Tiny Samples, Big Discoveries: New Method Uncovers Hidden Antibiotic Resistance Genes
Urbana, IL – In the escalating battle against antibiotic resistance, scientists at the University of Illinois Urbana-Champaign have developed a groundbreaking method to identify previously unknown resistance mechanisms lurking in even the smallest environmental samples.The technique,detailed in a recent paper,allows researchers to isolate and study genes from microbial DNA in quantities so minute,20,000 samples would barely weigh a single grain of sugar.
this innovation is critical as antibiotic resistance continues to rise globally, threatening the efficacy of life-saving medications. “With antibiotic resistance on the rise,it’s more vital than ever to understand the full diversity of mechanisms bacteria may be using to inactivate or avoid antibiotics,” explains Terence Crofts,senior author of the study and professor in the Department of Animal Sciences at the University of Illinois. “If we can get a clearer view of the antibiotic resistance genes that exist out in the surroundings,that will give biomedical researchers a chance to look out for them in the clinic and potentially design more effective drugs.”
The method, known as METa assembly, builds upon existing functional metagenomic library techniques.These libraries allow scientists to capture bacterial genes directly from the environment - soil, water, even stool samples – without needing to culture the microbes in a lab or fully sequence their genomes. METa assembly dramatically improves upon this process, requiring 100 times less DNA than standard methods. This is a game-changer for environments where microbes are scarce, or obtaining large samples is impractical.
How it Works: Harnessing E. coli to Find Resistance
Traditional gene finding frequently enough relies on sequencing vast amounts of DNA, but interpreting the function of these newly discovered genes can be a monumental task.METa assembly bypasses this challenge. Rather of sequencing everything, researchers use enzymes to break down environmental DNA into gene-sized fragments. These fragments are than inserted into E.coli bacteria - a readily cultivatable organism – which incorporates the foreign DNA into its own genetic makeup.
The brilliance of the technique lies in its simplicity. E. coli with antibiotic resistance genes will survive exposure to antibiotics, while those without will perish. “If E. coli has a resistance gene, it can survive an antibiotic.If it doesn’t, it dies,” Crofts explains. “We might have 10 million E. coli cells in a petri dish with 10 million unique random chunks of environmental DNA. If we expose it to a particular antibiotic and only 10 colonies survive, we know those 10 had a resistance gene.” Researchers can then easily sequence the DNA fragment from the surviving colonies to identify the specific resistance gene.
From Aquarium Tanks to the Human Gut
To demonstrate the power of METa assembly, the team tested it on samples from diverse environments: water from a large tank at Chicago’s Shedd Aquarium and a small swab sample of human fecal matter. The results were promising. They successfully identified previously unknown antibiotic resistance genes in both samples, highlighting the method’s versatility and sensitivity.
“Because aquatic samples are usually less dense with microbes, you usually can’t get as much DNA out of them, but we showed that we could still make good libraries from the aquarium sample,” Crofts said. The ability to generate libraries from such small fecal samples also holds significant potential for clinical applications, offering a less invasive way to study the complex microbial communities within the human gut.
This research represents a significant step forward in our ability to proactively address the growing threat of antibiotic resistance. By uncovering hidden resistance mechanisms, scientists can better prepare for emerging threats and develop new strategies to combat these increasingly resilient bacteria.
Learn More:
University of Illinois Urbana-Champaign News Release
University of illinois Urbana-Champaign Research Page
Terence Crofts Faculty Page
[METa assembly Publication](https://journals.asm.org/doi/10.
