OpGen to Offer Next-Generation Sequencing and PCR-based Coronavirus (2019-nCoV) Testing in Europe

OpGen, Inc. reported an update on the business of Curetis GmbH (“Curetis”), the other party to the planned business combination with OpGen. Today, Curetis announced that Ares Genetics GmbH, a Curetis Group company, and the Chinese genomics company BGI Group will collaborate in making molecular testing for the new coronavirus 2019-nCoV available in Europe.

2019-nCoV is a new coronavirus variant that has not been previously identified in humans but is responsible for the outbreak originating in the Chinese city of Wuhan and rapidly spreading globally with first cases identified and confirmed in Europe already. In response to this situation, and immediately after the occurrence of unexplained pneumonia in Wuhan on December 31, 2019, BGI was first to sequence the genome of the new 2019-nCoV virus and successfully developed a Real-Time (RT) Fluorescent PCR (polymerase chain reaction) kit for detecting 2019-nCoV, which can provide results in a few hours and has already obtained approval by the Chinese National Medical Products Administration.

In addition to the rapid detection kit based on RT-PCR technology, the DNBSEQ-T7 sequencing platform developed by BGI Group’s instrument and reagent subsidiary, MGI, passed the emergency approval procedure of the National Medical Products Administration, becoming the first officially approved testing products in China for surveillance, discovery and identification of unknown infectious diseases.

In Europe, BGI and MGI will work with their long-term strategic partner Ares Genetics to make its 2019-nCoV testing portfolio available to public health institutions and hospitals for outbreak monitoring, infection control, and epidemiology. Ares Genetics expects to provide next-generation sequencing services for 2019-nCoV out of its NGS laboratory in Vienna, Austria, for infection control and tracking of pathogen evolution from February 2020 onwards based on MGI’s DNBSEQ sequencing platform. Further, Ares Genetics and the Curetis Group will support BGI Group in the distribution of its PCR and NGS reagent kits to molecular testing laboratories in Europe that have the capability for 2019-nCoV testing with reagent kits initially being marketed for research use only prior to regulatory approval in Europe.

Ares Genetics is a digital diagnostics company utilizing artificial intelligence-powered molecular diagnostics to advance the field of infectious disease testing. Ares Genetics recently launched ARESupa – Universal Pathogenome Assay for the broad identification of bacterial pathogens and the accurate prediction of antibiotic susceptibility. The ARESupa test is based on the sequencing of bacterial DNA, combined with data analysis and interpretation powered by ARESdb, Ares Genetics’ unique, proprietary reference database on genetic antimicrobial resistance markers. The first generation of ARESupa is currently offered for non-diagnostic applications in epidemiology, infection control, and outbreak analysis for customers in the public health sector and the pharmaceutical industry. A laboratory-developed test (LDT) for human diagnostic use is under development.

“This collaboration highlights the importance of rapid testing technologies in tracking the evolution of and containing global outbreaks. We congratulate Curetis on their collaboration and commend them and BGI Group for their swift action to assist in the surveillance and identification of yet another infectious disease with cases across the globe,” said Evan Jones, Chairman & CEO of OpGen.

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Wuhan Coronavirus Detection Test Being Developed

It has been just three weeks since a brand new strain of coronavirus—2019-nCoV—was discovered in the Chinese city of Wuhan. But the novel virus which has spread rapidly over the past two weeks, causing respiratory illness, has become a growing concern for global health organizations. During the outbreak, the virus has sickened more than 500 patients and killed an estimated 17. The people that have died have, in general, had underlying medical conditions.

China confirmed human-to-human transmission of the virus on January 20, and the United States announced the first infection in this country on January 21, detected in a traveler returning from Wuhan. There is a quarantine in place in the city of Wuhan, grounding planes, preventing buses and trains from coming into or leaving the city, and halting all public transportation.

Co-Diagnostics, a molecular diagnostics company with a unique, patented platform for the development of molecular diagnostic tests, recently announced that it has completed principle design work for a PCR screening test for 2019-nCoV, intended to address the potential need for detection of the virus which could prove useful in the current outbreak in China.

“There are several challenges to developing a test for a virus so relatively new on the world stage, especially one with many closely-related genetic cousins such as SARS and MERS,” noted Dwight Egan, CEO of Co-Diagnostics.

The new test features the company’s patented CoPrimer technology. The company claims that their platform and the proprietary structure of CoPrimer molecules “dramatically enhances the output of molecular diagnostic tests conducted via real-time polymerase chain reaction tests.” They noted that it achieves this by creating reactions that are far more specific than competing PCR technologies and 2.5 million times more effective in reducing amplification errors.

