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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Technical requirements for any RMM might include the following:


    • Significantly reduced time-to-result when compared with conventional microbiological methods;

    • Automated, miniaturized and high-throughput technology platforms;

    • Increased sensitivity, accuracy, precision and reproducibility;

    • Detection of a single, viable microorganism without the requirement for cellular growth;

  • Enhanced detection of stressed organisms.


Business requirements might include:

    • Significant reduction of testing time to release products more rapidly;

    • Lower inventories (raw material, in-process material and finished product;

    • Prevention of back orders;

  • Reduction of repeat testing, deviations, OOS investigations and product rejection.


Regulatory uncertainty

Regulatory uncertainty is impeding the drug industry’s acceptance of RMMs and other new technologies today. Many drug companies view the existing regulatory system as rigid, and fear that FDA inspectors may not be familiar with recent advances in microbiology.

Quality and manufacturing professionals may have legitimate concerns or questions, ranging from fear of increased sensitivity in recovered microbial counts to concerns about the potential impact on existing acceptance criteria, uncertainties over the development of a meaningful validation and submission strategy, or doubts that a particular technology platform may be acceptable for use with a given product or process. Teams evaluating RMMs should be proactive, contact FDA, meet with the Agency’s microbiologists and discuss the best path forward. The spirit of FDA’s PAT Guidance views such communication as essential to advancing drug manufacturing technologies.

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.

Applications and opportunities

There are many opportunities for implementing RMMs in the pharmaceutical industry, including:


  • Raw material and component testing;
  • in-process and pre-sterilization/filtration bioburden;
  • fermentation and cell culture monitoring;
  • purified/process water testing;
  • environmental monitoring (e.g., surface, air, compressed gases, personnel);
  • bacterial endotoxin testing;
  • microbial limits;
  • antimicrobial effectiveness testing;
  • biological indicator survival studies;
  • sterility testing;
  • media fill failure investigation;
  • contamination incident assessment.


RMMs can be applied as PAT, when information about the microbial control of a manufacturing process can be obtained in real-time — for example, in purified water testing, in-process bioburden testing and environmental monitoring. In such cases, a company can apply RMMs to respond, immediately, to an OOS finding or an adverse trend, minimizing the impact to product or in-process material. The alternative is to wait for days until conventional testing results are available, after the opportunity to act has long passed.

Many RMMs offer increased sensitivity, accuracy, precision and reproducibility, and some can detect a single cell without the need for microbial growth. As more rapid method technology platforms are developed, instruments are being miniaturized to facilitate at-line, on-line and in-line applications at the site of manufacturing. RMMs can enhance risk-based analysis and microbial control strategies by offering a more robust understanding of manufacturing processes.

The following section provides an overview of the RMM platforms available or being developed, with a brief discussion of how they work.

Growth-based technologies rely on the measurement of biochemical or physiological parameters that reflect the growth of microorganisms. These types of systems require the organisms in a sample to proliferate, either on a solid or liquid medium, in order to be detected and/or quantified. Currently available growth-based technologies for the detection, enumeration and identification of microorganisms include:

    • the bioMérieux (Durham, N.C.) VITEK 2 and Bactometer systems;

    • the Biolog (Hayward, Calif.) Omnilog

    • ATP-bioluminescence systems such as Millipore’s (Billerica, Mass.) Milliflex Rapid System, the Celsis (Chicago) Advance Luminometer, and Pall’s (East Hills, N.Y.) PallChek Microbiology System;

  • Genomic Profiling Systems’ (Bedford, Mass.) Growth Direct, a new system, currently in development, that relies on the growth of microorganisms on agar.


Viability-based technologies use viability stains and/or cellular markers to detect and quantify microorganisms without the need for cellular growth. Today’s available technologies include:

    • the Chemunex (Princeton, N.J.) ScanRDI solid-phase cytometry platform;

  • flow-cytometry systems such as the Chemunex D-Count and BactiFlow, and the Advanced Analytical Technologies (Ames, Iowa) RBD 3000.


Artifact-based technologies rely on the analysis of cellular components or the use of probes that are specific for microbial target sites of interest. Examples include:

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