Tuesday, December 26, 2017

Fast Track Diagnostics and UgenTec Announce New Interpretation Software for All FTD Real-Time PCR Multiplex Kits

Fast Track Diagnostics S.à.r.l., one of the leading global suppliers of syndromic real-time PCR multiplexing kits, has been partnering for several months with UgenTec NV, an innovative European medical device software company that develops artificially intelligent PCR interpretation software.

From the first of January 2018, all Fast Track Diagnostics´ kits will be available on UgenTec´s FastFinder, a fully automated real-time PCR interpretation platform. This module will allow technicians to fully automate and standardise analysis of FTD´s kits with Applied Biosystems 7500 and LightCycler® 480 PCR platforms. The software will be developed for nearly all other clinical PCR machines by end of Q2 2018 and rolled out to users over that period.

The combination of Fast Track Diagnostics' kits and FastFinder’s artificial intelligence will considerably improve the processes within laboratories. The software is developed under ISO13485 standards and is CE IVD-certified.

“Fast Track Diagnostics strives constantly to deliver concrete and high quality solutions to healthcare specialists for the benefit of patients” said Bill Carman, Chief Executive Officer of Fast Track Diagnostics, “UgenTec´s knowledge on overcoming PCR interpretation challenges has brought the analysis time of FTD´s kits down to few minutes, bringing considerable efficiencies to the laboratory workflow.”

“Partnering with Fast Track Diagnostics will result in a strong increase in customer value” said Dr. Tom Martens, Managing Director at UgenTec “Their years of experience in manufacturing syndromic real-time PCR multiplexing kits combined with our IVD software knowledge will allow laboratories across the globe to decrease their eyes-on time drastically”.

Sunday, December 17, 2017

GenePOC Launches its GenePOC™ CDiff Test in the United States

GenePOC Inc. (GenePOC), a member of the Debiopharm Group™, is proud to announce the launch of its 2nd FDA cleared assay in less than 6 months, GenePOC™ CDiff, for use on the revogene™ instrument. The GenePOC CDiff test targets the toxin B gene of toxigenic C. difficile strains in unformed stool specimens obtained from patients suspected of having C. difficile infection (CDI). The test provides a novel and highly flexible alternative to assist clinicians in rapidly identifying, isolating and treating patients having CDI. Consequently, rapid management of patients having CDI will aid in preventing the spread of the bacteria - identified as an urgent threat in healthcare settings by the center for disease control (CDC).

About C. difficile infection in the US 

In the United States, CDI is the leading cause of infectious antibiotic-associated diarrhea with 293 000 infections per year[i] representing $4.8 billion in additional healthcare cost per year[ii]. CDI poses many challenges to health institutions, among which is being able to efficiently test the patients at risk.

Traditional testing methods for identification of toxigenic C. difficile, such as toxigenic culture and enzyme immunoassays (EIA), have been found to be labor intensive, to increase delays and, to have limited sensitivity[iii].

There exists a need for a faster and simpler testing algorithm. According to the 2010 guidance from the American Society for Microbiology, nucleic acid amplification tests detecting C. difficile toxin genes may be used as a stand-alone test[iv]. In fact, those molecular tests provide sensitive, specific and timely identification of patients with toxigenic C. difficile infection, and exhibit better performance than toxin EIAs[v].

According to Dr Nathan Ledeboer from the Medical College of Wisconsin, in Milwaukee: "It all starts with timely diagnosis of C. difficile infections to critically impact patient management and ensure proper implementation of infection control practices". Dr Nathan Ledeboer participated in a multicentric clinical trial, evaluating GenePOC CDiff test for use on the revogene instrument.

About GenePOC CDiff test 

The GenePOC CDiff assay is a qualitative in vitro diagnostic test to detect the toxin B (tcdB) gene of toxigenic C. difficile in unformed (liquid or soft) stool specimens obtained from patients suspected of having CDI. Performing this test enables healthcare professionals to detect the presence of toxigenic C. difficile within 70 minutes after loading the patient sample in the test cartridge or PIE. Early and accurate detection can lead to better control and management of CDI, which in turn can improve patient management and reduce the risk of transmission.

"A simple one-step algorithm to detect toxigenic C. difficile, using a clinical test with excellent performance, will inevitably contribute to better control the spread of CDI and reduce outbreaks" says Dr Patrice Allibert, CEO of GenePOC. "What makes our assay so unique is its right balance between sensitivity and specificity. This translates into the ability to identify patients with CDI from a single GenePOC CDiff test, a molecular test with less than 1% unresolved rate according to clinical trial results. Our test is performed on the affordable, user-friendly revogene instrument which can be directly connected to the hospital and laboratory information systems (LIS/HIS), for seamless transmission and communication of actionable results", Patrice Allibert continued.


i. Dubberke et al. Clin Infect Dis 2012; 55: S88-92.
ii. Lessa et al. N Engl J Med 2015; 372(9):825-834.
iii. Carroll KC. Tests for the diagnosis of Clostridium difficile infection: the next generation Anaerobe. 2011 Aug;17(4):170-4.
iv. Cohen SH, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the Society for Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA). Infect Control Hosp Epidemiol 2010; 31:431-55.
v. Wilcox MH, Planche T, Fang FC. What is the current role of algorithmic approaches for diagnosis of Clostridium difficile infection? J Clin Microbiol, 2010, vol. 48 (pg. 4347-4353).

University of Queensland Researchers Develop Rapid, Cheap Nucleic Acid Extraction Technology

Researchers at the University of Queensland have developed a rapid nucleic acid purification technology that obtains amplification-ready genetic material from difficult biological samples in less than 30 seconds.

In a study published in PLOS Biology, the researchers initially investigated the ability of certain chemicals to capture anionic DNA and RNA by spotting them on a piece of cellulose-based paper. While none of the chemical treatments produced reproducible amplification, the team found that the nucleic acids almost instantly bound to the untreated paper.

In addition, the cellulose-based paper retained the genetic material during a short washing step to remove contaminants, and they then eluted the material directly into an amplification reaction chamber.

"We used the adsorbing solvency of the paper to suck up a certain amount of the genetic sample, as determined by the size of the nucleic acid binding site," Michael Mason, a University of Queensland senior postdoctoral research fellow and co-first author on the paper, said in an interview.

Mason's team adapted the cellulose filter to develop an equipment-free nucleic acid extraction process that uses a dipstick made from the paper, with a small 8-mm2 DNA-binding surface and a long water-repellent handle made by filling the filter paper with paraplast wax.

The process involves homogenizing tissue in a tube containing appropriate lysis buffer and ball bearings to help break down the tissue, then using the dipstick to capture nucleic acids by dipping it into the lysate three times. The dipstick is then dipped up and down in a wash solution three times. Finally, the bound nucleic acids are eluted from the cellulose by putting the dipstick directly into the amplification mix three times.

While researchers have used other types of membranes to induce rapid nucleic acid extraction, including aluminum oxide and silica-based filters, the methods require relatively complex fabrication, multiple pipetting steps, or electrical equipment to help purify the nucleic acids.

To validate the new nucleic acid purification method, Mason's team matched the test against AMPure, a popular commercial rapid paramagnetic bead DNA extraction method sold by Beckman Coulter. They saw that the cellulose method purified amplifiable DNA significantly faster, in under 30 seconds compared to 14.5 minutes for AMPure purification.

While techniques like AMPure only take 10 minutes and do not require electrical equipment, Mason's team believes the tools required are too costly for external applications such as field-based point-of-need assays.  

"Importantly, the method achieves this speed and simplicity without the need for any pipetting, [and is] significantly cheaper, with consumables costing four times less than those required by the AMPure system, and does not require the initial investment of $685-$876 for the specialized magnet plate," the authors stated in the paper.    

According to the study, AMPure's paramagnetic beads cost $0.65 per sample, whereas the team's cellulose dipstick purification method costs $0.15 per sample, including plasticware and reagents. Mason explained that if the ball bearings used to homogenize the tissue are washed and reused, the cost for the cellulose dipstick purification could be further reduced to $0.06 per sample.

Mason and his team have filed a patent for the cellulose disc extraction method through UniQuest, a commercialization company for the University of Queensland. Mason said that UniQuest is currently in discussions with firms interested in commercializing the technology, but did not disclose them at this time.

"We haven't found [any] limitations, but we are looking into new uses for this technology, and we might find that we do need to increase the amount of DNA that binds onto the dipstick," Mason said.

Mason envisions the cellulose-based technology to be used in a wide range of situations, including clinical care and high school science classes. He also plans to use the technology to detect food pathogens, and his team is currently working with food-based molecular diagnostic projects in Papua New Guinea.

"You can have situations in the near future, like in hospitals, if a doctor suspects you have some sort of blood pathogen, he could actually take a drop of blood and perform the test right next to the bedside," Mason said.

