CRISPR is promising to tackle antimicrobial resistance, but remember bacteria can fight back
Experts looking to use the Nobel winning technology to target resistance genes and make bacteria sensitive to first line antibiotics again; but the bacteria have ways to fight back
EUROPEAN SOCIETY OF CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES
In the second new research review on this subject, Assistant Prof. Ibrahim Bitar, Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic, will give an overview of the molecular biology of CRISPR technology in explaining how it can used to tackle antimicrobial resistance.
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR associated genes (cas) are widespread in the genome of many bacteria and are a defence mechanism against foreign invaders such as plasmids and viruses. The CRISPR arrays are composed of a repeated array of short sequences, each originating from and exactly matching a nucleic acid sequence that once invaded the host.
Accompanying CRISPR sequences, there are 4-10 CRISPR-associated genes (cas), which are highly conserved and encode the Cas proteins. Cas proteins conduct adaptive immunity in prokaryotes (bacteria) based on immunological memories stored in the CRISPR array. The CRISPR/Cas system integrates a small piece of foreign DNA from invaders such as plasmids and viruses into their direct repeat sequences and will recognise and degrade the same external DNA elements during future invasions.
As the CRISPR/Cas systems integrate DNA from invading pathogens in chronical order, genotyping can be used to trace the clonality and the origin of the isolates and define them as a population of strains that were subjected to the same environmental conditions including geographic location (region) and community/hospital settings and eventually further extended to track pathogenic bacteria around human society.
CRISPR/Cas systems can also be employed for developing antimicrobial agents: introduction of self-targeting crRNAs will effectively and selectively kill target bacterial populations. Due to the shortage of available effective antimicrobial agents in treating multidrug-resistant (MDR) infections, researchers started to search for alternative methods to fight MDR infections rather than going through the process of developing new antimicrobial agents which can go on for decades. As a result, the concept of CRISPR/Cas-based selective antimicrobials was first developed and demonstrated in 2014. Vectors coding Cas9 and guide RNAs targeting genomic loci of a specific bacterial strain/species can be delivered to the target strain via bacteriophages or conjugative bacterial strains. In theory, delivery of the engineered CRISPR/Cas systems specifically eliminates target strains from the bacterial population, yet it is not that simple.
While these systems can seem a target for manipulation/intervention, all bacteria are regulated by multiple pathways to ensure the bacteria retains control over the process. Therefore, there remain several major challenges in using this system as an antimicrobial agent.
Most methods require delivery of the re-sensitised system by conjugation; the vector is carried by a non-virulent lab strain bacteria that is supposed to go and share the vector/plasmid through conjugation. The conjugation process is a natural process that the bacteria do which results in sharing plasmids among each other (even with other species). The percentage of conjugated (successfully delivered) bacteria in the total bacterial population is critical to the re-sensitised efficiency. This process is governed by several complicated pathways.
Bacteria also possess built-in anti-CRISPR systems, that can repair any damage caused by CRISPR-Cas systems. Defence systems that the bacteria uses to protect itself from foreign DNA often co-localise within defence islands (genomic segments that contain genes with similar function in protecting the host from invaders) in bacterial genomes; for example: acr (a gene that acts, with other similar variants, as a repressor of plasmid conjugative systems) often cluster with antagonists of other host defence functions (e.g., anti-restriction modification systems) and experts hypothesise that MGEs (mobile genetic elements) organise their counter defence strategies in “anti-defence” islands.
Assistant Professor Bitar concludes: “In summary, this method seems very promising as an alternative way of fighting antimicrobial resistance. The method uses the concept of re-sensitising the bacteria in order to make use of already available antibiotics – in other words, removing their resistance and making them vulnerable again to first-line antibiotics. Nevertheless, the bacterial pathways are always complicated and such systems are always heavily regulated by multiple pathways. These regulated pathways must be studied in depth in order to avoid selective pressure favoring anti-CRISPR systems activation, hence prevalence of resistance in a more aggressive manner.”
Experts developing way to harness Nobel Prize winning CRISPR technology to deal with antimicrobial resistance (AMR)
Antimicrobial resistance (AMR) is continuing to increase globally, with rates of AMR in most pathogens increasing and threatening a future in which every day medical procedures may no longer be possible and infections thought long dealt with could kill regularly again. As such, new tools to battle AMR are vitally needed.
In a new research review at this year’s ESCMID Global Congress (formerly ECCMID – Barcelona 27-30 April) shows how the latest CRISPR-Cas gene editing technology can be used to help modify and attack AMR bacteria. The presentation is by Dr Rodrigo Ibarra-Chávez, Department of Biology, University of Copenhagen, Denmark.
CRISPR-Cas gene editing technology is a groundbreaking method in molecular biology that allows for precise alterations to the genomes of living organisms. This revolutionary technique, which brought its inventors, Jennifer Doudna and Emmanuelle Charpentier, the Nobel Prize in Chemistry in 2020, enables scientists to accurately target and modify specific segments of an organism's DNA (genetic code). 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.
Dr Ibarra-Chávez says: “Fighting fire with fire, we are using CRISPR-Cas systems (a bacterial immunity system) as an innovative strategy to induce bacterial cell-death or interfere with antibiotic resistance expression – both hold promise as novel sequence-specific targeted ‘antimicrobials’.”
One line of their work involves creating guided systems against antimicrobial resistance genes could treat infections and prevent dissemination of resistance genes.
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. Dr Ibarra-Chávez explains how 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 his team is using are phage satellites, which are parasites of phages. He says: “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. 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 mechanisms to evade the action of the CRISPR-Cas system and delivery vectors can be vulnerable to anti-MGE defences. Thus Dr Ibarra-Chávez’s team and others are developing the use of anti-CRISPRs and defence inhibitors in the delivery payloads to counter these defences, to enable the CRISPR to arrive and attack the AMR genes in the cell.
Dr Ibarra-Chávez will also discuss 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.
He explains: “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.”
Dr Ibarra-Chávez has primarily focused on tackling resistance in Staphylococcus aureus and Escherichia coli. Now, in collaboration with Prof. Martha Clokie and Prof. Thomas Sicheritz-Pontén, his team will treat group A Streptococci necrotising soft tissue infection (flesh eating bacteria) using the combination approaches described above.
ARTICLE PUBLICATION DATE
26-Apr-2024
No comments:
Post a Comment