151
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CRISPR-Cas9 system: A genome-editing tool with endless possibilities. J Biotechnol 2020; 319:36-53. [DOI: 10.1016/j.jbiotec.2020.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
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152
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Adesanya O, Oduselu T, Akin-Ajani O, Adewumi OM, Ademowo OG. An exegesis of bacteriophage therapy: An emerging player in the fight against anti-microbial resistance. AIMS Microbiol 2020; 6:204-230. [PMID: 33134741 PMCID: PMC7595837 DOI: 10.3934/microbiol.2020014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/19/2020] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages (simply referred to as Phages) are a class of viruses with the ability to infect and kill prokaryotic cells (bacteria), but are unable to infect mammalian cells. This unique ability to achieve specific infectiousness by bacteriophages has been harnessed in antibacterial treatments dating back almost a decade before the antibiotic era began. Bacteriophages were used as therapeutic agents in treatment of dysentery caused by Shigella dysenteriae as far back as 1919 and in the experimental treatment of a wide variety of other bacterial infections caused by Vibriocholerae, Staphylococcussp., Pseudomonas sp. etc, with varying degrees of success. Phage therapy and its many prospects soon fell out of favour in western medicine after the Second World War, with the discovery of penicillin. The Soviet Union and other countries in Eastern Europe however mastered the craft of bacteriophage isolation, purification and cocktail preparation, with phage-based therapeutics becoming widely available over-the-counter. With the recent rise in cases of multi-drug resistant bacterial infections, the clamour for a return to phage therapy, as a potential solution to the anti-microbial resistance (AMR) crisis has grown louder. This review provides an extensive exposé on phage therapy, addressing its historical use, evidences of its safety and efficacy, its pros and cons when compared with antibiotics, cases of compassionate use for treating life-threatening antibiotic-resistant infections, the limitations to its acceptance and how these may be circumvented.
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Affiliation(s)
| | - Tolulope Oduselu
- Department of Medical Laboratory Science, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Olubusuyi M Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olusegun G Ademowo
- Department of Pharmacology & Therapeutics, College of Medicine, University of Ibadan, Ibadan, Nigeria
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153
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Tuminauskaite D, Norkunaite D, Fiodorovaite M, Tumas S, Songailiene I, Tamulaitiene G, Sinkunas T. DNA interference is controlled by R-loop length in a type I-F1 CRISPR-Cas system. BMC Biol 2020; 18:65. [PMID: 32539804 PMCID: PMC7296934 DOI: 10.1186/s12915-020-00799-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/20/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND CRISPR-Cas systems, which provide adaptive immunity against foreign nucleic acids in prokaryotes, can serve as useful molecular tools for multiple applications in genome engineering. Diverse CRISPR-Cas systems originating from distinct prokaryotes function through a common mechanism involving the assembly of small crRNA molecules and Cas proteins into a ribonucleoprotein (RNP) effector complex, and formation of an R-loop structure upon binding to the target DNA. Extensive research on the I-E subtype established the prototypical mechanism of DNA interference in type I systems, where the coordinated action of a ribonucleoprotein Cascade complex and Cas3 protein destroys foreign DNA. However, diverse protein composition between type I subtypes suggests differences in the mechanism of DNA interference that could be exploited for novel practical applications that call for further exploration of these systems. RESULTS Here we examined the mechanism of DNA interference provided by the type I-F1 system from Aggregatibacter actinomycetemcomitans D7S-1 (Aa). We show that functional Aa-Cascade complexes can be assembled not only with WT spacer of 32 nt but also with shorter or longer (14-176 nt) spacers. All complexes guided by the spacer bind to the target DNA sequence (protospacer) forming an R-loop when a C or CT protospacer adjacent motif (PAM) is present immediately upstream the protospacer (at -1 or -2,-1 position, respectively). The range of spacer and protospacer complementarity predetermine the length of the R-loop; however, only R-loops of WT length or longer trigger the nuclease/helicase Cas2/3, which initiates ATP-dependent unidirectional degradation at the PAM-distal end of the WT R-loop. Meanwhile, truncation of the WT R-loop at the PAM-distal end abolishes Cas2/3 cleavage. CONCLUSIONS We provide a comprehensive characterisation of the DNA interference mechanism in the type I-F1 CRISPR-Cas system, which is different from the type I-E in a few aspects. First, DNA cleavage initiation, which usually happens at the PAM-proximal end in type I-E, is shifted to the PAM-distal end of WT R-loop in the type I-F1. Second, the R-loop length controls on/off switch of DNA interference in the type I-F1, while cleavage initiation is less restricted in the type I-E. These results indicate that DNA interference in type I-F1 systems is governed through a checkpoint provided by the Cascade complex, which verifies the appropriate length for the R-loop.
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Affiliation(s)
- Donata Tuminauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Danguole Norkunaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Marija Fiodorovaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Sarunas Tumas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania.,Pressent Address: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania.
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154
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Kiga K, Tan XE, Ibarra-Chávez R, Watanabe S, Aiba Y, Sato'o Y, Li FY, Sasahara T, Cui B, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Azam AH, Suzuki M, Penadés JR, Cui L. Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria. Nat Commun 2020; 11:2934. [PMID: 32523110 PMCID: PMC7287087 DOI: 10.1038/s41467-020-16731-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/13/2020] [Indexed: 02/08/2023] Open
Abstract
The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes. CRISPR technology is emerging as a potential antimicrobial against antimicrobial-resistant bacteria. Here the authors develop a bacteriophage delivered Cas13a system for killing target bacteria and detecting bacterial genes.
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Affiliation(s)
- Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Sato'o
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Feng-Yu Li
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Bintao Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Moriyuki Kawauchi
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Tanit Boonsiri
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Taki
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Aa Haeruman Azam
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - José R Penadés
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan.
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155
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Bretaudeau L, Tremblais K, Aubrit F, Meichenin M, Arnaud I. Good Manufacturing Practice (GMP) Compliance for Phage Therapy Medicinal Products. Front Microbiol 2020; 11:1161. [PMID: 32582101 PMCID: PMC7287015 DOI: 10.3389/fmicb.2020.01161] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
Facing the emergence of difficult-to-treat bacterial infections, the perspective of using bacteriophages has re-gained interest in many countries. In terms of pharmaceutical classification in EU and United States, phages are considered as anti-infectious medicinal products and biological products, given the intended use and their live nature. During the production steps, the compliance with the Good Manufacturing Practice (GMP) represents the gold-standard to ensure the quality, safety and efficacy of medicinal products, either investigational or approved. In practice, the implementation of GMP rules for phage therapy medicinal products benefits from the long history of vaccine development. Accordingly, a well-structured strategy can be defined for each medicinal product, taking into account the specified indication (i.e., the target bacteria species, the infected site, the route of administration, the product composition). Based on the experience of different phage therapy medicinal products from the recent years, the most important requirements to achieve and claim GMP grade are reviewed here, including for genetically modified phages. Like all new medicinal products, the manufacturing of investigational phages incorporates significant challenges. However, the use of GMP-certified phages provides the best guarantee for the rigorous assessment of quality, safety and efficacy during the clinical development of phage medicinal products, thus appears as a key component for the successful development of phage therapy approaches.
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156
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Beta-Lactam Sensitive Bacteria Can Acquire ESBL-Resistance via Conjugation after Long-Term Exposure to Lethal Antibiotic Concentration. Antibiotics (Basel) 2020; 9:antibiotics9060296. [PMID: 32498393 PMCID: PMC7345503 DOI: 10.3390/antibiotics9060296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
Beta-lactams are commonly used antibiotics that prevent cell-wall biosynthesis. Beta-lactam sensitive bacteria can acquire conjugative resistance elements and hence become resistant even after being exposed to lethal (above minimum inhibitory) antibiotic concentrations. Here we show that neither the length of antibiotic exposure (1 to 16 h) nor the beta-lactam type (penam or cephem) have a major impact on the rescue of sensitive bacteria. We demonstrate that an evolutionary rescue can occur between different clinically relevant bacterial species (Klebsiella pneumoniae and Escherichia coli) by plasmids that are commonly associated with extended-spectrum beta-lactamase (ESBL) positive hospital isolates. As such, it is possible that this resistance dynamic may play a role in failing antibiotic therapies in those cases where resistant bacteria may readily migrate into the proximity of sensitive pathogens. Furthermore, we engineered a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-plasmid to encode a guiding CRISPR-RNA against the migrating ESBL-plasmid. By introducing this plasmid into the sensitive bacterium, the frequency of the evolutionarily rescued bacteria decreased by several orders of magnitude. As such, engineering pathogens during antibiotic treatment may provide ways to prevent ESBL-plasmid dispersal and hence resistance evolution.