In addition, Mason built an electronic amplification device that cost about A$30 ($23) using parts purchased on Ebay. He explained that this device "takes the tube out of the dipstick, performs the reactions, and returns the results quickly." Mason said that "doctors would know within an hour what's wrong with the patient."

New Salmonella Multiplex PCR Solution offers First Validated Assay for Simultaneous Detection of Three Salmonella Targets in One Rapid Test

Poultry and pork producers can now rapidly screen for 3 Salmonella targets with one rapid PCR test. The new Thermo Scientific RapidFinder Salmonella Multiplex PCR System is the first validated multiplex PCR assay for simultaneous detection of Salmonella species, Typhimurium and Enteritidis.

Thermo Fisher Scientific, a market leader in culture media, microbiology, molecular and mass spectrometry systems, has been awarded AOAC-RI Performance Tested MethodsSM certification for its RapidFinder Salmonella Multiplex PCR Detection Workflow. Validated for use on the Applied Biosystems Food Safety 7500 Fast System and the Applied Biosystems Food Safety QuantStudio 5 System, the workflow features simple sample preparation and results in as few as 16 hours from raw and cooked poultry and pork as well as production environment samples.

"Salmonella serovars Typhimurium and Enteritidis are most commonly associated with the disease in humans. As a result there are multiple strategies and regulations targeting a reduction in the contamination level of these serovars in the poultry and pork industries," said Bernd Hofmann, vice president, global marketing, microbiology, Thermo Fisher Scientific. "Identifying the serovar of any Salmonella strain quickly can bring substantial economic benefits to pork and poultry producers. To be able to detect three targets in as few as 16 hours now means product may be released two or three days sooner than when using conventional tests."

Many rapid methods are available to detect all Salmonella species but not all are capable of providing the serovar identity of a Salmonella strain if detected. To get that information the laboratory must run additional rapid tests, which can prove very expensive, or use a series of conventional biochemical and serological tests that can take several days to complete.

The RapidFinder Salmonella Multiplex PCR Solution offers:
  • Simple sample enrichment and PCR preparation protocols – fast & scalable for small to higher-throughput laboratories
  • Multiplexed, simultaneous detection of Salmonella species, Typhimurium and Enteritidis facilitating one-well screening and identification for maximum efficiency
  • TaqMan-based PCR probe technology for excellent sensitivity, specificity and reliability as evidenced through AOAC-RI Performance Tested MethodsSM (PTM) studies
  • Confidence in results – AOAC-RI PTM certification as part of an extensive validation program to address salmonella testing needs at all stages of the poultry and pork production process
In addition to the RapidFinder Salmonella Multiplex PCR Solution, Thermo Fisher Scientific provides real-time PCR-based workflow solutions and other methods to test for a broad range of food safety and quality indicators including other bacterial pathogens, meat species identification and GMO markers, as well as an expanding range of custom developed assays. All of our PCR solutions are designed to run on the Applied Biosystems 7500 Fast Real-Time PCR System which provides expansive molecular capability and streamlined testing processes which may reduce overall costs.

Sekisui Diagnostics Enters Strategic Alliance with Mesa Biotech Inc. for Molecular POC Testing System

Sekisui Diagnostics and Mesa Biotech Inc. announce a strategic alliance, to distribute the Mesa Biotech POC molecular system for Flu A/Flu B.   Sekisui Diagnostics will assume exclusive distribution of the Mesa Biotech POC system in the U.S. and Canada, pending FDA clearance.

The Mesa Biotech molecular dock and test cassette system provides physicians with rapid infectious disease diagnosis at the point of care with increased sensitivity and specificity over most rapid tests currently on the market by using nucleic acid PCR (polymerase chain reaction)amplification technology. The first test cassette will test for Flu A/Flu B with additional tests to be added over time.

"Sekisui Diagnostics is pleased to announce our new relationship with Mesa Biotech which will complement our existing rapid test portfolio," said Robert Schruender, President and COO of Sekisui Diagnostics. "This system is highly compatible with our business channels and relationships with distributors. It also offers the potential to strengthen our flu portfolio in the mid-to-long term by offering physicians 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."

"We are extremely excited to partner with Sekisui Diagnostics for the commercialization of Mesa Biotech's point of care PCR platform in North America," said Dr. Hong Cai, co-founder and CEO of Mesa Biotech. "Our PCR platform solution and pipeline coupled with Sekisui's Diagnostics commercial and supply chain expertise as well as their unparalleled field sales relationships brings tremendous synergy opportunities for both organizations."

About Sekisui Diagnostics

Sekisui Diagnostics is a global diagnostics company committed to improving patient's lives by providing innovative medical diagnostics to physicians and laboratories through a global commercial network.  Product lines include clinical chemistry and coagulation systems, reagents, point-of-care systems and rapid tests, as well as enzymes and specialty bio-chemicals.

About Mesa Biotech Inc.

Mesa Biotech designs, develops and manufactures next generation molecular diagnostic tests, bringing the superior diagnostic performance of nucleic acid PCR amplification to the point-of-care (POC). Mesa Biotech's System consists of a portable, palm-sized dock and a disposable, assay-specific test cassette. This patented system will allow healthcare professionals to access actionable, laboratory-quality results at the POC with greater sensitivity and specificity than current infectious disease rapid immunodiagnostic tests. Mesa Biotech's technology development has been funded to date by a series of grants and private equity investments.

Qvella Progresses on Rapid Sepsis Testing Platform With BioMérieux as New Investor

Toronto-based molecular diagnostics firm Qvella announced this week that it received $20 million in Series B funding, including support from a surprising new investor: BioMérieux.

A potential competitor in the rapid multiplex PCR diagnostics space, BioMérieux said that it will now explore collaborative opportunities in complementary markets around Qvella's field-activated sample treatment, or FAST technology.

BioMérieux sees Qvella's technology as an accompaniment to the BioFire FilmArray diagnostic platform, Frédéric Sweeney, vice president of corporate development and strategic financing said in an email, adding, "Technology that will help to advance microbiology and in vitro diagnostics is a strategic priority for BioMérieux."

Sweeney explained that BioMérieux has a dedicated team of business development professionals who explore and monitor companies, like Qvella, in order to make advancements in addressing growing healthcare threats, such as antimicrobial resistance.

Qvella has primarily focused its development on the fundamental problem of sample preparation, Sweeney further said, including automating the isolation, concentration, and lysis of a small number of pathogens in a whole blood sample.

BioFire FilmArray sample prep, meanwhile, uses silica beads to free the cell components, and magnetic beads to capture the DNA or RNA.

Overall, Qvella's technology "can be seen as a nice complement to many of BioMérieux’s other ranges of microbiology, immunoassay, or molecular biology products," Sweeney further said.

Qvella recently presented preliminary data and announced an updated timeline for the launch of its PCR-based, multiplex blood stream infection (BSI) panel.

The firm noted during a corporate workshop at the Association of Molecular Pathology meeting last month that its BSI test in development requires no extraction or purification. The test uses a fully integrated instrument with an easy-to-use graphical interface and disposable cartridges, and relies on a number of innovative core technologies to detect pathogens directly from whole blood in around 45 minutes.

Firstly, it employs a ribosomal target at the family or genus level to cast a wider net in capturing sepsis-causing pathogens, Qvella's CEO, Tino Alavie, said in a follow-up interview. The firm has balanced this, considering a treatment perspective as well as something that is manageable from a multiplexing perspective, in order "to give the most impactful response to clinicians," Alavie added.

At the AMP workshop, Qvella's scientific administrator Susan Novak reported that a version of the test with 16 reaction wells could detect up to 84 sepsis-causing species. These fit under one family-level, five genus-level, and 10 species-level categories, and covered greater than 90 percent of sepsis cases, according to Novak. The test was also able to identify polymicrobial cases in spiked-in samples.

Qvella's technology also uses a proprietary method for pathogenic cell isolation which involves a hemolysis step followed by centrifugal field and wash steps to generate a cell suspension, Alavie said. Qvella's FAST method is used to treat and lyse cells, after which pathogen nucleic acids can be subjected to array-based multiplex RT-PCR.

One person dies of sepsis every two minutes in the US and delays in initiation of appropriate antimicrobial therapies increase mortality, according to a 2011 review. A presentation at Qvella's workshop highlighted a gap in "rapid" sepsis diagnostics, namely that tests that rely on blood cultures are generally too slow to help in initial treatment decisions.

In the presentation, Larissa May, an emergency room physician who is also an antibiotic steward at the University of California, Davis, said that, from a stewardship perspective, the typical four days to identify a sepsis-causing pathogen is "frankly, unacceptable."

May highlighted that patients are often placed on early empiric, broad-spectrum antibiotic therapy while clinicians wait for lab results that can show the exact pathogen or pathogens that causing the infection. And, in patients with an unknown source of infection, certain pathogens may not be considered in the initial diagnosis, May said in a follow-up interview.

