Nanopore Technologies Develops Rapid Device for DNA Sequencing of Pathogens

The UK startup company Oxford Nanopore Technologies is speeding the discovery of pathogens with its MinION device, a portable, low-cost, real-time DNA and RNA sequencer. The MinION connects to the just-introduced MinIT hand-held AI supercomputer. The MinIT is a rapid analysis and device control accessory for nanopore DNA sequencing that arrives with genomics researchers.

The new hand-held AI supercomputer, powered by NVIDIA AGX is capable of sequence analysis in real time at any location. It is preconfigured with software for quick setup and easy operation of the MinION. The pocket-sized MinIT is powered by mains or separately available battery packs so that it can be used either in a lab environment or out in the field.

The new device as tested by the scientists helps in fighting viruses that destroy crops. It is mostly used in east Africa to characterize pathogens affecting Cassava plant. Researcher’s experiment as performed in a small farm in Tanzania characterizes the viruses responsible for cassava disease within 3 short hours. This helps the farmers with enough essential information to fight plant pathogens to improve crop productivity.

It also helps in onboard analysis of seawater, examining communities of marine microorganisms. Scientists seeking to understand biodiversity in the ocean and how climate change can affect microorganisms in the sea will get real-time data with the help of this AI supercomputer that could last weeks or months.

MinIT is now being shipped to scientists working across a variety of scientific disciplines. Many are working on healthcare applications, such as the rapid identification of infectious disease, cancer or other diseases. Others are focused on the plant or environmental science, or even using the technology in education.

MinIT is compatible with MinION, and also Flongle – an adapter for MinION that allows rapid, lower cost, smaller tests. Nanopore users have indicated that the MinIT will be used alongside MinION or Flongle in a variety of scenarios including rapid characterisation of infectious disease samples, cancer research, environmental analyses and food testing.

MinIT also comes preconfigured with software to run nanopore sequencing experiments, removing the need for configuration of a laptop. The instrument software MinKNOW, and real-time analysis platform for nanopore data, EPI2ME, can both be run on MinIT.

Karius and Duke Demonstrate Test Accurately Detects and Quantifies Microbial Cell-free DNA in Patients With Infective Endocarditis

Karius, a life sciences company transforming infectious disease diagnostics with genomics, along with Duke University, announced the positive results of a study demonstrating that the Karius® Test, a non-invasive blood test that detects pathogen DNA in plasma, accurately identified causative pathogens in patients with infective endocarditis even when blood cultures were negative due to pre-treatment with antibiotics.

"The diagnosis of infective endocarditis (IE) can be difficult, especially if it is caused by organisms that are hard to grow, or if the patient has recently received antibiotic therapy. The Karius diagnostic platform offers an exciting approach to identifying the cause of endocarditis in patients with this life-threatening condition," said Dr. Vance Fowler, professor in the Departments of Medicine and Molecular Genetics & Microbiology at Duke University Medical Center and a lead author of the study.

"The Duke Infective Endocarditis study demonstrates how the Karius Test can accurately identify the pathogen causing infective endocarditis even when the patient has been pre-treated with antibiotics," said Dr. David K. Hong, Vice President of Medical Affairs and Clinical Development at Karius. "The test's ability to detect and quantify over a thousand pathogens gives clinicians the unique ability to measure pathogen signal in patient plasma over time. This study shows great promise that microbial cell-free DNA as reported by the Karius Test can be a biomarker to aid in the diagnosis and monitoring of IE."

Findings 

Duke University researchers enrolled 30 hospitalized adult patients in a prospective study who were classified using the Duke Criteria for acute infective endocarditis. Blood samples were sent to the Karius laboratory, which uses next-generation sequencing to detect microbial cell-free DNA in patient plasma from over 1,000 pathogens including bacteria, DNA viruses, fungi, molds and eukaryotes.

The complete study results were presented yesterday as an oral abstract during IDWeek™ 2018: Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Infective Endocarditis (IE) Using the Karius Plasma Next Generation Sequencing (NGS) Test.

Study Overview

The Karius Test was performed on residual plasma samples collected within 24 hours of evaluation and whole blood samples collected within 48-72 hours of enrollment as well as on samples collected every 2-3 days for up to 7 time points until discharge. Of the 29 patients eligible for analysis, 24 patients enrolled in the study were evaluated to have definite infective endocarditis. Out of these, 21 patients had culture-positive disease. The Karius Test identified the same organism as cultures in 20 patients (95.2% sensitivity) and additionally identified Enterococcus faecalis in 1 out of the 3 culture-negative patients. Pathogen cell-free DNA signal decreased on antibiotic treatment with rapid declines after surgical procedures to remove the source of infection. The test identified pathogens causing the endocarditis episode in patients pre-treated with antibiotics up to 30 days prior to initial sample collection.

