NuGEN Ovation® Prokaryotic RNA-Seq Technology Penetrates Academic Market

Washington University in St. Louis and the University of Washington became the first two institutions to receive NuGEN's new Ovation® Prokaryotic RNA-Seq system through a limited-access program targeting medical and environmental microbial research centers.

NuGEN’s Ovation Prokaryotic RNA-Seq System is designed to enrich for mRNA in next-generation sequencing libraries. The resulting cDNA is compatible with NuGEN’s Encore™ NGS Library Systems as well as other library workflows using double-stranded cDNA as input for the creation of sequencing libraries. The firm says the platform can be applied to transcriptomes extracted from pure and mixed microbial cultures using a simple workflow, and generates reproducible transcriptome profiles across all prokaryotic species in the Eubacteria and Archaebacteria kingdoms.

Founded in 2000, San Carlos, CA-based NuGEN specializes in the development of solutions for high-sensitivity nucleic acid amplification and target preparation. The firm’s product family for sample preparation takes purified RNA, DNA, or cell lysates and prepares them for specific downstream analytical needs. The firm’s existing Ovation RNA-Seq System, launched in December 2009, has been developed as a fast and simple method for preparing amplified cDNA from total RNA, for RNA-Seq applications (transcriptome sequencing). The technology is driven by NuGEN’s Ribo-SPIA® technology, a rapid, simple and sensitive RNA amplification process it claims allows microgram quantities of cDNA to be prepared in approximately six hours, using just 500 pg total RNA.

Its Ovation and Applause™ RNA Amplification Systems for microarrays are part of a family of modularly designed, application-based products designed to allow whole transcriptome analysis from virtually any biological sample, regardless of the type, size, and source of the sample, NuGEN continues. For DNA sample preparation, the Ovation WGA System has been developed to offer linear amplification technology based on the SPIA® (Single Primer Isothermal Amplification) platform. RNA sample-preparation solutions include the Prelude Direct Lysis Module, the Ovation RNA Amplification Systems for microarrays and qPCR, the Applause RNA Amplification system based on the Ribo-SPIA technology, and post-amplification target-prep modules.

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North Bristol NHS Trust Invests In BioMérieux’s BacT/ALERT®

North Bristol NHS Trust recently chose to award their tender for Pathology Managed Equipment & Consumables Services to Roche Diagnostics Ltd. As part of that tender bioMérieux UK Ltd were chosen to provide a range of automation as part of the Microbiology solution. This included the BacT/ALERT 3D system for both Southmead and Frenchay hospitals, simplifying the integration of the two laboratories. Jon Mitchell, Laboratory Manager for both hospitals, explained: “The Trust identified financial advantages in moving to a Managed Service Contract and following an extensive tendering and evaluation process, selected bioMérieux as the service provider for blood and mycobacteria culture. We now use bioMérieux’s BacT/ALERT system in both of the Trust’s Microbiology laboratories, which allows the hospitals to share the same database for sample reporting and makes it much simpler to check and view patient results across health communities.”

“One big advantage is that the BacT/ALERT uses plastic bottles, which are lightweight and very robust, making it much easier and safer to transport samples from the patient to the laboratory,” Jon continued. “Using the same type of instrument to perform blood and mycobacteria culture makes training quicker and simpler which helps to reduce costs. Staff also only need to familiarise themselves with one piece of equipment, which is advantageous when rotating between sites. The BacT/ALERT is intuitive to use – the on-screen display makes identification of positive samples very easy – and it has proved very reliable.”

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Simple New Multi-Test System Detects Bacteria in < 7 Hours

Hygiena International Ltd launches the EnSURE; a small portable rapid detection system that can make several different test measurements using a new bioluminogenic test principle. The tests include Micro-Snap, Zymo-Snap and Super-Snap. Micro-Snap products will provide test results, indicating single figure organisms, in just 7 hours. They can be used to verify surface cleaning efficacy in industrial processing applications, plus product quality and safety for raw materials, processed food, cosmetics and pharmaceutical products together with both potable and process water supplies.

The system utilises a new bioluminogenic test principle in their existing patented snap valve device with a more sensitive luminometer, called EnSURE. The system has been validated for the detection of specific bacteria including Coliform, Enterobacteriaceae and E.coli at very low levels and in a variety of sample types. A new formulation and re-arrangement of the established ATP bioluminescence biochemistry, coupled to specific substrates, now enables the technology to detect specific bacteria with high sensitivity. Enzymes (such as beta-Galactosidase and beta-Glucuronidase) that are characteristic of specific target bacteria, utilise these substrates in a process that releases light which is detected in the sensitive EnSURE handheld luminometer.

