Scientists create the first CRISPR-based drug to target the microbiome


CRISPR-based targeting of new drug candidates E. coli in the gut microbiome is currently in phase 1 clinical trials. According to a new paper published in Nature Biotechnology, it may improve the well-being of blood cancer patients and reduce their death rate from E. coli infection.

Many people have contracted the infection from E. coli, which is especially seen as inconvenient and unpleasant. However, for some patients, such as those with blood cancer, there is a risk that the bacteria will transfer into the bloodstream. In that case, a E. coli infection can be fatal, with a fatality rate of between 15 and 20%.

The main remedy for such infections is the use of antibiotics, which have detrimental effects on the patient’s microbiome. The microbiome plays an important role in our physical and emotional well-being. In addition, a growing problem with antibiotic resistance makes such treatments less effective at treating infections.

CRISPR-based candidates leave the microbiome intact

An international team of scientists has now engineered the first published CRISPR-based candidate for a targeted drug E. coli directly and leave the microbiome intact. New paper in Natural Biotechnology, Antibacterial engineered phages CRISPR–Cas selectively reduced E. coli the ‘load on mice’ describes the development of the drug candidate to a stage where it is ready for testing in humans.

Through extensive use of synthetic biology, the team designed four bacterial viruses that used CRISPR technology to precisely kill unwanted bacteria.

“We believe that a narrow-spectrum drug with this efficacy could be of great benefit to cancer patients, including those with frequent serious infections that are difficult to treat with current antibiotics,” said Morten Otto Alexander Sommer, professor at DTU Biosustain, co. -founder of SNIPR Biomes, and lead author of this paper.

The work was carried out in collaboration with JAFRAL (Slovenia), JMI Laboratories (USA), and the Division of Infectious Diseases at Weill Cornell Medicine in the US.

Phage engineering to target E. coli

The team, based in the SNIPR Biome, screened a library of 162 naturally occurring phages (viruses that kill certain bacteria). They found that eight of these phages showed promise in targeting E. coli. They then engineered the phages through gene editing to enhance their ability to target E. coli.

This mixture of four phages, which they named SNIPR001, was highly effective at targeting bacteria in biofilms and reducing E. coli counts in a way that surpasses that of natural phages. Furthermore, they demonstrated that the phage cocktail was well tolerated in the intestines of mice and miniature pigs while reducing emergence E. coli. SNIPR001 is now under clinical development and has been granted a Fast Track designation (expedited review) by the US Food and Drug Administration.

General description of the SNIPR001 manufacturing process:

  1. Natural phages were screened with panels E. coli strains.
  2. Phages with broad activity against E. coli are tail fibers engineered and/or armed with the CRISPR–Cas system which contain specific sequences for E. colimake CAPs (Cas-armed phages).
  3. These CAPs were tested for host range, in vivo efficacy, and CMC specifications.

SNIPR001 consists of four complementary CAPs and is a new precision antibiotic that targets selectively E. coli to prevent bacteremia in hematological cancer patients who are at risk of neutropenia (low levels of white blood cells).

Blood cancer patients first in line

The reason this new development is of interest to blood cancer patients has to do with the side effects stemming from their chemotherapy treatment. This causes the patient’s bone marrow to produce less blood cells and inflammation of the intestines. The latter increases gut permeability allowing bacteria from the gut to travel into the bloodstream. This combination of side effects makes the patient susceptible to infections such as bacteria E. coli.

Currently, patients at risk (that is, those with low white blood cell levels) receive antibiotic treatment before their chemotherapy, but in some cases, E. coli show very high resistance to commonly used antibiotics. Also, antibiotics themselves have some side effects which in some cases reduce the effect of cancer treatment.

“We need a wider variety of options for treating these patients, preferably where we can specifically target the bacteria responsible to avoid side effects and not add to the problem of antibiotic resistance,” said Sommer.

In recent years, researchers have looked back at using phages to treat infections due to increasing antibiotic resistance. Before antibiotics became widely available, phages were widely used and studied in countries that were then part of the Soviet Union. However, there have been several clinical trials, and the results have not been conclusive, according to the paper.

“Through new technologies such as CRISPR, the use of phages in treating infections has become a viable pathway. As our results show, there is potential to enhance natural phages through genetic engineering. It is my hope that this approach can also serve as a blueprint for new antimicrobials targeting resistant pathogens,” added Sommer.

CRISPR, phages, and phage therapy

CRISPR technology is a way for scientists to edit DNA sequences in cells. It is based on the defense mechanisms that bacteria naturally use to protect themselves. CRISPR technology uses a molecule called Cas9, which works like a pair of scissors to cut DNA at specific places.

Once cut, DNA can be repaired, or new pieces can be added. Scientists can use these tools to create genetically modified organisms, discover new ways to treat genetic diseases, and learn more about how genes work.

Phages are small viruses that can kill certain bacteria. They are ubiquitous on Earth and help regulate bacterial populations and nutrient cycles. They infect and kill bacteria, and when the bacteria die, they release nutrients into the environment.

Scientists use phages to treat bacterial infections, which is called phage therapy. They identify and isolate phages that can kill certain strains of bacteria and use them to fight infections caused by those strains.

Phage therapy has several advantages over antibiotics, such as targeting specific bacteria without side effects and potentially reducing antibiotic resistance.


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