Microbial Process Design

Microbial Process Design

Click now to learn from Sue Schniepp, Distinguished Fellow at Regulatory Compliance Associates, as she describes microbial process design and how your team can improve contamination control. 



Human microbes live in every part of a human being, including the skin, gut, and nose. Trillions of microorganisms live inside the human body — often outnumbering human cells by 10 to 1. However, microorganisms only make up roughly 1 to 3 percent of the body’s mass because of their tiny size. Sometimes microbes in food can lead to illness, but it is more common for microbes in human body functions to safely live in their host. Additionally, many types of microbes provide unique qualities that help increase life expectancy and human survival in general.


Annex 1


microbial process designWhen it comes to microbial control and process design, there are unique drivers listed in the EU’s Annex 1 regulatory guidance that can help your organization. This regulatory compliance guidance contains different types of contamination control requirements.


Further, these drivers come in many different shapes and sizes, but all can impact manufacturing production if not carefully considered.


Sterile Preparations


Manufacturing sterile products covers a wide spectrum of decisions to be considered by the Quality team and manufacturing operations, including:


Sterile product types

  • Active substance
  • Sterile excipient
  • Packaging material
  • Finished dosage form

Packaging sizes

  • Single unit
  • Multiple units

Sterile processes

  • Automated systems
  • Manual processes


  • Biotechnology
  • Small molecule manufacturing
  • Closed systems


Additionally, one of the quality assurance goals of sterile product manufacturing is to minimize risk associated with microbial, particulate, and pyrogen contamination.


Process Design


Contamination sources are the focus of process design and are commonly due to microbial and cellular debris, as well as particulate matter. Understanding how your facility, equipment and employees contribute to uncleanness (whether intentional or not) is essential to contamination control. Lastly, process design should consider each contamination source individually and as a whole to achieve regulatory compliance.


Manufacturing Plant


The facility your product is manufactured in is the first gap analysis that should be conducted. For example, a food manufacturing plant will have a different set of needs to be considered than a pharmaceutical manufacturing environment. Each will have unique requirements based on equipment, environment and process. Further, pharmaceutical production follows unique FDA guidance recommendations that are unlike many commercialized products on the market.  




One of the first priorities your team should understand is clean room classifications and differences in a regulated clean room environment. There are many types of cleanroom services that can help with clean room design and preparing for regulatory compliance (e.g. ISO 7 or ISO 8).


For example, cleanliness standards and cleanroom supplies should be maintained and monitored for environmental conditions. Finally, airlocks for both personnel and equipment should include HEPA (High Efficiency Particulate Air) air filtration to increase air cleanliness and controls that reduce contaminants.




Restricted Area Barrier Systems (RABS) and isolators can help assure environmental conditions help minimize microbial contamination. Further, a reliable containment strategy should consider the types of human intervention that can impact the critical zone. This often goes hand-in-hand with the type of grade the zone is.


There are four primary types of critical zones:


  • Grade A: this area includes high risk operations that must consider air filtration, the aseptic processing line, and filling zone. Additionally, the stopper bowl, open ampoules and vials also must be studied based on contaminates & unidirectional air flow. Finally, process design & SOPs should minimize the number of operators who don’t use barrier protection or glove port
  • Grade B: this area is commonly a background cleanroom for Grade A aseptic preparation and filling zone. Most importantly, airflow visualization studies should show that air does not enter from any lower grade cleanrooms to Grade B. Air pressure differentials should be monitored to ensure clean airflow.
  • Grade C and D: These types of cleanroom spaces are used for lower risk manufacturing stages in the manufacturing process. The most often use class for Grade C and D are the preparation and filling of terminally sterilized


Finally, it is critically important when analyzing the grade of a zone when it comes to modular clean room or portable clean room designs. Make sure your cleanroom construction team understands the types of certified cleanroom principles that follow regulatory compliance.


