New gene-editing method to kill superbugs

MIT engineers have developed a new gene-editing system that can selectively kill bacteria carrying harmful genes that confer antibiotic resistance or cause disease.
"We've been interested in finding new ways to combat antibiotic resistance, and these papers offer two different strategies for doing that," said Timothy Lu, an associate professor at the Massachusetts Institute of Technology (MIT).
Most antibiotics work by interfering with crucial functions such as cell division or protein synthesis.
However, some bacteria, including the formidable MRSA (methicillin-resistant Staphylococcus aureus) and CRE (carbapenem-resistant Enterobacteriaceae) organisms, have evolved to become virtually untreatable with existing drugs.
In the study, graduate students Robert Citorik and Mark Mimee worked with Lu to target specific genes that allow bacteria to survive antibiotic treatment.

The CRISPR genome-editing system presented the perfect strategy to go after those genes.

CRISPR, originally discovered by biologists studying the bacterial immune system, involves 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 and colleagues 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 beta-lactam antibiotics, including carbapenems.
The genes encoding NDM-1 and other antibiotic resistance factors are usually carried on plasmids - circular strands of DNA separate from the bacterial genome - making it easier for them to spread through populations.

Researchers were able to specifically kill more than 99 per cent of NDM-1-carrying bacteria, while antibiotics to which the bacteria were resistant did not induce any significant killing.
They also successfully targeted another antibiotic resistance gene encoding SHV-18, a mutation in the bacterial chromosome providing resistance to quinolone antibiotics, and a virulence factor in enterohemorrhagic E coli.
The researchers showed that the CRISPR system could be used to selectively remove specific bacteria from diverse bacterial communities based on their genetic signatures, thus opening up the potential for "microbiome editing" beyond antimicrobial applications.
To get the CRISPR components into bacteria, researchers created two delivery vehicles - engineered bacteria that carry CRISPR genes on plasmids, and bacteriophage particles that bind to the bacteria and inject the genes.

Both of these carriers successfully spread the CRISPR genes through the population of drug-resistant bacteria.
The research was published in the journal Nature Biotechnology.