LOGFILE No. 1/2013 - Pharmaceutical Microbiology Labs


Good practices for Pharmaceutical Microbiology Laboratories

A review of the WHO Guidance

by Tim Sandle

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In late 2011 the World Health Organisation (WHO) reissued Annexe 2 of its Technical Report 961 (“Specifications for Pharmaceutical Preparations”). The Annexe consists of a guideline entitled ‘Good Practices for Pharmaceutical Microbiology Laboratories’. The guidance for pharmaceutical microbiology laboratories was originally written in 2009.

The reason for the relatively fast revision came about due to concerns from WHO GMP inspectors who reported that aspects of the guideline appeared either open to interpretation or had proven difficult for some laboratories to understand.

The Good Practices document has some similarities with the USP chapter <1117> “Microbiological Best Laboratory Practices” and together the two chapters are of importance given that there only other significant regulatory document is the FDA inspection guide “Microbiological Pharmaceutical Quality Control Labs”, which is now a little out of date and was last revised by the FDA in 1993. With regard to European GMPs and compendia there is no equivalent guidance or pharmacopoeial chapter.


The WHO document has a relatively narrow scope in terms of the perceived activities of a pharmaceutical microbiology laboratory and the scope is certainly inwards, in terms of the way a laboratory is run, rather than focusing outwards on the activities which laboratory staff might undertake. For example, the document is concerned with viable microbiological environmental monitoring within the laboratory but not with the activities of microbiology staff going into process areas to take airborne particle counts and to collect viable monitoring samples. This seems a little limited since the case for monitoring in an unclassified laboratory is somewhat debatable and the latter is something which occupies the time of many laboratory staff.

The guide has a glossary at the front in which a relatively short number of terms are defined. Here there are definitions of ‘precision’ and ‘robustness’ but not of ‘environmental monitoring’ or ‘bioburden’. I am not altogether certain how useful this list is and the scope of the definitions is either vague or lacks sufficient detail to be meaningful. Take, for example, ‘reference cultures’: “Collective term for reference strain and reference stocks”

Either the reader knows what is meant by a reference culture and its purpose for quality control and in which case the definition is superfluous; or the reader does not know and in which case the definition is not very informative.

The first main section of the document discusses personnel: staff who should be working in the microbiology laboratory. Here the requirement is limited. The document states that testing should be carried out and supervised by staff with experience and who hold an unspecified qualification. Whilst this is important the document disappointingly does not state that staff should hold a degree in an applicable bioscience subject.

The document is useful, however, in stating the need for supervision and for authorised personnel for the release of results from the laboratory. The document also outlines some of the basic training required for staff including aseptic technique, serial dilutions, working with hazardous cultures, and colony counting. Although there is not a great deal of detail, the section is important because common agreement, nationally or internationally, on microbiology laboratory training is lacking.

The second substantive section concerns laboratory premises. In this part reference is made to the need for dedicated areas for laboratory equipment, layout for operations, the separation of laboratories from production areas, and controlled access to microbiology areas. Reference is also made to cleaning and disinfection of the laboratory, spillage policy and hand sanitisation.

There is one statement in this section about Sterility Testing which makes an incorrect assumption that isolators are not being widely used regarding the classification of the room in which sterility testing takes place. With the sterility test environment a note is made about clean air classification being annual. This is out of step with ISO 14644 which requires the ISO class 5 clean air device to be classified six monthly.

Reference to environmental monitoring of sterility test areas and the trending of results is made.

The third main section concerns the validation to test methods. This is a relatively short section compared with USP <1227>. The section sates that pharmacopoeial test methods “are considered validated” but that specific products, when used against compendial test methods, must be shown to be suitable in terms of recovering microorganisms. There is a reference to the use of alternative test methods with a generalised list of validation requirements.

The fourth section concerns equipment, in terms of maintenance and calibration. The guidance is for a documented programme, which is useful as some laboratories do not have a calibration procedure or clearly defined acceptance criteria. References are made to national calibration standards and the need to assess items like pipettors and laboratory timers.

There is also some useful guidance for setting calibration intervals by tracking the period of drift for instrumentation from normal operating conditions. Special emphasis is given to temperature monitoring devices and incubators, which are critical for culture based methods. There are also sections on autoclaves and balances. With the former, on the oft debated issue of whether biological indicators should be used for laboratory autoclaves, there is no mention.

The fifth section concerns reagents and culture media. With reagents, there is a reference for the need to assess shelf life. The part on culture media is longer and there is mention of both media prepared in-house and media purchased from a vendor. With regard to growth promotion, in keeping with most laboratories, the requirement is to test each batch. There is also a statement about testing each shipment, which some might regard as excessive. There is a further stipulation about assessing transport requirements. This latter point is something which is not always addressed.

