How to reduce batch loss in biopharma production

Introduction

In biopharma, multiple batches of drug substance are produced every year. But according to a recent survey from BioPlan (1), a batch failure will occur on average every 64 weeks. In 2022, the average time between batch failures was 58 weeks (2). While these numbers show some improvement over previous surveys (3, 4), batch failure remains a costly concern for facilities producing biomolecules. While the causes are consistent in these surveys, the top causes can vary based on facility size and from year to year. The choice of equipment and supplier knowledge of your process can help minimize the risk for batch failure in your facility both at clinical stage and commercial scale. This article will explore some of the main causes of batch failure in the downstream purification steps and how manufacturers can assess their suppliers and manufacturing processes to reduce the risk.

Causes of batch loss and how to reduce your risk

Operator error

One of the top reasons for batch failure is operator error, for both commercial and clinical scale. Skilled operators are in high demand, and much time needs to be invested to recruit, train and retain people. Manufacturers often develop their own training programs; however, it can be useful to leverage training materials for equipment suppliers, if available.

Effective training can be in many formats, from self-directed online training to small group in-person training to immersive virtual or augmented reality modules. These tools may be provided free of charge from suppliers or require a fee or license for use.

 

 

Producing biologics can require expertise in multiple subject areas, from molecular biology and chemistry principles to materials and engineering. Operators must know how to program the software to safely and correctly operate the equipment, including packing and repacking columns if the facility isn't using prepacked columns. Batch records and data must be captured correctly and stored in the proper data management system. Operators should have a general understanding of what can potentially go wrong and how to mitigate or address the problem. They need to know when to schedule maintenance to keep equipment running properly and cleaning cycles so that bound impurities are removed from columns. An effective training program will give operators the confidence to keep the downstream purification processes running properly, know how to keep equipment running and avoid contamination, and know how to respond if and when a batch failure might occur.

 

 

Questions to consider:

Do your downstream equipment suppliers offer training materials for their equipment? Or for application training? What forms of training are offered? These may include self-paced online learning, virtual reality, classroom, hands-on and blended learning tools. Is training offered only when new equipment is installed or is it readily available to new operators and for refresher training?	Cytiva offers a number of training options including free online learning (registration required), and fee-based Fast Trak classroom, instructional videos and operator training programs. Training modules include application specific, regulatory topics, video-based instrument training, hands-on classroom courses and virtual reality modules. Onsite training is complementary for new equipment installation.
Do your downstream equipment suppliers have specialists available to help your operators determine root cause of a batch failure and how to restore the production line?	For customers who use both Cytiva downstream equipment and consumables, our specialists are available to help identify root cause for any problems that arise. When a production line uses products from multiple vendors, the investigation can become more complicated as different vendors won't have an understanding of other equipment used adjacent to their product.
Does the equipment software track the operators performing runs to help with data management?	Cytiva's UNICORN™ control software provides full data logging for all parameters for chromatography and other supported systems, including system data, run data and user data.

Equipment failure

Equipment failure is often cited as one of the main causes of batch failure. Equipment failure can take many forms during a purification step: a spike in pressure while loading a column with feed material, a leak in a valve or connector, a poor separation due to a poorly packed column or incorrectly programmed gradient, and so on. Equipment that is overdue for maintenance can also lead to failure of a critical component during a run, resulting in unplanned downtime and loss of a critical batch of drug substance. Some facilities keep critical spare parts on hand to minimize downtime.

Clear processes, regular maintenance and written SOP's can minimize the chance of future failures. Operator training also impacts the chances of equipment failure.

 

Modern equipment may include a range of sensors, data tracking for usage, and even predictive software to anticipate when maintenance should be performed before the equipment fails during a run. Drug manufacturers need to assess both hardware and software on new equipment against their needs for performance and data capture. Look for new generation chromatography systems that include industry standard components and high-quality sensors together with automation options for tracking and collecting critical information on every run.

 

 

Older equipment should be assessed for expected lifetime and tracked for replacement such that impact on production schedules in the facility are minimized.