Narrowing of antibiotic spectrum does not occur as early as needed due to current practice patterns and physician behavior, May said, including time constraints of traditional microbiologic testing and a reluctance among prescribers to switch therapies.

"Truly fast tests that [provide results] in less than an hour with high accuracy — with the caveat that this would not obviate the need for confirmatory culture — would enable a much-needed paradigm shift, moving from empiric to initial targeting therapy, earlier de-escalation, and ultimately improved patient outcomes due to more appropriate therapy and improved antibiotic stewardship in healthcare, including for critically ill patients," May said.

BioMérieux, meanwhile, has a company-wide focus on antibiotic stewardship. It's BacT/ALERT Virtuo blood culture platform was cleared by the US Food and Drug Administration earlier this year, and the firm has obtained new indications for its procalcitonin (PCT) diagnostic immunoassay which was recently cleared to guide antibiotic management in suspected sepsis and lower respiratory tract infections.

Subsidiary BioFire manufactures the FilmArray Blood Culture Identification (BCID) assay which was cleared by the FDA in 2013 and tests for 27 pathogens that can cause sepsis, including three common antibiotic resistance markers, in about one hour.

The BCID test has been demonstrated to have clinical benefits. For example, a study in 2015 showed it could lead to reduced use of broad-spectrum antimicrobials as well as earlier de-escalation. And a recent study of pediatric patients with sepsis showed clinical benefits of resistance testing in particular. Both studies also suggested that the clinical benefits of rapid diagnostic microbiological tools are enhanced with a concurrent antibiotic stewardship program, particularly one that includes things like templated comments to guide physician prescribing based on test results. However, although the BCID is faster than conventional culture methods — which can take days and require subculture and phenotypic susceptibility testing — the test still requires a positive blood culture.

Qvella has now lined up all the clinical trial sites for the BSI test, according to Novak.

The firm's timeline to launch includes: US pre-clinical trials from Q2 to Q3 2018; clinical trials, CE mark, and European launch from Q3 to Q4 2018; and FDA submission in Q1 2019.

PathoQuest and Mayo Clinic Enter into an Agreement to Conduct Study of iDTECT™ Blood in Patients with Febrile Neutropenia

PathoQuest, a life sciences leader focused on improving pathogen identification in biological samples, today announced that it will conduct research with Mayo Clinic to study the company’s proprietary iDTECT™ Blood test. Mayo Clinic will explore the use of iDTECT Blood in the context of a prospective study designed to confirm the utility of a next generation sequencing-based metagenomic approach to identify pathogens in patients with neutropenic fever. PathoQuest will work with Robin Patel, M.D., Chair, Division of Clinical Microbiology and Director of the Infectious Disease Research Laboratory at the Mayo Clinic to conduct the study.

PathoQuest, a life sciences leader focused on improving pathogen identification in biological samples, today announced that it will conduct research with Mayo Clinic to study the company’s proprietary iDTECT™ Blood test. Mayo Clinic will explore the use of iDTECT Blood in the context of a prospective study designed to confirm the utility of a next generation sequencing-based metagenomic approach to identify pathogens in patients with neutropenic fever. PathoQuest will work with Robin Patel, M.D., Chair, Division of Clinical Microbiology and Director of the Infectious Disease Research Laboratory at the Mayo Clinic to conduct the study.

About PathoQuest

PathoQuest, a spin out of Institut Pasteur, is a life sciences company offering a game changing metagenomics approach to improving pathogen detection in biological samples. PathoQuest’s technology combines a Next-Generation Sequencing (NGS) platform and a proprietary sample preparation process which is applicable to several types of samples with a proprietary pathogen genome sequence database and automated analysis pipeline.

PathoQuest has developed iDTECT Blood Test, the first and only clinical CE IVD metagenomic test in infectious disease. Using a single blood sample, the test provides clinicians and microbiologists with an improved method for detecting and identifying pathogens, particularly for immunocompromised patients with suspected infections. This new molecular diagnostic test is designed with the objective to improve antibiotic stewardship and lead to better patient care through precision medicine.

Based on the company’s technological platform, PathoQuest also offers biopharmaceutical companies a disruptive approach to secure production of biologics like vaccines and recombinant proteins. PathoQuest’s solution is currently being utilized by several major biopharma companies.

New Rapid Test for Valley Fever Should Help Reduce Diagnosis Delays

Valley fever cases in November saw a 50-percent spike over the previous month, leading experts at the University of Arizona Valley Fever Center for Excellence to predict a significant increase in cases in 2018.

Fortunately, the recent—and timely—approval of a new rapid assay test for Valley fever, developed with assistance from the University of Arizona, should reduce delays in diagnosing the respiratory fungal infections—a frequent problem in treating the disease, which is caused by spores endemic to soils in the U.S. Southwest.

The number of new Valley fever infections reported to the Arizona Department of Health Services has been relatively stable since 2013, but that may be starting to change, said John Galgiani, MD, director of the UA Valley Fever Center for Excellence and head of the Banner – University Medicine Valley Fever Program. For example, in November, more than 900 cases were reported, a 50-percent increase compared to October and the highest monthly total in the past two years. Although Arizona’s total number of cases for 2017 are only slightly more than in 2016, the accelerating monthly case numbers suggest the state may see a sharp increase in cases next year, he said.

“What seems clear is considerably more Valley fever infections are being reported right now,” Dr. Galgiani said. “Arizona clinicians need to be even more alert than usual if their patients develop pneumonia. On average, Valley fever causes one of every three cases of pneumonia in Phoenix, Tucson and surrounding areas. With infections increasing as they are now, pneumonia is even more likely to be due to our local fungal infection.”

Patients who develop persistent symptoms of pneumonia, such as fever, cough, chest pain, or shortness of breath, especially if associated with unusual skin rashes, joint pain or extreme fatigue, should ask their doctor whether they should be tested for Valley fever.

In 2011, more than 16,000 Valley fever infections of Arizonan residents were reported—a record for the state. In fall 2010, signs of that increase already were present, Dr. Galgiani said.

“We don’t know if 2018 will be like what we saw in 2011,” he added. “What we are seeing this fall, however, is very similar to how that epidemic [DM1] started seven years ago.”

Earlier this month, the U.S. Food and Drug Administration gave regulatory clearance for a molecular assay test for rapid detection of coccidioidomycosis (Valley fever, or cocci) using DxNA LLC’s GeneSTAT.MDx Coccidioides test and GeneSTAT System. That test (which reduces the time for results from as long as 21 days to the same day and without need for a Biosafety Level 3 lab to do culture testing) was developed using data licensed from the Translational Genomics Research Institute (TGen) and Northern Arizona University. Among sites that assessed the test were Banner Health and Laboratory Sciences at Banner – University Medical Center Phoenix and the UA BIO5 Institute, under Anne Wertheimer, PhD, associate director, Infectious Disease Research Core, and director, Diagnostic Laboratory Sciences, UA Applied Sciences Graduate Interdisciplinary Program.

“My lab in the UA BIO5 Institute was one of the three external validation and reproducibility testing sites and my team collected prospective, as well as a handful of retrospective, specimens,” Dr. Wertheimer said. “The assay was very robust for use by both entry-level as well as highly skilled technicians and eliminates exposure of lab personnel to a highly infectious culture.”

BIDMC Researchers Use Artificial Intelligence to Identify Bacteria Quickly and Accurately

Microscopes enhanced with artificial intelligence (AI) could help clinical microbiologists diagnose potentially deadly blood infections and improve patients’ odds of survival, according to microbiologists at Beth Israel Deaconess Medical Center (BIDMC). In a paper published in the Journal of Clinical Microbiology, the scientists demonstrated that an automated AI-enhanced microscope system is “highly adept” at identifying images of bacteria quickly and accurately. The automated system could help alleviate the current lack of highly trained microbiologists, expected to worsen as 20 percent of technologists reach retirement age in the next five years.

“This marks the first demonstration of machine learning in the diagnostic area,” said senior author James Kirby, MD, Director of the Clinical Microbiology Laboratory at BIDMC and Associate Professor of Pathology at Harvard Medical School. “With further development, we believe this technology could form the basis of a future diagnostic platform that augments the capabilities of clinical laboratories, ultimately speeding the delivery of patient care.”

Kirby’s team used an automated microscope designed to collect high-resolution image data from microscopic slides. In this case, blood samples taken from patients with suspected bloodstream infections were incubated to increase bacterial numbers. Then, slides were prepared by placing a drop of blood on a glass slide and stained with dye to make the bacterial cell structures more visible.