“One of the most important advantages of our CoPrimer platform,” explained Egan, “is its ability to reliably and accurately differentiate between similar genetic sequences, in order to reduce the likelihood of a false-positive diagnosis.” With a situation currently unfolding where at least 17 deaths have already been reported among the hundreds infected, Egan added, it is vital that healthcare professionals have access to the highest-quality diagnostic tools available, to be able to provide prompt and accurate diagnoses. “If the WHO takes the step of declaring the illness a global health emergency following collection of more data in the days and weeks to come, Co-Diagnostics will be well-positioned to quickly assist in providing these state-of-the-art tools to affected countries.”
The virus

Common human coronaviruses—including types 229E, NL63, OC43, and HKU1—typically cause mild to moderate upper-respiratory tract illnesses, like the common cold. And, according to the CDC, a coronavirus infection is not uncommon for many people.

Typically, the symptoms include runny nose, headache, dry cough, sore throat, and fever. However, more severe cases can result in more serious lower-respiratory tract infections such as viral pneumonia or bronchitis.

In 2003, the coronavirus SARS was at the center of a severe outbreak that affected thousands of people around the world and had a death rate of about 10%—resulting in nearly 800 deaths. MERS is another coronavirus known to cause severe illness, mostly in Saudi Arabia, which causes about 3 or 4 deaths out of every 10 patients reported with MERS. MERS cases continue to occur, primarily in the Arabian Peninsula. No human cases of SARS have been reported anywhere in the world since 2004.

Source: Genetic Engineering & Biotechnology News

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Indian Vice President Urges Global Cooperation to Detect the Wuhan Coronavirus

Vice-President M Venkaiah Naidu on Monday highlighted the need for global cooperation for early detection of new viruses and to contain serious fallout from the outbreak of epidemics.

The Vice-President, who visited the Hyderabad-based Centre for Cellular and Molecular Biology (CCMB), referred to the novel-strain of Coronavirus in China and pointed out that the disease was spreading across countries and is threatening to become a major public health crisis.

Referring to the vital role of the Indian Science and Technology Innovation (STI) system in achieving national goals as India aspires for sustainable and inclusive growth, the Vice-President made an appeal to the private sector to create a fund to finance innovative scientific projects aimed at addressing societal concerns.

Observing that investment in STI plays a major role in promoting research and developing cutting-edge technologies, he said funding for basic research must also be stepped up.
The Vice-President called upon scientists of CCMB and other scientific labs to find solutions to the challenges facing the world today like poverty, climate change, pollution, lack of clean drinking water, sanitation, increasing urbanisation and growing drug resistance.

He visited research facilities at CCMB and interacted with researchers and enquired about their work. He lauded CCMB’s effort in developing bacterial blight-resistant Samba Masuri rice variety in collaboration with the Indian Institute of Rice Research.

There is a need for CCMB to develop rapid DNA testing kits for the detection of rare diseases and many other genetic disorders. “It is important to predict and prevent genetic diseases as more than 70 million Indians are estimated to be suffering from genetic disorders,” Naidu said stating a report of the Organisation for Rare Diseases India. CCMB Director Dr Rakesh Mishra, Directors of CSIR labs, senior scientists and researchers were present.

Coronavirus: Patients from city test negative

Hyderabad: The swab samples of the patients at Fever Hospital, which were sent to the National Institute of Virology (NIV), Pune, have tested negative for coronavirus, which continues to spread in China and to other parts of the world. Fearing that they might have been infected by the virus, three persons hailing from Hyderabad but with a recent travel history to China had volunteered and got admitted to Fever Hospital.

Health officials collected the swab samples from the patients and sent them to NIV Pune for testing. “All the samples have come negative. The patients have cold but they do not have fever, throat pain or breathing-related issues. They will be kept under observation for a day or two before being discharged,” said Dr K Shankar, Superintendent, Fever Hospital.

Meanwhile, a team of experts from the Ministry of Health and Family Welfare (MoHFW) is expected to visit Hyderabad on Tuesday. The team will review coronavirus end-to-end preparedness for management of 2019-nCoV at airports, for thermal scanning of passengers and transferring of patients to hospitals for isolation. The team is also expected to visit Gandhi Hospital and Fever Hospital to oversee the preparations like isolation wards.

Source: Telangana Today

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Romer Labs® Introduces RapidChek® Campylobacter Test Kit

Romer Labs, a provider of diagnostic solutions for the agricultural, food, and feed industries, has announced that its RapidChek® line of solutions for pathogen testing will now include a test kit for Campylobacter.

RapidChek Campylobacter couples a sensitive immune-detection strip with a proprietary aerobic enrichment media. Poultry processors testing carcass rinses, turkey carcass swabs, and raw ground chicken get clear results within 20 minutes (after incubation), ensuring accuracy and enhancing compliance with emerging regulations in the United States.

RapidChek Campylobacter was developed in collaboration with a large poultry processor looking for an efficient way to comply with new U.S. Department of Agriculture regulations that require the industry to implement qualitative testing for the pathogen using enrichment-based procedures. RapidChek Campylobacter detects the three regulated species—C. jejuni, C. coli, and C. lari—in carcass rinses, raw ground chicken and turkey carcass swabs.

