Fluorescence-based lyobead assay for rapid phage detection in bioreactor systems

The National Institute of General Medical Sciences awarded Physical Sciences Inc. $311,847 on September 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to develop a fluorescence-based rapid phage detection system for industrial bioreactors.

Physical Sciences Inc. and the University of Connecticut are developing a lyobead assay platform that detects bacteriophage contamination in bioreactor systems within hours. The system uses a sampling chamber loaded with freeze-dried, thermally stable fluorescent reporter bacteria that reconstitute upon contact with bioreactor samples. Engineered E. coli strains mixed with the sample enable an integrated optical detection module to monitor fluorescence changes indicative of phage-induced bacterial lysis. A control chamber with sterile, phage-free sample establishes baseline fluorescence for comparison; if fluorescence drops beyond a set threshold, an alert triggers early intervention. The platform addresses phage contamination failures in bacterial fermentation processes used in biopharmaceutical, dairy, and biochemical manufacturing, where traditional mitigation methods have proven insufficient.

Performance occurs in Andover, Massachusetts, with work continuing through August 31, 2027. This is a Phase II Small Business Innovation Research award following successful Phase I feasibility demonstration.

Abstract

Phage contamination is a significant issue in bacterial fermentation processes, particularly in industries such as biopharmaceuticals, dairy, and biochemical manufacturing. In industrial settings where bacterial monocultures are used for efficiency, phage outbreaks can cause fermentation failures and substandard products, with traditional methods such as chemical disinfectants and strain rotation often failing to eliminate them. E. Coli and clostridium-based fermentations, common in biopharmaceutical production, are especially vulnerable due to regulatory constraints that limit mitigation strategies. Despite efforts including sanitation and genetic modifications to enhance bacterial resistance, phages continue to evolve and evade defenses, causing persistent contamination and significant financial setbacks. Physical sciences INC. (PSI), in collaboration with the university of connecticut (UCONN), proposes the development of a rapid phage detection system for early-stage identification of phage contamination in industrial bioreactors. This platform features a sampling chamber loaded with freeze-dried, thermally stable fluorescent reporter bacteria, which are reconstituted upon contact with bioreactor samples. Engineered E. Coli strains mixed with bioreactor samples enable an integrated optical detection module to monitor fluorescence changes, detecting phage-induced lysis within hours, eliminating the need for batch assays or complex sample prep. A control chamber with a sterile, phage-free sample establishes baseline fluorescence for accurate comparison. If fluorescence drops beyond a set threshold, an alert triggers early intervention. This system addresses a critical GAP in biomanufacturing, where phage contamination can cause costly fermentation failures and production delays. Following the successful feasibility demonstration in phase I, the proposed phase II effort will mature the technology and validate the phage detection system in an industrial bioreactor process at a local industry site. Additionally, a lyobead library will be developed, incorporating fluorescent strains of commonly used bacterial species in biomanufacturing to serve as standardized reference strains across various fermentation processes. Successful development of this technology will enable early detection of phage contamination, minimize production losses, and improve process reliability in industrial biomanufacturing.