In addition to Dr. Vance Fowler, Duke study authors include Pratik Shah MS, Felicia Ruffin MSN RN, Laura Winn, and Caitlin Drennan. Karius authors are Desiree Hollemon MSN, MPH, Hon Seng, Galit Meshulam-Simon PhD, Ka Lok Chan MS, Huy Quach, Timothy A. Blauwkamp PhD, and David K. Hong MD.

US Patent Issued to Liberian Scientist for Multiplex Infectious Disease Test

The United States Patent and Trademark Office (USPTO) has issued US Patent No. 10,072,309 to Dr. Dougbeh Chris Nyan for his invention of a rapid, real-time isothermal multiplex pathogen diagnostic test that detects and identifies many infections in less than an hour.

Nyan is a Liberian medical doctor and scientist with expertise in infectious diseases and developing simple diagnostic tests for hard-to-reach settings and the global healthcare community.

This proprietary technology is applicable to developing pathogen diagnostic test kits for simultaneous detection and differentiation of multiple infectious such as HIV/AIDS, Hepatitis B, C, and E, West Nile virus, Ebola, Malaria, Dengue, Lassa and Yellow fever viruses, West Nile virus, Zika, and a variety of other infectious. The technology was published in Nature-Scientific Reports and the International Journal of Infectious Diseases.

Accordingly, the Nyan-Test is capable of detecting at least 3-7 pathogens in less than an hour, thus enabling healthcare workers to identify infections and carry out specific treatment. The test is affordable, portable, cuts down detection time, and applicable to settings in the developing countries and vulnerable communities of the developed world. It can be used in early diagnosis, monitoring of the safety of blood products, and surveillance to prevent epidemics.

Nyan, a Mano name for second boy in a family, has intimated that his “invention will be produced to serve suffering humanity and contribute to the global fight against infectious diseases.”

His career in medicine and research spans over twenty-five years. He studied Zoology and Chemistry at the University of Liberia from where he was expelled by the military government of Samuel Doe in 1988 for his advocacy for democracy, press freedom, and human rights. He was arrested and imprisoned by the military government for his pro-democratic advocacy and later exiled and lived in Germany where he studied human medicine at the Charité Medical Faculty of the Humboldt University of Berlin.

He worked as scientist in infectious diseases at the US National Institutes of Health, the University of Pennsylvania School of Medicine, Naval Medical Research Center, the US Food and Drug Administration and in the biotechnology industry.

Dr. Nyan testified before the US Congress on September 17, 2014, during the Ebola outbreak in West Africa. He advocated for a sustained and coordinated support to the Ebola-affected countries of Liberia, Sierra Leone, Guinea, and Nigeria. He requested the U.S. Government to send health experts and technical personnel to the affected region.

He also advocated for the establishment of an African Center for Diseases Control and Prevention, now in Addis Ababa, Ethiopia.

In recognition of his invention, Dr. Nyan has received numerous awards and recognition including the prestigious 2017 African Innovation Award Special Prize for Social Impact, the Lifetime Achievement Award in Science and Medical Research form the Ward Fund, and the Science and Research Award from the Liberian Award.

Nyan’s multiplex test was also recognized as one of Top 3 Innovations by the Africa 2017 Business Forum in Egypt and recently exhibited as one of Top 50 Innovations at the Africa Innovation Summit 2018 in Kigali, Rwanda.

Nyan’s patented technology comes amid the rise of infectious diseases in vulnerable settings in Africa, Asia, and South America and disease re-emergence in neglected communities of the United States and other developed countries.

The Nyan-Test projects to be life-saving and contribute to quality healthcare globally, while providing a multi-billion dollar investment opportunity to the global business community. Dr. Nyan’s biotech startup, Shufflex Biomed, is now raising funds to produce version 2.0 of the test and carry out field studies in Africa and South America.

Patent Summary:

Title: Methods for real-time multiplex isothermal detection and identification of bacterial, viral, and protozoan nucleic acids.

