When doctors treat an infection, the goal can seem straightforward – identify the dangerous microbe and use appropriate antibiotics to kill it. But infections are rarely that simple. Bacteria and fungi live together in crowded communities where they compete for resources, alter each other’s behavior, and sometimes even unintentionally protect their neighbors.
As antibiotic resistance continues to rise, understanding these microbial communities is becoming increasingly important. Patients rarely experience infections caused by a single microbe. Instead, microbes exist within communities that constantly reshape their environment and each other. The combined selective pressures imposed by antibiotics and neighboring species make the evolution of resistance far more difficult to predict. Understanding the genetic basis of the distinct antibiotic-resistance strategies that bacteria develop in complex communities could help researchers develop better treatments for stubborn infections.
Pseudomonas aeruginosa is a bacterial pathogen that is notorious for its multidrug resistance. When other treatments fail, doctors often turn to colistin, a last-resort antibiotic. Colistin works by binding to the bacterial outer membrane, disrupting this protective barrier and ultimately killing the cell. However, colistin resistance has been increasing at an alarming rate, and understanding how that resistance emerges is an urgent medical priority.
Dr. Yu-Ying Phoebe Hsieh, a former postdoctoral fellow from the Malik lab in the Basic Sciences Division and the Dandekar lab in the UW Department of Microbiology, investigated how interactions between P. aeruginosa and the fungus Candida albicans influence the evolution of colistin resistance. Her previous work revealed that fungal neighbors can dramatically alter the path bacteria take toward resistance.
A key player in this process is magnesium. Like animals competing for food in a forest ecosystem, microbes compete for limited nutrients. In this case, C. albicans consumes magnesium from the environment, leaving less of this essential nutrient available for nearby bacteria.
P. aeruginosa rapidly responds to magnesium scarcity by modifying a key component of its outer membrane. This reversible response also slightly reduces the bacterium’s sensitivity to colistin. But Hsieh and colleagues discovered something even more striking. When grown alongside C. albicans and exposed to gradually increasing concentrations of colistin over 90 days, P. aeruginosa evolved to become nearly 100 times more resistant to the antibiotic.
However, the bacteria didn’t evolve resistance in the usual way. Instead of acquiring the standard mutations commonly associated with colistin resistance, they evolved a different strategy that was specific to the low-magnesium conditions created by the fungus.
In a recent study published in PLoS Biology, conducted in collaboration with the Ernst lab at the University of Maryland, the team set out to understand how this alternative form of colistin resistance arises. Using a combination of genetic and biochemical analyses, they tracked the mutations that appeared as resistant populations evolved and uncovered a key role for a magnesium-sensing pathway in driving resistance under low-magnesium conditions. They also identified mutations in genes that altered the structure of the bacterial outer membrane and in a gene involved in transporting magnesium across it.
Together, these changes revealed two previously unknown evolutionary pathways that allow P. aeruginosa to evade one of medicine's last-resort antibiotics.
Bacteria that followed the first route achieved colistin resistance by disrupting the structure of their outer membrane, preventing colistin from binding effectively. The strategy worked, but came at a cost to the bacteria. P. aeruginosa is naturally resistant to antibiotics that target processes inside the cell, like vancomycin and rifampicin, because these drugs cannot easily cross the protective outer membrane. But in bacteria that evolved colistin-resistance through this pathway, the damaged membrane becomes more permeable, allowing these antibiotics to reach their targets inside the cell. In other words, gaining resistance to one antibiotic made P. aeruginosa susceptible to several others.
The second pathway tells a different story. Although these bacteria carry mutations in genes involved with building the outer membrane, they did not develop the same membrane defects. These bacteria maintain the integrity of their outer membrane and retain their resistance to other antibiotics. Colistin can still bind to their membranes, suggesting that resistance arose through an entirely different mechanism. Exactly how these bacteria evade colistin remains unclear, but they appear to have found a way to become resistant without incurring the evolutionary trade-off experienced by the first group.
These trade-offs could create new therapeutic opportunities. If resistant bacteria weaken their own membranes to escape colistin, clinicians may exploit that vulnerability by pairing colistin with antibiotics that otherwise cannot penetrate cells. The researchers also identified the molecular signaling pathway responsible for sensing magnesium as a key driver of resistance evolution under low magnesium conditions. Drugs that disrupt magnesium sensing could potentially prevent certain forms of resistance from emerging in the first place.
These findings add to the growing realization that antibiotic resistance is not simply a genetic problem – it is also an ecological one. The fungal neighbors in this study fundamentally altered the evolutionary options available to P. aeruginosa, steering it toward resistance strategies that would not otherwise have emerged. To understand how resistance emerges and spreads, scientists need to look beyond individual microbes and consider the communities they inhabit.
Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium Member Dr. Harmit Malik contributed to this research.
The spotlighted research was funded by the Cystic Fibrosis Foundation, the National Institutes of Health, and the Howard Hughes Medical Institute.
Hsieh YP, O’Keefe IP, Wang Z, Sun W, Yang H, Vu LM, Smalley NE, Ernst RK, Dandekar AA, and Malik HS. 2026. Magnesium depletion by Candida albicans unleashes two unusual modes of colistin resistance in Pseudomonas aeruginosa with different fitness costs. PLoS Biology. DOI: 10.1371/journal.pbio.3003673.
Science Spotlight writer Thamiya Vasanthakumar is a postdoctoral research fellow in the Campbell Lab at Fred Hutch. As a structural biologist, she uses cryogenic electron microscopy (cryoEM) to visualize the molecular structures of receptors found on the surface of immune cells.