Rethinking "Critical Aseptic": Balancing Contamination Control and Process Efficiency in Gene Therapy Manufacturing

In the highly manual world of gene therapy manufacturing, the balance between contamination risk and operational efficiency is a delicate one. The complex nature of these products, combined with stringent regulatory expectations for aseptic processing, demands a more nuanced approach, especially when determining when and where to apply the designation of “critical aseptic.”

 

A Narrow Definition with Broad Implications

Traditionally, regulatory guidance and industry practice have centered the concept of "aseptic" processing around the final, post-filtration stages of manufacturing. FDA’s Sterile Drug Products Produced by Aseptic Processing – Current Good Manufacturing Practice defines a critical area as one “in which the sterilized drug product, containers, and closures are exposed to environmental conditions that must be designed to maintain product sterility” (FDA, 2004).

Similarly, EU GMP Annex 1 describes aseptic preparation/processing as “the handling of sterile product, containers and/or devices in a controlled environment in which the air supply, materials and personnel are regulated to prevent microbial, endotoxin/pyrogen and particle contamination” (Annex 1, 2022).

However, this downstream focus overlooks a critical fact: in gene therapy manufacturing, some of the highest risks of microbial contamination exist upstream, well before sterilizing filtration.

 

The Risk Upstream

Due to the nature of gene therapy products, traditional sterilization methods such as heat, radiation, or ethylene oxide are not applicable. Instead, sterile filtration serves as the final sterility-assuring step. Yet, it’s upstream of this point, during cell culture and vector production, that the environment is most conducive to microbial contamination. The warm, humidified, and nutrient-rich conditions needed to grow host cells are also ideal for microbial growth.

Despite this, upstream manufacturing processes are often designated as “low bioburden” rather than “aseptic,” in part to reduce the complexity and cost of operating under stringent Grade A/ISO 5 conditions. While this may make sense from a logistical and financial standpoint, the decision must be weighed against the true contamination risks, not just the regulatory labels.

 

The Risk Hammock: A Visual Model of Real Risk

The concept of the “risk hammock”, as introduced by Sigma-Aldrich (MilliporeSigma), helps visualize this issue (MilliporeSigma, 2021). The idea is that microbial risk across a bioprocess is not flat or evenly distributed. Instead, when plotted, the highest points of risk often appear upstream and in cell culture, where conditions favor microbial ingress and growth.

The risk is then lessened during downstream purification steps, where nutrient-rich media is traded for buffers and a series of filtrations, conditions which are less conducive to microbial proliferation. Risk then rises again during sterile filtration and filling operations as these terminal steps in the process have the greatest potential to impact the safety and quality of the product.

This model encourages a shift away from over-focusing on final fill and filtration, and toward a whole-process perspective that identifies and controls contamination where it is most likely to occur.

Figure 1: Gene therapy manufacturing “risk hammock”

 

More Than a Designation: A Mindset

One of the most critical elements of this whole-process mindset is ensuring that contamination control principles are consistently applied throughout manufacturing, not just where formal aseptic designations exist.

That includes:

• Aseptic behavior: Not to be confused with “aseptic technique” (which applies to manipulations under Grade A air supply), aseptic behavior refers to actions and habits that prevent contamination (e.g., high standards of personal hygiene and cleanliness, proper gowning, frequent glove sanitization, minimizing movement, and maintaining spatial awareness) regardless of whether one is working in Grade A or a lower-grade area. These behaviors should be embedded into every individual and every process, regardless of designated criticality.

• Cleaning and disinfection: Cleaning and disinfection are more than “going through the motions”. These operations must be designed with the appropriate agents, tools, and textiles to accomplish their distinct purpose. Cleaning methods must be deliberate and designed for removal of gross contamination and residues. Disinfection must be thorough and performed consistently across all cleanroom grades. All surfaces, equipment, and environments must be managed with the same mindset: preventing contamination.

• Transfer disinfection: Materials entering controlled environments must be appropriately disinfected at every transition. Each transfer step, even in lower-grade areas, presents an opportunity for contamination to gain entry into the cleanroom. Manual transfer disinfection is a known vulnerability, and this risk should be addressed with the implementation of a highly effective sporicidal disinfectant and robust operator training and awareness.

Even in Grade C or D environments, these principles are vital. In the absence of terminal sterilization, the quality of the final product is only as strong as the weakest control applied at any point in the process.

 

Practical Considerations for Gene Therapy Manufacturing

Modern gene therapy manufacturing increasingly relies on sterile, single-use technologies to reduce cleaning burden and cross-contamination risks. Still, no system is foolproof. The risk of contamination is influenced not just by equipment and consumables, but by human intervention, material flow, and environmental control.

By applying a contamination control mindset consistently across the process, manufacturers can protect product quality while balancing efficiency. That means assessing microbial risk early, training staff beyond formal aseptic technique, and ensuring facility and procedural design supports contamination control principles, regardless of room classification.

Using a risk-based approach guided by concepts like the risk hammock, manufacturers can prescribe appropriate controls to areas of the highest risk, rather than relying solely on formal designations like “critical aseptic” or “low bioburden”.

 

A Call for Rethinking

Rather than rigidly assigning “critical aseptic” designations based solely on regulatory definitions tied to final fill, manufacturers of gene therapies should adopt a risk-based approach. This approach should recognize:

• The heightened contamination risks upstream, especially in cell culture.

• The inability to terminally sterilize gene therapy products by traditional methods.

• The importance of foundational contamination control principles throughout the entire process.

This shift in perspective is not about loosening standards, it’s about aligning resources, behaviors, and environmental controls to where the risks truly lie rather than treating aseptic designation as a switch flipped only at the point of sterile filtration.

Adopting a whole-process contamination control strategy, grounded in aseptic behavior, robust cleaning and disinfection, and intelligent risk-based decision-making, allows manufacturers to protect product quality while maintaining operational efficiency.

Are you wanting to discuss more ways to add contamination control measures in your gene therapy manufacturing facility? Contact your Sales Representative to learn more about our contamination control assessments.

 

References: 

1. U.S. Food & Drug Administration. Guidance for Industry: Sterile Drug Products Produced by Aseptic Processing – Current Good Manufacturing Practice. 2004. https://www.fda.gov/media/71026/download 

1. European Commission. EudraLex Volume 4 – EU Guidelines for Good Manufacturing Practice for Medicinal Products for Human and Veterinary Use: Annex 1 – Manufacture of Sterile Medicinal Products. 2022. https://health.ec.europa.eu/system/files/2022-08/202208_annex1_en_0.pdf 

1. MilliporeSigma. Bioburden Control in Bioprocessing: Building an Aseptic Control Strategy That Protects Product Quality. 2021. https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/pharmaceutical-and-biopharmaceutical-manufacturing/bioburden-aseptic-control-strategy/bioburden-control-bioprocessing