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Bacteriophage genome engineering for phage therapy to combat bacterial antimicrobial resistance as an alternative to antibiotics

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Abstract

Bacteriophages (phages) are viruses that mainly infect bacteria and are ubiquitously distributed in nature, especially to their host. Phage engineering involves nucleic acids manipulation of phage genome for antimicrobial activity directed against pathogens through the applications of molecular biology techniques such as synthetic biology methods, homologous recombination, CRISPY-BRED and CRISPY-BRIP recombineering, rebooting phage-based engineering, and targeted nucleases including CRISPR/Cas9, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Management of bacteria is widely achieved using antibiotics whose mechanism of action has been shown to target both the genetic dogma and the metabolism of pathogens. However, the overuse of antibiotics has caused the emergence of multidrug-resistant (MDR) bacteria which account for nearly 5 million deaths as of 2019 thereby posing threats to the public health sector, particularly by 2050. Lytic phages have drawn attention as a strong alternative to antibiotics owing to the promising efficacy and safety of phage therapy in various models in vivo and human studies. Therefore, harnessing phage genome engineering methods, particularly CRISPR/Cas9 to overcome the limitations such as phage narrow host range, phage resistance or any potential eukaryotic immune response for phage-based enzymes/proteins therapy may designate phage therapy as a strong alternative to antibiotics for combatting bacterial antimicrobial resistance (AMR). Here, the current trends and progress in phage genome engineering techniques and phage therapy are reviewed.

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Abbreviations

AIDS:

Acquired immunodeficiency syndrome

AMR:

Antimicrobial resistance

CRISPY-BRED:

CRISPR/Cas9-bacteriophage recombineering with electroporated DNA

CRISPY-BRIP:

CRISPR/Cas9-bacteriophage recombineering with infectious particles

CRISPR-plasmid:

Clustered regularly interspaced short palindromic repeats-plasmid

CRISPR-Cas:

Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins

CRISPR/Cas9:

Clustered regularly interspaced short palindromic repeats/Cas9

DNA:

Deoxyribonucleic acid

DSBs:

DNA double-strand breaks

dsDNA:

Double-stranded DNA

EPA:

Environmental protection agency

FDA:

Food and drug administration

FQs:

Fluoroquinolones

HDR:

Homology-directed repair

HIV:

Human immunodeficiency virus

HR:

Homologous recombination

MDR Bacteria:

Multidrug-resistant bacteria

NHEJ:

Nonhomologous end joining

ORFs:

Open reading frames

RNA:

Ribonucleic acid

ssDNA:

Single-stranded DNA

TALENs:

Transcription activator-like effector nucleases

tRNA:

Transfer RNA

UN:

United Nations

USA:

United States of America

ZFNs:

Zinc-finger nucleases

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  1. Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144401, Punjab, India

    Sani Sharif Usman & Evangeline Christina

  2. Department of Biological Sciences, Faculty of Science, Federal University of Kashere, P.M.B. 0182, Gombe, Nigeria

    Sani Sharif Usman

  3. Department of Molecular Biology and Genetics, Istanbul AREL University, 34537, Istanbul, Türkiye

    Abdullahi Ibrahim Uba

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Sani Sharif Usman and Evangeline Christina conceived the idea; Sani Sharif Usman designed the review and gathered the information; Sani Sharif Usman, Abdullahi Ibrahim Uba and Evangeline Christina wrote the manuscript. The authors read and approved the final manuscript as well as agreed to authorship and submission of the manuscript for review.

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Usman, S.S., Uba, A.I. & Christina, E. Bacteriophage genome engineering for phage therapy to combat bacterial antimicrobial resistance as an alternative to antibiotics. Mol Biol Rep 50, 7055–7067 (2023). https://doi.org/10.1007/s11033-023-08557-4

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