CRISPR/Cas has gotten a lot of attention in recent years because it is a genome-editing system that is simpler than zinc finger technology. Science named the technology one of its top 10 breakthroughs of 2013. (See BioWorld Today, Dec. 20, 2013.)

Now, a team from MIT has described the use of the CRISPR system to target bacteria by their sequences.

"CRISPR can be repurposed as a sequence-specific antimicrobial," senior author Timothy Lu told BioWorld Today, "which is a very different way to think about antibiotics."

CRISPR/Cas9 is a genome-editing system that targets specific genes and induces double-stranded DNA breaks in them. In their work, Lu and his graduate students Robert Citorik and Mark Mimee used both bacteriophages and plasmids to specifically target drug resistance and virulence genes, which enabled them to selectively kill off carbapenem-resistant enterobacteriaceae (CRE) and enterohemorrhagic Escherichia coli (EHEC).

Both CRE and EHEC illustrate the problems with currently used antibiotics. Different types of bacteria – including E. coli – can become CRE if they acquire the resistance gene for carbapenem antibiotics, and EHEC can cause very severe disease and can kill its victims. An outbreak in Germany in 2011 caused nearly 3,000 cases of severe disease and killed 18 individuals.

But E. coli is normally a harmless resident of the human gut. In fact, they benefit their hosts, both by producing vitamin K and by preventing the colonization of the gut by pathogenic bacteria. For that reason, antibiotics that kill E. coli indiscriminately can actually lay the groundwork for other, nastier bacteria to come in and colonize the now-empty niche. Specifically targeting dangerous forms of the E. coli while leaving the harmless ones untouched could make antibiotics less risky and less toxic.

If gene targeting is an unusual way to think about antibiotics, Lu is also unusual in his honesty about what one might expect from such antibiotics.

"We're never going to be able to develop a perfect therapy," because developing resistance is in the nature of bacteria. Instead, "it will be a constant back and forth. . . . What we're trying to do is to develop a pipeline of therapies that can be engineered" to parry each bacterial volley as it comes.

Beyond antibiotics, Lu said that "there's a spectrum of applications" the CRISPR technology can address. Getting those applications developed into something practical will take differing amounts of time. Quickest will be diagnostic applications – in fact, one such application is already on the market. Food safety start-up Sample6 Technologies, where Lu is on the board, markets a test for food-borne bacterium Listeria monocytogenes, which can cause serious food poisoning.

In the work, which was published in the Sept. 21, 2014, online issue of Nature Biotechnology, Lu and his colleagues showed they were able to detect bacterial strains with specific gene sequences in them, using CRISPR combined with a signaling molecule. In the medical world, such technology could, for example, quickly test whether a patient suffering from a Staphylococcus aureus infection had a bug that was resistant to methicillin, or from a pathogenic E. coli strain.

CRISPR systems that could manipulate the gut microbiome might have both research and therapeutic applications. Among the largest scientific shifts in the past few years has been the realization just how much the human microbiome affects the body – and how much its composition can influence everything from weight to the immune system and cancer risk. (See BioWorld Today, Aug. 26, 2009, July 15, 2013, and Aug. 19, 2014.)

Efforts in both research and therapeutics, however, are complicated by the fact that although it is possible to manipulate the gut microbiome by adding species, as well as by transplants, there is currently no easy way to remove specific bacterial strains. Using CRISPR could provide tools to study more nuanced changes to the microbiome, as well as therapies to specifically get rid of unwanted denizens of the gut.

In their Nature Biotechnology paper, the team did show that treatment with CRISPR systems targeting various different sequences could kill bacteria outright, re-sensitize them to antibiotics to which they had grown resistant and improve the survival of moth larvae infected with E. coli. Lu and his colleagues now are working on targeting a greater number of different gene sequences, on improving delivery technology and on testing whether the approach works in mammals.

He was clear that "there's a lot of technological and regulatory hurdles to overcome" before any CRISPR-based drugs might make it to the market. Any clinical applications of the approach are years in the future.

"But," he added, "the enabling technology is there."