DNA-based PCR Test Accurately Predicts Antibiotic Resistance

A rapid high-throughput PCR test developed by OpGen “accurately and reliably” predicted antibiotic resistance in common bacteria at a rate of 90% or higher, researchers reported.

According to a study published in Antimicrobial Agents and Chemotherapy, the researchers evaluated more than 7,500 highly antibiotic-resistant clinical isolates of Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa for antibiotic-resistance genes and compared them with phenotypic resistance across penicillins, cephalosporins, carbapenems, aminoglycosides, trimethoprim-sulfamethoxazole, fluoroquinolones and macrolides.

“In the most comprehensive study of its kind, OpGen’s informatics technology (Acuitas Lighthouse) rapidly predicted antibiotic resistance to 15 antibiotics accurately and reliably, with an average positive predictive value of 90%,” G. Terrance Walker, PhD, senior vice president of research and development at OpGen, told Infectious Disease News. “On a larger scale, the paper supports a potential breakthrough in the global effort to speed up the rapid detection of antimicrobial resistance.

“Today, phenotypic methods based on bacterial growth are the standard of care. It can take days to provide results to patients. However, DNA testing can be completed in just hours and represents an attractive potential solution. Showing that DNA testing can be used to accurately predict antibiotic resistance has been a critical challenge that scientists have been working on for many years. This paper demonstrates that a well-defined set of DNA markers can potentially be used to perform rapid, accurate antibiotic resistance detection in key pathogens.”

Walker and colleagues reported testing 2,919 E. coli isolates, 1,974 K. pneumoniae isolates, 1,150 P. mirabilis isolates and 1,484 P. aeruginosa isolates, of which 34% originated in hospitals in North America, 23% in Europe, 13% in Asia, 12% in South America, 7% in Africa and 1% in Oceania, according to the study. Another 9% of tested isolates were of unknown origin.

According to the study, they “developed statistical methods to predict phenotypic resistance from resistance genes for 49 antibiotic-organism combinations, including gentamicin, tobramycin, ciprofloxacin, levofloxacin, trimethoprim-sulfamethoxazole, ertapenem, imipenem, cefazolin, cefepime, cefotaxime, ceftazidime, ceftriaxone, ampicillin, and aztreonam.”

The findings revealed that the test’s average positive predictive value for genotypic prediction of phenotypic resistance was 91% for E. coli, 93% for K. pneumoniae, 87% for P. mirabilis and 92% for P. aeruginosa, according to the study.

OpGen expects the first FDA clearances for the test this year, Walker noted.

“In high-risk patients needing urgent care and patients with complicated urinary tract infections, the faster determination of appropriate antibiotic therapy translates to improved health outcomes, lower hospital costs and better antibiotic stewardship,” Walker said. “OpGen’s technology is the application of precision medicine to infectious disease management, which has become more complex with the proliferation of antimicrobial resistance.”

Read more

Advanced Detection Tool to Limit the Spread of Devastating Tree Pathogens

Seeking to prevent the introduction and spread of quarantine tree pathogens, the EU Horizon 2020-funded project HOMED (HOlistic Management of Emerging forest pests and Diseases) supports the development of an innovative tool for on-site detection of pathogens. The tool was developed by a team of scientists from the Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR) and the Department of Agrifood Production and Environmental Sciences (DISPAA), University of Florence and is described in an open access paper, published in the journal AMB Express.

Invasive alien species in trees and plants can have severe economic, ecological and sociological impact. Due to international trade, tourism and other human activities, non-native pathogens spread into new environments, causing a major threat to biodiversity, economy and human health. An effective framework for early warning and rapid response is a crucial element to intercept biological invasions of plant pathogens.

The HOMED-supported innovative tool works for on-site detection of quarantine pathogens, such as Xylella fastidiosa, Ceratocystis platani and Phytophthora ramorum. These are three of the most devastating pathogens of trees and ornamental plants accidentally introduced to Europe, which are causing epidemics with heavy consequences.

