CRISPR-based antimicrobials to obstruct antibiotic-resistant and pathogenic bacteria

Araya, Dennise Palacios; Palmer, Kelli L.; Duerkop, Breck A.

doi:10.1371/journal.ppat.1009672

Cited by 30 publications

(26 citation statements)

References 32 publications

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“…CRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR associated protein) is a bacterial adaptive immune system that uses DNA-encoded, RNA-mediated, or DNA-targeting processes to counter the invasion of bacteria by foreign genetic material and mobile genetic elements, such as plasmids and phages [ 140 , 141 , 142 ]. CRISPR-Cas are genomic engineering tools offering promising new leads as programmable sequence-specific antimicrobials [ 140 , 143 ]. These gene-editing tools can target quantitatively, specifically, and selectively bacterial genomes to reduce or eliminate antibiotic resistance and create new opportunities to treat MDR infections [ 140 , 141 , 142 , 143 , 144 ].…”

Section: Strategies Targeting Antimicrobial-resistant Enzymesmentioning

confidence: 99%

“…CRISPR-Cas are genomic engineering tools offering promising new leads as programmable sequence-specific antimicrobials [ 140 , 143 ]. These gene-editing tools can target quantitatively, specifically, and selectively bacterial genomes to reduce or eliminate antibiotic resistance and create new opportunities to treat MDR infections [ 140 , 141 , 142 , 143 , 144 ]. CRISPR-Cas systems can discriminate between pathogenic and commensal bacteria and are potentially capable of selectively removing AMR genes from bacterial populations and bacterial virulence factors, or sensitizing bacteria to an antibiotic by eliminating plasmids harboring antibiotic resistance genes [ 143 , 145 ].…”

Section: Strategies Targeting Antimicrobial-resistant Enzymesmentioning

confidence: 99%

“…Within all Cas proteins, the ones used that show the most promise for AMR include (i) CRISPR-Cas9, an RNA-guided-DNA cleavage, (ii) dCas9, (iii) nSpCas9:rAPOBEC1, and (iv) Cas13a [ 146 ]. CRISPR-Cas offers new potential with respect to AMR [ 140 , 141 , 142 , 143 , 144 , 145 , 146 , 147 , 148 , 149 , 150 , 151 ]. Further studies are needed to address the limitations while focusing on in vivo experiments [ 145 ], such as (1) the delivery issues addressed by the use of phage-delivery and phagemids, conjugative plasmids, to polymeric nanoparticles; (2) the side effects of potential off-target modifications in the host’s genome [ 145 , 152 , 153 , 154 , 155 ].…”

Section: Strategies Targeting Antimicrobial-resistant Enzymesmentioning

confidence: 99%

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Progress in Alternative Strategies to Combat Antimicrobial Resistance: Focus on Antibiotics

et al. 2022

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Antibiotic resistance, and, in a broader perspective, antimicrobial resistance (AMR), continues to evolve and spread beyond all boundaries. As a result, infectious diseases have become more challenging or even impossible to treat, leading to an increase in morbidity and mortality. Despite the failure of conventional, traditional antimicrobial therapy, in the past two decades, no novel class of antibiotics has been introduced. Consequently, several novel alternative strategies to combat these (multi-) drug-resistant infectious microorganisms have been identified. The purpose of this review is to gather and consider the strategies that are being applied or proposed as potential alternatives to traditional antibiotics. These strategies include combination therapy, techniques that target the enzymes or proteins responsible for antimicrobial resistance, resistant bacteria, drug delivery systems, physicochemical methods, and unconventional techniques, including the CRISPR-Cas system. These alternative strategies may have the potential to change the treatment of multi-drug-resistant pathogens in human clinical settings.

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Section: Strategies Targeting Antimicrobial-resistant Enzymesmentioning

confidence: 99%

Section: Strategies Targeting Antimicrobial-resistant Enzymesmentioning

confidence: 99%

Section: Strategies Targeting Antimicrobial-resistant Enzymesmentioning

confidence: 99%

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Progress in Alternative Strategies to Combat Antimicrobial Resistance: Focus on Antibiotics

et al. 2022

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“…For example, Manipulated cas9 and crRNA of the methicillin resistance gene (mecA) of a phagemid (pDB121:: mecA) for treating a clinical isolate of Staphylococcus aureus showed a reduction of the disease by 49.6% after treatment. 8 , 83 , 84 Studies using a mouse skin colonization model showed that CRISPR/Cas9 in S. aureus significantly reduced S. aureus skin colonization compared to other treatment conditions. 101 Another study by Rodrigues, McBride, Hullahalli, Palmer, Duerkop, chemotherapy 102 showed that CRISPR/Cas9, which targets the erythromycin resistance gene ermB, significantly reduced the overall development of erythromycin-resistant E. faecalis in the intestine after treatment.…”

