CRISPR Could Serve as an Invaluable Tool for Combating Bacterial Antibiotic Resistance

CRISPR Could Serve as an Invaluable Tool for Combating Bacterial Antibiotic Resistance

One of the biggest problems in medicine is not finding new antibiotics to treat bacterial infections, although that is certainly important, but making sure that the ones that have been developed continue to work. Unfortunately, antibiotic resistance is now a major problem and one that will get considerably worse.

Currently several strains of bacteria are resistant to most of the treatments that used to be so effective. For example, Neisseria gonorrhoeae which causes gonorrhea and Clostridioides difficile, which causes infectious diarrhea.

Antibiotic resistance is considered a public health crisis now. Figures from the Centers for Disease Control and Prevention show there are around 2.8 million infections involving antibiotic resistant bacteria each year and 35,000 people die as a result. Last year, the Organization for Economic Co-operation and Development estimated that in 30 years, around a million individuals in the United States will have died from antibiotic resistant bacterial infections.

Researchers at the University of California San Diego School of Medicine may have found a solution: The CRISPR-Cas9 gene editing tool. CRISPR-Cas9 is being used to make edits to the DNA of cells to remove harmful mutations and to replace defective genes and clinical trials in humans have now started in the United States. This tool could also potentially be used to tackle antibiotic resistance.

The researchers have developed a modified version of CRISPR-Cas9 called Pro-AG. Pro-AG does not target human DNA, instead it is being used to deactivate a gene in bacteria that provides antibiotic resistance. Remove the resistance and standard antibiotic treatments will continue to work. The Pro-AG system takes its name from pro-active genetics, which relates to the inheritance of preferred traits.

One of the main problems with targeting resistance in bacteria is the plasmids: Circular forms of DNA that can replicate independently of the bacterial genome. Multiple plasmids exist inside bacterial cells and they can transfer antibiotic resistance to other bacteria.

Pro-AG performs a cut and repair of the antibiotic-resistant gene which disrupts its activity. The system has a self-amplifying editing mechanism that improves in efficiency through a positive feedback loop and the Pro-AG system works at 2.5 orders of magnitude greater than the cut and destroy methods currently being used.

The researchers tested the Pro-AG system in cultures of ampicillin-resistant bacteria with high numbers of plasmids and were able to insert genetic payloads into the resistance gene and thus disrupt the resistance process.

“A human delivery system carrying Pro-AG could be deployed to address conditions such as cystic fibrosis, chronic urinary infections, tuberculosis and infections associated with resistant biofilms that pose difficult challenges in hospital settings,” said Nizet, distinguished professor of Pediatrics and Pharmacy and the faculty lead of the UC San Diego Collaborative to Halt Antibiotic-Resistant Microbes (CHARM).

In addition to treating diseases in patients, the system could also be used to target populations of resistant bacteria in the environment, such as in sewers to remove antibiotic resistance in populations of Clostridioides difficile.

The technique is detailed in the paper – A bacterial gene-drive system efficiently edits and inactivates a high copy number antibiotic resistance locus – which was recently published in the journal Nature Communications. DOI: 10.1038/s41467-019-13649-6

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