Wednesday, September 23, 2015

BioDetection Instruments Awarded Grant by the U.S. FDA

Biodetection Instruments has recently been awarded a Small Business Innovation and Research (SBIR) Phase I grant by the Food and Drug Administration. The $150,000 grant, awarded September 10, 2015, supports BioDetection Instruments in the development of an automated food pathogen screening system with integrated sample concentration. The Phase I study will focus on the detection of Salmonella in ready-to-eat (RTE) foods with Salmonella Typhimurium as a model pathogen.

BioDetection Instruments is developing an integrated system for rapid and sensitive screening of foodborne pathogens in a sample-in-answer-out format. The system is based on integration of patented sample preparation technology and patent-pending self-contained microfluidic assay cartridge technology. The automated system can address the limitations of current microbial detection methods, e.g., laboriousness and tediousness (culture methods), complexity and high skill requirement (PCR), lack of sensitivity (lateral flow immuno-strip tests) or specificity (conventional ATP bioluminescence). The system will be fully automated, requiring minimal operator training.

The United States enjoys one of the safest food supplies in the world, but contamination of food products by microbial pathogens remains a major concern of our society. It is estimated that contaminated food causes 48 million illnesses, 128,000 hospitalizations, and 3,000 deaths in the U.S. each year. Nontyphoidal Salmonella, e.g., Salmonella Typhimurium, is one of the top five pathogens causing foodborne illnesses in the United States. To prevent the introduction of contaminated food products into the food supply chain, monitoring of foodborne pathogens is a critical control point. Unfortunately, currently detection of bacterial pathogens in food and other matrices still heavily relies on culture methods, which are extremely time-consuming, often taking up to 48 hours or more. Rapid and sensitive detection of bacterial pathogens in food products will help prevent foodborne infections and thus help protect the public health. It will also help reduce medical costs and productivity losses.

Although research associated with this grant focuses on the detection of viable Salmonella, the technology is applicable to other foodborne pathogens, and has broad commercial utility.

BioDetection Instruments, Inc. is developing innovative new technologies for the rapid detection of pathogens. BioDetection Instruments’ products can improve the safety and quality of the world’s food and water supply. BioDetection Instruments™ is a VIC Technology Venture Development™ portfolio company.

The New USP Chapter 1223: An Overview in Two Publications

On June 1, 2015, a substantially modified USP chapter <1223>, Validation of Alternative Microbiological Methods, was published in the second supplement to USP38/NF33 with an official date of 1st December 2015. Two recently published papers provide an overview of the chapter's most notable changes and compare the revision with what is recommended in the Parenteral Drug Association (PDA) Technical Report Number 33 and the proposed revision to European Pharmacopoeia (Ph. Eur.) chapter 5.1.6.

Both papers, authored by rapid methods expert Dr. Michael J. Miller, are referenced below and contain links to view the articles in their entirety.

2015. Miller, M.J. A Fresh Look at USP <1223> Validation of Alternative Microbiological Methods and How the Revised Chapter Compares with PDA TR33 and the Proposed Revision to Ph. Eur. 5.1.6. American Pharmaceutical Review. 18(5): 22-35.

2015. Miller, M.J. Rapid Methods Update: Revisions to a United States Pharmacopeia Chapter. European Pharmaceutical Review. 20(4): 38-43.

Roche Receives US FDA CLIA Waiver for Flu A/B Test for Use on its cobas Liat PCR System

Roche announced that the US Food and Drug Administration (FDA) has granted CLIA (Clinical Laboratory Improvement Amendments) waiver for cobas influenza A/B test for use on its cobas Liat System.

It is the first CLIA-waived, real-time polymerase chain reaction (PCR) test to detect influenza A and B in 20 minutes. It targets highly conserved regions of the influenza A and B genomes to provide broad strain coverage of over 30 commonly found strains of influenza A and B. Coupled with the CLIA waived cobas Strep A test, the cobas influenza A/B test can now be used by healthcare providers in non-traditional testing sites, including physician offices, emergency rooms, health department clinics, pharmacy clinics and other healthcare facilities.

“Today’s CLIA waiver for the cobas influenza A/B test allows real-time PCR technology, the gold standard in molecular testing, to be utilized at the point of care to accurately and quickly detect and differentiate influenza A and B,” said Roland Diggelmann, COO, Roche Diagnostics.

“Effective management of influenza relies on accurate detection within 48 hours of onset, which can be challenging with current turnaround times for lab-based test results. The cobas influenza A/B test provides lab-quality PCR results in ~20 minutes, enabling health care providers in all settings to give prompt and confident diagnosis and treatment to patients.”

An estimated three to five million individuals develop influenza each year worldwide, and 250,000 to 500,000 die from the virus. Patients at highest risk include children, the elderly and pregnant women. The CLIA waived cobas influenza A/B test for the cobas Liat PCR System offers an effective, new diagnostic tool to clinicians for the upcoming flu season and provides faster diagnosis and treatment for patients in primary and urgent care settings.

The cobas influenza A/B test is the second assay on the cobas Liat System to receive CLIA waiver, following the cobas Strep A test, which received CLIA waiver in May 2015. The cobas Liat Analyzer, cobas influenza A/B test and cobas Strep A test are CE marked, FDA cleared and CLIA waived.

Utilizing PCR technology, the cobas Liat System fully automates the testing process, simplifies workflow and enables healthcare professionals to perform molecular testing in a variety of settings with speed, reliability and minimal training. Definitive results are generated in 20 minutes or less to aid a treatment decision. In addition to the existing tests for flu A/B and Strep A, assays for other infectious diseases are in development.

Real-time PCR is widely recognized as the gold standard for molecular testing. It is highly accurate and offers a low limit of detection (LOD) to detect viruses in patients with low viral load, such as some adults with influenza infection. PCR is also extremely versatile, offering capabilities with high multiplex testing (e.g. influenza A, influenza B and RSV in the same test), quantification (viral load count), and detection. Additionally, compared to physician clinical management, rapid antigen testing and other point-of-care testing methods, real-time PCR has demonstrated improved detection of influenza.

