# A platform for genome mining of multidrug-resistant pathogens to develop therapeutic phages using synthetic biology

> **NIH NIH R21** · GENEVA FOUNDATION · 2021 · $103,947

## Abstract

PROJECT SUMMARY/ABSTRACT
Multidrug resistant [MDR] pathogens represent a global health threat and a challenge for modern medicine;
and, as bacterial resistance to new antibiotics is now outpacing the antibiotic development effort, it is critical to
develop new effective antimicrobial alternatives. The antimicrobial resistance crisis is bringing new interests
worldwide to develop phage-based therapies. Over the last decade, efforts in the U.S. to produce phage
therapeutics targeting different bacterial pathogens have shown promising results, including successful
treatments of life-threatening infections in human patients. Safety of phage therapy is still a concern in the
U.S.; however FDA has highlighted requirements for phage preparation: they need to be safe, pure, potent,
exclusively lytic, non-transducing, and lacking undesirable genes (antibiotic resistance, virulence factors) and
bacterial endotoxins.
If bacteriophages for therapy have historically been isolated from natural environments, recent progresses in
phage genetics and genome engineering have proven successful to generate synthetic, strictly lytic derivatives
targeting pathogens. The development of synthetic phages against MDR pathogens would require pipelines to
accelerate our knowledge on newly discovered phages and their potential for synthetic biology. Critical insights
into their biology, i.e. genome structure, phage replication cycle, genetic content (essential genes versus
dispensable [antibiotic resistance and virulence genes]), interaction with the target host, are a prerequisite.
Here, we propose a platform to (i) mine the genomes of MDR pathogens, a gold mine to identify dormant
lysogenic phages directly from within their natural host; and (ii) develop high-throughput pipelines to quickly
gain knowledge on the phage biology to guide our efforts to engineer synthetic phages as therapeutics.
We will use the Group A Streptococcus (GAS), a “Concerning Threat” on the 2019 CDC “18 MDR pathogens”
Watch List, as our model. We showed that Tn-seq could identify functional lysogenic phages from cryptic ones
in GAS genomes, and mutations to reboot dormant prophages into their lytic cycle. In Aim 1, we will produce
the critical knowledge to guide decision on what phages to select for therapeutic potential using synthetic
biology: we will experimentally assess phage genome organization, phage replication/transduction
mechanisms, host range and cell surface receptor(s). In Aim 2, we will implement a design-build-test-learn
cycle" pipeline to optimize the synthetic biology effort, i.e. deletion of undesirable genes and addition of
“payload” genes, to enhance their potential as therapy phages. Finally, we will use in vivo model of wound
infection to test the efficacy of the synthetic phages we generated. Our overarching goal is to develop the tools
and experience to apply our synthetic biology phage-engineering platform to other MDR pathogens.

## Key facts

- **NIH application ID:** 10130308
- **Project number:** 1R21AI156850-01
- **Recipient organization:** GENEVA FOUNDATION
- **Principal Investigator:** Yoann Stephane Le Breton
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $103,947
- **Award type:** 1
- **Project period:** 2021-02-18 → 2023-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10130308

## Citation

> US National Institutes of Health, RePORTER application 10130308, A platform for genome mining of multidrug-resistant pathogens to develop therapeutic phages using synthetic biology (1R21AI156850-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10130308. Licensed CC0.

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