This unique, portable and self-contained package de-skills and simplifies the microbiological testing process, while maintaining sensitivity and particularly high specificity. Testing can be undertaken by an individual in laboratory conditions, but can also be successfully applied at field or site locations by health and safety technicians without the need for additional personnel or laboratory equipment.

Coliforms and E.coli are important indicators of hygiene, quality and safety. The detection of low levels of specific bacterial contamination can be determined and measured within a normal working 8 hour shift using the Micro-Snap system; whereas other test methods can take up to 1 - 2 days to show results. Additional diagnostic bioluminogenic substrates under investigation are being engineered to detect pathogens such as Listeria monocytogenes, MRSA and ESBL.

Hygiena Zymo-Snap detects enzymes of industrial importance such as Alkaline Phosphatase, providing a 5 minute test of pasteurisation efficiency for food safety in the dairy industry. The new Super-Snap provides the greatest sensitivity and robustness for surface hygiene monitoring for the most demanding cleaning verification applications such as allergen control programs. The EnSURE instrument together with Micro-Snap, Zymo-Snap and Super-Snap provides a simple, rapid, multi-test platform with many industrial applications and is particularly well suited for the dairy industry because several key quality and safety tests can all be performed on the same low cost system.

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AdvanDx Receives FDA 510(k) Clearance for GNR Traffic Light™ PNA FISH®

AdvanDx announced that it has received FDA 510(k) clearance for its GNR Traffic Light™ PNA FISH® test. GNR Traffic Light PNA FISH is the first test capable of simultaneously identifying Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa directly from positive blood cultures containing Gram-negative rods in less than 90 minutes. The test is the latest addition to AdvanDx's easy-to-use, molecular-based PNA FISH diagnostics platform designed to provide rapid, therapy-guiding results that enable clinicians to provide early, effective therapy for patients with Gram-negative bloodstream infections (BSI). Every year, close to 875,000 patients in the United States contract bloodstream infections, leading to over 150,000 deaths and $12 billion in patient care costs. The infection is detected when a culture of the patient's blood (i.e. a blood culture) turns positive with bacteria or yeast. Rapid and accurate identification of the specific infecting pathogen is crucial to ensure early and appropriate therapy and save patient lives.

Gram-negative BSIs are considered some of the most serious hospital-acquired infections and afflict more than 100,000 patients annually in the US. The majority of these infections, approximately 70 to 80%, are caused by E. coli, K. pneumoniae and P. aeruginosa. Increasing resistance to a multitude of antibiotic agents, especially in P. aeruginosa and increasingly in K. pneumoniae, along with slow conventional laboratory testing methods that take 2 to 3 days to identify the causative pathogen, complicate therapy decisions for clinicians. As a result, up to one third of patients afflicted by Gram-negative BSIs initially receive inappropriate antibiotic therapy which in turn leads to higher mortality rates of up to 40%, longer hospital stays and significant extra costs.

GNR Traffic Light PNA FISH will enable microbiology labs to identify and report E. coli, K. pneumoniae and P. aeruginosa from positive blood cultures 1 to 2 days earlier than traditional methods. The rapid results will provide clinicians a "head start" on selecting appropriate and effective therapy for patients with Gram-negative bloodstream infections which studies show may improve clinical outcomes, reduce incidence of adverse events and shorten hospital length of stay.

PNA FISH is an easy-to-use and highly sensitive and specific fluorescence in situ hybridization (FISH) assay that uses PNA (peptide nucleic acid) probes to target species specific ribosomal RNA (rRNA) in live bacteria and yeast. The unique properties of the non-charged, peptide backbone of PNA probes enable the use of FISH assays in exceedingly complex sample matrixes, such as blood and blood cultures, and this in turn facilitates the development of very simple, yet very accurate tests that don't require the extensive sample preparation necessary for other nucleic acid technologies.

PNA FISH tests enable microbiology labs to provide rapid and accurate identification of bloodstream pathogens directly from positive blood cultures in hours instead of days. Clinical studies show that rapid identification of bloodstream pathogens using PNA FISH tests leads to more appropriate patient therapy that saves lives and reduces unnecessary antibiotic use, patient length of stay and hospital costs.

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First Commercial Method for Top 6 Non-O157 Shiga Toxigenic E. coli

BioControl Systems, Inc. has become the first manufacturer to develop a PCR method for the detection of the top 6 non-O157 serotypes of Shiga Toxigenic E.coli (STEC) as defined by the United States Department of Agriculture Food Safety Inspection Service (USDA FSIS).

