1
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Gruzdev N, Katz C, Yadid I. Curing of a field strain of Salmonella enterica serovar Infantis isolated from poultry from its highly stable pESI like plasmid. J Microbiol Methods 2024; 222:106959. [PMID: 38782300 DOI: 10.1016/j.mimet.2024.106959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Salmonella enterica serovar Infantis (S. infantis) is an important emerging pathogen, associated with poultry and poultry products and related to an increasing number of human infections in many countries. A concerning trend among S. infantis isolates is the presence of plasmid-mediated multidrug resistance. In many instances, the genes responsible for this resistance are carried on a megaplasmid known as the plasmid of emerging S. infantis (pESI) or pESI like plasmids. Plasmids can be remarkably stable due to the presence of multiple replicons and post-segregational killing systems (PSKs), which contribute to their maintenance within bacterial populations. To enhance our understanding of S. infantis and its multidrug resistance determinants toward the development of new vaccination strategies, we have devised a new method for targeted plasmid curing. This approach effectively overcomes plasmid addiction by leveraging the temporal overproduction of specific antitoxins coupled with the deletion of the partition region. By employing this strategy, we successfully generated a plasmid-free strain from a field isolate derived from S. infantis 119,944. This method provides valuable tools for studying S. infantis and its plasmid-borne multidrug resistance mechanisms and can be easily adopted for plasmid curing from other related bacteria.
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Affiliation(s)
- Nadya Gruzdev
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel
| | - Chen Katz
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel
| | - Itamar Yadid
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel; Tel-Hai College, Upper Galilee 1220800, Israel.
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2
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Aliakbari M, Karkhane AA. In vivo cloning of PCR product via site-specific recombination in Escherichia coli. Appl Microbiol Biotechnol 2024; 108:400. [PMID: 38951186 PMCID: PMC11217044 DOI: 10.1007/s00253-024-13239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/02/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Over the past years, several methods have been developed for gene cloning. Choosing a cloning strategy depends on various factors, among which simplicity and affordability have always been considered. The aim of this study, on the one hand, is to simplify gene cloning by skipping in vitro assembly reactions and, on the other hand, to reduce costs by eliminating relatively expensive materials. We investigated a cloning system using Escherichia coli harboring two plasmids, pLP-AmpR and pScissors-CmR. The pLP-AmpR contains a landing pad (LP) consisting of two genes (λ int and λ gam) that allow the replacement of the transformed linear DNA using site-specific recombination. After the replacement process, the inducible expressing SpCas9 and specific sgRNA from the pScissors-CmR (CRISPR/Cas9) vector leads to the removal of non-recombinant pLP-AmpR plasmids. The function of LP was explored by directly transforming PCR products. The pScissors-CmR plasmid was evaluated for curing three vectors, including the origins of pBR322, p15A, and pSC101. Replacing LP with a PCR product and fast-eradicating pSC101 origin-containing vectors was successful. Recombinant colonies were confirmed following gene replacement and plasmid curing processes. The results made us optimistic that this strategy may potentially be a simple and inexpensive cloning method. KEY POINTS: •The in vivo cloning was performed by replacing the target gene with the landing pad. •Fast eradication of non-recombinant plasmids was possible by adapting key vectors. •This strategy is not dependent on in vitro assembly reactions and expensive materials.
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Affiliation(s)
- Moein Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Asghar Karkhane
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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3
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Gupta SS, Hamza Kh M, Sones CL, Zhang X, Sivaraman GK. The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems. Funct Integr Genomics 2024; 24:110. [PMID: 38806846 DOI: 10.1007/s10142-024-01362-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/30/2024]
Abstract
With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.
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Affiliation(s)
- Sobin Sonu Gupta
- Founder & CEO at Times of Biotech, Navelim Bicholim, Goa-403505, India
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Muneeb Hamza Kh
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Collin L Sones
- Founder and CTO of Highfield Diagnostics, Zepler Institute of Photonics and Nanoelectronics, University of Southampton, SO17 1BJ, Southampton, UK
| | - Xunli Zhang
- School of Engineering & Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India.
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4
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Zhang H, Chen B, Wang Z, Peng K, Liu Y, Wang Z. Resensitizing tigecycline- and colistin-resistant Escherichia coli using an engineered conjugative CRISPR/Cas9 system. Microbiol Spectr 2024; 12:e0388423. [PMID: 38385691 PMCID: PMC10986596 DOI: 10.1128/spectrum.03884-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Tigecycline and colistin were referred to as the "last resort" antibiotics in defending against carbapenem-resistant, Gram-negative bacterial infections, and are currently widely used in clinical treatment. However, the emergence and prevalence of plasmid-mediated tet(X4) and mcr-1 genes pose a serious threat to the therapeutic application of tigecycline and colistin, respectively. In this research, a tigecycline- and colistin-resistant bacteria resensitization system was developed based on efficient and specific DNA damage caused by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Associated Protein 9 (Cas9) nucleases. A conjugation method was used to deliver the resensitization system, which harbors two single-guide RNAs targeting tet(X4) and mcr-1 genes and constitutively expressed Cas9. The conjugation efficiency was nearly 100% after conjugation condition optimization in vitro, and the resensitivity efficiency for clinical isolates was over 90%. In addition, when performing resensitization in vivo, the resistance marker was replaced with a glutamate-based, chromosomal, plasmid-balanced lethal system to prevent the introduction of additional resistance genes in clinical settings, making this strategy a therapeutic approach to combat the in vivo spread of antibiotic resistance genes (ARGs) among bacterial pathogens. As a proof of concept, this resensitive system can significantly decrease the counts of tigecycline- and colistin-resistant bacteria to 1% in vivo. Our study demonstrates the efficacy and adaptability of CRISPR-Cas systems as powerful and programmable antimicrobials in resensitizing tet(X4)- and mcr-1-mediated, tigecycline- and colistin-resistant strains, and opens up new pathways for the development of CRISPR-based tools for selective bacterial pathogen elimination and precise microbiome composition change. IMPORTANCE The emergence of plasmid-encoded tet(X4) and mcr-1 isolated from human and animal sources has affected the treatment of tigecycline and colistin, and has posed a significant threat to public health. Tigecycline and colistin are considered as the "last line of defense" for the treatment of multidrug-resistant (MDR) Gram-negative bacterial infections, so there is an urgent need to find a method that can resensitize tet(X4)-mediated tigecycline-resistant and mcr-1-mediated colistin-resistant bacteria. In this study, we developed a glutamate-based, chromosomal, plasmid-balanced lethal conjugative CRISPR/Cas9 system, which can simultaneously resensitize tet(X4)-mediated tigecycline-resistant and mcr-1-mediated colistin-resistant Escherichia coli. The counts of tigecycline- and colistin-resistant bacteria decreased to 1% in vivo after the resensitization system was administered. This study opens up new pathways for the development of CRISPR-based tools for selective bacterial pathogen elimination and precise microbiome composition change.
