Bacteria develop antibiotic resistance more slowly if they have to fight two threats at once

Disease-causing bacteria can become resistant to antibiotics with astonishing speed. But if the bacteria have to fight a predator at the same time as being exposed to antibiotics, the evolution of antibiotic resistance slows down.

Perhaps we should feel sorry for this batch of the bacteria Pseudomonas fluorescens. As if it’s not bad enough that it has to float in a liquid containing an antibiotic, a substance that can inhibit its growth or even kill it, it also has to fight a predator determined to eat it at the same time.

Usually Pseudomonas fluorescens, like most other bacteria in the world, can develop the ability to resist the effects of antibiotics surprisingly quickly through mutations in their genes.

Similarly, the bacteria can usually protect themselves from predators for example by clumping together in big groups, which the predator then has trouble eating.

But fighting the battle on two fronts is proving to be too much for this colony of Pseudomonas fluorescens. The bacteria’s ability to counter the effects of the antibiotic, or devise a strategy to avoid being eaten by the predator, are both being slowed down.  

Although we might pity the bacteria’s plight, this, from a human perspective, can be considered a positive thing since bacteria resistant to antibiotics pose a serious global health problem.

A five-year study to match real-life environment 

“The way bacteria evolve to become resistant to antibiotics has been studied extensively in laboratory settings,” says Teppo Hiltunen, a microbial ecologist at the University of Helsinki.

“But usually the studies have been simple and exposed bacteria to only one threat at a time: the antibiotic. In real life bacteria are interacting with their environment and living in communities consisting of multiple organisms, and they encounter multiple threats at once.”

That’s why Hiltunen and his colleagues at the Max Planck Institute for Evolutionary Biology in Plön, Germany, and the University of Jyväskylä in Finland, devised an experiment in which the bacteria were exposed to two threats at once to better mimic the situation in real life.

The results of the five-year study have now been published in the journal Nature Ecology and Evolution. The consortium found that when bacteria has to fight two threats, or stress factors, at once, its ability to evolve slows down when compared to a situation where is it is fighting only one threat.

While the finding cannot immediately be put to use in fighting antibiotic-resistant bacteria, since more research is needed, it is an important indication of how processes that are ecological (in other words, related to the environment) on the one hand and evolutionary (in other words, related to genes) on the other are linked and make the evolutionary processes more complex than we currently understand.

Resistance to antibiotics in only eleven days

Bacteria are masters of survival. They can adapt to new conditions and develop the ability to counter threats such as pesticides or predators with astonishing speed. One of their enemies is antibiotics, a group of medications that are widely used to treat bacterial infections in humans and promote the growth and health of animals.

Bacteria can gain resistance to antibiotics either through evolution – by developing mutations in genes – or by acquiring antibiotic-resistance genes from another bacteria.

The increasing ability of disease-causing bacteria to resist antibiotic treatment is considered one of the most dangerous emerging threats to human health. According to estimates, bacteria and other micro-organisms resistant to antibiotics and other drugs will, by 2050, cause more deaths than cancer as infections become more difficult or even impossible to treat.

Bacteria’s ability to mutate is exemplified by an experiment captured on video by a group of scientists at Harvard Medical School. The scientists divided a large petri dish into ten slots each filled with agar, a jelly-like substance used in scientific experiments. Each slot contained an antibiotic with the concentration growing from the sides towards the center. In 11 days, E. coli bacteria in the dish were able to mutate so many times that they were able to reach the center of the dish and survive in a concentration of antibiotics that was a thousand times higher than what the bacteria in the dish had originally been able to endure.

Antibiotics in water and soil can trigger the evolution of resistance

Antibiotics that enter soil and the water supply via waste water and accumulate there in low concentrations can make the antibiotic-resistance problem worse, as they can trigger the evolution of resistance in bacteria even though these concentrations are so low that they inhibit bacterial growth only slightly or not at all.

“Antibiotic resistance is essentially an evolutionary problem requiring an understanding of evolutionary biology,” Teppo Hiltunen notes.

