Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance

Abstract

The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.

Keywords: Anti-CRISPR proteins; Antibiotic resistance genes; CRISPR-Cas system; Horizontal gene transfer; Mobile genetic elements.

Fig. 1

Acr-phages cooperation to suppress CRISPR-Cas system immunity. Bacteria use CRISPR-Cas systems to protect themselves against bacteriophages (phages), and some phages produce anti-CRISPR proteins that inhibit immune system function. Acr-phages often need to cooperate to overcome CRISPR-Cas system resistance. During the initial stages of infection, anti-CRISPR proteins produced by phage genomes suppress the host bacterium's initial immune response, which predisposes the cell to successful infection by other phages in the population. When Acr-phages encounter CRISPR-Cas system immunity, the production of anti-CRISPR does not guarantee phage replication; but instead, if the number of Acr-phages falls below a critical threshold, the host bacterium survives. Viral replication occurs only if multiple Acr-phage genomes deliver a sufficient dose of anti-CRISPR to a single cell.

Fig. 2

CRISPR-Cas9 System-based Approaches to combat bacterial infection. ARGs can be carried on a plasmid and/or a chromosome, conferring resistance toward antibiotic treatment. The antibiotic-resistant bacteria are transduced with engineered phages carrying the CRISPR-Cas9 system. Identification and cleavage of the ARG sequence on a plasmid or chromosome by sgRNA/Cas9 complex causes bacterial cell re-sensitization or death, respectively.

Fig. 3

Schematic illustration of engineered anti-CRISPR gene-containing phages in suppressing bacterial infections. Normally, phage infection activates the bacterial CRISPR-Cas system, which prevents phage replication by cleavage of phage genomes, resulting in preserving bacterial homeostasis, and eventually bacterial growth. EATPs suppress the bacterial CRISPR-Cas system-mediated adaptive immunity to protect their associated phage genomes by producing anti-CRISPR proteins, resulting in a large quantity proliferation of phages and, eventually, host bacteria's lysis.