The test requirements for culture media and the acceptance criteria are the same as the harmonised microbial enumeration chapters (USP <61> and Ph. Eur. 2.6.12). The preparation of media, in keeping with cGMP, is addressed as per any production batch manufacture.

The media section also includes a part on the resuscitation of microorganisms, which is quite useful.

The sixth section addresses reference materials and cultures. The advice for storing cultures, subculturing and limiting the number of passages is consistent with the pharmacopoeias.

The seventh and eighth sections overlap a little and address sampling and sample handling. With sampling, the need to test samples promptly and to keep chilled where appropriate is useful but there is little with regard to sampling methods and no mention of aseptic techniques. The part relating to sample handling describes rudimentary logging procedures.

The ninth section is very short and emphasises the importance of contaminated waste disposal. The tenth part is also brief and describes the importance of internal laboratory quality control (laboratory controls). This section really should contain more information and a description of laboratory deviations is clearly lacking.

The eleventh section is about testing procedures and does not go into any meaningful detail. The twelfth and final section addresses test reports and touches on the debate on reporting quantitative results: is it “not detected for a defined unit” or “zero”?

The WHO document is supported by some appendices on classifying different parts of the laboratory environment and some suggested maintenance periods for various items of equipment, which seems a little out of place to me as this would depend very much on the item, the manufacturer and the performance of the equipment in the laboratory.

Comparison of WHO, USP and FDA

The WHO document, despite some limitations, does stand as a useful adjunct to the USP chapter and the FDA inspection guide. To give an overview, I have highlighted similarities and differences in the table below.

Alert and action levels Yes No No
Aseptic techniques No In part No
Autoclaves Yes No No
Balances Yes No No
Cleaning and disinfection Yes No No
Contaminated waste disposal Yes No No
Contract test facilities No No Yes
Culture media: manufacturing Yes Yes Yes
Culture media: testing Yes Yes No
Deviations/OOS No No No
Environmental monitoring of micriobiolgy laboratory Yes No No
Equipment calibration Yes In part No
Equipment qualification Yes In part No
Laboratory design/premises Yes Yes  
Laboratory management    In part Yes Yes
Laboratory staff Yes Yes No
Method validation: alternative methods Yes No No
Method validation: pharmacopoeial Yes In part Yes
Microoraganisms: use in the laboratory  Yes Yes No
Microorganisms: reference cultures  Yes Yes No
Non-sterile product tests  No No Yes
Quality control  Yes No No
Reagents  Yes No No
Reference cultures  Yes Yes No
Sampling  Yes Yes No
Sterility testing environment (cleanroom)  Yes No Yes
Temperature monitoring devices  Yes In part No
Test procedures  Yes Yes No
Test records  Yes Yes Yes
Training  In part Yes No
Waste disposal  Yes In part No


The WHO document is a mixed affair. In some areas there is no mention of new technologies or the operation of commonplace technology like Laboratory Information Management Systems (LIMS); in other areas it lacks any detail (such as reagents), in others it provides unhelpful information (such as the parameters for alternative methods), yet in other cases it provides useful advice, especially in terms of laboratory equipment, or at least thought provoking material, as with the test requirements for culture media. It also shies away from, fortunately in my view, any references to saving time, money or resources. A quality based guide should focus on just that – best practice – and leave the budgetary aspects to other types of publications.

This assessment of the WHO guidance has been generally critical and this reflects the fragmented and inadequate nature of regulatory guidance on microbiology laboratories, where there is a paucity of regulatory guidance within GMPs and pharmacopoeias. The guidance which is available is lacking information or does not go into sufficient detail in order for the laboratory manager to rely on such documents alone in establishing best practices. Furthermore, the information presented within different guidances is often contradictory.

There is a clear void to be filled with the need for a clear, concise and practical guide to the operation of microbiology laboratories operating in a GMP environment.


Food and Drug Administration. “Guide to Inspections of Microbiological Pharmaceutical Quality Control Laboratories” (July 1993). At: www.fda.gov/ICECI/Inspections/InspectionGuides/ucm074914.htm

USP. 2010. <1117> Microbiological Best Laboratory Practices.
USP 33

World Health Organisation. “Good Practices for Pharmaceutical Microbiology Laboratories”. At: http://apps.who.int/prequal/info_general/documents/TRS961/TRS961_Annex2.pdf

About the Author:

Tim Sandle is Head of Microbiology at BioProducts Laboratory. He is currrently chairman of the Pharmig LAL Action Group and serves on the UK Blood Service Cleaning and Disinfection Committee. He has written and contributed to many papers and books, including "Microbiology and Sterility Assurance in Pharmaceuticals and Medical Devices" and "Cleanroom Management in Pharmaceuticals and Healthcare".

E-Mail: tim.sandle@bpl.co.uk

Web: www.pharmig.blogspot.com

This article is republished with permission from GMP REVIEW, VOL.11 NO.3 OCTOBER 2012.

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