Rapid Microbiological Methods Online Master Class - April 1-2, 2020

For the first time ever, I am offering my intensive two-day Rapid Microbiological Methods Master Class online! This will take place on Wednesday and Thursday, April 1st and 2nd, 2020, from 10:00 AM EDT to 2:30 PM EDT. This live, online class will discuss the same industry best practices I have taught in similar training programs around the world. Attendees will be immersed in discussions regarding current regulatory policies and expectations, guidance on rapid sterility testing for gene and cell therapies (ATMP), validation strategies, statistical analysis, technology reviews and return-on-investment considerations. For the complete agenda and information on how to register, please visit http://rapidmicromethods.com/events/masterclass-april2020.php.

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Portable Nanohole Device Will Rapidly Diagnose Sepsis

EPFL researchers have developed a highly sensitive and portable optical biosensor that stands to accelerate the diagnosis of fatal conditions like sepsis. It could be used by ambulances and hospitals to improve the triage process and save lives. Their press release and associated reference paper are provided below.

Sepsis claims one life every four seconds. It is the primary cause of death in hospitals, and one of the ten leading causes of death worldwide. Sepsis is associated with the body’s inflammatory response to a bacterial infection and progresses extremely rapidly: every hour that goes by before it is properly diagnosed and treated increases the mortality rate by nearly 8%. Time is critical with sepsis, but the tests currently used in hospitals can take up to 72 hours to provide a diagnosis.

Many scientists are working on this critical issue, including those at Abionic, an EPFL spin-off. Researchers at the Laboratory of Bionanophotonic Systems (BIOS) at EPFL’s School of Engineering have just unveiled a new technology. They have developed an optical biosensor that slashes the sepsis diagnosis time from several days to just a few minutes. Their novel approach draws on recent developments in nanotechnology and on light effects at a nano scale to create a highly portable, easy-to-use device that can rapidly detect sepsis biomarkers in a patient’s bloodstream. And their device takes just a few minutes to deliver a result, like a pregnancy test.

Because the biosensor uses a unique plasmonics technology, it can be built from small, inexpensive components, yet it can achieve an accuracy on par with gold-standard laboratory methods. The device can screen a large panel of biomarkers and be adapted for the rapid diagnosis of a number of diseases. It was installed at Vall d’Hebron University Hospital in Spain and used in blind tests to examine patient samples from the hospital’s sepsis bank. The researchers’ technology is patent-pending, and their findings were recently published in Small.

Trapping biomarkers in nanoholes

The device employs an optical metasurface – in this case a thin gold sheet containing arrays of billions of nanoholes. The metasurface concentrates light around the nanoholes so as to allow for exceptionally precise biomarker detection. With this type of metasurface, the researchers can detect sepsis biomarkers in a blood sample with nothing more than a simple LED and a standard CMOS camera.

L'appareil est compact et abordable© Alain Herzog / EPFL 2020

The researchers begin by adding a solution of special nanoparticles to the sample that are designed to capture the biomarkers. They then distribute this mixture on the metasurface. “Any nanoparticles that contain captured biomarkers are trapped quickly by antibodies on the nanoholes,” says Alexander Belushkin, the lead author of the study. When an LED is applied, those nanoparticles partially obstruct the light passing through the perforated metasurface. “These nano-scale interactions are imaged by the CMOS camera and digitally counted in real-time at high precision,” says Filiz Yesilkoy, the study’s co-author. The generated images are used to rapidly determine whether disease biomarkers are present in a sample and, if so, in what concentration. They used the new device to measure the blood serum levels of two important sepsis relevant biomarkers, procalcitonin and C-reactive protein. Doctors can use this information to accelerate the triage of sepsis patients, ultimately saving lives.

“We believe our low-cost, compact biosensor would be a valuable piece of equipment in ambulances and certain hospital wards,” says Hatice Altug, the head of BIOS. Scientists already have possible applications in mind. “There is an urgent need for such promising biosensors so that doctors can diagnosis sepsis accurately and quickly, thereby keeping patient mortality to a minimum,” say Anna Fàbrega and Juan José González, lead doctors at Vall d’Hebron University Hospital.

Reference

Alexander Belushkin, Filiz Yesilkoy, Juan Jose González‐López, Juan Carlos Ruiz‐Rodríguez, Ricard Ferrer, Anna Fàbrega, Hatice Altug, Rapid and Digital Detection of Inflammatory Biomarkers Enabled by a Novel Portable Nanoplasmonic Imager, Small

Source: École polytechnique fédérale de Lausanne (EPFL)

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Imperial College Scientists Win €22.5m EU Funding to Develop Rapid Test Based on Gene Signatures

A rapid test to diagnose severe illnesses, using personalised gene signatures, is being developed by scientists at Imperial College London.

The new approach could speed up diagnosis times for many serious conditions including pneumonia, tuberculosis, sepsis, meningitis, and inflammatory and immune diseases, to under two hours.

The landmark project, involving an international consortium led by Imperial, has been awarded a major EU grant worth €22.5m over five years, to develop the test and bring it to hospitals across Europe. The current stepwise process of diagnosing infectious and inflammatory diseases involves doing many different blood tests and scans which can be slow and inefficient, meaning that there may be significant delays before the right treatment is given.

