The "Low Bioburden" Myth: Why Aseptic Process Simulations Are Mandatory in Open Filling Lines

Even when drug substance processes are classified as “low bioburden,” aseptic process simulations (APS) are not optional, especially when open filling operations are performed in Grade A laminar airflow (LAF) zones with a Grade C background.

Regulatory bodies such as the FDA and EMA consistently enforce the requirement for media fills across all aseptic processes. Ignoring this mandate can, and frequently does, lead to warning letters, recalls, or import alerts. 

This article explores the critical role of APS for low bioburden drug substances in open processing scenarios, referencing EU Annex 1 (2022), PDA Technical Report 90 (TR90), ICH Q9(R1), and key FDA enforcement cases. 

Isolator-Based Aseptic Handling in a Controlled Environment.

Regulatory Position: APS is Not Optional in Aseptic Filling

EU GMP Annex 1 (2022) is crystal clear on this point: 

“Periodic verification of the effectiveness of the controls in place for aseptic processing should include an APS using a sterile nutrient media and/or surrogate in place of the product” and should “imitate as closely as possible the routine aseptic manufacturing process and include all the critical manufacturing steps” (Annex 1, Section 9.32–9.33). 

Annex 1 further clarifies that the principles apply not just to finished sterile products but also to sterile product types and low bioburden biological intermediates: 

“...some of the principles and guidance…may be used to support the manufacture of other products that are not intended to be sterile such as certain liquids, creams, ointments and low bioburden biological intermediates…where the control and reduction of microbial, particulate and endotoxin/pyrogen contamination is considered important.” (Annex 1, Scope, Section 1). 

Open processing, by its nature, carries high contamination risk due to operator proximity, interventions, and equipment exposure. Thus, APS is required to simulate and verify the process under actual conditions, including worst-case interventions. 

Low Bioburden ≠ Low Risk 

A “low bioburden” classification upstream does not mitigate contamination risks introduced during downstream aseptic handling. Microbial ingress during open filling is primarily driven by: 

• Operator interventions 

  
  

• Airflow disruptions 

• Surface contamination

• Improper gowning or technique 

  
  

Aseptic process simulations help verify not just the process, but also operator performance. 

As emphasised in PDA Technical Report No. 90: 

“Aseptic operator trainees should only be permitted to perform interventions upon successful participation with a process simulation.” 

ICH Q9(R1): Risk-Based Doesn’t Mean Risk-Ignored 

ICH Q9(R1) on Quality Risk Management encourages the application of scientific knowledge and evidence to support decision-making. It does not permit bypassing control measures based on assumptions or incomplete rationale: 

“The level of effort, formality and documentation of the quality risk management process should be commensurate with the level of risk.” (ICH Q9(R1), Section 3).

In other words, if the risk of contamination during open filling is high, and it is, then a highly formal, documented risk control (like APS) is required. 

What the FDA Has to Say: Real-World Warning Letters 

Numerous FDA warning letters underscore that media fills are expected and must simulate all aseptic operations, even for intermediates or low bioburden processes. 

📌 Daewoo Pharmaceutical Co., Ltd (2025) 

Cited for failing to ensure that media fills reflected actual commercial operations, undermining confidence in the aseptic process. 

“Your media fills failed to accurately simulate commercial operations.” 

📌 Staska Pharmaceuticals, Inc (2025) 

Cited for incomplete simulation of challenging operational conditions during media fills.  

“Your media fills were not performed under the most challenging or stressful conditions.” 

📌 Aspen Pharmacare Holdings Limited (2025) 

Flagged for poor aseptic practices and lack of thorough operator assessment. 

“In 2022, your firm identified contamination in two media fill batches…You identified the root cause as poor aseptic behaviour…Your firm did not perform a sufficiently comprehensive evaluation of aseptic behaviour of operators as part of this recurrent trend.” 

These cases make it clear: the FDA expects media fills to comprehensively represent all aseptic handling, including that of low bioburden substances. 

PDA TR90 & CCS Principles: Media Fills as a Control Pillar 

PDA TR90 reinforces that aseptic process simulations are an essential element of personnel qualification and cleanroom behaviour oversight. APS supports operator training, qualification, and behavioural assessment by: 

• Simulating real production tasks and interventions under expected operating conditions 

  
  

• Reinforcing good aseptic technique and identifying poor practices 

  
  

• Supporting regular retraining and qualification based on performance 

  
  

Media fill outcomes, observation programs, and operator qualification trends should feed back into the site’s contamination control strategy and overall risk evaluation process. 

When Exemptions Don't Apply

Some facilities may attempt to justify the absence of APS using arguments such as: 

• Closed filling systems (but still allow open setup or sampling) 

  
  

• Sterile filtration as a final step 

  
  

• Historical process performance 

  
  

These arguments fall short under regulatory scrutiny unless every risk is scientifically justified, and mitigated by validated controls. As Annex 1 notes: 

“Processes, equipment, facilities, and manufacturing activities should be managed in accordance with QRM principles…Where alternative approaches are used, these should be supported by appropriate rationale, risk assessment and mitigation, and should meet the intent of this Annex.” (Annex 1, Section 2, Principle).

So, What Are Your Options?

If you're performing open aseptic filling of a low bioburden drug substance, here are the four realistic options to remain compliant: 

Option 1: Close the Process

Fully enclose the process using sealed, closed systems with sterile transfer and filtration. 

Pros: 

• Eliminates need for APS if no open handling occurs 

• Minimizes human intervention and contamination risk 

  
  

Cons: 

• High initial CAPEX (engineering redesign, new equipment) 

• May not be feasible for all products or facilities 

• Still requires validation and risk assessments 

Option 2: Use Isolators or RABS 

Implement isolator or Restricted Access Barrier Systems to separate operators from product during filling. 

Pros: 

• Substantially reduces risk of contamination 

• Allows for better control and reproducibility 

• Viewed favourably by regulators (Annex 1 encourages use) 

  
  

Cons: 

• Still requires APS 

• High cost and complexity to install and qualify 

• Requires rigorous decontamination cycles 

Option 3: Perform APS (Media Fills) 

Conduct well-designed aseptic process simulations that replicate the worst-case production scenario. 

Pros: 

• Meets regulatory expectations explicitly 

• Demonstrates validated operator technique and process control 

• Low relative cost vs. facility redesign 

  
  

Cons: 

• Operationally burdensome 

• Requires microbial incubation infrastructure and sterility evaluation 

• Must be repeated periodically (e.g., semi-annually) 

Option 4: Build the Best “Defence Package” Possible 

Develop a science-based CCS and QRM framework showing how your process meets or exceeds Annex 1 intent without APS. 

Pros: 

• May delay need for APS in edge cases 

• Could be viable for niche products (e.g., ATMPs, intermediates not administered directly) 

  
  

Cons: 

• Very high burden of proof 

• Requires in-depth risk assessments, barrier justification, operator training, and robust EM data 

• Still likely to attract scrutiny without APS 

APS Is Still the Gold Standard

Open filling in a Grade A environment with a Grade C background, even for low bioburden APIs, is inherently high risk. Aseptic process simulations remain the gold standard for validating sterility assurance.

Unless you can close the system or implement isolators/RABS, you are obligated under both EU Annex 1 and FDA CGMPs, to perform APS.

Skipping this step is not only risky for patients, but for your compliance status as well. 

📌 Need help designing or remediating your contamination control program? 

Pharmalliance Consulting Ltd offers hands-on support, training, and gap assessments to ensure your aseptic operations are regulatory-ready and quality-driven. Get in touch with our team of contamination control experts to start your compliance journey today.