Rapid microbiology: Solutions for the next stage

Posted: 20 July 2006 | | No comments yet

Rapid microbiology is an exciting field for the development of new technologies and applications. There are significant challenges to be overcome and in doing so, great prospects for microbiologists and the companies that provide cutting-edge equipment.

European Pharmaceutical Review spoke to the industry’s leading vendors to hear what they have to offer in terms of insight and technology. We have also included commentary from two well-recognised names in the field: Michael J. Miller of Eli Lilly and Don Singer, member of the USP Microbiology and Sterility Assurance Expert Committee.

The vendor’s perspective

Three vendors outline their perspective on the technologies that are currently available and what the future holds for Rapid Microbiological Methods (RMM).

A leaner solution from Celsis

Celsis is renowned for its ATP Bioluminescence and next-generation Adenylate Kinase-enhanced (AK) bioluminescence technologies for product screening. Through an exclusive licensing agreement, Celsis has developed AKuScreenTM: an adenylate kinase-enhanced bioluminescence assay that delivers results in 18 hours for bacteria and yeast and as little as 24 hours for bacteria, yeast and mold.

Efforts targeted to meet the needs of the biopharmaceutical industry have resulted in the development of the recently launched RapiScreen Biologics kit which is now in use by several biopharmaceutical companies for in-process and/or finished product screening.

Validation is an important element of implementing any new technology in the pharmaceutical setting. According to Judy Madden, Vice President, Strategic Development at Celsis, a thorough validation program for their technology includes three key elements: Sample Effects, Spiking Studies and Parallel Testing. “Sample Effects is an evaluation of how the product sample interfaces with the method,” says Madden, “Spiking Studies involve spiking samples with low levels of known organisms to demonstrate detection. Finally, Parallel Testing requires side-by-side testing of product using both old and new methods to demonstrate equivalency of the method.”

Technology must be evaluated in terms of its suitability for the products and facilities in which it will be implemented and the incremental value that the technology will bring to the manufacturing process. “Instruments and/or protocols that look interesting in a tech center may not be suitable for less-resourced manufacturing environments in other parts of the world,” says Madden, “nor may the information that they provide by relevant to the economics of efficient manufacturing. We constantly ask ourselves the questions “What information does our customer need and when do they need to have it?”

Where regulatory approval is concerned, like all contributors to this article, Madden supports the fact that other industries, such as food manufacturing, have made significantly more progress towards the implementation of rapid microbiological methods, although regulatory approval does not represent the same challenge it once did. “The use of Comparability Protocols and the more recent PAT initiative are proving to be invaluable to industry.”

One of the most difficult assessments to make when implementing any new technology is that of value-for-money. Madden insists that in this respect, no one makes purchase decisions based on technology alone. “In order to understand the economics of implementing our technology, Celsis worked in collaboration with a management consulting firm and one of our global customers as they evaluated the financial impact of implementing Celsis technology in their manufacturing facilities worldwide. The result of that collaboration was a financial model that projects the Five-Year Net Present Value and Payback Period associated with the investment. The model takes into consideration the impact of reduced inventories and working capital requirements along with the reduced costs associated with earlier identification of contamination events when they occur. We use this model with virtually all of our customers to help them make informed decisions about our technology.”

Madden believes that there will be an increase in the implementation of rapid methods in the pharmaceutical industry will accelerate during the next five years. In line with the industry’s commitment to more efficient manufacturing, Celsis’ message remains that there is no better way to improve efficiency than by taking multiple days out of manufacturing cycle times.

Automation and standardisation from MIDI

Craig J. Kunitsky, Global Marketing Director for MIDI, Inc. identifies four key technologies as leaders in microbial identification: fatty acid analysis by gas chromatography; biochemical enzyme assays, 16S and 28S rRNA gene sequencing and DNA ribotyping.