The researchers believe diagnosis can be made accurately and rapidly on the first blood sample taken when a patient attends a hospital or health centre, by identifying the pattern of genes switched on in each patient’s blood.

Unique gene signatures

The team of scientists, led by Imperial’s Professor Michael Levin from the Department of Infectious Disease, believe that the test could completely change the way patients are diagnosed.

The work will build on over a decade of research into the pattern of genes switched on in the blood in different conditions.

The team’s previous research discovered that each disease is associated with a unique pattern of genes that are switched on or off – which form a ‘molecular signature’ – which can be used to rapidly identify each disease.

Earlier studies using the technique found that it could predict a bacterial infection with 95-100 per cent accuracy.

The international group will build a ‘library of gene signatures’ where the signatures of all common infectious and inflammatory diseases will be stored and made publicly available.

By comparing the pattern of genes in each patient’s blood sample with the signature of all diseases in the ‘gene signature library’, the diagnosis in each individual can be made rapidly.

Currently if a patient enters hospital with symptoms such as a high fever and feeling unwell they could go through a whole series of investigations, such as blood tests, spinal fluid samples, MRI and CT scans, while medics try to identify the cause.

Patients can also be treated with antibiotics unnecessarily as a precaution in case they have a bacterial infection. Investigations can take days or weeks before an accurate diagnosis is made, delaying treatment, taking up resources and costing vast amounts of money.

Gene library

The team will spend the next two years building the library of gene signatures covering all common conditions.

In parallel to the search for diagnostic signatures, engineering and industry members of the team will develop novel device prototypes that can quickly and accurately determine gene expression in a blood sample – this is done by measuring the number of RNA molecules each gene is making.

They will turn this into a rapid test platform that can measure the small number of genes needed to diagnose most common infectious and inflammatory diseases. In the final stage they will conduct a trial of the new diagnostic approach compared to current diagnosis.

The team believe that measurement of 100-150 genes will enable identification of all common infectious and inflammatory diseases, and that this can be achieved within 1-2 hours, so a final diagnosis can be made rapidly and avoiding unnecessary investigations and treatment.

New approach to diagnosis

The scientists have called this new approach Personalised Molecular Signature Diagnosis (PMSD) and they aim to conduct the first pilot trials in UK and European hospitals in 2023 and 2024.

Project lead, Professor Michael Levin, from the Department of Infectious Disease at Imperial College London, said: “We’re very confident that identifying the pattern of genes switched on in each patient will enable us to make an accurate diagnosis rapidly, as every disease has its own unique signature.

“The ambition is to develop a rapid test that will make the correct diagnosis based on the gene signature on the first blood sample taken when a patient arrives in hospital, and with the result within 1-2 hours. In the future the whole basis of medical diagnosis could be based on molecular signatures.”

Dr Myrsini Kaforou, from the Department of Infectious Disease, said: “This award has resulted from several years collaborative and cross disciplinary work, linking the strength of Imperial in computational biology and big data analysis, genomics, and clinical medicine and engineering, with partner institutions across Europe.

"The DIAMONDS project has drawn from strengths of different departments at Imperial, and reflects what can be achieved in cross disciplinary research.”

The project, named DIAMONDS (Diagnosis and Management of Febrile Illness using RNA Personalised Molecular Signature Diagnosis), involves teams in Austria, France, Germany, Greece, Italy, Latvia, Slovenia, Netherlands, Spain, Switzerland, Taiwan, Gambia, Australia, Nepal and the UK.

The group will recruit thousands of patients from across Europe with conditions caused by infections, and inflammation. It is being funded by the EU’s Horizon 2020 Research and Innovation Actions.

The project is very multidisciplinary, also including the team of Dr. Pantelis Georgiou from the Department of Electrical and Electronic Engineering, who will be developing a rapid point of care test using microchip technology to detect the gene signatures, and Dr Jethro Herberg, Clinical Senior Lecturer in Paediatric Infectious Diseases, who was previously involved with the PERFORM study.

The team’s previous projects, ILULU, EUCLIDS and PERFORM have successfully identified gene patterns for several conditions such as tuberculosis, Kawasaki disease, bacterial and viral infections.

The EU has awarded Professor Michael Levin nearly 60 million euros since 2006. This vital funding paved the way for early studies and collaborations with partners across Europe.

In 2006, the EU awarded Professor Levin and his team 5 million euros to study tuberculosis. This initial grant enabled his team to begin using molecular signatures to diagnose TB.

Then in 2012, Professor Levin was awarded a 12 million euros grant to study the genetic factors that influence children’s susceptibility to bacterial infections. The EUCLIDS project, funded by the European Union’s Seventh Framework Programme for Research (FP7), involved 14 partner institutions in six countries.

In 2016, the EU awarded the team a further 18 million euros to develop a rapid test to allow medics to quickly identify bacterial infection in children. The PERFORM project built on their previous research that showed bacterial illnesses can be identified by a particular patterns of genes and proteins.

The new DIAMONDS project has been awarded 22.5 million to bring the revolutionary approach to diagnosis to hospitals across Europe.

