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Contamination Control Through Cleaning and Disinfection: Reviewing the Strategy

A fundamental element of any contamination control strategy (CCS) is the control of bioburden to prevent microbial contamination of products and processes. A significant weapon in the armoury of tools available to the manufacturing site for microbiological control will be the site’s implementation of cleaning and disinfection processes in their classified areas.

As stated in the European Union Annex 1: Manufacture of Sterile Medicinal Products, the process is multi-staged. For example, cleaning is the removal of physical and chemical contamination, often in preparation for the subsequent application of a disinfectant agent, and disinfection is the use of a chemical agent with biocidal activity against microorganisms.

Cleaning and disinfection are vital to microbial control within a classified area. While it seems simple enough to soak surfaces with chemicals, the devil is in the details to achieve consistent and effective contamination control. Moreover, Annex 1 gives some significant detail on what is required regarding cleaning and disinfection, stating “The disinfection process should be validated. Validation studies should demonstrate the suitability and effectiveness of disinfectants in the… manner in which they are used and should support the in-use expiry periods of prepared solutions.”

Now, whether working on the construction of a new clean room suite, or working with an established operation, the validation of the disinfection process requires thought.

Disinfectant Validation Considerations

A scientist piping liquid into a petri dish

The first thing to understand is that there is no regulatory test method for performing disinfection validation in a pharmaceutical setting. United States Pharmacopoeia (USP) (1) chapter <1072> is commonly referenced. However, this is not a prescriptive method but rather a guidance document of points to consider. Another approach is to use standards such as the European Norms (EN). Disinfectant suppliers use these methods to demonstrate a biocidal label claim for a particular disinfectant.

Nonetheless, the methods are not designed with only the pharmaceutical industry in mind. Following these methods without adaptation to reflect pharmaceutical manufacturing conditions may lead to failures in the validation. Reputable disinfectant suppliers to the pharmaceutical industry are aware of these pitfalls, and they can readily advise you on the best methods to employ when looking to validate a new sanitizer and disinfectant.

Local environmental isolates must be used within disinfectant validation. A reference organism such as those from the American Type Culture Collection (ATCC) are considered to be the standard example of a particular species. First and foremost, it is a rare facility that finds its most common environmental monitoring isolates to be the same species as the reference organisms. Therefore, the site must include its commonly recovered environmental isolates in the disinfectant validation, as it is well understood that different strains within the same species will have different levels of sensitivity to chemical disinfectants.

How the disinfectant is used in a facility will also impact the disinfectant validation method. Three factors that will heavily influence the validation outcome include the test surface, the wet contact time and the method of disinfectant application, i.e., manual wiping.

Test methods suppliers use to create sanitizer and disinfectant label claims are based on using a single test surface; a coupon made of stainless steel. While stainless is a significant component of manufacturing equipment and facilities, it is not often the most prevalent surface compared to wall or floor materials. Different surfaces will have an impact on how a disinfectant will cover a surface. For example, a hydrophobic surface will reduce the surface area that disinfectant droplets will cover. These surface properties should be assessed ahead of validation.

The wet contact time used in the validation at a site must reflect how and where the disinfectant is used in practice. It is often desirable in areas of high airflow (where there is a significant drying effect) to have as short a contact time as possible to avoid repeated reapplications of disinfectant. Lack of consideration of actual conditions may lead to the development of unachievable wet contact times in a cleanroom setting.

An important element of a disinfection process is incorporating mechanical action when applying a chemical agent to a surface. Mechanical action, like wiping or mopping on a surface, may enable a disinfectant to increase the area of coverage by overcoming surface tension on hydrophobic surfaces. A correct application technique will also remove any potential physical or chemical contamination remaining on a surface. Finally, mechanical action can also aid in removing any organisms, such as bacterial spores, which a broad-spectrum biocide may not destroy.

Management of Disinfectant Residues

The EU Annex also discusses the importance of removing residues from surfaces – “For disinfection to be effective, prior cleaning to remove surface contamination should be performed. Cleaning programs should effectively remove disinfectant residues.” This includes residues created by the manufacturing process or from the application of certain disinfectants.

Residues need to be removed first for disinfectants to be effective. Chemical disinfection requires the direct contact between the microbial cell and the chemical molecules. Physical residues may prevent this contact either though shielding the microorganisms from direct contact, or through chemical deactivation from reactive substances in the residue. The residues themselves are also a potential risk to the manufacturing process, either as a source of physical or chemical contamination. A contamination control strategy should review the residue risks within the facility and determine the appropriate measures to manage them.

A gowned scientist wiping down a metal surface 

Rotation of Disinfectants

6 different spray bottles containing various ECOLAB disinfectant products

Use of more than one type of disinfectant has been a recommendation of Annex 1 for a long time. The Annex provides further information on a rotational strategy for disinfectant use but the current text in the Annex may lead to a degree of interpretation as to what this means – “More than one type of disinfecting agent should be employed to ensure that where they have different modes of action and their combined usage is effective against all bacteria and fungi. Disinfection should include the periodic use of a sporicidal agent.”

One simple explanation can be to rotate disinfectants relative to the organisms which are to be controlled. This should be based on which type of microorganisms represent a risk to the facility, process or products manufactured. To be clear, there is no regulatory requirement to rotate biocides with the same biocidal claims i.e., two bactericides, but to ensure the rotation addresses the relevant microbicidal needs.