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Affiliation(s)
- Haijie Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Bo Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zeyu Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Kai Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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5
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Leung PB, Matanza XM, Roche B, Ha KP, Cheung HC, Appleyard S, Collins T, Flanagan O, Marteyn BS, Clements A. Shigella sonnei utilises colicins during inter-bacterial competition. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001434. [PMID: 38376387 PMCID: PMC10924462 DOI: 10.1099/mic.0.001434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024]
Abstract
The mammalian colon is one of the most densely populated habitats currently recognised, with 1011-1013 commensal bacteria per gram of colonic contents. Enteric pathogens must compete with the resident intestinal microbiota to cause infection. Among these enteric pathogens are Shigella species which cause approximately 125 million infections annually, of which over 90 % are caused by Shigella flexneri and Shigella sonnei. Shigella sonnei was previously reported to use a Type VI Secretion System (T6SS) to outcompete E. coli and S. flexneri in in vitro and in vivo experiments. S. sonnei strains have also been reported to harbour colicinogenic plasmids, which are an alternative anti-bacterial mechanism that could provide a competitive advantage against the intestinal microbiota. We sought to determine the contribution of both T6SS and colicins to the anti-bacterial killing activity of S. sonnei. We reveal that whilst the T6SS operon is present in S. sonnei, there is evidence of functional degradation of the system through SNPs, indels and IS within key components of the system. We created strains with synthetically inducible T6SS operons but were still unable to demonstrate anti-bacterial activity of the T6SS. We demonstrate that the anti-bacterial activity observed in our in vitro assays was due to colicin activity. We show that S. sonnei no longer displayed anti-bacterial activity against bacteria that were resistant to colicins, and removal of the colicin plasmid from S. sonnei abrogated anti-bacterial activity of S. sonnei. We propose that the anti-bacterial activity demonstrated by colicins may be sufficient for niche competition by S. sonnei within the gastrointestinal environment.
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Affiliation(s)
- P. B. Leung
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - X. M. Matanza
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - B. Roche
- Universite de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9002, F-67000 Strasbourg, France
| | - K. P. Ha
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - H. C. Cheung
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - S. Appleyard
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - T. Collins
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - O. Flanagan
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - B. S. Marteyn
- Universite de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9002, F-67000 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), F-67000 Strasbourg, France
- Institut Pasteur, Université de Paris, Inserm U1225, Unité de Pathogenèse des Infections Vasculaires, F-75015 Paris, France
| | - A. Clements
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
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6
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Castañeda-Barba S, Top EM, Stalder T. Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era. Nat Rev Microbiol 2024; 22:18-32. [PMID: 37430173 DOI: 10.1038/s41579-023-00926-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/12/2023]
Abstract
Antimicrobial resistance (AMR) poses a substantial threat to human health. The widespread prevalence of AMR is, in part, due to the horizontal transfer of antibiotic resistance genes (ARGs), typically mediated by plasmids. Many of the plasmid-mediated resistance genes in pathogens originate from environmental, animal or human habitats. Despite evidence that plasmids mobilize ARGs between these habitats, we have a limited understanding of the ecological and evolutionary trajectories that facilitate the emergence of multidrug resistance (MDR) plasmids in clinical pathogens. One Health, a holistic framework, enables exploration of these knowledge gaps. In this Review, we provide an overview of how plasmids drive local and global AMR spread and link different habitats. We explore some of the emerging studies integrating an eco-evolutionary perspective, opening up a discussion about the factors that affect the ecology and evolution of plasmids in complex microbial communities. Specifically, we discuss how the emergence and persistence of MDR plasmids can be affected by varying selective conditions, spatial structure, environmental heterogeneity, temporal variation and coexistence with other members of the microbiome. These factors, along with others yet to be investigated, collectively determine the emergence and transfer of plasmid-mediated AMR within and between habitats at the local and global scale.
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Affiliation(s)
- Salvador Castañeda-Barba
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA.
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7
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Lammens EM, Volke DC, Schroven K, Voet M, Kerremans A, Lavigne R, Hendrix H. A SEVA-based, CRISPR-Cas3-assisted genome engineering approach for Pseudomonas with efficient vector curing. Microbiol Spectr 2023; 11:e0270723. [PMID: 37975669 PMCID: PMC10715078 DOI: 10.1128/spectrum.02707-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The CRISPR-Cas3 editing system as presented here facilitates the creation of genomic alterations in Pseudomonas putida and Pseudomonas aeruginosa in a straightforward manner. By providing the Cas3 system as a vector set with Golden Gate compatibility and different antibiotic markers, as well as by employing the established Standard European Vector Architecture (SEVA) vector set to provide the homology repair template, this system is flexible and can readily be ported to a multitude of Gram-negative hosts. Besides genome editing, the Cas3 system can also be used as an effective and universal tool for vector curing. This is achieved by introducing a spacer that targets the origin-of-transfer, present on the majority of established (SEVA) vectors. Based on this, the Cas3 system efficiently removes up to three vectors in only a few days. As such, this curing approach may also benefit other genomic engineering methods or remove naturally occurring plasmids from bacteria.
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Affiliation(s)
| | - Daniel Christophe Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kaat Schroven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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8
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Chen BC, Chen YZ, Lin HY. An Introduced RNA-Only Approach for Plasmid Curing via the CRISPR-Cpf1 System in Saccharomyces cerevisiae. Biomolecules 2023; 13:1561. [PMID: 37892243 PMCID: PMC10604987 DOI: 10.3390/biom13101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
The CRISPR-Cas system has been widely used for genome editing due to its convenience, simplicity and flexibility. Using a plasmid-carrying Cas protein and crRNA or sgRNA expression cassettes is an efficient strategy in the CRISPR-Cas genome editing system. However, the plasmid remains in the cells after genome editing. Development of general plasmid-curing strategies is necessary. Based on our previous CRISPR-Cpf1 genome-editing system in Saccharomyces cerevisiae, the crRNA, designed for the replication origin of the CRISPR-Cpf1 plasmid, and the ssDNA, as a template for homologous recombination, were introduced for plasmid curing. The efficiency of the plasmid curing was 96 ± 4%. In addition, we further simplified the plasmid curing system by transforming only one crRNA into S. cerevisiae, and the curing efficiency was about 70%. In summary, we have developed a CRISPR-mediated plasmid-curing system. The RNA-only plasmid curing system is fast and easy. This plasmid curing strategy can be applied in broad hosts by designing crRNA specific for the replication origin of the plasmid. The plasmid curing system via CRISPR-Cas editing technology can be applied to produce traceless products without foreign genes and to perform iterative processes in multiple rounds of genome editing.