Professor Levin said: “The EU has been our most valuable source of funding and has enabled us to establish a wonderful network of researchers in different countries working together, with exchange of ideas and movement of young scientists between countries.

“We were able to pull in expertise of the best laboratories from across Europe. It opened up a new way of doing research that wouldn’t have been possible without the EU funding.”

Source: Imperial College London

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Pocket-Sized DNA Sequencers Could Stop Food-Borne Pathogen Outbreaks as Soon as They Start

I recently reviewed an interesting story on food-borne pathogen outbreaks and the need to rapidly detect microorganisms to minimize the impact on people's lives. In a recent Massive Science article, microbiologist Bhavya Singh describes the use of a pocket-sized DNA sequencer that makes it easier to detect outbreaks before they cause significant harm. The article is reprinted below.

A few months ago, the Canadian Food Inspection Agency (CFA) recalled frozen chocolate eclairs due to a possible Salmonella infection.

That’s just one. In the past year alone, there have been enough food-related outbreaks that I have now made it a regular habit to check for food recalls on the CFA website. Unfortunately, the biannual recall of romaine lettuce is the least of our worries. From leafy greens to herbal tea, food recalls due to pathogenic outbreaks are on the rise. The U.S. Center for Disease Control and Prevention (CDC) reports that 1 in 6 Americans are affected by food-borne pathogens, with roughly 3,000 people dying due to these illnesses. These statistics make food-borne pathogens a public health concern that affects everyone.

To combat this problem, scientists are now using a portable device to sequence DNA from food and detect infection-causing organisms in just a few hours. Being able to identify an infected product before it causes a pathogenic outbreak can save lives, and current research will finally allow us to do that.

The Oxford Nanopore MinION is a pocket-sized DNA sequencer – it’s smaller than a typical smartphone, and significantly faster at producing data than most sequencers currently in use. Current full-genome sequencing technologies require over 24 hours to go from DNA extraction to analysis, without including the extra time to culture and grow pathogens. Overall, it can take days. Days. That is more than enough time for infected food to travel from grocery stores to homes.

Perhaps the most exciting feature of this technology is that sequences can be analyzed in real-time, making this process even faster by reducing the data processing time typically required for sequencing data.

A joint study from the University of Massachusetts and New England Biolabs recently put the MinION to the test for detecting viable food pathogens. The researchers chose to use RNA sequencing, as opposed to DNA sequencing, to address one of the major issues with DNA-based analyses: the inability to differentiate between DNA from viable and living pathogens, versus background DNA. Since RNA is less stable than DNA and has a shorter life once cells have died, it is relatively safer to assume that any detected RNA is from living pathogens. The MinION had a turnaround time of just 6.5 hours to sequence the transcriptomes of multiple bacteria, from the first step to the final analysis. Another recent study that instead employed DNA sequencing was able to sequence the entire genome of a Salmonella strain with a total turnaround time of 10 hours, without including the 24 hours it took to grow the bacterial cultures prior to DNA extraction.

Current standard procedures for identifying outbreaks can also be a huge financial barrier. Isolating, culturing (for identification, older techniques often need to create more pathogen than a sample provides), and sequencing microorganisms requires expensive laboratory equipment and facilities. Unfortunately, these facilities might not be accessible in places where outbreaks can cause the most damage. Even the size of most sequencers can be a barrier to fast detection – most instruments cannot be picked up and carried from site to site, making them very impractical for the food industry, particularly in situations where something needs to be analyzed on-site.

Another research group, known as the Tree Lab, has been conducting a study in East Africa to see if the MinION’s success could be replicated in the field. The lack of access to equipment can require agricultural scientists to transport samples to third-party services, which are often in different countries. Delays caused by transportation, data analysis, and communication can increase the timeline of pathogen detection to a staggering six months. Such a large turnaround time hinders the quick decision-making that is required to protect crops and manage disease outbreaks. The Tree Lab aimed use a MinION to cut this timeline down to just a few hours, compared to the grueling months when relying on conventional approaches.  Instead of sending samples away for analysis, the researchers wanted to carry out every step of the procedure on-site, with local scientists and farmers. This would circumvent a lot of the previous caveats, such as the exorbitant costs, the potential of sample degradation and contamination during travel, and the arduous and memory-intensive task of sharing extremely large amounts of sequencing data over the internet.

With farm conditions that included no access to laboratories, reliable electricity, or internet connection, the researchers collected samples from cassava plants. As the fourth largest source of food in the world, cassava is a staple for 800 million people in the world. Unfortunately, pathogens such as the cassava mosaic begomoviruses can cause devastating damage to crop yields.

In their Cassava Virus Action Project, members of the Tree Lab were able to sequence and detect the cassava mosaic begomovirus in under four hours. In addition to the speed of the portable DNA sequences, this was made possible by a rapid DNA extraction technique, which further cut down the time it would typically require to culture and grow pathogens before extracting DNA. Pre-installed and pre-curated databases also circumvented the need for high-powered computers for data analysis.

While these results are promising, there are a few things to consider before portable DNA sequencers can become standard procedure for pathogen surveillance.