For most sites rotational control will be against bacteria, bacterial spores, moulds and yeasts. Unless the site is working with living cells, then a virucidal product will not be required. A broad-spectrum biocide will be effective against everything except the most resistant of organisms – the bacterial endospore. Therefore, based upon risk, a good rotational policy will be to use a broad-spectrum biocide (as described above) rotated with a sporicide.

An additional benefit to be brought by simplifying the approach to rotation will be to reduce the number of disinfectants in use by a site. This will make management of the correct biocide rotation easier, reduce the risk of error, reduce the cost of disinfection and reduce the impact on the environment. If a site also selects low residue biocides as part of the rotational policy, this will also positively impact on residue management.

Contamination Control for Material Transfer

A critical chink in the armour of the cleanroom defences is the movement of goods and materials from the uncontrolled warehouse to the cleanrooms, and into highest classified areas. A well-defined transfer disinfection process will address the potential for contamination to enter critical areas or equipment such as isolators.

A good transfer disinfection process will cover two elements. The movement of routine items, for example consumables, gowning materials and monitoring equipment. The second part of the process is to manage the entry of non-routine items. Annex 1 recognises the contamination risk non-routine items pose and promotes disinfection to mitigate the risk – “Any unapproved items that require transfer should be pre-approved as an exception. Appropriate risk assessment and mitigation measures should be applied and recorded as per the manufacturer’s CCS and should include a specific disinfection and monitoring programme approved by quality assurance.”

A gowned up scientist spraying down a white cloth with a disinfectant spray 

Any assessment looking at the contamination risks of material transfer should consider the following factors:

  • Is a disinfection process in place? If so, are the selected disinfectants capable of covering the range of microbial contamination expected to be seen, including bacterial endospores?
  • Has the site determined the compatibility of the materials to be disinfected with the chemicals used?

Does the method of disinfection consider the flexible surfaces often seen, contact time in high airflow areas and the degree of manual dexterity and focus required? If the answer to these questions is to utilise the “spray and pray technique”, then there may be some gaps in the CCS.

Procedures and People

A gowned worker clearning a RABs system while another scientist looks on through an observation window

As with all aspects of GMP, documenting the cleaning and disinfection process will go a long way in demonstrating the site has control of the risks it has identified in its CCS. Standard Operating Procedures (SOPs) should detail the types of disinfectants used, methods of application and details such as contact time, rotation, and residue removal. For transfer disinfection the SOP should be able to differentiate the routine from non-routine items. Non-routine items should go through a prescribed risk assessment which includes cleaning, disinfection and any associated environmental monitoring.

As most readers will be aware it is people and their behaviours that represent one of the biggest risks to contamination in the cleanroom environment, especially from the microorganisms that are found on, in and coming off them. A fundamental part of managing human-borne contamination is the cleanroom gowning process and within that, correct hand hygiene.

Good hand hygiene practices should always start with washing of the hands with soap and water. Soap breaks down any grease or fats that will be present on the hands, representing contamination risks in themselves and providing a hiding place for microbes to shelter under. Hand washing should be prescribed in detail with visual guides available at the sink. A good template to use is the WHO (World Health Organization) hand washing guides.

Soaps and alcohol gels should be suitable for use in a cleanroom environment. They should not be scented or contain an attractive colourant. The alcohols should be of the correct concentration and be suitable for direct contact with skin. This is a very different formulation to the alcohol disinfectants used on gloves.


A site’s contamination control strategy forms the backbone of its planned defences against contamination. As shared in this article, good cleaning and disinfection practices form a significant element of this strategy, addressing contamination risks from people, materials and surfaces. Reputable suppliers of disinfectants should have the expertise to identify gaps within contamination control strategies for cleaning and disinfection, and to support remediation of those gaps. If the preparation of a CCS for cleaning and disinfection seems a daunting task, engage your supplier for support. Ecolab and Bioproducts Laboratory have collaborated on just such a task, with a published article “Opportunity mapping: Deploying risk analysis to improve transfer disinfection”, from Dr Tim Sandle in support (2). For more information, visit

Two gowned scientists at an observation window looking into a facility


Globally there are different terminologies in use for chemical agents that kill microorganisms, Annex 1 utilises the terms disinfection / disinfectant – however this may be applicable for the term’s sanitization/ sanitizer.


  1. United States Pharmacopeia (USP), Chapter <1072> Disinfectants and Antiseptics
  2. Opportunity mapping: Deploying risk analysis to improve transfer disinfection, Dr Tim Sandle, BP

About the Author

David KeenDavid Keen, is director of microbiology consulting services and validation with Ecolab Life Sciences and the current chair of Pharmig, the professional organisation promoting excellence in microbiology.

He is an environmental monitoring and investigation specialist, and expert in sterility assurance including sterile isolator operations, Pharma water systems and biofilm management.

He has long experience as a pharmaceutical microbiologist in the pharma industry and his experience includes sterility assurance for dose forms ranging from bulk API to small molecule sterile injectables.

He is well versed in dealing with regulatory inspections (MHRA, FDA, TGA etc), internal and external auditing, and working with customers to solve complex microbiological issues and devising the most efficient and robust cleanroom disinfection strategies.

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