Biosafety/Biocontainment Plan Guidance: Appendix 1

Principles of decontamination, sterilization, and disinfection


Decontamination can include a number of processes that render an area, device, item, or material safe to handle (i.e., safe in the context of being reasonably free from a risk of disease transmission). The primary objective is to reduce the level of microbial contamination so that infection transmission is eliminated. The decontamination process may include a cleaning step prior to disinfection or sterilization.[1]


Cleaning is a process that can be an important adjunct in the decontamination process by removal of organic and inorganic materials from objects and surfaces prior to sterilization or disinfection. This process can remove a large number of microorganisms as well and the organic matter protecting them. Cleaning is normally accomplished manually or mechanically using water with detergents or enzymatic products.  Liquid for cleaning should be treated as liquid biohazardous waste.


Some chemical germicides used as disinfectants do, in fact, kill large numbers of spores, though high concentrations of the chemical germicides and several hours of exposure may be required. Non-sporicidal disinfectants may differ in their capacity to accomplish disinfection. Some germicides rapidly kill only the vegetative forms of bacteria such as staphylococci and streptococci, some forms of fungi, and lipid-enveloped viruses, whereas others are effective against such relatively resistant organisms as Mycobacterium tuberculosis var. bovis, non-lipid viruses, and most forms of fungi.[2]

The effectiveness of a disinfection procedure is controlled by several factors, including:

  • Nature and number of contaminating microorganisms (especially the presence of bacterial spores)
  • Amount of organic matter present (e.g., soil, feces, and blood)
  • Type and condition of instruments, devices, and materials to be disinfected
  • Temperature
  • Time
  • pH
  • Water hardness
  • Other chemicals used (e.g., mixing with certain detergents)


Results from sterilization procedures, however, can only be expressed in terms of the probability of viable organisms surviving after a sterilization procedure.[3] A probability level of less than one in one million microbial survivors (10-6) after treatment is a commonly accepted measure of sterility. This is referred to as the “sterility assurance level.”[4]

Decontamination of Solid and Liquid Wastes

All laboratory waste materials, contaminated animal or plant materials, and personal protective equipment (PPE) that are contaminated with BSAT should be decontaminated prior to removal from BSAT registered containment areas. However, there are situations when equipment used for terminal decontamination such as autoclaves, incinerators, digesters, renderers, or effluent decontamination systems (EDS), are located outside of registered BSAT spaces.

If the solid waste decontamination area (e.g., such as autoclave rooms, digester or renderer rooms, and incinerator facilities) is not inside the containment barrier of the laboratory, an entity should ensure the following practices are in place (Note: The area would not need to be listed on an entity registration or separately registered as long as the area is not used for the storage of BSAT solid waste):

  • Ensure that a person who has FSAP approved access to BSAT (approved by FSAP to have access to BSAT subsequent to a FBI security risk assessment) transports solid BSAT waste.  For a Tier 1 BSAT, or material contaminated with a Tier 1 BSAT, the person also must be enrolled in the entity’s personnel suitability program.
  • Transport waste by FSAP approved staff using personal protective equipment (PPE) deemed appropriate for the agent or toxin as determined by a risk assessment.
  • Transport solid waste to the decontamination unit in leak-proof sealed containers. The outside surface of these containers must be decontaminated with an appropriate disinfectant before being removed from containment. Place the container in the decontamination apparatus.  The container must remain sealed until the decontamination cycle is completed.
  • Start the decontamination unit as soon as the material is placed in the unit. The FSAP approved person must confirm to his satisfaction that the decontamination cycle has begun. This person is not required to remain in the area during the entire decontamination cycle but only to be reasonably assured that the cycle has begun.
  • The FSAP approved person confirms that the decontamination cycle, using system settings validated to render the contaminated material non-infectious or non-toxic, has been completed according to system specifications.
  • Keep the decontamination unit on a maintenance schedule. Maintenance schedules usually include periodic spot-checks for problems, semi/annual service, and re-certification by a qualified technician.
  • Create a process for verifying all parameters of the decontamination cycle have been attained (e.g., recording tape, biological indicators, probes, etc.).
  • Maintain written documentation that the decontamination procedure is validated for the specific agent, toxin, and/or material decontaminated.
  • Maintain a chain of custody document for solid waste that leave registered spaces for decontamination.
  • Check if the decontamination apparatus is working properly and is adequately maintained.

The entity incident response plan should include a plan for material that leaves the laboratory to be decontaminated offsite and for material that remains in the building. Ideally, waste should not be transported through an unregistered area. If the entity has no other option, include a description in the entity’s incident response plan addressing how the entity will deal with a spillage or release. The plan must also include procedures for documenting unintended spills or accidents during transport. There is a requirement for the notification of the appropriate Federal, state, and/or local officials and first responders in the event of an offsite spill.

Ensure that procedures are in place for decontamination of personnel and the PPE worn by personnel responding to a spill. As needed, include medical surveillance after potential exposure to select agents and
toxins during the clean-up process.

Any departure from a standardized method protocol should be revalidated. The entity could validate the autoclaved decontamination method used with a biological indicator, such as Geobacillus stearothermophilus.

Liquid waste that is not decontaminated in the solid waste decontamination stream may be decontaminated by several means. Contaminated liquid from showers may be disinfected by chemical disinfectant following manufacturer’s specifications including purging the plumbing trap before and after the shower. Contaminated liquid waste may be decontaminated by holding in a container or sink with a chemical disinfectant for the appropriate amount of time. An EDS, while not required, may also be utilized if large amounts of liquid waste, such as liquid from showers and from animal holding facilities, are generated. If the entity has an EDS, the entity should conduct the following practices:

  • Restrict access to the EDS. Non-FSAP-approved staff or visitors should be monitored and allowed controlled access for official duties only.
  • Create and maintain written documentation that the decontamination procedure is validated for the specific agent, toxin, and/or material being decontaminated.
  • Validate any changes in standardized methods.
  • Keep a regular maintenance schedule. Maintenance schedules may include daily or monthly checks or regular service.
  • Validate the EDS system under actual in-use conditions that may include high levels of bioburden or high matrix content, such as in infected animal holding areas.
    • This may include use the solid waste decontamination process above for disposing of animal bedding and/or high volume of fecal matter.
  • Maintain training records that the EDS operation staff have been trained on how to respond to leaks and spills.
  • Inspect the pipe leading from the containment area to the EDS to ensure it is sealed at least annually. A double walled pipe is preferred.
  • Put procedures and structures in place to contain more liquid than the EDS system would process in the event a spill of the liquid from the EDS tanks (e.g. a berm surrounding the EDS tanks that holds greater volumes than the tanks).
  • Ensure that procedures are in place for the cleanup and decontamination of a spill from the EDS.

[1] Fraise, AP. (2004) Decontamination of the environment and medical equipment in hospitals. In Principles and Practices of Disinfection, Preservation and Sterilization, 4th edition edsFraise, AP, Lambert, PA and Maillard J-Y,p 565.

[2] BMBL, p 327

[3] Lambert, PA. (2004) Sterilization. In Principles and Practices of Disinfection, Preservation and Sterilization, 4th edition edsFraise, AP, Lambert, PA and Maillard J-Y,p 389.

[4] Baird, RM. (2004) Sterility assurance: concepts, methods and problems. In Principles and Practices of Disinfection, Preservation and Sterilization, 4th edition edsFraise, AP, Lambert, PA and Maillard J-Y,p 526-539.

Page last reviewed: September 9, 2020