Next, they trained a convolutional neural network (CNN) – a class of artificial intelligence modeled on the mammalian visual cortex and used to analyze visual data – to categorize bacteria based on their shape and distribution. These characteristics were selected to represent bacteria that most often cause bloodstream infections; the rod-shaped bacteria including E. coli; the round clusters of Staphylococcus species; and the pairs or chains of Streptococcus species.

“Like a child, the system needed training,” said Kirby. “Learning to recognize bacteria required a lot of practice, making mistakes and learning from those errors.”

To train it, the scientists fed their unschooled neural network more than 25,000 images from blood samples prepared during routine clinical workups. By cropping these images – in which the bacteria had already been identified by human clinical microbiologists – the researchers generated more than 100,000 training images. The machine intelligence learned how to sort the images into the three categories of bacteria (rod-shaped, round clusters, and round chains or pairs), ultimately achieving nearly 95 percent accuracy.

Next, the team challenged the algorithm to sort new images from 189 slides without human intervention. Overall, the algorithm achieved more than 93 percent accuracy in all three categories. With further development and training, Kirby and colleagues suggest the AI-enhanced platform could be used as fully automated classification system in the future.

In the meantime, Kirby suggests automated classification can ameliorate the shortage of human technologists by helping them work more efficiently, “conceivably reducing technologist read time from minutes to seconds,” he said.

While human technologists routinely provide highly accurate diagnoses, demand for these highly skilled workers exceeds supply in the United States. Nine percent of lab technologists remain unfilled, and that number is expected to dramatically increase as technologists of the Baby Boomer generation begin to retire in droves, according to a 2014 survey from the American Society for Clinical Pathology.

What’s more, these images can be sent remotely, bringing the highest level expertise anywhere the internet reaches. That’s critical, as rapid identification and delivery of antibiotic medications is the key to treating bloodstream infections, which can kill up to 40 percent of patients who develop them. Each day a patient goes untreated is linked with an increased risk of mortality.

In addition to its clinical uses, the new tool could also have applications in microbiology training and research, Kirby noted.

“The tool becomes a living data repository as we use it,” he said. “And could be used to train new staff and ensure competency. It can provide unprecedented level of detail as a research tool.”

In addition to Kirby, study authors include co-lead authors, postdoctoral fellow, Kenneth P. Smith, Ph.D., and, medical microbiology fellow, Anthony D. Kang, Ph.D., both members of the Department of Pathology at BIDMC.

This work was supported by the Harvard Clinical and Translational Science Center (National Center for Research Recourses and the National Center for Advancing Translational Science, National Institutes of Health Award UL1 TR001102) and by financial contributions from Harvard University and its affiliated academic healthcare centers. Anthony Kang was supported by the United States Army’s Long Term Health Education and Training program as an American Society for Microbiology Committee on Postgraduate Educational Programs Fellow at BIDMC. Kenneth Smith was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (F32 AI124590).

Thursday, November 23, 2017

Biological Threats to be Detected by Griffith University

Griffith University researchers have developed a system that can quickly detect airborne biological threats.

Professor Igor Agranovski, of the School of Engineering, has developed a system that collects aerosolised micro-organisms and finds the threats, such as fungi spores, viruses and bacteria. Such a system could be crucial to soldiers in the field or post-event investigations.

The researchers won contracts with the Australian Defence Force (ADF) through the Defence Innovation Fund to complete the prototyping of the system. It follows on from Professor Jin Song Dong’s contract in June to develop autonomous underwater vehicles.

Aerosolisation is when a physical substance is converted into particles small and light enough to be suspended and transmitted in the air. That could be through a spray, like and aerosol nebuliser, or through a natural process, like a sneeze or cough.

“I started my research in the area of bioaerosols in the year of 2000 in collaboration with colleagues from the University of Cincinnati, USA,” Professor Agranovski said.

“When the system is complete and being used it will be capable of early detection of presence on airborne pathogenic microorganisms, enabling more timely use of personal protective equipment (PPE) and the launch of corresponding sanitary and quarantine actions.

“This will improve human protection, and not just armed services people. It could used in any civilian circumstance where there is a possibility of contact with airborne pathogens.”

Griffith Enterprise has been working closely with several researchers whose work could have defence application for a number of years.

The Defence Innovation Hub was launched in December 2016, and has invested around $20 million in industry and research organisations across Australia to mature and further develop defence technologies. Its expects to spend a total of $1.6 billion.

Minister for Defence Industry, Hon Christopher Pyne announced the new projects as boosts to ADF capability.

“These investments will drive growth in defence industry and innovation whilst focusing on the capability needs required to ensure Australia’s national security now and into the future,” Minister Pyne said.

“I look forward to seeing more of these valuable and exciting ideas as we harness the innovation potential of Australia’s defence industry through the Defence Innovation Hub.”

Nanoparticles Used in Malaria Diagnosis Test

The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.

Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases. An early diagnosis is vital for the timely and right kind of therapy. There are five different types of parasites at the origin of the disease. Plasmodium falciparum is causing malaria tropica and it is particularly harmful for infants and pregnant women in the African sub-Saharan region.

To diagnose malaria with conventional diagnostic tools and to identify the parasite causing the infection takes experienced and well-trained personnel and a well-equipped laboratory. Both are scarce in Africa or even anywhere else outside specialized health care centers.

That is the reason why the NanoFRET project partners come together to develop the whole blood rapid diagnostic test to detect just this special type of parasite. Funding is granted by the German Federal Ministry of Education and Research (BMBF) within the framework of the VIP+ program (“Validation of the innovation potential of scientific research”).

In the body, infectious germs produce large amounts of specific proteins that accumulate in the blood. These proteins will be detected by a new tool developed by the project consortium led by the project coordinator Dr. Rolf Fendel (University of Tübingen). At the Fraunhofer IME, the team around Dr. Torsten Klockenbring sets out to develop antibodies able to identify proteins from the malaria parasite. These antibodies are coupled to novel fluorescent nanoparticles, which Dr. Sofia Dembski and her “Theranostik” team — part of the Translational Center Regenerative Therapies — developed at the Fraunhofer ISC.

The detection of the pathogen in a blood sample will be based on a special technique (time-resolved fluorescence resonance energy transfer (TR-FRET) in combination with the antibodies and the nanoparticles.

However, there is one challenge to overcome: The fluorescent properties of the nanoparticles have to be adapted so that the autofluorescence of blood cannot affect the result.

Testing will take place with samples from malaria patients and a non-infected control group. Samples will be gathered, characterized and used to define the test parameters. The study will be performed by Dr. Andrea Kreidenweiss from the Institute of Tropical Medicine (University of Tübingen) at the Centre de Recherches Médicales de Lambaréné (CERMEL) located in Gabon, a collaboration partner of long standing.

In a next step upon establishing a reliable method, it will be tested in a diagnostic study at the CERMEL. The evaluation will consider sensitivity, specificity, and practicability under real conditions. If the test proves to be suitable, the project partners will design a prototype kit. The test kit must be producible at low cost and should enable an early diagnosis with malaria tropica.

The project is planned to be completed by late 2019. If successful, the project partners will adapt the test method to other infectious diseases and then find industry partners to develop the next generation of rapid diagnostic tools.

Source: Fraunhofer Institute for Silicate Research ISC

IIT Hyderabad Develops Device to Diagnose Infectious Diseases

A team of researchers from Indian Institute of Technology, Hyderabad, has developed a new device that promises to help detect infectious diseases at low costs and very early.

The device uses a biochip and a nanomaterial based on Zinc Oxide. As a proof of concept it has been demonstrated in rapid detection of malaria.

The biochip comprises of a sensing platform integrated with a three-electrode system. The sensing electrode consists of antibody conjugated nanofibers. In the case of the device which has been tested, nanofibres were conjugated with histidine-rich protein II antibodies, which are specific to malarial antigen. Upon recognizing the presence of even a trace of malaria’s biomarkers in blood serum, the device registered a signal. It is calibrated to assess the quantitative level of infectious biomarker present in the sample. Samples obtained from a hospital were tested using the device.

The device can also quantify the extent of infection and does not require a trained technician to use it. “It can be used as a point of care device. It will be particularly useful in rural areas where diagnostic facilities are not available readily. People in endemic areas can keep the device at home and when someone in the house falls sick, they test if there is infection,” Shiv Govind Singh, leader of the team, said while speaking to India Science Wire.

The device is highly sensitive. It can detect malaria parasite at a concentration of even as low as a trillionth of a gram in a millilitre. This means it can detect minutest presence of a parasite, and help detect the infection on day one itself.

Dr. Singh said he and his team members were working on taking the device to the next level wherein the diagnosis could be transmitted to a medical professional via a smart phone. In addition, they are working on a device through which several diseases could be detected in one go.

