Filtration Validation Guide: 5 Hidden Risks and How to Avoid Them – Insights from 13,000+ Validation Cases

Why did the filter integrity test fail but the quality of the liquid drug product was fine?

Why did the reused filter element pass the integrity test, but the liquid drug product was still contaminated by bacteria?

In filtration processes, validation data is the bottom line of safety. But small oversights in process details may cause all efforts to come to nothing.

Cobetter Validation Center has identified five high-risk scenarios by conducting over 13,000 process validation studies, including chemical compatibility, extractables/leachables, integrity test, bacterial challenge, and more. Each study shows how minor process issues can lead to major failures — and more importantly, how to predict risks from the accumulation of verification and avoid losses through precise selection of filters.

A Deep Validation Library

Over the past 14 years, we've worked with more than 1,500 clients and completed 13,000+ validation studies and 30,000+ reports. These cover a wide range of solutions — from small-molecule drugs to biologics and intermediates. About 5% involve more complex products like liposomes, high-viscosity fluids, and microspheres. The validations span across clarification, ultrafiltration, virus removal, sterile filtration, and single-use assemblies.

A Solid Data Foundation

We’ve built a strong database covering USP <665> / BPOG extractables studies for all of our products. A comprehensive internal mass spectrometry database and toxicology database of extractables and leachables.

Complete In-House Analysis Capabilities

Our lab is equipped with advanced instrumentation and analytical capabilities for chromatography, mass spectrometry, spectroscopy, surface analysis, performance testing, and microbiological analysis.

Five High-Risk Scenarios in Process Validation: From Passively Dealing with Problem to Actively Avoiding It in Advance

Risk 1: Chemical Compatibility – Wrong Selection of Material Causes Hidden Failures

Cases 1: Company A selected PES cartridge filter to process a solution containing over 80% benzyl alcohol, based on the compatibility table that PES is fine with alcohols like methanol and ethanol. But during validation at Cobetter, the membrane shrank and deformed after contact with the liquid.

Case 2: Company B used PES membrane filter to process an injection solution containing N,N-dimethylformamide (DMF). Cobetter’s validation showed that the filter membrane was dissolved by the solvent.

How to Avoid Risk:

High-Concentration Organic Solvents: In API production, common solvents like ethyl acetate, acetone, and dichloromethane are used for dissolution, crystallization, or washing. For these solutions, PTFE filters should be preferred choice to avoid risks of incompatibility and high levels of extractables.

Heated Alcohol-Based Solutions: PVDF or PTFE membranes are preferred choice because PES membrane can swell or deform under these conditions.

Special Seal Material Selection: For esters and ketones at mild temperatures, EPDM seals are suitable. For long exposure at high heat, switch to fluoropolymer-coated or fully fluorinated (FFKM) seals. Avoid silicone or FKM (fluoroelastomer) in these cases. For harsher solvents like THF, dichloromethane, or diethyl ether, fluoropolymer options are strongly recommended.

Risk 2: Extractables and Leachables (E&L) – The Hidden Safety Risk

Recommended Solutions:

Organic phase > 50%:

PTFE or PVDF membranes are strongly recommended. Use PES and nylon with caution as these materials tend to have more additives, which can lead to higher extractables and potential safety concerns.

High-risk solutions (e.g., nucleic acid therapies, blood products, antibody drugs):

These biologics often require stricter compatibility studies due to their complex molecular structures, process sensitivity, lower stability, or tighter regulations. For these solutions, it's recommended to include advanced analyses like LC-MS and ICP-MS (when needed) to monitor potential leachables more precisely.

Risk 3: Bacterial Challenge Test (BCT) Failure – Process Parameters Make or Break It

The goal of a bacterial challenge test is to show that, under simulated process conditions, the filter can consistently retain high concentrations of standard bacteria or related microorganisms suspended in the product or surrogate fluid.

However, product characteristics can impact the results. Based on real BCT penetration cases, we’ve identified three high-risk scenarios involving process fluids with challenging characteristics.

Risk 4: Product-Wet Integrity Testing – The Commonly Overlooked “Testing Trap”

Why run product-wet integrity tests?

The goal is to set an integrity standard based on the actual solution to avoid false passes or false failures. This means wetting the filter with the real process fluid (not water or a substitute solvent), then verifying integrity metrics like bubble point and diffusion flow. This ensures the result truly reflects the filter’s retention performance.

When should you consider product-wet integrity testing?

• If the filter is hard to clean after filtration due to solution properties — recommended
• If you want to simplify or shorten the rinse process — recommended
• If the formulation is unstable or prone to precipitation — not recommended

Risk 5: Filter Reuse - Looks Cost-Effective, But It’s a Hidden Risk

In a reuse lifespan study from Company A, membrane samples were taken from scaled-down test filters and observed under SEM. Results showed visible cracking in the membrane (see Figure 5).

Figure 5. Membrane from PES filter in the reuse lifespan study

Sterile-grade filters that pass integrity testing after reuse may still fail bacterial challenge tests (BCT). This isn’t just theoretical—it happens in real cases. This mismatch mainly comes from the difference in test principles: integrity testing uses indirect physical indicators, while BCT directly verifies microbial retention.

The table below shows real-world examples and root causes. For sterile filtration, single-use per batch is strongly recommended in line with regulatory standards.