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Affiliation(s)
- Bo-Chou Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan;
| | - Yu-Zhen Chen
- Department of Food Science and Technology, Hungkuang University, Taichung 433, Taiwan;
| | - Huan-Yu Lin
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan;
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9
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Sheng H, Wu S, Xue Y, Zhao W, Caplan AB, Hovde CJ, Minnich SA. Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance. PLoS One 2023; 18:e0291520. [PMID: 37699034 PMCID: PMC10497133 DOI: 10.1371/journal.pone.0291520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Pathogenic Escherichia coli and Salmonella enterica pose serious public health threats due to their ability to cause severe gastroenteritis and life-threatening sequela, particularly in young children. Moreover, the emergence and dissemination of antibiotic resistance in these bacteria have complicated control of infections. Alternative strategies that effectively target these enteric pathogens and negate or reduce the need of antibiotics are urgently needed. Such an alternative is the CRISPR-Cas9 system because it can generate sequence-specific lethal double stranded DNA breaks. In this study, two self-transmissible broad host range conjugative plasmids, pRK24 and pBP136, were engineered to deliver multiplexed CRSIPR-Cas9 systems that specifically target Enterohemorrhagic and Enteropathogenic strains of E. coli (EHEC and EPEC), S. enterica, and blaCMY-2 antibiotic resistance plasmids. Using in vitro mating assays, we show that the conjugative delivery of pRK24-CRISPR-Cas9 carrying guide RNAs to the EPEC/EHEC eae (intimin) gene can selectively kill enterohemorrhagic E. coli O157 eae+ cells (3 log kill at 6 h) but does not kill the isogenic Δeae mutant (P<0.001). Similar results were also obtained with a pBP136 derivative, pTF16, carrying multiplexed guide RNAs targeting E. coli eae and the S. enterica ssaN gene coding for the type III secretion ATPase. Another pBP136 derivative, TF18, carries guide RNAs targeting S. enterica ssaN and the antibiotic resistance gene, blaCMY-2, carried on the multi-drug resistant pAR06302. Introduction of pTF18 into bacteria harboring pAR06302 showed plasmids were cured at an efficiency of 53% (P<0.05). Using a murine neonate EPEC infection model, pTF16 was delivered by a murine derived E. coli strain to EPEC infected mice and showed significant reductions of intestinal EPEC (P<0.05). These results suggest that establishing conjugative CRISPR-Cas9 antimicrobials in the intestinal microbiome may provide protection from enteric pathogens and reduce antibiotic resistance without disrupting the normal microbiota.
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Affiliation(s)
- Haiqing Sheng
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah Wu
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Yansong Xue
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Wei Zhao
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Allan B. Caplan
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Carolyn J. Hovde
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Scott A. Minnich
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
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10
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Mayorga-Ramos A, Zúñiga-Miranda J, Carrera-Pacheco SE, Barba-Ostria C, Guamán LP. CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance. ACS Infect Dis 2023; 9:1283-1302. [PMID: 37347230 PMCID: PMC10353011 DOI: 10.1021/acsinfecdis.2c00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Indexed: 06/23/2023]
Abstract
The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.
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Affiliation(s)
- Arianna Mayorga-Ramos
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Johana Zúñiga-Miranda
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Saskya E. Carrera-Pacheco
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Carlos Barba-Ostria
- Escuela
de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170902, Ecuador
| | - Linda P. Guamán
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
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11
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Xiao Y, Zhang Y, Xie F, Olsen RH, Shi L, Li L. Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System. Int J Mol Sci 2023; 24:10585. [PMID: 37445761 DOI: 10.3390/ijms241310585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.
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Affiliation(s)
- Yawen Xiao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Yan Zhang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Fengjun Xie
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
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12
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Devi V, Harjai K, Chhibber S. Repurposing prokaryotic clustered regularly interspaced short palindromic repeats-Cas adaptive immune system to combat antimicrobial resistance. Future Microbiol 2023; 18:443-459. [PMID: 37317864 DOI: 10.2217/fmb-2022-0222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Despite achieving unparalleled progress in the field of science and technology, the global health community is still threatened by the looming pressure of infectious diseases. One of the greatest challenges is the rise in infections by antibiotic-resistant microorganisms. The misuse of antibiotics has led to the present circumstances, and there is seemingly no solution. There is imminent pressure to develop new antibacterial therapies to curb the rise and spread of multidrug resistance. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas, having immense potential as a gene-editing tool, has gained considerable attention as an alternative antibacterial therapy. Strategies, aiming to either eliminate pathogenic strains or to restore sensitivity to antibiotics, are the main focus of research. This review deals with the development of CRISPR-Cas antimicrobials and their delivery challenges.
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Affiliation(s)
- Veena Devi
- Department of Microbiology, Panjab University, Chandigarh, 160014, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, 160014, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, 160014, India
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13
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Lennox-Hvenekilde D, Bali AP, Gronenberg LS, Acevedo-Rocha C, Sommer MOA, Genee HJ. Metabolic engineering of Escherichia coli for high-level production of free lipoic acid. Metab Eng 2023; 76:39-49. [PMID: 36639019 DOI: 10.1016/j.ymben.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023]
Abstract
L-Lipoic acid (LA) is an important antioxidant with various industrial applications as a nutraceutical and therapeutic. Currently, LA is produced by chemical synthesis. Cell factory development is complex as LA and its direct precursors only occur naturally in protein-bound forms. Here we report a rationally engineered LA cell factory and demonstrate de novo free LA production from glucose for the first time in E. coli. The pathway represents a significant challenge as the three key enzymes, native Octanoyltransferase (LipB) and Lipoyl Synthase (LipA), and heterologous Lipoamidase (LpA), are all toxic to overexpress in E. coli. To overcome the toxicity of LipB, functional metagenomic selection was used to identify a highly active and non-toxic LipB and LipA from S. liquefaciens. Using high throughput screening, we balanced translation initiation rates and dual, orthogonal induction systems for the toxic genes, LipA and LpA. The optimized strain yielded 2.5 mg free LA per gram of glucose in minimal media, expressing carefully balanced LipB and LipA, Enterococcus faecalis LpA, and a truncated, native, Dihydrolipoyllysine-residue acetyltransferase (AceF) lipoylation domain. When the optimized cell factory strain was cultivated in a fed-batch fermentation, a titer of 87 mg/L free LA in the supernatant was reached after 48 h. This titer is ∼3000-fold higher than previously reported free LA titer and ∼8-fold higher than the previous best total, protein-bound LA titer. The strategies presented here could be helpful in designing, constructing and balancing biosynthetic pathways that harbor toxic enzymes with protein-bound intermediates or products.
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Affiliation(s)
- David Lennox-Hvenekilde
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark; Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | - Anne P Bali
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | | | | | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Hans J Genee
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark.
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14
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Gu S, Zhang J, Li L, Zhong J. Repurposing the Endogenous CRISPR-Cas9 System for High-Efficiency Genome Editing in Lacticaseibacillus paracasei. ACS Synth Biol 2022; 11:4031-4042. [PMID: 36414383 DOI: 10.1021/acssynbio.2c00374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Lactobacilli such as Lacticaseibacillus (Lcb) paracasei are generally regarded as safe and health-promoting microbes, and have been widely applied in food and pharmaceutical industries. However, the genetic bases of their beneficial properties were mostly uncertain because of the lack of effective genetic manipulation tools. The type II CRISPR-Cas9 system is the largest family present in lactobacilli, but none of them yet have been developed for genetic modifications. Here, we establish the first endogenous CRISPR-Cas9 genome-editing system in lactobacilli. With a validated protospacer adjacent motif (PAM) and customized single guide RNA (sgRNA) expression cassette, the native CRISPR-Cas9 system was reprogrammed to achieve gene deletion and chromosomal insertion at over 90% efficiency, as well as nucleotide substitution at ≥50% efficiency. We also effectively accomplished deletions of large genomic fragments (5-10 kb) and simultaneous deletion of multiple genes at distal loci, both of which are the first cases in lactobacilli when either endogenous or exogenous CRISPR-Cas systems were employed. In addition, we designed a controllable plasmid-targeting sgRNA expression module and integrated it into the editing plasmid. The all-in-one vector realized gene deletion and plasmid curing at high efficiency (>90%). Collectively, the present study develops a convenient and precise genetic tool in Lcb. paracasei and contributes to the genetics and engineering of lactobacilli.
