# Using genetics and multi-scale imaging to understand the mechanisms underlying mycobacteriophage host choice

> **NIH NIH R21** · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · 2021 · $250,961

## Abstract

PROJECT SUMMARY
The arms race between humans and bacterial pathogens is accelerating. There is a clear need for the
development of new tools and strategies to confront antibiotic resistance. In recent years, phage have returned
as a possible lifeboat when antibiotics fail. Recent successes, including the treatment of a disseminated drug-
resistant Mycobacterium abscessus (Mab) infection with a personalized phage cocktail2, motivate the continued
refinement of this innovative therapy. Advances in phage engineering have made it possible to modify phages
so that they are constitutively bactericidal and with potentially tunable host ranges3. This is appealing as clinical
isolates of the M. abscessus complex have variable phage susceptibility profiles – most likely because they are
genetically very diverse, with oversized accessory genomes. Furthermore, the multitude of phage defense
systems identified in the model organism Mycobacterium smegmatis suggests that orthogonal systems exist in
non-tuberculous mycobacteria (NTMs). To be able to specify phage host choice for genetically diverse NTMs,
shared phage receptors used for host recognition need to be identified, and conserved phage defense systems
need to be characterized.
 Antibiotics are first-line therapies for bacterial infections. But phage therapies may be able to complement
the current standard of care. Many studies have described increased sensitivities to antibiotics in bacteria that
have acquired resistance to phage. Combination antibiotic/phage therapies take advantage of this phenomenon,
but to formulate more effective combinations, a better understanding is needed of the interplay between drug
and phage pharmacokinetics/pharmacodynamics and the underlying genetic relationships driving resistance and
susceptibility.
 Very little is known about the mycobacteriophage determinants of specificity. Even more mysterious, are
the host factors that regulate, and function directly as receptors for phage. This project presents an experimental
workflow to identify and characterize phage resistance mechanisms in Mab clinical isolates due to 1) dedicated
phage defense systems 2) spontaneous mutations and 3) attachment inhibition. In the first aim, forward genetic
screens will be employed to identify genes of interest. In the second aim, function and mechanism will be
characterized, and in the third aim it will be determined whether acquisition of resistance is associated with
changes in antibiotic sensitivity.

## Key facts

- **NIH application ID:** 10127964
- **Project number:** 1R21AI156772-01
- **Recipient organization:** HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH
- **Principal Investigator:** Eric J. Rubin
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $250,961
- **Award type:** 1
- **Project period:** 2020-12-01 → 2022-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10127964

## Citation

> US National Institutes of Health, RePORTER application 10127964, Using genetics and multi-scale imaging to understand the mechanisms underlying mycobacteriophage host choice (1R21AI156772-01). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10127964. Licensed CC0.

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