We are running out of antibiotics to treat the drug-resistant bacteria that have been emerging in recent years. In the US alone, drug-resistant tuberculosis, staphylococcus and other superbugs infect over 2 million people and claim at least 23,000 lives every year. Now a new study reveals how engineers have found a way to turn one of the superbugs’ own weapons on themselves.

illustration of mrsa bacteriaShare on Pinterest
Superbugs like MRSA have acquired genes that make them virtually untreatable with antibiotics.

Writing in Nature Biotechnology, Timothy Lu, an associate professor of biological engineering and electrical engineering and computer science at Massachusetts Institute of Technology (MIT), and colleagues explain how they used CRISPR (clustered regularly interspaced short palindromic repeats) – a gene-editing system that bacteria use to defend against virus attack – to target the superbugs themselves.

Most antibiotics work by disrupting essential bacterial processes like cell division and protein synthesis. But superbugs like MRSA (methicillin-resistant Staphylococcus aureus) and CRE (carbapenem-resistant Enterobacteriaceae) have acquired genes that make them virtually untreatable with drugs that work in this way.

Prof. Lu says we are at a “crucial moment,” with “fewer and fewer new antibiotics available, but more and more antibiotic resistance evolving.”

Prof. Lu and his team have been looking for new ways to tackle antibiotic resistance, and the new paper describes one such strategy.

CRISPR is a part of the immune system of bacteria that helps them fight bacteriophages (viruses that infect bacteria). It contains instructions for making tools in the form of proteins. One such protein, called Cas9, is an enzyme that cuts DNA. It attaches to an RNA “guide” that tells it where to cut.

In their study, Prof. Lu and colleagues describe how they used this feature of CRISPR against bacteria. They designed their own RNA guide to target genes for antibiotic resistance. One such gene codes for an enzyme known as NDM-1.

Bacteria that carry the NDM-1 gene are among the most drug-resistant superbugs around. The gene allows them to resist a broad range of beta-lactam antibiotics, including carbapenems. NDM-1 genes are usually carried on plasmids – rings of DNA that are separate from the bacterial genome – making it easier for them to spread to other bacteria populations.

By using CRISPR with Cas9 to target NDM-1, the researchers were able to selectively kill over 99% of bacteria carrying NDM-1 – while antibiotics to which the bacteria were resistant killed hardly any of them.

They then used the system to target another gene called SHV-18, a mutation in the bacterial chromosome that makes them resistant to quinolone antibiotics. It is also known to be a virulence factor in enterohemorrhagic E. coli, a strain that can cause severe foodborne disease.

As an added bonus, the team also found, using their unique genetic signatures, they could get CRISPR to selectively target and kill specific bacteria in mixed colonies. This opens up the prospect of “microbiome editing” – using a sniper approach instead of the scatter-gun that broad-spectrum antibiotics employ.

In their study, the team successfully demonstrated two ways of delivering CRISPR to target bacteria. One method used engineered bacteria to carry the CRISPR genes on plasmids (which readily spread to the target bacteria), and the other used virus particles that bind to the bacteria to inject the genes.

They also showed the CRISPR system led to increased survival in waxworm larvae infected with a harmful form of E. coli.

The team is currently testing the system on mice, and look forward to the day when the technology can be modified to treat infections and remove unwanted bacteria in humans.

Ahmad Khalil, an assistant professor of biomedical engineering at Boston University, and who was not involved in the study, says:

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.”

The National Institutes of Health, the Office of Naval Research, the Defense Threat Reduction Agency, the US Army Research Laboratory, the US Army Research Office, and the Ellison Foundation all contributed funds to the research.

Meanwhile, in August 2014, a team from MIT’s Koch Institute for Integrative Cancer Research writing in Nature, showed how CRISPR enables faster study of the role of mutations in tumor development.