Harnessing CRISPR to Battle Antimicrobial Resistance


A novel approach using this emerging technology looks to interfere with antibiotic resistance expression and reduce this global health issue.


CRISPR-Cas can cut the DNA at designated spots. This action facilitates either the deletion of unwanted genes or the introduction of new genetic material into an organism's cells, paving the way for advanced therapies.

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) gene editing technology is a Nobel Prize-winning method that allows for precise alterations to the genomes of living organisms.

CRISPR-Cas enables researchers to target and modify specific segments of an organism's DNA. Functioning like molecular ‘scissors’ with the guidance of guide RNA (gRNA), CRISPR-Cas can cut the DNA at designated spots. This action facilitates either the deletion of unwanted genes or the introduction of new genetic material into an organism's cells, paving the way for advanced therapies.

Separately, antimicrobial resistance (AMR) causes an estimated 1.2 million deaths per year, globally. This issue continues to be a major challenge in health care.

With CRISPR-Cas, it seems an appropriate, potential strategy to address AMR, and possibly aid in reducing this public health issue. HIV is another area within infectious disease that is looking at CRISPR-Cas technology to aid in fighting that virus.

‘Induce Bacterial Cell-Death’
At the ongoing ESCMID Global Congress, new research shows how the CRISPR-Cas gene editing technology can be used to help modify and attack AMR bacteria. A presentation was by Rodrigo Ibarra-Chávez, PhD, Department of Biology, University of Copenhagen, Denmark.

One area of their studies involves creating guided systems against antimicrobial resistance genes could treat infections and prevent dissemination of resistance genes.

“Fighting fire with fire, we are using CRISPR-Cas systems as an innovative strategy to induce bacterial cell-death or interfere with antibiotic resistance expression,” Ibarra-Chávez said in a previously released statement.

What You Need to Know

CRISPR-Cas gene editing technology shows promise as an innovative strategy to combat AMR.

Researchers are exploring the use of mobile genetic elements (MGEs) and phage satellites, which are parasites of phages, as delivery mechanisms for CRISPR-Cas systems.

To address the adaptability of bacteria and the risk of developing resistance to CRISPR-Cas systems, researchers advocate for combinatorial strategies.

Mobile genetic elements (MGEs) are parts of the bacterial genome that can move about to other host cells or also transfer to another species. These elements drive bacterial evolution via horizontal gene transfer. Repurposing mobile genetic elements (MGEs) and choosing the delivery mechanism involved in the antimicrobial strategy is important for reaching the target bacterium.

A phage is a virus that infects bacteria, and it is also considered MGE, as some can remain dormant in the host cell and transfer vertically. The MGEs Ibarra-Chávez's team is using are phage satellites, which are parasites of phages. 

“These phage satellites hijack parts of the viral particles of phages to ensure their transfer to host cells. In contrast to phages, satellites can infect bacteria without destroying them, offering a step-change over existing methods involving phages and thus developing an arsenal of viral particles that are safe to use for applications such as detection and modification via gene delivery," Ibarra-Chávez said. "Phage particles are very stable and easy to transport and apply in medical settings. It is our task to develop safe guidelines for their application and understand the resistance mechanisms that bacteria can develop.”

Bacteria can evolve to evade the action of the CRISPR-Cas system and delivery vectors can be vulnerable to anti-MGE defenses. Ibarra-Chávez’s team and others are developing the use of anti-CRISPRs and defense inhibitors in the delivery payloads to counter these defenses, to enable the CRISPR to arrive and attack the AMR genes in the cell.

During the conference, Ibarra-Chávez discussed how combination strategies employing CRISPR-Cas systems could promote antibiotic susceptibility in a target bacterial population. Phages have a particular selective pressure on AMR cells, which can improve the effect of some antibiotics. Similarly, using CRISPR-Cas in combination with phages and/or antibiotics, it is possible to suppress the mechanisms of resistance that infectious bacteria may develop by targeting such virulence/resistance genes, making these therapies safer.

“Bacteria are particularly good at adapting and becoming resistance. I believe we need to be cautious and try using combinatorial strategies to avoid the development of resistance, while monitoring and creating guidelines of new technologies,” he said.

Next Steps in the Research
Ibarra-Chávez has focused primarily on tackling resistance in Staphylococcus aureus and Escherichia coli, and is currently working with others in finding ways to combat group A Streptococci necrotizing soft tissue infection.

“Both [approaches] hold promise as novel sequence-specific targeted antimicrobials,” Ibarra-Chávez concluded.

Ibarra-Chávez R. How to use CRISPR-Cas to combat AMR. Poster # 3749 Presented at ESCMID. April 27-30, 2024. Barcelona, Spain.

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