Section: Applying Crispr-cas System As An Alternative Antimicrobialsmentioning

confidence: 99%

Multidrug-Resistant Microbial Therapy Using Antimicrobial Peptides and the CRISPR/Cas9 System

Getahun¹,

Ali²,

Taye³

et al. 2022

VMRR

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The emergence and spread of multidrug-resistant microbes become a serious threat to animal and human health globally because of their less responsiveness to conventional antimicrobial therapy. Multidrug-resistant microbial infection poses higher morbidity and mortality rate with significant economic losses. Currently, antimicrobial peptides and the CRISPR/Cas9 system are explored as alternative therapy to circumvent the challenges of multidrug-resistant organisms. Antimicrobial peptides are small molecular weight, cationic peptides extracted from all living organisms. It is a promising drug candidate for the treatment of multidrug-resistant microbes by direct microbial killing or indirectly modulating the innate immune system. The CRISPR/Cas9 system is another novel antimicrobial alternative used to manage multidrug-resistant microbial infection. It is a versatile gene-editing tool that uses engineered single guide RNA for targeted gene recognition and the Cas9 enzyme for the destruction of target nucleic acids. Both the CRISPR/Cas9 system and antimicrobial peptides were used to successfully treat nosocomial infections caused by ESKAPE pathogens, which developed resistance to various antimicrobials. Despite, their valuable roles in multidrug-resistant microbial treatments, both the antimicrobial peptides and the CRISPR/Cas systems have various limitations like toxicity, instability, and incurring high manufacturing costs. Thus, this review paper gives detailed explanations of the roles of the CRISPR/Cas9 system and antimicrobial peptides in circumventing the challenges of multidrug-resistant microbial infections, its limitation and prospects in clinical applications.

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“…The past decade has been fundamental in the exploration of novel therapeutic approaches to control bacterial infections. Pioneering studies have demonstrated that engineered CRISPR-Cas systems can be used as sequence-specific antimicrobials to target the bacterial chromosome, thereby killing or inhibiting pathogens, or to eliminate plasmids harboring drug-resistance genes (7, 8). CRISPR-Cas are natural defense mechanisms that work as adaptive immune systems against MGEs (9).…”

Section: Introductionmentioning

confidence: 99%

Efficacy of plasmid-encoded CRISPR-Cas antimicrobial is affected by competitive factors found in wildEnterococcus faecalisisolates

Araya

Islam

Moni

et al. 2022

Preprint

Self Cite

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Enterococcus faecalis is a leading cause of hospital-acquired infections. These infections are becoming more difficult to treat due to the increasing emergence of E. faecalis strains resistant to last resort antibiotics. Over the past decade, multiple groups have engineered the naturally occurring bacterial defense system CRISPR-Cas as a sequence-specific antimicrobial to combat antibiotic-resistant bacteria. We have previously established that the type II CRISPR-Cas system of E. faecalis can be reprogrammed as a CRISPR-Cas antimicrobial and delivered to antibiotic-resistant recipients on a conjugative pheromone-responsive plasmid. Using a co-culture system, we showed sequence-specific depletion of antibiotic resistance from E. faecalis model strains, both in vitro and in vivo. Although this and other studies have demonstrated the potential use for CRISPR-Cas as an antimicrobial, most have deployed the system against model bacterial strains. Thus, there is limited knowledge on how effective these potential therapies are against recently isolated and uncharacterized strains with limited laboratory passage, which we refer to here as wild strains. Here, we compare the efficacy of our previously established CRISPR-Cas antimicrobials against both E. faecalis model strains and wild E. faecalis fecal isolates. We demonstrate that these wild isolates can antagonize the CRISPR-Cas antimicrobial donor strain via competitive factors like cytolysin. Furthermore, we show that the wild isolates can effectively prevent delivery of the CRISPR-Cas antimicrobial plasmids, consequently avoiding CRISPR-Cas targeting. Our results emphasize the requisite to study CRISPR-Cas antimicrobials against wild strains to understand limitations and develop delivery systems that can endure competitive interspecies interactions in the gut microenvironment and effectively deliver CRISPR-Cas antimicrobials to their intended targets.

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CRISPR-based antimicrobials to obstruct antibiotic-resistant and pathogenic bacteria

Cited by 30 publications

References 32 publications

Progress in Alternative Strategies to Combat Antimicrobial Resistance: Focus on Antibiotics

Progress in Alternative Strategies to Combat Antimicrobial Resistance: Focus on Antibiotics

Multidrug-Resistant Microbial Therapy Using Antimicrobial Peptides and the CRISPR/Cas9 System

Efficacy of plasmid-encoded CRISPR-Cas antimicrobial is affected by competitive factors found in wildEnterococcus faecalisisolates

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