Influenza is an acute respiratory illness caused by infection with the influenza virus. Influenza viruses consist of three types: influenza A, influenza B and influenza C. In the US, influenza A/H1N1, A/H3N2 and influenza B are the predominant seasonal viruses. Influenza A and B viruses are among the leading causes of respiratory infections, estimated to affect 5-10 per cent of adults and 20-30 per cent of children every year worldwide. Influenza is primarily spread by breathing in infected droplets formed when a person with the flu sneezes, coughs, or talks. Symptoms include fever, cough, headache, fatigue, muscle pain, sore throat, and runny nose. Elderly people, young children, and people with weakened immune systems or chronic medical conditions can be at high risk for serious disease. Each year, approximately 3 to 5 million people develop severe illness and 250,000 to 500,000 people die from the flu.

Stanford-led Group Validates Multiplex Tropical Pathogen PCR for Plasmodium Species Detection

Identifying the cause of febrile illnesses can be a challenge, particularly in some tropical and sub-tropical areas of the world where patients can be exposed to different pathogens whose symptoms mimic each other.

To help address this, researchers at Stanford University School of Medicine have been developing a single-reaction multiplex PCR assay that can detect and differentiate the causative agents of dengue fever, leptospirosis, and malaria — three pathogens endemic to such regions.

Specifically, the assay is designed to detect dengue viruses DENV-1 to -4 using a pan-DENV design, as well as all species of Leptospira bacteria, and the five Plasmodium parasite species known to be cause malaria in humans, with a specific call-out for P. falciparum.

A study published online earlier this month in the Journal of Clinical Microbiology showed that the test, dubbed the DLM assay, compared favorably to microscopy and the BinaxNow Malaria rapid diagnostic test from Alere specifically in detecting Plasmodium falciparum.

Many molecular assays separately target the individual causative agents of dengue, leptospirosis, and malaria, but the multiplexed detection of all three pathogens makes the DLM assay unique, Benjamin Pinsky, a co-author on the study and an assistant professor of pathology and infectious diseases at Stanford University Medical Center, told GenomeWeb in an email.

Many other molecular tests for malaria require whole blood or dried blood spots, but the current study is among the first to analyze serum and plasma.

The study was conducted using samples obtained by co-author Wellington Oyibo at the University of Lagos College of Medicine in Nigeria, where P. falciparum is the predominant species.

"The DLM assay uses a pan-Plasmodium primer-probe set that detects all five of the Plasmodium species that infect humans but does not distinguish between them; a separate P. falciparum-specific primer-probe set that utilizes a different fluorescent label allows a call-out for P. falciparum," Pinsky explained.

The DLM assay itself was described last year, also in JCM. The goal of the current study was to compare the DLM assay with gold-standard microscopy and rapid antigen testing for P. falciparum.

On serum or plasma from 317 patients, the assay showed 97 percent sensitivity and 93.5 percent specificity for P. falciparum. A rapid immunoassay from Alere was shown to be similarly sensitive, and both were superior to microscopy, which has a sensitivity of 79 percent.

The mean specimen volume was 70 microliters, but when the researchers constrained their analysis to sample volumes  of greater than 75 microliters, the sensitivity and specificity of the DLM test for P. falciparum improved to 99 percent and 97.5 percent, respectively, possibly due to detection of lower parasitemia in higher volumes.

Pinsky says his group plans to compare the test to PCR-based Plasmodium tests in the future. Meanwhile, it has used this assay "to test thousands of samples from around the world, including samples collected from febrile patients in Nicaragua, Brazil, Sri Lanka, Kenya, and Cameroon."

The dengue virus component of the DLM assay has been licensed, Pinsky said, and the licensee intends to use it as a companion diagnostic for a dengue therapeutic that is entering human clinical trials.

"We are working with this company, as well, to license the DLM assay," he said, but noted that the company requested he not reveal its name at the present time.

At this point, the DLM assay would need to be run in a laboratory capable of molecular diagnostic testing because it runs on a standard real-time PCR platform and requires sample preparation.

"However, the goal is to provide this and other assays for undifferentiated systemic febrile illnesses in a format that can be performed near-care or at the point-of-care," Pinsky said.

This may eventually involve isothermal amplification methods like recombinase polymerase amplification (RPA) or loop-mediated isothermal amplification (LAMP). Furthermore, the group has "already started working with both academic laboratories and diagnostics companies on adapting our existing assays to PCR-based sample-to-answer systems," Pinsky said.

Indeed, for single-plex assays at least, this appears to be feasible. An isothermal Leptospira assay was recently developed using TwistAmp chemistry from Alere subsidiary TwistDx, as reported by GenomeWeb. Another group has also reported using RPA to build a lateral flow P. falciparum assay, and a malaria assay from Eiken Chemical that uses LAMP was made commercially available with CE marking about two years ago.

Pinsky said his group has also developed other tests, including ones for viruses such as chikungunya, Zika, Yellow Fever, West Nile, O'nyong nyong, Mayaro, and Rift Valley Fever.

"These assays have been designed to be compatible in multiplex with each other as well as [with] the components of the DLM assay, so that regional panels can be designed to best detect the pathogens important in a particular area," Pinsky said.

A number of molecular diagnostics makers, including BioMérieux subsidiary BioFire Diagnostics and German assay developer Hahn-Schickard, are currently developing or considering multiplex PCR panels for undifferentiated febrile illness, sometimes also referred to as "traveler's panels." Metagenomic sequencing using Oxford Nanopore MinIon is another possible method to pinpoint the cause of UFI, as recently discussed.

Wayne State to Develop New Rapid Tests for Infants with Serious Infections

Prashant Mahajan, M.D., professor of Pediatrics and Emergency Medicine, chief of the Division of Emergency Medicine in the Department of Pediatrics at Wayne State University and Children's Hospital of Michigan, has been awarded a five-year, $5.76 million grant (1R01HD085233) by the Eunice Kennedy Shriver National Institute of Child Health & Human Development of the National Institutes of Health. Dr. Mahajan and his collaborators will study how febrile infants - babies 2 months or younger who are brought to emergency rooms with invasive bacterial infections - can avoid invasive procedures such as lumbar punctures, overuse of antibiotics and unnecessary hospitalizations through a new, rapid and more accurate testing to be developed by their research team.