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Affiliation(s)
- Shujie Gu
- University of Chinese Academy of Sciences, Beijing 100039, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Li
- University of Chinese Academy of Sciences, Beijing 100039, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin Zhong
- University of Chinese Academy of Sciences, Beijing 100039, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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15
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Liang M, Zhang J, Yang Y, Xia Y, Liu L, Liu L, Wang Q, Gao X. Nattokinase enhances the preventive effects of Escherichia coli Nissle 1917 on dextran sulfate sodium-induced colitis in mice. World J Microbiol Biotechnol 2022; 39:8. [PMID: 36350434 DOI: 10.1007/s11274-022-03452-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
Nattokinase with excellent anti-thrombotic, anti-inflammatory, anti-tumor, and anti-hypertension properties has been used in the development of several healthcare products in many countries. The probiotic Escherichia coli Nissle 1917 (EcN) with anti-inflammatory effect is commonly used to treat inflammatory bowel disease. To determine whether nattokinase could enhance the therapeutic efficacy of EcN in colitis, a recombinant E. coli Nissle 1917 strain (EcNnatto) with nattokinase-expressing ability was successfully constructed, and the protective effect of the engineered strain on mice with experimental chronic colitis was investigated. Although both EcN and EcNnatto strains substantially alleviated the clinical symptoms and pathological abnormalities in colitis mice by regulating gut flora and maintaining intestinal barrier function, the EcNnatto strain was found to perform better than the control strain, based on a further increase in colon length and a downregulation in pro-inflammatory cytokines (IL-6 and TNF-α). Nattokinase expressed in EcN attenuated DSS-induced epithelial damage and restored the mucosal integrity by upregulating the levels of tight junction proteins, including ZO-1 and occludin. The expression level of Lgr5, a marker of intestinal stem cells, was also increased. Moreover, constitutively expressed nattokinase in EcN reversed the gut microbial richness and diversity in colitis mice. Based on our findings, nattokinase could strengthen the capacity of EcN to treat intestinal inflammation.
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Affiliation(s)
- Manyu Liang
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jing Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yanhong Yang
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yi Xia
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Lintao Liu
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Li Liu
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Qin Wang
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiaowei Gao
- School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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A Defect in Lipoprotein Modification by Lgt Leads to Abnormal Morphology and Cell Death in Escherichia coli That Is Independent of Major Lipoprotein Lpp. J Bacteriol 2022; 204:e0016422. [PMID: 35938851 PMCID: PMC9487459 DOI: 10.1128/jb.00164-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lgt is an essential enzyme in proteobacteria and therefore a potential target for novel antibiotics. The effect of Lgt depletion on growth, morphology, and viability was studied in Escherichia coli to assess whether absence of Lgt leads to cell death. Two Lgt depletion strains were used in which lgt was under the control of an arabinose-inducible promoter that allowed regulation of Lgt protein levels. Reduced levels of Lgt led to severe growth and morphological defects that could be restored by expressing lgt in trans, demonstrating that only Lgt is responsible for the distorted phenotypes. In the absence of major lipoprotein Lpp, growth defects were partially restored when low levels of Lgt were still present; however, lgt could not be deleted in the absence of Lpp. Our results demonstrate that Lpp is not the main cause of cell death under conditions of Lgt depletion and that other lipoproteins are important in cell envelope biogenesis and cell viability. Specific inhibitors of Lgt are thus promising for the development of novel antibiotics. IMPORTANCE Incomplete maturation and envelope mislocalization of lipoproteins, through inhibition or mutations in lipoprotein modification enzymes or transport to the outer membrane, are lethal in proteobacteria. Resistance to small-molecule inhibition or the appearance of suppressor mutations is often directly correlated with the presence of abundant outer membrane lipoprotein Lpp. Our results show that Lgt, the first enzyme of the lipoprotein modification pathway, is still required for growth and viability in the absence of Lpp and thus is necessary for the function of other essential lipoproteins in the cell envelope. This adds credence to the hypothesis that Lgt is essential in proteobacteria and an attractive target for the development of novel antibiotics.
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17
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Sundaramoorthy NS, Shankaran P, Gopalan V, Nagarajan S. New tools to mitigate drug resistance in Enterobacteriaceae - Escherichia coli and Klebsiella pneumoniae. Crit Rev Microbiol 2022:1-20. [PMID: 35649163 DOI: 10.1080/1040841x.2022.2080525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Treatment to common bacterial infections are becoming ineffective of late, owing to the emergence and dissemination of antibiotic resistance globally. Escherichia coli and Klebsiella pneumoniae are the most notorious microorganisms and are among the critical priority pathogens listed by WHO in 2017. These pathogens are the predominant cause of sepsis, urinary tract infections (UTIs), pneumonia, meningitis and pyogenic liver abscess. Concern arises due to the resistance of bacteria to most of the beta lactam antibiotics like penicillin, cephalosporin, monobactams and carbapenems, even to the last resort antibiotics like colistin. Preventing influx by modulation of porins, extruding the antibiotics by overexpression of efflux pumps, mutations of drug targets/receptors, biofilm formation, altering the drug molecules and rendering them ineffective are few resistance mechanisms that are adapted by Enterobacteriaeceae upon exposure to antibiotics. The situation is exacerbated due to the process of horizontal gene transfer (HGT), wherein the genes encoding resistance mechanisms are transferred to the neighbouring bacteria through plasmids/phages/uptake of free DNA. Carbapenemases, other beta lactamases and mcr genes coding for colistin resistance are widely disseminated leading to limited/no therapeutic options against those infections. Development of new antibiotics can be viewed as a possible solution but it involves major investment, time and labour despite which, the bacteria can easily adapt to the new antibiotic and evolve resistance in a relatively short time. Targeting the resistance mechanisms can be one feasible alternative to tackle these multidrug resistant (MDR) pathogens. Removal of plasmid (plasmid curing) causing resistance, use of bacteriophages and bacteriotherapy can be other potential approaches to combat infections caused by MDR E. coli and K. pneumoniae. The present review discusses the efficacies of these therapies in mitigating these infections, which can be potentially used as an adjuvant therapy along with existing antibiotics.
