CRISPR-Cas: A Promising Tool For Combatting Antibiotic-Resistant Staphylococcus aureus

By Dr. Chinta SidharthanReviewed by Lily Ramsey, LLMAug 12 2024

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) systems evolved in bacteria as defense mechanisms against bacteriophages but have proven to be an extremely valuable tool in genetic engineering and for the detection of various microorganisms, including disease-causing pathogens.

In a recent review published in Heliyon, researchers examined using CRISPR-Cas systems in various studies to detect and treat Staphylococcus aureus.

​​​​​​​Study: The application of CRISPR-Cas system in Staphylococcus aureus infection. Image Credit: Ivan Marc/Shutterstock.com

Staphylococcus aureus Infections

Although S. aureus is normally found among the bacterial flora in the human body, when the body undergoes a low immunity state for a variety of reasons, the proliferation of S. aureus can cause a range of infections from food poisoning and skin infections such as boils, sores, and abscesses to potentially life-threatening conditions such as endocarditis, meningitis, and pneumonia.

Apart from the genes constituting its core genome and some core-variable genes, S. aureus also carries mobile genetic elements that can be horizontally transferred between S. aureus cells.

These mobile genetic elements facilitate pathogenic evolution and the acquisition and spread of antimicrobial resistance.

Antibiotic-resistant strains of S. aureus are responsible for a large proportion of nosocomial infections and significantly increase the rates of morbidity and mortality. They are also responsible for substantial disability-adjusted life-years.

CRISPR-Cas System

The CRISPR-Cas system has exhibited high specificity and sensitivity in the detection of pathogens, and studies have found that it plays a role in inhibiting the spread of antimicrobial-resistant genes between S. aureus cells by preventing horizontal gene transfer.

The evolutionary role of the CRISPR-Cas system was to protect the bacteria and archaea cells against invading bacteriophages or genetic elements such as plasmids.

The mechanism through which CRISPR-Cas protected the bacteria involved the generation of specific double-stranded breaks in the deoxyribonucleic acid (DNA) of invading viruses or mobile genetic elements.

This ability of CRISPR-Cas to target specific sequences and generate double-stranded breaks was leveraged not only for gene editing but also for studying the resistance and virulence genes in bacteria, leading to the development of more accurate diagnostic techniques and targeted treatment methods.

The system consists of repetitive nucleotide sequences or repeats interspersed with spacers, which are non-repetitive sequences. Ribonucleic acid (RNA) guides, known as CRISPR RNA or crRNA, are used to guide the nucleases or Cas proteins to the targeted site of the invading genetic element or viral genetic material and cleave them.

There are two classes of CRISPR-Cas systems, each with specific applications and distinct mechanisms of action.

CRISPR-Cas Applications in S. aureus Infections

CRISPR-Cas systems provide a precise and efficient method to understand and treat the pathogenicity of bacteria such as S. aureus. Its role in gene editing is vital to deciphering the pathways and mechanisms contributing to various bacteria' drug resistance and pathogenicity.

Compared to traditional gene editing methods, the CRISPR-Cas9 system provides a rapid, marker-free gene manipulation method to conduct gene knockouts to study the function of specific genes in S. aureus and their contributions to pathogenicity.

The use of programmed and optimized guide RNA or crRNA can further improve the various applications of the CRISPR-Cas9 system, including insertion, deletion, activation, or repression of genes.

The review discussed several CRISPR-based systems developed for S. aureus editing, including a combination of Streptococcus pyogenes Cas9 with a plasmid system expression CRISPR-Cas9.

The CRISPR interference system, which uses a catalytically inactive Cas9 protein, has also been used extensively for gene silencing and knockdown experiments. However, the inactive Cas9 protein causes toxicity in high concentrations.

The application of CRISPR-Cas systems has been especially important in detecting S. aureus, including the methicillin-resistant strain, with high sensitivity and specificity.

The CRISPR-Cas13a system has proven extremely accurate in detecting the target DNA even at very low concentrations and has been used extensively in the food industry to detect S. aureus contamination.

Combining the accuracy and specificity of CRISPR-Cas-based detection methods with nucleic-acid amplification technologies such as polymerase chain reaction, recombinase polymerase amplification, and loop-mediated isothermal amplification have further enhanced the detection performance and have been applied widely to differentiate infections caused by methicillin-resistant S. aureus (MRSA) from other bacterial infections.

Other CRISPR-based detection methods include CRISPR-mediated DNA-fluorescence in-situ hybridization (FISH), which can distinguish between the methicillin-resistant and methicillin-sensitive strains of S. aureus.

The ability of CRISPR-Cas systems to target and cleave specific sequences also provides a promising treatment method for re-sensitizing or eliminating strains of S. aureus that are resistant to drugs.

The delivery of CRISPR-Cas9 antimicrobials using bacteriophages has been applied to selectively target MRSA without damaging the host's microbiome.

Furthermore, CRISPR-Cas systems can also be used to edit bacteriophages to enhance their bactericidal activity and use them to specifically target S. aureus.

Studies have found that modified bacteriophages have been effective against biofilm-associated infections, providing a promising approach to treating persistent bacterial infections.

Conclusions

To conclude, CRISPR-Cas systems provide a promising option for rapidly detecting pathogens and developing effective antimicrobial therapies. However, off-target effects, toxicity, and inefficient delivery continue to pose challenges.

Furthermore, the evolution of anti-CRISPR systems in bacteria exacerbates the severity of antimicrobial-resistant bacterial infections.

Further research is required to improve the efficiency and applications of CRISPR-Cas systems in antimicrobial therapy.