Abstract: Herein disclosed are rapid real-time isothermal multiplex methods of detecting, identifying and quantifying bacterial, viral, and protozoan nucleic acids in a sample. These include contacting the sample with two or more sets of pathogen-specific reverse transcription loop-mediated isothermal amplification primers and novel oligofluorophores specific for the target bacterial, viral, and parasitic nucleic acids of interest such as human immunodeficiency virus, Ebola virus, Marburg virus, Yellow fever virus, hepatitis-B virus, Lassa fever virus, Plasmodium, hepatitis-C virus, hepatitis-E virus, dengue virus, Chikungunya virus, Japanese Encephalitis virus, Middle Eastern Respiratory Syndrome Corona virus, Mycobacterium, West Nile virus, Cytomegalovirus, Parvovirus, Leishmania, Trypanosoma, and Zika virus nucleic acids, under conditions sufficient to produce detectable real-time amplification signals in about 10 to 40 minutes. The amplification signals are produced by pathogen-specific fluorogenic labels included in one or more of the primers. Also, novel reaction and sample lysis buffers, primers, and kits for rapid multiplex detection, quantification, and identification of bacterial, viral, and protozoan nucleic acids by real-time isothermal amplification are herein disclosed.

First Light Biosciences Develops a Novel Method for Rapidly Determining Effective Antibiotics for Treating Infections

First Light Biosciences, a provider of innovative diagnostic tests for fighting life-threatening infections and combating the spread of antibiotic resistance, today announced they will be presenting a scientific poster detailing their novel MultiPath™ technology for rapidly detecting infections, identifying pathogens, and determining the optimum antimicrobial therapy at IDWeek in San Francisco next week.

"IDWeek is the premier, international, scientific meeting of healthcare professionals in infectious diseases and healthcare epidemiology and prevention, including researchers, clinicians, quality and patient safety practitioners, epidemiologists, and public health officials, as well as those who see HIV and pediatric patients."  With more than 6000 attendees and hosted by internationally recognized organizations such as the Society for Healthcare Epidemiology of America (SHEA), the Infectious Disease Society of America (IDSA), The HIV Medicine Association (HIVMA), and the Pediatric Infectious Diseases Society (PIDS), IDWeek provides a unique opportunity for practitioners in the industry to gather and learn from each other's knowledge and experiences.

During the poster session, Lauren Priess, Senior Research Associate from First Light, will be discussing the poster entitled, "A New Method for Rapid Phenotypic AST Directly from Patient Samples." The poster highlights a study demonstrating the value of MultiPath technology for addressing important drawbacks of current infectious disease diagnostics.

The pathogens causing life-threatening infections are frequently resistant to antibiotics. Because current culture-based antimicrobial susceptibility tests (ASTs) take days to identify the appropriate targeted antimicrobial therapy, broad-spectrum therapies are generally prescribed initially. This empiric therapy may be medically sub-optimal or even ineffective and often results in treatment of uninfected patients, which accelerates the spread of antibiotic resistance.

The poster introduces the MultiPath technology and demonstrates its potential for detecting infections, identifying pathogens, and determining the appropriate targeted therapy in 4 hours rather than several days as required by current methods. The study demonstrates the method's unique potential to determine the effective antibiotic directly from patient samples including samples infected by multiple pathogens and samples containing large numbers of contaminating non-pathogenic microbes.

"We are excited to have the opportunity to present the results of this study at IDWeek," said Don Straus, Founder and Chief Scientific Officer at First Light Biosciences. "The results of this study demonstrate MultiPath technology's unique potential to determine the optimum treatment for life-threatening syndromic infections in any type of sample in just a few hours."

First Light will be presenting their poster on Friday, October 5th from 12:30 PM - 1:45 PM, and will be happy to answer questions throughout the event.

About First Light Biosciences

First Light Biosciences is developing and preparing to commercialize, innovative diagnostic products for rapid, sensitive and cost-saving detection of life-threatening infections, and combating the spread of antibiotic resistance.  Don Straus is the company's Founder and primary inventor of the company's core scientific technology. Based on its proprietary MultiPath™ detection technology, First Light's products combine the clinical performance of the most advanced commercial laboratory tests with speed, cost-effectiveness, and ease-of-use. The tests rapidly detect infections, identify infectious agents, and determine effective targeted antibiotic therapy. This will improve patient outcomes, reduce healthcare costs, and prevent inappropriate use of powerful antibiotics.

HHS Partners to Develop Faster Tests to Identify Bacterial Infections

A test that may reduce, from days to hours, the time needed to diagnose patients with bacterial infections and determine how well an antibiotic will work against specific infections will receive advanced development support from the U.S. Department of Health and Human Services’ (HHS) Office of the Assistant Secretary for Preparedness and Response (ASPR).

