Rapid Microbiological Methods for a New Generation

These are exciting times, as 19th-century microbiological methods make way for rapid detection, quantification and characterization technologies.

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

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One of the greatest contributions to the field of microbiology came from the kitchen. In the 1880s, scientist Walter Hesse was searching for a solid medium that could be used to cultivate bacteria. The material had to be stable at high temperatures, and had to allow different types of microbes to be separated easily. Fanny Angelina, Hesse’s wife and laboratory assistant, had the answer: Agar-Agar, a gelling agent that she used in her jellies and puddings. This simple kitchen ingredient revolutionized the science of microbiology, allowing the separation and culturing of microbes to become a routine procedure.


Rapid Microbiological Methods: LabChip from Agilent Technologies
LabChip technology uses microfluidics to separate and analyze samples for microbial identification. Samples are run through microscopic channels inside the chip. Courtesy of Agilent Technologies.

Now, almost 125 years later, microbiology agar is the most important and widely used microbial growth medium available today. Fanny would be proud . . . but should we be?

The growth of microbial cells on agar surfaces may provide critical information about the number and the type of organisms that are present in a sample, but it can take days or even weeks to get results. In many cases, individual organisms cannot be isolated due to confluent growth, necessitating subculturing onto additional agar media, further delaying the time to result. In addition, many microbes may not replicate when cultured on artificial media after they’ve been deprived of nutrients or exposed to sublethal concentrations of preservatives, disinfectants, heat or decontaminating gases.

The modern microbiological laboratory needs more innovative approaches to microbial detection, identification and enumeration. Fortunately, technology is now available — or close to being available — that will speed up microbiological analysis, allowing aseptic manufacturing to embrace the concepts of Process Analytical Technology (PAT). This article surveys the various Rapid Microbiological Methods (RMMs) that are now available (or are in development) to the pharmaceutical industry.

PAT and FDA’s acceptance of rapid methods

The PAT initiative describes a regulatory framework that encourages the voluntary development and implementation of innovative approaches in pharmaceutical development, manufacturing and quality assurance (Pharmaceutical Manufacturing, November/December 2004, p. 41). Many new technologies are currently available that provide information on physical, chemical, and microbiological characteristics of materials to improve process understanding and to measure, control and/or predict product quality and performance. However, RMMs have not yet been widely implemented within the pharmaceutical industry due to concerns about validation and the need to prove the technologies’ “comparability” with existing methods, worries about return on investment (ROI) and regulatory uncertainty.

Many forward-looking microbiologists working at pharmaceutical companies are frustrated by their management’s hesitancy to approve the use of RMMs. Typically, these managers fear that the company won’t be able to make a compelling case to regulators that the new methods work as well or better than technologies that the company already uses, or that there’s not enough guidance available to validate a new method and/or laboratory system. This simply is not true. Companies that have conducted successful validations or those that are now qualifying new systems have relied on guidelines presented in PDA Technical Report #33, “Evaluation, Validation and Implementation of New Microbiological Testing Methods.” Published in 2000, this document provides information on validation protocol design, testing and acceptance criteria, and installation, operational and performance qualification strategies.

But demonstrating comparability of the new technology is only one part of the overall strategy for embracing RMMs. Management may also be concerned that:


    • Technologies may be incompatible with product and/or processes;

    • Staff may not understand what the required method sensitivity or specificity should be (e.g., detection levels and for what types of microorganisms);

    • Technologies may require significant operator training and qualification;

  • Technology vendors won’t be able to provide support during the initial assessment, validation exercises, and most importantly, after the system has been placed in service for routine use.


Due diligence is essential, from both a technical and a business perspective, when implementing RMMs, to ensure that any technology selected will be the best possible fit for the application involved.

Making a business case for RMMs

RMMs are not inexpensive. The overhead alone can run into the hundreds of thousands of U.S. dollars, required for:


  • initial feasibility assessment;
  • development of user requirements;
  • testing protocols and SOPs;
  • training;
  • execution of the validation program;
  • documentation;
  • regulatory submission;
  • technology transfer;
  • site implementation.


These expenses don’t include the costs for the equipment itself, or testing costs, which tend to be higher than those for established technologies.

At any pharmaceutical company, corporate management will demand to know what ROI it can expect from these new technologies. In order to provide the most accurate information, any team exploring the use of RMMs must include someone from the company’s financial or business planning department. Their expertise will ensure that the budget is accurate, and that the team makes a strong business case for the technology. In many cases, the long-term benefits of RMMs will far outweigh the short-term costs.

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