As with Celsis, Kunitsky highlights the importance of vendor service in the context of validation. “Is the technology Part 11 compliant and can the vendor assist in validating this compliance?” asks Kunitsky, “are documentation and protocols available from the vendor? Are lab personnel trained and how do you go about testing new technologies?”

When asked how MIDI products offer value-for-money, Kunitsky refers to his own checklist:

  • Offer the largest environmental library in the industry
  • Create an easy-to-use, standardised sample preparation
  • Automate all sample processing and naming to reduce subjective errors
  • Minimise the cost per sample by having no proprietary kits, proprietary media or offline tests required
  • Offer the ability to identify microbes by both Phenotypic and Genotypic technologies from the same platform
  • Offer the ability to do near real-time strain tracking at no additional cost after each identification
  • Offer an easy-to-perform validation procedure

“New microbial identification technology should provide several advantages over the existing technology being used,” states Kunitsky, “including, but not limited to advantages in total costs, including implementation, material costs, labour and maintenance; accuracy; speed of analysis; size of libraries; ruggedness and sensitivity.”

For the next five years Kunitsky anticipates the use of more polyphasic approaches to identification, e.g. a phenotypic method combined with a genotypic method, where greater accuracy is required.

Comprehensive customer support from AES Chemunex

AES offers its renowned Solid Phase Cytometry; ChemScanRDI and Flow Cytometry; D-Count, BactiFlow ALS and BactiFlow.

“As a vendor we have to take into account that the validation of a new method is a concern for the industrial sites implementing RMM due to the additional workload that comes in addition to the routine operation of the laboratory,” says Xavier Grand-Maison, Product Manager & Marketing Engineer, AES Chemunex. “For validation, dedicated human resources are necessary for a period of time from several weeks to several months. To facilitate the smooth introduction of the new technology in the companies, AES Chemunex offers users comprehensive Fast Track Validation Support and Routine Use services. This includes on-site training, practical advice and a full series of documentation.”

Testament to AES’ validation is that fact that GlaxoSmithKline has received FDA approval to use ChemScanRDI for routine microbiological analysis of their pharmaceutical grade water.

AES Chemunex has completed a Drug Master File (DMF) for the detection of viable microorganisms using laser scanning cytometry on solid phase (ChemScanRDI).

“The U.S. and European Pharmacopeias (USP and EP) have already proposed general chapters on rapid microbiological methods. The planned USP informational chapter <1223>, ‘Validation of Alternative Microbiological Methods,’ provides guidance for validating methods that can be used as alternatives to official Compendial microbiological methods. The proposed informational EP chapter 5.1.6, ‘Alternative Methods for Control of Microbiological Quality,’ describes alternative methods for the control of microbiological quality.”

Grand-Maison believes there is a long list of reasons that justify the cost and time required to select, procure and implement new technologies:

  • Final product testing in minutes
  • Rapid detection of problems (Raw materials ? Final product)
  • Immediate response to contamination incidents
  • Rapid confirmation of corrective action effectiveness
  • Real time trending of the production process
  • Decrease inventory holding and warehouse costs
  • Decrease product losses
  • Minimise production disruption
  • Increase production flexibility
  • Increase profitability

The industrial perspective

Donald Singer, Member of USP Microbiology and Sterility Assurance Expert Committee

Essentially there are three main categories that RMM technology has been marketed to: identification, quantitative (enumeration) microbiology and qualitative (presence/absence) microbiology. There are many different ways to categorise the different types of technologies being marketed as rapid microbiology. The biologist’s categories of technologies are: growth-based (e.g. bioluminescence), viability-based (e.g. flow cytometry), cellular component-based (e.g. fatty acid profiles) and nucleic acid-based (e.g. PCR). Some systems are completely automated, and others are semi-automated.

In terms of applications for these technologies in the pharmaceutical industry, I don’t feel there are any ‘best’ applications, but there are some which find a very good fit. Most systems are off-the-shelf and they have to fit the user’s needs as is, which can be problematic for the microbiologist and their laboratory. Customised systems are a better approach, with the microbiologist participating in the design of a system for their use.

