Rapid and sensitive Mycoplasma detection in antibody bioprocessing via RPA-CRISPR/Cas12a

Mycoplasma species are prevalent microbial contaminants in the production of biological products, such as monoclonal antibodies, posing significant threats to the safety and efficacy of these products. Current regulatory guidelines as well as pharmacopoeias mandate the demonstration of the absence of Mycoplasma in the cell culture and further downstream processing to ensure product safety. Despite recent advancements in sensitive detection techniques for Mycoplasma in eucaryotic expression systems, these methods remain complex and time-consuming. There is a pressing need for a rapid, simple, and sensitive process analytical technology (PAT) for Mycoplasma detection. Here, we report the first development and application of a recombinase polymerase amplification (RPA)-assisted CRISPR-Cas12a (RPA-CRISPR/Cas12a) system spcifically tailored for Mycoplasma detection in biopharmaceutical production. This system combines the high-sensitivity isothermal nucleic acid amplification capabilities of RPA with the trans-cleavage activity of CRISPR-Cas12a reporter probes, enabling the rapid and accurate detection of Mycoplasma, accommodating various experimental requirements and application scenarios. By designing RPA universal primers and crRNA targeting the highly conserved sequences of Mycoplasma 16S rRNA and optimizing reaction conditions, we achieved dual-specific recognition with unprecedented efficiency in bioprocessing samples. All tested Mycoplasma specimens were detectable with limits between 10 and 0.1 copies/μL, with the whole process taking less than 1 hour. We further evaluated the feasibility of this method in detecting Mycoplasma in the cell culture of antibody products and further downstream processing samples. This method reduces the risk of false-positive signals due to non-specific amplification, enhancing detection sensitivity and specificity while significantly reducing analysis, representing the first PAT-compatible method for rapid Mycoplasma monitoring in antibody manufacturing, thereby providing robust assurance for the quality and safety of biological products.