Antibiotic Persistence Emerges from Cell-State-Driven Transcriptional Reprogramming.

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• Antibiotic persistence enables bacterial survival without resistance, leading to treatment failure.
• Redundancy in persistence mechanisms and population heterogeneity complicate study.
• Bulk analyses are insufficient to understand transient persister formation.

Purpose of the Study:

• Investigate how transcriptional heterogeneity and redundant stress responses influence bacterial persistence.
• Utilize single-cell RNA sequencing to resolve the molecular basis of persistence in *Klebsiella pneumoniae*.
• Establish a systems-level framework for understanding persistence.

Main Methods:

• Single-cell RNA sequencing in *Klebsiella pneumoniae*.
• Functional assays to assess bacterial survival and persistence.
• Analysis of transcriptional variation across different growth phases.
• Genetic (e.g., *rpoS* deletion) and environmental (e.g., nutrient supplementation) perturbations.

Main Results:

• Transcriptional heterogeneity within an isogenic population contributes to survival.
• Distinct transcriptional responses are induced and co-contribute to persistence.
• Pre-treatment cell state and antibiotic mechanism shape survival responses.
• Perturbations altering cell states modified persistence frequencies.

Conclusions:

• Transcriptional heterogeneity, influenced by pre-treatment cell states, is biologically significant for persistence.
• A systems-level framework explains persistence mechanisms.
• Modulating bacterial cell states offers strategies to improve antibiotic efficacy.