CRISPR gene-drive technology reverses antibiotic resistance in bacteria

Antibiotic resistance is a rapidly escalating global health crisis. The emergence of “superbugs” – bacteria that have evolved to resist drug treatments – threatens to reverse decades of progress in fighting infectious diseases, with projections estimating more than 10 million deaths worldwide annually by 2050.

A New Approach to Combating Resistance

Scientists are increasingly turning to innovative technologies to address this urgent threat. Researchers at the University of California San Diego have recently applied advanced genetic tools to directly counteract antibiotic resistance, focusing on areas where these resistant bacteria thrive, including hospitals, sewage treatment plants, animal husbandry operations, and fish farms.

Leveraging CRISPR Technology

The laboratories of Professors Ethan Bier and Justin Meyer at UC San Diego School of Biological Sciences have developed a novel method for removing antibiotic resistance elements from bacterial populations. This new technology, called pPro-MobV, builds upon the principles of gene drives – a technique already being explored to disrupt the spread of harmful traits in insects, such as those that cause malaria.

Did You Know? In 2019, the initial Pro-AG concept was developed through collaboration between Professor Bier’s lab and the group led by Professor Victor Nizet at UC San Diego School of Medicine.

“With pPro-MobV we have brought gene-drive thinking from insects to bacteria as a population engineering tool,” said Bier. “With this new CRISPR-based technology we can take a few cells and let them go to neutralize AR in a large target population.”

The initial Pro-AG concept, developed in 2019, involves introducing a genetic cassette that copies itself between bacterial genomes, effectively disabling antibiotic resistance. This cassette targets antibiotic resistance genes carried on plasmids – circular DNA structures within bacterial cells – restoring the bacteria’s sensitivity to antibiotics.

Spreading the Solution

Building on this foundation, the researchers created pPro-MobV, a system that spreads these antibiotic-disabling CRISPR cassette components through a process resembling bacterial “mating,” known as conjugal transfer. As detailed in the journal npj Antimicrobials and Resistance, this next-generation system utilizes naturally occurring tunnels between bacterial cells to distribute the key disabling elements.

Importantly, the researchers demonstrated the effectiveness of pPro-MobV within bacterial biofilms – complex communities of microorganisms that adhere to surfaces and are notoriously difficult to eradicate with conventional cleaning methods. Biofilms contribute significantly to disease spread and are present in the majority of serious infections, partly because they create a protective barrier against antibiotics.

Expert Insight: The ability to target antibiotic resistance within biofilms is particularly significant, as these structures represent a major clinical challenge in both healthcare settings and enclosed environments like aquafarms and wastewater treatment facilities.

Bier noted, “The biofilm context for combatting antibiotic resistance is particularly important since this is one of the most challenging forms of bacterial growth to overcome in the clinic or in enclosed environments such as aquafarm ponds and sewage treatment plants.” He also highlighted that reducing the transmission of resistance from animals to humans – estimated to account for roughly half of all cases – could have a substantial impact.

Future Possibilities

The research team also discovered that components of this genetic system could be delivered by bacteriophages, viruses that naturally prey on bacteria. These engineered phages are already being developed to combat antibiotic resistance by overcoming bacterial defenses and introducing disruptive elements. The pPro-MobV elements could potentially work in conjunction with these engineered viruses.

As a safety measure, the system incorporates a process called homology-based deletion, allowing for the removal of the gene cassette if desired. Meyer stated, “This technology is one of the few ways that I’m aware of that can actively reverse the spread of antibiotic-resistant genes, rather than just slowing or coping with their spread.”

Frequently Asked Questions

What is pPro-MobV?

pPro-MobV is a new CRISPR-based technology developed by researchers at UC San Diego to remove antibiotic resistance elements from bacterial populations. It is a second-generation tool building on previous work and utilizes a process similar to gene drives.

Where do antibiotic-resistant bacteria commonly flourish?

Antibiotic-resistant bacteria are known to flourish in hospital settings, sewage treatment areas, animal husbandry locations, and fish farms.

How does pPro-MobV work within bacterial biofilms?

pPro-MobV spreads antibiotic CRISPR cassette components via conjugal transfer, utilizing naturally created bacterial mating tunnels to distribute disabling elements even within the protective structure of biofilms.

As research continues, could this technology offer a turning point in the fight against antibiotic resistance and the growing threat of superbugs?