First, the Tree Lab conducted an excellent proof-of-concept experiment to show that portable DNA sequencers can be used in the field, where laboratory equipment and scientific experts are not readily available. However, transitioning out of current procedures and using portable DNA sequencers in practice will take time and additional investments. Secondly, while Nanopore sequencing is incredibly fast, one major trade-off is the reduced sequencing quality, which can affect the ability of bioinformatics tools to detect the source of the DNA sequences. Lastly, phasing out current technologies and introducing pocket sequencers will require large amounts of training, changes in current rapid-response procedures, and advances in other bioinformatics tools to aid in accurate detection and analysis of pathogens.

Currently, most food-borne pathogens are only detected after people get ill. Surveillance patterns of these cases are then used to find the source of the outbreak and identify the contaminated food. This outbreak is controlled by removing the contaminated food from shelves and homes. While scientist are making strides in streamlining pathogen detection, we have a long way to go. Until then, it doesn’t hurt to periodically check for food recalls on your local government websites.

Source: Massive Science

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Early Detection of Viruses in Biopharma

Researchers in Carnegie Mellon University’s Department of Chemical Engineering (ChemE) are collaborating with leading biotechnology company Genentech, a member of the Roche Group, and LumaCyte, a biotechnology instrumentation company based in Charlottesville, VA, to develop an advanced biomanufacturing technology for adventitious agent testing, or testing for unexpected viral infections during the production of biopharmaceuticals.

The research recently received funding from the National Institute for Innovation in Manufacturing Biopharmaceuticals (NIIMBL) to develop and test technologies for improving the safety testing of biologic medicines during production and prior to release. This project, which aims to rapidly and accurately detect viral infectivity in biopharmaceuticals, was one of the first four proposals funded by NIIMBL. The team, which includes Carnegie Mellon, Genentech, and LumaCyte, will receive $1.5 million in funding from NIIMBL over 18 months.

When using biological materials such as mammalian cell lines to produce pharmaceuticals, manufacturers face the risk of viruses infecting the batch. Currently, testing for adventitious agents such as viruses happens late in the manufacturing process—but the research team, which includes ChemE Professor Jim Schneider and Adjunct Professor Todd Przybycien, are developing technologies to test biopharmaceutical batches while they are being produced.

“If you don’t find out about infection until very late in the process, you will have wasted a lot of time and money as more downstream equipment and product becomes infected,” says Schneider. “Current infection detection techniques, such as cell-based assays and polymerase chain reaction, can take days to complete. Our methods can provide readout in less than 15 minutes, which enables a routine, continuous type of testing that could detect infections almost as soon as they take hold.”

Rapid DNA analysis has been in development for a number of years by Schneider and Przybycien, who is also a professor of chemical and biological engineering at Rensselaer Polytechnic Institute. Using a rapid DNA analysis technique developed in Schneider’s lab, the team is detecting viruses and bacteria in process streams used to make biologic pharmaceutical projects. By performing rapid electrophoresis, the researchers can separate tagged and untagged DNA in a sample, indicating the presence of virus or bacteria in biologic process streams.

The researchers aim to combine their method with LumaCyte’s LFC and Radiance technology for a faster, more reliable, and more cost-effective solution. LumaCyte’s Radiance and Carnegie Mellon’s patented rapid DNA analysis platform will combine to rapidly detect the presence of virus and/or bacteria in bio process streams.

“The focus of NIIMBL is to translate existing technologies into biomanufacturing contexts,” said Schneider. “One of the top priorities that the industry has identified is rapid adventitious agent screening. As one of the first four projects funded by NIIMBL, this research with LumaCyte and Genentech shows our commitment to collaboration between academia and the pharmaceutical industry."

NIIMBL is an Innovation Institute designed to revolutionize domestic biopharmaceutical manufacturing. Funded through a $70 million cooperative agreement with the National Institute of Standards and Technology (NIST) in the U.S. Department of Commerce, NIIMBL funds and collaborates on innovative manufacturing technologies that bring life-saving and life-enhancing products to market faster and at reduced cost, while maintaining safety and efficacy.

LumaCyte is an analytical instrument development company headquartered in Charlottesville, VA. LumaCyte produces a label-free cell analysis and sorting instrument called Radiance that does not require the use of antibody or genetic labelling for analysis of cells. Applications of LumaCyte’s label-free platform technology include viral infectivity for vaccine manufacturing, cell and gene therapy, cancer biology, infectious disease, and pre-clinical drug discovery.

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New Diagnostics to be Highlighted at the European Congress of Clinical Microbiology & Infectious Diseases (ECCMID) in Amsterdam

A number of companies will be highlighting their new technologies at the 29th Annual European Congress of Clinical Microbiology and Infectious Diseases (ECCMID). ECCMID is being held on April 13 – 16, 2019 in Amsterdam, Netherlands. Below you will find prep releases from some of these companies.