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Affiliation(s)
- Niranjana Sri Sundaramoorthy
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Prakash Shankaran
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Vidhya Gopalan
- Department of Virology, Kings Institute of Preventative Medicine, Guindy, Chennai, Tamil Nadu, India
| | - Saisubramanian Nagarajan
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
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18
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Li P, Wan P, Zhao R, Chen J, Li X, Li J, Xiong W, Zeng Z. Targeted Elimination of blaNDM-5 Gene in Escherichia coli by Conjugative CRISPR-Cas9 System. Infect Drug Resist 2022; 15:1707-1716. [PMID: 35422639 PMCID: PMC9004731 DOI: 10.2147/idr.s357470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/19/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Plasmid-borne carbapenem resistance gene blaNDM-5 accelerates the dissemination of carbapenem-resistant Enterobacteriaceae. To efficiently eliminate the blaNDM-5-harboring plasmid and sensitize the antibiotic-resistant bacteria to meropenem, we used the CRISPR-Cas9 system for combating the carbapenem-resistant Escherichia coli (E. coil). Methods A series of CRISPR-Cas9 plasmids was constructed, and specific guide RNAs(sgRNA) were designed to target the blaNDM-5 gene. We used chemically transformation or conjugation delivery methods, and the elimination efficiency in each recipient strains was evaluated by plate counting, PCR and quantitative real-time PCR (qPCR). Antimicrobial susceptibility test was carried out by using the broth microdilution method. In addition, we assessed the effect of the CRISPR-Cas9 system of adaptive immunity on the prevention of the exogenous resistant plasmids pNDM-5 by introducing the system into E coli J53. Results The results showed that pCas9, pCas9-oriT and pBAD-Cas9-oriT can effectively eliminate blaNDM-5 in E. coli with >94.00% elimination efficiency. The blaNDM-5-harboring E. coli successfully restored their susceptibility to meropenem, with eight-fold reduction of minimum inhibitory concentration (MIC) values (from 16 µg/mL to 0.06 µg/mL). The E. coli J53 strain containing plasmid pCas9-N reduced the number of transconjugants by 26-fold. Conclusion The CRISPR-Cas9 system achieved plasmid clearance and simultaneous re-sensitization to meropenem in E. coli. The CRISPR-Cas9 system could block the horizontal transfer of plasmid pNDM-5. The conjugative delivery of CRISPR-Cas9 provides a new tool for the removal of resistance plasmids and sensitize the recipient to carbapenem. It provides a therapeutic approach to counteract the propagation of blaNDM-5 gene among clinical pathogens.
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Affiliation(s)
- Peisi 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
| | - 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
| | - 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
| | - Jin 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
| | - Jie 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
| | - 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
- Correspondence: Zhenling Zeng; Wenguang Xiong, Tel +862085281204, Fax +862085284896, Email ;
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Lee KZ, Mechikoff MA, Parasa MK, Rankin TJ, Pandolfi P, Fitzgerald KS, Hillman ET, Solomon KV. Repurposing the Homing Endonuclease I-SceI for Positive Selection and Development of Gene-Editing Technologies. ACS Synth Biol 2022; 11:53-60. [PMID: 35007422 DOI: 10.1021/acssynbio.1c00340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prokaryote genomes encode diverse programmable DNA endonucleases with significant potential for biotechnology and gene editing. However, these endonucleases differ significantly in their properties, which must be screened and measured. While positive selection screens based on ccdB and barnase have been developed to evaluate such proteins, their high levels of toxicity make them challenging to use. Here, we develop and validate a more robust positive selection screen based on the homing endonuclease I-SceI. Candidate endonucleases target and cure the I-SceI expression plasmid preventing induction of I-SceI-mediated double strand DNA breaks that lead to cell death in E. coli. We validated this screen to measure the relative activity of SpCas9, xCas9, and eSpCas9 and demonstrated an ability to enrich for more active endonuclease variants from a mixed population. This system may be applied in high throughput to rapidly characterize novel programmable endonucleases and be adapted for directed evolution of endonuclease function.
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Affiliation(s)
- Kok Zhi Lee
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
| | - Michael A. Mechikoff
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
| | - Mrugesh Krishna Parasa
- Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Drive, West Lafayette, Indiana 47907-2093, United States
- Department of Chemical & Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Tyler J. Rankin
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, United States
| | - Paula Pandolfi
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, United States
| | - Kevin S. Fitzgerald
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
| | - Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, 155 South Grant Street, West Lafayette, Indiana 47907, United States
| | - Kevin V. Solomon
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
- Department of Chemical & Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, 155 South Grant Street, West Lafayette, Indiana 47907, United States
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, Indiana 47907-2022, United States
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Backes N, Phillips GJ. Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales. EcoSal Plus 2021; 9:eESP00062020. [PMID: 34125584 PMCID: PMC11163844 DOI: 10.1128/ecosalplus.esp-0006-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022]
Abstract
Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.
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Affiliation(s)
- Nicholas Backes
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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21
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Wu Y, Battalapalli D, Hakeem MJ, Selamneni V, Zhang P, Draz MS, Ruan Z. Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections. J Nanobiotechnology 2021; 19:401. [PMID: 34863214 PMCID: PMC8642896 DOI: 10.1186/s12951-021-01132-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is spreading rapidly around the world and seriously impeding efforts to control microbial infections. Although nucleic acid testing is widely deployed for the detection of antibiotic resistant bacteria, the current techniques-mainly based on polymerase chain reaction (PCR)-are time-consuming and laborious. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance (AMR). The CRISPR-Cas system is an adaptive immune system found in many prokaryotes that presents attractive opportunities to target and edit nucleic acids with high precision and reliability. Engineered CRISPR-Cas systems are reported to effectively kill bacteria or even revert bacterial resistance to antibiotics (resensitizing bacterial cells to antibiotics). Strategies for combating antimicrobial resistance using CRISPR (i.e., Cas9, Cas12, Cas13, and Cas14) can be of great significance in detecting bacteria and their resistance to antibiotics. This review discusses the structures, mechanisms, and detection methods of CRISPR-Cas systems and how these systems can be engineered for the rapid and reliable detection of bacteria using various approaches, with a particular focus on nanoparticles. In addition, we summarize the most recent advances in applying the CRISPR-Cas system for virulence modulation of bacterial infections and combating antimicrobial resistance.
