CRISPR-Cas Vs. Anti-CRISPR Proteins: The Battle Over Antibiotic Resistance In Bacteria

By Dr. Chinta SidharthanReviewed by Lily Ramsey, LLMJul 30 2024

The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) system evolved in bacteria to restrict horizontal gene transfer and as a defense mechanism against bacteriophages.

However, mobile genetic elements such as phages and plasmids have evolved a system known as anti-CRISPR proteins to counteract bacteria's CRISPR-Cas-based defenses.

In a recent review published in Heliyon, researchers discussed the relationship between antibiotic resistance in bacteria and the interactions between the CRISPR-Cas system and anti-CRISPR proteins.

​​​​​​​Study: Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance​​​​​​​. Image Credit: Prostock-studio/Shutterstock.com

Antibiotic Resistance In Bacteria

Horizontal gene transfer occurs when genetic material is exchanged between two organisms that do not have a parent-offspring relationship. The process is vital to bacterial adaptation, especially in acquiring virulence genes and antibiotic resistance.

Horizontal gene transfer can occur between bacteria of different genera, and the spreading of antibiotic resistance genes across genera increases the risk of novel antibiotic-resistant bacterial strains.

Antibiotic resistance genes are also found in mobile genetic elements and can be transferred between bacteria through the various mechanisms of horizontal gene transfer.

These mechanisms include the uptake of free deoxyribonucleic acid (DNA) known as transformation, transduction, where the transfer of genes is mediated by viruses such as phages, and conjugation, which is mediated by plasmids.

CRISPR-Cas Systems and Antibiotic Resistance

The CRISPR-Cas and restriction-modification systems evolved in bacteria as defense mechanisms against phage infection and to prevent the loss of their genome through horizontal gene transfer.

The transfer of mobile genetic elements can be restricted by the CRISPR-Cas system, which also provides the bacteria with heritable immunity against various foreign nucleic acids.

CRISPR-Cas systems play a complex role in antibiotic resistance in bacteria by facilitating and inhibiting antibiotic resistance genes. On one hand, CRISPR-Cas systems prevent the uptake of mobile genetic elements that might benefit the bacteria, such as antibiotic-resistance genes.

Examples include Klebsiella pneumoniae, where CRISPR-Cas systems prevent the uptake of plasmids containing the beta-lactamase gene, conferring antibiotic resistance in carbapenem-sensitive strains and increasing the sensitivity of these strains to antibiotics.

Conversely, antibiotic-sensitive strains of K. pneumoniae and Enterococcus faecalis are found to lack CRISPR-Cas-associated defense mechanisms, increasing their ability to carry out horizontal gene transfer.

On the other hand, CRISPR-Cas systems can also increase antibiotic resistance in bacteria such as Francisella novicida by enhancing membrane integrity and improving the bacteria’s resistance to antibiotics that target the bacterial membrane.

In some bacteria, such as Vibrio cholerae and Neisseria meningitidis, CRISPR-Cas systems are linked to increased transduction rates, allowing greater acquisition of antibiotic-resistance genes.

The decreased permeability of the bacterial envelope in Campylobacter jejuni due to the regulation of ribosomal proteins by the CRISPR-Cas system type II has been found to increase its resistance to the antibiotic erythromycin.

Various studies suggest that factors such as the isolation time of the strain, host, geography, antibiotic type, and bacterial species influence the relationship between antibiotic resistance and CRISPR-Cas systems.

The researchers believe that more research is necessary to understand this relationship and its implications in treating bacterial diseases and infections.

Anti-CRISPR Proteins

The mobile genetic elements have developed a counter-defence mechanism against the CRISPR-Cas system using 50 families of anti-CRISPR proteins that can prevent the effective functioning of various CRISPR systems.

These anti-CRISPR proteins were first identified in bacteriophages that infected Pseudomonas aeruginosa, but have since been identified in phages, plasmids, and genomes of various archaea and bacteria.

Suppressing CRISPR-Cas systems by anti-CRISPR proteins has significantly improved horizontal gene transfer in bacteria and the acquisition of antibiotic-resistance genes.

Anti-CRISPR proteins in P. aeruginosa showed a positive association with resistance to multiple antibiotics such as phenicol, beta-lactam, fosfomycin, and aminoglycoside drugs.

Mobile genetic elements such as phages and plasmids can also carry anti-CRISPR proteins and increase the spread of antibiotic-resistance genes.

However, studies have found that successfully replicating viruses carrying anti-CRISPR proteins requires adequate doses or a critical threshold of anti-CRISPR proteins to overcome the CRISPR-Cas-based immunity of the bacterial host. Inadequate doses of anti-CRISPR proteins can result in a failed infection.

Using CRISPR-Cas Systems Against Antibiotic Resistance

The genome-editing ability of CRISPR-Cas systems can be used to reduce or prevent antibiotic resistance. The type II CRISPR-Cas9 system is especially useful due to its adaptability and simplicity.

Using a single single-guide ribonucleic acid (sgRNA) in Cas 9 to detect specific DNA sequences and cause double-stranded breaks can target antibiotic resistance genes.

CRISPR-Cas systems against bacterial antibiotic resistance can be either genome-focused or pathogen-focused.

In the former approach, the CRISPR-Cas systems can target bacteria's antibiotic resistance and virulence genes and restore their susceptibility to antibiotics.

The pathogen-focused approach involves delivering CRISPR-Cas systems into bacteria using phages or plasmids, and targeting the chromosomal genes of pathogenic bacteria, selectively eliminating pathogenic strains. Both approaches are potentially promising as compared to traditional antimicrobial methods.

Conclusions

Overall, the researchers presented a comprehensive view of CRISPR-Cas systems as a defense mechanism in bacteria against mobile genetic elements and horizontal gene transfer and how this defense mechanism either counters or confers antibiotic resistance.

The review also explained the counter mechanism developed against CRISPR-Cas systems in the form of anti-CRISPR proteins and how these proteins enhance antibiotic resistance in various bacterial species.

While CRISPR-Cas systems could potentially be used to combat antibiotic resistance in bacteria, these findings highlight the need for more research on optimizing their therapeutic efficacy against antibiotic resistance.