The researchers will investigate whole genome RNA expression profiles to define RNA biosignatures that allow precise diagnosis of isolated bacterial infections, isolated viral infections and bacterial-viral co-infections. The investigators will also validate the RNA biosignatures on a novel, PCR-based platform that has a rapid turnaround time of two to four hours, as opposed to current methods of bacterial cultures that often take up to 48 hours for results.

The evaluation of well-appearing febrile infants continues to be challenging and controversial for clinicians. Their immune system is immature and even otherwise normal infants are unable to protect themselves from invasive bacterial diseases such as meningitis, bacteremia and urinary tract infections. Fever is the most common reason for infants to be brought to emergency departments and approximately 250,000 very young febrile infants are taken to emergency rooms across the United States annually. In addition, many more are brought to pediatricians and other health care settings and thus, this continues to be one of the most vexing issues in pediatrics.

Dr. Mahajan said that less than 5 percent of febrile infants will have an invasive or serious bacterial illness. These infants are clinically indistinguishable from the majority of the febrile infants with non-bacterial illness. However, the outcomes, such as bacterial meningitis, severe sepsis and potentially death, are devastating. More importantly, the current standard use of bacterial cultures for diagnosis is suboptimal. In particular, culture results are reported after 24 to 48 hours are not helpful for clinical decision-making at the patient's bedside.

Dr. Mahajan and his collaborators, Dr. Octavio Ramilo of Nationwide Children's Hospital, The Ohio State University, and Dr. Nathan Kuppermann of the University of California, Davis Medical Center, have been researching the evaluation of the febrile infant for 15 years and have been continuously funded in their efforts since 2008. The investigative team initially received a $600,000 Targeted Issues Grant (H34MC08509) from Heath Resources Services Administration (HRSA) as part of the Emergency Medical Services for Children to create an infrastructure to study febrile infants in U.S. emergency departments through a federally supported network of approximately 20 pediatric emergency departments called Pediatric Emergency Care Applied Research Network. After establishing the infrastructure, Dr. Mahajan and his collaborators were awarded $3.15 million (R01HD062477) from the NICHD to further define and validate the bacterial and non-bacterial biosignatures of febrile infants. Their findings demonstrated that it is possible to identify bacterial infections from non-bacterial infections by RNA biosignatures in emergency departments with 95 percent accuracy.

"This award will aid in the development of a potentially paradigm-shifting approach of a new, more precise, efficient and rapid laboratory diagnostic strategies," Dr. Mahajan said. "This would allow for a less-invasive, quicker and more accurate cost-effective evaluation of young febrile infants while bringing this exciting technology to patient's bedside. If successful, it will substantially impact the care of thousands of febrile infants across the world."

"Dr. Mahajan's research is highly timely and translational in nature in that it will allow for greater accuracy and enhance antibiotic stewardship among the most vulnerable of all children, very young infants," said Steven E. Lipshultz, M.D., chair of Pediatrics at Wayne State University's School of Medicine and pediatrician-in-chief of Children's Hospital of Michigan.

"Dr. Mahajan's research offers much promise to very sick infants, their parents and health care professionals," said Gloria Heppner, Ph.D., associate vice president for Research at Wayne State University. "His work will assist in quickly and accurately diagnosing them, and ultimately will aid in determining the best treatment method, with potentially lower costs and better results."

UK Team Using Oxford Nanopore Sequencer to Develop Rapid Urinary Tract Infection Dx

Researchers in the UK are working on a rapid sequencing-based diagnostic test for severe urinary tract infections using Oxford Nanopore Technologies' MinIon platform.

The goal is to develop a test that can identify the pathogen involved and predict its antibiotic susceptibility within six hours of taking a urine sample and at a cost that is "attractive to hospital laboratories," according to Justin O'Grady, a medical microbiologist at the University of East Anglia's Norwich Medical School and one of the project's leaders.

Members of his team presented early results from a pilot study last weekend at the American Society for Microbiology's Interscience Conference of Antimicrobial Agents and Chemotherapy in San Diego, which was held jointly with the International Congress of Chemotherapy and Infection. They plan to submit their results for publication in a journal in the near future.

More than 30,000 patients in the UK each year are diagnosed with Escherichia coli bacteremia, or blood infections, the majority of which start as urinary tract infections. At the moment, severe urinary tract infections that can lead to urosepsis, where the infection spreads into the bloodstream, are diagnosed by cell culture, O'Grady said, which takes about two days and tells doctors about the pathogen and its antibiotic susceptibility.

A sequencing-based test could potentially deliver this information faster, which could be essential for patients in intensive care units with suspected urosepsis. O'Grady's team has been interested in using DNA sequencing for clinical microbiology for a while, and has been participating in Oxford Nanopore's MinIon Access Program since last summer. Last fall, he and his colleagues published a paper on using the MinIon to characterize antibiotic resistance islands in Salmonella.

"We knew there would be sufficient bacteria present in urine samples, and we knew that this technology would work quite well for this application," he told GenomeWeb, "so we decided to test urinary tract infection samples from the local hospital and see if we could detect these organisms and their resistance genes using this technology."

For their pilot study, the researchers analyzed 10 urine samples from patients treated at the Norfolk & Norwich University Hospital, as well as two control samples that were spiked with E. coli bacteria, one of which had been previously analyzed with Illumina sequencing technology.

To prepare the samples for sequencing, they developed a protocol to enrich for pathogen DNA that includes differential centrifugation to remove human cells and a lysis step that selectively breaks up human cells and destroys their DNA. This is followed by automated bacterial DNA extraction using a Roche MagNA Pure system.

After library preparation, sequencing, and bioinformatic analysis, the scientists were able to identify the pathogen species correctly in six of the clinical urine samples. For the first four samples, the sequence data yield was too low because they were run on early versions of the MinIon flow cell or because human DNA was not adequately removed, but all later samples worked well.

