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In 2002, the FDA Science Board hosted several discussions over the state of pharmaceutical manufacturing. During these meetings, it became obvious that the pharmaceutical industry faced numerous challenges regarding the understanding and control of manufacturing processes, and that there were significant opportunities for improvement. The information gathered during these meetings resulted in the development of a shared vision for the future that would benefit not only the FDA but also the industry as well. Today, this vision is more commonly known as the "desired state" for pharmaceutical manufacturing in the 21st Century.

Recommendations for how the industry can achieve the "desired state" were incorporated into a number of regulatory initiatives that encourage the pharmaceutical industry to implement risk-based approaches, to apply modern quality management techniques to all aspects of pharmaceutical production and quality assurance, and to adopt new scientific and technological advances to help understand, better control, and continuously improve manufacturing processes. These include Quality by Design (QbD) and Process Analytical Technology (PAT). For pharmaceutical microbiologists, the implementation of novel technology platforms, such as RMMs, allows the industry a means for meeting these expectations from a microbial control perspective.

Quality by Design (QbD)

QbD is a systematic approach to developing formulations and manufacturing processes to ensure predefined product quality. This concept supports a continuous improvement model, emphasizes product and process understanding and process control, and is based on sound science and quality risk management principles.

One of the basic fundamentals of the GMPs is that quality should be built-in or should be by design, and product cannot be tested into compliance. In essence, when an appropriate QbD product development and manufacturing strategy exists, release testing should seldom result in an out of specification result. Furthermore, if we properly design and validate our processes and include analytical testing points throughout manufacturing, release testing can be reduced or eliminated. This is the basis for Process Analytical Technology (PAT), and RMMs can also serve to support this initiative.

Process Analytical Technology (PAT)

Published in 2004, the FDA PAT initiative describes a regulatory framework that encourages the voluntary development and implementation of innovative approaches in pharmaceutical development, manufacturing and quality assurance. PAT is a system for designing, analyzing, and controlling manufacturing through timely measurements of critical quality and performance attributes of raw and in-process materials and processes with the goal of ensuring predefined product quality and improving manufacturing efficiencies.

The term “analytical” in "PAT" is viewed broadly to include chemical, physical, microbiological, mathematical, and risk analysis. Many new technologies are currently available that provide information on these attributes to improve process understanding and to measure, control and/or predict product quality and performance. Companies that introduce PAT into their routine operations may realize reduced production cycle times by using on-, in-, and/or at-line measurements and controls, an elimination of rejects, scrap, and re-processing, the use of real-time release, and an increase in automation that improves operator safety and the reduction of human errors. Actually, RMMs are now being used in support of the PAT initiative. In fact, the very first FDA PAT approval was for an ATP bioluminescence rapid method that replaced the compendial Microbial Limits Test.

The FDA also understands that to enable successful implementation of PAT, flexibility, coordination, and communication with manufacturers is critical. The recommendations provided in the PAT initiative are intended to alleviate the fear of delay in approval as a result of introducing new manufacturing technologies, including RMMs. Therefore, PAT may be implemented through reduced reporting strategies, the use of comparability protocols, and by way of inspections.

Pharmaceutical cGMP's for the 21st Century: A Risk-Based Approach

This 2004 initiative is designed to use an integrated systems approach to regulating pharmaceutical product quality, and is based on science and engineering principles for assessing and mitigating risks related to poor product and process quality. We are encouraged to use the latest scientific advances in pharmaceutical manufacturing and technology to achieve the FDA's vision of the future desired state of pharmaceutical manufacturing:

  • Product quality and performance are ensured through the design of effective and efficient manufacturing processes
  • Product and process specifications are based on a mechanistic understanding of how formulation and process factors affect product performance
  • Continuous real-time quality assurance
  • Relevant regulatory policies and procedures are tailored to accommodate the most current level of scientific knowledge
  • Risk-based regulatory approaches recognize the level of scientific understanding of how formulation and manufacturing process factors affect product quality and performance and the capability of process control strategies to prevent or mitigate the risk of producing a poor quality product

