Microbiological safety cabinets: Best cleaning protocol

Published: 13-Apr-2023

What should you be doing to keep your Microbiological Safety Cabinets (MSCs) clean, and how often should you be doing it? Charis Hickey from Biopharma Group explains

Microbiological Safety Cabinets (MSCs) are a vital part of many research labs, often with multiple users working in the same cabinet over the course of the day, running different tests and/or experiments. This means that having stringent cleaning protocols for these workhorses of the lab, is crucial.

Microbiological safety cabinets: Best cleaning protocol

Incorrect, or ineffective cleaning of a cabinet can potentially lead to cross-contamination no matter how careful users are. This can create a situation whereby revenue is lost due to downtime of the cabinet, accuracy of tests and/or samples could be jeopardised, and the efficacy and product/user safety is affected. Additionally, it can also lead to costly product recalls or, for a company, perceived reputational damage. Improper cleaning methods can also conceivably reduce the lifespan of the safety cabinet, thus providing a lower return on investment (ROI).

An area often overlooked in terms of how to care for it, is the stainless steel within your safety cabinet. Stainless steel is not corrosion-proof, it is corrosion-resistant and owes this resistance to a thin, chromium oxide film on the metal's surface. Therefore, cleaning practices and protocols need to have a balance between ensuring that the cabinet is clear of contaminants and maintaining the integrity of the surface.

No cleaning agent is 100% safe of course. If used inappropriately, some cleaning agents are too aggressive and therefore not recommended for use on lab equipment such as safety cabinets and fume hoods.

Some examples would be highly oxidative agents, strong acids, and highly concentrated salt solutions. Instead, as highly experienced in the airflow equipment field, we would recommend* disinfecting agents based on alcohol (70% ethanol or 70% isopropanol), or alternatively disinfecting agents based on QUATS (quaternary ammonium salts) as detailed below.

Before and after every application

Clean with 70% ethanol or isopropanol solution. Ensure this covers the worksurface and 10cm of the back wall including plug sockets as these are high touch points, but often missed from general cleaning practices.

If the SOP requires strong solutions such as Virkon to clean the surface then, after cleaning, wash thoroughly with pre-treated water ONLY. Water quality should be maintained between 50 Kohms-cm and 1 Megohm-cm (electrical resistivity). Feed water quality outside this range, may lead to surface damage.

At least once a week

Remove all 4 work surface trays and use a non-abrasive stainless-steel polish or mild detergent and non-abrasive cleaning pad to scrub all areas constructed of stainless steel. Be sure to thoroughly rinse the area after cleaning is complete.

Additional protection can be obtained by using products that can be implemented alongside your cleaning regime, such as the Bactiscan or Bactiscope (available from EIT International) which can instantly identify whether any unwanted bacterial or biofilm contaminants are still present, using unique wave-alternating UV light technology.

For laboratories, using ATP swab testing the Bactiscan and/or Bactiscope can make ATP testing more efficient and effective.


A microbiological safety cabinet should be serviced annually at a minimum, or every 6 months if a key piece of lab equipment is being used regularly. This will ensure that the cabinet airflow and HEPA filters are functioning as per BSEN:12469, making the cabinet and lab compliant for any regulatory audits and product pathway transparency.

Microbiological safety cabinets in containment level 3 or 4 (CL3 /CL4) laboratories should be tested, validated and decontaminated at least every 6 months, as recommended by Advisory Committee on Dangerous Pathogens (ACDP).

Assessing the integrity of the metallic surfaces is also possible using the MAG3 (also available from EIT International) this can highlight cracks, pinholes and general surface defects developed as a result of corrosion which could harbour unwanted contaminants. A handheld scanning unit that does not rely on dye penetrant methods could easily be incorporated into a servicing and maintenance programme.

Cleaning your safety cabinet should be as important as the experiments and tests you perform in it. By maintaining it regularly and following stringent cleaning protocols, you can benefit from several positive outcomes such as:

  • Reduced chance of cross-contamination
  • Compliance with applicable regulatory legislation is easier to achieve
  • The cabinet can work more efficiently
  • The lifespan of your capital equipment is extended, which means lower total cost of ownership and improved return on investment

Annex 1 revision

Contamination control is one of the focus items in the newly published “Annex 1” document under its Contamination Control Strategy which comes into effect from August 2023, demonstrating understanding and commitment to its growing importance. 

“The assessment of risks (hazards) across the entire manufacturing process (QRM), and having a coherent and comprehensive contamination control strategy (CCS) in response, are anchored firmly in the new Annex 1,” said 3idimension Cleanroom’s Principal Consultant, Conor Murray.

Whether you operate in a sterile laboratory environment or not, the need to meet compliance requirements will still apply, as such, moving to an operating model that has a clearly defined contamination control strategy that includes stringent cleaning protocols will only become even more critical.

You can obtain an early heads-up of the important changes that Annex 1 will bring to cleanrooms and associated controlled environments. from an authoritative source.

*Cleaning methods and protocols vary depending on the lab and the method we suggest here is based on our own experience and expertise.


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