Microfluidics Platform for Rapid, High-throughput Screening of Therapeutic Bacteriophages Based on Patient Bacterial Isolates

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PROJECT SUMMARY—Felix Biotechnology is developing a microfluidics platform for rapid, high-throughput screening of therapeutic bacteriophages that target disease-causing bacteria. Federal agencies, multiple companies, and infectious disease specialists in major academic medical centers across the US are advancing the use of phages for a broad range of applications including the treatment of multi-drug resistant bacterial infections and the prevention of food-borne illnesses. While these efforts show great promise, the narrow host range of most phages limits the commercial and clinical potential of phages as a generalized tool. Engineering phage with expanded host ranges may provide a possible solution, but researchers lack the necessary understanding of the genetic factors that determine host range. Collecting data on genetic variation in host range is time consuming, expensive, and low throughput. In preliminary studies, Felix demonstrated 1) the ability to reliably combine bacteria and phage in reproducible ratios in single droplets using a co-flow focusing device, 2) the ability to co-culture bacteria and phage in the droplets and observe phage-specific killing of target bacteria, and 3) the ability to optimize the ratio of bacteria to phage to achieve ≥ 99.9% killing in susceptible strains. In this proof-of-concept Phase I SBIR, Felix proposes to tag phages and bacteria with unique oligonucleotide-based barcodes prior to combining them in droplets, sort droplets where phage successfully kills the bacteria, unify the respective barcodes (“epicPCR”) by merging droplets where phage kill bacteria with PCR reagents and then fusing the barcodes identifying the specific phage and specific bacteria that were involved. The droplets would then be lysed and the pool of hybrid barcodes would be sequenced, giving us information on and sequence- unified amplicons for detecting a lytic pairing. Felix will then demonstrate the ability to distinguish correctly paired phage/bacteria in a 10 x 10 matrix of different phages and bacteria. Aim 1. Validate the use of oligonucleotide barcodes for identifying phage/bacteria pairing in droplets. Milestone / Success Metric: Validation of 20 unique oligonucleotide-based barcodes (10 phage, 10 bacteria). Aim 2. Demonstrate the ability of barcodes to correctly identify phage/bacteria pairs when starting with a matrix of 10 different phages and 10 different bacteria. Milestone / Success Metric: ≥ 80% agreement between traditional plaquing assay and the microfluidics assay. Go/No-Go Criterion for Advancing to Phase II: At least 80% agreement between plaquing and microfluidics assays for identifying phage/host pairs is sufficient to warrant further optimization. Impact—Successful proof-of- concept would support further development of a microfluidics device with a target product profile capable of screening a matrix of 1,000 x 1,000 with ≥ 95% agreement with traditional plaquing assays. This would provide orders of magnitude more data than current methods, providing the volume of data needed to accurately identify the genetic basis of host range and engineer phages with expanded host range. These advances could accelerate the use of phages as a sustainable first-line treatment for bacterial disease.