Sterile Drug Products Produced by Aseptic Processing - cGMP

Published in 2004, this document updates the 1987 FDA guidance primarily with respect to personnel qualification, cleanroom design, process design, quality control, environmental monitoring, and review of production records. With regard to RMMs, the guidance recommends the use of rapid genotypic methods for microbial identification, as these methods have been shown to be more accurate and precise than biochemical and phenotypic techniques. The guidance also states that these methods are especially valuable for investigations into significant microbiological adverse events, such as sterility test failures and contaminated media fills. The guidance additionally confirms that other suitable microbiological tests (e.g., rapid methods) can be considered for environmental monitoring, in-process control testing, and finished product release testing after it has been demonstrated that these new methods are equivalent or better than conventional methods.

2008 Guidance for Industry: RMMs for Sterility Testing of Cellular and Gene Therapy Products

In February 2008, the FDA published their draft guidance on the validation of growth-based RMMs for sterility testing of cellular and gene therapy products. The guidance addressed considerations for method validation and determining equivalence of an RMM to sterility assays described in Title 21 Code of Federal Regulations (CFR), 610.12 (21 CFR 610.12). Additionally, the guidance specifically applied to somatic cellular therapy and gene therapy products that are regulated within the Center for Biologics Evaluation and Research (CBER) or other products that are also subject to sterility testing under 21 CFR 610.12. However, the guidance was not intended for human cells, tissues, and cellular and tissue products (HCT/Ps), HCT/Ps which are regulated as medical devices under 21 CFR Part 820, or for other pharmaceutical products that would normally be regulated by the Center for Drug Evaluation and Research (CDER).

The FDA realized that many cell-based products couldn’t be cryopreserved or otherwise stored without affecting viability and potency. Furthermore, most cell-based products are manufactured using aseptic manipulations because they cannot undergo sterile filtration or terminal sterilization. Furthermore, rapid and effective testing was needed because many cell-based products have a potentially short dating period, which often necessitates administration of the final product to a patient before sterility test results are available. Because of the challenges associated with cell-based products, there was a significant need to develop, validate, and implement sterility test methods that are more rapid than the sterility test methods described in 21 CFR 610.12.

For these reasons, the draft guidance provided direction on how to demonstrate that an alternative or rapid method is equivalent to a test method specified in 21 CFR Part 610, such as the sterility testing described in 21 CFR 610.12. It was also expected that an applicant demonstrate in a Biologics License Application (BLA) or supplement to a BLA that the alternative method will provide assurances of the safety, purity, potency and effectiveness of the biological product equal to or greater than the assurances provided by the specified method (21 CFR 610.9).

It is also important to note that the principles of RMM validation described in the draft guidance applied only to growth-based RMMs. Growth-based RMMs, like traditional methods of detecting viable microorganisms as described in 21 CFR 610.12, rely on the ability to recover and detect organisms from the product and demonstrate their viability by multiplication in liquid media. Therefore, the specific recommendations in this draft guidance document may not be applicable for non-growth-based RMMs that detect microbiological surrogates, such as Adenosine Triphosphate (ATP) or nucleic acids. For these reasons, the guidance focused solely on RMMs that provided qualitative results (i.e., detection of microorganisms).

The guidance stated that RMMs have the potential to replace the traditional methods for microbiological testing in the manufacturing process, including component (e.g., raw material, excipient) testing, in-process testing, drug substance testing and drug product in its final container.

Reliance on validated sterility testing methods is a critical element in assuring the safety of a product. Therefore, the draft guidance specified that proper validation of critical methods, including RMMs, demonstrate that the methods are suitable for their intended purpose and provides assurance that the results obtained are accurate and reproducible. Also included in the guidance were an overview of validation criteria that should be assessed, including limit of detection, specificity, ruggedness and robustness, what microorganisms to use, controls, and what method comparison studies to consider.

Proposed Rule: Amendments to Sterility Test Requirements for Biological Products

Sweeping changes were later proposed for the sterility testing of biological products. In June 2011, the FDA recommended to amend the sterility test requirements to provide manufacturers of biological products greater flexibility and to encourage use of the most appropriate and state-of-the-art test methods for assuring the safety of biological products. They took this action as part of FDA’s continuing effort to review and, as necessary, update the biologics regulations.