The Biomedical Advanced Research and Development Authority (BARDA), part of ASPR, will sponsor the advanced development of the new testing technology under an 18-month, approximately $9.3 million contract with SeLux Diagnostic, Inc of Charlestown, Massachusetts.

SeLux is developing a phenotypic test; it identifies bacteria based on observable physical or biochemical characteristics of the bacteria. Based on the characteristics, the test identifies the class of bacteria and which antibiotics are best for treating that particular bacterial infection.

Faster information to select the best antibiotic can speed a patient’s recovery, which means fewer days spent in a hospital and better outcomes for patients. The ability to match bacteria more precisely to the drugs that will combat the infection also could curb antibiotic resistant infections.

“Antibiotic resistance is a growing threat to public health and to the health security of the United States,” said BARDA Director Rick Bright, Ph.D. “In a bioterrorism incident, antibiotic resistant infections could be devastating. We will need innovative tools for precision medicine to save lives.”

BARDA is sponsoring the development of two test systems from SeLux.  The company’s first-generation test system may be able to provide results using bacteria isolated from patient samples 24 hours faster than current state-of-the-art methods and may be able to provide results from blood samples three days faster than the current methods. The company’s second-generation test system may be able to provide results the same day that the test is started.

The tests are designed to be used in hospital and commercial laboratories. Rapid information on bacteria and how susceptible they are to antibiotics would help doctors make earlier, better-informed decisions about how best to treat infections.

BARDA funding will support necessary work for the company to apply for U.S. Food and Drug Administration (FDA) approval. The agreement can be extended to fund additional work up to a total of approximately $36 million through 2023.

In addition to SeLux’s diagnostic test systems, BARDA is supporting development of other antibiotic susceptibility tests that can distinguish between bacterial and viral infections. BARDA also is working with federal partners to develop other tests that identify bacterial infections and the bacteria’s susceptibility to specific antibiotics. These efforts are part of the HHS commitment to combat antimicrobial resistance and to support antibiotic stewardship. To encourage antimicrobial stewardship further, ASPR provides hospitals and health care coalitions with guidance and the latest information on antibiotic resistant infections and new tools to combat them.

About HHS, ASPR and BARDA

HHS works to enhance and protect the health and well-being of all Americans, providing for effective health and human services and fostering advances in medicine, public health, and social services. The mission of HHS’s Office of the Assistant Secretary for Preparedness and Response (ASPR) is to save lives and protect Americans from 21st century health security threats. Within ASPR, BARDA invests in the advanced research and development, acquisition, and manufacturing of medical countermeasures – vaccines, drugs, therapeutics, diagnostic tools, and non-pharmaceutical products needed to combat health security threats.

Nigeria Government to Deploy GeneXpert Systems to Improve TB Diagnosis

As Part of national efforts to improve the diagnosis of tuberculosis (TB), the Minister of Health, Prof. Isaac Adewole said that the Federal Government plans to deploy GeneXpert machines in 774 local government council areas across the federation.

Adewole disclosed this plan at the Public Private Mix (PPM) Summit for Tuberculosis (TB) Control in Nigeria, which took place in Lagos recently.

According to Adewole, a total of 391 GeneXpert machines have so far been installed at 310 sites across the country for this purpose of improving the diagnosis of TB and to make the diagnosis rapid.

However, to ensure universal access to TB diagnosis, the Federal Government targets to have at least one machine per LGC area across the federation.

The GeneXpert diagnostic technology is a a diagnostic tool that has high sensitivity in diagnosing TB.

TB is an infectious disease usually caused by bacterium Mycobacterium (MTB). TB generally affects the lungs, but can also affect other parts of the body. Most TB infections do not have symptoms, in which case it is known as latent TB.

About 10 per cent of latent infections progress to active disease which, if left untreated kills about half of those infected. The classic symptoms of active TB are a chronic cough with blood-containing sputum, fever, night sweats and weight loss.

The PPM summit was organised by the Federal Ministry of Health (FMOH) in collaboration with the World Health Organisation (WHO), Stop TB Partnership Nigeria and the Tuberculosis Control Programme in Lagos State.

Giving the background to some of the challenges in tackling TB, it was said that inadequate Gene Expert machines meant for the diagnosis of the killer disease remains a huge challenge to curbing the high prevalence of TB in communities.