Julie Sundgaard, managing director, Romer Labs North America says, “We have been hearing from our customers in the poultry sector that they need a rapid, reliable test for Campylobacter that doesn’t need specialized and expensive equipment to comply with new regulations. With the RapidChek Campylobacter test kit, we provide them with the solution they have been looking for.

The procedure is simple—an all-in-one aerobic enrichment media requires no additional supplements for preparation, and the whole test can be learned with minimal training. We know that resource management is an issue for poultry processors. This is why we made sure that our kit can be stored at room temperature and has a long shelf life. Third-party certifications are pending.”

Source: Food Safety Magazine

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WHO Approves India’s Cost-Effective TB Test

A technology to diagnose tuberculosis (TB), and its multi-drug resistant variant, faster and at a lower cost by Indian researchers has received approval from the World Health Organisation (WHO).

The WHO’’s Global TB Programme has included TrueNat TB test, a new molecular test that detects TB as well as resistance to the drug Rifampicin in about 90 minutes, in its rapid communication document on molecular investigative procedure in laboratory medicine and pharmacology.

Talking about its significance, director general Indian Council of Medical Research (ICMR), and secretary Department of Health Research, Dr Balram Bhargava, in a statement said that WHO endorsement of the technology would enable low and middle-income countries to procure TrueNat for TB and Rifampicin resistance, which will help in eliminating the disease in developing countries.

At 2.7 million new infections, India is home to almost a quarter of world’s TB patients. The Indian government has set an ambitious target of eliminating the disease by 2025- five years before the global target.

The TrueNat assay kit is highly cost-effective compared to GeneXpert and can be used in peripheral centres without an air conditioned laboratory as it runs on battery which can be solar powered.

The kit works in two steps. In the first step, the DNA is extracted from the sputum and the second stage involves detection of tuberculosis and multi-drug resistant TB.

Supported by the Department of Health Research (DHR), Ministry of Health and DBT, various indigenous technologies developed by Indian scientists and companies for detection of multi-drug resistant (MDR)/extensively drug-resistant (XDR) TB were reviewed.

The most promising kits were selected by an expert group and those were subjected to a double-blind validation in comparison to standard tests at four national reference laboratories of the country.

After a stringent review, a series of validation, subsequent feasibility studies and continuous follow-up, the ‘’TrueNat MTB & Rif’’ assay was found to be on par with the internationally recognized molecular assay Gene Xpert in terms of sensitivity and specificity and detection of rifampicin resistance.

This was taken up by National TB Elimination Programme after recommendations from ICMR.

As part of WHO’’s pre-qualification process, ICMR funded Indian centres of the FIND-coordinated multi-central, prospective field evaluation study in four countries -- India, Ethiopia, Peru and Papua-New Guinea.

Based on the interim analysis of data, WHO included TrueNat as test to diagnose TB, replacing sputum smear microscopy, and to sequentially detect rifampicin resistance in view of its high diagnostic accuracy. The study has completed enrolment at all sites and a final analysis would be undertaken soon by FIND, Geneva, the ICMR statement further read.

Source: hindustantimes

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PathogenDx Becomes First Sponsor of Illinois Hemp Growers Association

PathogenDx, Inc., the Arizona based technology company which has developed an Ultra-rapid DNA-based customized pathogen testing platform for the cannabis, food and agricultural sectors, announced today a partnership with the Illinois Hemp Growers Association (IHGA). The partnership, which includes a sponsorship, comes at a time when the hemp industry is gaining momentum as a cash crop in America.

Illinois has always been synonymous with the agriculture of corn and soybeans, but since the U.S. Farm Bill made hemp production legal in December 2018, Illinois has grabbed hold of the opportunity to establish itself as a leader in industrial hemp production. Like many crops, farmers and producers need to safeguard their plants from pathogens that can destroy profits and threaten public health.

PathogenDx's clean testing technologies are used by more than 90 laboratories around the country to help ensure regulatory approval for growers, processors and supporting businesses. The company's EnviroX clean testing solution allows growers, processors and producers to get biomass rapidly tested for dozens of pathogens that are wreaking havoc on the industry, as well as swab production and storage facilities to mitigate contamination of the product regardless of the stage of process it is in.

"We have the opportunity to build a safe supply chain right from the start - not one that only catches tainted product when it hits the lab or is already in the public realm," said Milan Patel, Co-Founder and CEO of PathogenDx. "We are excited to partner with IHGA to set a new safety standard for the burgeoning hemp industry that will protect farmers and consumer health."

"We are pleased to announce that the Illinois Hemp Growers Association is being sponsored by PathogenDx," said Rachel Berry, Founder and CEO of the IHGA. "Our partnership will bring awareness to and help establish standards of product purity that are critical to the developing Illinois hemp industry."

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Ontera and QuantuMDx Collaborate to Advance Sepsis Diagnosis

Ontera, Inc., and QuantuMDx Group Limited have announced a collaboration to create a next-generation solution for blood stream infection and drug resistance detection. The technology will be based on QuantuMDx’s rapid cell/sample preparation technology, Capture-XT®, and Ontera’s powerful nanopore biosensor, currently utilized in their SAM and DUO Nano platforms.