In downstream purification processes, the quality of a packed column can have a high impact on the quality and yield of a batch of drug substance. A poorly packed column can cause poor retention of the target molecule, co-evolution of target molecule and impurities, batch to batch variations for the purification step and possible cross-contamination issues. The column hardware must be compatible with the properties of the chromatography resin being packed, to produce a well-packed column. Packing a modern resin in an older column may not allow the resin to be packed well enough to take advantage of the higher flow properties. For use with modern chromatography resin families that are more rigid to allow higher flow rates, look for columns which use axial compression to achieve a highly stable packed bed. Using older generation columns will not allow the user to use these resins at their optimal flow rates or with the best column packing. Prepacked columns could be an option for users who wish to eliminate the need for column packing, unpacking, cleaning and revalidation steps in their process; however, these may only be available up to a particular volume.

Learn more:

ÄKTA process™ CFG chromatography system

AxiChrom™ chromatography columns

ReadyToProcess™ prepacked columns

UNICORN™ control software

OptiRun™ Connect

Questions to consider when evaluating a downstream equipment supplier:

Does the downstream equipment have controls in place (e.g. warnings, sensors) that can assist operators in assessing a situation before or after it results in a batch failure?	Cytiva's UNICORN™ software for chromatography and other systems includes warnings and alarms to assist in preventing damage to equipment. The result log files include details needed for root cause analysis if a run failure occurs. Each run produces a batch record (result file) that includes all system and run parameters from that run.
Does the equipment record a batch record that has all details needed for an investigation into a batch failure?
Does your downstream equipment have the ability to adapt to different feed viscosities and titers to avoid over pressure alarms?	Cytiva's ÄKTA™ chromatography systems can be programmed to adjust the flow based on flow or pressure feedback to remain within the safe working range for the system and column. Watch commands can stop a run if pressure or flow max set points are exceeded.
Does the downstream equipment have remote monitoring capability to react quickly to any issue seen during a purification step?	Cytiva's UNICORN™ control software has remote capability (system dependent) to allow users to view active runs and in some cases to remotely adjust the run parameters if needed. All changes are added to the result file run log.
Does the column supplier offer training and support for column packing? Does the equipment have protocols (method/recipe templates) for automated column packing and verification? Can the software track column usage and cleaning schedules?	Cytiva's pilot and process chromatography systems have method templates for automated column packing of AxiChrom™ columns. Column performance testing is recorded including column efficiency (HETP) and asymmetry. Protocols are available in Cytiva's column packing handbook and in online application notes. The column logbook function can log usage of each individual column to track usage and cleaning frequency. Operator training (see section above) for column operation and packing is available in several formats.
Does the supplier offer regular preventive maintenance and service coverage to minimize downtime in your facility? How long does it take to schedule an unplanned service visit?	Predictive maintenance uses sensors and data to predict asset maintenance schedules. Cytiva offers many forms of service support, including OptiRun™ Connect to provide faster support and minimize downtime.

HETP = height equivalent to a theoretical plate

Bioburden and batch contamination

One of the biggest concerns for biomanufacturers is the risk of contamination, which jeopardizes product safety and can result in millions of dollars of lost product and lost productivity. Two ways to control for bioburden in downstream processes are (1) develop effective cleaning methods for packed columns and stainless steel equipment that keep microbial levels contained and (2) incorporate single-use and disposable equipment into your process, eliminating the need for cleaning altogether. If purification steps can be connected in series, this can eliminate potential entry points for contamination by reducing the number of handling steps (which can produce an added benefit of increased product yields). The quality of the raw materials from every supplier must also be assessed and tested when it arrives at your facility.

Working with cleanable equipment and columns

If stainless steel systems and glass columns are in use, every entry point (e.g. connections, valves, sensors) and transfer points from one process step to the next has potential for bioburden contamination. Rigorous cleaning methods must be used to control for bioburden and cross-product contamination. Usually this is done using sodium hydroxide (NaOH) solutions or similar caustics. Peracetic acid (PAA) also has been shown to have sporicidal properties. Check the specifications for the equipment to determine the levels of NaOH that can be tolerated and the contact time needed. Cytiva performs extensive testing of the cleanability of its chromatography systems, columns and chromatography resins, which can be found in several application notes listed below.