Also, the MinIon identified the same acquired resistance genes in the control sample as the Illumina platform. However, the bioinformatic pipeline sometimes called the same gene multiple times because it did not generate a consensus sequence from the noisy MinIon reads first. In the future, this can be fixed by increasing sequencing coverage and developing consensus calling, O'Grady said.

In the six successful clinical samples, resistance gene profiles derived from the MinIon data agreed well with culture-based drug resistance profiles. But because the culture-based tests did not cover all the resistance genes the MinIon found, they need to confirm the MinIon results by comparing them with Illumina sequencing data, which they are currently generating.

The entire assay currently takes about 12 hours, including a couple of hours to process the sample and extract the DNA, two hours of library preparation, and the remainder for sequencing and data analysis.

The first part — identifying the pathogen — can now be done within the first five minutes of sequencing, using an application called "What's in my pot?" or WIMP that Oxford Nanopore recently introduced for its Metrichor analysis framework. This enables the analysis of the sequence reads in real time, O'Grady said.

After that, the run needs to continue for a few more hours to ensure sufficient coverage of the pathogen genome, so no resistance genes are missed in the analysis that follows. "What we're not good at doing so far is detecting single nucleotide variants that lead to drug resistance in chromosomal resistance genes," O'Grady said. "That will improve with improving technology and a greater yield of sequence data."

He and his colleagues are now working on bringing the assay time down to six hours, which they hope to achieve within the next month or so. In part, this will rely on Oxford Nanopore adding an antibiotic resistance gene database to its Metrichor framework, which would allow the resistance analysis to become automated and proceed in real time. They are also planning to test new flow cells from Oxford Nanopore that double the speed of data acquisition, as well as new library prep kits that reduce the time required for that process.

The assay currently costs on the order of $1,000, he said, including about $900 for the flow cell, $100 for library prep reagents, and $50 for "everything else." However, at its user meeting this spring, Oxford Nanopore talked about plans to introduce 'pay-as-you-go' sequencing for as little as $20 per 2 gigabases, he said, sufficient "to tell us everything we would need" about a sample. "If you could get down to that range, $20 per sample, that would really make a huge difference" for clinical applications, he said.

Getting the test into routine clinical use would require validation studies, though, as well as changes to the workflow, who would analyze the data, and how the results would be presented to doctors. "That would take time," O'Grady said. "But the technology is there."

In parallel to the urine test, he and his colleagues are developing a similar, blood-based test for sepsis, which is more challenging than urine because there is much more human DNA in blood than pathogen DNA. They have already developed strategies to enrich the pathogen DNA and have achieved "some good results" from sequencing so far, he said.

DuPont BAX System Real-Time PCR Assay for Salmonella Receives AOAC-RI Validation Extension

The AOAC Research Institute (AOAC-RI) has approved a method extension for the DuPont BAX System real-time PCR assay for Salmonella to include enrichment protocols using Actero Salmonella Enrichment Media from FoodChek™ Systems. Included in this method extension are protocols for two new sample types – milk chocolate and chocolate liquor – and shortened protocols for dry pet food and environmental sponges.

“Chocolate products have become a higher-priority food type for Salmonella testing, but are difficult to test with rapid molecular methods due to the inhibitory properties of chocolate,” says Morgan Wallace, DuPont Nutrition & Health senior microbiologist and validations leader for Diagnostics. “By combining the robust formulation of Actero media for enhanced Salmonella enrichment and the sensitivity of PCR processing and automated detection with the BAX System real-time PCR assay, this new AOAC-approved method for milk chocolate and chocolate liquor provides customers with an accurate, reliable testing method that can easily fit with a standard laboratory workflow.”

In addition to providing Salmonella testing of these new sample types, this proprietary media helps to provide faster, simpler enrichment procedures for testing products with the BAX System method. “Actero Salmonella Enrichment Media reduces the total enrichment time for sample types such as pet food and environmental swabs by about 7 to 9 hours compared to enrichment with standard enrichment media. This time savings, combined with the reduced media volume required, can help improve food safety testing efficiencies and the financial bottom line for food companies and commercial testing laboratories alike,” said William J. Hogan, FoodChek™ chairman, president and CEO.

The DuPont BAX System provides advanced, automated testing for foodborne pathogens, spoilage organisms and other microbes in raw ingredients, finished products and manufacturing environments. The system breaks down samples at the genetic level using the power of the polymerase chain reaction (PCR), then uses target-specific primers to automatically detect the presence or absence of the target bacterial DNA and provide clear yes-or-no results. With certifications and regulatory approvals around the world, the BAX System is recognized as one of the most advanced pathogen testing systems available to the food industry today.

Rapid Test Helps Detect Dangerous Bacteria in Milk

Now, a fluorescent paper strip can within minutes detect pathogens in milk samples from cattle suffering from brucellosis. This disease can be transmitted to humans through contact or consumption of unpasteurized milk and undercooked meat of infected animals.

Researchers from the Institute of Chemical Technology (ICT), Matunga have developed a cost-effective diagnostic tool that can detect the presence of Brucella abortus, the bacterium causing brucellosis.

“There are no laboratory facilities in rural areas to detect brucellosis, and samples have to be transported to cities,” said Swati Vyas, a research student at the department of pharmaceutical sciences.

“The strip that we have developed is similar to a pregnancy detection kit and can be done in 15 minutes,” said Vyas.

Currently, there are two tests to detect the bacteria– PCR and ELISA – which cost between Rs 25,000 and Rs 45,000 for testing 100 samples. Both the tests require skilled personnel and complex instrumentation. PCR does not yield accurate results, said the researchers.

“When we dropped a few microlitres of infected milk, the two fluorescent bands glowed, indicating contamination. Only one band glowed for bacteria-free samples,” added Vyas.

“The test could be useful for the food industry that maintains large herds of cattle for milk and milk products,” said Vandana Patravale, Professor, department of pharmaceutical sciences and technology.