The combined technologies should enable clinicians to quickly interrogate blood specimens of those presenting with sepsis signs and symptoms, allowing guided ‘right first time’ care management, at the bedside.

Sepsis affects more than 30 million people worldwide every year, leading to an estimated 6 million deaths.¹ If it’s not recognized early and managed promptly with targeted antibiotics, sepsis can lead to septic shock, multiple organ failure and death.

QuantuMDx’s revolutionary Capture-XT® technology captures, concentrates and enriches targeted pathogens from a large sample volume, quickly enabling visual diagnosis and downstream utilization, such as drug-susceptibility analysis, PCR, NGS and now nanopore detection, with this collaboration.

Ontera’s single pore platform provides fast amplification of multiple bacterial targets, differentiation between antibiotic resistant and susceptible strains. The company uses silicon nanopore for in-minutes quantitative measurement of nucleic acids, proteins and small molecules, avoiding time-consuming laboratory procedures that can delay lifesaving, fast and precise treatment.

“Sepsis is one of the hardest diseases to detect. It’s like looking for a needle in a haystack, due to the low concentration of organisms in the blood stream that cause disease,” says Jonathan O’Halloran, Chief Scientific Officer at QuantuMDx. “Our early prototype testing has already shown sensitivity in the range required for this kind of test and performed in minutes from spiked bacteria in whole blood. We haven’t even pushed the technology yet, but it has the potential to become a paradigm-shifting, powerful device. And, by including drug resistance in the assay to enable right first time prescribing, the impact of this partnership could be profound.”

“Today, 30% of patients receive inappropriate antimicrobial therapy. By not only identifying sepsis but also resistance to most common antibiotics in less than 30 minutes, we will transform the sepsis landscape and impact lives,” says Murielle Thinard McLane, CEO of Ontera. “We have set out on a mission to democratize access to molecular information to create a more sustainable planet. This collaboration with QuantuMDx is a major proof point along that mission.”

Notes:

WHO 2019
Sepsis arises when the body’s response to any infection injures its own tissues and organs. If not recognized early and managed promptly, it can lead to septic shock, multiple organ failure and death. It is a serious complication of infection in all countries and particularly in low- and middle-income countries it represents a major cause of maternal and neonatal morbidity and mortality. (WHO 2019)

About Ontera

Ontera, a leader in silicon-based nanopore sensing, was founded with the idea that better information is needed to enhance human and environmental health in a sustainable way. The company aims to democratize access to molecular information through its series of nanopore based platforms, making it accessible at the point of need: easy, fast and cost effective.

About QuantuMDx

QuantuMDx Group is a multinational company with a global vision of empowering the world to control and eradicate disease by making transformative, quality point-of-care diagnostic technologies universally accessible. QuantuMDx has operations and strategic partnerships in the United States, Asia, Europe and Africa – keeping it at the forefront of molecular diagnostics.

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Illuminating Anthrax

The Defense Threat Reduction Agency’s Chemical and Biological Technologies Department (DTRA CB) has a new test that reduces the time needed to determine clearance decontamination for anthrax (anthrax clearance). Anthrax clearance means that anthrax spores are no longer detectable in a laboratory test of an environmental sample. Clearance testing ensures that decontamination efforts have reduced the hazard to a level that does not threaten the warfighter. Current clearance tests can take up to two days.

DTRA CB’s faster test, called the Bacteriophage Rapid Anthrax Viability Evaluation System (BRAVES), produces results in 6–8 hours. BRAVES is an adaptation of a commercial, off-the-shelf technology. DTRA CB supported the adaptation effort, which was performed by government researchers at the U.S. Army Corps of Engineers Engineer Research and Development Center Construction Engineering Research Laboratory and the Naval Surface Warfare Center Dahlgren Division.

BRAVES rapidly detects living anthrax spores in multiple environmental samples at one time. Additional research is necessary to evaluate the new test’s efficacy in the environmental conditions where warfighters operate. Researchers will also compare the new test’s ability to identify viable anthrax spores across various samples (plywood, concrete, fabric, water, soil), collected before and after a decontamination. Outstanding assessments aside, BRAVES is showing promise as a new anthrax clearance test.

BRAVES overcomes disadvantages associated with current anthrax clearance methods that include the standard polymerase chain reaction (PCR) test, the plate culture assay, and quantitative PCR. Standard PCR takes 12–18 hours to complete and does not differentiate dead spores from living or viable spores that can become infectious. The plate culture assay test requires 1–2 days to complete, is demanding in labor, and needs its results verified by sophisticated laboratory equipment that, in turn, needs skilled technicians to operate and an environmentally controlled setting to store. Quantitative PCR also needs equipment that is impractical for the field, and its results take over 24 hours to yield.

