New method based on mRNA sequencing may be helpful to tackle antibiotic resistance

Sweden: Researchers state in a research published in Nature Microbiology that a new method called 5PSeq can reveal bacterial reactions to antibiotics in five minutes. 5PSeq is simple to use and is based on sequencing the mRNA (messenger RNA) the bacteria break down as they synthesise proteins. 

 The measurements reveal how the bacteria are affected by different environmental factors, such as antibiotic treatments and other types of stress.

“We are confident and hope that this can be one of many tools that doctors need to tackle antibiotic resistance, which is a serious and growing problem,” says principal investigator Vicent Pelechano, associate professor at the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet.

Rapid test for clinical use

The researchers tested the method on 96 bacterial species from different phyla in complex clinical samples taken, for example, from faecal matter and the vagina, but also in compost samples. After only a few minutes, they could see whether or not the bacteria responded to antibiotic treatment; the effect was most salient after about half an hour.

3N Bio is a company that Dr Pelechano and some of his colleagues have started up in the KI Innovations incubator to develop the method and create a rapid molecular test for clinical use. They have now received financing from the Swedish Research Council to demonstrate proof of concept for such a test in collaboration with the Karolinska University Hospital.

“It’s crucial that doctors can quickly find the right antibiotics for seriously ill patients with bacterial infections to reduce the unnecessary use of antibiotics,” says Dr Pelechano. “Current methods of testing antibiotic resistance can take hours or even days, but often treatment needs to be given more promptly than that to avoid serious consequences for the patient. Because of this, a broad-spectrum antibiotic is often prescribed, which increases the risk of resistance.”

Examine how bacteria interact

Apart from measuring antibiotic resistance, the method can help researchers understand how bacteria handle stress and interact with each other and their hosts. The researchers will continue to study complex gut samples to examine how the bacterial communities interact in our gut and contribute to health and disease.

Reference:

Huch, S., Nersisyan, L., Ropat, M. et al. Atlas of mRNA translation and decay for bacteria. Nat Microbiol (2023). https://doi.org/10.1038/s41564-023-01393-z.