Requiring minimum equipment and easy to transport the new diagnostic tool can be also used by non-scientists to quickly and reliably check the health status of live trees and plants. Such user-friendly and compact tools greatly reduce the time usually necessary to take and analyse samples, thus allowing prompt reaction and increasing chances of confinement.

HOMED recognises the need for action and engages forest managers, biosecurity agencies, policy makers and environmental NGOs in the project with the goal to manage emerging forest diseases and thus preserve biodiversity.

Applying a holistic approach, HOMED improves strategies of risk assessment and management by targeting the successive phases of invasion, and developing mitigation methods for each phase - prevention, detection and diagnosis, surveillance, eradication and control tools.

The newly developed detection tool can be used to check the health status of live trees or tree parts, reducing time of analyses and in this way allowing a prompt reaction and potential control of environmental and economic losses. The tool allows a complete analysis in only 30 minutes time and can be applied as point-of-care diagnostics and represents a great advantage to preventing introductions and for applying control measures.

Author and HOMED partner Dr. Alberto Santini comments:

"The use of rapid, specific and sensitive point-of-care methods like the LAMP assays developed in this study could enable phytosanitary services to make immediate management decisions, helping in containing environmental and economic losses. The application of such a portable diagnostic tool, requiring minimum equipment and a few, if any, specific scientific skills could be profitably used to check the health status of live trees or tree parts at the points of entry or in field, thus reducing time of analyses and allowing a prompt reaction."

Read more

binx health Receives CE Mark For Rapid Chlamydia And Gonorrhea Test For Mass Markets

binx health™, the pioneer in anywhere care today announced that its proprietary Chlamydia and Gonorrhea (CT/NG) test has received European CE Mark approval. The new multiplex test works with the binx io platform, delivering a laboratory-quality result in about 30 minutes, creating a new model for "test-and-treat" care for two of the most prevalent Sexually Transmitted Infections (STIs) globally.

More than one million STIs are acquired worldwide every day with chlamydia and gonorrhea representing two of the most prevalent1.  Recent data released by the European Centre for Disease Prevention and Control (ECDC) notes a striking rise in the cases of gonorrhea – up 17% between 2016 and 2017 across the reporting EU/EEA countries, with some countries noting year-over-year spikes of more than 40%2.  Similarly, in the United States, infection rates have risen an astonishing 67% since 2013, with rates continuing to be highest in the 20-24 year-old age group.3

Today, the majority of CT/NG tests are sent to central laboratories, meaning there can be up to a seven day waiting period from first visit to treatment, during which time patients may continue to spread infection, with up to 40% of positive patients never returning for treatment4. binx is positioned to radically change this paradigm, enabling patients and consumers to leave a retail pharmacy, primary care office, clinic, urgent care facility and any other brick-and-mortar location, with treatment in hand in a single visit (while the binx point-of-care platform is not yet available in the United States, the company recently completed its multi-center clinical study for submission to FDA for 510(k) clearance). The binx io platform is designed for ease-of-use, enabling non-laboratory-trained users to run a test with the same accuracy as a central lab test, making it ideal for use in a variety of approved medical and consumer settings.

"Achieving a 30-minute diagnostic turnaround time for two of the most common STIs is a major public health breakthrough," explains Howard Heller, MD MPH, binx health's Chief Medical Officer. "Rapid results equal rapid, appropriate treatment.  This new panel enables a path to not just same day, but same visit testing and treatment, eliminating an immense barrier to care and cure."

"Modern healthcare delivery requires tools that meet consumers' needs where they live, work and shop," said Jeffrey Luber, binx health's Chief Executive Officer. "Doing this effectively means delivering fast, accurate, cost-effective solutions at brick-and-mortar locations, as well as physician-ordered, medical guideline-based testing online, that work to bring consumers from 'worry to well' in the locations most convenient for them. Through scientific rigor, guideline-based testing, and an 'anywhere' mindset that puts the consumer at the center of all we do, today we embark on a path to deliver omnichannel, high quality care in family health, starting with young people and STIs as our launching point."

