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      Phage engineering and phage‐assisted CRISPR‐Cas delivery to combat multidrug‐resistant pathogens

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          Abstract

          Antibiotic resistance ranks among the top threats to humanity. Due to the frequent use of antibiotics, society is facing a high prevalence of multidrug resistant pathogens, which have managed to evolve mechanisms that help them evade the last line of therapeutics. An alternative to antibiotics could involve the use of bacteriophages (phages), which are the natural predators of bacterial cells. In earlier times, phages were implemented as therapeutic agents for a century but were mainly replaced with antibiotics, and considering the menace of antimicrobial resistance, it might again become of interest due to the increasing threat of antibiotic resistance among pathogens. The current understanding of phage biology and clustered regularly interspaced short palindromic repeats (CRISPR) assisted phage genome engineering techniques have facilitated to generate phage variants with unique therapeutic values. In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR‐Cas9‐assisted phage engineering for effective and more specific targeting of bacterial pathogens. Lastly, we discuss techniques that either help to increase the fitness, specificity, or lytic ability of bacteriophages to control an infection.

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          Most cited references175

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          The global burden of nontyphoidal Salmonella gastroenteritis.

          To estimate the global burden of nontyphoidal Salmonella gastroenteritis, we synthesized existing data from laboratory-based surveillance and special studies, with a hierarchical preference to (1) prospective population-based studies, (2) "multiplier studies," (3) disease notifications, (4) returning traveler data, and (5) extrapolation. We applied incidence estimates to population projections for the 21 Global Burden of Disease regions to calculate regional numbers of cases, which were summed to provide a global number of cases. Uncertainty calculations were performed using Monte Carlo simulation. We estimated that 93.8 million cases (5th to 95th percentile, 61.8-131.6 million) of gastroenteritis due to Salmonella species occur globally each year, with 155,000 deaths (5th to 95th percentile, 39,000-303,000 deaths). Of these, we estimated 80.3 million cases were foodborne. Salmonella infection represents a considerable burden in both developing and developed countries. Efforts to reduce transmission of salmonellae by food and other routes must be implemented on a global scale.
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            Origins and evolution of antibiotic resistance.

            Antibiotics have always been considered one of the wonder discoveries of the 20th century. This is true, but the real wonder is the rise of antibiotic resistance in hospitals, communities, and the environment concomitant with their use. The extraordinary genetic capacities of microbes have benefitted from man's overuse of antibiotics to exploit every source of resistance genes and every means of horizontal gene transmission to develop multiple mechanisms of resistance for each and every antibiotic introduced into practice clinically, agriculturally, or otherwise. This review presents the salient aspects of antibiotic resistance development over the past half-century, with the oft-restated conclusion that it is time to act. To achieve complete restitution of therapeutic applications of antibiotics, there is a need for more information on the role of environmental microbiomes in the rise of antibiotic resistance. In particular, creative approaches to the discovery of novel antibiotics and their expedited and controlled introduction to therapy are obligatory.
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              CRISPR–Cas9 Structures and Mechanisms

              Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific double-stranded breaks in target DNA. Target recognition strictly requires the presence of a short protospacer adjacent motif (PAM) flanking the target site, and subsequent R-loop formation and strand scission are driven by complementary base pairing between the guide RNA and target DNA, Cas9–DNA interactions, and associated conformational changes. The use of CRISPR–Cas9 as an RNA-programmable DNA targeting and editing platform is simplified by a synthetic single-guide RNA (sgRNA) mimicking the natural dual trans-activating CRISPR RNA (tracrRNA)–CRISPR RNA (crRNA) structure. This review aims to provide an in-depth mechanistic and structural understanding of Cas9-mediated RNA-guided DNA targeting and cleavage. Molecular insights from biochemical and structural studies provide a framework for rational engineering aimed at altering catalytic function, guide RNA specificity, and PAM requirements and reducing off-target activity for the development of Cas9-based therapies against genetic diseases.
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                Author and article information

                Contributors
                suri28@hanyang.ac.kr , suresh.ramakris@gmail.com
                vijaisingh15@gmail.com , vijai.singh@indrashiluniversity.edu.in
                Journal
                Bioeng Transl Med
                Bioeng Transl Med
                10.1002/(ISSN)2380-6761
                BTM2
                Bioengineering & Translational Medicine
                John Wiley & Sons, Inc. (Hoboken, USA )
                2380-6761
                06 August 2022
                March 2023
                : 8
                : 2 ( doiID: 10.1002/btm2.v8.2 )
                : e10381
                Affiliations
                [ 1 ] Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
                [ 2 ] School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry United Kindgom
                [ 3 ] Department of Microbiology Gargi College, University of Delhi New Delhi India
                [ 4 ] Center for Biomedicine and Community Health International School, Vietnam National University Hanoi Vietnam
                [ 5 ] Faculty of Applied Sciences International School, Vietnam National University Hanoi Vietnam
                [ 6 ] Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea
                [ 7 ] Hanyang Biomedical Research Institute Hanyang University Seoul South Korea
                [ 8 ] College of Medicine Hanyang University Seoul South Korea
                [ 9 ] Department of Clinical Laboratories Sciences College of Applied Medical Sciences, Taif University Taif Saudi Arabia
                Author notes
                [*] [* ] Correspondence

                Suresh Ramakrishna, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.

                Email: suri28@ 123456hanyang.ac.kr and suresh.ramakris@ 123456gmail.com

                Vijai Singh, Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India.

                Email: vijaisingh15@ 123456gmail.com and vijai.singh@ 123456indrashiluniversity.edu.in

                Author information
                https://orcid.org/0000-0001-5154-8779
                https://orcid.org/0000-0002-6642-7096
                https://orcid.org/0000-0002-5485-9190
                https://orcid.org/0000-0001-7690-5517
                https://orcid.org/0000-0002-4596-2022
                https://orcid.org/0000-0001-7379-3994
                https://orcid.org/0000-0002-6688-0106
                https://orcid.org/0000-0002-4038-1085
                https://orcid.org/0000-0002-6394-4370
                Article
                BTM210381
                10.1002/btm2.10381
                10013820
                36925687
                e99ec668-c21c-44fd-9fd4-5d1603d329fa
                © 2022 The Authors. Bioengineering & Translational Medicine published by Wiley Periodicals LLC on behalf of American Institute of Chemical Engineers.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 30 June 2022
                : 23 March 2022
                : 16 July 2022
                Page count
                Figures: 4, Tables: 2, Pages: 23, Words: 19717
                Funding
                Funded by: Indian Council of Medical Research , doi 10.13039/501100001411;
                Award ID: 5/3/8/41/ITR‐F/2022‐ITR
                Award ID: 5/3/8/63/ITR‐F/2020
                Funded by: Korean Fund for Regenerative Medicine (KFRM)
                Award ID: 22A0304L1‐01
                Funded by: National Research Foundation of Korea , doi 10.13039/501100003725;
                Award ID: 2018M3A9B5024066
                Award ID: 2021M3A9H3015389
                Award ID: 2021R1I1A1A01049524
                Funded by: Taif University Researchers Supporting Program
                Award ID: TURSP‐2020/128
                Categories
                Review Article
                Review Articles
                Custom metadata
                2.0
                March 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.6 mode:remove_FC converted:14.03.2023

                crispr‐cas9 system,infection,microflora,multidrug resistance,pathogens,phage

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