Unlike other tests, BRAVES produces light to signal the number of viable spores present in a sample. Here’s how the new test functions: soil or another environmental sample is added to a broth containing nutrients for germinating viable spores and growing the parent bacterium Bacillus anthracis. The broth also includes antibiotics and a genetically engineered bacteriophage (a small virus) called the Wβ. Bacteriophages infect certain bacteria, and the Wβ infects B. anthracis.

If a sample has viable anthrax spores, then the spores germinate into vegetative cells that are capable of causing the anthrax infection. Wβ infects the vegetative cells and replicates itself and, in the process, makes the luciferase protein, the same type of protein that makes a firefly glow. The mixture of sample and broth incubate for 6–8 hours, and the luciferase protein produces bioluminescence, thereby causing each living anthrax cell to illuminate. The antibiotic in the broth kills all nonanthrax bacteria in the sample, so the light generated is only due to viable anthrax spores.

Typically, researchers expect an anthrax clearance test to detect spores at a number below the amount required to infect humans. BRAVES exceeds this expectation. Laboratory tests reveal that the new test identifies as few as 1,000 B. anthracis viable spores (about 10 times less than a human infectious dose) in a gram of normal soil.
The new Wβ-mediated bioluminescent technology achieves anthrax clearance at 10% of the cost, labor, and laboratory space needed by current methods — a logistical improvement.

BRAVES is faster in determining anthrax clearance than competing state-of-the-art methods, thereby enabling warfighters to more quickly establish the success of their decontamination efforts. For warfighters, a quicker achievement of clearance means a quicker return to the mission and a quicker return home.

Source: https://www.dvidshub.net/

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New Paper-Based Test for Early Lyme Diagnosis

A new paper in the journal ACS Nano reports the development of an incredibly cheap and highly sensitive test to diagnose Lyme disease in its earliest stages, when it can be most easily, effectively and inexpensively treated.

Lyme disease

The tick-borne disease called Lyme disease is caused by a bacterium that produces both acute and chronic symptoms and signs. Ticks are usually picked up while walking through infested areas. The disease initially manifests as a bull’s-eye or target rash, which is characteristic of the disease. However, this is not universally present in all individuals with Lyme disease. Thus about 10% to 20% of these patients are likely to be diagnosed much later when they come down with delayed manifestations such as arthritis or palpitations. This makes it necessary to find a way to diagnose it more sensitively and earlier in its course.

Every year, about 300,000 Americans come down with Lyme disease, caused by the bacterium Borrelia burgdorferi, making it the most common infectious disease caused by any vector-borne agent. Black-legged ticks of the Ixodes genus are responsible for carrying this bacterium.

The first symptoms occur within 30 days, and include the rash, fever, chills, headache and muscle pains. Prompt antibiotic treatment can arrest the course of the disease. If untreated, the disease progresses to nerve palsy, especially of the facial nerve, neurological pain, joint pain and swelling, and palpitations due to heart block. This is seen in up to a fifth of all patients.

Diagnosis of Lyme disease

While the disease can be diagnosed directly by detecting the nucleic acid of the organism, or by culturing the bacterium, these are time-consuming and not as sensitive as could be desired. The issue is that the bacterium is present for only a short time and in low concentrations in the blood, making direct detection of the bacterium a challenge.

Indirect detection by blood tests that detect specific antibodies to the bacterium is also disappointing, especially in the early stages, when it is most necessary to diagnose it in order to start appropriate treatment.

Currently, a two-tier testing procedure is the diagnostic standard: first a sensitive enzyme immunoassay or immunofluorescence assay, followed by a Western blot for confirmation by picking up specific antibodies. However, this is sensitive and specific only with late Lyme disease, though treatment is most effective and cheapest in early disease. Besides, most patients are seen with early disease. Thirdly, the set up for this type of testing is expensive, requires upscale infrastructure, and trained technicians, making it non-feasible for the very populations where the tick bites are most likely to happen.

The study

The current study was motivated by the need to come up with a rapid, convenient and cheap diagnostic test that would show the presence of the infection early in the disease course. They used existing knowledge about paper-based assays and deep machine learning to come up with a new, cheap and fast test for early-stage Lyme disease.

The researchers designed a small device that is meant to find the presence of the bacterium in blood samples. It uses a stack of functionalized papers as the basic material and a sensing membrane. The paper stack is functionalized with seven bacterial antigens as well as an artificial peptide, localized in 13 spots. The device is exposed to the serum which flows vertically through the stacks, so that the antibodies to the bacteria can bind to the spots. The bound antibodies are then treated with a color-changing solution that will show how much bound antibody is present.

The colored spots are photographed using a customized smart phone-based reader. The analysis of the color changes is then carried out based on a neural network developed for this study, which is capable of deep learning to determine if the sample is negative for the disease or positive. This is based on the presence of antibody binding to an optimal antigen/peptide target subset selected by the deep learning algorithm.

The device was tested on 50 samples, some of which were positive and some negative for the early stages of Lyme disease.