Mesa Biotech to Introduce Expanded Molecular POC Testing Portfolio at the European Congress of Clinical Microbiology and Infectious Diseases

Mesa Biotech Inc., a privately-held, molecular diagnostic company that has developed an affordable and easy to operate PCR (polymerase chain reaction) testing platform designed specifically for point-of-care (POC) infectious disease diagnosis, today announced it will demonstrate its expanded, novel Accula™ Test System at the 29th Annual European Congress of Clinical Microbiology and Infectious Diseases (ECCMID). ECCMID is being held on April 13 – 16, 2019 in Amsterdam, Netherlands and the Accula System will be on exhibit in Booth 1.1C. Mesa Biotech has obtained CE Mark in the European Union (EU), as well as 501(k) clearance and CLIA Waiver from the U.S. Food and Drug Administration (FDA) on both its Accula Flu A/Flu B and RSV tests.

The Accula System, recently named 2019 Frost & Sullivan Price/Performance Global Value Leader, is a palm-sized, reusable dock with disposable test cassettes. The novel molecular test system offers the simplicity, convenience and procedural familiarity of traditional POC rapid immunoassays, while providing the superior sensitivity, specificity and information content of laboratory-based PCR testing. Test results are available in approximately 30 minutes to guide same day treatment decisions. Both the Accula Flu A/Flu B and RSV tests are indicated for use with nasal swab collection that is less invasive than nasopharyngeal swabs and allows for a more comfortable specimen collection experience for the patient.

"We are excited to introduce our expanded PCR test platform at ECCMID," said Hong Cai, Co-founder and Chief Executive Officer, Mesa Biotech, Inc. "As our product offerings continue to increase, we are carefully selecting additional strategic distributors to add to our growing international network."

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 disposable, 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.

T2 Biosystems and Clinicians to Share Clinical Data in Integrated Symposium and Poster Presentations at the European Congress of Clinical Microbiology & Infectious Diseases (ECCMID)

T2 Biosystems, Inc., an emerging leader in the development of innovative medical diagnostic products for critical unmet needs in healthcare, announced today that the Company will host an integrated symposium highlighting key clinical data about the T2Bacteria® and T2Candida® panels at the European Congress of Clinical Microbiology & Infectious Diseases (ECCMID) in Amsterdam on Monday, April 15, at 16:00-18:00 Central European Time (CET). ECCMID will take place April 13-16 at the Amsterdam RAI Exhibition and Convention Center.

Additionally, seven leading clinicians and users of T2Direct Diagnostics™ will offer scientific presentations during ECCMID that will highlight the most recent scientific data on the Company’s FDA-cleared T2Bacteria and T2Candida Panels. The Company will also present the first patient case studies with the T2Resistance™ Panel, which recently received FDA Breakthrough designation and is pending CE mark for commercial availability in Europe. All presentations will demonstrate the potential for these panels to significantly improve infectious disease management for patients in real clinical settings.

“I have seen firsthand how the rapid detection of bacterial and fungal pathogens with T2Direct Diagnostics can improve patient outcomes, better manage broad-spectrum antimicrobial usage and combat antibiotic resistance,” said Neil Clancy, MD, University of Pittsburgh Medical Center, who is one of the integrated symposium speakers.

The T2Bacteria and T2Candida Panels are able to identify sepsis-causing pathogens within 3 to 5 hours directly from whole blood, instead of days required with blood culture based diagnostics. This gives clinicians actionable information much earlier than was previously possible, allowing them to make more informed treatment plans for escalation or de-escalation of antimicrobial therapy.

Dr. Clancy continued, “When diagnosing and treating infectious diseases, time is of the essence. I am proud to be one of the clinicians here at ECCMID using T2Direct Diagnostics and believe that we must continue to spread awareness about this rapid diagnostic technology to improve patient care.”

T2 Biosystems will showcase its latest innovations at Booth #1.22. The Company will also host an educational event, “Rapid Diagnostics Direct from Whole Blood: A Solution for Fast and Appropriate Antimicrobial therapy,” which will be co-chaired by Prof. Karsten Becker, MD, University Hospital Münster and Prof. Emmanuel Roilides, MD Aristotle University of Thessaloniki; and it will include the following presentations:

Integrated Symposium

-- “Rapid Diagnostics Direct from Whole Blood: A Solution for Fast and Appropriate Antimicrobial Therapy,” on Monday, April 15 from 16:00-18:00 CET in Hall D; presenters include: • Prof. Michael Bauer, MD, Jena University (Jena, Germany) • Dr. Cornelius (Neil) Clancy, University of Pittsburgh Medical Center (Pittsburgh, PA) • Dr. Giulia De Angelis, Institute of Microbiology, UniversitàCattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli (Rome, Italy) • Dr. Thomas Walsh, New York Presbyterian Hospital (New York, NY)

Poster Presentations

-- Development of a highly sensitive assay for the detection of carbapenem-resistance genes from whole blood by T2 magnetic resonance, on Sunday, April 14, from 13:30-14:30 CET (Tom Lowery) -- Real-life diagnostic performance of T2Candida among ICU patients with risk factors for invasive candidiasis, on Tuesday, April 16 from 12:30-13:30 CET (Maiken Arendrup) -- The T2Bacteria assay is a sensitive and rapid detector of bacteraemia that can be initiated in the emergency department and has potential to favourably influence subsequent therapy, on Tuesday, April 16 from 12:30-13:30 CET (Christopher Voigt) -- The T2Bacteria Panel is a rapid detector of bacteraemia and has potential to guide therapy in patients with haematological malignancies and haematopoietic stem cell transplantation: a pilot study of non-culture molecular diagnosis, on Tuesday, April 16 from 12:30-13:30 CET (Thomas J. Walsh) -- Evaluation of a molecular technology magnetic resonance for the direct identification of pathogens from blood samples in paediatric patients with suspected sepsis, on Tuesday, April 16 from 12:30-13:30 CET (Paola Bernaschi)

