Tuesday, September 28, 2010

The Next Generation MicroSEQ® Microbial ID System

Life Technologies Corporation announced the launch of its next-generation, high throughput genotypic MicroSEQ® Microbial ID System for the identification of bacteria and fungi within a pharmaceutical manufacturing environment. Powered by the new 3500 Series Genetic Analyzer, this new system offers enhanced throughput, ease-of-use features while maintaining the accuracy required by the pharmaceutical industry to rapidly identify microbial contaminations. To review their entire press release, please visit our RMM News Page at http://rapidmicromethods.com/files/news.html.

Saturday, September 18, 2010

Recently Added Rapid Method News Articles

We have recently added a number of news articles that highlights rapid method technologies and related information. Here is a preview:

  • Identification of Clinically Significant Microorganisms
  • Bruker Introduces the MALDI Sepsityper™ Kit for Rapid MALDI Biotyper Microbial Identification from Positive Blood Cultures
  • Rapid Micro Biosystems Names Julie Sperry to Post of Chief Commercial Officer

To view these articles, please visit our News Page or click on http://rapidmicromethods.com/files/news.html.

New Paper on Rapid Sterility Testing

Scientists at Alcon Laboratories have recently published a paper on the use of the Chemunex ScanRDI as a rapid alternative to the pharmacopoeial sterility test. Two sterility test methods, the ScanRDI rapid sterility test and the United States Pharmacopeia/European Pharmacopoeia/Japanese Pharmacopoeia (USP/EP/JP) compendial sterility test, were compared withrespect to the limits of detection for the presence of viable microorganisms in aqueous solutions at low inoculation levels. Eight microorganisms were evaluated, seven compendial microorganisms (Clostridium sporogenes, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus subtilis, Aspergillus niger, Candidaalbicans) and the Gram-positive anaerobe Propionibacterium acnes. The number of viable organisms was estimated using the ScanRDI method and the conventional sterility test method using most probable number methodology. The mean difference between the methods was computed and 95% confidence intervals around the mean difference were estimated. The ScanRDI method was found to be numerically superior and statistically non-inferior to the compendial (USP/EP/JP) sterility test with respect to the limits of detection for all organisms tested.

PDA members may download the article for free from the PDA Journal website. The full reference is provided below. For a comprehensive list of rapid method published papers, please visit our Reference Page.

2010. Smith, R.; Von Tress, M.; Tubb, C.; Vanhaecke, E. Evaluation of the ScanRDI as a Rapid Alternative to the Pharmacopoeial Sterility Test Method: Comparison of the Limits of Detection. PDA Journal of Pharmaceutical Science and Technology. 64(4): 356-363.

PDA Technical Report No. 50, Alternative Methods for Mycoplasma Testing

PDA Technical Report No. 50, Alternative Methods for Mycoplasma Testing, is now published. The scope of the TR is the application of non-culture testing methodology, including nucleic acid amplification and other assays, for the detection of mycoplasmas in cell cultures and biotech products. The TR describes assay procedures, assay validation, demonstration of comparability to reference methods, and potential applications for alternative methods. PDA members may be downloaded the TR for free until October 14, 2010.

Sunday, September 5, 2010

New paper on viable but not culturable (VBNC) cells and RMMs

Jeanne Moldenhauer has recently published a paper on viability-based RMMs and the types of indicators or markers used in these systems. She writes that some RMMs still rely on the growth of microorganisms, while others are based on viability methods to detect and quantify microorganisms without the need for microbial growth. The use of viability methods has both benefits and challenges, the latter including the potential for obtaining a false positive response (i.e., a viable count from a non-viable cell). A link to Jeanne's paper may be found on our RMM References Page (http://rapidmicromethods.com/files/references.html) under the General Overviews section. The full reference is below:

2010. Moldenhauer, J. Use of a Viability Test Method. Does It Mean What You Think? American Pharmaceutical Review. 13(5): 22-29.

Automating the Micro QC Lab (Part 3)

In continuation of my conversation with Steve Delity, President and CEO of Rapid Micro Biosystems, on the benefits of automation in the pharmaceutical microbiology lab, I asked him to share advice he gives to companies considering an automated vs. a non-automated method.

Michael - Moving from a manual operation to an automated lab is a significant leap. How would you advise companies that are considering using a non-automated rapid method initially, then moving to a more automated option?