“This test is a platform technology, and we are researching further for rapid detection of other microbial infections,” Patravale added.The team has now applied for a patent.

Thursday, September 10, 2015

Micro Imaging Technology Adds Enterococcus Faecalis to Its Catalog of Identifiers

Micro Imaging Technology, Inc. announced that its MIT 1000 System can now identify Enterococcus faecalis, a bacterial species found in human feces and in the intestines of many warm-blooded animals; occasionally found in urinary infections and in blood and heart lesions in cases of subacute endocarditis. E. faecalis can cause life-threatening infections in humans, especially in the hospital environment, where the naturally high levels of antibiotic resistance found in E. faecalis contribute to its pathogenicity. E. faecalis has been frequently found in root canal-treated teeth which are about nine times more likely to harbor the bacteria than cases of primary infections.

"This is a significant step forward for MIT 1000 technology," said Dr. David Haavig, Micro Imaging Technology's Chief Scientist. "The completion of this Identifier demonstrates the sensitivity of this non-biological bacterial identification technology. This new Identifier gives our MIT 1000 the ability to identify a species of the genus Enterococcus. Our other Identifiers give the MIT 1000 the ability to identify Salmonella Choleraesuis, as well as Listeria genus and Staphylococcus genus, where each genus consists of multiple species, some of which can be pathogenic."

Identifiers give the MIT 1000 System the ability to identify bacteria. All Identifiers, including this new E. faecalis Identifier, as well as all future Identifiers, use the same simple chemical-free, very low-cost, one-minute sample preparation procedure and two-minute average hands-off test with no modification or addition to the MIT 1000 System. The MIT 1000 is a rapid, bacterial cell-based detection and identification system that can identify pathogenic bacteria, now including E. faecalis, in three minutes (average).

Meanwhile, MIT is working on Staphylococcus aureus, Methicillin resistant S. aureus (MRSA), and Listeria monocytogenes Identifiers.

Micro Imaging Technology, Inc. is a California-based public company that is also registered to do business under the name Micro Identification Technologies. MIT has developed and patented the MIT 1000, a stand-alone, rapid, optically-based, software driven system that can identify pathogenic bacteria and complete an identification test, after culturing, in three (3) minutes (average) at the lowest cost per test when compared to any other conventional method. It does not rely on chemical or biological agents, conventional processing, fluorescent tags, gas chromatography or DNA analysis. The process requires only clean filtered water and a sample of the unknown bacteria. Revenues for all rapid testing methods exceed $5 billion annually -- with food safety accounting for over $3.5 billion, which is expected to surpass $4.7 billion by this year according to BCC Research. In addition, the recently passed "New" U.S. Food Safety Bill is expected to further accelerate the current annual growth rate of 6.6 percent.

In June 2009, the AOAC Research Institute (AOAC RI) awarded the Company Performance Tested Methods SM (PTM) certification for the rapid identification of Listeria. The AOAC RI provides an independent third party evaluation and expert reviews of methods and will award PTM certification to methods that demonstrate performance levels equivalent or better than other certified bacteria identifying methods. The MIT System underwent hundreds of individual tests, including ruggedness and accuracy, to earn AOAC RI's certification for the identification of Listeria.

Rapid Test Kits for Dengue Inaccurate, Indian Govt. to Ban Them Soon

The Indian government plans to ban the sale of rapid diagnostic test kits used for ‘quick’ detection of dengue infection as it does not provide accurate results, an official said on Tuesday. ‘Talks are going on with experts of the Indian Council of Medical Research (ICMR). We may ban the sale of rapid diagnostic kits, which are believed not to be reliable,’ Director General of Health Services (DGHS) Jagdish Prasad said.

The union health ministry has also decided to seek reports from individual hospitals in Delhi — including the All India Institute of Medical Sciences, Ram Manohar Lohia Hospital and Safdarjung Hospital — to ensure that there is no fudging of dengue numbers reported in the national capital. Prasad said the ministry only recommends ELISA-based kits, which are provided by the National Institute of Virology (NIV) at 499 sentinel surveillance hospitals and 15 apex referral laboratories to facilitate free diagnosis.

The decision comes a day after the Municipal Corporation of Delhi (MCD) said the city has witnessed 1,259 dengue cases with two deaths till September 5 — 38 times higher than 2014 during when, only 33 cases were recorded in the corresponding period. The number was 255 in 2013, 17 in 2012 and 104 in 2011. In 2010, however, the number was 1,512 till September 5.

Nanoporous Gold Sponge Makes DNA Detector: Possible New Rapid Tests for Human, Animal, Plant Pathogens

In two recent papers in Analytical Chemistry, a group from the UC Davis Department of Electrical and Computer Engineering demonstrated that they could detect nucleic acids using nanoporous gold, a novel sensor coating material, in mixtures of other biomolecules that would gum up most detectors. This method enables sensitive detection of DNA in complex biological samples, such as serum from whole blood.

"Nanoporous gold can be imagined as a porous metal sponge with pore sizes that are a thousand times smaller than the diameter of a human hair," said Erkin Seker, assistant professor of electrical and computer engineering at UC Davis and the senior author on the papers. "What happens is the debris in biological samples, such as proteins, is too large to go through those pores, but the fiber-like nucleic acids that we want to detect can actually fit through them. It's almost like a natural sieve."

Rapid and sensitive detection of nucleic acids plays a crucial role in early identification of pathogenic microbes and disease biomarkers. Current sensor approaches usually require nucleic acid purification that relies on multiple steps and specialized laboratory equipment, which limit the sensors' use in the field. The researchers' method reduces the need for purification.

"So now we hope to have largely eliminated the need for extensive sample clean-up, which makes the process conducive to use in the field," Seker said.

The result is a faster and more efficient process that can be applied in many settings.

The researchers hope the technology can be translated into the development of miniature point-of-care diagnostic platforms for agricultural and clinical applications.

"The applications of the sensor are quite broad ranging from detection of plant pathogens to disease biomarkers," said Seker.

