Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis

Antimicrob Agents Chemother. 2024 May 2;68(5):e0118523. doi: 10.1128/aac.01185-23. Epub 2024 Apr 8.

Abstract

Transcriptional responses in bacteria following antibiotic exposure offer insights into antibiotic mechanism of action, bacterial responses, and characterization of antimicrobial resistance. We aimed to define the transcriptional antibiotic response (TAR) in Mycobacterium tuberculosis (Mtb) isolates for clinically relevant drugs by pooling and analyzing Mtb microarray and RNA-seq data sets. We generated 99 antibiotic transcription profiles across 17 antibiotics, with 76% of profiles generated using 3-24 hours of antibiotic exposure and 49% within one doubling of the WHO antibiotic critical concentration. TAR genes were time-dependent, and largely specific to the antibiotic mechanism of action. TAR signatures performed well at predicting antibiotic exposure, with the area under the receiver operating curve (AUC) ranging from 0.84-1.00 (TAR <6 hours of antibiotic exposure) and 0.76-1.00 (>6 hours of antibiotic exposure) for upregulated genes and 0.57-0.90 and 0.87-1.00, respectfully, for downregulated genes. This work desmonstrates that transcriptomics allows for the assessment of antibiotic activity in Mtb within 6 hours of exposure.

Keywords: Mycobacterium tuberculosis; antibiotic response; novel diagnostics; transcriptomics.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Antitubercular Agents / pharmacology
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Bacterial / drug effects
  • Humans
  • Microbial Sensitivity Tests
  • Mycobacterium tuberculosis* / drug effects
  • Mycobacterium tuberculosis* / genetics
  • Transcriptome* / genetics

Substances

  • Anti-Bacterial Agents
  • Antitubercular Agents