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157
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Francisella novicida CRISPR-Cas Systems Can Functionally Complement Each Other in DNA Defense while Providing Target Flexibility. J Bacteriol 2020; 202:JB.00670-19. [PMID: 32284320 DOI: 10.1128/jb.00670-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/11/2020] [Indexed: 01/03/2023] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immune systems that facilitate protection of bacteria and archaea against infection by external mobile genetic elements. The model pathogen Francisella novicida encodes a CRISPR-Cas12a (FnoCas12a) system and a CRISPR-Cas9 (FnoCas9) system, the latter of which has an additional and noncanonical function in bacterial virulence. Here, we investigated and compared the functional roles of the FnoCas12a and FnoCas9 systems in transformation inhibition and bacterial virulence. Unlike FnoCas9, FnoCas12a was not required for F. novicida virulence. However, both systems were highly effective at plasmid restriction and acted independently of each other. We further identified a critical protospacer-adjacent motif (PAM) necessary for transformation inhibition by FnoCas12a, demonstrating a greater flexibility for target identification by FnoCas12a than previously appreciated and a specificity that is distinct from that of FnoCas9. The effectors of the two systems exhibited different patterns of expression at the mRNA level, suggesting that they may confer distinct benefits to the bacterium in diverse environments. These data suggest that due to the differences between the two CRISPR-Cas systems, together they may provide F. novicida with a more comprehensive defense against foreign nucleic acids. Finally, we demonstrated that the FnoCas12a and FnoCas9 machineries could be simultaneously engineered to restrict the same nonnative target, thereby expanding the toolset for prokaryotic genome manipulation.IMPORTANCE CRISPR-Cas9 and CRISPR-Cas12a systems have been widely commandeered for genome engineering. However, they originate in prokaryotes, where they function as adaptive immune systems. The details of this activity and relationship between these systems within native host organisms have been minimally explored. The human pathogen Francisella novicida contains both of these systems, with the Cas9 system also exhibiting a second activity, modulating virulence through transcriptional regulation. We compared and contrasted the ability of these two systems to control virulence and restrict DNA within their native host bacterium, highlighting differences and similarities in these two functions. Collectively, our results indicate that these two distinct and reprogrammable endogenous systems provide F. novicida with a more comprehensive defense against mobile genetic elements.
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158
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Ferriol-González C, Domingo-Calap P. Phages for Biofilm Removal. Antibiotics (Basel) 2020; 9:antibiotics9050268. [PMID: 32455536 PMCID: PMC7277876 DOI: 10.3390/antibiotics9050268] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
Biofilms are clusters of bacteria that live in association with surfaces. Their main characteristic is that the bacteria inside the biofilms are attached to other bacterial cells and to the surface by an extracellular polymeric matrix. Biofilms are capable of adhering to a wide variety of surfaces, both biotic and abiotic, including human tissues, medical devices, and other materials. On these surfaces, biofilms represent a major threat causing infectious diseases and economic losses. In addition, current antibiotics and common disinfectants have shown limited ability to remove biofilms adequately, and phage-based treatments are proposed as promising alternatives for biofilm eradication. This review analyzes the main advantages and challenges that phages can offer for the elimination of biofilms, as well as the most important factors to be taken into account in order to design effective phage-based treatments.
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Affiliation(s)
| | - Pilar Domingo-Calap
- Department of Genetics, Universitat de València, 46100 Valencia, Spain;
- Institute for Integrative Systems Biology, ISysBio, Universitat de València-CSIC, 46910 Valencia, Spain
- Correspondence: ; Tel.: +34-963-543-261
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159
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Cooper RM, Hasty J. One-Day Construction of Multiplex Arrays to Harness Natural CRISPR-Cas Systems. ACS Synth Biol 2020; 9:1129-1137. [PMID: 32271547 DOI: 10.1021/acssynbio.9b00489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems are prokaryotic immune systems that have proliferated widely not only in bacteria and archaea, but also much more recently, in human biological research and applications. Much work to date has utilized synthetic sgRNAs along with the CRISPR nuclease Cas9, but the discovery of array-processing nucleases now allows the use of more compact, natural CRISPR arrays in heterologous hosts, in addition to organisms with endogenous systems. Unfortunately, the construction of multiplex natural CRISPR arrays remains technically challenging, expensive, and/or time-consuming. This limitation hampers research involving natural CRISPR arrays in both native and heterologous hosts. To address this problem, we present a method to assemble CRISPR arrays that is simple, rapid, affordable, and highly scalable-we assembled 9-spacer arrays with 1 day's worth of work. We used this method to harness the endogenous CRISPR-Cas system of the highly competent bacterium Acinetobacter baylyi, showing that while single spacers are not always completely effective at blocking DNA acquisition through natural competence, multiplex natural CRISPR arrays enable both nearly complete DNA exclusion and genome editing, including with multiple targets for both. In addition to demonstrating a CRISPR array assembly method that will benefit a variety of applications, we also find a potential bet-hedging strategy for balancing CRISPR defense versus DNA acquisition in naturally competent A. baylyi.
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Affiliation(s)
- Robert M. Cooper
- BioCircuits Institute, University of California, San Diego, La Jolla, California 92093, United States
- San Diego Center for Systems Biology, La Jolla, California 92093, United States
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, California 92093, United States
- San Diego Center for Systems Biology, La Jolla, California 92093, United States
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
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160
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Liu H, Li H, Liang Y, Du X, Yang C, Yang L, Xie J, Zhao R, Tong Y, Qiu S, Song H. Phage-delivered sensitisation with subsequent antibiotic treatment reveals sustained effect against antimicrobial resistant bacteria. Am J Cancer Res 2020; 10:6310-6321. [PMID: 32483454 PMCID: PMC7255016 DOI: 10.7150/thno.42573] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/25/2020] [Indexed: 12/31/2022] Open
Abstract
Temperate phages integrated with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas systems have been gaining attention as potential strategies for combating bacteria resistant to antimicrobials. To further advance this technology, phage recombination procedure should be improved, and the bactericidal effect should be examined in detail and compared with conventional lytic phage strategy. The possibility of the emergence of mutational resistance, a phenomenon commonly observed with lytic phage therapy, should be illustrated. Methods: Here, we developed a novel one-step cloning method to fulfil the recombination of CRISPR/Cas9 system within the genome of a new isolated lysogenic Escherichia coli phage. Then, we proposed and developed a phage-delivered resistance eradication with subsequent antibiotic treatment (PRESA) strategy. The removal efficiency and antimicrobial effect of the plasmids were analysed. Long-term antimicrobial effect was evaluated by continued OD600 monitoring for 240 hours to illustrate the potential mutational resistance, compared with the lytic phage strategy. The treatment effect of PRESA was evaluated in vivo by determining bacterial loads in the skin and intestine of infected mice, in contrast with lytic phage therapy. Genome sequencing was performed to identify mutations in bacterial cells treated with phage strategies. Results: Phage-delivered CRISPR targeting efficiently eradicated and blocked the transfer of the antibiotic resistance plasmid. PRESA decreased the bacterial load by over 6- and 5-logs in vitro and in vivo, respectively. Importantly, while lytic phages induced mutational phage resistance at 24 h in vitro and 48 hours in vivo, PRESA demonstrated a constant effect and revealed no resistant mutants. Genes involved in DNA mismatch repair were upregulated in cells undergoing Cas9-based plasmid cleavage, which may reduce the development of mutations. Conclusion: The PRESA strategy for eradicating resistant bacteria showed high bactericidal efficacy and a sustained inhibition effect against resistant bacteria. By restoring the efficacy of low-cost antibiotics, PRESA could be developed as an efficient and economical therapy for infections of antibiotic resistant bacteria.