For example, in agriculture, scientists could detect whether a certain pathogen exists on a plant without seeing any symptoms. And in sepsis cases in humans, doctors might determine bacterial contamination much more quickly than at present, preventing any unnecessary treatments.

Other authors of the studies were Pallavi Daggumati, Zimple Matharu, and Ling Wang in the Department of Electrical and Computer Engineering at UC Davis.

This work is funded by the UC Davis Research Investments in the Sciences and Engineering (RISE) program, which encourages interdisciplinary work to solve problems facing the world today, as well as the UC Lab Fees Research Program and the National Science Foundation.

New E. Coli Test Reportedly Shows Results in Less Than 24 Hours

The standard methods of detecting the presence of E. coli O157 in meat products use cultures and microbiological assays and can take 48 hours or more to get a result. Meanwhile, the clock is ticking on a given product’s shelf life.

As a result, according to a recent research report on the food safety testing industry published in QA Magazine, the technological focus has been shifting to faster techniques to get definitive results.

“Rapid testing methods such as PCR (Polymerase Chain Reaction) and immunoassay-based techniques are used to ensure timely analysis of a larger sample size and thereby reduce the time for food safety testing. These advanced technologies also ensure the detection of food contaminants of biological as well as chemical origins,” the report stated.

Researcher Yadira Tejeda, a Ph.D. candidate at the University of Western Ontario in London, Ontario, has reportedly developed a method of more quickly detecting E. coli O157 contamination in meat products.

The process is similar to a pregnancy test, where one line indicates a negative result and two lines indicates a positive one. She is now working with a small business to validate the method and test its feasibility.

“I work with E. coli O157 because it has caused many epidemics, and has contaminated both raw and ready-to-cook meats; for example, burgers, sausages, beef and pork. In these circumstances, the products had to be removed from the market,” Tejeda says.

She notes that there are several collaborative programs in Canada with other countries, including Mexico, her native country.

“This is something that pleases me very much because there is a possibility of doing something to impact my home country,” she says.

3M's Next Generation Molecular Detection Assay for Listeria monocytogenes Earns AOAC-PTM Validation

3M Food Safety announced today that its 3M™ Molecular Detection Assay 2 – Listeria monocytogenes has been approved by the AOAC® Performance Tested MethodsSM program (Certification 081501). The approval certifies that the next generation test kit is now equivalent or better than standard reference methods.

Achieving AOAC PTM status required a rigorous, independent laboratory examination of 3M’s unique molecular test method’s ability to accurately detect Listeria monocytogenes within a variety of foods. Food samples analyzed during the validation study included beef hot dogs, queso fresco cheese, vanilla ice cream, 4 percent milk fat cottage cheese, 3 percent chocolate whole milk, romaine lettuce, bagged raw spinach, cold smoked salmon, deli turkey, raw chicken, cantaloupe, and various environmental surfaces (plastic, stainless steel, concrete).

“Third-party validations enable customers to meet internal and/or external requirements, and also provide them with added confidence in their testing,” said John David, global marketing supervisor with 3M Food Safety. “We know our customers relied on having the original 3M Molecular Detection Assays validated, so pursuing validations such as AOAC PTM for the next generation tests was always in our plan.”

Developed in response to customer engagement and ongoing desire to work with food processors to protect the world’s food supply, the latest Listeria monocytogenes assay is one of two test kits that were expanded on the innovative 3M™ Molecular Detection System platform. The 3M Molecular Detection System is based on unique isothermal DNA amplification and bioluminescence detection technologies and designed around food processors’ needs for a real-time pathogen detection approach that’s faster and simpler while also more accurate. The new test now provides a faster time-to-result – as little as 24 hours of enrichment – and features a streamlined workflow that is 30 percent faster than first generation assay.

PathoGenetix Begins Production of the Resolution Microbial Genotyping System

PathoGenetix announces commercial launch and shipment of the Resolution Microbial Genotyping System for rapid bacterial serotyping and strain typing.

Production of commercial instruments for sales and delivery was a key milestone for the Genome Sequence Scanning Technology.

The RESOLUTION Microbial Genotyping System is fully automated and includes the instrument, pathogen databases, bioinformatics and data analysis software, and pathogen-specific assays. The RESOLUTION System has been developed for food safety testing and foodborne illness outbreak investigations. Protocols have been developed that enable the analysis of food and clinical samples, providing molecular serotype and strain type for target pathogens in as few as five hours, without the need for a pure culture isolate.

The RESOLUTION System is based on PathoGenetix’s proprietary Genome Sequence Scanning™ (GSS™) technology, initially developed to detect bio-threat pathogens in environmental samples under a five-year, $50-million contract through the Department of Homeland Security. The breakthrough genotyping technology isolates and analyzes DNA direct from complex mixtures—without the need for a pure culture isolate—and provides molecular serotype and strain type information for target bacteria in just five hours. The strain type information provided by GSS is comparable to pulsed field gel electrophoresis (PFGE), the current gold standard for pathogen identification.

The RESOLUTION has a comprehensive Pathogen Library that includes 371 strains of Salmonella, 402 strains of E.coli and 53 strains of Listeria enabling significantly improved rapid and accurate identification of Salmonella and E.coli strains. With Resolution software, the end user has ability to add new strains to the library.

Working with its sister-company, Fluid Management Systems, Inc. (FMS), PathoGenetix has made a significant investment in the design over the past year and has begun commercial production of the RESOLUTION System at the PathoGenetix-FMS facility in Watertown, MA.

“PathoGenetix’ president Hamid Shirkhan quotes: It is exciting to be part of the development and launch of a break-through life saving technology for food safety and public health.”

Rapid Micro Biosystems Announces the Commercial Availability of the Growth Direct MultiTest System

Rapid Micro Biosystems, the provider of automated, rapid, non-destructive detection and enumeration technologies in microbiology, today announced the continued expansion of the Growth Direct(TM) product line with the launch of the Growth Direct MultiTest System.  The technology automates the incubation, detection, and results reporting steps for bioburden, environmental monitoring and sterility testing -- within a single instrument.  The proven method is based on the detection of the natural auto-fluorescence of microorganisms, and can detect growing colonies in about half the time of the traditional tests, providing time and resource savings.

