Bridging Regulatory and Technical Challenges in Continuous Manufacturing of Biologics

The biopharmaceutical industry is experiencing a transformative shift from traditional fed-batch processes to Continuous Manufacturing (CM), particularly in biologics production. CM offers significant advantages, including increased efficiency, cost-effectiveness, and enhanced product quality. However, this transition presents a unique set of regulatory and technical challenges that organizations must navigate to realize the potential of CM fully (1–3).

Core Guidelines for CM in Biologics Production

In July 2023, the ICH implemented the Q13 guideline in Europe, offering a framework for developing, operating, and managing CM processes in pharma. The following table provides an overview of key International Council for Harmonisation (ICH) guidelines relevant to CM in biologics. Each guideline addresses specific aspects of development, quality, and lifecycle management, offering a comprehensive framework to support the implementation and regulation of CM processes in the biopharmaceutical industry.

The FDA’s draft guidance (2025) on “Complying With 21 CFR 211.110” emphasizes robust, risk-based approaches to maintaining processes in a “state of control” throughout the lifecycle (4). This includes monitoring Critical Quality Attributes (CQAs) and employing Process Analytical Technology (PAT) to enhance real-time monitoring and process reliability.

Key Regulatory and Technical Challenges in Continuous Manufacturing of Biologics:

1. Upstream Processing Complexities:
   • Cell Line Stability: Ensuring long-term viability and genetic stability of cell lines during extended continuous cultures is critical. Biologics involve living organisms with longer growth phases, making full CM implementation challenging, especially for mammalian cell cultures (5,6).
   • Media Optimization: Balancing nutrient levels is essential to maintain consistent cell viability and product quality. This requires meticulous optimization of culture media and feeding strategies to support sustained cell growth and productivity (7).
   • Real-Time Monitoring: Implementing robust PAT tools for continuous monitoring of critical process parameters is vital. PAT enables real-time adjustments, ensuring process control and product consistency. However, the implementation can be costly and technologically demanding (8,9).
2. Downstream Processing Integration:
   • Continuous Purification Validation: Demonstrating the effectiveness of continuous purification steps, including viral inactivation and filtration, is necessary to meet regulatory standards. Continuous downstream processes must ensure impurity removal and product quality equivalent to traditional batch methods (10,11).
   • Multi-Column Chromatography: Validating novel technologies like multi-column chromatography is essential for consistent impurity removal across cycles. This requires thorough validation studies to demonstrate robustness and reproducibility (5,10).
3. Data Management and Integrity:
   • Large Data Volumes: CM generates extensive real-time data. Managing and summarizing this data effectively while ensuring compliance with data integrity regulations (e.g., FDA’s 21 CFR Part 11) is a significant challenge. Robust data management systems are necessary to handle the volume and complexity of data (12).
   • Process Validation: Providing comprehensive validation data covering the entire duration of continuous processes is essential for regulatory approval. This includes demonstrating consistent product quality throughout prolonged production runs (13).
4. Comparability Studies:
   • Product Equivalence: Demonstrating that products from CM are equivalent to those from batch processes in terms of quality, safety, and efficacy is critical. This involves thorough analytical comparability studies and may require additional clinical data if significant differences are observed.
   • Regulatory Expectations: Addressing potential requirements for additional clinical data necessitates early engagement with regulatory authorities to define acceptable comparability criteria and study designs (14,15).
5. Risk Management and Control Strategies:
   • Thorough Risk Assessments: Identifying and mitigating risks unique to CM processes, such as equipment failures or deviations that could impact product quality, is crucial. Risk assessments should be integrated into the overall quality management system (16).
   • Integration into Control Strategies: Ensuring that risk management is seamlessly incorporated into process control strategies helps maintain consistent product quality and compliance (17).
6. Regulatory Considerations and Gaps:
   • • Batch Definition and Validation: Defining what constitutes a “batch” in CM is complex due to the continuous nature of the process. Regulatory guidelines require clear batch definitions and validation data from consecutive batches produced at commercial scale.
     • Quality by Design (QbD): Integrating QbD principles into CM for biologics is still evolving. A comprehensive understanding of process parameters and CQAs is essential to develop a robust control strategy.
     • Regulatory Guidelines: While the ICH Q13 guideline provides a framework for CM, gaps remain, especially regarding process transfer and scaling for biologics. Early and transparent communication with regulatory authorities is crucial to navigate uncertainties and align expectations. To enable global consistency in adopting ILM (in-line monitoring) and RTR (real-time release) for new and existing products, there is a need for harmonized regulatory guidelines and active agency involvement, as differing requirements across regions currently complicate implementation and supply chains.
     • FDA Guidance on Advanced Manufacturing: The FDA’s draft guidance under 21 CFR 211.110 highlights the need for robust methods to ensure blend uniformity in advanced manufacturing, including continuous manufacturing and 3D printing (4). It emphasizes pairing process models with in-process testing to maintain a state of control. This approach addresses challenges in isolating in-process materials during CM and ensures compliance with GMP requirements, particularly when unplanned disturbances occur.
   • Equipment Design and System Integration: In biologics, additional gaps arise in designing single-use systems for extended runs, balancing microbial contamination risks, and material traceability under strict bioprocessing conditions. Biologics also face unique challenges in the long-term bioreactor performance and scalability of perfusion systems.
   • Process Control and Monitoring: Biologics require comprehensive real-time quality and microbial contamination control, which demands sophisticated PAT for product-specific CQAs (e.g., protein aggregation). Sampling strategies must focus on contamination prevention and ensure bioprocess consistency over prolonged runs.
   • Adventitious Agent Control: Unlike chemical entities, therapeutic proteins require vigilant adventitious agent control, such as viral clearance, especially under prolonged continuous runs. Implementing rapid testing technologies can improve real-time contamination detection, but regulatory validation of these tools for continuous processes remains challenging.
   • Process Validation and Run Time: Biologic CM needs validation of bioreactors and chromatography systems for sustained performance, focusing on viral clearance and product stability over extended runs. Process Performance Qualification (PPQ) is essential, particularly in documenting the robustness of viral removal and sterilization steps.
   • Stability Considerations: Biologics require specific stability testing to monitor protein integrity, potency, and aggregation over extended CM durations, considering that minor variations can significantly impact therapeutic efficacy.
   • Regulatory Submissions: Emphasis should be placed on contamination controls, material traceability, and extended validation data for viral clearance. Lifecycle management must account for bioprocess adjustments across biologics to address contamination and stability, ensuring ongoing compliance with regulatory expectations
7. Operational Challenges:
   • • Scaling Up: CM technologies feasible at small scales may not directly translate to large-scale manufacturing without significant adjustments. Hybrid approaches—combining batch upstream processes with continuous downstream processes—can be a practical interim solution.
     • Cost Implications: While CM can reduce long-term operational costs, the initial investment in advanced equipment, automation, and workforce training can be substantial, posing a barrier for some organizations.
8. End-to-End Continuous Manufacturing for Biologics