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Affiliation(s)
- Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Mohammed J Hakeem
- Department of Food Science and Human Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Venkatarao Selamneni
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pengfei Zhang
- Department of Central Laboratory, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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22
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Clifton BE, Fariz MA, Uechi GI, Laurino P. Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation. Nucleic Acids Res 2021; 49:12467-12485. [PMID: 34761260 PMCID: PMC8643618 DOI: 10.1093/nar/gkab1067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
The tRNA modification m1G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Muhammad A Fariz
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Gen-Ichiro Uechi
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
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23
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Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe 2021; 29:1620-1633.e8. [PMID: 34597593 PMCID: PMC8585504 DOI: 10.1016/j.chom.2021.09.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 02/23/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022]
Abstract
Temperate phages are pervasive in bacterial genomes, existing as vertically inherited islands termed prophages. Prophages are vulnerable to predation of their host bacterium by exogenous phages. Here, we identify BstA, a family of prophage-encoded phage-defense proteins in diverse Gram-negative bacteria. BstA localizes to sites of exogenous phage DNA replication and mediates abortive infection, suppressing the competing phage epidemic. During lytic replication, the BstA-encoding prophage is not itself inhibited by BstA due to self-immunity conferred by the anti-BstA (aba) element, a short stretch of DNA within the bstA locus. Inhibition of phage replication by distinct BstA proteins from Salmonella, Klebsiella, and Escherichia prophages is generally interchangeable, but each possesses a cognate aba element. The specificity of the aba element ensures that immunity is exclusive to the replicating prophage, preventing exploitation by variant BstA-encoding phages. The BstA protein allows prophages to defend host cells against exogenous phage attack without sacrificing the ability to replicate lytically. BstA is an abortive infection protein found in prophages of Gram-negative bacteria aba, a short DNA sequence within the bstA locus, acts as a self-immunity element aba gives BstA-encoding prophages immunity to BstA-driven abortive infection Variant BstA proteins have distinct and cognate aba elements
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Affiliation(s)
- Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK; Biozentrum, University of Basel, Basel, Switzerland
| | - Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Ella V Rodwell
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Arthur Bowers-Barnard
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Natalia Quinones-Olvera
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Boston, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.
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24
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He YZ, Kuang X, Long TF, Li G, Ren H, He B, Yan JR, Liao XP, Liu YH, Chen L, Sun J. Re-engineering a mobile-CRISPR/Cas9 system for antimicrobial resistance gene curing and immunization in Escherichia coli. J Antimicrob Chemother 2021; 77:74-82. [PMID: 34613377 DOI: 10.1093/jac/dkab368] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 09/06/2021] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES In this study, we developed an IS26-based CRISPR/Cas9 system as a proof-of-concept study to explore the potential of a re-engineered bacterial translocatable unit (TU) for curing and immunizing against the replication genes and antimicrobial resistance genes. METHODS A series of pIS26-CRISPR/Cas9 suicide plasmids were constructed, and specific guide RNAs were designed to target the replication gene of IncX4, IncI2 and IncHI2 plasmids, and the antibiotic resistance genes mcr-1, blaKPC-2 and blaNDM-5. Through conjugation and induction, the transposition efficiency and plasmid-curing efficiency in each recipient were tested. In addition, we examined the efficiency of the IS26-CRISPR/Cas9 system of cell immunity against the acquisition of the exogenous resistant plasmids by introducing this system into antimicrobial-susceptible hosts. RESULTS This study aimed to eliminate the replication genes and antimicrobial resistance genes using pIS26-CRISPR/Cas9. Three plasmids with different replicon types, including IncX4, IncI2 and IncHI2 in three isolates, two pUC19-derived plasmids, pUC19-mcr-1 and pUC19-IS26mcr-1, in two lab strains, and two plasmids bearing blaKPC-2 and blaNDM-5 in two isolates were all successfully eliminated. Moreover, the IS26-based CRISPR/Cas9 system that remained in the plasmid-cured strains could efficiently serve as an immune system against the acquisition of the exogenous resistant plasmids. CONCLUSIONS The IS26-based CRISPR/Cas9 system can be used to efficiently sensitize clinical Escherichia coli isolates to antibiotics in vitro. The single-guide RNAs targeted resistance genes or replication genes of specific incompatible plasmids that harboured resistance genes, providing a novel means to naturally select bacteria that cannot uptake and disseminate such genes.
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Affiliation(s)
- Yu-Zhang He
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xu Kuang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Teng-Fei Long
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Gong Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hao Ren
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bing He
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jin-Ru Yan
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Ping Liao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ya-Hong Liu
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Jian Sun
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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25
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Abstract
In the age of antibiotic resistance and precise microbiome engineering, CRISPR-Cas antimicrobials promise to have a substantial impact on the way we treat diseases in the future. However, the efficacy of these antimicrobials and their mechanisms of resistance remain to be elucidated. We systematically investigated how a target E. coli strain can escape killing by episomally-encoded CRISPR-Cas9 antimicrobials. Using Cas9 from Streptococcus pyogenes (SpCas9) we studied the killing efficiency and resistance mutation rate towards CRISPR-Cas9 antimicrobials and elucidated the underlying genetic alterations. We find that killing efficiency is not correlated with the number of cutting sites or the type of target. While the number of targets did not significantly affect efficiency of killing, it did reduce the emergence of chromosomal mutations conferring resistance. The most frequent target of resistance mutations was the plasmid-encoded SpCas9 that was inactivated by bacterial genome rearrangements involving translocation of mobile genetic elements such as insertion elements. This resistance mechanism can be overcome by re-introduction of an intact copy of SpCas9. The work presented here provides a guide to design strategies that reduce resistance and improve the activity of CRISPR-Cas antimicrobials.
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26
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Tailoring the evolution of BL21(DE3) uncovers a key role for RNA stability in gene expression toxicity. Commun Biol 2021; 4:963. [PMID: 34385596 PMCID: PMC8361080 DOI: 10.1038/s42003-021-02493-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Gene expression toxicity is an important biological phenomenon and a major bottleneck in biotechnology. Escherichia coli BL21(DE3) is the most popular choice for recombinant protein production, and various derivatives have been evolved or engineered to facilitate improved yield and tolerance to toxic genes. However, previous efforts to evolve BL21, such as the Walker strains C41 and C43, resulted only in decreased expression strength of the T7 system. This reveals little about the mechanisms at play and constitutes only marginal progress towards a generally higher producing cell factory. Here, we restrict the solution space for BL21(DE3) to evolve tolerance and isolate a mutant strain Evo21(DE3) with a truncation in the essential RNase E. This suggests that RNA stability plays a central role in gene expression toxicity. The evolved rne truncation is similar to a mutation previously engineered into the commercially available BL21Star(DE3), which challenges the existing assumption that this strain is unsuitable for expressing toxic proteins. We isolated another dominant mutation in a presumed substrate binding site of RNase E that improves protein production further when provided as an auxiliary plasmid. This makes it easy to improve other BL21 variants and points to RNases as prime targets for cell factory optimisation.
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27
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A transposon-associated CRISPR/Cas9 system specifically eliminates both chromosomal and plasmid-borne mcr-1 in Escherichia coli. Antimicrob Agents Chemother 2021; 65:e0105421. [PMID: 34339270 PMCID: PMC8448152 DOI: 10.1128/aac.01054-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The global spread of antimicrobial-resistant bacteria has been one of the most severe threats to public health. The emergence of the mcr-1 gene has posed a considerable threat to antimicrobial medication since it deactivates one last-resort antibiotic, colistin. There have been reports regarding the mobilization of the mcr-1 gene facilitated by ISApl1-formed transposon Tn6330 and mediated rapid dispersion among Enterobacteriaceae species. Here, we developed a CRISPR/Cas9 system flanked by ISApl1 in a suicide plasmid capable of exerting sequence-specific curing against the mcr-1-bearing plasmid and killing the strain with chromosome-borne mcr-1. The constructed ISApl1-carried CRISPR/Cas9 system either restored sensitivity to colistin in strains with plasmid-borne mcr-1 or directly eradicated the bacteria harboring chromosome-borne mcr-1 by introducing an exogenous CRISPR/Cas9 targeting the mcr-1 gene. This method is highly efficient in removing the mcr-1 gene from Escherichia coli, thereby resensitizing these strains to colistin. The further results demonstrated that it conferred the recipient bacteria with immunity against the acquisition of the exogenous mcr-1 containing the plasmid. The data from the current study highlighted the potential of the transposon-associated CRISPR/Cas9 system to serve as a therapeutic approach to control the dissemination of mcr-1 resistance among clinical pathogens.
