Wednesday 17 February 2021

Microbiological Characterisation during routine operations and reference data through start up when establishing microbiological control and qualifications of the control state


Microorganisms are found in pharmaceutical ingredients, water for pharmaceutical use, the manufacturing environment, intermediates, and in finished products. Microbiologists are frequently required not only to count the number of “colony forming units” (CFU) but also to identify the contaminants in order to assist in product investigations and environmental monitoring excursions. The microbiologist should understand the typical profile of microorganisms found in the facility ('microflora') for different conditions, including[i]:


a) Start-up, following shutdown or maintenance

b) Routine operations


With these, the profile for different grades of cleanrooms and cleanrooms used for different activities (such as a wash-bay compared with an autoclave preparation area) should be noted.


For a new facility, extensive environmental monitoring will allow for the 'norm' to be established. Routine environmental monitoring can then be used to track whether this 'norm' is maintained and variances from the norm may indicate an out-of-control situation.


A change in profile may lead to a review of:


a) Cleaning and disinfection,

b) Maintenance of HVAC systems,

c) Changes with personnel behaviours and practices,

d) Helping with corrective and preventative actions

e) In relation to non-sterile products, when the potential for the organism to survive in a process or to cause spoilage of the product is taken into account.


Although each facility is different, some general patterns for cleanrooms will be[ii]:


·         An association between the microorganisms commonly found in cleanrooms and those which are transient to (short-term or long term-residents on) human skin. Here the Micrococci and Staphylococci dominate.

·         In addition, other types of microorganisms present in cleanrooms, such as Bacillus spp. or Corynebacterium spp., are those present in soil. Such microorganisms may be transferred into the cleanrooms via personnel, dust, and material transfer.

·         Occasional, low-level incidences of microorganisms resident within the human body can also be detected.

·         In lower-grade cleanrooms, where there is a water source, some microorganisms associated with water systems will be detected, such as Pseudomonads (albeit often in relatively low numbers; otherwise the cleaning and sanitization regime may be considered to be ineffective).


Although common types of microorganisms have been outlined, each facility will vary due to[iii]:


a) Cleanrooms

·         Cleanroom types and uses

·         Grade, temperature and humidity

·         Geographical location

·         Gowning requirements

·         Certain locations of the body are more likely to release organisms than others


b) Microbial identification method

·         Phenotypic or genotypic

·         Databases [size, orientation (clinical or industrial)


e) Periodic reclassification of microorganisms


f) Limitations of environmental monitoring methods


g) Culturability (some research suggests that less than 10% of bacteria found in cleanrooms are culturable)


h) Seasonality and time of sampling


Therefore it is incumbent upon the microbiologist to understand, to profile, and to trend their own facility.

[i]Sandle, T. (2011): “Environmental Monitoring.” In Saghee, M.R.; Sandle, T.; and Tidswell, E.C. (Eds.): Microbiology and Sterility Assurance in Pharmaceuticals and Medical Devices, Business Horizons, New Delhi,, India, pp. 293-326

[ii] Sandle, T. (2011): “A Review of Cleanroom Microflora: Types, Trends, and Patterns,” PDA J. Pharm. Sci. Tech., Vol. 65, No. 4, July–August 2011, pp. 392-403

[iii] Halls, N. (2004): “Effects and Causes of Contamination Control in Sterile Manufacturing.” In Microbiological Contamination Control in Pharmaceutical Cleanrooms; Halls, N., Ed.; CRC Press: Boca Raton, FL; pp 8 –12

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

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