December 11, 2017

Prepare for an FDA bioburden inspection

By Anastasia G. Lolas, M.Sc., President and Founder of Visionary Pharma Consulting LLC, former FDA reviewer and inspector

Not sure how to best approach a bioburden problem when an FDA inspection is imminent? Anastasia Lolas, former FDA Biologics License Application (BLA) reviewer and inspector focusing on microbiology, shares her expert tips.


Even with effective prevention, bioburden incidents can occur. A best-practices response will not only help you be prepared for any upcoming FDA inspection, it may also yield valuable insights to help improve processes and procedures.

Review, document, and prepare

First, address the problem early with a comprehensive review of data, investigation, root cause analysis, and risk assessment. Second, document these activities thoroughly, including all supporting data. Third, plan and execute corrective and preventive measures. Finally, prepare to present the approach, data, and conclusions to FDA inspectors.

Expectations from the FDA

Ultimately, the inspector wants to understand the “hows” and the “whats” of the incident. The FDA inspector expects to discuss:

  • What was the problem or event?
  • How was it investigated?
  • What were the results of the investigation?
  • What was the root cause of the incident?
  • What were the results of the risk assessment of the bioburden impact on the final drug substance, and affected lots?
  • What corrective and preventive actions (CAPA) were taken?
  • Were the implemented actions effective?
  • What was the disposition decision of the affected lots, and why?

If the facility is preparing for a pre-license or preapproval inspection, notify the FDA promptly about a bioreactor contamination issue, and work with the FDA to determine next steps. Additionally, the facility must be manufacturing the drug substance in the filed application during the inspection.

Finding the root cause

First and foremost, identify the organism or organisms. Identification points to the source of the organism. Is it of waterborne, environmental, or human origin?

The presence of bacterial endotoxins points to waterborne Gram-negative organisms. A waterborne organism points to biofilm, inadequate cleaning, or inadequate practices for managing cleaned equipment, water hoses and any other aqueous solutions.

A Gram-positive sporeformer (e.g., Bacillus) or mold is of environmental (e.g., soil) origin. These organisms ingress into cleanrooms through transfer of materials, personnel, and equipment. The spores then ingress into the process through contact with the materials, equipment, personnel, and environment. The presence of these organisms may also indicate inadequate disinfection practices. Spores are resistant to typical disinfectants and require a sporicidal application.

While a complete investigation may fail to definitively identify the true root cause, it is important to consider all potential entry points and contributing causes.

Extent of microbial contamination

It is essential that the investigation include non-routine sampling of several surfaces to determine the full extent of the contamination. For example, if bioburden is found in the eluate from a column, swab the column on various locations, particularly at the column boundary. This is an area that many companies fail to address by not sampling enough to identify the cause and extent of the problem.

Perform a historical review to identify any similar issues in the past. Review the maintenance history of the implicated equipment as well, including any associated change controls, corrective actions, related equipment, environmental monitoring data, equipment and walk-down inspections, and automation sequences.

Assessment of potential impact on drug substance

Identify and assess all batches affected by this problem. One of the most common FDA 483 observations is that investigations were not expanded to include other batches, and investigations did not capture all affected batches. A comprehensive risk and impact assessment of drug substance and lot disposition will include:

  • Evaluation of the organism, its significance, pathogenicity, ability to produce toxins, endotoxins, virulence factors, metabolites, and by-products.
  • Assessment of bioburden entry downstream of the location where the problem was detected, and the potential presence in the drug substance and drug product.
  • Assessment of the downstream presence of metabolites and toxins, and potential presence in the drug substance and drug product. This includes evaluation of whether toxins, endotoxins, and metabolites can be removed adequately by the chromatography and filtration steps.
  • Downstream assessments should include all in-process data, buffer solutions, filtration steps and filters, and factors such as hold times that may allow for proliferation of the organism and production of metabolites.
  • Assessment of whether the identified metabolites can affect the stability of the drug substance over its shelf life.

Corrective and preventive actions, and lot disposition

Document all the assessments and the resulting corrective actions, preventive actions and effectiveness checks as well as the decision for lot disposition. Sometimes, additional studies may be needed to gather data to support the risk and impact assessments and final lot disposition. Thorough discovery and disposition of all affected lots is a critical final step in preventing potentially contaminated or sub-potent drug products from reaching the market and patients.

A valuable opportunity

Utilizing the findings to evaluate identical or similar equipment at the site and at other company sites will identify improvement opportunities. Implementing identified improvements in maintenance and operation practices globally will prevent and reduce the risk of future bioburden incidents throughout operations.

Make the inspector’s job easy

Present all events and data in a clear and logical way. While an FDA inspection may not be pre-announced, having well organized and thorough documentation on hand will facilitate clear communications. Take the opportunity to rehearse your presentation. Bioburden incidents are high on the inspectors’ lists and are usually selected for review during an inspection.

Remember, you share a goal with the FDA: the safety, purity and potency of the drug you bring to market. Approach any FDA inspection with a spirit of cooperation and transparency. A thorough investigation will result in effective corrective and preventive actions that can help you prevent future bioburden incidents.

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