Contamination Control

Root Cause Analysis - Contamination Control Plan Development of a contamination control plan is critical to the success of aseptic, terminal sterilization and non-sterile manufacturing facilities.  This is most obvious in the aseptic arena, where the FDA has issued clear regulatory guidance on the need for control of contamination at all stages of the process.  What is less obvious is the even greater need for a plan to address contamination control in non-sterile manufacturing.  This need only becomes obvious after a problem has arisen, frequently a problem in contamination control that requires product recall.  The challenge in non-sterile production is different from that in aseptic production, of course.  In aseptic production we try to exclude all microorganisms from the finished product, in non-sterile we wish to control the types and numbers of microorganisms in the finished products.  Recent regulatory action has extended this consideration even into the realm of personal care products (cosmetics, toiletries and soaps).

Historically, diverse markets such as pharmaceuticals, medical devices, diagnostics and personal care products have operated under very different CGMP.  However, the considerations for contamination control are similar and can be approached from the perspective of root cause analysis.   This type of “Cause and Effect” diagram can be an excellent learning tool for the contamination control team as well as leading to valuable insights in the determination of likely routes of contamination after the fact, but can also be used as a proactive learning tool for the development of the Contamination Control Plan.  For those more comfortable with Six Sigma procedures this can be revisited as an Ishikawa Diagram.   The main point here is to identify, and come to agreement, on the likely causes of potential problems.

A more traditional proactive approach risk management might be through use of FMEA (Failure Risk Mode Evaluation Analysis) which can be extremely useful in determining the most important aspects of control for your process.   Let the experts at the Microbiology Network assist your company in developing a comprehensive contamination control plan that will provide consistency across your facilities, as well as a solid basis for the control of chemical and microbiological contamination in your finished products.

Areas to address

Phases of Manufacturing Operation

  1. Commissioning and initial start-up
  2. Ongoing Operations
  3. Shut-down for regular maintenance
  4. Start-up after scheduled shut-down

These phases will not have the same level of contamination control. In fact, the third and fourth phases may well have different levels of control to be addressed. A good plan will discuss the concerns specific to each of these phases.

This program, and the protocol governing the program, are essential documents useful in documenting the rationale and methods used to accomplish three tasks:

  • Minimizing the bioburden throughout the manufacturing processes
  • Minimizing the level of batch residual cross-over contamination
  • Minimizing the level of cleaning material residual contamination

Validated methods

All measures of bioburden in a facility will be indirect. We cannot count bacterial cells on a surface or in the air. We must transfer the microorganisms to an agar plate (or some other mechanism) and count colony forming units. If we make the assumption that the transfer of microorganisms from the air or from a surface to agar is consistent, then we can use these numbers to estimate trends over time. This assumes that the nutrient agar is capable of growing the microorganisms to visible colonies. As residual disinfectant on a surface may impede the growth of microorganisms, neutralizers are frequently incorporated into the growth media (Dey-Engley Agar, MCTA, etc.).  The Contamination Control Plan should describe the sampling methods used, and how these methods are to be validated for the conditions of use.

The facility should be disinfected regularly using validated sanitizers and sporicides. The contamination control plan should describe the methods for testing and rationale for acceptance of materials to be used in the ongoing program of disinfection. The plan should ideally describe the in vitro or laboratory tests to evaluate the sanitizers, including the identification of the most resistant microorganisms found in the facility as well as the most difficult-to-disinfect materials in the facility. This is also where the method for on-going evaluation of the sanitizers based on environmental monitoring data will be recorded. The choice of disinfection regimens should be reevaluated annually, and the contamination control plan should describe how this evaluation will occur.

It is also critical to have appropriate microbiological methods for the relevant specifications – plate counts under 20 CFU are notoriously unreliable.  Traditionally the “countable range” for a standard sized petri dish is 25-250 (or 30-300) CFU/plate.  These lower limits (Limits of Quantification) are routinely ignored when setting product and environmental specifications, sacrificing accuracy and precision.  Similarly, the upper limit (250 or 300 CFU/plate) are set for particular microorganisms on standard sized plates, smaller plates or organisms that produce larger colonies will have lower numbers as there upper limit, requiring dilutions to as appropriate to measure the same specification.

Know the enemy

A successful Contamination Control Plan is geared to providing the most useful information on the microorganisms present while at the same time showing fiscal responsibility. The FDA aseptic processing guidance document recommends genetic identification of all organisms isolated from the manufacturing environment on a regular basis. This is a laudable goal, but few of us have anything near the required budget to accomplish this task, and in all honesty it is reasonable to wonder if it is really necessary. The numbers of CFU from validated sites (viable air and surface, non-viable) is sufficient to provide a measure of the state of control of the facility. However, periodic cataloging of the resident microflora will provide you with a good check on the continued effectiveness of the disinfectants in use. Shifts of bioburden to spore forming microorganisms will be strong evidence of the need for use of a sporicidal agent. Occasionally, this effort will also pick up shifts among non-spore-forming organisms – this is not due to “resistance” but rather ecological shifts towards species more naturally resistant to the disinfectant in use.

The considerations in the non-sterile facility are similar, as we need proof that the sanitization program used is effective and the regular use of sporicidal agents appropriate.  The contamination control plan must address how the sanitization program will be monitored for efficacy.