The proposed rule and it’s advantages were very similar to the 2008 draft guidance for industry: that manufacturers of innovative products, such as cell and gene therapy products, as well as manufacturers of currently approved products, may benefit from sterility test methods with rapid and advanced detection capabilities.

The proposed rule also stated that advances in technology (in recent years) have allowed the development of new sterility test methods that yield accurate and reliable test results in less time and with less operator intervention than the currently prescribed methods. Some examples of novel methods with the potential to detect viable contaminating microorganisms that the FDA identified included ATP bioluminescence, chemiluminescence and carbon dioxide head space measurement. Therefore, the proposed rule was not limited to the use of growth-based RMMs, but was now promoting the potential to use non-growth-based RMMs as an alternative to the compendial sterility test.

To summarize, the FDA proposed to amend 21 CFR 610.12 to promote improvement and innovation in the development of sterility test methods, to address the challenges of novel products that may be introduced to the market in the future, and to potentially enhance sterility testing of currently approved products. This proposed revision would provide manufacturers the flexibility to take advantage of modern methods as they become available, provided that these methods meet certain criteria.

With respect to validation, USP General Chapter 1223, “Validation of Alternative Microbiological Methods,” was also referenced. Validation of a microbiological method is the process by which it is experimentally established that the performance characteristics of the method meet the requirements for the intended application. For sterility testing, this means that the test can consistently detect the presence of viable contaminating microorganisms.

FDA proposed to eliminate the prescribed sterility test methods found in 21 CFR 610.12 and instead allow the use of sterility test methods that are validated in accordance with established protocols, to be capable of consistently detecting the presence of viable contaminating microorganisms. If an established USP compendial sterility test method is used, a manufacturer must verify that this established method is suitable for application to the specific product; however, FDA considered established USP compendial sterility test methods to already have been validated using an established validation protocol, so their accuracy, specificity, and reproducibility need not be re-established to fulfill the proposed validation requirement. In contrast, novel methods and any methods that deviate from the USP compendial sterility test methods would require a detailed validation.

As an example, when validating non-culture-based methods, the feasibility of identifying microorganisms from a contaminated sample should be evaluated. And if a method does not have the capability to identify microorganisms to the species level, the validation protocol should require that an additional method for species identification be utilized for investigation of detected contaminants. Next, the test organisms selected should reflect organisms that could be found in the product, process, or manufacturing environment. Finally, the validation study design should contain the appropriate controls to evaluate the product sample’s potential to generate false positive and false negative results. Validation of the sterility test should be performed on all new products, and repeated whenever there are changes in the test method that could potentially inhibit or enhance detection of viable contaminating microorganisms.

The Final Rule is Published in 2012

On May 3, 2012, the FDA amended the sterility test requirements for biological products in their Final Rule, “Amendments to Sterility Test Requirements for Biological Products.” With an effective date of June 4, 2012, the rule revises the sterility requirements for most biological products under Title 21 of the CFR, subchapter F, parts 600 through 680 (21 CFR parts 600 through 680) 1 and is intended to promote improvement and innovation in the development of sterility test methods by allowing manufacturers the flexibility needed for sterility testing of some novel products that may be introduced to the market, enhancing sterility testing of currently approved products, and encouraging manufacturers to utilize scientific and technological advances in sterility test methods as they become available.

Many changes have been put in place; for example, the Final Rule:

  • eliminates specified sterility test methods, culture media formulae and culture media test requirements, such as incubation conditions (time and temperature) and visual examination requirements
  • eliminates specified membrane filtration procedure requirements for certain products
  • eliminates specified sterility test requirements for most bulk material
  • modifies the repeat sterility test requirements, so that repeat tests will occur only once for each lot, if due to laboratory error or faulty materials
  • replaces the sample size or amount requirement with a requirement that the sample be appropriate to the material being tested
  • replaces the storage and maintenance requirements for cultures of test organisms used to determine the ‘‘growth-promoting qualities’’ of culture media
  • requires that the sterility test be appropriate to the material being tested such that the material does not interfere with or otherwise hinder the test

The Final Rule also provides very specific guidance when it comes to RMMs, especially as they relate to validation. For example, a novel method is required to be validated in accordance with an established protocol to demonstrate that the test is capable of consistently detecting the presence of viable microorganisms. Additionally, method validation is a well-recognized activity and can be performed without comparison to a ‘‘referee’’ test method. Specifically, there is no single ‘‘referee’’ test method that would work for all products and that some novel methods cannot be easily compared to culture-based methods such as USP Chapter 71 because these testing methods do not measure microbial growth.

