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Updated: Mar 21, 2026

Population and Single-Cell Analysis of Antibiotic Persistence in Escherichia coli
Published on: March 24, 2023
In Vitro Emergence of High Persistence upon Periodic Aminoglycoside Challenge in the ESKAPE Pathogens
Joran Elie Michiels1, Bram Van den Bergh1, Natalie Verstraeten1
1Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
Abstract:
Health care-associated infections present a major threat to modern medical care. Six worrisome nosocomial pathogens-Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.-are collectively referred to as the "ESKAPE bugs." They are notorious for extensive multidrug resistance, yet persistence, or the phenotypic tolerance displayed by a variant subpopulation, remains underappreciated in these pathogens. Importantly, persistence can prevent eradication of antibiotic-sensitive bacterial populations and is thought to act as a catalyst for the development of genetic resistance. Concentration- and time-dependent aminoglycoside killing experiments were used to investigate persistence in the ESKAPE pathogens. Additionally, a recently developed method for the experimental evolution of persistence was employed to investigate adaptation to high-dose, extended-interval aminoglycoside therapy in vitro We show that ESKAPE pathogens exhibit biphasic killing kinetics, indicative of persister formation. In vitro cycling between aminoglycoside killing and persister cell regrowth, evocative of clinical high-dose extended-interval therapy, caused a 37- to 213-fold increase in persistence without the emergence of resistance. Increased persistence also manifested in biofilms and provided cross-tolerance to different clinically important antibiotics. Together, our results highlight a possible drawback of intermittent, high-dose antibiotic therapy and suggest that clinical diagnostics might benefit from taking into account persistence.
Insights
The study reveals that common hospital pathogens, known as ESKAPE bugs, can develop increased persistence, a tolerance to antibiotics, when exposed to high-dose, intermittent therapy. This persistence can hinder treatment and may promote antibiotic resistance.
Area of Science:
- Microbiology
- Infectious Diseases
- Pharmacology
Background:
- Health care-associated infections (HAIs) pose a significant threat, often caused by multidrug-resistant pathogens.
- The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are major contributors to HAIs.
- Bacterial persistence, a non-heritable tolerance to antibiotics, is an underappreciated factor in treatment failure and resistance development.
Purpose of the Study:
- To investigate the phenomenon of bacterial persistence in ESKAPE pathogens.
- To determine if high-dose, extended-interval aminoglycoside therapy promotes persistence in these bacteria.
- To explore the impact of increased persistence on antibiotic tolerance and biofilm formation.
Main Methods:
- Concentration- and time-dependent aminoglycoside killing assays were performed on ESKAPE pathogens.
- Experimental evolution was used to simulate adaptation to high-dose, extended-interval aminoglycoside therapy in vitro.
- Persistence levels were quantified, and cross-tolerance to other antibiotics was assessed in planktonic and biofilm states.
Main Results:
- ESKAPE pathogens demonstrated biphasic killing kinetics, indicating the formation of persister cells.
- In vitro adaptation to intermittent high-dose aminoglycoside therapy resulted in a significant (37- to 213-fold) increase in persistence without the emergence of genetic resistance.
- Elevated persistence was observed in biofilms and conferred cross-tolerance to various clinically relevant antibiotics.
Conclusions:
- Intermittent, high-dose antibiotic therapy may inadvertently promote bacterial persistence, potentially complicating infection eradication.
- Persistence in ESKAPE pathogens can increase tolerance to multiple antibiotics and is exacerbated by simulated clinical dosing regimens.
- Clinical strategies and diagnostics should consider bacterial persistence as a critical factor in managing HAIs and combating antibiotic resistance.
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