Validation or better yet, suitability testing, should go to the basics: 1) identify the purpose and identify the measurement, 2) define the criteria that makes scientific sense, 3) show sensitivity of technology is adequate for the criteria and the purpose intended, and 4) generate ongoing data to prove criteria is acceptable and technology is adequate. Remember that validation or suitability of a ‘new’ technology could be an ongoing effort. It shouldn’t be considered ‘done’ until sufficient data has been collected that can show confidence and reliability in generating appropriate data to help make decisions.

When implementing new technologies, the primary step, which is the most important, is ensuring parameters that support suitability testing (such as accuracy, limit of detection, limit of quantitation, whichever are most appropriate) are capable of meeting intended use and value. Adequate learning and training in the technology is another key step that should be included. Building staff confidence in the new technology compared to use of classical methods, as well as using the technology along with classical methods, is a way to develop understanding and acceptance of the changes.

Regulatory approval

Regulatory approval will depend on regulatory authority (geographical differences). In the U.S., comparability is now the method of choice, whether in formalised presentation of just following the intent of the guidance on comparability protocols as written by the FDA. The key step is communications with the FDA from the beginning and throughout the implementation process. In other countries, a similar approach is probably a good beginning along with communications with the relevant Authority. What is actually required in other countries is not clear yet and is developing slightly slower.

Selection and procurement

First identify the need, then seek understanding of the technologies that exist, and then partner with a new technology supplier to develop processes that fit the need. Value will be limited if you try to force fit a technology into a need.

Innovation and new approaches in science are requirements to be a leader in any industry. Other leadership competencies are seeking improvements in profitability and quality. Time, cost and labour are all included in a cost/benefit evaluation that should be performed for any new technology being considered for development or implementation.

The USP committee has been informally monitoring technologies in industry as they relate to compendial article quality testing and process monitoring. New technologies could change the scientific approach to quality by design. Yet, successes in specific companies are not easily communicated due to the competitive nature of our industry.

The road ahead

Due to the newness of many technologies being trialed, and due to the global nature of many companies, implementations may be global instead of localised. Of course, there are still differences in regulatory acceptance. The U.S. FDA seems to be a bit quicker in accepting adequately developed and validated systems, also based on strong communications with the agency up front and throughout the process. There is another ironic reality, though, and that is that the ‘best kept secret’ in industry is that over-the-counter consumer products (food, cosmetics, and drugs) around the world have been testing or using ‘new’ technologies for years. What can we learn from them?

In the next five years I anticipate more customised solutions, more partnerships with vendors, and continuing development in areas such as RNA technologies, will continue the expansion of development, acceptance and implementation of new technologies. I think it is highly probably for technologies to become more focused on use in process-monitoring than in end-product quality testing.

Michael J. Miller, Ph.D., Senior Research Fellow, Eli Lilly and Company

There are a wide range of currently available technologies that will span growth-based, viability-based, artifact-based and genetic-based platforms. A few key technologies in each group are presented below:

Growth-based systems rely on the measurement of carbohydrate or physiological parameters that reflect growth of microbes. These include ATP-bioluminescent detection platforms and a number of microbial identification systems.

Viability-based technologies utilise stains or cellular markers to detect and enumerate microorganisms without the need for microbial growth. Some of these technologies include flow and solid-phase cytometry.

Artifact-based systems rely on the analysis of cellular components or the use of probes that are specific for target sites of interest. For example, currently available technologies use fatty acid analysis, MALDI and SELDI Time-of-Flight mass spectrometry, and endotoxin analysis.

Finally, genetic-based technologies make use of DNA sequencing, 16S rDNA typing and DNA amplification (PCR).