The MultiTest System expands the existing Growth Direct(TM) technology platform currently used in FDA regulated manufacturing facilities.

"Companies have been looking for a way to increase their efficiency, reduce errors and deliver results more quickly across the portfolio of tests they conduct," states Julie Sperry, Chief Commercial Officer. "The Growth Direct MultiTest is unique in its ability to run all the applications concurrently on the same system."

"Using a single, automated, self-contained microbial QC testing system changes the way that businesses view rapid methods for their quality control labs," said Robert Spignesi, President and CEO of Rapid Micro Biosystems. "Companies now have the option to perform all their key tests on a single platform versus the inefficiencies in validation, training and maintenance of deploying unique solutions for each application.  This allows QC labs to see the benefits while minimizing their up-front investment."

PositiveID Achieves Firefly Dx Development Milestone With the Production of Injection-Molded PCR Chips

PositiveID Corporation, a developer of biological detection and diagnostics solutions, announced that it successfully achieved a new milestone in the development of its Firefly Dx PCR (polymerase chain reaction) prototype pathogen detection system (“prototype system”) with the production of the Company’s first article, molded PCR chips for the Firefly Dx cartridge.

The completion of injection-molded PCR chips represents the next stage of product maturity for the Firefly Dx prototype system. This advancement will enable the Company to produce large quantities of PCR chips at a lower cost, thereby enabling higher throughput of testing data and cost-effective field applications. PositiveID will now be able to incorporate and optimize additional assays on its Firefly Dx cartridge with a disposable PCR chip.

PositiveID’s Firefly Dx is designed to provide real-time, accurate diagnostic results in a handheld device, thereby leading to treatment scenarios at the point of need that are not possible with existing systems, which require lab-based equipment, highly trained personnel, and can take hours or even days to provide results. Firefly’s applications include point-of-need, lab-quality, detection of pathogenic organisms; agricultural and food screening in both domestic sectors and developing countries; and detection of biological agents associated with weapons of mass destruction.

“We continue to be encouraged by our sustained progress with the development and testing of the Firefly Dx prototype system,” stated William J. Caragol, Chairman and CEO of PositiveID. “This latest milestone is significant because it allows us to make our PCR chips disposable, which, we believe, represents another proof statement that Firefly Dx can fill a critical requirement for point-of-need, rapid, and cost-effective biological detection.”

New Assay Could Revolutionize Diagnosis and Treatment of Life-Threatening Fungal Disease

Invasive Fungal Disease (IFD) is an emerging global health problem associated with high mortality rates in severely immunocompromised patients, such as those undergoing intensive chemotherapy or stem cell transplantation, and in patients suffering immune compromising conditions such as AIDS. The most common causative agents of this disease have been identified as Candida and Aspergillus species, between them accounting for nearly 90% of all reported IFD.

These infections are difficult and time-consuming to diagnose, so at-risk patients are often administered a course of expensive and potentially toxic prophylactic anti-fungal drugs.

But the launch of a new, rapid PCR-based test for the detection of Candida and Aspergillus DNA extracted from blood samples, could make diagnosis quicker and more accurate, reducing the need for anti-fungal therapy for most patients.

Renishaw Diagnostics’ first assay, Fungiplex, is a CE-IVD certified test designed for use on the RenDx Multiplex Assay System, an automation and detection platform that allows processing of up to 45 samples in a single run. The assay identifies 12 Candida and Aspergillus species using a unique detection technology known as surface enhanced resonance Raman spectroscopy (SERRS).

Rupert Jones, General Manager of Renishaw Diagnostics, said, “The CE-IVD launch of our RenDx platform and first assay marks a significant milestone, not just in the progress made here at Renishaw Diagnostics but more importantly, for infectious disease diagnostics throughout Europe. The extensive target menu for the Fungiplex assay, together with the high sensitivity that can be achieved through our exceptional detection technology, has the potential to aid earlier diagnosis, reduce overall spend and improve patient outcomes for those susceptible to these life threatening infections. We are looking forward to working with clinicians and laboratories to bring this assay into routine clinical use.”

NIH Funds Effort to Develop PCR Test to Diagnose Infections in Infants

The National Institutes of Health has recently awarded a Wayne State University researcher a five-year grant to develop a PCR-based platform for the diagnosis of infections in febrile infants.

An estimated 500,000 febrile infants are admitted to emergency departments annually in the US, around 10 percent of which will have an invasive bacterial infection such as bacteremia or meningitis, according to the grant's abstract. Current methods for diagnosing these patients, however, are often invasive and can lead to the overuse of empirical antibiotics and unnecessarily hospitalizations.

To address this unmet need, and with the support of the NIH funding, Wayne State's Prashant Mahajan and colleagues are working to establish a panel of blood-based RNA signatures used to diagnose isolated bacterial and viral infections, as well as co-infections, in febrile infants.

The panel will then be validated using a novel and rapid PCR platform in a prospective, multi-center, cross-sectional study of febrile infants under evaluation for bacterial infections.

The grant project began on August 21, and is worth $1.4 million in its first year.

Tanzania: WHO Approves Korean HIV Rapid Test Kits Suspended in 2011

A South Korean made HIV rapid test kit, SD Bioline HIV 1/2 3.0 whose use was suspended in 2011 by World Health Organization due to accuracy concerns has been pre-qualified for use by member countries.

WHO Department of Essential Medicines and Health Products Director, Mercedes Gonzales said the rapid test kits have been re approved following corrective measures taken by Standard Diagnostics Inc., of South Korea which manufactures the kits.

"Following our guidance and advice, Standard Diagnostics took a number of corrective measures to improve their test's quality and the product was subsequently prequalified on May 20, 2013," Mr Gonzales told 'Daily News' in an emailed response to questions sent.

Ministry of Health and Social Welfare suspended use of SD Bioline HIV rapid test kits immediately after WHO suspended them from its pre-qualified list of kits in 2011, following discovery of defective lots which did not give correct readings.