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161
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Song W, Sun HX, Zhang C, Cheng L, Peng Y, Deng Z, Wang D, Wang Y, Hu M, Liu W, Yang H, Shen Y, Li J, You L, Xiao M. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic Acids Res 2020; 47:W74-W80. [PMID: 31114893 PMCID: PMC6602508 DOI: 10.1093/nar/gkz380] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/03/2019] [Accepted: 05/17/2019] [Indexed: 01/21/2023] Open
Abstract
Identifying active prophages is critical for studying coevolution of phage and bacteria, investigating phage physiology and biochemistry, and engineering designer phages for diverse applications. We present Prophage Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria. Combining sequence similarity-based matching and genetic features-based machine learning classification, we developed a novel scoring system that exhibits higher accuracy than current tools in predicting active prophages on the validation datasets. The option of skipping similarity matching is also available so that there's higher chance for novel phages to be discovered. Prophage Hunter provides a one-stop web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and annotate the function of phage proteins. Prophage Hunter is freely available at https://pro-hunter.bgi.com/.
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Affiliation(s)
- Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Basic Medical Sciences, Qingdao University, Qingdao 266071, China
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Carolyn Zhang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Li Cheng
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Ye Peng
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Dan Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yun Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Ming Hu
- Department of Basic Medical Sciences, Qingdao University, Qingdao 266071, China
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.,South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
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162
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
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Tagliaferri TL, Guimarães NR, Pereira MDPM, Vilela LFF, Horz HP, Dos Santos SG, Mendes TADO. Exploring the Potential of CRISPR-Cas9 Under Challenging Conditions: Facing High-Copy Plasmids and Counteracting Beta-Lactam Resistance in Clinical Strains of Enterobacteriaceae. Front Microbiol 2020; 11:578. [PMID: 32425894 PMCID: PMC7203346 DOI: 10.3389/fmicb.2020.00578] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/16/2020] [Indexed: 01/21/2023] Open
Abstract
The antimicrobial resistance (AMR) crisis urgently requires countermeasures for reducing the dissemination of plasmid-borne resistance genes. Of particular concern are opportunistic pathogens of Enterobacteriaceae. One innovative approach is the CRISPR-Cas9 system which has recently been used for plasmid curing in defined strains of Escherichia coli. Here we exploited this system further under challenging conditions: by targeting the blaTEM–1 AMR gene located on a high-copy plasmid (i.e., 100–300 copies/cell) and by directly tackling blaTEM–1-positive clinical isolates. Upon CRISPR-Cas9 insertion into a model strain of E. coli harboring blaTEM–1 on the plasmid pSB1A2, the plasmid number and, accordingly, the blaTEM–1 gene expression decreased but did not become extinct in a subpopulation of CRISPR-Cas9 treated bacteria. Sequence alterations in blaTEM–1 were observed, likely resulting in a dysfunction of the gene product. As a consequence, a full reversal to an antibiotic sensitive phenotype was achieved, despite plasmid maintenance. In a clinical isolate of E. coli, plasmid clearance and simultaneous re-sensitization to five beta-lactams was possible. Reusability of antibiotics could be confirmed by rescuing larvae of Galleria mellonella infected with CRISPR-Cas9-treated E. coli, as opposed to infection with the unmodified clinical isolate. The drug sensitivity levels could also be increased in a clinical isolate of Enterobacter hormaechei and to a lesser extent in Klebsiella variicola, both of which harbored additional resistance genes affecting beta-lactams. The data show that targeting drug resistance genes is encouraging even when facing high-copy plasmids. In clinical isolates, the simultaneous interference with multiple genes mediating overlapping drug resistance might be the clue for successful phenotype reversal.
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Affiliation(s)
- Thaysa Leite Tagliaferri
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Natália Rocha Guimarães
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Liza Figueiredo Felicori Vilela
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Simone Gonçalves Dos Santos
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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164
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Xiong S, Liu X, Deng W, Zhou Z, Li Y, Tu Y, Chen L, Wang G, Fu B. Pharmacological Interventions for Bacterial Prostatitis. Front Pharmacol 2020; 11:504. [PMID: 32425775 PMCID: PMC7203426 DOI: 10.3389/fphar.2020.00504] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/31/2020] [Indexed: 12/16/2022] Open
Abstract
Prostatitis is a common urinary tract condition but bring innumerable trouble to clinicians in treatment, as well as great financial burden to patients and the society. Bacterial prostatitis (acute bacterial prostatitis plus chronic bacterial prostatitis) accounting for approximately 20% among all prostatitis have made the urological clinics complain about the genital and urinary systems all over the world. The international challenges of antibacterial treatment (emergence of multidrug-resistant bacteria, extended-spectrum beta-lactamase-producing bacteria, bacterial biofilms production and the shift in bacterial etiology) and the transformation of therapeutic strategy for classic therapy have attracted worldwide attention. To the best of our knowledge currently, there is not a single comprehensive review, which can completely elaborate these important topics and the corresponding treatment strategy in an effective way. This review summarizes the general treatment choices for bacterial prostatitis also provides the alternative pharmacological therapies for those patients resistant or intolerant to general treatment.
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Affiliation(s)
- Situ Xiong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoqiang Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Institute of Urology, Nanchang, China
| | - Wen Deng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Institute of Urology, Nanchang, China
| | - Zhengtao Zhou
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Institute of Urology, Nanchang, China
| | - Yulei Li
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Institute of Urology, Nanchang, China
| | - Yechao Tu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Luyao Chen
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Gongxian Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Institute of Urology, Nanchang, China
| | - Bin Fu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Institute of Urology, Nanchang, China
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165
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Wan P, Cui S, Ma Z, Chen L, Li X, Zhao R, Xiong W, Zeng Z. Reversal of mcr-1-Mediated Colistin Resistance in Escherichia coli by CRISPR-Cas9 System. Infect Drug Resist 2020; 13:1171-1178. [PMID: 32368108 PMCID: PMC7184118 DOI: 10.2147/idr.s244885] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022] Open
Abstract
Purpose The plasmid-borne mobilized colistin resistance gene (mcr-1) was discovered in 2015. Subsequently, the rapid horizontal transfer of mcr-1 gene to diverse bacterial species poses a serious threat to public health, which urgently needs the introduction of novel antimicrobial strategies. Therefore, the purpose of this study is to sensitize bacteria to colistin and reduce the propagation of mcr-1 gene by curing mcr-1-harboring plasmid in Escherichia coli (E. coli) using the CRISPR-Cas9 system. Methods Two sgRNAs specific to mcr-1 gene were designed and cloned into plasmid pCas9. The recombinant plasmid pCas9-mcr was transformed into E. coli carrying pUC19-mcr-1 or pHNSHP45, separately. The elimination efficiency in strains was evaluated by PCR and quantitative real-time PCR (qPCR). The antimicrobial susceptibility test was performed using the broth microdilution method. Results In this study, we constructed the high copy number plasmid pUC19-mcr-1 and recombinant plasmid pCas9-m1 or pCas9-m2, which contain 20 nt or 30 nt sgRNA sequences targeted to mcr-1, respectively. PCR and qPCR results showed that mcr-1-harboring plasmids could be efficiently eliminated, and there was no significant correlation between sgRNA lengths and curing efficiency. However, when comparing restructured high copy number plasmid (pUC19-mcr-1) to natural resistance plasmid (pHNSHP45) in eliminating efficiency, we found that the content of plasmid backbone had an influence on efficiency. Furthermore, the conjugation assays verified that the engineered CRISPR-Cas9 system in bacteria or in bacteria genome can protect the recipient from plasmid-borne mcr-1 transfer via conjugation. Additionally, sequence analysis showed that three different types of defects in CRISPR-Cas9 system lead to escape mutants. Conclusion We presented a method that only one plasmid-mediated CRISPR-Cas9 system can be used to efficiently resensitize E. coli to colistin. Moreover, this system provided a great potentiality to counteract the propagation of mcr-1 among bacterial pathogens.