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28
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Ji X, Lu P, Hu Y, Xue J, Wu J, Zhang B, Zhang Y, Dong L, Lv H, Wang S. Function Characterization of Endogenous Plasmids in Cronobacter sakazakii and Identification of p-Coumaric Acid as Plasmid-Curing Agent. Front Microbiol 2021; 12:687243. [PMID: 34248908 PMCID: PMC8267800 DOI: 10.3389/fmicb.2021.687243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Virulence traits and antibiotic resistance are frequently provided by genes located on plasmids. However, experimental verification of the functions of these genes is often lacking due to a lack of related experimental technology. In the present study, an integrated suicide vector was used to efficiently and specifically delete a bacterial endogenous plasmid in Cronobacter sakazakii. The pESA3 plasmid was removed from C. sakazakii BAA-894, and we confirmed that this plasmid contributes to the invasion and virulence of this strain. In addition, the pGW1 plasmid was expunged from C. sakazakii GZcsf-1, and we confirmed that this plasmid confers multidrug resistance. We further screened plasmid-curing agents and found that p-coumaric acid had a remarkable effect on the curing of pESA3 and pGW1 at sub-inhibitory concentrations. Our study investigated the contribution of endogenous plasmids pESA3 and pGW1 by constructing plasmid-cured strains using suicide vectors and suggested that p-coumaric acid can be a safe and effective plasmid-curing agent for C. sakazakii.
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Affiliation(s)
- Xuemeng Ji
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Ping Lu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical Collage, Tianjin, China
| | - Yaozhong Hu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jing Wu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Bowei Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Lu Dong
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Huan Lv
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
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29
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Lan YJ, Tan SI, Cheng SY, Ting WW, Xue C, Lin TH, Cai MZ, Chen PT, Ng IS. Development of Escherichia coli Nissle 1917 derivative by CRISPR/Cas9 and application for gamma-aminobutyric acid (GABA) production in antibiotic-free system. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107952] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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30
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Martin-Pascual M, Batianis C, Bruinsma L, Asin-Garcia E, Garcia-Morales L, Weusthuis RA, van Kranenburg R, Martins Dos Santos VAP. A navigation guide of synthetic biology tools for Pseudomonas putida. Biotechnol Adv 2021; 49:107732. [PMID: 33785373 DOI: 10.1016/j.biotechadv.2021.107732] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Pseudomonas putida is a microbial chassis of huge potential for industrial and environmental biotechnology, owing to its remarkable metabolic versatility and ability to sustain difficult redox reactions and operational stresses, among other attractive characteristics. A wealth of genetic and in silico tools have been developed to enable the unravelling of its physiology and improvement of its performance. However, the rise of this microbe as a promising platform for biotechnological applications has resulted in diversification of tools and methods rather than standardization and convergence. As a consequence, multiple tools for the same purpose have been generated, whilst most of them have not been embraced by the scientific community, which has led to compartmentalization and inefficient use of resources. Inspired by this and by the substantial increase in popularity of P. putida, we aim herein to bring together and assess all currently available (wet and dry) synthetic biology tools specific for this microbe, focusing on the last 5 years. We provide information on the principles, functionality, advantages and limitations, with special focus on their use in metabolic engineering. Additionally, we compare the tool portfolio for P. putida with those for other bacterial chassis and discuss potential future directions for tool development. Therefore, this review is intended as a reference guide for experts and new 'users' of this promising chassis.
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Affiliation(s)
- Maria Martin-Pascual
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Luis Garcia-Morales
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem 4206 AC, The Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, the Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands; LifeGlimmer GmbH, Berlin 12163, Germany.
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31
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Abstract
Plasmids have largely contributed to the spread of antimicrobial resistance genes among Staphylococcus strains. Knowledge about the fitness cost that plasmids confer on clinical staphylococcal isolates and the coevolutionary dynamics that drive plasmid maintenance is still scarce. In this study, we aimed to analyze the initial fitness cost of plasmids in the bacterial pathogen Staphylococcus aureus and the plasmid-host adaptations that occur over time. For that, we first designed a CRISPR (clustered regularly interspaced palindromic repeats)-based tool that enables the removal of native S. aureus plasmids and then transferred three different plasmids isolated from clinical S. aureus strains to the same-background clinical cured strain. One of the plasmids, pUR2940, obtained from a livestock-associated methicillin-resistant S. aureus (LA-MRSA) ST398 strain, imposed a significant fitness cost on both its native and the new host. Experimental evolution in a nonselective medium resulted in a high rate pUR2940 loss and selected for clones with an alleviated fitness cost in which compensatory adaptation occurred via deletion of a 12.8-kb plasmid fragment, contained between two ISSau10 insertion sequences and harboring several antimicrobial resistance genes. Overall, our results describe the relevance of plasmid-borne insertion sequences in plasmid rearrangement and maintenance and suggest the potential benefits of reducing the use of antibiotics both in animal and clinical settings for the loss of clinical multidrug resistance plasmids.
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32
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Roy S, Naha S, Rao A, Basu S. CRISPR-Cas system, antibiotic resistance and virulence in bacteria: Through a common lens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:123-174. [PMID: 33685595 DOI: 10.1016/bs.pmbts.2020.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas system, antibiotic resistance and virulence are different modes of survival for the bacteria. CRISPR-Cas is an adaptive immune system that can degrade foreign DNA, antibiotic resistance helps bacteria to evade drugs that can threaten their existence and virulence determinants are offensive tools that can facilitate the establishment of infection by pathogens. This chapter focuses on these three aspects, providing insights about the CRISPR system and resistance mechanisms in brief, followed by understanding the synergistic or antagonistic relationship of resistance and virulence determinants in connection to the CRISPR system. We have addressed the discussion of this evolving topic through specific examples and studies. Different approaches for successful detection of this unique defense system in bacteria and various applications of the CRISPR-Cas systems to show how it can be harnessed to tackle the increasing problem of antibiotic resistance have been put forth. World Health Organization has declared antibiotic resistance as a serious global problem of the 21st century. As antibiotic-resistant bacteria increase their footprint across the globe, newer tools such as the CRISPR-Cas system hold immense promise to tackle this problem.
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Affiliation(s)
- Subhasree Roy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Ankur Rao
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India.
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33
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Kan A, Gelfat I, Emani S, Praveschotinunt P, Joshi NS. Plasmid Vectors for in Vivo Selection-Free Use with the Probiotic E. coli Nissle 1917. ACS Synth Biol 2021; 10:94-106. [PMID: 33301298 PMCID: PMC7813132 DOI: 10.1021/acssynbio.0c00466] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Escherichia
coli Nissle 1917 (EcN) is a probiotic
bacterium, commonly employed to treat certain gastrointestinal disorders.