For columns that are used for multiple cycles, the hardware can be cleaned thoroughly when the column is unpacked and repacked, following the manufacturer's specifications (as the column is fully exposed to the facility environment during these steps, proper handling and testing is required to avoid potentially introducing bioburden into the column hardware). For cleaning a column that is in use, the cleaning methods will depend on the properties of the chromatography resin as well as the hardware. Cleaning cycles are required at regular intervals to maintain the performance of the column. The more cycles you can use a resin in the packed column, the more product you can produce before needing to replace the resin. While most ion exchange and multimodal resins will tolerate cleaning with sufficient levels of NaOH, many protein A resins are not base-stable, leading to loss of the Protein A ligand after several cleaning cycles. These types of affinity resins are exposed directly to the feed from the bioreactor, which puts them most at risk of experiencing contamination, while historically being least stable to rigorous cleaning. New generation base-stable resins for protein A and protein L affinity capture steps provide new options that can be cleaned with minimal ligand loss, thus extending the useful resin lifetime and controlling bioburden in the critical capture columns.

 

 

Working with single-use equipment, prepacked columns and disposable consumables

The introduction of single-use equipment with disposable flow paths in the 2000's, together with the introduction of prepacked columns and disposable membrane devices provided new options for virtually eliminating the risk of bioburden in a facility. The use of single-use equipment shifts the responsibility to the supplier to ensure that raw materials in flow kits and manifolds are free from microbial contamination and show no extractables and leachables (E&L) that could impact the drug product.

For prepacked columns, the supplier also takes the cost, skill set and time needed for column packing and verification. While most pre-packed columns can be reused for multiple batches if suitable cleaning steps can be tolerated by the resin and the hardware, they can also be implemented as single-use consumables, for example, when purifying viral vectors or antibody-drug conjugates (ADCs) where cross-contamination would be a serious concern. The use of disposable membrane devices for purifications steps also can help reduce concerns about bioburden.

 

 

Tips for minimizing the risk of bioburden:

• Establish a cleaning schedule for every column and stainless steel system, and testing methods to verify that bioburden is being controlled effectively
• Explore whether unit operations can be connected, reducing the number of potential entry points for contamination and handling steps
• Ensure that operators are fully trained on equipment usage and aseptic handling in the cleanroom
• Switch to single-use and disposable products that reduce the risk of bioburden and cross-contamination carryover between batches
• Switch to newer generation chromatography resins or membranes that have higher tolerance for cleaning solutions. This may allow you to get more cycles out of every product, reducing your overall cost for producing the drug substance.

Learn more:

MabSelect PrismA™ protein A affinity resin

MabSelect™ VL protein L affinity resin

Mustang™ membranes

ÄKTA ready™ single-use chromatography systems

Infographic: Extreme costs of a bioburden incident

Conclusion

Batch failure is a question of when, not if it happens. Manufacturers can minimize the impact on their downstream operations by implementing effective training programs for operators, ensuring that equipment failure is avoided as much as possible through regular maintenance and controls in the run methods, and preventing bioburden incidents through rigorous testing and cleaning of equipment or use of single-use products where possible. Cytiva supports customers by providing GMP products designed to minimize the chances of batch failure, and next generation chromatography resins that tolerate more rigorous cleaning methods to minimize bioburden. Cytiva also has experienced specialists and field engineers to assist customers, as well as training programs and regulatory support documentation for equipment.

REFERENCES

1. BioPlan 20^th Annual Report and Survey of Biopharmaceutical Manufacturing Capacity and Production. https://www.bioplanassociates.com/20th/
2. Bioprocessing Sees Continued Improvements In Batch Failure Reductions In 2022. https://www.bioprocessonline.com/doc/bioprocessing-sees-continued-improvements-in-batch-failure-reductions-in-0001
3. Average batch failure rate worsens. https://www.genengnews.com/insights/average-batch-failure-rate-worsens/
4. Biotech Facilities Average a Batch Failure Every 40.6 Weeks. https://www.bioprocessintl.com/bioanalytical-methods/biotech-facilities-average-a-batch-failure-every-40-6-weeks

Application notes for cleaning equipment and packed columns

Reducing bioburden during packing/repacking of AxiChrom columns

Sanitization of ÄKTA pilot 600 chromatography system using NaOH

Cleaning components/external surfaces of ÄKTA process™ systems

Cleaning-in-place of ÄKTA process™ with sodium hydroxide

CIP of ÄKTA process™ to remove S. aureus

Sodium hydroxide sanitization of AxiChrom™ columns packed with chromatography resin

Effect of sanitization with a sporicidal agent on MabSelect PrismA chromatography resin

Extractables in single-use systems used in ADC manufacturing

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