About T2 Biosystems

T2 Biosystems, a leader in the development and commercialization of innovative medical diagnostic products for critical unmet needs in healthcare, is dedicated to improving patient care and reducing the cost of care by helping clinicians effectively treat patients faster than ever before. T2 Biosystems’ products include the T2Dx® Instrument, T2Candida® Panel, and T2Bacteria® Panel and are powered by the proprietary T2 Magnetic Resonance (T2MR®) technology. T2 Biosystems has an active pipeline of future products, including products for the detection of additional species and antibiotic resistance markers of sepsis pathogens, and tests for Lyme disease.

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Sherlock Biosciences Launches to Provide Better, Faster and More Affordable Diagnostic Testing Worldwide Through Engineering Biology

Sherlock Biosciences, an Engineering Biology company dedicated to making diagnostic testing better, faster and more affordable, announced its launch and initial financing of $35 million. The financing includes a $17.5 million non-dilutive grant and an investment from the Open Philanthropy Project with support from additional undisclosed investors.

Sherlock is using Engineering Biology tools, including CRISPR and Synthetic Biology, to create a new generation of molecular diagnostics that can rapidly deliver accurate and inexpensive results for a vast range of needs in virtually any setting.

“Our founders have created some of the most important breakthroughs in modern science through advances in the field of Engineering Biology, the practice of designing and building biological systems into tools that can enhance human health,” said Rahul K. Dhanda, Sherlock’s co-founder, president and CEO. “We are building Sherlock to transform these breakthroughs into a new and powerful generation of molecular diagnostics that will enable users to make more effective decisions in both clinical and non-clinical settings worldwide – including hospitals, industrial settings, low-resource settings and at home.”

The company takes its name from one of its foundational platform technologies, SHERLOCK™ (Specific High-sensitivity Enzymatic Reporter unLOCKing), which is licensed from the Broad Institute of MIT and Harvard. SHERLOCK was developed by a team led by co-founder and chair of Sherlock’s scientific advisory board Feng Zhang, Ph.D., and collaborators, as a method for identifying specific genetic targets using CRISPR. SHERLOCK can detect genetic fingerprints across multiple organisms or sample types and has been described in four papers published in the journal Science.

The company is also developing INSPECTR™ (INternal Splint-Pairing Expression Cassette Translation Reaction), a Synthetic Biology-based molecular diagnostics platform developed by a team led by co-founder James J. Collins, Ph.D., at the Wyss Institute for Biologically Inspired Engineering at Harvard University. The technology, licensed from Harvard’s Office of Technology Development, can be programmed to distinguish targets based on a single nucleotide without an instrument, at room temperature.

Used as stand-alone tools or in combination, these platforms allow for the detection and quantification of targets without complex instruments and in a variety of potential settings. The flexibility and modularity of these platform technologies open a wide range of potential applications and actionable insights in areas including precision oncology, infection identification, food safety, at-home testing, and disease detection in the field.

The company will employ a strategy of selective partnering and direct product development to apply these technologies into a wide range of settings and applications. The financing will be used to advance development programs and design new assays.

“Engineering Biology-based tools have broad potential to transform not just the treatment of disease but also how diseases are diagnosed,” said co-founder James Collins, Ph.D. “Sherlock Biosciences will make a significant difference in the world by bringing the power of Synthetic Biology and CRISPR to diagnostic development.”

“We believe Sherlock Biosciences offers an enormous opportunity to improve human health worldwide by delivering fast, accurate and simple diagnostic testing. It is especially encouraging that the broad potential of its technologies is matched by co-founders and a team who are deeply experienced scientists, entrepreneurs and clinicians,” said Heather Youngs, program officer for scientific research at the Open Philanthropy Project. “Development of this technology could both reduce viral pandemic threats and benefit healthcare more broadly. We are excited to support Sherlock’s efforts to realize the potential of diagnostics and propel this technology into the mainstream.”

“Our team has the expertise and technology to transform diagnostics with a powerful set of Engineering Biology tools to enable rapid test design and deployment, an essential component of addressing many healthcare needs, including the growing problem of resistant bacteria,” said co-founder Deborah Hung, M.D., Ph.D. “After early experiments, our tools were quickly used in a wide range of geographies with real patient samples, confirming that we can swiftly respond to urgent healthcare needs.”

“We founded Sherlock Biosciences to improve health worldwide through the development of disruptive molecular diagnostics. We are delighted to have the support of the Open Philanthropy Project and our investors as we develop Sherlock’s platforms to achieve that goal,” said co-founder David Walt, Ph.D. “Existing molecular diagnostic tools are often limited in their effectiveness because they are costly, labor-intensive, and are not mobile. We believe that Sherlock is poised to overcome those challenges by creating tests that are faster, less expensive and easier to use than currently available molecular diagnostics.”