The research team included Brince Paul and Asisa Kumar Panigrahi (IIT Hyderabad) and Dr. Vikrant Singh from School of Medicine, University of California. The study results have been published in journal ACS Applied Materials and Interfaces. (India Science Wire)

Horse Diseases Diagnosed with Smartphone and Test Kit

Researchers in Illinois have used a smartphone in conjunction with a credit-card-sized test kit to diagnose four respiratory diseases in horses.

The low-cost, portable, smartphone-integrated system is said to be able to address the challenges of diagnosing infectious diseases in resource-limited settings, or in situations where a result is needed immediately.

The system has reportedly achieved detection limits comparable to those obtained by laboratory-based methods and instruments, in about 30 minutes.

Findings published in Analytical Chemistry showed the system was able to detect four horse respiratory diseases – equine herpesvirus-1, equine herpesvirus-4, Streptococcus equi, and S. Zooepidemicus. A related report in Biomedical Microdevices explained how the system was used to detect and quantify the presence of Zika, Dengue, and Chikungunya virus in a droplet of whole blood.

For the research effort, horses were used as an animal model for respiratory diseases in man and in food animals. The team of researchers is working on a next-generation chip that will have four more tests available.

“You can often more easily develop diagnostic tools for human use by coming in to development from the animal side of things first,” explains Dr David Nash, a key researcher involved in the project.

“Many diseases show up first in animals, kind of the canary in the coal mine,” says Nash, who is a private practice equine expert and veterinarian in Kentucky.

Discussing the financial impact of infectious disease outbreaks in horses, he says: “It’s costly to horse owners and trainers, and disrupts the business operations of all equine sports.

“Consider this — on December 25, 2016 a single horse stabled at the Fair Grounds Race Course in New Orleans experienced a fever and subsequently developed neurological symptoms.

“The state diagnostic lab was 100 miles away and was closed for the Christmas holiday. The end result was an equine herpesvirus-1 (EHV-1) outbreak that resulted in the quarantine of over 200 horses at the racetrack and a serious financial loss for horse owners and the racetrack owner.

“Imagine the consequences if they ever had to postpone the Kentucky Derby due to a disease outbreak.”

The technology is intended to enable clinicians to rapidly diagnose disease in their office or in the field, resulting in earlier, more informed patient management decisions, while markedly improving the control of disease outbreaks.

The system uses a commercial smartphone to acquire and interpret real-time images of an enzymatic amplification reaction that takes place in a silicon microfluidic chip that generates green fluorescence and displays a visual read-out of the test.

The system is composed of an unmodified smartphone and a portable 3D-printed cradle that supports the optical and electrical components, and interfaces with the rear-facing camera of the smartphone.

The software on the smartphone gathers information about the tests conducted on the microfluidic card, patient-specific information, and the results from the assays, that are then communicated to a cloud storage database.

“This project is a game changer,” says Nash.

“This is the future of medicine – empowered front-line healthcare professionals. We can’t stop viruses and bacteria, but we can diagnose more quickly.

“We were able to demonstrate the clear benefit to humankind, as well as to animals, during the proposal phase of the project, and our results have proved our premise.

“Next, I want to go into the field, multiple sites, multiple geographic locations, and test in real-world situations.”

University of Illinois graduate student and research assistant Fu Sun sees this project as fulfillment of one of her primary career objectives:

“I entered graduate school with the hope to make a better world by developing biomedical devices that can facilitate effective disease prevention, diagnosis, or treatment.”

The system represents the only platform to date that can multiplex detection of viral and other nucleic acid targets on a portable point-of-care setup using one droplet of bodily fluid, including whole blood.

Importantly, the system is capable of detecting multiple nucleic acid targets at the same time and, thus, is capable of identifying coinfections of multiple pathogen strains. By generating a positive/negative determination of the presence of specific pathogens, the mobile system can assist physicians in rapid point-of-care decision-making for treatment and quarantine response that is currently not possible with tests performed at central laboratory facilities.

The multidisciplinary group inolved in the project included personnel from University of Illinois at Urbana-Champaign and the University of Washington at Tacoma.

GNA Biosolutions Releases Laser PCR Platform for Research Use in Europe

German firm GNA Biosolutions last week announced the commercial launch of its Pharos V8 platform, a real-time PCR system for research use in Europe.

The device uses GNA's laser PCR technology, which operates on the same principles as standard nucleic acid amplification but instead uses nanomaterials to control temperature cycles at the nanometer scale instead of heating and cooling down the entire solution.

"We add nanoparticles to the mastermix of the reaction … for instantaneous heating and cooling," said Lars Ullerich, managing director of business development at the company. "We get to real-time PCR results within 10 minutes, from start to finish of the amplification and detection mechanism."

According to Ullerich, the technology accelerates the PCR reaction times by a factor of ten and opens the door for application in multiple time-sensitive settings. Researchers can process small and large volumes of solution, up to 100 microliters, on the system due to the nanoparticles. Ullerich described the Pharos V8 platform as a semi-quantitative device that has built-in real time detection. He also noted that the platform is currently not able to perform real-time PCR relative to a standard that would allow researchers to determine copy number, hence the "semi-quantitative" label.

Several academic groups and companies are attempting to push the 10-minute boundary for real-time PCR. For instance, a group headed by Carl Wittwer, a professor of pathology at the University of Utah School of Medicine, has pushed the limits of PCR detection using an intercalating dye to determine extension rates, measured as nucleotides per second per molecule of polymerase. Wittwer's team developed the technique to work on a real-time PCR platform, and has recorded producing efficient and specific DNA amplification in 15 to 60 seconds. But that work was only theoretical and has not been implemented in a commercial platform.

The Pharos V8 platform uses 8-strip PCR tubes instead of cartridges, allowing researchers to adapt their existing real-time assays to the company's mastermix for a small fee. GNA said that the device is amenable to samples prepared by any number of conventional methods.

With a team of 30 employees, GNA designed the Pharos V8 to be an open platform for customers who need "to provide a  very quick answer and who need to use this answer to release material". GNA CEO Frank Krieg-Schneider envisions the test being used for "anything from food testing, to quality control, to human [in vitro diagnostics]."

Because the Pharos V8 platform and reagents are not IVD/CE marked, GNA emphasized that the system is meant for lab-developed tests that can be accelerated by a factor of 10. GNA will provide generic kits so that customers, which could include labs in Europe and the US, can design their own tests to run on the instrument. This week the company launched the Pharos V8 Universal Assay Kit for DNA amplification alongside its platform.

"It is important to mention that use of the instrument for 'near' diagnostic purposes is meant for Europe," Krieg-Schneider explained. "At this point, for the US market, the instrument will be for research purposes only."

GNA has also developed industrial partnerships over the past few years, but did not disclose them at this time. Ullerich said that the firm offers additional services including nucleic acid detection, modular instrument components, and custom molecular assays.

"We are interested in infectious disease testing because we think it's very time-sensitive, and that's where speed matters a lot, and we're developing assays for quickly detecting hospital-acquired diseases," Krieg-Schneider added.

GNA's Pharos V8 device costs an end user €25,000 ($29,498) with a cost of €1.50 for each Laser PCR reaction running on the universal assay accompanying the platform. According to Ullerich, the Pharos V8 is currently available for sale only in the EU for research use, which "does not impede diagnostic laboratories to employ the device for their lab-developed tests."At this time, the firm has not finalized its distribution strategy for the EU or beyond.

GNA previously developed the Pharos 400 two years ago, a prototype device used as a part of a research project funded by IMI2, a public-private partnership between the EU's Horizon 2020 research and European Federation of Pharmaceutical Industries and Associations. Called FiloDiag, the GNA-led research team is developing real-time laser PCR and RNA-based assays to detect Ebola infection. Ullerich explained that the test is in final stages of research, which will "ultimately lead to a point-of-care system that will be something like a CLIA-waived instrument, [as] it will come with a cartridge that has a dedicated test on board."

GNA has also received funding from the German Federal Ministry of Education and Research regarding research on the rapid detection of methicillin-resistant Staphylococcus aureus and multidrug resistant gram-negative bacteria in hospitals.

GNA plans to launch a DNA amplification kit during Q1 2018. In addition, it plans to launch a one-step RT-PCR kit, which will enable users to run RNA amplification.

VTT Develops Disposable Optical Test Substrate for Detecting Harmful Microbes

Harmful microbes and toxic micromolecules in food and drinking water can cause serious health problems around the world. For her PhD thesis, VTT researcher Sanna Uusitalo has developed a disposable optical test substrate for use in microbial detection. The aim is to enable cost-effective detection of harmful microbes and toxins.

Uusitalo developed the optical detection of microbial cells using Raman spectroscopy to increase measurement sensitivity via SERS (surface-enhanced Raman scattering) amplification. SERS measurement is based on Raman scattering, whose intensity is increased by the oscillation of free electrons in metal. In some cases, the method can identify a sample to a precision-level of one molecule. The disposable SERS measuring substrate is patterned using a roll-to-roll production method and coating the substrate with thin gold plating. "The more sensitive the SERS process becomes in the case of challenging cell measurements, the more applications it will have in the future. It would provide a fast and simple method of microbial identification compared to traditional cell cultures and enable the fast identification of microbes in cases, say, of food poisoning, or rapid purity analysis in food industry production facilities," says Uusitalo.