The findings

The results showed that it was over 96% specific and picked up almost 86% of positive samples. This is much higher than that of existing tests, which is below 50%. Moreover, the test is completed in about 15 minutes rather than the more than 24 hours of existing two-tier testing. It also comes at an incredibly low cost of only 42 cents compared to the above $400 cost of conventional serologic testing.

Implications

This kind of testing methodology will allow point-of-care testing for Lyme disease in the earliest stages. The possible advantages of this novel application, besides those mentioned above, include the ability to optimize the selection of antigens, to achieve the desired balance of false positives and false negatives in the final diagnostic phase, and the potential for the development and inclusion of more sensitive and stable antigens that can allow a still more improved performance.

Reference:

Point-of-Care Serodiagnostic Test for Early-Stage Lyme Disease Using a Multiplexed Paper-Based Immunoassay and Machine Learning, Hyou-Arm Joung, Zachary S. Ballard, Jing WuDerek K. Tseng, Hailemariam Teshome, Linghao Zhang ,Elizabeth J. Horn, Paul M. Arnaboldi, Raymond J. Dattwyler, Omai B. Garner, Dino Di Carlo, Aydogan Ozcan, ACS Nano 2019, https://doi.org/10.1021/acsnano.9b08151

Source: News-Medical.net

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The Combined Use of Two Rapid Tests is Effective for Accurate Diagnosis of Chronic Chagas Disease in the Field

The combined use of two commercially available rapid diagnostic tests is effective for accurately diagnosing chronic Chagas disease in the field, according to a study funded by the Inter-American Development Bank (IDB) and led by the Barcelona Institute for Global Health (ISGlobal), an institution supported by “la Caixa” in collaboration with CEADES and Mundo Sano Foundation. The performance observed indicates that these tests could be used to diagnose chronic Chagas in highly endemic regions with poorly equipped laboratories.

A complicated diagnosis in the field

The acute phase of infection by Trypanosoma cruzi – the causal agent of Chagas disease – is typically asymptomatic and goes unnoticed. Disease diagnosis often occurs during the chronic stage, when symptoms appear. The conventional serological tests (ELISAs) used to diagnose the disease are not practical to perform since they require equipped laboratories. In contrast, rapid diagnosis tests (RDTs) are easy to use, do not need cold storage, and require small quantities of blood.

In a previous study, the research team had already suggested using two rapid tests as an alternative to serological techniques for Chagas diagnosis. “We have now taken the RDTs to the field, to test them in screening campaigns performed by mobile teams,” explains Julio Alonso-Padilla, ISGlobal researcher and coordinator of the study. The authors used 685 samples obtained in the Chaco region of Bolivia to compare results from both RDTs – either combined or separately – with the standard serological tests performed in laboratory. They found that the combined use of both RDTs had a sensitivity (i.e. the capacity to detect positive cases) of 97% and a specificity (i.e. the capacity to discern negative cases) of 96.1%, compared to the standard algorithm (based on ELISAs).

The results, published in PLoS NTDs, showed a high prevalence of infection in the region: 44% of analysed samples were positive. “The results of this study support the use of rapid diagnostic tests as an alternative to conventional serological methods in the Chaco and other highly endemic regions,” says Alonso-Padilla.

Reference

Lozano D, Rojas L, Mendez S, et al. Use of rapid diagnostic tests (RDTs) for conclusive diagnosis of chronic Chagas disease – field implementation in the Chaco region. Plos NTDs. doi: 10.1371/journal.pntd.0007877

Source: Barcelona Institute for Global Health

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Scientists Identify Harmful Bacteria Based on its DNA at a Very Low Cost

Currently, the detection of food poison outbreaks caused by bacteria takes a long time and is expensive, but this does not have to be the case in the future. Researchers from the Department of Food Science at the University of Copenhagen have found a method for the precise identification of bacteria in just a few hours on a mobile-phone-sized device that costs about 200 times less than alternative approaches.

A new bacterial identification method, called ON-rep-seq, examines selective, strain-specific fragments of the bacterial genome, allowing the generation of results that earlier required DNA sequencing of the entire bacterial genome or tedious approaches like pulsed field gel electrophoresis, which previously has been the golden standard for strain-level typing of microorganisms. Hence, the method has the potential to change the approach utilized for investigating food-based disease outbreaks by making analysis much less time- and cost consuming.

Currently, bacterial detection and identification based on bacterial DNA requires expensive instrumentation and many hours of work by highly trained specialists. Let’s imagine, for example, there is a suspected Salmonella outbreak. Usually in order to locate its origin, not only will investigators have to analyze many samples, but the analysis has to be precise in order to distinguish one bacterial strain from another.

“Our new method allows identification and typing of hundreds of samples in less than two hours, and we expect that this will even be reduced to "real time" in a short period of time,” says one of the researchers behind the study, Lukasz Krych, Associate Professor at the Department of Food Science at the University of Copenhagen, Denmark.

Method builds on a device that was used for DNA sequencing in space

The new method is based on nanopore sequencing, which is a new, real-time DNA sequencing approach “that will definitely revolutionize the future of DNA sequencing” according to Lukasz Krych.