While hybrid systems are increasingly adopted, moving towards end-to-end CM—where both upstream and downstream processes are fully continuous—is the next significant advancement.

• Benefits: Offers significant reductions in production time, enhanced product consistency, and increased manufacturing flexibility.
• Challenges: Overcoming technical hurdles in process synchronization and equipment design and maintaining product quality over extended periods are required.
• Industry Efforts: Companies like Amgen and Evotec actively pursue end-to-end CM solutions by investing in advanced technologies and automation.

Implications for Medical Writing and Regulatory Teams:

• Comprehensive Documentation: Detailed descriptions of CM processes, control strategies, and validation data are crucial, particularly in preparing CTD Module 3 for regulatory submissions.
• Clarity and Organization: Presenting complex technical information in an accessible and well-structured manner facilitates regulatory review and approval.
• Regulatory Alignment: Staying updated with evolving guidelines and ensuring submissions meet all regulatory expectations is imperative for compliance.
• Interdisciplinary Collaboration: Working closely with technical, quality, and regulatory teams helps gather necessary information and ensures consistency across documentation.

Looking Ahead: The Future of Continuous Manufacturing in Biologics

The future of CM in biologics is promising, offering potential benefits such as shorter production times, improved sterility, and enhanced product consistency. Success in this endeavor hinges on the following:

• Regulatory Engagement: Early and ongoing dialogue with regulatory authorities to proactively clarify expectations, address challenges, and facilitate smoother regulatory reviews.
• Technological Investment: Commitment to advanced equipment, automation, and robust process control strategies to support continuous operations.
• Skilled Workforce: Developing in-house expertise in CM technologies and regulatory requirements through targeted training and capacity building.

Conclusion:

Transitioning to Continuous Manufacturing in biologics is a complex but rewarding endeavor. By addressing regulatory and technical challenges head-on, the industry can unlock CM’s full potential, delivering high-quality biologics more efficiently and affordably to patients worldwide.

