Application of nanopore long-read sequencing to sterility testing for cell therapy products

Abstract Compendial sterility testing for bacteria and fungi can take 7–14 days, which is too long for testing autologous cell therapy products with short manufacturing times of two weeks or less. To create a rapid, agnostic sterility test that can meet the needs of autologous cell therapies, we developed a 16S and 18S amplicon sequencing methodology using the Oxford Nanopore MinION platform to detect microbial contaminants. Reads are classified metagenomically and a machine-learning algorithm is used to assess if a sample is contaminated. Using spiked T-cell cultures, this methodology could detect sample sterility status and identify any microbial species present in T-cell cultures, including the USP <71> organisms, to a limit of detection of 10 CFU/ml. This breakthrough has the potential to improve the safety and efficiency of cell therapy manufacturing, leading to better patient outcomes and a more streamlined production process. Biography Dr. Stacy Springs is the Executive Director at the MIT Center for Biomedical Innovation (CBI). The Center integrates the Institute’s technical, scientific, and management expertise to solve complex biopharmaceutical challenges. CBI leads multi-stakeholder, multidisciplinary research and educational initiatives with real world impact, including MIT's Biomanufacturing Consortium (BioMAN) and its Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB). Dr. Springs is a principal investigator on several research programs in biologics manufacturing, from application of data analytics and PAT in the continuous production of monoclonal antibodies, viral vectors, and vaccines; to development of innovative rapid sterile tests and new approaches to adventitious agent contamination through long-read sequencing. Stacy is part of the leadership of SMART CAMP, an interdisciplinary research group focused on Critical Analytics for Manufacturing Personalized-Medicine at the Singapore–MIT Alliance for Research and Technology (SMART) and serves as the Chair of Landmark Bio’s Science and Technology Committee. Her research interests include biopharmaceutical development and manufacturing, risk management, regulatory and translational science, and food safety and food supply chains. She holds a PhD in Chemistry from The University of Texas at Austin and gained postdoctoral training in protein and biophysical chemistry at Princeton University.