“We need to recognize how resistance develops in natural environments and moves from environmental bacteria to clinically relevant pathogens. In order to understand this, we need to study antibiotic-resistance evolution in more complex settings, for example, by adding species interactions as we did here.”

Genetic mutations changed as one threat grew into two

In Hiltunen’s laboratory, the bacterium Pseudomonas fluorescence had to cope with both antibiotics and the single-cell predator organism Tetrahymena thermophila.

After just a short time, the team of researchers noticed that the bacterial population was changing: the bacteria were much slower and less effective in developing resistance and protecting themselves from being consumed than bacteria in the treatments that were only exposed to one of these stress factors.

Moreover, resistance against the antibiotic was much less common.

“The bacteria were clearly unable to optimize both attributes at the same time,” says the study co-author Lutz Becks of the Max Planck Institute.

In the next step, the scientists analysed the genetic basis of these adaptations. Their results show that mutations for improved protection from predators appear consistently in the same way in the bacterial genome if only the predators are present.

The same applies to mutations that cause resistance to antibiotics.

However, as soon as the bacteria have to fight both predators and antibiotics at the same time, different patterns of mutations occur. This causes both the bacteria’s protection against predators and resistance to antibiotics to evolve more slowly and be less efficient.

Because the bacteria are less able to protect themselves from predators if they are confronted by the predatory ciliates and antibiotics simultaneously, their numbers are fewer than when they only have to defend themselves from one threat at a time. Several threats therefore appear to have a strong influence on whether and how often resistance to antibiotics develops and how large the population of bacteria can become.

“This kind of interaction between bacteria and ciliates is very common in environments such as wastewater treatment plants, soil and water bodies,” Teppo Hiltunen says.

“Our finding is part of a bigger puzzle starting to come into clearer focus at the moment, where researchers are figuring out that we need to have a broader view of antibiotic-resistance evolution accounting for the interplay between ecology and evolution.”

More trouble for the antibiotic-resistant bacteria, less trouble for human kind – or that is the hope.

Original study: “Dual-stressor selection alters eco-evolutionary dynamics in experimental communities,” Nature Ecology & Evolution

Teppo Hiltunen leads the Research Group on Experimental Evolution and chairs the HiLife – Helsinki Institute of Life Science’s Grand Challenge project on combatting antimicrobial drug resistance.

Read moreJohannes Cairns: Behind the Paper – "Coming to terms with complexity: Eco-evolutionary dynamics under more than one selection pressure"

HiLIFE Grand Chal­lenge pro­jects 2018–2021

The HiLIFE – Helsinki Institute of Life Science Grand Challenge projects collect together life science research strengths at the University of Helsinki and collaborating organizations such as Helsinki University Hospital HUS and National Resources Institute of Finland LUKE. The Grand Challenges are aimed to be inclusive and interdisciplinary to form an environment where new ideas are born at the edges of research fields. 

The Grand Challenge program provides up to 1 360 000 euros seed funding for the projects. Funding of up to 70 000 euros is provided to each project and additional funding can be proposed for e.g. scientific meetings, defined subprojects, or to support external grants for these high quality nuclei.

Grand Challenge project on com­bat­ting an­ti­mi­cro­bial drug res­ist­ance:

Chair: Teppo Hiltunen
Vice-chair: Liisa Holm
Number of participating PI’s at start: 16
Partner organisations: Aalto UniversityFinnish Food Authority Ruokavirasto 

The rapid rise in antibiotic-resistant pathogens is one of the grand challenges in life sciences. This project aims to harness cutting-edge microbiological and sequencing technologies and bioinformatics to 1) revolutionize infection diagnostics enabling early recognition and personalized treatment of hospital-acquired infections and 2) enable epidemiological inference and understand associations between microbiome, drug responses, and treatment outcomes. Furthermore, the project will develop quantitative strategies to combat antimicrobial resistance (AMR) in originating hotspots including food production settings and sewage treatment plants.

In­tro­du­cing the HiLIFE Grand Chal­lenge pro­jects 2018–2021