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Affiliation(s)
- Peng Wan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Shiyun Cui
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Zhenbao Ma
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Lin Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Xiaoshen Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Ruonan Zhao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, People's Republic of China.,National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, People's Republic of China
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Gholizadeh P, Köse Ş, Dao S, Ganbarov K, Tanomand A, Dal T, Aghazadeh M, Ghotaslou R, Ahangarzadeh Rezaee M, Yousefi B, Samadi Kafil H. How CRISPR-Cas System Could Be Used to Combat Antimicrobial Resistance. Infect Drug Resist 2020; 13:1111-1121. [PMID: 32368102 PMCID: PMC7182461 DOI: 10.2147/idr.s247271] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Rapid emergence of antibiotic-resistant bacteria has made it harder for us to combat infectious diseases and to develop new antibiotics. The clustered regularly interspaced short palindromic repeats - CRISPR-associated (CRISPR-Cas) system, as a bacterial adaptive immune system, is recognized as one of the new strategies for controlling antibiotic-resistant strains. The programmable Cas nuclease of this system used against bacterial genomic sequences could be lethal or could help reduce resistance of bacteria to antibiotics. Therefore, this study aims to review using the CRISPR-Cas system to promote sensitizing bacteria to antibiotics. We envision that CRISPR-Cas approaches may open novel ways for the development of smart antibiotics, which could eliminate multidrug-resistant (MDR) pathogens and differentiate between beneficial and pathogenic microorganisms. These systems can be exploited to quantitatively and selectively eliminate individual bacterial strains based on a sequence-specific manner, creating opportunities in the treatment of MDR infections, the study of microbial consortia, and the control of industrial fermentation.
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Affiliation(s)
- Pourya Gholizadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d’Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Khudaverdi Ganbarov
- Department of Microbiology, Baku State University, Baku, Republic of Azerbaijan
| | - Asghar Tanomand
- Department of Basic Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Tuba Dal
- Department of Clinical Microbiology, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Mohammad Aghazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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167
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Phage-Mediated Molecular Detection (PMMD): A Novel Rapid Method for Phage-Specific Bacterial Detection. Viruses 2020; 12:v12040435. [PMID: 32290520 PMCID: PMC7232155 DOI: 10.3390/v12040435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
Bacterial infections pose a challenge to human health and burden the health care system, especially with the spread of antibiotic-resistant populations. To provide effective treatment and improved prognosis, effective diagnostic methods are of great importance. Here we present phage-mediated molecular detection (PMMD) as a novel molecular method for the detection and assessment of bacterial antibiotic resistance. This technique consists of a brief incubation, of approximately ten minutes, of the biological sample with a natural bacteriophage (phage) targeting the bacteria of interest. This is followed by total RNA extraction and RT-PCR. We applied this approach to Staphylococcus aureus (SA), a major causative agent of human bacterial infections. PMMD demonstrated a high sensitivity, rapid implementation, and specificity dependent on the phage host range. Moreover, due to the dependence of the signal on the physiological state of the bacteria, PMMD can discriminate methicillin-sensitive from methicillin-resistant SA (MSSA vs. MRSA). Finally, we extended this method to the detection and antibiotic sensitivity determination of other bacteria by proving PMMD efficacy for Bacillus anthracis.
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168
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Reuter M, Kruger DH. Approaches to optimize therapeutic bacteriophage and bacteriophage-derived products to combat bacterial infections. Virus Genes 2020; 56:136-149. [PMID: 32036540 PMCID: PMC7223754 DOI: 10.1007/s11262-020-01735-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022]
Abstract
The emerging occurrence of antibiotic-resistant bacterial pathogens leads to a recollection of bacteriophage as antimicrobial therapeutics. This article presents a short overview of the clinical phage application including their use in military medicine and discusses the genotypic and phenotypic properties of a potential "ideal" therapeutic phage. We describe current efforts to engineer phage for their improved usability in pathogen treatment. In addition, phage can be applied for pathogen detection, selective drug delivery, vaccine development, or food and surface decontamination. Instead of viable phage, (engineered) phage-derived enzymes, such as polysaccharide depolymerases or peptidoglycan-degrading enzymes, are considered as promising therapeutic candidates. Finally, we briefly summarize the use of phage for the detection and treatment of "Category A priority pathogens".
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Affiliation(s)
- Monika Reuter
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Detlev H. Kruger
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
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169
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McKitterick AC, LeGault KN, Angermeyer A, Alam M, Seed KD. Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: insights from a natural arms race. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180089. [PMID: 30905288 PMCID: PMC6452262 DOI: 10.1098/rstb.2018.0089] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CRISPR-Cas systems function as adaptive immune systems by acquiring nucleotide sequences called spacers that mediate sequence-specific defence against competitors. Uniquely, the phage ICP1 encodes a Type I-F CRISPR-Cas system that is deployed to target and overcome PLE, a mobile genetic element with anti-phage activity in Vibrio cholerae. Here, we exploit the arms race between ICP1 and PLE to examine spacer acquisition and interference under laboratory conditions to reconcile findings from wild populations. Natural ICP1 isolates encode multiple spacers directed against PLE, but we find that single spacers do not interfere equally with PLE mobilization. High-throughput sequencing to assay spacer acquisition reveals that ICP1 can also acquire spacers that target the V. cholerae chromosome. We find that targeting the V. cholerae chromosome proximal to PLE is sufficient to block PLE and is dependent on Cas2-3 helicase activity. We propose a model in which indirect chromosomal spacers are able to circumvent PLE by Cas2-3-mediated processive degradation of the V. cholerae chromosome before PLE mobilization. Generally, laboratory-acquired spacers are much more diverse than the subset of spacers maintained by ICP1 in nature, showing how evolutionary pressures can constrain CRISPR-Cas targeting in ways that are often not appreciated through in vitro analyses. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
- Amelia C McKitterick
- 1 Department of Plant and Microbial Biology, University of California , 111 Koshland Hall, Berkeley, CA 94720 , USA
| | - Kristen N LeGault
- 1 Department of Plant and Microbial Biology, University of California , 111 Koshland Hall, Berkeley, CA 94720 , USA
| | - Angus Angermeyer
- 1 Department of Plant and Microbial Biology, University of California , 111 Koshland Hall, Berkeley, CA 94720 , USA
| | - Munirul Alam
- 2 International Centre for Diarrhoeal Disease Research , Dhaka , Bangladesh
| | - Kimberley D Seed
- 1 Department of Plant and Microbial Biology, University of California , 111 Koshland Hall, Berkeley, CA 94720 , USA.,3 Chan Zuckerberg Biohub , San Francisco, CA 94158 , USA
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170
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Zheng Y, Li J, Wang B, Han J, Hao Y, Wang S, Ma X, Yang S, Ma L, Yi L, Peng W. Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering. Front Bioeng Biotechnol 2020; 8:62. [PMID: 32195227 PMCID: PMC7064716 DOI: 10.3389/fbioe.2020.00062] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/24/2020] [Indexed: 12/18/2022] Open
Abstract
Establishment of production platforms through prokaryotic engineering in microbial organisms would be one of the most efficient means for chemicals, protein, and biofuels production. Despite the fact that CRISPR (clustered regularly interspaced short palindromic repeats)–based technologies have readily emerged as powerful and versatile tools for genetic manipulations, their applications are generally limited in prokaryotes, possibly owing to the large size and severe cytotoxicity of the heterogeneous Cas (CRISPR-associated) effector. Nevertheless, the rich natural occurrence of CRISPR-Cas systems in many bacteria and most archaea holds great potential for endogenous CRISPR-based prokaryotic engineering. The endogenous CRISPR-Cas systems, with type I systems that constitute the most abundant and diverse group, would be repurposed as genetic manipulation tools once they are identified and characterized as functional in their native hosts. This article reviews the major progress made in understanding the mechanisms of invading DNA immunity by type I CRISPR-Cas and summarizes the practical applications of endogenous type I CRISPR-based toolkits for prokaryotic engineering.