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FDA, CDC, and CMS Launch Task Force to Facilitate Rapid Availability of Diagnostic Tests During Public Health Emergencies

The U.S. Food and Drug Administration, Centers for Disease Control and Prevention (CDC) and the Centers for Medicare and Medicaid Services (CMS) announced the launch of the Tri-Agency Task Force for Emergency Diagnostics. This task force has been created to help leverage the expertise of each agency to advance rapid development and deployment of diagnostic tests in clinical and public health laboratories during public health emergencies.

“Public health emergencies, like Ebola outbreaks, remind us that we’re a global community when it comes to public health protection. Bacteria and viruses don’t respect territorial boundaries. It takes a sustained, robust and globally coordinated effort to protect our nation and the global community from various infectious disease threats. We’re all in this together. To that end, the FDA knows that collaborating with our federal partners to employ our collective expertise, experiences from previous incidents, and resources will better assist in a global response. We also believe that this task force could lead to more innovation for diagnostic tests as developers will see a more predictable federal regulatory response through the agencies’ coordination,” said Jeffrey Shuren, M.D., J.D., director of the FDA’s Center for Devices and Radiological Health. “This task force will help our agencies better collaborate to prepare for, and respond to, public health threats, including identifying threats and ensuring the appropriate diagnostics are in place to support efforts in the field.”

The FDA, CDC and CMS each play a critical role in responding to public health emergencies, including identifying threats, regulating medical products, and providing oversight for laboratories. The agencies have robust teams of scientists, researchers and policy experts that are dedicated to preparing the U.S. for rapid disaster response.

Diagnostic tests—such as those that can detect pathogens like the Ebola and Zika viruses—can be quickly made available to meet response needs during a crisis through the Emergency Use Authorization (EUA) process. The FDA has authority to issue an EUA for the use of diagnostic tests during public health emergencies, provided criteria are met. The CDC is responsible for providing agent-specific subject matter expertise in epidemiology, laboratory expertise and guidance to clinicians and laboratories responding to the emergency. The CDC and other federal laboratories are often the ones developing new tests to respond to emergency needs. CMS has authority to ensure quality testing at laboratories through the Clinical Laboratory Improvement Amendments (CLIA). CMS provides guidance, even during public health emergencies, to laboratories on meeting CLIA requirements to ensure laboratories produce accurate, reliable and timely results.

Prior to this partnership, feedback from the clinical laboratory community indicated that there was uncertainty about how to implement the diagnostic tests once they received an EUA; particularly, the community was uncertain about meeting CLIA regulations under an EUA to allow labs to start testing specimens.

“During public health emergencies, ensuring the health and safety of patients through quality laboratory testing will remain the focus of CMS,” said Kate Goodrich, director of the Center for Clinical Standards and Quality and CMS Chief Medical Officer. “Timely implementation of EUA diagnostic assays in the US healthcare system is dependent upon laboratories understanding the instructions for use and applying them to the patient samples received for testing. As part of this taskforce, it is our goal to provide clear and consistent guidance to laboratories on the application of CLIA requirements for these emergency assays.”

By standardizing collaboration efforts, the federal partners hope to address issues related to implementation of diagnostic tests authorized for emergency use under an EUA, as well as other unmet needs and gaps in preparing and responding to global health threats. The task force will provide a forum for each agency to coordinate, provide consultation, and improve the availability of diagnostic tests during public health emergencies. In addition, to assist in public health preparedness, the task force will work to define, refine and streamline interagency approaches for the implementation of EUA diagnostic tests. The hope is that the task force will enable an even more efficient federal government response for making diagnostic tests available in the event of a public health emergency.

“Time and time again, we’re reminded that disease knows no borders. While our globalized world and modern transportation help promote economic prosperity, these features also facilitate the spread of emerging infectious diseases,” said Chesley Richards, CDC’s Deputy Director for Public Health Science and Surveillance. “In the past 15 years alone, we’ve faced serious global outbreaks of deadly pathogens. During public health emergencies, it is critical for diagnostic tests to be made available and adopted quickly into clinical and public health laboratories for rapid patient care.”

The FDA, an agency within the U.S. Department of Health and Human Services, protects the public health by assuring the safety, effectiveness, and security of human and veterinary drugs, vaccines and other biological products for human use, and medical devices. The agency also is responsible for the safety and security of our nation’s food supply, cosmetics, dietary supplements, products that give off electronic radiation, and for regulating tobacco products.

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“0D” Microarrays Of Live Bacteria Using AC Electrokinetics On A Chip

Bacteria have been around for over a billion years and have developed remarkable capabilities to not only cause deadly infections but also to survive adverse environmental conditions (1, 2). This has led to a rich cellular diaspora with diverse geno- and phenotypic variability that is important to characterize owing to its dire implications on mankind.

Researchers are constantly evolving strategies that allow them to study complex cellular processes like cell-cell interactions, cellular metabolic activity, gene function, response to external stimuli (3-7), host-pathogen interactions, and surface-associated redox activities (8) at a single cell level. The foremost requirements of these single cell test platforms are to distinguish, isolate, manipulate, immobilize, and characterize cells in an easy and reproducible manner.