Control incoming bioburden

The first step in any control program is to control contamination at the very beginning of the process. This includes raw materials (excipients, API, water, etc) and the primary containers. All materials should be tested for incoming bioburden against documented acceptance criteria. Part of the incoming bioburden will also be any water used as an excipient to the process.   The GMPs for pharmaceuticals, biologics, medical devices and diagnostics all provide instruction on this point.

Appropriate gowning

The gowning methods and materials are of critical importance to minimization of contamination.   The primary source of contamination in most controlled areas will be the personnel and the Contamination Control Plan must address this whether it is designed for aseptic gowning procedures or protection of personnel in non-sterile manufacturing facilities.   All personnel should be well-trained in appropriate gowning practice and behavior. The Contamination Control Plan should describe the rationale for the level of gowning chosen, the frequency of gown cleaning, behavior and the acceptable gown materials for the type of manufacturing process.


Operator training is critical to contamination control. No supervisor can be present at all locations at all times. Each operator must be aware of his or her role in contamination control and how to minimize the risk to batch integrity.   Minimal skill sets in relation to product protection and sampling should be described by job function in the Contamination Control Plan.

Controlled Environments

Control and monitoring of the environment is another critical element of the contamination  control plan. Large portions of this can be addressed by the corporate Environmental Monitoring Master Plan (which provides rationale and consistency for a single EM  philosophy across the different facilities of the corporation) or the site Environmental Master Plan (which provides consistency and detailed instruction for the various manufacturing buildings at a given site).  However, the Contamination Control Plan should cite the relevant documents and their role in contamination control.

The appropriate Environmental Monitoring (EM) plan for non-sterile manufactures and for API manufacturers is not well-defined from a regulatory sense. There are no strong recommendations such as those seen for the environmental monitoring of aseptic facilities; however the absence of regulatory guidance is not the same thing as the absence of need for the activity. EM is useful for determining the state of control of the facility and so is an important part of the monitoring program for all manufacturers.

Validated Sanitization and Sporicidal Procedures

The efficacy of the sanitizers and sporicides used in the program must be demonstrated in a study designed to test their efficacy on the materials of construction and against resident microorganisms found in the facilities governed by the Contamination Control Plan.  This can be done optimally in a four-step process:

  1. Suspension test of efficacy
    This is a screening effort using your candidate agents against lab strains of indicator organisms as well as a variety of the microorganism species found in your facility.  The goal of this assay is to determine the “most resistant” microorganism(s) for the next step.
  2. Coupon study
    Using the representative organisms (gram positive, gram negative, spore former, yeast and mold) and organism(s) identified in the previous study, test the efficacy of the sanitizing agents on coupons of materials found in the facility.  The purpose of this test is to demonstrate efficacy on these materials using the appropriate application procedures.
  3. “Mock” Sanitization Study
    This study provides real-world evidence of efficacy.  Let a representative room go untouched for a period of time to become “contaminated”.  Take bioburden samples throughout the room, then sanitize the surfaces and repeat the bioburden sampling.  The samples taken after cleaning should be far less contaminated than the first set.
  4. Confirm from Environmental Monitoring
    The final step in validating the sanitization program will be ongoing evidence that the program allows the facility to operate in a state of control.

Well-defined and Understood Manufacturing Processes

The manufacturing process should be evaluated for its potential to limit or eliminate bioburden. The two common methods for performing this is either a HACCP-type or a FMEA approach. The use of organic solvents, heat, or other inhospitable activities can greatly reduce bioburden of a process. The contribution of compression (and associated shear), for example, should be evaluated for a potential reduction in risk of excessive microbial contamination, The contribution of the finished product water activity should also contribute to this analysis.  Process bioburden reduction steps shoudl be factored into the Contamination Control Plan on a  process-by-process basis.

Of particular importance in this evaluation for the potential for microbial contamination of the process are cleaning steps, equipment hold times, HVAC, control level of environments for critical tasks, open-system vs closed-system operations, and bioburden monitoring (among others specific to your process). As an example of the importance of the bioburden control point issue, there is a strong regulatory expectation in Europe that products sterilized by filtration should have a pre-filtration bioburden of not more than 10 CFU/100 mL immediately before the sterilizing filter (or be subjected to dual filtration in series).

Finally the Contamination Control Plan should cite the need clear SOPs on all aspects of manufacturing, monitoring and control. These SOPs are critical for training, documentation and batch release.

Minimization of Batch Residual Cross-over Contamination

The contamination control plan should also address the potential for a batch to be contaminated by material from the previous batch manufactured using that equipment. Obviously, the contamination control plan should describe the methods by which this likelihood is minimized.

The concern over batch residual cross-over is most relevant when there is more than one product manufactured at a site. This concern has little to do with the sterility of the finished
product, and is relevant to sterile and non-sterile manufacture alike.

Minimization of Cleaning Material Residual Contamination

Validation of cleaning procedures is essential to demonstrate not only that the cleaning procedure effectively cleans and sanitizes the manufacturing equipment, but also that residual cleaning material is removed to prevent contamination of the next batch manufactured.

The Microbiology Network

The Microbiology Network can assist in all aspects of contamination control.  Our network of internationally-recognized experts will assist in developing your Contamination Control Plan as a proactive step to prevent issues, or as part of remedial activities to correct a situation recently brought to light.