Already used extensively within the food industry for the rapid detection of E.coli O157:H7 in beef and fresh produce, Assurance GDS® (Genetic Detection System) now combines the latest advancements in molecular technology and food microbiology to provide a new method for the detection of the six major non-O157 serotypes of STEC (O26, O45, O103, O111, O121, and O145).

“The Assurance GDS pathogen detection system is ideally suited to handle the challenges of detecting this specific group of E.coli, defined only by their O antigens and 3 key pathogenicity genes”, states Geoff Bright Group Product Manager. “The method includes a proprietary IMS-based sample preparation procedure specifically targeting the top 6 O serogroups followed by PCR analysis for the detection of the eae and stx1 or stx2 genes. This combined approach meets the USDA FSIS criteria for detection of STEC and helps ensure the STEC genetic targets are only detected in the serogroups of concern, preventing false positives from other O serogroups and eliminating the need for additional down stream PCR analysis” explains Bright.

With Assurance GDS, producers can obtain results for both E.coli O157:H7 and the top 6 non-O157 STEC from a single enriched sample after just 10 hours of incubation. The use of a common enrichment media for both assays helps streamline testing programs and control costs by eliminating the need to prepare duplicate samples. The ability to quickly test and release product, particularly in the beef and fresh produce industries, can have a significant financial impact on an organization's bottom line.

In addition to non-O157 STEC, the Assurance GDS platform includes assays for E.coli O157:H7, Shiga Toxin Genes, Salmonella, Listeria spp., Listeria monocytogenes, and Cronobacter.

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FDA Awards SDIX Method Equivalency for Salmonella Enteritidis Detection in Poultry Houses and Eggs

SDIX™, a leading supplier of rapid detection solutions to the $1 billion food pathogen testing market, announced that its RapidChek® SELECTTM Salmonella Enteritidis (SE) test system has been reviewed by the U.S. Food and Drug Administration (FDA) and determined to be equivalent in accuracy, precision and sensitivity to their current standard methods for poultry house environmental drag swabs and pooled egg testing. For pooled egg testing, SDIX’s method is considered by FDA as equivalent to its standard test without a 96-hour hold period, thus delivering results with a substantial time and cost advantage.

Recently, SDIX’s test also earned Performance-Tested Methods (PTM) certification from the AOAC Research Institute (AOAC-RI). The AOAC PTM certification also validated the RapidChek SELECT SE method as equivalent to the FDA methodology for detecting SE in poultry house environments and pooled eggs. With the added FDA equivalency determination, SDIX’s test can help the approximately 3,300 egg producers comply with the new FDA regulations and significantly reduce contamination levels from those being experienced today by providing a more sensitive and accurate detection of SE.

The FDA Final Rule dictates that if SE is found in the layer environment, eggs must then be screened for the presence of SE in order to keep any contaminated eggs from reaching the consumer market. With this FDA equivalency ruling, SDIX can offer U.S. egg producers an easier, faster, and cost effective way to comply with that FDA regulation.

According to the USDA and the Center for Disease Control’s (CDC) FoodNet surveillance system Salmonella is not only the most common food-borne bacterial pathogen with over 1 million estimated cases annually in the US, but it is also responsible for more hospitalizations and more deaths – almost 400 annually-- than any other food pathogen. Over 500 million eggs were recalled from this past summer’s SE outbreak with reports of approximately 1,800 cases of Salmonella poisoning from tainted eggs.

Tim Lawruk, Food Safety Market Manager at SDIX, said, “The RapidChek® SELECTTM SE test system can deliver results for environmental samples from the layer house one full day faster than the current FDA method and with substantially increased sensitivity and accuracy. These benefits enable egg producers to identify SE in the environment before it contaminates eggs, which helps ensure safer eggs and reduces the possibility of a costly egg recall. This ability to screen for SE quickly and accurately is especially relevant today given the recent egg recalls. For egg testing, the RapidChek SELECT method can provide SE test results 5 days faster than the FDA method, which has a substantial effect on product storage and release for the egg producers.” Continuing, Mr. Lawruk said, “Obtaining both AOAC-RI certification and FDA method equivalency provides egg producers complete confidence that deploying SDIX’s rapid methods not only provides great financial benefits, but also ensures that they are complying with the testing requirements of the FDA Final Rule.” The new testing system is comprised of the RapidChek® SELECTTM Salmonella Enteritidis detection system for screening environmental drag swabs or pooled eggs and the RapidChek® CONFIRMTM Salmonella Enteritidis immunomagnetic separation system for confirmation of environmental presumptive positive samples.