The conventional methods widely used for single cell isolation include fluorescence- or magnetic-activated cell sorting (FACS/MACS), micromanipulation, microdissection, and manual cell picking. While FACS/MACS need high cellular loads, large sample volumes and specific treatment of cells prior to analysis, the remaining techniques have quite a low throughput and require highly-skilled labor for carrying out the experiments. Other methods for cell capture include ink-jet printing on molecularly-patterned templates (9) or dip-pen nanolithography (10), but they again, suffer from poor reproducibility, high cost, and our inability to reuse the substrate.

With recent advances in the field of microfluidics, manipulation and separation of cells on the basis of their dielectric properties, using external electric fields has garnered significant attention. This approach offers numerous advantages such as a high extent of miniaturization, low sample volume, controlled fluid dynamics, ease of sample handling, high throughput, great precision, automation, and label-free operation.

Motivated by these factors, we exploited an electrokinetic phenomenon called alternating current (AC) dielectrophoresis to collect live bacterial cells into grid-like patterns, with each node containing a single cell (see image below). This electric field-assisted assembly not only provided high spatio-temporal control over several thousands of cells simultaneously, but the dynamically-formed cellular arrays were also fully reversible meaning that both the cells and the chips could be retrieved at the end of each capture cycle. This study was recently published in Biosensors and Bioelectronics (111, 2018, 159–165) and showed that model Gram-negative bacteria S.typhi and E.coli can be trapped inside micropatterned conductive circular well electrodes by applying AC electric fields (5 MHz, 5-20 Vpp) across a few microliters of cell suspension.

Dynamic electropatterning of live bacteria into single microwell arrays using AC electrokinetics. The bacteria were fluorescently tagged to allow visualization. Image courtesy Meenal Goel & Shalini Gupta

Shrinking the size of the individual electrodes down to 5 μm allowed single cells to be captured per well with 90% efficiency. This trapping of cells took place due to positive dielectrophoresis that attracted them toward regions of high electric field intensity (microwells in our case). The cells remained alive during the one-hour-long operation, and the overall collection efficiency (from bulk to the surface) was also found to be around 90%.

The potential biotechnological application of our chip was demonstrated in two ways. First, the two cell types were mixed in suspension and collected together using the chip. Counting their relative concentration in the 2D matrix using their phenotypic traits allowed us to directly estimate cellular bulk concentrations in the mixture without generating any calibration curves. Both the total time taken and the volume of the sample used was a fraction of the conventional methods. In the second case, the chip was integrated with an impedance spectroscope to carry out rapid cell viability testing. The response of dielectrophoretically-trapped bacteria against a known antimicrobial peptide was recorded at different drug concentrations and found to be ultrasensitive, reducing the overall time for drug susceptibility testing to just under an hour. This is a significant reduction over standard clinical methods that take several hours to produce outcomes.

In the future, our technology could be used for a wide range of applications including multiplexed sensing, rapid single bacterial profiling in heterogeneous populations, and ultrafast drug susceptibility testing to reduce the use of broad-spectrum antibiotics and, hence, the emergence of new antibiotic-resistant strains.

These findings are described in the article entitled Electric-field driven assembly of live bacterial cell microarrays for rapid phenotypic assessment and cell viability testing, recently published in the journal Biosensors and Bioelectronics. This work was conducted by Meenal Goel, Abhishek Verma, and Shalini Gupta from the Indian Institute of Technology Delhi.

Source: Science Trends

References:

1. Turner, N. A., Harris, J., Russell, A. D., Lloyd. D. 2000. J. Appl. Microbiol. 89, 751–759.
2. Davey, M. E., O’Toole, G. A., 2000. Microbiol. Mol. Biol. Rev. 64, 847–867.
3. Flaim, C.J., Chien, S., Bhatia, S.N., 2005. Nat. Methods 2, 119–125.
4. Hung, P.J., Lee, P.J., Sabounchi, P., Lin, R., Lee, L.P., 2005. Biotechnol. Bioeng. 89, 1–8.
5. Lee, M.Y., Dordick, J.S., 2006. Curr. Opin. Biotechnol. 17, 619-27.
6. van der Meer, J.R., Belkin, S. 2010. Nat. Rev. Microbiol. 8, 511–522.
7. Ziauddin, J., Sabatini, D.M., 2001. Nature 411, 107–10.
8. Potma, E. O., de Boeij, W. P., van Haastert, P. J. M., Wiersma., D. A. 2001. Proc. Natl. Acad. Sci. 98, 1577–1582.
9. Xu, Luping, Robert, Lydia, Ouyang, Qi, Taddei, François, Chen, Yong, Lindner, Ariel B., Baigl, Damien, 2007. Nano Lett. 7, 2068–2072.
10. Kim, J., Shin, Y.-H., Yun, S.-H., Choi, D.-S., Nam, J.-H., Kim, S.R., Moon, S.-K., Chung, B.H., Lee, J.-H., Kim, J.-H., Kim, K.-Y., Kim, K.-M., Lim, J.-H., 2012. J. Am. Chem. Soc. 134, 16500–16503.

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