Water Systems


A water treatment plant is one of the most critical elements of microbial process design. The water filter system should minimize both particulates and pyrogens to help reduce the potential for contamination. Further, special attention should be given to the different types of water filter products used & how they are monitored and maintained over time. Nevertheless, water flow should remain forceful & consistent through water filtration pipes to minimize microbial adhesion & the risks associated with biofilm formation.


Sterilizing Agent


When using a pure steam generator as a sterilizing agent, the design should be correctly purified. Additionally, these agents of sterilization should be designed & validated to confirm steam quality meets both chemical levels and endotoxin levels. For the same reason, measure your steam quality for any additional additives that can cause either contamination of your product or manufacturing equipment.


Central Vacuum System


Understanding when gases come into contact with the product or container surfaces is critical during process design. For example, here are process design concepts to validate proper chemical, particulate, and microbial quality:


  • Relevant parameters (e.g. oil and water content) should be specified in the documentation
  • Consider the use cases inside the facility & type of gas being used during the process
  • Respect the gas generation system & if the design complies with the Pharmacopoeia monograph


Gases used in aseptic processes should always be filtered through a sterilizing filter. If your sterilizing filter is used on a batch basis, consider integrity testing the results during batch certification. Finally, any backflow from vacuum systems or pressure systems can produce hazards to the product. Have your quality team consistently review the mechanisms that prevent backflow when the systems are shut down.


Hydraulic Systems


Manufacturing equipment connected by hydraulics or heating & cooling systems, when possible, should be preferably outside the filling room. Equally important, pump hydraulics or fluid hydraulics located in the filling room should include design controls to contain any spillage. Leaks from these types of systems could pose a contamination risk to the product that should be detectable.


Finally, incorporating an indication system can help monitor leakage scenarios where contamination can become an urgent problem. This can include manufacturing technology such as tank gauges, a tank level sensor, and advanced water level monitor functionality. 


About RCA’s Pharmaceutical Consulting Services 


Regulatory Compliance Associates (RCA) has helped thousands of pharmaceutical companies meet regulatory, compliance, quality assurance, and remediation challenges. With more than 20 years of experience with FDA, Health Canada, EU and global regulatory agencies worldwide, Regulatory Compliance Associates® offers leading pharmaceutical consultants. We’re one of the few pharma consulting companies that can help you navigate the challenges associated with industry regulations.


Our pharmaceutical consulting firm includes over 500 seasoned FDA, Health Canada & EU compliance consultants and regulatory affairs experts who understand industry complexities. It’s a pharma consultancy founded by regulatory compliance executives from the pharmaceutical industry. Every pharmaceutical industry consultant on the Regulatory Compliance Associates team knows the unique inner workings of the regulatory process. 


Client Solutions


Whether you’re in the product planning, development or pharmaceutical lifecycle management stage or need a remediation strategy for a compliance crisis, Regulatory Compliance Associates will guide you through every pharmaceutical consulting step of the regulatory process and create a customized approach depending on your product and your pharma company’s individual needs. Our regulatory compliance clients include:


  • Companies new to FDA, Health Canada or EU regulations and regulatory compliance
  • Start-up organizations with novel submissions to 510(k) submissions from multi-national corporations
  • Investment firms seeking private equity due diligence for pre-acquisition and post-deal research
  • Law firms seeking pharmaceutical consulting firm expertise in the remediation of warning letters, consent decrees, 483’s or import bans


Regulatory Affairs


Regulatory affairs is Regulatory Compliance Associates backbone. We exceed other pharma consulting companies with industry experts experienced in complexities of the pharmaceutical and biopharmaceutical industries. Our pharma consulting expertise spans all facets and levels of Regulatory Affairs, from Regulatory Support for New Products to Life Cycle Management, to other services like Outsourced Regulatory Affairs, Submissions, Training, and more.


