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USP (1117) Microbiological Best Laboratory Practices

Scott Sutton, Ph.D.
This article first appeared in the PMF Newsletter of August, 2006 and is protected by copyright to PMF. It appears here with permission.


The USP finalized a series of chapters this summer. Past issues of the newsletter have discussed four of these:

There is a need to set some base level of microbiological laboratory standards. Therefore, after several rounds of discussion (stretching over a couple years), the AMB has presented a draft chapter entitled “<1117> Good Microbiological Laboratory Practices” (1). The response to this initial proposal was spirited. Comments can in from industry and FDA on this initial proposal, and a draft revision was published in 2004 (2). This revision was well-received (few comments) and made effective (with minor changes) in August of 2006 (3).

Chapter Organization

The chapter is meant to provide minimum guidance for microbiological practices in the pharmaceutical environment. As such, it is organized into topics of importance to the microbiologist:

  • Media Preparation and Quality Control
  • Maintenance of Microbiological Cultures
  • Maintenance of Laboratory Equipment
  • Laboratory Layout and Operations
  • Training of Personnel
  • Documentation
  • Maintenance of Laboratory Records
  • Interpretation of Assay Results

Media Preparation and Quality Control

The quality of work in a microbiological laboratory depends on the quality of the culture media. It is essential to use the correct media for the purpose at hand, although the correct media is not always obvious. For example, water testing is commonly done with R2A agar, but many facilities use TSA for this purpose. The recommendation is provided that the choice of media should be consistent, appropriate and justified.

The chapter spends some time on media preparation as well. The recommendations include accurate weighing of dehydrated components, the use of high quality (USP Purified) water, completely dissolving the dehydrated media or individual ingredients, and the need to control the heating of the media to avoid damaging heat-labile components of the media. Some recommendations on the labeling and packaging of media are also provided.

An entire section is devoted to the question of media storage and the effects this might have on the media quality. Excesses of heat and cold are to be guarded against, as is the potential for dehydration of poured plates. Some guidance is also provided in quality control for molten media used in pour plates.

The quality control of the media is a critical concern. Interestingly, initially some of the most passionate commentary on the chapter dealt with the “excessive” amount of space provided to media quality checks. Since the initial release in 2003, however, the harmonized Sterility Tests and the harmonized Microbial Limits Tests have both incorporated stringent media quality checks.

Maintenance of Microbiological Cultures

Second only to media, safeguarding the stock cultures is the most important component of a successful microbiology laboratory. These must be handled carefully at all times to avoid contamination.

The care of the cultures starts upon receipt. A careful stock culture curator will confirm the identity of the received cultures, even if they come from as respected a source as a national culture collection. Mistakes can happen. The use of an incorrect strain in a compendial test could bring the results of weeks or months of work into question.

The chapter reinforces the compendial preference for the “seed lot technique” in culture maintenance. Critical to this is the need to go into your containers of stock culture only once, and in restricting the number of passages. Now, it must be stated that there is nothing magic about the number 5. This number gained popularity in the compendia through its use in the Sterility Test, and has been maintained for consistency. The point to the practice is that a careful lab will safeguard the purity and identity of their stock cultures by limiting the potential for “drift” due to excessive transfers.

Maintenance of Laboratory Equipment

This section was included more for the sake of completeness than because of concerns peculiar to the microbiology laboratory. Most lab equipment in the microbiology laboratory is subject to the standard validation practices of IQ, OQ, and PQ. As is common, periodic calibration/maintenance may be required for the particular equipment based on its nature, and performance verification checks should also be performed regularly. The frequency will depend on characteristics and use of the equipment.

Laboratory Layout and Operations

The need for this section stems from the concern that too few facilities understand or plan for the separation of samples from a microbiological perspective. The success of a laboratory can be enhanced by the thoughtful separation of samples likely to have contamination from those that are expected to be sterile.

Training of Personnel

The chapter states plainly what should be common sense in recommending that microbiologists and managers in the pharmaceutical support lab should have academic training in microbiology or allied health sciences. This recommendation is in line with current best practice for biosafety as laid out in the 5th Edition of the Center for Disease Control’s (CDC) manual “Biosafety in Microbiological and Biomedical Laboratories (BMBL).” (4)

In addition to the recommendation that the microbiology staff have studied a relevant subject while in school, the proposed guidance chapter points out a fundamental link between training and the unit’s SOP system. It recommends that the SOP system should be comprehensive and serve as basis of the training program. This proposal also recommends that performance assessments be done periodically and should demonstrate competency in core activities of the lab.

Documentation and Maintenance of Laboratory Records

Like the section on equipment maintenance, this section was included only for the sake of completeness.

Interpretation of Assay Results

This section was initially entitled “OOS Investigations” it was renamed “Microbial Data Deviation Investigations” out of deference to the work underway by a PDA task force. However, during the writing process it became clear that the scope of this section was broader than merely investigations, and so the current title was settled upon almost by the process of elimination. A discussion of the inherent variability of microbiological data was necessary in this chapter. One view of good laboratory practices could be structured around determining practices that minimize variability in the microbiology lab. However, because we are dealing with such low numbers on plates (frequently less than 20 CFU/plate) and the real opportunities for human error in tests that may run over a month to completion, the microbiologist must always be aware of the role that random chance has in the data and be on guard against over-interpreting the results of a study.

This section of the proposed guidance document is intended to be both a discussion of the limitations of compendial test methodologies and a guide to developing methods of investigating test failures. It discusses the difference between a test that has failed, a test that should be invalidated and a test that should be repeated for confirmation.


The proposed chapter <1117> Good Microbiological Laboratory Practices” was developed in response to repeated requests from industry for guidance in this area. This chapter is meant to provide guidance to workers and to regulators in evaluating the operations of the QC microbiology lab.

This article is an updated version of an article by the author that originally appeared in the PMF Newsletter vol. 11 no.2 (2004).


  1. USP. 2006. <1117> Microbiological Best Laboratory Practices. USP 29 Suppl 2 pp. 3804-3807.
  2. USP. 2003. <1117> Good Microbiological Laboratory Practices. Pharmacopeial Forum 29(3):842- 850.
  3. USP. 2004. <1117> Microbiological Best Laboratory Practices. Pharmacopeial Forum 29(3):1713- 1721.
  4. CDC. 2007. Biosafety in Microbiological and Biomedical Laboratories (BMBL) 5th Edition http://www.cdc.gov/od/ohs/biosfty/bmbl5/ bmbl5toc.htm released to the web in February, 2007.


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