In its evaluation report released in 2013, WHO said the pre-qualification of SD Bioline follows thorough investigations which included site visits of the global health body's experts to make sure that major changes have been made to guarantee safety and standards.

"SD Bioline HIV-1/2 3.0 was accepted for the WHO list of prequalified diagnostics on the basis of data submitted and publicly available information in May 2013," the global health body's report stated. Standard Diagnostics Inc. submitted an application for prequalification of SD Bioline HIV-1/2 3.0.

Based on the established prioritization criteria, SD Bioline HIV-1/2 3.0 was given priority for prequalification. "The information submitted in the product dossier was reviewed by WHO staff and external experts (assessors) appointed by WHO in accordance with the internal report on the screening and assessment of a product dossier.

Based on the product dossier screening and assessment findings, a recommendation was made to accept the product dossier for SD Bioline HIV -1/2 3.0 for prequalification," the WHO report said.

The WHO experts report further noted that its inspectors visited the Korean manufacturer's factory to see the equipment used.

"A comprehensive second re-inspection was performed at the sites of the legal manufacturer of SD Bioline HIV -1/2 3.0 at 156-68 Hagal-dong Giheung-gu, Yongin-si, Kyonggi-do 446-930, Republic of Korea and 473-4 Bora-dong Giheung-gu, Yongin-si, Kyonggi-do, 446-904, Republic of Korea in November 2012," the report noted.

The inspection was based on 'ISO 13485:2003 Medical devices - Quality management systems -Requirements for regulatory purposes' and other internationally recognized standards relevant to the manufacture of in vitro diagnostics, the WHO report noted.

The manufacturer has committed to continuing improvements in the quality management system particularly in the areas of clear lines of authority, identification and traceability, warehousing and clarity of work instructions and batch manufacturing records, the report concluded.

Lab-on-a-Disc Platform Combines Microfluidics and Raman Microscopy for Rapid Detection of Urinary Tract Infections

A Lab-on-a-Disc platform developed by a German and Irish team of researchers combines modern microfluidic techniques with fast optical diagnostics to dramatically cut the time to detect bacterial species that cause urinary tract infections—a major cause of sepsis—from 24 hours to within 70 minutes. Illustration courtesy of Ute Neugebauer/Jena University Hospital

Urinary tract infections can quickly move from being a merely miserable experience to a life-threatening condition. Untreated cases may trigger sepsis, which occurs when the immune system, in an attempt to fight off the infection, inadvertently activates body-wide inflammation that can cause blood clots and leaky blood vessels.

Sepsis is a major killer and accounts for about half of the hospital deaths in the U.S. by some estimates. Hospital patients often acquire urinary tract infections via infected catheters and so untreated infections are a huge problem faced by healthcare providers around the world. Early diagnosis could save lives and reduce healthcare costs. With this motivation in mind, a team of researchers in Germany and Ireland set out to speed up the detection process for bacteria that cause urinary tract infections.

In the journal Biomicrofluidics, from AIP Publishing, the team describes creating a Lab-on-a-Disc platform that combines microfluidics and Raman microscopy, a modern optical detection method.

Their medical diagnostics device is designed to harness centrifugal force -- akin to the circular swing of a “Chair-o-Plane” carnival ride, in which a fast rotation creates a force that causes the seats to drift radially away from the ride's center -- to capture the tiny bacteria directly from patients’ samples of bodily fluids…in this case, urine.

The work involves extremely small sample sizes, on the scale of a small raindrop, so the device needed to be a microfluidic one.
“Our device works by loading a few microliters of a patient’s urine sample into a tiny chip, which is then rotated with a high angular velocity so that any bacteria is guided by centrifugal force through microfluidic channels to a small chamber where ‘V-cup capture units’ collect it for optical investigation,” explains Ulrich-Christian Schröder, a PhD student at the Jena University Hospital and Leibniz Institute of Technology in Germany.

The team’s concept then adds Raman spectroscopy to its centrifugal microfluidic platform. “Raman spectroscopy uses the way light interacts with matter to produce ‘unique scattering,’ the equivalent of a molecular fingerprint, which can then be used to identify the types of bacteria present,” says Ute Neugebauer, group leader at the Jena University Hospital and Leibniz Institute of Technology.

What exactly does the team’s medical device detect? “In our pilot study, we were able to identify Escherichia coli (more commonly known as E. coli) and Enterococcus faecalis -- two species known to cause urinary tract infections -- within 70 minutes, directly from patients’ urine samples,” said Schröder.

The speedy diagnosis marks a tremendous reduction in the wait time compared to the lengthy lag -- often 24 hours or more -- associated with methods routinely used to identify bacteria and diagnose urinary tract infections today, so the team’s device shows great potential for improving the future of medical diagnostics.

The team envisions general practitioners, a.k.a. family doctors, using the device to rapidly -- while a patient waits -- identify the bacteria causing an infection directly within the patient’s bodily fluid so that they can prescribe the appropriate medication and treatment. “Our pilot study brings us a step closer toward realizing this vision,” said Neugebauer.

The team will continue toward its goal of developing an easy-to-use spectroscopy-based point-of-care medical device for fast and reliable diagnostics. “The next step will involve implementing antibiotic susceptibility testing and automating the sample pre-treatment steps,” Neugebauer explained. “Our ultimate vision is to apply the concepts behind our device to enable diagnostics devices for use with other bodily fluids.”

The article, "Rapid, culture-independent, optical diagnostics of centrifugally captured bacteria from urine samples," is authored by Ulrich-Christian Schröder, Frank Bokeloh, Mary O’Sullivan, Uwe Glaser, Katharina Wolf, Wolfgang Pfister, Jürgen Popp, Jens Ducrée, and Ute Neugebauer. It was published in the journal Biomicrofluidics on Aug. 11, 2015. After that date, it can be accessed at:

The authors of this paper are affiliated with Jena University Hospital, Leibniz Institute of Photonic Technology Jena, Dublin City University, and Friedrich Schiller University.

Source: American Institute of Physics (AIP)