# Synthetic Genomics to Improve a Phage-Based Diagnostic for Multi-Drug Resistant Bacteria

> **NIH NIH R21** · J. CRAIG VENTER INSTITUTE, INC. · 2020 · $268,375

## Abstract

Abstract
Multi-drug resistant TB (MDR-TB) is caused by Mycobacterium tuberculosis (Mtb) strains that are
resistant to two front-line antibiotics, isoniazid (INH) and rifampin (RIF), in the recommended TB
treatment regimen. The World Health Organization (WHO) estimates the prevalence of MDR-TB
at approximately 50 million people worldwide, expanding by nearly 500,000 new cases each
year. A more alarming development is the increase in and global distribution of extremely drug-
resistant TB (XDR-TB), defined as Mtb resistant to INH, RIF and key second-line drugs.
Early recognition of patients with M/XDR-TB and selection of appropriate antibiotics to which their
isolates are susceptible would improve patient outcomes and assist in TB control efforts. While
culturing of microorganisms to determine viability remains the gold standard for infectious disease
diagnostics and phenotypic antibiotic susceptibility test (AST), the slow growth of Mtb delays AST
results beyond practical utility for patient management or infection control. There are presently no
satisfactory options for early, rapid (< 24 hr.), and sensitive detection of Mtb antibiotic resistance.
Thus, there is a desperate need to identify a rapid diagnostic AST to prevent drug failure, relapse,
and death from M/XDR-TB.
Sequella developed a rapid (<1 day), relatively sensitive (≤102 colony forming units), test to
interrogate the metabolic potential of clinical Mtb isolates without culture when exposed to TB
drugs. Recombinant phage engineered to contain the B-SMART™ cassette take over the
metabolism of Mtb and immediately direct the cell to synthesize multiple copies of a unique nucleic
acid sequence not otherwise present in either the phage or Mtb. Antibiotics reduce B-SMARTTM
signal because they interfere with cellular metabolism (transcription and translation), thus phage
are not able to produce the signal and the readout is a phenotypic characterization of drug
susceptibility. B-SMART™ signal sequence is optimized for nucleic acid amplification (NAA)
testing and can be detected by any NAA method.
This R21 proposal will improve the sensitivity of the phage used in B-SMART™ by using a cutting-
edge synthetic genomics approach to improve its signal to noise ratio and test the optimized B-
SMART™ in Mtb clinical isolates. Once the phage is optimized and we test the sensitivity of the
assay with the various TB drugs in a research laboratory setting, we will develop a clinical
laboratory protocol in a subsequent application for 1) detection of live Mtb in patient sputum
samples, 2) use in either centralized laboratories or a point-of-care setting, or both, 3) validation
the B-SMART™ AST using FDA guidelines, and 4) preparation for commercial launch.

## Key facts

- **NIH application ID:** 9941031
- **Project number:** 5R21AI146703-02
- **Recipient organization:** J. CRAIG VENTER INSTITUTE, INC.
- **Principal Investigator:** Sanjay Vashee
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $268,375
- **Award type:** 5
- **Project period:** 2019-06-03 → 2023-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9941031

## Citation

> US National Institutes of Health, RePORTER application 9941031, Synthetic Genomics to Improve a Phage-Based Diagnostic for Multi-Drug Resistant Bacteria (5R21AI146703-02). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/9941031. Licensed CC0.

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