New Method Identifies Whole Bacterial Genomes without DNA Amplification

The global overuse of antibiotics is fueling the rise of antibiotic-resistant bacteria, posing a formidable challenge to the treatment of bacterial diseases. Antibiotics, pivotal in combating bacterial infections, are losing efficacy. Addressing this crisis necessitates a shift toward using fewer antibiotics, and a novel method has emerged to facilitate this transition by identifying bacteria more easily and rapidly.

“We have developed a simple tool that can identify all of the genetic material in bacteria. This allows us to find out more quickly what kind of bacteria a sick person or animal is affected by, or what kind of bacteria are found in food or the environment. We can then also decide whether it is necessary to use antibiotics against the bacterium, and if so what kind, so we don’t have to use as much medication,” explains Professor Erika Eiser from Norwegian University of Science and Technology, senior author of the paper published in PNAS. 

The novel technique eliminates the need for gene amplification, a time-consuming step in the analysis process. By employing a method previously confined to simulations, the researchers can analyze the bacterium's DNA comprehensively, saving both time and resources.

The method employs colloids—particles dissolved in a liquid—grafted with different DNA variants to identify short sequences of bacterial DNA. This enables rapid identification of bacteria, as the DNA sequences cause colloids to clump together in distinct ways.

“Using this method, we saw how as few as five E. coli bacteria caused the colloids to create clusters,” says Professor Eiser.