Authors:

Mélissa Bou Jaoudeh

Innovation Product Development Officer

Research & Innovation

ProductLife Group

Alaa Abdellatif, PhD

Innovation Product Development Officer

Research & Innovation

ProductLife Group

References:

1. Drobnjakovic M, Hart R, Ivezic N, Srinivasan V. towards continuous biomanufacturing.
2. Boskabadi MR, Ramin P, Kager J, Sin G, Mansouri SS. KT-Biologics I (KTB1): A dynamic simulation model for continuous biologics manufacturing. Computers & Chemical Engineering. 2024 Sep 1;188:108770.
3. Hutchinson N. From Development to Delivery: How Continuous Manufacturing is Redefining the Commercial Landscape for Biologics.
4. Research C for DE and. Considerations for Complying with 21 CFR 211.110 [Internet]. FDA; 2025 [cited 2025 Jan 13]. Available from: https://www.fda.gov/regulatory-information/search-fda-guidance-documents/considerations-complying-21-cfr-211110
5. Khanal O, Lenhoff AM. Developments and opportunities in continuous biopharmaceutical manufacturing. mAbs. 2021 Jan 1;13(1):1903664.
6. Strube J, Ditz R, Kornecki M, Huter M, Schmidt A, Thiess H, et al. Process intensification in biologics manufacturing. Chemical Engineering and Processing – Process Intensification. 2018 Nov;133:278–93.
7. O’Flaherty R, Bergin A, Flampouri E, Mota LM, Obaidi I, Quigley A, et al. Mammalian cell culture for production of recombinant proteins: A review of the critical steps in their biomanufacturing. Biotechnology Advances. 2020 Nov;43:107552.
8. Quality & Regulatory Solutions for PAT in Continuous Manufacturing | Pharmaceutical Engineering [Internet]. 2024 [cited 2024 Oct 31]. Available from: https://ispe.org/pharmaceutical-engineering/september-october-2020/quality-regulatory-solutions-pat-continuous
9. Kornecki M, Schmidt A, Lohmann L, Huter M, Mestmäcker F, Klepzig L, et al. Accelerating Biomanufacturing by Modeling of Continuous Bioprocessing—Piloting Case Study of Monoclonal Antibody Manufacturing. Processes. 2019 Aug 1;7(8):495.
10. Jungbauer A, Satzer P, Duerauer A, Azevedo A, Aires-Barros R, Nilsson B, et al. Continuous downstream processing. Separation and Purification Technology. 2024 Jun;338:126439.
11. Where Do We Stand On Adopting Continuous Manufacturing For Biologics? [Internet]. [cited 2024 Jul 31]. Available from: https://www.bioprocessonline.com/doc/where-do-we-stand-on-adopting-continuous-manufacturing-for-biologics-0001
12. Guidance for Industry – Part 11, Electronic Records; Electronic Signatures — Scope and Application.
13. Holzberg TR, Watson V, Brown S, Andar A, Ge X, Kostov Y, et al. Sensors for biomanufacturing process development: facilitating the shift from batch to continuous manufacturing. Current Opinion in Chemical Engineering. 2018 Dec;22:115–27.
14. Manser B, Glenz M. Regulatory and Quality Considerations of Continuous Bioprocessing. In: Subramanian G, editor. Process Control, Intensification, and Digitalisation in Continuous Biomanufacturing [Internet]. 1st ed. Wiley; 2022 [cited 2024 Jul 10]. p. 351–75. Available from: https://onlinelibrary.wiley.com/doi/10.1002/9783527827343.ch10
15. Q13 Continuous Manufacturing of Drug Substances and Drug Products.
16. Nasr MM, Krumme M, Matsuda Y, Trout BL, Badman C, Mascia S, et al. Regulatory Perspectives on Continuous Pharmaceutical Manufacturing: Moving From Theory to Practice. Journal of Pharmaceutical Sciences. 2017 Nov;106(11):3199–206.
17. Tian G, Koolivand A, Arden NS, Lee S, O’Connor TF. Quality risk assessment and mitigation of pharmaceutical continuous manufacturing using flowsheet modeling approach. Computers & Chemical Engineering. 2019 Oct;129:106508.

We welcome your thoughts and experiences on adopting Continuous Manufacturing in biologics. What challenges have you faced, and how are you overcoming them? Let’s collaborate and drive innovation together!