Two bacterial shutdown modes explain antibiotic persistence and relapse

New study reveals that bacteria can survive antibiotic treatment through two fundamentally different "shutdown modes," not just the classic idea of dormancy. The researchers show that some cells enter a regulated, protective growth arrest, a controlled dormant state that shields them from antibiotics, while others survive in a disrupted, dysregulated growth arrest, a malfunctioning state marked by vulnerabilities, especially impaired cell membrane stability. This distinction is important because antibiotic persistence is a major cause of treatment failure and relapsing infections even when bacteria are not genetically resistant, and it has remained scientifically confusing for years, with studies reporting conflicting results. By demonstrating that persistence can come from two distinct biological states, the work helps explain those contradictions and provides a practical path forward: different persister types may require different treatment strategies, making it possible to design more effective therapies that prevent infections from coming back.

Antibiotics are supposed to wipe out harmful bacteria. Yet in many stubborn infections, a small number of bacterial cells manage to survive, only to re-emerge later and cause relapse. This phenomenon, known as antibiotic persistence, is a major driver of treatment failure and one reason infections can be so difficult to fully cure.

For years, persistence has largely been blamed on bacteria that shut down and lie dormant, essentially going into a kind of sleep that protects them from antibiotics designed to target active growth. But new research led by PhD student Adi Rotem under the guidance Prof. Nathalie Balaban from Hebrew University reveals that this explanation tells only part of the story.

The study shows that high survival under antibiotics can originate from two fundamentally different growth-arrest states, and they are not just variations of the same "sleeping" behavior. One is a controlled, regulated shutdown, the classic dormancy model. The other is something entirely different: a disrupted, dysregulated arrest, where bacteria survive not by protective calm but by entering a malfunctioning state with distinct vulnerabilities.

"We found that bacteria can survive antibiotics by following two very different paths," said Prof. Balaban. "Recognizing the difference helps resolve years of conflicting results and points to more effective treatment strategies."

Two "survival modes" and why they matter

The researchers identified two archetypes of growth arrest that can both lead to persistence, but for very different reasons:
1) Regulated growth arrest: A protected dormant state
In this mode, bacteria intentionally slow down and enter a stable, defended condition. These cells are harder to kill because many antibiotics rely on bacterial growth to be effective.
2) Disrupted growth arrest: Survival through breakdown
In the second mode, bacteria enter a dysregulated and disrupted state. This is not a planned shutdown, but a loss of normal cellular control. These bacteria show a broad impairment in membrane homeostasis, a core function needed to maintain the integrity of the cell.
That weakness could become a key treatment target.

A framework that could transform antibiotic strategies

Antibiotic persistence plays a role in recurring infections across a wide range of settings, from chronic urinary tract infections to infections tied to medical implants. Yet despite intense research, scientists have struggled to agree on a single mechanism explaining why persister cells survive. Different experiments have produced conflicting results about what persisters look like and how they behave.

This study offers an explanation: researchers may have been observing different types of growth-arrested bacteria without recognizing they were distinct.

By separating persistence into two different physiological states, the findings suggest a future where treatments could be tailored, targeting dormant persisters one way, and disrupted persisters another.

How the researchers saw what others missed

The team combined mathematical modeling with several high-resolution experimental tools, including: 

• Transcriptomics, to measure how bacterial gene expression shifts under stress
• Microcalorimetry, to track metabolic changes through tiny heat signals
• Microfluidics, allowing scientists to observe single bacterial cells under controlled conditions

Together, these approaches revealed clear biological signatures distinguishing regulated growth arrest from disrupted growth arrest, along with the specific vulnerabilities of the disrupted state.