The research project was carried out in collaboration with the polish company GenXone S.A., which helped to set up a bioinformatics pipeline that is needed to perform fast and efficient analysis of the sequencing data.

The smallest ever sequencer offered by Oxford Nanopore Technologies, called MinION, is a $999 hand-held, USB-powered device that became commercially available in 2015. A year later it was taken to the International Space Station, where it achieved the first DNA sequencing in history performed in zero-gravity conditions. Despite the indisputable revolution in DNA sequencing offered by MinION, it quickly became clear that the data generated with the device are still not perfect due to e.g. sequencing errors while the analysis remained relatively expensive to perform (app. $150 per bacterium).

Small device with fast and cheap analysis offers huge opportunities within food safety

The scientists from the Department of Food Science at the University of Copenhagen have found a way to utilize this technology to analyze hundreds of bacteria at a time, cutting costs to less than $2 per bacterium, while at the same time increasing the accuracy to more than 99%.

“Our method can be used both within food safety, where you can quickly find disease-causing or health-promoting bacteria, and also in the health sector, where you will be able to perform certain analyses that you are not even considering today because of the price and time-consuming nature of traditional analysis," says another of the researchers behind the study, Post Doc Josue Leonardo Castro Mejia.

At the moment, there are several companies testing the method to implement in their systems for establishing rapid screening programmes for thousands of strains.

Source: University of Copenhagen

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Taiwan Hospital Promotes Drug-Resistant Superbug Detection Method

Chang Gung Memorial Hospital in Linkou, Taoyuan has developed artificial intelligence (AI)-based research technology that can rapidly detect antibiotic-resistant superbugs and better guide the correct administration of antibiotics, a hospital representative said Thursday.

Staphylococcus aureus or staph, the most dangerous of all the many common staphylococcal bacteria, is the best known drug-resistant superbug, Wang Hsin-yao (王信堯), a clinical pathologist/microbiologist in the Department of Laboratory Medicine at the hospital, said at the press event held to publicize the research.

Noting that staph claims millions of lives every year, Wang said that the overuse and misuse of antibiotics are key factors contributing to the growing antibiotic resistance of staph and even the appearance of heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA), an emerging superbug with implicit drug resistance to vancomycin.

The antibiotic vancomycin is the last line of defense against the community-associated methicillin-resistant S. aureus, according to Wang.

To find a method to identify superbugs, the hospital, in conjunction with Chang Gung University and National Central University, developed the AI technology after two years of research. Integrated with a mass spectrometer it achieves 80 percent medication accuracy, Wang said.

The mass spectrometer is one of the most popular mass spectrometry instruments used in biology, due to its rapid and precise identification of the genus and species of an extensive range of bacteria.

The superbug detection model developed by the hospital can provide rapid and accurate reports regarding hVISA/VISA and thereby guide the correct administration of antibiotics in treatment of S. aureus infection, according to Wang.

The research results won a gold medal at the 2017 Taipei International Invention Show & Technomart and were published in the October 2018 issue of Frontiers in Microbiology, a leading international journal in its field, publishing rigorously peer-reviewed research in the field of microbiology.

The technology will be used to detect other superbugs, Wang said, adding that the hospital is currently experimenting with the method to expand its application.

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25-Minute Test Could Simplify Initial Diagnosis of Urinary Tract Infections

Biological Engineers at the University of Bath have developed a test that could help medics quickly diagnose urinary tract infections (UTIs), using a normal smartphone camera.

Similar in principle to a pregnancy test, the process can identify the presence of harmful E. coli bacteria in a urine sample in just 25 minutes. As well as being far faster than existing testing, it could make accurate UTI testing more widely available in developing nations and remote regions thanks to its potential to be made portable, and far more cheaply than existing lab-based tests.

E. coli is present in 80 percent of bacterial UTIs, so if it is found it tells medical professionals that an antibiotic treatment is needed.

As well as a smartphone camera, the test, which could be adapted to detect a variety of bacterial infections, takes advantage of widely-available reagents and new micro-engineered materials. Researchers say the simplicity of the test, which has now passed the proof-of-concept stage, could deliver a new way to quickly identify treatments for patients in poorer or remote regions.

Described in the journal Biosensors and Bioelectronics, the test uses antibodies to capture bacterial cells in very thin capillaries within a plastic strip, detecting and identifying the cells optically rather than through the microbiological methods currently used.

Dr. Nuno Reis, from Bath's Department of Chemical Engineering, led the development of the test. He says: "The test is small and portable—so it has major potential for use in primary care settings and in developing countries.

"Currently, bacterial infections in UTIs are confirmed via microbiological testing of a urine sample. That is accurate, but time-consuming, taking several days. We hope that giving medical professionals the ability to quickly rule in or rule out certain conditions will allow them to treat patients more quickly and help them make better decisions about the prescription of antibiotics."