About binx health 

binx health™  is the pioneer in anywhere care for consumers where they live, work and shop. We do this with (1) proprietary, rapid desktop PCR instruments for retail pharmacy, urgent care, primary care, health centers, and any other brick-and-mortar location where onsite, on demand testing and rapid results on par with central lab testing, are paramount, and (2) mobile solutions for at-home, physician-ordered testing that aim to bring consumers from "worry-to-well" in the palm of their hands. Starting with sexually-transmitted infections, we aim to reverse trends of rising infections among young people, and move into broader family health through the expansion of our point-of-care and at home offerings. binx health's investors include financial investors, Johnson & Johnson Innovation, Novartis Venture Fund, LSP Venture Capital, BB Biotech, RMI Investments and Technology Venture Partners and strategic investors, Consort Medical (whose wholly owned subsidiary Bespak are the makers of the company's low-cost, proprietary multi-plex cartridges) and China-based Wondfo Biotech.

Read more

RIT Professor Develops Device to Better Detect Ebola Virus

A faculty-researcher at Rochester Institute of Technology has developed a prototype micro device with bio-sensors that can detect the deadly Ebola virus. With this type of device, those infected can be treated earlier, and the early detection process can potentially decrease the spread of infections.

Ke Du, a faculty-researcher in RIT’s Kate Gleason College of Engineering, developed a microfluidic device that utilizes CRISPR gene-editing technology to monitor and detect the nucleic acid markers that indicate Ebola virus. The virus is highly contagious and there is limited treatment once an individual has been diagnosed, he said. There are several prominent strains of Ebola, and his research team has focused on the EBOV strain, which has a high mortality rate.

“If an individual travels from one infected community to another, they can easily spread the epidemic. That is why before any symptoms of Ebola, such as cough or fever present, individuals can take a blood test before being allowed to travel,” said Du, an assistant professor of mechanical engineering. He leads a multidisciplinary team of engineers and biochemists developing a rapid point-of care system and biochemistry array for in-field pathogen diagnosis. According to early results, the team has found that the Ebola RNA in test environments can be detected within five minutes by combining automated sample processing, fluorescence sensing and a unique CRISPR-Cas13a assay originated from a bacterial adaptive immune system.

The microfluidic device is an automated and small chip with a highly sensitive fluorescence sensing unit embedded into the device. Physicians take patient samples and add them into the device where Ebola RNA can be seen by activating the CRISPR mechanism. Du is also developing a device that could detect multiple virus strains from Ebola to influenza and zika, for example.

Du’s research was published in the April 2019 issue of ACS Sensors. The article “Rapid and Fully Microfluidic Ebola Virus Detection with CRISPR-Cas13a,” features an international and multidisciplinary team assessing the use of CRISPR technology—gene editing technology—to improve virus detection. The group members are from University of California, Berkeley; Tsinghua Berkeley Shenzhen Institute (China); Dong-A University (Korea); Texas Biomedical Research Institute; and Boston University.

“For this work, we are trying to develop a low-cost device that is easy to use especially for medical personnel working in developing countries or areas where there are outbreaks. They’d be able to bring hundreds of these devices with them for testing, not just one virus or bacteria at one time, but many different kinds,” he explained.

Researchers have tried for the past 40 years to develop an effective Ebola vaccine. Early detection remains an important strategy for controlling outbreaks, the most recent in the Congo, where more than 1,000 individuals have died, according to the Centers for Disease Control.

“If you look at this like influenza, and people don’t look at it as a virus which also can kill people each year. Some strains may not be as deadly as Ebola, but we know that infectious diseases, regardless of the type, are problems that can threaten the public,” Du said. “I grew up in China and experienced the 2002-2004 SARS outbreak. I have seen many people lose their relatives and friends because of infectious diseases. If we can have early detection systems to help screen for all types of diseases and patterns, this can be very useful because it can provide information to medical doctors and microbiologists to help develop the vaccines, and early detection and identification can control and even prevent outbreaks.”

Read more