Harnessing the CRISPR-Cas Systems to Combat Antimicrobial Resistance

Abstract

The emergence of antimicrobial-resistant (AMR) bacteria has become one of the most serious threats to global health, necessitating the development of novel antimicrobial strategies. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system, known as a bacterial adaptive immune system, can be repurposed to selectively target and destruct bacterial genomes other than invasive genetic elements. Thus, the CRISPR-Cas system offers an attractive option for the development of the next-generation antimicrobials to combat infectious diseases especially those caused by AMR pathogens. However, the application of CRISPR-Cas antimicrobials remains at a very preliminary stage and numerous obstacles await to be solved. In this mini-review, we summarize the development of using type I, type II, and type VI CRISPR-Cas antimicrobials to eradicate AMR pathogens and plasmids in the past a few years. We also discuss the most common challenges in applying CRISPR-Cas antimicrobials and potential solutions to overcome them.

Keywords: CRISPR-Cas system; antimicrobial resistance; genome targeting; phage delivery; plasmid curing.

Figure 1

Stages of the CRISPR-Cas adaptive immunity. CRISPR-Cas immunity consists of three stages: adaptation, crRNA biogenesis, and interference. During adaptation, a DNA fragment of the invading genetic elements, such as a phage genome, is captured and incorporated into the CRISPR array to generate a new spacer (pink). During crRNA biogenesis, the entire CRISPR array is transcribed into a long pre-crRNA which is further processed into mature crRNAs. During interference, the crRNA specifically recognizes a target protospacer sequence in the invaders by base pairing and guides the Cas effector to destruct the targets.

Figure 2

Working mechanisms and delivery of CRISPR-Cas antimicrobials. (A) Antimicrobial applications based on the endogenous and heterogeneous CRISPR-Cas systems are shown using the phage-based delivery as an example. In the strains containing an active CRISPR-Cas system (upper panel), a single mini-CRISPR element is required to express a crRNA to guide the endogenously expressed Cas effector to specifically destruct the host genome or cure the AMR plasmid, which results in the killing or re-sensitizing of the AMR pathogens, respectively. Mini-CRISPR and cas genes can also be co-delivered into the target cells to achieve bacterial genome destruction or plasmid curing (lower panel). (B) Delivery strategies for CRISPR-Cas antimicrobials: phage-based delivery (left), conjugative plasmid-based delivery (middle), and nanoparticle-based delivery (right).