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Affiliation(s)
- Yanli Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jie Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Baiyang Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jiamei Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Yile Hao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Shengchen Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiangdong Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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171
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Liang C. New Opportunities to Meet the Grand Challenges in Infectious Diseases. Front Genome Ed 2020; 2:1. [PMID: 34713210 PMCID: PMC8525069 DOI: 10.3389/fgeed.2020.00001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
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172
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Sharma SG, Sharma NR, Sharma M. Impact of Human Microbiome on Health. MICROBIAL DIVERSITY, INTERVENTIONS AND SCOPE 2020. [PMCID: PMC7315774 DOI: 10.1007/978-981-15-4099-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human genome in the recent years, by the advent of technological advancements, has emerged as a major prolocutor for reciprocity between the human body and the food consumed. As known, microbiome comprises all the genetic materials within a microbiota and can thereby be also referred to as metagenome of the microbiota. Contemporary researches have revealed the influence of microbiome not only on human mind and health status, but also in wide range of disease switching, ranging from cardio-metabolic diseases, allergies and obesities to life-threatening diseases such as cancer. Though the complete mechanism of many diseases is yet unclear, research works have revealed that the metabolites, nutrients and microbes can be regarded as the key players for such physiological state. The major approach of this chapter is to enlighten the interrelationship of the microbiome on the human health either in a synergistic or in an antagonistic manner.
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Affiliation(s)
- Shiwani Guleria Sharma
- School of Bioengineering and Biosciences, Lovely Professional Univeristy, Phagwara, Punjab India
| | - Neeta Raj Sharma
- School of Bioengineering and Biosciences, Lovely Professional Univeristy, Phagwara, Punjab India
| | - Mohit Sharma
- Molecular Genetics Laboratory, Dayanand Medical College and Hospital, Ludhiana, Punjab India
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173
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Li Y, Peng N. Endogenous CRISPR-Cas System-Based Genome Editing and Antimicrobials: Review and Prospects. Front Microbiol 2019; 10:2471. [PMID: 31708910 PMCID: PMC6824031 DOI: 10.3389/fmicb.2019.02471] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
CRISPR-Cas systems adapt “memories” via spacers from viruses and plasmids to develop adaptive immunity against mobile genetic elements. Mature CRISPR RNAs guide CRISPR-associated nucleases to site-specifically cleave target DNA or RNA, providing an efficient genome engineering tool for organisms of all three kingdoms. Cas9, Cas12, and Cas13 are single proteins with multiple domains that are the most widely used CRISPR nucleases of the Class 2 system. However, these CRISPR endonucleases are large in size, leading to difficulty for manipulation and toxicity for cells. Most archaeal genomes and half of the bacterial genomes encode different types of CRISPR-Cas systems. Therefore, developing endogenous CRISPR-Cas systems-based genome editing will simplify manipulations and increase editing efficiency in prokaryotic cells. Here, we review the current applications and discuss the prospects of using endogenous CRISPR nucleases for genome engineering and CRISPR-based antimicrobials.
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Affiliation(s)
- Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Large Phenotypic and Genetic Diversity of Prophages Induced from the Fish Pathogen Vibrio anguillarum. Viruses 2019; 11:v11110983. [PMID: 31653117 PMCID: PMC6893619 DOI: 10.3390/v11110983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023] Open
Abstract
Vibrio anguillarum is a marine pathogenic bacterium that causes vibriosis in fish and shellfish. Although prophage-like sequences have been predicted in V. anguillarum strains, many are not characterized, and it is not known if they retain the functional capacity to form infectious particles that can infect and lysogenize other bacterial hosts. In this study, the genome sequences of 28 V. anguillarum strains revealed 55 different prophage-related elements. Chemical and spontaneous induction allowed a collection of 42 phage isolates, which were classified in seven different groups according to a multiplex PCR assay. One shared prophage sequence, p41 (group III), was present in 17 V. anguillarum strains, suggesting that this specific element is very dynamically exchanged among V. anguillarum populations. Interestingly, the host range of genetically identical phages was highly dependent on the strains used for proliferation, indicating that phenotypic properties of phages were partly regulated by the host. Finally, experimental evidence displayed that the induced phage ɸVa_90-11-287_p41 was able to lysogenize V. anguillarum strain Ba35, and subsequently spontaneously become released from the lysogenized cells, demonstrating an efficient transfer of the phage among V. anguillarum strains. Altogether, the results showed large genetic and functional diversity and broad distribution of prophages in V. anguillarum, and demonstrated the potential of prophages as drivers of evolution in V. anguillarum strains.
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175
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Conjugative Delivery of CRISPR-Cas9 for the Selective Depletion of Antibiotic-Resistant Enterococci. Antimicrob Agents Chemother 2019; 63:AAC.01454-19. [PMID: 31527030 DOI: 10.1128/aac.01454-19] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
The innovation of new therapies to combat multidrug-resistant (MDR) bacteria is being outpaced by the continued rise of MDR bacterial infections. Of particular concern are hospital-acquired infections (HAIs) that are recalcitrant to antibiotic therapies. The Gram-positive intestinal pathobiont Enterococcus faecalis is associated with HAIs, and some strains are MDR. Therefore, novel strategies to control E. faecalis populations are needed. We previously characterized an E. faecalis type II CRISPR-Cas system and demonstrated its utility in the sequence-specific removal of antibiotic resistance determinants. Here, we present work describing the adaption of this CRISPR-Cas system into a constitutively expressed module encoded on a pheromone-responsive conjugative plasmid that efficiently transfers to E. faecalis for the selective removal of antibiotic resistance genes. Using in vitro competition assays, we show that these CRISPR-Cas-encoding delivery plasmids, or CRISPR-Cas antimicrobials, can reduce the occurrence of antibiotic resistance in enterococcal populations in a sequence-specific manner. Furthermore, we demonstrate that deployment of CRISPR-Cas antimicrobials in the murine intestine reduces the occurrence of antibiotic-resistant E. faecalis by several orders of magnitude. Finally, we show that E. faecalis donor strains harboring CRISPR-Cas antimicrobials are immune to uptake of antibiotic resistance determinants in vivo Our results demonstrate that conjugative delivery of CRISPR-Cas antimicrobials may be adaptable for future deployment from probiotic bacteria for exact targeting of defined MDR bacteria or for precision engineering of polymicrobial communities in the mammalian intestine.
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176
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Whitfill T, Oh J. Recoding the metagenome: microbiome engineering in situ. Curr Opin Microbiol 2019; 50:28-34. [PMID: 31622928 DOI: 10.1016/j.mib.2019.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/19/2019] [Accepted: 09/06/2019] [Indexed: 12/24/2022]
Abstract
Synthetic biology has enabled a new generation of tools for engineering the microbiome, including targeted antibiotics, protein delivery, living biosensors and diagnostics, and metabolic factories. Here, we discuss opportunities and limitations in microbiome engineering, focusing on a new generation of tools for in situ genetic modification of a microbiome that hold particular promise in circumventing these limitations.
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Affiliation(s)
- Travis Whitfill
- Azitra, Inc., 400 Farmington Ave, Farmington, CT 06032, United States
| | - Julia Oh
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT 06032, United States.
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177
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Dunne M, Rupf B, Tala M, Qabrati X, Ernst P, Shen Y, Sumrall E, Heeb L, Plückthun A, Loessner MJ, Kilcher S. Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. Cell Rep 2019; 29:1336-1350.e4. [DOI: 10.1016/j.celrep.2019.09.062] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/07/2019] [Accepted: 09/19/2019] [Indexed: 01/08/2023] Open
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178
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Songailiene I, Rutkauskas M, Sinkunas T, Manakova E, Wittig S, Schmidt C, Siksnys V, Seidel R. Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length. Cell Rep 2019; 28:3157-3166.e4. [PMID: 31533038 PMCID: PMC6859484 DOI: 10.1016/j.celrep.2019.08.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 12/24/2022] Open
Abstract
The multi-subunit type I CRISPR-Cas surveillance complex Cascade uses its crRNA to recognize dsDNA targets. Recognition involves DNA unwinding and base-pairing between the crRNA spacer region and a complementary DNA strand, resulting in formation of an R-loop structure. The modular Cascade architecture allows assembly of complexes containing crRNAs with altered spacer lengths that promise increased target specificity in emerging biotechnological applications. Here we produce type I-E Cascade complexes containing crRNAs with up to 57-nt-long spacers. We show that these complexes form R-loops corresponding to the designed target length, even for the longest spacers tested. Furthermore, the complexes can bind their targets with much higher affinity compared with the wild-type form. However, target recognition and the subsequent Cas3-mediated DNA cleavage do not require extended R-loops but already occur for wild-type-sized R-loops. These findings set important limits for specificity improvements of type I CRISPR-Cas systems.
