**9.1 The clustered regularly interspaced short palindromic repeats – CRISPR-associated (CRISPR-Cas) system**

The clustered regularly interspaced short palindromic repeats – CRISPRassociated (CRISPR-Cas) system is a bacterial adaptive immune system, which is used for controlling antibiotic-resistant strains. Moreover, the programmable Cas nuclease of this system can totally diminish or reduce the resistance of bacteria to antibiotics [93].

The Cas (CRISPR-associated) nucleases identify a specific sequence of DNA by establishing a complex with a CRISPR-RNA (crRNA) that has sequence homology to the target4,5. The crRNA-Cas complex binds to the target and leads to DNA damage [95].

Interestingly, the CRISPR-Cas system is precise and easily programmable, so CRISPR-based tools for genome editing are magnificently applied nowadays in eukaryotes and prokaryotes [96].

Eukaryotic cells can repair DNA breaks using the error-prone non-homologous end joining (NHEJ) mechanisms but most prokaryotes lack NHEJ mechanisms, wherefore continuous DNA damage leads to cell death if not repaired through homologous recombination. This phenomenon has been exploited for the development of CRISPR-Cas based antimicrobials [95]. The most important advantage for CRISPR-Cas antimicrobials is the discrimination and elimination of specific bacteria at the strain level such as *E. coli* [95, 96].

CRISPR-Cas provides acquired immunity against viruses and plasmids. In the treatment of *E. coli*, CRISPR-encoded immunity is provided by transcription of the repeat-spacer array, followed by transcript processing into small crRNAs (CRISPR RNAs), which are then used in combination with Cas proteins as guides to interfere with invasive DNA or RNA. In *E. coli*, few model systems have been established to study of CRISPR/Cas functionality [97].

The CRISPR2 and CRISPR4 systems present in the *S. thermophilus* DGCC7710 genome belong to the TypeIII (Mtube) and Type I (*E. coli*), respectively. Differences between types can be observed in terms of repeat, spacer, and Cas gene content and sequence. The multiplicity of CRISPR/Cas systems in *S. thermophilus* is explained by their susceptibility to horizontal gene transfer, and phage selective pressure [98].

#### **9.2 Phage therapy**

Bacteriophages are bacteria-specific viruses, which can specifically infect and lyse bacteria. Phage therapy has been used to treat MDR *E. coli* that are resistant to last resort antibiotics. It is considered one of the most effective weapons for combating MDR *E. coli* [99, 100].

An example of phages used to treat *E. coli* is VB\_EcoS-Golestan which is a virulent phage that belongs to *Kagunavirus* genus of *Guernseyvirinae* subfamily, *Siphoviridae* family. VB\_EcoS-Golestan has many advantages in the treatment of UPEC specifically such as broad host range specificity, a rapid adsorption time, large burst size, and high stability at a wide range of pH and temperatures, which makes it a promising agent against *E. coli* infections [101].

Since phage therapy is still an under-study therapeutic approach, further development of this method requires biological characterization of bacteriophages such as their host specificity, genome diversity, and adaption to their bacterial hosts.

#### **9.3 Nanoparticles**

Nowadays, nanoparticles are one of the safest, cost-effective, and most effective bactericidal materials, which can be efficiently used as carriers of therapeutic agents [102].

Unfortunately, one of the major obstacles facing us when using silver nanoparticles is their high toxicity toward mammalian cells but to a lesser extent than pathogenic bacterial cells [103]. On the other hand, silver is less dangerous to mammalian cells than other metals [104]. Silver nanoparticles (Ag NPs or nanosilver), a kind of nanosized silver particle, are widely used NPs and show strong broad-spectrum biocidal effects on pathogenic bacteria, including MDR *E. coli* [104, 105].

Escherichia coli *(*E. coli*) Resistance against Last Resort Antibiotics and Novel Approaches… DOI: http://dx.doi.org/10.5772/intechopen.104955*

Furthermore, Gold NPs may become useful in the development of antibacterial strategies due to their polyvalent effects, versatility in surface modification, and nontoxicity [106, 107].

Cui et al. could develop a strategy to fight against MDR bacteria via presenting inactive small organic molecules, such as 4, 6-diamino-2-pyrimidinethiol on gold NPs (Au\_DAPT NPs), which act on *E. coli* such as disorganizing cell membranes, binding to nucleic acids, and inhibiting protein synthesis [108].

The Gold NPs antibacterial mechanism of action is to change membrane potential and inhibit ATP synthase activities to decrease the ATP level, indicating a general decline in metabolism; and inhibition of the ribosome subunit for tRNA binding, resulting in a collapse of biological process [108, 109].
