment to empower FilmArray® users to better serve patients and improve outcomes.”

Judy Daly, Ph.D., Professor of Pathology at the University of Utah and Director of Microbiology Laboratories at Primary Children’s Medical Center in Salt Lake City, Utah was the principal investigator at one site for the FDA clinical studies of FilmArray® RP2. Dr. Daly states: “The FilmArray® Respiratory Panel 2 assay is robust, simple-to-use, and provides rapid detection of 21 respiratory pathogens in about 45 minutes. In our experience, the FilmArray® RP2 enables us to provide faster, more accurate, and more comprehensive results and helps improve detection of respiratory pathogens and clinical actionability.”

The FilmArray® RP2 is compatible for use on the FilmArray® 2.0 and FilmArray® Torch systems. The Company plans to continue to make the current FilmArray® RP panel commercially available.

About the FilmArray® System:

The FilmArray® System is an FDA-cleared and CE-marked multiplex PCR system that integrates sample preparation, amplification, and detection into one closed system. The FilmArray® System requires only two minutes of hands-on time and has a total run time of about 45 to 65 minutes, depending on the panel. The FilmArray® System has the largest infectious disease pathogen menu commercially available composed of:

• FilmArray® Respiratory Panel, a comprehensive panel of 20 respiratory viruses and bacteria performed directly on nasopharyngeal swabs in viral transport media.
• FilmArray® Respiratory Panel 2 (RP2), a comprehensive panel of 21 respiratory viruses and bacteria performed directly on nasopharyngeal swab-associated transport media.
• FilmArray® Respiratory Panel 2 plus (RP2plus), currently CE-marked and under review with the US FDA, a comprehensive panel of 22 respiratory viruses and bacteria performed directly on nasopharyngeal swab-associated transport media.
• FilmArray® RP EZ for the detection of 11 viral and 3 bacterial pathogens associated with respiratory infections. FDA cleared and CLIA-waived for use in the US only.
• FilmArray® Blood Culture Identification (BCID) Panel, capable of identifying 27 of the most common causes of bloodstream infections and associated antimicrobial resistance directly from positive blood culture.
• FilmArray® Gastrointestinal (GI) Panel, for identification of 22 of the most common viral, bacterial and parasitic causes of infectious diarrhea directly from stool in Cary Blair transport media.
• FilmArray® Meningitis/Encephalitis (ME) Panel, identifying 14 bacterial, viral, and fungal causes of meningitis and encephalitis directly from cerebrospinal fluid.

Read more