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Affiliation(s)
- Inga Songailiene
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Marius Rutkauskas
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Tomas Sinkunas
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Sabine Wittig
- HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Carla Schmidt
- HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania.
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany.
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179
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Potential Benefits and Risks for Soil Health Derived From the Use of Organic Amendments in Agriculture. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9090542] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The use of organic amendments in agriculture is a common practice due to their potential to increase crop productivity and enhance soil health. Indeed, organic amendments of different origin and composition (e.g., animal slurry, manure, compost, sewage sludge, etc.) can supply valuable nutrients to the soil, as well as increase its organic matter content, with concomitant benefits for soil health. However, the application of organic amendments to agricultural soil entails a variety of risks for environmental and human health. Organic amendments often contain a range of pollutants, including heavy metals, persistent organic pollutants, potential human pathogens, and emerging pollutants. Regarding emerging pollutants, the presence of antibiotic residues, antibiotic-resistant bacteria, and antibiotic-resistance genes in agricultural amendments is currently a matter of much concern, due to the concomitant risks for human health. Similarly, currently, the introduction of microplastics to agricultural soil, via the application of organic amendments (mainly, sewage sludge), is a topic of much relevance, owing to its magnitude and potential adverse effects for environmental health. There is, currently, much interest in the development of efficient strategies to mitigate the risks associated to the application of organic amendments to agricultural soil, while benefiting from their numerous advantages.
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180
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Wang P, He D, Li B, Guo Y, Wang W, Luo X, Zhao X, Wang X. Eliminating mcr-1-harbouring plasmids in clinical isolates using the CRISPR/Cas9 system. J Antimicrob Chemother 2019; 74:2559-2565. [PMID: 31203365 DOI: 10.1093/jac/dkz246] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/06/2019] [Accepted: 05/17/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES To eliminate mcr-1-harbouring plasmids and MDR plasmids in clinical Escherichia coli isolates. METHODS Plasmid pMBLcas9 expressing Cas9 was constructed and used to clone target single-guide RNAs (sgRNAs) for plasmid curing. The recombinant plasmid pMBLcas9-sgRNA was transferred by conjugation into two clinical E. coli isolates. The curing efficiency of different sgRNAs targeting conserved genes was tested. The elimination of targeted plasmids and the generation of transposase-mediated recombination of p14EC033a variants were characterized by PCR and DNA sequencing. RESULTS In this study, four native plasmids in isolate 14EC033 and two native plasmids in isolate 14EC007 were successfully eliminated in a step-by-step manner using pMBLcas9. Moreover, two native plasmids in 14EC007 were simultaneously eliminated by tandemly cloning multiple sgRNAs in pMBLcas9, sensitizing 14EC007 to polymyxin and carbenicillin. In 14EC033 with two mcr-1-harbouring plasmids, IncI2 plasmid p14EC033a and IncX4 plasmid p14EC033b, a single mcr-1 sgRNA mediated the loss of p14EC033b and generated a mutant p14EC033a in which the mcr-1 gene was deleted. An insertion element, IS5, located upstream of mcr-1 in p14EC033a was responsible for transposase-mediated recombination, resulting in mcr-1 gene deletion instead of plasmid curing. CONCLUSIONS CRISPR/Cas9 can be used to efficiently sensitize clinical isolates to antibiotics in vitro. For isolates with multiple plasmids, the CRISPR/Cas9 approach can either remove each plasmid in a stepwise manner or simultaneously remove multiple plasmids in one step. Moreover, this approach can be used to delete multiple gene copies by using only one sgRNA. However, caution must be exercised to avoid unwanted recombination events during genetic manipulation.
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Affiliation(s)
- Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Dongmei He
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Baiyuan Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiongjian Luo
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xuanyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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181
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Shapiro RS, Chavez A, Collins JJ. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat Rev Microbiol 2019; 16:333-339. [PMID: 29599458 DOI: 10.1038/s41579-018-0002-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genetic manipulation of microorganisms has been crucial in understanding their biology, yet for many microbial species, robust tools for comprehensive genetic analysis were lacking until the advent of CRISPR-Cas-based gene editing techniques. In this Progress article, we discuss advances in CRISPR-based techniques for the genetic analysis of genetically intractable microorganisms, with an emphasis on mycobacteria, fungi and parasites. We discuss how CRISPR-based analyses in these organisms have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - James J Collins
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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182
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Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
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183
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Shabbir MAB, Shabbir MZ, Wu Q, Mahmood S, Sajid A, Maan MK, Ahmed S, Naveed U, Hao H, Yuan Z. CRISPR-cas system: biological function in microbes and its use to treat antimicrobial resistant pathogens. Ann Clin Microbiol Antimicrob 2019; 18:21. [PMID: 31277669 PMCID: PMC6611046 DOI: 10.1186/s12941-019-0317-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022] Open
Abstract
The development of antibiotic resistance in bacteria is a major public health threat. Infection rates of resistant pathogens continue to rise against nearly all antimicrobials, which has led to development of different strategies to combat the antimicrobial resistance. In this review, we discuss how the newly popular CRISPR-cas system has been applied to combat antibiotic resistance in both extracellular and intracellular pathogens. We also review a recently developed method in which nano-size CRISPR complex was used without any phage to target the mecA gene. However, there is still challenge to practice these methods in field against emerging antimicrobial resistant pathogens.
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Affiliation(s)
- Muhammad Abu Bakr Shabbir
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Muhammad Zubair Shabbir
- Quality Operation Laboratory at University of Veterinary and Animal Sciences, Lahore, 54600 Pakistan
| | - Qin Wu
- National Reference Laboratory of Veterinary Drug Residues and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Sammina Mahmood
- Department of Botany, University of Education, Bank Road Campus, Lahore, Pakistan
| | - Abdul Sajid
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, 23200 Pakistan
| | - Muhammad Kashif Maan
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Saeed Ahmed
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Umer Naveed
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland UK
| | - Haihong Hao
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Zonghui Yuan
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- National Reference Laboratory of Veterinary Drug Residues and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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184
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CTX phage of Vibrio cholerae: Genomics and applications. Vaccine 2019; 38 Suppl 1:A7-A12. [PMID: 31272871 DOI: 10.1016/j.vaccine.2019.06.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/22/2019] [Accepted: 06/11/2019] [Indexed: 01/03/2023]
Abstract
The bipartite genome of Vibrio cholerae is divided into two circular non-homologous chromosomes, which harbor several genetic elements like phages, plasmids, transposons, integrative conjugative elements, and pathogenic islands that encode functions responsible for disease development, antimicrobial resistance, and subsistence in hostile environments. These elements are highly heterogeneous, mobile in nature, and encode their own mobility functions or exploit host-encoded enzymes for intra- and inter-cellular movements. The key toxin of V. cholerae responsible for the life-threatening diarrheal disease cholera, the cholera toxin, is coded by part of the genome of a filamentous phage, CTXϕ. The replicative genome of CTXϕ is divided into two distinct modular structures and has adopted a unique strategy for its irreversible integration into the V. cholerae chromosomes. CTXϕ exploits two host-encoded tyrosine recombinases, XerC and XerD, for its integration in the highly conserved dimer resolution site (dif) of V. cholerae chromosomes. CTXϕ can replicate only in the limited number of Vibrio species. In contrast, the phage integration into the bacterial chromosome does not rely on its replication and could integrate to the dif site of large numbers of gram-negative bacteria. Recent pangenomic analysis revealed that like CTXϕ, the bacterial dif site is the integration spot for several other mobile genetic elements such as plasmids and genomic islands. In this review we discuss about current molecular insights into CTXϕ genomics and its replication and integration mechanisms into hosts. Particular emphasis has been given on the exploitation of CTXϕ genomics knowledge in developing genetic tools and designing environmentally safe recombinant live oral cholera vaccine strains.