– When I speak with companies considering either an automated or non-automated rapid solution, I try to help them explore a few areas. First, I look to uncover where they expect to find the greatest benefit. Certainly, rapid detection provides a clear advantage to the current, manual method in reduced time to results, and not surprisingly, that is the benefit I hear most often. But, as we continue to explore the operation, companies start to realize there are other considerations that need to be addressed. For example, there are risks inherent in any manual process, even a rapid method, such as data entry errors or inconsistency of processes. Could that decrease confidence in the “non-automated” rapid method?

The second area I try to understand is the impact to the operation of the rapid method. Will the “non-automated’ rapid method add steps to the already cumbersome manual process? If there are additional steps, how will that affect the ability for the lab to handle current and future sample workloads? Will there be an increase in resource requirements in the lab, and therefore and increased cost? I often speak with businesses that focus too much on their need for a rapid method, and overlook these types of impacts, missing opportunities for additional benefits through automation.

It is important for the business to understand both the benefits and shortcomings with a non-automated solution. The right answer will be different for each situation, based on how these attributes are weighted. Companies considering both non-automated and automated rapid methods should weigh the importance, benefits and risks to find their optimal solution. And for those technologies that can provide both rapid results and automation, businesses can get the best of both worlds.

In the final part of this series, we talk about automation and validation. Stay tuned.

Friday, September 3, 2010

Next Generation Genome Sequencing

I recently came across an interesting article in the July/August 2010 issue of Australian Life Scientist. It discusses technological advances in the field of genome sequencing that are overcoming cost and speed limitations and opening the door to new applications. Here is an overview of what was discussed:

It took nearly two decades to go from the release of the first semi-automated genome sequencer in the mid-1980s to the launch of Roche’s flagship 454 FLX next generation sequencer in 2005. The 454 is now one of three major players in the next gen market whose impact on the world of genomics cannot be underestimated. Just five years later we are poised to embrace another new wave of sequencing technology. Next gen sequencers, exemplified by Illumina's Solexa Genome Analyzer and the APplied Biosystems SOLiD System, together with 454, are likely to continue to be adapted for myriad use rather than being superceded by the next next gen technology platforms.

The new wave of sequencers, sometimes called the third gen, are creating deal of excitement because they will likely enable scientists to reach the goal of the $US1000 human genome. The third generation of sequencing technology sees single molecules of DNA being sequenced without the need for cloning or PCR amplification and the inherent biases these procedures introduce. There are generally two types of detection methods for single molecule sequencing: those that rely on fluorescence and CCD capture, and those that don’t. Instruments that use the first of these detection methods include the Helicos Heliscope, launched in 2008; Pacific Biosciences single molecule real time sequencing (SMRT) machines, which have been shipped to their first customers; and Life Technologies-VisiGen system, which relies on fluorescence resonance energy transfer (FRET), and Life Technologies expects the first instrument will be placed later this year.

The third generation

The two non-fluorescing technologies operate via quite different methods, with detection systems based on tiny changes in electrical current or pH, thus removing the most expensive components, and associated costs, of sequencing instruments. Both nanopore sequencing, from Oxford Nanopore Technologies (ONT), and Ion Torrent, from Mass Genomics (which was just acquired by Life Technologies), are based on silicon chips. The ONT chip contains hundreds of wells each covered by a lipid bilayer that contains a nanopore – which is a hole around one nanometre in diameter – with each pore an individual electrical channel.

Sequencing is based on exonuclease cleavage of the single DNA strand and detection occurs when the cleaved nucleotide falls through the pore, transiently disrupting the current. The change in current amplitude is unique for each base (A,G,C,T and 5-Methylcytosine - the direct reading of which is unique to nanopore technology). ONT plan to commercialise their nanopore sequencing system by the end of 2010.

Ion Torrent, while also relying on advances in semi-conductor technology, sequences by monitoring DNA synthesis. Single types of nucleotides are sequentially flooded across the chip. Nucleotide incorporation into the new DNA strand results in the release of a H+ ion, which is detected by the pH sensitive dielectric layer. These breadbox–sized benchtop instruments come with an iPod, pre-installed with an application to monitor runs and cycles in real time. The Ion Torrent Personal Genome Machine (PGM) sequencer is just making its way into American research labs now.

Second generation sequencing redux

The third generation upstarts may be on their way, but that doesn’t mean second generation sequencers don’t have more yet to give. Improvements to the technology continue to be made on a number of fronts. They include an increase in the number of wells/reads per plate, superior base-calling algorithms and CCD detection rates and resolution (so the depth of sequencing required can be reduced for the same accuracy), and creation of scaled-down versions of instruments that, cost-wise, will put them in reach of the smaller research laboratories.