The Final Rule also provides definitions and expectations for testing criteria that should be considered during validation:

  • The Limit of Detection reflects the lowest number of microorganisms that can be detected by the method in a sample matrix. This is necessary to define what is considered contaminated.
  • Specificity is the ability of the test method to detect a range of organisms necessary for the method to be suitable for its intended use. This is demonstrated by challenging the sterility test with a panel of relevant organisms in the sample matrix.
  • Ruggedness is the degree of reproducibility of results obtained by analysis of the same sample under a variety of normal test conditions, such as different analysts, different instruments, and different reagent lots.
  • Robustness is the capacity of the test method to remain unaffected by small, but deliberate, variations in method parameters, such as changes in reagent concentration or incubation temperatures.

Next, the Final Rule provides additional comment on the use of non-growth-based RMMs. For example, the feasibility of identifying microorganisms from a contaminated sample should be evaluated during validation. If a method does not have the capability to identify microorganisms to the species level, the validation protocol should require that an additional method for species identification be utilized for investigation of detected contaminants. Second, the validation study design should contain the appropriate controls to evaluate the product sample’s potential to generate false-positive and false negative results. Third, written procedures must include the composition of test components, test parameters, including the acceptance criteria, and the controls used to verify the test method’s ability to consistently detect the presence of viable contaminating microorganisms. Finally, the volume of test material that results in a dilution of the product should not inhibit or otherwise hinder the detection of viable contaminating microorganisms.

Lastly, the Final Rule specifies that a manufacturer who desires to utilize an alternate sterility test method other than the one approved in its BLA must submit a BLA supplement in accordance with 21 CFR 601.12(b).

FDA Strategic Plan for Regulatory Science

The core responsibility of FDA is to protect consumers by applying the best possible science to its regulatory activities - from pre-market review of efficacy and safety to post-market product surveillance to review of product quality. In the last few years, rapid advances in innovative science have provided new technologies to discover, manufacture and assess novel medical products, and to improve food safety and quality; FDA must both keep pace with and utilize these new scientific advances in order to accomplish its mission to protect and promote the health of the United States.

To meet this need, FDA developed its August 2011 strategic plan for regulatory science, the science of developing new tools, standards, and approaches to assess the safety, efficacy, quality, and performance of FDA-regulated products. This plan identifies eight priority areas of regulatory science where new or enhanced engagement is essential to the continued success of FDA’s public health and regulatory mission.

One of the priority areas, Support New Approaches to Improve Product Manufacturing and Quality, outlines the application of novel technologies to product development and innovative analytical approaches, including rapid methods for the detection of microbial contamination.

More specifically, analytical technologies are rapidly changing and leading to dramatic improvements in sensitivity, resolution, and precision in the determination of product structure and the detection of contaminants. In order to better reduce the risk of microbial contamination of products, the following needs will be addressed:

  • Develop sensitive, rapid, high-throughput methods to detect, identify, and enumerate microbial contaminants and validate their utility in assessing product sterility
  • Develop and evaluate methods for microbial inactivation/removal from pharmaceutical products that are not amenable to conventional methods of sterilization
  • Evaluate the impact of specific manufacturing processes on microbial contamination
  • Develop reference materials for use by industry and academia to evaluate and validate novel methods for detecting microbial contamination

Each of these needs fall within the FDA’s Quality by Design initiative, which includes understanding the manufacturing process and identifying the key steps for obtaining and assuring a pre-defined final product quality. We have discussed this new strategic plan in our RMM Blog, and a PDF of the plan may be downloaded from our References Page.