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185
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186
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Neil K, Allard N, Jordan D, Rodrigue S. Assembly of large mobilizable genetic cargo by double recombinase operated insertion of DNA (DROID). Plasmid 2019; 104:102419. [PMID: 31247227 DOI: 10.1016/j.plasmid.2019.102419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 01/21/2023]
Abstract
There is an important need to develop new therapeutic tools to modulate the gene content of microbiomes. A potential strategy for microbiome engineering relies on the delivery of genetic payloads by conjugative plasmids. Yet, the introduction of large DNA molecules in conjugative plasmids can be challenging. Here, we describe the Double Recombinase Operated Insertion of DNA (DROID), an efficient method to assemble large DNA molecules without introducing antibiotic resistance genes or other unwanted sequences in the final construct. We exemplify this method by demonstrating that the Bxb1 integrase and FLP recombinase can be used successively to stably insert a relatively large DNA cargo consisting of a CRISPR-Cas9 system in a conjugative plasmid. We further show that the resulting CRISPR-Cas9 mobilization system was able to cure a multi-copy antibiotic resistance plasmid in a target bacterium. In addition to its utility for DNA payload integration in conjugative plasmids, the DROID method could readily be adapted to a multitude of other applications that require the manipulation of large DNA molecules.
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Affiliation(s)
- Kevin Neil
- Department of Biology, University of Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Nancy Allard
- Department of Biology, University of Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - David Jordan
- Department of Biology, University of Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Rodrigue
- Department of Biology, University of Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Centre de recherche du CHUS, Sherbrooke, QC J1H 5N4, Canada.
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187
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Selective antimicrobial activity of cell lytic enzymes in a bacterial consortium. Appl Microbiol Biotechnol 2019; 103:7041-7054. [DOI: 10.1007/s00253-019-09955-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/20/2019] [Accepted: 05/28/2019] [Indexed: 12/30/2022]
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188
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Chevallereau A, Meaden S, van Houte S, Westra ER, Rollie C. The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180094. [PMID: 30905293 PMCID: PMC6452272 DOI: 10.1098/rstb.2018.0094] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2018] [Indexed: 01/07/2023] Open
Abstract
CRISPR-Cas immune systems are present in around half of bacterial genomes. Given the specificity and adaptability of this immune mechanism, it is perhaps surprising that they are not more widespread. Recent insights into the requirement for specific host factors for the function of some CRISPR-Cas subtypes, as well as the negative epistasis between CRISPR-Cas and other host genes, have shed light on potential reasons for the partial distribution of this immune strategy in bacteria. In this study, we examined how mutations in the bacterial mismatch repair system, which are frequently observed in natural and clinical isolates and cause elevated host mutation rates, influence the evolution of CRISPR-Cas-mediated immunity. We found that hosts with a high mutation rate very rarely evolved CRISPR-based immunity to phage compared to wild-type hosts. We explored the reason for this effect and found that the higher frequency at which surface mutants pre-exist in the mutator host background causes them to rapidly become the dominant phenotype under phage infection. These findings suggest that natural variation in bacterial mutation rates may, therefore, influence the distribution of CRISPR-Cas adaptive immune systems. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
| | | | | | - Edze R. Westra
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9EZ, UK
| | - Clare Rollie
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9EZ, UK
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189
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Abstract
Our bodies are colonized by a complex ecosystem of bacteria, unicellular eukaryotes and their viruses that together play a major role in our health. Over the past few years tools derived from the prokaryotic immune system known as CRISPR-Cas have empowered researchers to modify and study organisms with unprecedented ease and efficiency. Here we discuss how various types of CRISPR-Cas systems can be used to modify the genome of gut microorganisms and bacteriophages. CRISPR-Cas systems can also be delivered to bacterial population and programmed to specifically eliminate members of the microbiome. Finally, engineered CRISPR-Cas systems can be used to control gene expression and modulate the production of metabolites and proteins. Together these tools provide exciting opportunities to investigate the complex interplay between members of the microbiome and our bodies, and present new avenues for the development of drugs that target the microbiome. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
| | - David Bikard
- Synthetic Biology Group, Department of Microbiology, Institut Pasteur, Paris 75015, France
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190
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Kim J, Kim GH, Lee NG, Lee JS, Yoon SS. Whole-Genome Sequencing and Genomic Analysis of a Virulent Bacteriophage Infecting Bacillus cereus. Intervirology 2019; 61:272-280. [PMID: 31071714 DOI: 10.1159/000499068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 02/17/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Infants with a weak immune system are prone to infection with Bacillus cereus, which is commonly found in natural environments. With the aim of achieving better control of this pathogenic bacterium, in the present study we characterized a new bacteriophage, ΦBC01. METHODS Bacteriophage particles were analyzed by transmission electron microscopy. Factors influencing adsorption were identified in a double-layer plaque assay. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was conducted to determine the size of major structural proteins. The complete genome of the phage was analyzed. RESULTS Bacteriophage particles (105.3 ± 3.1 nm icosahedral head and 208.8 ± 3.6 nm contractile tail) were identified as Myoviridae. ΦBC01 was found to have host specificity to B. cereus. Major structural proteins of ΦBC01 showed 2 well-pronounced bands of 99 and 56 kDa. The 158,385-bp genome sequence of ΦBC01 was determined: 56 of the 239 open reading frames were annotated, indicating involvement in bacteriophage DNA manipulation, cell lysis, packaging, virion structure, and other functions. CONCLUSION Because of characterization and genotyping of a new bacteriophage from soil samples containing earthworms, this study provides a baseline for the development of alternatives to antibiotics.
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Affiliation(s)
- Jaegon Kim
- Department of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Gyeong-Hwuii Kim
- Department of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Na-Gyeong Lee
- Department of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Jin-Sun Lee
- Department of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Sung-Sik Yoon
- Department of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea,
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191
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Tang C, Liu C, Han Y, Guo Q, Ouyang W, Feng H, Wang M, Xu F. Nontoxic Carbon Quantum Dots/g-C 3 N 4 for Efficient Photocatalytic Inactivation of Staphylococcus aureus under Visible Light. Adv Healthc Mater 2019; 8:e1801534. [PMID: 30941911 DOI: 10.1002/adhm.201801534] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/15/2019] [Indexed: 01/08/2023]
Abstract
The widespread use of antibiotics has caused the rapid emergence of antibiotic-resistant bacterial strains and antibiotic resistance genes in the past few decades. Photocatalytic inactivation, a promising approach for the killing of pathogens, efficiently avoids the problems induced by antimicrobial drugs. However, traditional photocatalysts usually have some disadvantages, such as high costs of raw materials, ultraviolet ray excitation, and potential leaching of toxic metals. Here, a metal-free heterojunction photocatalyst, denoted as CQDs/g-C3 N4 , is synthesized through incorporating carbon quantum dots (CQDs) on graphitic carbon nitride (g-C3 N4 ), which significantly enhances photocatalytic inactivation of Staphylococcus aureus (S. aureus) compared with pure g-C3 N4 in vitro. CQDs/g-C3 N4 causes a rapid increase of intracellular reactive oxygen species levels and destruction of cell membranes under visible light, eventually leading to death of bacteria. The efficacy of CQDs/g-C3 N4 is further examined by a mouse cutaneous infection model of S. aureus. CQDs/g-C3 N4 markedly reduces the bacterial loads and prompts lesion recovery in mice, as compared with g-C3 N4 -treated group. In vivo and in vitro toxicity analyses show that the side effects of CQDs/g-C3 N4 are negligible. Considering the efficient photocatalytic inactivation and nontoxicity of CQDs/g-C3 N4 , this visible-light-driven photocatalyst paves a brand new avenue for the treatment of S. aureus infection.