The lack of rapid diagnostics for UTIs has in many cases led to a catch-all prescription of potentially unnecessary antibiotics, which increases the risk of bacteria becoming resistant to treatment—accepted as one of the biggest threats to global health and development.

How the test works

The test is carried out by passing a urine sample over a ridged plastic micro-capillary strip, containing an immobilizing antibody able to recognize E. coli bacterial cells. If E. coli is present in the sample, antibodies in the reagents will bind with it, stopping it from passing through the section of plastic strip. Finally, an enzyme is added that causes a change in color that can be picked up by a smartphone camera.

The system also measures the concentration of E. coli in the sample by analyzing an image taken by the camera. The procedure is simple and could be manually operated or fully automated without any need for a mains power supply.

Aims to overcome regulators' concerns on smartphone use

To date, bodies such as the United States Food & Drug Administration (FDA) have not granted approval to techniques that use smartphones—citing the potential for both non-lab conditions and software updates to the phone to make tests unscientific. But Dr. Reis hopes that the way the test uses a variable scale to digitally compare the pixels within an image will convince regulators to allow the treatment to move toward eventual production.

Dr. Reis adds that wealthier nations could also benefit from adopting the methodology, as it could make testing within primary care facilities such as GP surgeries more viable, reducing the need to send samples to central labs for testing.

He says: "The UK and wealthy countries have seen a big shift to decentralized diagnostics to reduce the load on national or regional labs and provide doctors with important tools to make informed diagnoses.

"Driving more of this will bring better outcomes to patients in terms of speeding up the process, but will also lower the cost to healthcare providers. We are not talking about replacing centralized diagnostics services but providing the first point of contact with affordable and rapid tools to support prescription of antibiotics and avoid their overuse."

The next step for the process is clinical trials, which will require collaboration with clinical and commercial partners. Beyond this, the team will shortly begin working on refining the test to allow for the detection of other bacteria and their concentrations, which will help prescribe correct dosages and avoid the overuse of antibiotics.

Dr. Reis concludes: "The smartphone solves one of the biggest problems of the decentralizing of diagnostics because their capabilities are actually very sophisticated in certain conditions. They offer the same functionality as sophisticated scanners that have until now been available only in labs."

Source: University of Bath

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A Fast and Inexpensive Device to Capture and Identify Viruses

A device to quickly capture and identify various strains of virus has been developed, according to researchers at Penn State and New York University.

Currently, virologists estimate that 1.67 million unknown viruses are in animals, a number of which can be transmitted to humans. Known viruses, such as H5N1, Zika and Ebola have caused widespread illness and death. The World Health Organization states that early detection can halt virus spread by enabling rapid deployment of countermeasures.

“We have developed a fast and inexpensive handheld device that can capture viruses based on size,” said Mauricio Terrones, distinguished professor of physics, chemistry, and materials science and engineering at Penn State. “Our device uses arrays of nanotubes engineered to be comparable in size to a wide range of viruses. We then use Raman spectroscopy to identify the viruses based on their individual vibration.”

This device, called a VIRRION, has a wide range of possible uses. For farmers, for example, early detection of a virus in the field can save an entire crop. Early detection of a virus in livestock can save a herd from illness. Humans also will benefit by the detection of viruses in minutes rather than in days with current methods. Because of its size and low cost, such a device would be useful in every doctor’s office as well as in remote locations when disease outbreaks occur.

“Most current techniques require large and expensive pieces of equipment,” Terrones said. “The VIRRION is a few centimeters across. We add gold nanoparticles to enhance the Raman signal so that we are able to detect the virus molecule in very low concentrations. We then use machine learning techniques to create a library of virus types.”

According to Professor Elodie Ghedin, a virologist at NYU, "The VIRRION enables the rapid enrichment of virus particles from any type of sample — environmental or clinical — which jump-starts viral characterization. This has applications in virus emergence, virus discovery and in diagnosis. Eventually, we hope to use this device for the capture and sequencing of single virions, giving us a much better handle on the evolution of the virus in real time."

Added lead author Ying-Ting Yeh, an assistant research professor in the Terrones group, "We synthesized a gradient of aligned carbon nanotube forest arrays to capture different viruses according to their size and detect them in-situ using Raman spectroscopy. We designed and assembled a portable platform that enriches virus particles from several milliliters of clinical samples in a couple of minutes.”

The work is published in Proceedings of the National Academy of Science. Titled “A rapid and label-free platform for virus capture and identification from clinical samples,” the paper’s co-authors are Ying-Ting Yeh, an assistant research professor in Terrones’ group; Kristen Gulino, Tsui-Wen Chou and Bin Zhou, all of NYU; and YuHe Zhang, Aswathy Sabestien, Zhong Lin, Istvan Albert, Huaguang Lu and Venkataranman Swaminathan, all of Penn State.

The National Science Foundation Growing Convergence Research Big Idea, the Thrasher Research Fund, an Infectious Disease Research Exchanges Grant from Princeton University and the startup fund from Penn State supported this work.

Source: Penn State News

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