FDA's Perspectives on RMM Validation

The appropriate pathway for rapid microbiology submissions to FDA is best determined through direct dialogue with the Agency. The PAT initiative recommends discussion with FDA regarding all aspects of implementation for new process analytical methods, and until RMMs become more widespread in the pharmaceutical industry, Dr. Riley suggests that it may be simplest to implement new rapid methods on a post-approval basis. However, firms may also include RMMs in their original product submissions as well. Both of these options are discussed in more detail below.

Within the U.S., PDA TR#33 and USP <1223> can serve as a jumping off point for discussions with the FDA on the validation of a RMM (please visit our Validation Page for detailed information regarding these guidance documents). However, a firm may also develop their own validation strategy, as long as it is scientifically sound and defendable. The latter may include incorporating the guidance from Ph. Eur. chapter 5.1.6.

Each of these guidance documents describes the basics for validation, including validation parameters and acceptance criteria that might be appropriate for each parameter. And while it is important that each validation parameter be addressed, the user may not need to perform all of the work themselves. For example, ruggedness and robustness are better suited to be performed by the RMM vendor. However, the vendor can also provide additional validation test data, either by providing the data directly to the end user or by submitting the data to the FDA within a Drug Master File (DMF). If a vendor's DMF has been submitted, then the end user would, in many cases, only have to provide test data that is not covered in the DMF, as well as product-specific data associated with the RMM being qualified.

There are a number of options for qualifying a RMM that will be used to support the manufacture of FDA-regulated drug product. If the RMM will be used with a new product, a firm may include the RMM in a new drug application (NDA) or an abbreviated new drug application (ANDA). If the RMM will be used with an existing product, and the RMM will replace a microbiology method that has been included in the product's original regulatory submission, then it may be necessary to file a post-approval change or prior-approval supplement in the relevant Chemistry, Manufacturing and Controls (CMC) sections for that product. Once a RMM has been approved, either in an NDA, ANDA or a prior-approval supplement, subsequent product filings may include the RMM in an Annual Product Report. Another option is to file a Comparability Protocol to manage the validation of the proposed RMM.

A Comparability Protocol (CP) is a well-defined, detailed, written plan (and prior-approval supplement) for assessing the effect of specific CMC changes in the identity, strength, quality, purity, and potency of a specific drug product as these factors relate to the safety and effectiveness of the product. The CP describes the changes that are covered under the protocol and specifies the tests and studies that will be performed, including the analytical procedures that will be used, and acceptance criteria that will be achieved to demonstrate that specified CMC changes do not adversely affect the product. In terms of RMMs, the CP is a validation protocol to demonstrate that the RMM is suitable for its intended use. Furthermore, the CP can be particularly useful for changes of a repetitive nature, such as the use of a RMM for multiple products or processes.

Because the CP is reviewed by the FDA, deficiencies in the validation plan can be corrected prior to performing the studies, eliminating the need to repeat some or all of the testing. Once the CP is approved by the FDA, the experiments are carried out, and if they meet the acceptance criteria provided in the CP, the FDA is notified via a Special Report [as per 21 CFR 314.81(b)(3)(ii)], the latter which is submitted to the relevant application(s). The Special Report references the approved CP and includes a brief description of the RMM and its use, confirmation that the acceptance criteria have been met, and the date of implementation. The report can be as small as one page, because there is no need to communicate any of the testing data back to the FDA. Additionally, a reduced reporting category can be used to notify the FDA that the RMM is being implemented, such as a Changes Being Effected (CBE)-30 or CBE-0. For example, when using a CBE-0 notification process, a firm can immediately implement the RMM for routine use.

The same CP can be used (without going through another review and approval process) to subsequently validate the same RMM for additional products or samples, as long as the CP acceptance criteria are met. In this case, the same approved reduced reporting notification method can be used. It should also be noted that a number of companies have already used these same strategies for RMM approvals associated with drug product that is sold in the U.S.

