Rapid and ultrasensitive identification of multi-resistant germs

Bacteria that can no longer be controlled with various antibiotics pose a major threat to our health. Medical professionals need information quickly about existing resistance in the case of a bacterial infection in order to be able to react quickly and correctly.

Cantilever systems as an alternative

Classical methods for detecting resistance are based on culturing bacteria and testing their sensitivity to a spectrum of antibiotics. It takes 48 to 72 hours to obtain results, and some bacterial strains are also difficult to culture. Much faster are molecular biological tests that amplify resistance genes or specific short segments in the genome using PCR (polymerase chain reaction). However, even this method does not provide satisfactory results for every bacterium.

An alternative is offered by methods that use tiny spring bars (cantilevers). These cantilevers bend detectably when, for example, RNA molecules bind on their surface. RNA molecules are "working transcripts" of genes and serve, among other things, as instructions for the construction of proteins. RNA molecules can also be used to detect resistance genes in the genetic material of bacteria.

Without labeling and duplication

A team of scientists from the Department of Physics, the Department of Biomedicine and the Swiss Nanoscience Institute at the University of Basel has now presented a cantilever test system in the scientific journal "Global Challenges" with which they were able to detect RNA from individual bacteria that indicate resistance to antibiotics. With the new cantilever system, the samples for analysis do not have to be amplified or labeled.

First, the researchers fixed sections of three genes associated with resistance to vancomycin onto the cantilevers. They then allowed an RNA extract from bacteria to flow over the spring bars prepared in this way. If RNA molecules of the resistance genes were present, binding of the matching RNA pieces on the prepared cantilevers occurred. This binding leads to a deflection of the spring bars in the nanometer range, which can be detected with the aid of a laser.

Clear signal also for point mutations

Not only resistance genes could be detected with this method, but also single point mutations associated with resistance genes. For this study, the researchers used point mutations coupled with genes responsible for resistance to ampicillin and other beta-lactam antibiotics. "The big advantage of the method we developed is its speed and sensitivity," said François Huber, Ph.D., first author of the paper. "We were able to detect tiny amounts of specific RNA pieces within five minutes." The amounts detected, when it came to single mutations, were equivalent to about 10 bacteria.

When detecting entire resistance genes, the researchers got a clear signal from an amount of RNA equivalent to a single bacterium. "If we can detect specific genes or mutations in the genome of the bacteria, we know which antibiotic resistances the bacteria have," explains Prof. Dr. Adrian Egli from the University Hospital Basel, whose team was significantly involved in the study.  "For our work in the hospital, it would be desirable to get reliable and sensitive information about the resistance of germs this quickly."

Scientific article: Global Challenges: Huber et al. (2020) - Rapid and Ultrasensitive Detection of Mutations and Genes Relevant to Antimicrobial Resistance in Bacteria

Source: nano.swiss - Schnelle und sensitive Identifizierung multiresistenter Keime

Image source: Wikimedia Commons: Uwe Gille – Antibiogram-Mueller-Hinton