She believes that the first general application of the method will be in explosives detection or the analysis of environmental toxins. Portable Raman measuring devices are already on the market for the analysis of larger sample volumes. Future R&D will also lead to portable SERS measuring devices for measuring very low sample volumes.

Uusitalo's doctoral thesis, "Detection of small molecules and microbial cells by surface-enhanced Raman spectroscopy using roll-to-roll produced substrates", which focuses on Raman spectroscopy, will be examined at 12 noon on 24 November at the University of Oulu.

VTT Technical Research Centre of Finland Ltd is the leading research and technology company in the Nordic countries. We use our research and knowledge to provide expert services for our domestic and international customers and partners, and for both private and public sectors.

Medical University of Vienna Team Shows Roche PCR Test Suitable for Rapid Neonatal Sepsis Diagnosis

Medical University of Vienna researchers have shown that a Roche PCR test has superior sensitivity rates and can more rapidly identify pathogens in the blood of neonatal patients than traditional blood culture testing.

As a result, the researchers deemed the Roche SeptiFast Mgrade PCR test using a modified DNA extraction protocol acceptable for rapid detection of neonatal sepsis alongside conventional blood culture. The researchers published their findings last week in the journal PLOS One.

Sepsis is among the leading causes of neonatal mortality, and prematurely born neonates experience the highest incidence and mortality of sepsis among all age groups, according to a review published last year in Current Opinion in Pediatrics.

The review noted that in the US, 36 percent of neonates born before they have completed 28 weeks of gestation "suffer at least one episode of a bloodstream infection during their birth in hospitals, with up to a 50 percent associated mortality."

"Routinely, hospitals hold a low-birth-weight baby and start them on prophylactic antibiotic treatment while drawing cultures during the first 48 hours," Darshna Tanna, Roche's lifecycle leader for microbiology, said in an interview. "The quicker you can rule out a bacterial infection, the quicker you can get babies off empirical treatment and out of the neonatal intensive care unit."

The researchers in Vienna prospectively analyzed 212 episodes of suspected late-onset sepsis in neonatal patient samples using the SeptiFast diagnostic test with the modified DNA extraction protocol. They compared the results with those from blood culture, laboratory biomarkers, and clinical signs of sepsis.

Using a blood volume of 100 μL, the test demonstrated a sensitivity of 90.2 percent "for the diagnosis of blood-culture positive sepsis episodes; a moderately high number of positive test results in episodes without infection potentially due to contamination during blood drawing and processing; and an increased pathogen detection rate in patients with clinical sepsis," the researchers said.

"The most important message in this study is that there is great need for a rapid and adequate treatment of neonatal sepsis in order to reduce the leading causes of mortality of preterm babies," Tanna said. "Methods in the past have been based on adult requirements of blood, ranging from 5 to 10 mls per bottle, but this study has been able to show that a modified DNA extraction yielding 100 μL is sufficient for the rapid, molecular detection of bacterial pathogens."

The time to detection for the Roche test is within 5 to 6 hours, and traditional cultures require at least 48 to 120 hours to yield a positive result, Tanna said. She noted that other PCR technologies offer targeted panels but don't offer the level of multiplexing and pathogen spectrum that is available on the SeptiFast test, which detects and identifies the 25 most common pathogens known to cause to blood stream infections and is designed to be run on the company's LightCycler 2.0 qPCR platform.

In neonatal sepsis testing, the gold standard for many years has been traditional blood culture testing, which takes longer and requires more blood than physicians would like, Tanna said.

"You can imagine that a tiny, premature baby has a limited amount of blood to offer and there is the added difficulty of a peripheral venipuncture on such a tiny individual," Tanna noted. "A routine sepsis workup requires sampling of blood for cultures, hematology, and clinical chemistry. Therefore, any method that offers the possibility of collecting less blood is welcome to these patients."

The study by the Vienna researchers recommends that blood culture be used along with PCR in testing neonates for sepsis.

"In this study, clinicians are using SeptiFast as an additive test, so they are continuing to use blood culture testing, the gold standard, but when they add the use of SeptiFast the sensitivity of the test rises from 50 percent to 90 percent," Tanna noted.

SeptiFast has received CE marking and is available in Europe and other countries that accept the mark, but it is not commercially available in the US. Roche said it doesn't have plans to seek US Food and Drug Administration clearance for the test, but that SeptiFast is one among a portfolio of diagnostic products it is offering and developing to combat the growing rate of sepsis infections and to combat antimicrobial resistance that can occur from over prescription of antibiotics.

The firm markets assays for its fully automated Cobas 4800 real-time PCR system that target and identify antibiotic resistant organisms such as MRSA, C. difficile, and vancomycin-resistant organisms. Additionally, the company provides sepsis biomarker tests that run on its Elecsys electrochemical analyzer, including c-reactive protein, interleukin-6, lactate, and procalcitonin, which is perhaps the most important marker according to Tanna and "has a very high negative predictive value and sensitivity to bacterial infections."

The Vienna researchers in their study cautioned that the benefit of rapid pathogen detection "has to be balanced against the considerable risk of contamination, loss of information on antibiotic sensitivity pattern, and increased costs."

PCR and other molecular technologies are likely to be most effective in neonatal sepsis and general sepsis diagnosis and treatment when they are paired with a phenotypic antibiotic sensitivity analysis tools that analyzes the sensitivity of a pathogen to an antibiotic treatment, Tanna noted. "To identify the correct pathogen and get the right drug-bug combination, you want to know what type of antibiotic to use, its concentration for the patient, and the length of time it should be administered," she said.

For that, Roche is developing Smarticles technology that consists of DNA-delivery bioparticles combined with custom-designed DNA molecules that cause live bacteria to produce light. In the presence of antibiotics, susceptible bacteria targeted by bioparticles will remain dark, while drug-resistant bacteria produce light quickly and efficiently, Roche said.

The firm purchased Smarticles technology with the acquisition of GeneWeave BioSciences in 2015. The technology is not yet commercially available, and Roche did not provide a timeline for its expected release.

In the market for sepsis testing, Roche has several competitors that offer a combination of molecular and immunochemistry assays, including established companies such as BioMérieux and Thermo Fisher Scientific, and emerging firms such as T2 Biosystems and Accelerate Diagnostics.

In September, T2 said it had filed a 510(k) premarket submission for its T2Bacteria Panel with the US Food and Drug Administration. The panel runs on the FDA-cleared T2Dx instrument and identifies pathogens associated with sepsis within hours instead of days, T2 Biosystems said at the time of its submission.

In February, the FDA cleared Accelerate Diagnostics' test kit and instrument platform for identifying organisms that cause bloodstream infections. Similar to Roche's Smarticles technology, the kit provides information about antibiotic sensitivity. It can identify bacteria or yeast from a positive blood culture in about 1.5 hours.

Roche is "looking internally at several technologies to do direct-from-sample identification of pathogens," in the context of sepsis diagnosis and treatment, Tanna said.

She also noted that the firm had recently inked an R&D agreement with Inotrem to collaborate on developing a companion diagnostic test for a septic shock treatment in clinical trials.

Under the terms of the agreement, Roche and Inotrem will develop a prototype assay for quantitative measurement of soluble plasma circulating protein (sTREM-1) in septic shock patient samples. The test would run on Roche's Elecsys immunochemistry platform.

Akonni Biosystems Awarded NIH Grant to Develop a Low-Cost, Simple, Rapid Point-Of-Care Test for Tuberculosis

Akonni Biosystems, a molecular diagnostics (MDx) company that develops, manufactures, and intends to market advanced MDx systems, today announced receipt of a $300K Commercial Readiness Pilot (CRP) grant from the National Institutes of Health (NIH). Unlike other kinds of NIH research grants, CRP grants are intended to facilitate the transition of previously-funded Phase II projects to the commercialization stage, including activities related to clinical trials and regulatory submissions.  This grant in particular will help Akonni accelerate the commercialization of its proprietary TruArray® MDR-TB test on its TruDx®3000 sample-to-answer diagnostic platform.

According to the World Health Organization (WHO), tuberculosis (TB) continues to cause significant mortality and morbidity throughout the world, recently surpassing HIV as the single largest killer of all infectious diseases. Of all diseases, TB represents one of, if not the greatest, health disparities between socioeconomic classes. Further compounding this health disparity is the prevalence of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) cases. Each year there are approximately 500,000 new cases of MDR-TB, 10% of which have XDR-TB. Current diagnostic methodologies, available primarily to affluent healthcare communities, utilize microbial cultures, which require sophisticated laboratories and weeks before a result can be determined. In addition, difficulties for lower socioeconomic persons to commute and/or follow up with their physicians can result in a lack of appropriate treatment, potentially leading to further drug resistance.