Utilizing a Research Exemption

It may be appropriate to utilize a Research Exemption process when generating new RMM data in an active manufacturing area. The FDA has acknowledged the industry's concerns that an increased amount of process data may in fact indicate a problem in a product that meets its current registered release methods, and this may also apply to data generated by RMMs under evaluation and/or validation. In response to this concern, the FDA introduced the "safe harbor" or "research exemption" concept during numerous meetings of the Advisory Committee for Pharmaceutical Science and the PAT Sub-committee. The concept is designed to encourage the industry to investigate tools that will provide increased process information without the fear of having a negative impact on the ability to release products that meet all aspects of the company's current registered quality control strategy. A strategy for operating under a research exemption may include:

  • Designating all data generated by the RMM under investigation are for research purposes only
  • All GMP decisions, including batch release, are based on the current approved and validated methods
  • An internally approved, written document and/or a Comparability Protocol should be used to communicate this strategy within the company and/or to the FDA.

Internal research exemption documents should explain the nature of the technology under review, an overview of the testing plan and that the data generated by the new technology will not be used for making GMP decisions. This document should also be readily available for review in the event an inspector asks questions about the technology under review.

It is also worth noting that the research exemption concept is not currently recognized by European regulators.

Publications by FDA's Microbiology Review Staff

In 2006, Drs. David Hussong and Robert Mello (New Drug Microbiology Staff at CDER) published a paper entitled, "Alternative Microbiology Methods and Pharmaceutical Quality Control." The paper stated the following: "New microbiology methods can offer advantages of speed and precision for solving microbiological problems associated with materials or environmental influences. Neither Corporate economics nor regulatory attitudes should be a barrier to the use of new testing technologies or different measurement parameters. In fact, if we are to increase our understanding of quality-based products and processes, then quality by design principles and risk analysis methods must be extended to the development of new microbiological technologies. This approach will drive process engineering to yield real, measurable gains in microbiological product quality assurance."

Dr. Bryan Riley, New Drug Microbiology Staff at CDER, published a 2004 paper entitled, "Rapid Microbiology Methods in the Pharmaceutical Industry. Dr. Riley wrote, "The use of rapid microbiology methods by the pharmaceutical industry should offer many advantages. Receiving microbiology test results sooner will provide for better control and understanding of the manufacturing process via faster feedback. Appropriate validation of rapid microbiology methods is necessary to ensure that the test is suitable for its intended purpose. However, it should be noted that the existing traditional microbiological test methods leave a lot of room for improvement. Therefore, it is not necessary to demonstrate that a new rapid method is flawless, only that it is not inferior to the current method, and will thereby provide equivalent assurance of microbial quality. Current FDA initiatives (i.e., PAT and GMPs for the 21st Century) should help assure industry of the agency's understanding of the potential importance of rapid microbiology methods. These initiatives should also convince industry that FDA will assess rapid methods scientifically and not place undue regulatory burdens on firms interested in using these methods. There are many exciting potential uses for rapid microbiology methods in the pharmaceutical manufacturing process, and industry should not feel that FDA will be a hindrance to the appropriate use of these methods."

Both of these papers may be downloaded from our References Page.

Presentations by FDA's Microbiology Review and Compliance Staff

Discussions by the U.S. FDA have reinforced their acceptance of RMM technologies within the pharmaceutical industry. For example, during the PDA 2nd Annual Global Conference on Pharmaceutical Microbiology (2007), Dr. Brenda Uratani, consumer safety officer for the Center for Drug Evaluation and Research (CDER), described the benefits of using a RMM, and these included automating the testing process, electronic capture of test data and information creation, the ability to initiate investigations earlier as compared with conventional methods, the reduction of risk associated with microbial contamination, and the use of the data as a continuum for process improvement.

During the 2010 PDA 5th Annual Global Conference on Pharmaceutical Microbiology, Dr, David Hussong, Director, New Drug Microbiology Staff at CDER, stated that RMMs are very important for meeting QbD principles, smart processing and PAT, that CDER actively encourages the use of new technologies, and the regulatory mechanisms for implementation of RMMs are evolving.


The FDA has made significant progress in understanding, accepting and encouraging the use of RMMs. For firms wishing to implement RMMs in support of product sold in the U.S., it is very helpful to discuss your plans with the FDA as early as possible, and this can be done through informal meetings via telephone or more formally via face-to-face meetings with the Agency's RMM subject matter experts.