However, bringing the Gene Expert machine closer to various communities would therefore remove the hindrance obstructing rapid diagnosis of the medical condition.

Nigeria has the 2nd highest burden of TB in Africa.Nigeria has a country is among the 14th countries considered by the WHO as being high burden not only for Tb, but also for TB/HIV and multi-drug resistance ( MDR-TB).

Country Representative of the WHO in Nigeria, Dr. Wondimagegnehu Alemu who was represented by Dr. Lynda Ozor, said expanding quality TB diagnostic coverage nationwide was necessary as a measure to stop the spread of new TB infections.

He also called for the optimisation of the existing Gene EXpert diagnostic machine (390).
According to him, involving the private sector in tackling TB would ensure that the vision of reaching more Nigerians that were affected by TB and those at risk of infection, could be reached this 2018 and beyond.

OpGen Partners with NY State Department of Health and Merck’s ILÚM Health Solutions to Detect Antimicrobial-Resistant Infections

OpGen, Inc. announced a groundbreaking collaboration with the New York State Department of Health (“DOH”) and ILÚM Health Solutions, LLC (“ILÚM”), a wholly owned subsidiary of Merck’s Healthcare Services and Solutions, to develop a state-of-the-art research program to detect, track, and manage antimicrobial-resistant infections at healthcare institutions statewide. OpGen will work together with DOH’s Wadsworth Center and ILÚM to develop an infectious disease digital health and precision medicine platform that connects healthcare institutions to DOH and uses genomic microbiology for statewide surveillance and control of antimicrobial resistance.

The DOH, ILÚM and OpGen will work collaboratively to build a sustainable, flexible infectious diseases reporting, tracking and surveillance tool for antimicrobial resistance that can be applied across New York State. The goal of this project is to improve patient outcomes and save healthcare dollars by integrating real-time epidemiologic surveillance with rapid delivery of resistance results to care-givers via web-based and mobile platforms. ILÚM is leading the project with the implementation of its technology platform. OpGen is providing its Acuitas® AMR Gene Panel for rapid detection of multidrug-resistant bacterial pathogens along with its Acuitas Lighthouse® Software for high resolution pathogen tracking.

“We are proud to be a part of this groundbreaking initiative throughout the State of New York, and to collaborate with Wadsworth and ILÚM to help develop the blueprint for how governments and healthcare facilities can detect, track, and manage antimicrobial-resistant infections,” said Evan Jones, CEO, OpGen. “As part of the collaboration, OpGen will receive a $1.5 million contract for the 12-month demonstration portion of the project, with the potential for full implementation during the next five years, should certain milestones be achieved by all parties involved. We look forward to working with the Wadsworth Laboratories and to serving the people of the State of New York.”

The precision medicine solutions provided by OpGen and ILÚM to accomplish the goals of the project are:

• The OpGen Acuitas AMR Gene Panel u.5.47, a distributed, rapid diagnostics platform capable of detection and identification of multidrug-resistant bacterial pathogens in under three hours and for use with the Acuitas Lighthouse Software.  Together, these products can rapidly identify and locate antibiotic resistance threats in healthcare institutions and networks.  Both systems are commercially available for Research Use Only (RUO) and are anticipated to be submitted for FDA clearance after completion of ongoing and planned clinical trials. In future iterations, OpGen’s Acuitas technologies are anticipated to provide custom testing solutions to supplement evolving Wadsworth Laboratory testing and New York State’s DOH surveillance needs.
• The OpGen Acuitas Lighthouse Software includes Acuitas Lighthouse epidemiology dashboards with high-resolution pathogen tracking through healthcare facilities, to cities, regions, as well as the entire state. 
• ILÚM’s technology platform, a Commercial Off The Shelf (COTS) solution which assembles and streams analyzed health data from across locations and health care systems. This data includes laboratory test results, pharmacy, orders, and ADT (admissions, discharges, transfers). The platform offers patient and program-specific data analytics and visualization capabilities to users via a web application and a mobile device application.  Also, it enables case browsing, patient monitoring, detection and prioritization and performance monitoring and reporting for disease management, including actionable insights in support of quality improvement efforts, disease surveillance, pathway adherence, and ultimately impacting outcomes.

New York State Health Commissioner Dr. Howard A. Zucker said, "Under Governor Cuomo's leadership, New York State is setting the standard in addressing the threat of antimicrobial resistance.  New York's Wadsworth Center is uniquely qualified to partner with OpGen and ILÚM Health Solutions as part of our response to this public health concern."