In order to effectively address this global epidemic, a low-cost, simple, and rapid point-of-care (POC) test that accurately detects TB and its resistance to first-line drugs is needed. Currently available TB diagnostics lack the sensitivity, specificity, multiplexing capacity, and/or affordability needed to achieve this goal. As such, Akonni is committed to commercializing a POC MDR-TB diagnostic that offers the sensitivity of culture methods, specificity of nucleic acid methods, and a broad coverage of clinically relevant mutations, at a fraction of the cost of existing molecular methods. "Funding from this grant will help accelerate critical elements of our commercialization plan for the MDR-TB test on the TruDx3000, including ISO 13485 certification and subsequent regulatory approvals," said Christopher Cooney, Principal Investigator on this project and Director of Engineering for Akonni.

Sunday, November 12, 2017

Scientists Develop Sensor-Based Technique to Identify Bacteria that Cause Throat Infections

Indian scientists have developed a new sensor-based technique for detecting the presence of S. pyogenes bacteria, the most common cause of throat infections. It is claimed to be a quick and cost-effective.

The device, a DNA chip-based sensor, consists of a carbon electrode embedded with gold nanoparticles to improve electronic properties. Many small-sized DNA probes are located on the modified chip. They attach themselves to the target DNA samples of bacteria taken from throat swabs of the patient.

The new sensor has been found to be better than earlier reported sensors due to its ability to pick up bacterial DNA even if present in small numbers, within 30 minutes. It correctly distinguishes S. pyogenes from other bacteria, according to the study published in International Journal of Biological Macromolecules.

“The aim was to develop a rapid, accurate, sensitive, specific and cost-effective method for detection of S. pyogenes. The current methods of detection S. pyogenes infection are culture test, biochemical assays, polymerase chain reaction, genetic markers. And these methods are time-consuming, expensive, are unable to pick up the bacteria if present in small numbers and may even wrongly identify other bacteria as S. pyogenes,” Professor Ashok Kumar from the Institute of Genomics and Integrative Biology, who led the research, told India Science Wire.

Based on this technique, he said, several other infection-causing microbes can be identified to prevent the disease by taking medical treatment at early stage of infection.

The most common cause of throat infections in humans is S. pyogenes bacteria. If left untreated it may damage human heart valves resulting in a severe form of rheumatic heart disease. Early diagnosis can prevent damage of human heart valves by taking timely and correct medical care.

The team of researchers included Swati Singh and Ankur Kaushal from the CSIR-Institute of Genomics and Integrative Biology, Delhi, and Dr. Shashi Khare from the National Centre for Disease Control, Delhi.


Several infectious pathogens are found in human whose detection is essential for rapid cure of diseases. The most commonly found pathogen in human is Streptococcus pyogenes which leads to a wide range of infections from mild pharyngitis to rheumatic heart disease. An ultrasensitive DNA chip based sensor was developed for quick identification of pathogen S. pyogenes from patient throat swab samples. The amperometric response was measured after hybridization of specific probe with single stranded genomic DNA (ssG-DNA) from the patient samples. The DNA chip was characterized by FTIR, SEM and validated with suspected patient real samples. The sensitivity of the DNA chip based sensor was found 951.34 (μA/cm2)/ng DNA and lower limit of detection (LOD) was 130 fg/6 μL samples. The DNA chip based sensor is highly specific and takes only 30 min for identification of specific pathogen.

Tuesday, November 07, 2017

Smartphone Diagnosis Via Card-Mounted Lab-on-a-Chip Differentiates Similar Viruses

Infectious disease is still the biggest causes of human death and disability worldwide, and are a particularly acute problem in developing countries where easy access to clinics equipped with up-to-date diagnostic equipment is often limited. But the rapid spread of smartphones has put advanced technology into the hands of many more people, and leveraging their capabilities for healthcare applications has become a subject of great interest.

The US team, spread across electrical engineering, bioengineering and mathematics departments at the Universities of Illinois at Urbana-Champaign and the University of Washington at Tacoma, developed a lab-on-a-chip system that can be mounted on a very portable credit card-sized carrier and read by the camera on an unmodified smartphone, providing diagnostics almost as sensitive and accurate as those of clinic-based equipment but potentially at a fraction of the cost. Moreover, the team claims, it can distinguish between diseases with similar symptoms, allowing the right treatment — or quarantine, if necessary — to be administered quickly.

The team was led by two Illinois professors, electrical engineer Brian Cunningham and bioengineer Rashid Bashir, and Tacoma Prof David Hirschberg, affiliated with science and mathematics at the School of Interdisciplinary Arts and Sciences. Also on board was Ian Brooks of the National Centre for Supercomputing Applications in Urbana-Champaign, and David Nash, a Kentucky-based specialist in respiratory diseases in horses.

“You can often more easily develop diagnostic tools for human use by coming in to development from the animal side of things first,” Nash explained. “Many diseases show up first in animals, kind of the canary in the coal mine.” Moreover, he stressed, disease outbreaks in horses are a major financial drain on a locally-important industry, and as diagnostic labs tend to be far apart, there is a need for this kind of technology.

The lab-on-a-chip is equipped to carry out enzymatic tests on small samples of blood or sputum, and indicates results by inducing a green fluorescence that can be easily detected by a standard phone camera. The card is accompanied by a 3D-printed cradle that contains optics and electronics and holds the card and the phone at the optimum distance with the rear-mounted camera of the phone positioned over the chip’s readout section. Software on the phone gathers information about the tests on the card, patient-specific information, and uploads the test results to a cloud server.

The project’s results have been published in two papers. In Analytical Chemistry, the team describes detection of four equine diseases, and in Biomedical Devices, they discuss how the system detected and quantified the presence of three mosquito-borne viruses — Dengue fever, Zika and Chikungunya, which all have similar early symptoms but different outcomes and require specific treatment— from a single drop of whole blood.

“This project is a game changer,” Nash said. “This is the future of medicine – empowered front-line healthcare professionals. We can’t stop viruses and bacteria, but we can diagnose more quickly. We were able to demonstrate the clear benefit to humankind, as well as to animals, during the proposal phase of the project, and our results have proved our premise. Next, I want to go into the field, multiple sites, multiple geographic locations, and test in real-world situations.”

What’s more, he added, it could not have been done without a multidisciplinary team. “I can’t envision going into a project without engineers now,” he said.

Rapid Micro Biosystems Awarded a Contract by Biomedical Advanced Research and Development Authority (BARDA) for the Implementation of a Rapid Sterility Test for Vaccines

Rapid Micro Biosystems, a leading provider of automated, non-destructive, rapid microbial detection, is pleased to announce the receipt of a $7.3 million contract from the Biomedical Advanced Research and Development Authority (BARDA) for the implementation of a rapid sterility test for vaccines. This awarded grant is part of BARDA’s Advance Development of Medical Countermeasures for Pandemic Influenza, which focuses on improving the government’s responsiveness to future pandemic threats. When combined with Rapid Micro Biosystems’ automated Growth Direct™ detection system, the rapid sterility test will result in faster release of vaccines and other sterile products. Timely delivery of these products carries multiple public benefits, principally in facilitating rapid responses to pandemic or emerging infections, agents of bioterrorism, and availability of life saving medicines.

“Our continuing relationship with BARDA demonstrates the critical need for rapid sterility testing as part of our response to immediate health threats,” said Robert Spignesi, Chief Executive Officer at Rapid Micro Biosystems.

“Our unique detection technology will show contamination within hours and will provide results in half the time of the traditional 14-day test,” said Edward Ognibene, Vice President Development at Rapid Micro Biosystems.

The team at Rapid Micro Biosystems has extensive experience in product development, manufacturing, and service of rapid microbial quality control products, and has previously worked successfully with BARDA to develop the fundamental technology for a rapid sterility test.  Upon completion of the program, the resulting product will make valuable improvements to the quality control release of sterile vaccines and other lifesaving pharmaceutical products and will immediately benefit the public.

Quidel Receives FDA Clearance for Its Point-of-Care Sofia® Lyme FIA

Quidel Corporation (“Quidel”), a provider of rapid diagnostic testing solutions, cellular-based virology assays and molecular diagnostic systems, announced today that it has received 510(k) clearance from the United States Food and Drug Administration (FDA) to market its Sofia Lyme FIA for the rapid differential detection of human IgM and IgG antibodies to Borrelia burgdorferi from serum and plasma specimens from patients suspected of B. burgdorferi infection. The test is intended for use with the Sofia analyzer to aid in the diagnosis of Lyme disease.

