Phage Foundry: A High-Throughput Platform for Rapid Design and Development of Countermeasures to Combat Emerging Drug-Resistant Pathogens

Authors:

Brady Cress²* ([email protected]), Mohamad Alayouni¹, Archana Anand⁴, Adam P. Arkin², Hans Carlson¹, Adam Deutschbauer¹, Darian Doakes², Michael Hajkowski⁴, Jamie Inman¹, Alexey Kazakov¹, Britt Koskella², Petr Leiman⁵, Catherine Mageeney⁶, Ryan Melnyk¹, Mark Mimee³, Harshini Mukundan¹, Avery Noonan¹, Denish Piya¹, Ella Rotman³, Hemaa Selvakumar¹, Antoine Snijders¹, Jessica Trinh⁶, Simon Roux¹, Vivek K. Mutalik¹ (PI)

Institutions:

¹Lawrence Berkeley National Laboratory; ²University of California–Berkeley; ³University of Chicago; ⁴San Francisco State University;
⁵University of Texas Medical Branch; ⁶Sandia National Laboratory

Goals

There is an urgent need to develop effective antimicrobials to address the public health crisis arising from antimicrobial-resistant (AMR) bacteria. Phages represent a promising alternative to antibiotics as they tend to specifically target a few bacterial hosts and can therefore be applied as precise antimicrobials without collateral disruption of the microbiome. However, isolation of phages against a bacterial strain of interest currently relies on a tedious workflow and may not be achieved in a timely manner.

Abstract

In this project, this team is building the largest collection of phages (“phage banks”) targeting a panel of ESKAPE pathogens AMR pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) and a plant pathogen (Pseudomonas syringae). The phage bank consisting of natural phages may not necessarily represent the optimal genotype for therapeutic use. The group will overcome this limitation by directed evolution of natural phages towards broadening the host-range and by pre-adapting phages to common bacterial resistance mechanisms.

In addition, the group will also develop technologies to rapidly engineer effective phages in the absence of optimal phages in the phage bank. Specifically, researchers aim to learn phage engineering design principles by applying CRISPR-based genome-scale phage functional genomics, determining which phage genes are dispensable and which are useful for host-range engineering. The group will also use CRISPR-Cas tools to build synthetic phages and will apply “rebooting” technologies to facilitate in vitro phage engineering. Taken together, the new resources and capabilities developed as part of the Biopreparedness Research Virtual Environment (BRaVE) Phage Foundry should enable a broader and more efficient use of phages as therapeutics.

Funding Information

This material by Biopreparedness Research Virtual Environment (BRaVE) Phage Foundry at Lawrence Berkeley National Laboratory is based upon work supported by the DOE Office of Science BER program under contract number DE-AC02-05CH11231.