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Dynacare Selects Bruker's MALDI Biotyper for Next-Generation Microbial ID

Bruker today announced that Dynacare Laboratories in Milwaukee, Wisconsin, after careful internal evaluation, has purchased a Bruker MALDI Biotyper system as their next-generation rapid microbial identification system. The MALDI Biotyper has obtained the IVD-CE Mark in selected European countries, and Bruker is planning to submit the MALDI Biotyper to the U.S. FDA for clearance.

The MALDI Biotyper is a MALDI-TOF mass spectrometry based platform for rapid molecular identification of bacteria, yeast and fungi. Its carefully curated database includes quality-controlled entries of over 3,900 strains from 2,000 well-characterized microbial species. Starting from a cultured colony, identification is performed by matching the measured protein fingerprint against the proprietary MALDI Biotyper database. Including data acquisition and database search, a scored list of identification proposals is automatically presented to the microbiologist in minutes. Multiple colonies can be spotted on a single target, and about 30-60 identifications can be performed every hour. The MALDI Biotyper offers considerably faster time-to-result (TTR), high specificity, very low false positive rates, low operational costs, and low technical barriers for new operators. Bruker has installed over 200 MALDI Biotyper systems worldwide in research and routine clinical laboratories for microbiology, and the MALDI Biotyper is rapidly becoming a new standard for robust, rapid microbial identification in Europe.

Dr. Nathan Ledeboer, Assistant Professor of Pathology at the Medical College of Wisconsin and Medical Director of Microbiology and Molecular Diagnostics for Dynacare, stated: "MALDI-TOF is going to revolutionize identification in clinical microbiology. It will reduce the turnaround of clinical cultures, decrease laboratory errors, and reduce laboratory costs. We plan to use the MALDI Biotyper for microbial identifications currently performed by phenotypic methods, and expect to see improvements in time to result, workflow and consumables costs. Dynacare also plans to investigate the use of the MALDI Biotyper to replace 16s rDNA sequencing for identification. It will bring microbiology into the 21st century. We are pleased that Dynacare Laboratories will be the fifth clinical laboratory in nation - and the only laboratory in Wisconsin - to implement this new, advanced technology."

Mr. George Goedesky, Executive Director for Business Development of Bruker Daltonics, said: "We have enjoyed collaborating with Dynacare, and we are very pleased they have selected the MALDI Biotyper for use both in their research and their routine microbial identification production facility. We look forward to continuing to work with Dynacare on further applications of the MALDI Biotyper microbiology platform."

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MIT Receives First Production Rapid Microbial Identification Systems Manufactured by OSI Optoelectronics

Micro Identification Technologies, Inc. (MIT) announced that it received the first production MIT 1000 System from OSI Optoelectronics (OSIO), a subsidiary of OSI Systems on December 24, 2010 and stated that initial test results are superb. MIT contracted with OSIO in 2010 to manufacture MIT's Rapid Microbial Identification System, the MIT 1000. OSIO has manufacturing facilities in California, Malaysia and India.

"All of OSIO's world class facilities are ISO 9001:2000 certified, FDA registered and GMP compliant making them a perfect company to fabricate MIT's Systems for its food safety applications and its planned pharmaceutical and clinical diagnostic applications," stated John Ricardi, MIT's Executive Vice President and Chief Operating Officer. Mr. Ricardi further added that, "While initially the Systems will be constructed in OSIO's Hawthorne-California facility, as volume increases, fabrication will move to one of their lower labor cost facilities in either Malaysia or India and thus provide the capability for MIT to maintain or improve future profit margins and price competiveness." Mr. Ricardi continued, "OSIO fabricates the photodiode detectors that are used in the MIT 1000 and plans to supply other components. In addition, their experience with MIT's System and targeted markets enables them to both accelerate and help us to ensure that our current and future product designs meet the stringent requirements of those industries -- capabilities that will insure deliveries of Systems early in 2011."

The MIT 1000 Rapid Microbial Identification System can identify bacteria in less than five minutes after culturing at a cost of less than 10 cents per test and is a certified AOAC Research Institute (RI) test method for Listeria, one of three bacteria (the others are Salmonella and E.coli) that are responsible for most of the worldwide food contamination events. The Company is in the process of preparing the MIT 1000 to become AOAC RI certified later this year for the presence of all "three" bacteria with a single mouse click.

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