As your partner, we can negotiate the potential assessment minefield of regulatory compliance services with insight, hindsight, and the clear advantage of our breadth and depth of knowledge and regulatory compliance consulting. We offer the following pharma consulting regulatory affairs services for pharmaceutical companies.


  • New Product Support
  • Product Lifecycle
  • Other Regulatory Services
  • Combination Products


Compliance Assurance


The regulations process surrounding pharmaceutical companies can be tricky for even the most experienced industry veteran to understand. Just one misstep could mean significant and lasting consequences for your business. At Regulatory Compliance Associates, we offer the pharma consulting experience and pharma consultants necessary to guide you through the quality compliance process.


  • Assessments
  • Audits
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  • Preparation and Training
  • Inspection Readiness
  • Data Integrity


Quality Assurance


Regulatory Compliance Associates Quality consulting includes assessments, strategy, implementations, staff augmentations, and identification of quality metrics to ensure continuous improvement. Our pharma consultants understand the strategic thinking needed to align your business needs and goals. Regulatory Compliance Associates quality assurance services include quality experts with experience spanning major corporations and start-ups. Our pharmaceutical consulting firm knows firsthand how to achieve, maintain, and improve quality, and we excel in transferring pharma consulting knowledge to your organization.


  • 21 CFR Part 11
  • Data Integrity
  • Manufacturing Support
  • Facility Support
  • Quality Metrics


Remediation Services 


Regulatory Compliance Associates has a proven remediation services approach to managing FDA Warning Letters, Consent Decrees, Remediation and other serious regulatory situations. Our pharma consultants know how to partner with executive, legal, and communication teams. Each RCA pharma consulting Expert will develop a response that will be accepted by the regulatory agency and be realistic to execute.


Regulatory Compliance Associates pharma regulatory consultants will develop a comprehensive proof book of documented evidence demonstrating the corrective action taken to remediate non-compliant issues. In addition, each Regulatory Compliance Associates pharma consulting Expert understands compliance enforcement. We’ll prepare a comprehensive pharma consulting strategy to assist in your remediation efforts, drive continuous improvement, and maintain regulatory compliance with the regulations.


  • Regulatory Action
  • Regulatory Compliance
  • Regulatory Enforcement
  • Warning Letter
  • 483 Observation
  • Oversight Services
  • Risk Management Plan


About Regulatory Compliance Associates


pharmaceutical consultantsRegulatory Compliance Associates® (RCA) provides pharmaceutical consulting to the following industries for resolution of life science challenges:



We understand the complexities of running a life science business and possess areas of expertise that include every facet of R&D, operations, regulatory affairs, quality, and manufacturing. We are used to working on the front lines and thriving in the scrutiny of FDA, Health Canada, MHRA and globally-regulated companies.


As your partners, we can negotiate the potential minefield of regulatory compliance and regulatory due diligence with insight, hindsight, and the clear advantage of our unique expertise and experience.


  • Founded in 2000
  • Headquartered in Wisconsin (USA)
  • Expertise backed by over 500 industry subject matter experts
  • Acquired by Sotera Health in 2021


About Sotera Health


The name Sotera Health was inspired by Soteria, the Greek goddess of safety, and reflects the Company’s unwavering commitment to its mission, Safeguarding Global Health®.


Sotera Health Company, along with its three best-in-class businesses – Sterigenics®Nordion® and Nelson Labs®, is a leading global provider of mission-critical end-to-end sterilization solutions and lab testing and advisory services for the healthcare industry. With a combined tenure across our businesses of nearly 200 years and our industry-recognized scientific and technological expertise, we help to ensure the safety of over 190 million patients and healthcare practitioners around the world every year.


We are a trusted partner to 5,800+ customers in over 50 countries, including 40 of the top 50 medical device companies and 9 of the top 10 pharmaceutical companies.


Commitment to Quality


Our Certificate of Registration demonstrates that our Quality Management System meets the requirements of ISO 9001:2015, an internationally recognized standard of quality.


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