Bacterial clusters inside hydrogels. Blue: wild type Pseudomonas aeruginosa, Yellow: FM4-64 staining of the bacterial outer membrane). Credit: Sourabh Monnappa ©2026 EPFL
EPFL researchers have shown that physical pressure helps the pathogenic bacterium Pseudomonas aeruginosa survive antibiotic treatment.
Pseudomonas aeruginosa is an opportunistic pathogen that can cause acute and chronic infections. Responsible for many hospital-acquired infections, it is also a major concern for people with cystic fibrosis, whose lungs are clogged with thick mucus that promotes its growth.
P. aeruginosa also thrives within biofilms, where bacteria surround themselves with a self-made elastic matrix that protects them. Treatments often fail due to antibiotic resistance, but tolerance allows bacteria to survive antibiotic exposure without carrying the genetic changes that define resistance.
A team led by Alexandre Persat at EPFL has now shown that confinement itself can make P. aeruginosa more tolerant to antibiotics. The study, published in PNAS, shows that as bacteria grow in tight elastic materials, they are subjected to pressure that changes their physiology and helps them survive several types of antibiotic treatment.
Building a controlled squeeze
To isolate the effect of physical pressure, the researchers grew single P. aeruginosa cells inside water-rich synthetic gels that allow nutrients and small molecules pass through while still pushing back as bacterial clusters grow. By changing the stiffness of the gel, the team could control how much the material pushed back as bacterial clusters expanded, a setup that separated mechanics from chemistry.
The researchers then checked that the gels did not block antibiotic movement. Fluorescent tests showed that small molecules and a colistin-like antibiotic reached the bacterial clusters quickly. This meant that any change in survival could not be explained simply by poor drug penetration.
Stiffer surroundings, higher survival
The team first tested colistin, a last-resort antibiotic used against some hard-to-treat infections. Bacteria growing in confinement survived colistin better than bacteria growing freely in liquid culture. At one tested dose, confined cells showed about a 10-fold drop in survival, while free-living cells showed about a 1,000-fold drop.
The scientists then investigated whether the gel's stiffness also affected bacterial survival. They found that bacteria in stiffer hydrogels, which created higher growth-induced pressure, survived better than bacteria in softer gels. At a higher colistin dose, clusters in stiff gels survived about 10 times better than clusters in soft gels. Imaging also showed more live cells in stiff conditions.
The same pattern appeared beyond one laboratory strain. Confinement increased colistin tolerance in another laboratory strain and in two clinical isolates from people with cystic fibrosis. The team also tested the antibiotics tobramycin, ciprofloxacin, and meropenem. All across them, confined bacteria survived better than free-living bacteria, with stronger protection in stiffer gels.
More than slower growth
Physical confinement does more than just compress bacteria; it also slows their growth. Cells in stiffer gels formed smaller clusters and became shorter. Slower growth likely explained part of the effect, especially for antibiotics whose activity depends on bacterial growth.
But when the researchers released bacteria from the gels, the cells quickly resumed normal growth. However, even after release from confinement, bacteria remained less sensitive to antibiotics, suggesting that the effects of mechanical pressure can persist beyond the confined state.
To identify the mechanisms, the team used transposon sequencing, a genetic screening method that tests which genes matter under specific conditions. The screen pointed to genes involved in the bacterial cell envelope, membrane remodeling, ion transport, and stress responses.
The work shows that the physical environment of an infection can affect whether antibiotics succeed. This does not mean pressure alone explains treatment failure. Infection sites also involve immune responses, nutrient changes, mucus, tissue structure, and biofilms. But the study adds mechanics to the list of factors that shape bacterial survival.
For patients, the long-term value lies in better ways to understand stubborn infections. For researchers and clinicians, it suggests new targets: not only the bacteria's genes or metabolism, but also how bacteria interact with the materials around them. It could also guide the design of biomaterials that resist bacterial colonization or make bacteria easier to kill.
