# Deconvoluting drug interactions using M. tuberculosis physiologic processes: transcriptional disaggregation of the BPaL regimen in vivo

## TL;DR

This study introduces a new method to understand how tuberculosis drugs interact by measuring their effects on bacterial processes in mice.

## Contribution

SEARCH-TB is introduced as a novel pharmacodynamic approach using transcriptional profiling to evaluate drug interactions in tuberculosis.

## Key findings

- SEARCH-TB revealed drug-specific transcriptional responses in Mtb within 2 days of treatment.
- Bedaquiline dominated pairwise drug combinations, while pretomanid-linezolid showed intermediate effects.
- The three-drug BPaL regimen produced a greater transcriptional response than expected from pairwise combinations.

## Abstract

A key challenge in preclinical tuberculosis drug development is identifying
optimal antibiotic combinations. Drug interactions are complex because one
drug may affect Mycobacterium tuberculosis
(Mtb) physiology in a way that alters the activity of
another drug. Conventional pharmacodynamic evaluation based on
colony-forming units (CFU) does not provide information about this
physiologic interaction because CFU enumerates bacteria but does not give
information about the drug’s effect on bacterial cellular processes.
SEARCH-TB is a novel pharmacodynamic (PD) approach that uses targeted
in vivo transcriptional profiling to evaluate drug
effects on Mtb physiology. To evaluate SEARCH-TB’s
capacity to elucidate drug interactions, we deconstructed the BPaL
(bedaquiline, pretomanid, and linezolid) regimen in the BALB/c high-dose
aerosol mouse infection model, measuring the effect of 2-, 7-, and 14-day
treatment with drugs in monotherapy, pairwise combinations, and as a
three-drug combination. Monotherapy induced drug-specific
Mtb transcriptional responses by day 2 with continued
evolution over 14 days. Bedaquiline dominated pairwise combinations with
pretomanid and linezolid, whereas the pretomanid-linezolid combination
induced a transcriptional profile intermediate between either drug. In the
three-drug BPaL regimen, adding both pretomanid and linezolid to bedaquiline
yielded a greater transcriptional response than expected, based on pairwise
results. This work demonstrates that physiologic perturbations induced by a
single drug may be modified in complex ways when drugs are combined. This
establishes proof of concept that SEARCH-TB provides a highly granular
readout of drug interactions in vivo, providing information
distinct from CFU burden and suggesting a future where regimen selection is
informed by in vivo molecular measures of
Mtb physiology.