The push for PAT, both in Europe and the U.S., prompts us to think about in-process microbiological control and RMM’s fit nicely into this area. For example, a number of currently available RMM’s can be used to monitor the manufacturing environment during a production campaign, the pharmaceutical-grade water that is being used as well as in-process bioburden, all in real-time. In the event a contaminant is detected, some of the newer identification systems that do not rely on growth may be used for a rapid ID. What we are working toward is to move quality control upstream to the critical processing steps rather than at the end (i.e., finished product/process testing). This is one of the components of Quality by Design.


One of the main issues associated with validation of these new technologies is that a company must have a robust validation strategy in place. For many years, one of the main barriers to implementing RMM’s was the lack of appropriate guidance documents for method and system validation. Fortunately, this is not the case today. All of the components of a robust validation strategy are currently available, either in the Pharm. Eur. Chapter 5.1.6, the draft USP chapter <1223>, the PDA Technical Report #33, and in the Encyclopedia of Rapid Microbiological Methods, co-published by the PDA and Davis Healthcare International, and edited by Dr. Michael J. Miller.


First and foremost, a company needs a champion; one who will assemble the right resources and develop a strategy for the applications and financial justifications needed to convince their management that RMM’s is a viable opportunity. Next, the firm must understand what technologies are available for the application(s) they intend to address. When the right technology is married with an application, and the return-on-investment is understood, then feasibility studies and ultimately formal validation studies may be conducted. An in-depth review of validation and implementation strategies may be found in the Encyclopedia of Rapid Microbiological Methods.

Regulatory uncertainty is impeding the pharmaceutical industry’s acceptance of RMMs and other new technologies today. There still exists a perception that the regulatory authorities are unfamiliar with RMM technologies and that the approval process is difficult to navigate. Specifically, there are significant differences in the regulatory approval process between Europe and the U.S., especially for previously approved products. For example, RMM’s that would be considered for use in a PAT application (e.g., monitoring of in-process bioburden or purified water systems) could utilize the comparability protocol approach when registering the new technology/method with the FDA. The comparability protocol is reviewed and agreed upon upfront, and the firm can take advantage of reduced reporting structures, such as a CBE-0, when the protocol has been successfully executed. This type of regulatory infrastructure does not exist in Europe today, and firms may need to submit a validation package for each product/process and wait for responses from all of the member bodies before obtaining approval. This European approval process may take over a year, as compared with the FDA comparability protocol process which can occur in as little as a few weeks. Furthermore, the potential need to submit multiple supplementary applications for the use of RMMs for post-approved products (many which can be considered as a Type-2 variation) is a significant challenge for the implementation of these technologies within Europe. It would be advantageous if the EMEA and the local regulatory authorities worked toward streamlining the processes by which RMMs are reviewed and accepted.

Selection and procurement

A financial justification and return-on-investment assessment should be conducted to ensure that the chosen technology will add the greatest value to the company once it is implemented.

Examples of what a firm might review to justify the implementation of a technology may include the changes associated with:

  • testing cycle time
  • repeat testing
  • OOS investigations
  • lot rejection
  • raw material, in-process and finished goods inventory holdings
  • warehouse space
  • back order avoidance
  • improved in-process monitoring

Although there are too few numbers of actual RMM imple­ment­a­tion success stories to compare the European vs. US experience, it appears that European companies have been working on the implementation of these technologies longer than in the U.S.; however, the regulatory approval process is more challenging in Europe than in the U.S. (see comments above). I believe that as more and more companies work with the Regulatory authorities in validating these technologies we will see a greater number of implementation case studies in the years ahead.

The next step for RMMs is to further miniaturise and automate the detection, counting and identification of microorganisms that may be found in our processes and products. For example, new platforms utilising optical spectroscopy, Lab-On-A-Chip or microfluidics systems, microarrays or biochips, biosensors and nanotechnology are currently being made available or are in development. Also, the push for Quality by Design and PAT-based monitoring and control of our development and manufacturing processes will promote the implementation of RMMs at a greater rate than that which we see today.