Emergence of antimicrobial resistance in bacteria tracked in real time
Single-cell genomics technology could transform understanding of how bacterial populations evolve and combat the growing problem of antibiotic resistance
Cutting-edge technology has allowed scientists to watch in real time how bacteria develop antimicrobial resistance, new research published in shows Microbial Genomics.
Single-cell genomics and analysis, pioneered at the Earlham Institute in Norwich, could help chart the occurrence of genetic mutations that allow bacteria to resist antibiotics, opening up new and much-needed avenues to combat the rise in superbugs.
Antibiotic resistance describes how bacteria have changed and evolved through random mutations in their DNA in response to antibiotics, which are usually prescribed to fight bacterial infections. However, due to their overuse in medicine and agriculture, antibiotics are found in most ecosystems today.
This misuse of antibiotics, along with other factors including poor hygiene, has played a role in the spread of what are known as superbugs — infectious bacteria that are resistant to common antibiotics. With no new antibiotics in development, scientists are trying to better understand the genetic origins of this resistance.
In this study, a collaboration between researchers from the Earlham Institute and the Quadram Institute, funded by a BBSRC Tools and Resources Development Fund (TRDF), researchers exposed strains of salmonella to low levels of ciprofloxacin, a common antibiotic used to treat bacterial infections.
By regularly sampling and sequencing individual cells in the population, they were able to track mutations as they emerged and record any that helped the bacteria evade treatment.
The team was able to identify specific mutations in individual cells that are known to be responsible for resistance. They were also able to detect fluctuations in the population; whether all resistant bacteria had a common ancestor or whether several bacteria had mutated independently.
“The evolution of bacteria is like a deck of cards; The environment is playing a card and the bacteria have to beat the dealer,” he said Study author Dr. Matt Bawn, postdoctoral fellow at the Earlham Institute and Quadram Institute.
“If there are more subpopulations, the bacteria have more cards and can increase their chances of success.”
If scientists can “cheat” by seeing the bacterium’s hand, they can analyze population diversity and understand exactly how adaptable and likely their survival will be – leading to more personalized treatments for common bacterial infections.
previous in vitro Evolutionary studies have used a technique called “mass sequencing” to analyze the genetic variation that occurs in evolving populations, in which all of the individual genomes within a population are sequenced together.
Although this allows scientists to see the differences between populations at different time points, it does not link these differences to individual cells or allow for the identification of subpopulations that share similar genetic traits, such as B. a specific mutation that confers antibiotic resistance.
Single cell sequencing is a rapidly developing technology that makes it possible to identify individual cells and subpopulations. More commonly used to study human cells, for example in cancer or developmental biology, the technology can also provide a much higher-resolution view of bacterial genomes, helping to reveal genetic changes that might otherwise have been missed.
dr Johana Hernandez, joint first author and former EI postdoc, currently Head of Genomic Surveillance at Secretaria Distrital de Salud, Colombia, said: “The application of single cell technology to bacteria is still relatively new – for this study we had to develop approaches to isolate single cells and then read the tiny amount of DNA present in it.
“We were really amazed at the amount of data we were able to generate from each cell; sometimes we could read almost the entire genome of a single cell — and we could use that data to pinpoint mutations that differentiate one cell from another.”
“This makes it a perfect tool to study bacterial evolution and the emergence of AMR.”
dr Iain Macaulay, Group Leader for Technical Development at Earlham Institute, said: “Single-cell techniques bring the kind of resolution that is absolutely fundamental to the identification of genetic diversity. In this way, we can begin to recognize those cells or subpopulations that have acquired a change in their DNA that has the potential to make the bacteria more resilient.
“In a way, it allows us to create a ‘family tree’ of the bacteria as they develop and see the branches of that tree where resistance is emerging.”
This work suggests that microbes are developing resistance faster than we discover and develop new antibiotics. There is hope for new alternatives, but researchers are cautious.
“Considering how easily bacterial populations adapt to our current antibiotics,” he says dr Bawn“there is no guarantee that future solutions will be viable for long.
“This single-cell approach has the potential to future-proof new antibacterial treatments like phage therapy by studying how they affect bacterial evolution with greater resolution than ever before.”
In the future, the researchers hope to expand their single-cell approach and determine if it could provide a route to developing treatments that reduce bacterial virulence by limiting population diversity.