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Affiliation(s)
- Chenyi Tang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and RecyclingSchool of Environmental Science and EngineeringZhejiang Gongshang University Hangzhou 310012 Zhejiang China
| | - Chao Liu
- Department of Infectious DiseasesThe Second Affiliated HospitalZhejiang University School of Medicine Hangzhou 310009 Zhejiang China
| | - Yu Han
- Department of Infectious DiseasesThe Second Affiliated HospitalZhejiang University School of Medicine Hangzhou 310009 Zhejiang China
| | - Qiaoqi Guo
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and RecyclingSchool of Environmental Science and EngineeringZhejiang Gongshang University Hangzhou 310012 Zhejiang China
| | - Wei Ouyang
- Department of Infectious DiseasesThe Second Affiliated HospitalZhejiang University School of Medicine Hangzhou 310009 Zhejiang China
| | - Huajun Feng
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and RecyclingSchool of Environmental Science and EngineeringZhejiang Gongshang University Hangzhou 310012 Zhejiang China
| | - Meizhen Wang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and RecyclingSchool of Environmental Science and EngineeringZhejiang Gongshang University Hangzhou 310012 Zhejiang China
| | - Feng Xu
- Department of Infectious DiseasesThe Second Affiliated HospitalZhejiang University School of Medicine Hangzhou 310009 Zhejiang China
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192
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Mathieu J, Yu P, Zuo P, Da Silva MLB, Alvarez PJJ. Going Viral: Emerging Opportunities for Phage-Based Bacterial Control in Water Treatment and Reuse. Acc Chem Res 2019; 52:849-857. [PMID: 30925037 DOI: 10.1021/acs.accounts.8b00576] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Water security to protect human lives and support sustainable development is one of the greatest global challenges of this century. While a myriad of water pollutants can impact public health, the greatest threat arises from pathogenic bacteria that can be harbored in different components of water treatment, distribution, and reuse systems. Bacterial biofilms can also promote water infrastructure corrosion and biofouling, which substantially increase the cost and complexity of many critical operations. Conventional disinfection and microbial control approaches are often insufficient to keep up with the increasing complexity and renewed relevance of this pressing challenge. For example, common disinfectants cannot easily penetrate and eradicate biofilms, and are also relatively ineffective against resistant microorganisms. The use of chemical disinfectants is also curtailed by regulations aimed at minimizing the formation of harmful disinfection byproducts. Furthermore, disinfectants cannot be used to kill problematic bacteria in biological treatment processes without upsetting system performance. This underscores the need for novel, more precise, and more sustainable microbial control technologies. Bacteriophages (phages), which are viruses that exclusively infect bacteria, are the most abundant (and perhaps the most underutilized) biological resource on Earth, and hold great promise for targeting problematic bacteria. Although phages should not replace broad-spectrum disinfectants in drinking water treatment, they offer great potential for applications where selective targeting of problematic bacteria is warranted and antimicrobial chemicals are either relatively ineffective or their use would result in unintended detrimental consequences. Promising applications for phage-based biocontrol include selectively suppressing bulking and foaming bacteria that hinder activated sludge clarification, mitigating proliferation of antibiotic resistant strains in biological wastewater treatment systems where broad-spectrum antimicrobials would impair pollutant biodegradation, and complementing biofilm eradication efforts to delay corrosion and biofouling. Phages could also mitigate harmful cyanobacteria blooms that produce toxins in source waters, and could also serve as substitutes for the prophylactic use of antibiotics and biocides in animal agriculture to reduce their discharge to source waters and the associated selective pressure for resistant bacteria. Here, we consider the phage life cycle and its implications for bacterial control, and elaborate on the biochemical basis of such potential application niches in the water supply and reuse cycle. We also discuss potential technological barriers for phage-based bacterial control and suggest strategies and research needs to overcome them.
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Affiliation(s)
- Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Houston, Texas 77005, United States
| | - Pengxiao Zuo
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Marcio L. B. Da Silva
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Houston, Texas 77005, United States
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193
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Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations. Nat Biotechnol 2019; 37:755-760. [DOI: 10.1038/s41587-019-0105-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/13/2019] [Indexed: 01/21/2023]
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194
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Engineering Bacteriophages as Versatile Biologics. Trends Microbiol 2019; 27:355-367. [DOI: 10.1016/j.tim.2018.09.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 01/21/2023]
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195
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Monteiro R, Pires DP, Costa AR, Azeredo J. Phage Therapy: Going Temperate? Trends Microbiol 2019; 27:368-378. [DOI: 10.1016/j.tim.2018.10.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/29/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023]
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196
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Abstract
Infectious diseases remain a global threat contributing to excess morbidity and death annually, with the persistent potential for destabilizing pandemics. Improved understanding of the pathogenesis of bacteria, viruses, fungi, and parasites, along with rapid diagnosis and treatment of human infections, is essential for improving infectious disease outcomes worldwide. Genomic loci in bacteria and archaea, termed clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, function as an adaptive immune system for prokaryotes, protecting them against foreign invaders. CRISPR-Cas9 technology is now routinely applied for efficient gene editing, contributing to advances in biomedical science. In the past decade, improved understanding of other diverse CRISPR-Cas systems has expanded CRISPR applications, including in the field of infectious diseases. In this review, we summarize the biology of CRISPR-Cas systems and discuss existing and emerging applications to evaluate mechanisms of host-pathogen interactions, to develop accurate and portable diagnostic tests, and to advance the prevention and treatment of infectious diseases.
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197
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Rowan-Nash AD, Korry BJ, Mylonakis E, Belenky P. Cross-Domain and Viral Interactions in the Microbiome. Microbiol Mol Biol Rev 2019; 83:e00044-18. [PMID: 30626617 PMCID: PMC6383444 DOI: 10.1128/mmbr.00044-18] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.
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Affiliation(s)
- Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Eleftherios Mylonakis
- Infectious Diseases Division, Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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198
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Parmeciano Di Noto G, Molina MC, Quiroga C. Insights Into Non-coding RNAs as Novel Antimicrobial Drugs. Front Genet 2019; 10:57. [PMID: 30853970 PMCID: PMC6395445 DOI: 10.3389/fgene.2019.00057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/24/2019] [Indexed: 12/21/2022] Open
Abstract
Multidrug resistant bacteria are a serious worldwide problem, especially carbapenem-resistant Enterobacteriaceae (such as Klebsiella pneumoniae and Escherichia coli), Acinetobacter baumannii and Pseudomonas aeruginosa. Since the emergence of extensive and pan-drug resistant bacteria there are few antibiotics left to treat patients, thus novel RNA-based strategies are being considered. Here, we examine the current situation of different non-coding RNAs found in bacteria as well as their function and potential application as antimicrobial agents. Furthermore, we discuss the factors that may contribute in the efficient development of RNA-based drugs, the limitations for their implementation and the use of nanocarriers for delivery.
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Affiliation(s)
- Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Carolina Molina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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199
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Wu ZY, Huang YT, Chao WC, Ho SP, Cheng JF, Liu PY. Reversal of carbapenem-resistance in Shewanella algae by CRISPR/Cas9 genome editing. J Adv Res 2019; 18:61-69. [PMID: 30809393 PMCID: PMC6374997 DOI: 10.1016/j.jare.2019.01.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/26/2022] Open
Abstract
Emergence of carbapenem-resistant S. algae is a severe problem. Re-sensitization of S. algae to carbapenem by CRISPR/Cas9 genome editing. The blaOXA-55-like gene is essential for carbapenem resistance in S. algae. One-plasmid genome editing system for CRISPR/Cas9 genome editing in S. algae. CRISPR/Cas9 genome editing is a promising approach to validate the gene function.
Antibiotic resistance in pathogens is a growing threat to human health. Of particular concern is resistance to carbapenem, which is an antimicrobial agent listed as critically important by the World Health Organization. With the global spread of carbapenem-resistant organisms, there is an urgent need for new treatment options. Shewanella algae is an emerging pathogen found in marine environments throughout the world that has increasing resistance to carbapenem. The organism is also a possible antibiotic resistance reservoir in humans and in its natural habitat. The development of CRISPR/Cas9-based methods has enabled precise genetic manipulation. A number of attempts have been made to knock out resistance genes in various organisms. The study used a single plasmid containing CRISPR/Cas9 and recE/recT recombinase to reverse an antibiotic-resistant phenotype in S. algae and showed blaOXA-55-like gene is essential for the carbapenem resistance. This result demonstrates a potential validation strategy for functional genome annotation in S. algae.
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Affiliation(s)
- Zong-Yen Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Wen-Cheng Chao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shu-Peng Ho
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan.,Department of Physical Therapy, Shu-Zen Junior College of Medicine and Management, Kaohsiung City, Taiwan.,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
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200
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Abstract
Bacteriophages, discovered about a century ago, have been pivotal as models for understanding the fundamental principles of molecular biology. While interest in phage biology declined after the phage "golden era," key recent developments, including advances in phage genomics, microscopy, and the discovery of the CRISPR-Cas anti-phage defense system, have sparked a renaissance in phage research in the past decade. This review highlights recently discovered unexpected complexities in phage biology, describes a new arsenal of phage genes that help them overcome bacterial defenses, and discusses advances toward documentation of the phage biodiversity on a global scale.
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Affiliation(s)
- Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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