A benign bacterium armed with a designer, CRISPR-based weapon has been used to eliminate a harmful bacterium from the guts of mice while leaving all other microbes unharmed.
The approach could give us a new way of tackling antibiotic-resistant infections of the gut and skin, says at the University of Sherbrooke in Canada, and also help treat a wide range of diseases by editing the microbiome.
Others have shown that this approach works in cells growing in dishes but Rodrigue鈥檚 team is the first to get it to work effectively in animals. 鈥淎nd if it works in mice, it should also work in other animals, including people,鈥� he says.
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CRISPR is best known as a gene-editing tool, but it can also be programmed to kill bacterial cells that have specific bits of DNA inside them. The hard part is that doing this requires getting a CRISPR system inside every single one of the bacterial cells that you want to kill. 鈥淭he real challenge is the delivery,鈥� says Rodrigue.
One way to deliver CRISPR is to exploit circular bits of DNA within bacteria known as conjugative plasmids. These carry genes that make the bacteria pass them on to other bacterial cells via a process called conjugation.
Rodrigue鈥檚 team tested lots of different conjugative plasmids in a common group of bacteria to find the one that was most effective at transferring itself. The group then evolved it in the lab to make it even more efficient.
The team added the genes for a CRISPR system targeting an antibiotic-resistant strain of E. coli, and put the plasmid inside a benign bacterium used as a probiotic. When the CRISPR-armed probiotic bacteria were given to mice, they eliminated 99.9 per cent of the E. coli bacteria in four days.
Next, the team targeted a bacterium called Citrobacter rodentium that damages the guts of mice it infects. The CRISPR-armed probiotic bacteria cured infections within four days. 鈥淚t completely eliminated the Citrobacter rodentium,鈥� says Rodrigue.
The team has now begun testing the method in pigs, where it could provide an alternative to the antibiotics widely used by farmers.
The method is very efficient, says at Columbia University in New York. 鈥淥verall, an approach like this is certainly possible.鈥�
But there are potential risks with such efficient conjugative plasmids, says Chavez. If something went wrong, the plasmids might end up spreading undesirable genes.
To ensure nothing like this can happen, Rodrigue plans to ensure that the plasmids don鈥檛 persist after treatment. One way to do this is to delete the genes that the plasmids need to replicate, so they soon die out.
Another is to make the CRISPR system target and destroy the plasmids after a certain delay 鈥� a timed self-destruct system. 鈥淭hat鈥檚 the next step in terms of biocontainment,鈥� says Rodrigue.
The CRISPR-armed probiotic bacteria effectively act as a highly selective antibiotic. They could be used to treat infections wherever bacteria can survive in the body, from the skin to the bladder.
In addition, many medical conditions, from cancer to 颁谤辞丑苍鈥檚, are associated with changes in people鈥檚 microbiome, says Rodrigue. It often isn鈥檛 clear where these changes are a cause or a consequence.
Having a tool that allows us to alter the microbiome will help us find out, and could lead to new treatments. 鈥淲e could use this as a way of changing the microbiome to favour health rather than disease,鈥� says Rodrigue.
Molecular Systems Biology