“With the clearance of the Sofia Lyme FIA, we are now able to detect the microorganism associated with Lyme disease more rapidly in near patient settings. This is another example of our ability to provide simple, cost-effective solutions for physician offices and hospitals that previously had to wait several days for send-out Lyme results,” said Douglas Bryant, president and chief executive officer of Quidel Corporation.

Lyme disease is the most common tickborne disease in North America and Europe1. In the United States, Lyme disease is caused by the bacterium, Borrelia burgdorferi, transmitted through the bite of an infected blacklegged tick. (1, 2)

Patients infected with B. burgdorferi may experience symptoms associated with three stages: early localized disease, early disseminated disease, and late persistent disease1. The most characteristic symptom of early localized disease is the appearance of erythema migrans (EM) on the skin1,3. EM may also be accompanied by flu-like symptoms days or weeks after infection3. In the second stage, early disseminated disease, untreated patients may begin to see neurological and rheumatological manifestations, and less commonly, dermatological, cardiac, or ophthalmological manifestations. These symptoms generally appear weeks to months after infection1. If the disease continues to be left untreated, late persistent disease may also follow months or years later with continued progression of manifestations in the joints, heart, skin, and nervous system. (2, 3)

Early detection and treatment of Lyme disease can help resolve symptoms and prevent progression of the disease1. The primary means of identifying B. burgdorferi infection is detection of the body’s IgM and IgG antibody response by way of immunoassay3. Detection of IgM antibodies to B. burgdorferi is generally most significant in the earlier stages of the disease. Conversely, detection of IgG antibodies has proven to be significant for longer periods, as the antibodies may remain detectable years after infection.

The Sofia analyzer and Sofia Lyme FIA combine unique immunofluorescence chemistry, advanced lateral flow technology, and failure alert and fail-safe systems designed to ensure reliable, objective, diagnostic results within 10 minutes of application of the patient's specimen. The Sofia Lyme FIA is the first to provide differentiated results for both IgM and IgG on a single test.

  1. Wormser, G. P., Dattwyler, R. J., Shapiro, E. D., Halperin, J. J., Steere, A. C., Klempner, M. S., Nadelman, R. B. (2006). The Clinical Assessment, Treatment, and Prevention of Lyme Disease, Human Granulocytic Anaplasmosis, and Babesiosis: Clinical Practice Guidelines by the Infectious Diseases Society of America. Clinical Infectious Diseases, 43(9), 1089-1134.
  2. CDC. http://www.cdc.gov/lyme/diagnosistesting/LabTest/TwoStep/index
  3. Aguero-Rosenfeld, M. E., Wang, G., Schwartz, I., & Wormser, G. P. (2005). Diagnosis of Lyme Borreliosis. Clinical Microbiology Reviews, 18(3), 484-509.

Luminex Corp. Announces FDA Clearance for ARIES Group A Strep Assay

Luminex Corporation announced that it has received FDA clearance for the ARIES® Group A Strep Assay, a moderate complexity, sample to answer test for the direct detection of Streptococcus pyogenes from throat swab specimens using the ARIES® System. This is the sixth assay the FDA has cleared for use on Luminex's ARIES® Systems in the last 24 months.

Fast and accurate diagnosis of Group A Streptococcus infections is critical to ensuring that appropriate antibiotic therapy is started promptly. For example, accurate diagnosis of Group A β-hemolytic Streptococcus pyogenes is crucial for determining the optimal treatment since physical examination alone is not sufficient to distinguish between pharyngitis caused by Group A β-hemolytic Streptococcus pyogenes and viral pharyngitis, or non-GAS bacterial organisms such as Fusobacterium necrophorum. Invasive cases of this infection lead to as many as 1,600 deaths in the United States each year, according to CDC estimates.

"In order for us to support the highest level of patient care at our children's hospital, we require fast time to results, especially when it comes to dealing with infectious diseases," said Dr. Jennifer Dien Bard, Director, Clinical Microbiology and Virology Laboratory at the Children's Hospital Los Angeles. "Having tests that are easy to use and require only minimal hands-on time are key. The Luminex Group A Strep Assay has performed very well in our lab, and is a welcome addition to the ARIES® System test menu."

Dr. Ted E. Schutzbank, Technical Director, Specialized Testing and Microbiology at Ascension/St. John Providence added: "While the use of rapid antigen detection kits has been the standard of care in physicians' offices for years, the sensitivity of these tests has always been questionable, requiring follow-up testing of negative results, typically by bacterial culture. Delaying treatment while awaiting lab results can lead to serious short-term sequelae such as scarlet fever, or long-term complications such as rheumatic fever. Replacement of rapid antigen testing by the ARIES® Group A Strep Assay will allow for a much faster definitive diagnosis of these infections and greatly enhanced patient care by ensuring timely administration of antibiotic therapy."

Overuse of antibiotics has caused the resistance of numerous species of bacteria, so accurate diagnosis is pivotal to mitigating unnecessary antibiotic use and guiding appropriate patient treatment. Molecular testing for respiratory pathogens has been shown to improve infection control efforts and reduce the use of unnecessary antibiotics, duration of treatment, length-of-stay, and hospital admissions.

"We are pleased to continue the rapid expansion of our infectious diseases portfolio with the FDA clearance of the ARIES® Group A Strep Assay," said Homi Shamir, President and Chief Executive Officer of Luminex. "Our broad respiratory offering provides both targeted assays, like the ARIES® Group A Strep Assay, and customizable disease state panels. With our breadth of respiratory testing options, clinicians have access to the testing flexibility necessary to quickly adapt to the varying clinical needs of their patients."

The ARIES® Group A Strep Assay, a real-time polymerase chain reaction (PCR)-based qualitative in vitro diagnostic test, is part of Luminex's comprehensive respiratory testing menu that also includes the ARIES® Bordetella Assay, ARIES® Flu A/B & RSV Assay, NxTAG® Respiratory Pathogen Panel, and VERIGENE® Respiratory Pathogens Flex Test.

New Sensor Provides Real-Time Detection of Bacteria and other Contaminants In Water

Water quality monitoring currently occurs mainly at water supply intakes or water treatment plants, rather than along water distribution lines or at the point of use. This is inadequate because negative changes can occur in water quality between the water source and your faucet. It is essential to monitor this key natural resource for various contaminants, such as toxic heavy metal ions, within water distribution and treatment systems.

Accurate and accessible detection technologies are necessary to ensure continuous water quality control and early warning capabilities to avoid public safety catastrophes like the ongoing Flint water crisis in Michigan.

During the AVS's 64th International Symposium & Exhibition, being held Oct. 29-Nov. 3, 2017, in Tampa, Florida, Junhong Chen, distinguished professor of mechanical engineering, materials science and engineering at the University of Wisconsin-Milwaukee, will present his work about inventing a graphene-based sensing platform for real-time, low-cost detection of various water contaminants. The new sensor detects heavy metals, bacteria, nitrates and phosphates.

"Our technology addresses an unmet need for real-time, low-cost monitoring of critical contaminants in drinking water," said Chen. "Water plays an important role in the economic world, but only 3 percent of the available water is potable, and with increasing demand, the need for safe drinking water is rising."

Graphene, a single layer of carbon atoms arranged in a 2-D honeycomb lattice, is a promising nanomaterial thanks to its unique structure and electrical properties.

"Intrinsic graphene is a zero-gap semiconductor that has remarkably high electron mobility (100 times greater than that of silicon), which makes it attractive for sensitive, high-speed chemical and biological sensors due to its high sensitivity to electronic perturbations," he said.

The sensor works by placing graphene-based nanosheets that are semiconducting between an electrode gap. The electrical conductivity of the graphene material changes with the binding of substances, called analytes, to its surface and their chemical constituents are identified and measured.

"The magnitude of the conductivity change can be correlated to the concentration of analyte, and the technology also involves the functionalization of the graphene material surface with specific probes that can target a specific analyte," said Chen.

The sensor is based on a field-effect transistor (FET) device with reduced graphene oxide (rGO) as its sensing channel. "The working principle of the sensor is that the rGO conductivity (usually measured in resistance) changes with the binding of chemicals such as heavy metals to probes anchored on the rGO surface," he said. "So the presence of the chemicals can be determined by measuring the sensor resistance change."

By deploying these real-time sensors to monitor water contaminants in water distribution systems, according to Chen, they could provide early warning of chemical and biological contamination in water, improving water safety and public health benefits.

"The platform technology can also be further engineered to detect various analytes for food and beverages, as well as for biomedical applications," said Chen.

Chen has launched a startup, NanoAffix Science LLC, to commercialize his water-quality sensing technology. With funding from the National Science Foundation and in partnership with several water companies, they've already developed a prototype of a hand-held device for rapid, low-cost detection of lead ions in drinking water. "We're now refining the prototype to make it a commercial product in the near future," said Chen.