Two New Technologies To Fight Superbugs

Most antibiotics work by interfering with crucial functions such as cell division or protein synthesis. However, many bacteria are resistant and untreatable with current drugs.

Timothy Lu, an associate professor of biological engineering and electrical engineering and computer science at MIT, has developed two new technologies for combating drug-resistant bacteria, reports MIT News.

In a new Nature Biotechnology study, Lu targets specific genes that allow bacteria to survive antibiotic treatment using the CRISPR genome-editing system that can disable any target gene.

CRISPR uses a set of proteins that bacteria use to defend themselves against bacteriophages (viruses that infect bacteria). One of these proteins, a DNA-cutting enzyme called Cas9, binds to short RNA guide strands that target specific sequences, telling Cas9 where to make its cuts.

Lu designed their RNA guide strands to target genes for antibiotic resistance, including the enzyme NDM-1, which allows bacteria to resist a broad range of antibiotics. When the researchers used the CRISPR system against NDM-1, they were able to specifically kill more than 99 percent of NDM-1-carrying bacteria.

The researchers are now testing this approach in mice.

"This work represents a very interesting genetic method for killing antibiotic-resistant bacteria in a directed fashion, which in principle could help to combat the spread of antibiotic resistance fueled by excessive broad-spectrum treatment," said Ahmad Khalil, an assistant professor of biomedical engineering at Boston University.

Another tool Lu has developed to fight antibiotic resistance is a technology called CombiGEM. This system, described in theProceedings of the National Academy of Sciences, allows scientists to rapidly search for genetic combinations that sensitize bacteria to different antibiotics.

Lu created a library of 34,000 pairs of bacterial genes, which also includes barcodes. These barcodes allow the researchers to rapidly identify the genes without having to sequence the entire strand of DNA.

"You can take advantage of really high-throughput sequencing technologies that allow you, in a single shot, to assess millions of genetic combinations simultaneously and pick out the ones that are successful," Lu said.

The researchers delivered combinations of genes into drug-resistant bacteria and treated them with different antibiotics. For each antibiotic, they identified gene combinations that enhanced the killing of target bacteria by 10,000- to 1,000,000-fold.

"This platform allows you to discover the combinations that are really interesting, but it doesn't necessarily tell you why they work well," Lu said. "This is a high-throughput technology for uncovering genetic combinations that look really interesting, and then you have to go downstream and figure out the mechanisms."

Once scientists understand how these genes influence antibiotic resistance, they could try to design new drugs that mimic the effects, according to Lu.