Microbiology is Vital to Compliance to Annex 1 and Risk-Based Regulation

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On November 23, 2023, the PDA Ireland Chapter hosted an event on Microbiology – The Key to Compliance with Annex 1 and Risk Based Regulations. This sold-out event was led by industry leaders, experts, regulators, and pharmaceutical company representatives and was attended by professionals from across Ireland as well as overseas.

The latest revision of the Annex 1 came into force in August 2023 and remains a hot topic within the industry.1 Discussion during the event centered on Annex 1 compliance, with some key takeaways related to specific topics arising from the guidelines.

Knowledge and Training

The updated Annex 1 discusses education, training, and knowledge in multiple sections throughout the document and this topic was a common theme throughout the presentations at the event. In the area of sterile product manufacturing, it is critical that manufacturers have appropriately trained and educated personnel, and in sufficient numbers, to support the manufacture and ensure quality of the product(s).

It is widely recognized that in the case of sterile manufacturing, personnel pose the greatest risk of introducing microbial contamination to the process. With that in mind, it is essential to consider the knowledge base of all personnel who may be required to access the production environment, be that frequently or infrequently.

It is essential that personnel on-site have an appropriate level of understanding of aseptic awareness and cleanroom behavior. Simply providing training in this area is not sufficient. Instead, the trainee must show an understanding of the topic and the impact of microbial contamination on the process, product and, most importantly, the patient.

The accessibility of the training material and its mode of delivery should be considered in that it should be tailored to the target audience in its design and should be innovative. Examples for companies to consider include role swapping and “a day in the life” lab visits, and even virtual reality.


The revision of Annex 1 clearly calls out the use of quality risk management (QRM) to identify potential risks to quality and the implementation of a contamination control strategy (CCS). Many companies may have a CCS in place or are in the process of developing or revising their existing strategy.

During this process it is important to remember that the CCS must not be designed to simply fit the process, since this will not result in an effective CCS. Rather, the CCS process should serve to determine and assess whether the level of control within the unit operations is suitable, and to identify areas of deficiency and proposed mitigations for these deficiencies.

When developing the CCS, it is important to ensure appropriate input. This means that the responsibility for CCS development should not rest with a single individual or group but should include all the relevant stakeholders and subject matter experts. In fact, as was noted in the event, this is what inspectors expect.

Those who have a hands-on understanding of the process must be included in the CCS process, including personnel on the shop floor who have real working knowledge of the manufacturing process, equipment, and cleanroom environment. A CCS should be a live document driving continuous improvement and, as such, should be periodically reviewed and updated where necessary. It is also important to consider the design and language used within the CCS and the audience it is targeting to ensure engagement and adherence across all departments.

Sterility Assurance

Sterility assurance offers a level of confidence that a product is sterile. However, monitoring processes and testing do not offer sterility assurance. In other words, you cannot test compliance into a product. Sterility assurance is achieved through multiple practices and procedures that should form a holistic sterility assurance program for an aseptically manufactured product.1

It was the presenters’ experience that the role of sterility assurance governance is commonly assumed by one person. However, given the criticality of sterility assurance in terms of the quality, safety, and efficacy of sterile medicinal products and challenges that can occur with respect to its implementation and control, it is important to ensure that this area is suitably supported and resourced.

It should be embedded within the company culture that sterility assurance is the responsibility of all personnel on site. Manufacturers should leverage the knowledge base of personnel working in sterility assurance and in microbiology laboratories.

Personnel with backgrounds in these areas should frequently be present on the shop floor to impart knowledge, coach, and promote continuous improvement. Access to this expertise for all relevant departments should also be facilitated and consideration afforded to the development of area “champions” within this sphere. Educating people, promoting quality culture and a sense of process ownership engages teams and promotes best practice.

Challenges in Cell and Gene Therapy Manufacturing

Another topic discussed at the event was the challenges that companies face during the manufacture of cell and gene therapy (CGT) products. CGTs are a rapidly growing area within the biopharmaceutical industry.

The manufacture of these products is, however, quite different to standard sterile or aseptic products in that the process relies heavily on manual processing activities.3 The products also typically have a short shelf life, which presents challenges in terms of testing for sterility as sterility test turnaround times are lengthy, with a minimum lead time of 14 days for traditional sterility test methods.4

Additionally, there are no downstream processing activities to purify the product and remove contaminants as the cell itself is the product. Therefore, control of the process and the prevention of contamination ingress is paramount.

The risks associated with the manufacturing process must be clearly identified, understood, and mitigated. As mentioned above, the process for manufacturing of CGT products is heavily reliant on personnel and manual activities.

The speaker noted that due to the manual nature of these processes, it is critical to provide personnel with the correct training and qualify them appropriately. Effective assessments demonstrating competency and proficiency are key in this area.

It is also important to remember to continue to make training packages effective through review and re-designing as required based on training engagement and success rates. The need for fresh perspective in the design and delivery of training is needed here to ensure the required standard of knowledge and skills are retained.

In accordance with Annex 1, when designing the aseptic process simulation (APS) for a CGT product the APS must be as close to the real commercial process as possible.1 As the presenter noted, the approach to APS for CGTs is different to a standard fill finish APS because of the manual nature of the CGT production process.

As such, a dedicated company global/local procedure should be considered where a company has multiple facilities. Consideration must be given to appropriate risk assessment and justification of interventions, and the APS strategy should outline what interventions are to be simulated and at what frequency.

When considering the grouping of interventions, this should be based on the similarity of the activity/task performed. Annex 1 describes the requirement that operators involved with manual filling activities need to be requalified every six months. As such, the number of APS runs to be completed by a site could also be determined by the number of operators present.

The presenter emphasized that this is a factor to be accounted for during planning activities, as all activities to be performed by the operator must be simulated in the APS to the same extent as the during the commercial process. This can result in the requirement for numerous APS runs to facilitate the (re)qualification of all operators semi-annually for manually filled products. Filling operations that are completed automatically require an annual requalification of its operators.


The new revision of the Annex 1 describes the importance of qualification, training, behavior, and experience as key areas in minimizing contamination risk to sterile product manufacture. Throughout the event the focus on the criticality of ensuring that personnel are appropriately educated and knowledgeable in the principles concerning the protection of sterile products was emphasized.

When considering contamination risk factors to the sterile manufacturing process, manufacturers should ensure that the area of personnel knowledge, training and awareness is addressed appropriately.

About the Author

Noelle Clifford is Manager Consultant at Cencora PharmaLex.


  1. EudraLex Volume 4 Good Manufacturing (GMP) Guidelines – Annex 1, Manufacture of Sterile Medicinal products (2022) . Accessed through: https://health.ec.europa.eu/system/files/2022-08/20220825_gmp-an1_en_0.pdf
  2. European Pharmacopoeia 11.4 , section 2.6.1 – Sterility (2023). Accessed through https://pheur.edqm.eu/home
  3. Cell & Gene Newsletter – Proposed best practices for cell & gene therapy aseptic process simulation (2023). Accessed through https://www.cellandgene.com/doc/proposed-best-practices-for-cell-gene-therapy-aseptic-process-simulation-0001
  4. Journal of Clinical Microbiology – Sterility testing for cellular therapies: What is the role of the clinical microbiology laboratory (2020). Accessed through https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315024/

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The contents of this blog are solely the opinion of the author and do not represent the opinions of PharmaLex GmbH or its parent Cencora Inc. PharmaLex and Cencora strongly encourage readers to review the references provided with this blog and all available information related to the topics mentioned herein and to rely on their own experience and expertise in making decisions related thereto.

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