It is fast emerging as an important target for the development of
therapeutic engineered bacteria, benefiting from the wealth of knowledge
of E. coli biology and ease of manipulation.
Bacterial synthetic biology projects commonly utilize engineered plasmid
vectors, which are simple to engineer and can reliably achieve high
levels of protein expression. However, plasmids typically require
antibiotics for maintenance, and the administration of an antibiotic
is often incompatible with in vivo experimentation
or treatment. EcN natively contains plasmids pMUT1 and pMUT2, which
have no known function but are stable within the bacteria. Here, we
describe the development of the pMUT plasmids into a robust platform
for engineering EcN for in vivo experimentation,
alongside a CRISPR-Cas9 system to remove the native plasmids. We systematically
engineered both pMUT plasmids to contain selection markers, fluorescent
markers, temperature sensitive expression, and curli secretion systems
to export a customizable functional material into the extracellular
space. We then demonstrate that the engineered plasmids were maintained
in bacteria as the engineered bacteria pass through the mouse GI tract
without selection, and that the secretion system remains functional,
exporting functionalized curli proteins into the gut. Our plasmid
system presents a platform for the rapid development of therapeutic
EcN bacteria.
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Affiliation(s)
- Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Ilia Gelfat
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Sivaram Emani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Harvard College, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Pichet Praveschotinunt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Neel S. Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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Tissue-Specific Delivery of CRISPR Therapeutics: Strategies and Mechanisms of Non-Viral Vectors. Int J Mol Sci 2020; 21:ijms21197353. [PMID: 33027946 PMCID: PMC7583726 DOI: 10.3390/ijms21197353] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 02/07/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome editing system has been the focus of intense research in the last decade due to its superior ability to desirably target and edit DNA sequences. The applicability of the CRISPR-Cas system to in vivo genome editing has acquired substantial credit for a future in vivo gene-based therapeutic. Challenges such as targeting the wrong tissue, undesirable genetic mutations, or immunogenic responses, need to be tackled before CRISPR-Cas systems can be translated for clinical use. Hence, there is an evident gap in the field for a strategy to enhance the specificity of delivery of CRISPR-Cas gene editing systems for in vivo applications. Current approaches using viral vectors do not address these main challenges and, therefore, strategies to develop non-viral delivery systems are being explored. Peptide-based systems represent an attractive approach to developing gene-based therapeutics due to their specificity of targeting, scale-up potential, lack of an immunogenic response and resistance to proteolysis. In this review, we discuss the most recent efforts towards novel non-viral delivery systems, focusing on strategies and mechanisms of peptide-based delivery systems, that can specifically deliver CRISPR components to different cell types for therapeutic and research purposes.
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CRISPR-Cas9-Mediated Carbapenemase Gene and Plasmid Curing in Carbapenem-Resistant Enterobacteriaceae. Antimicrob Agents Chemother 2020; 64:AAC.00843-20. [PMID: 32631827 DOI: 10.1128/aac.00843-20] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Combating plasmid-mediated carbapenem resistance is essential to control and prevent the dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Here, we conducted a proof-of-concept study to demonstrate that CRISPR-Cas9-mediated resistance gene and plasmid curing can effectively resensitize CRE to carbapenems. A novel CRISPR-Cas9-mediated plasmid-curing system (pCasCure) was developed and electrotransferred into various clinical CRE isolates. The results showed that pCasCure can effectively cure bla KPC, bla NDM, and bla OXA-48 in various Enterobacteriaceae species of Klebsiella pneumoniae, Escherichia coli, Enterobacter hormaechei, Enterobacter xiangfangensis, and Serratia marcescens clinical isolates, with a >94% curing efficiency. In addition, we also demonstrated that pCasCure can efficiently eliminate several epidemic carbapenem-resistant plasmids, including the bla KPC-harboring IncFIIK-pKpQIL and IncN pKp58_N plasmids, the bla OXA-48-harboring pOXA-48-like plasmid, and the bla NDM-harboring IncX3 plasmid, by targeting their replication and partitioning (parA in pKpQIL) genes. However, curing the bla OXA-48 gene failed to eliminate its corresponding pOXA-48-like plasmid in clinical K. pneumoniae isolate 49210, while further next-generation sequencing revealed that it was due to IS1R-mediated recombination outside the CRISPR-Cas9 cleavage site resulting in bla OXA-48 truncation and, therefore, escaped plasmid curing. Nevertheless, the curing of carbapenemase genes or plasmids, including the truncation of bla OXA-48 in 49210, successfully restore their susceptibility to carbapenems, with a >8-fold reduction of MIC values in all tested isolates. Taken together, our study confirmed the concept of using CRISPR-Cas9-mediated carbapenemase gene and plasmid curing to resensitize CRE to carbapenems. Further work is needed to integrate pCasCure in an optimal delivery system to make it applicable for clinical intervention.
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Ibarra-Chávez R, Haag AF, Dorado-Morales P, Lasa I, Penadés JR. Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All. BIODESIGN RESEARCH 2020; 2020:5783064. [PMID: 37849900 PMCID: PMC10530653 DOI: 10.34133/2020/5783064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/17/2020] [Indexed: 10/19/2023] Open
Abstract
Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.
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Affiliation(s)
- Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andreas F. Haag
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Pedro Dorado-Morales
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra-Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Complejo Hospitalario de Navarra-Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Gawin A, Ertesvåg H, Hansen SAH, Malmo J, Brautaset T. Translational regulation of periplasmic folding assistants and proteases as a valuable strategy to improve production of translocated recombinant proteins in Escherichia coli. BMC Biotechnol 2020; 20:24. [PMID: 32393331 PMCID: PMC7216727 DOI: 10.1186/s12896-020-00615-0] [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: 12/18/2019] [Accepted: 04/24/2020] [Indexed: 01/02/2023] Open
Abstract
Background Advantages of translocation of recombinant proteins to the periplasm in Escherichia coli include simplified downstream processing, and improved folding and in vivo activity of the target protein. There are, however, problems encountered in the periplasmic production that can be associated with the incorrect formation of disulfide bonds, incomplete cleavage of the signal peptide, and proteolytic degradation. A common strategy used to overcome these difficulties involves manipulating the cellular levels of proteases and periplasmic folding assistants like chaperones, signal peptide peptidases or thiol-disulfide oxidoreductases. To date, this has been achieved by plasmid-based over-expression or knockouts of the relevant genes. Results We changed the translation efficiencies of five native E. coli proteins, DsbA, DsbB, Skp, SppA, and DegP, by modifying the strength of their ribosome binding sites (RBS). The genomic RBS sequences were replaced with synthetic ones that provided a predicted translation initiation rate. Single- and double-gene mutant strains were created and tested for production of two pharmaceutically relevant proteins, PelB-scFv173–2-5-AP and OmpA-GM-CSF. Almost all the single-gene mutant strains showed improved periplasmic production of at least one of the recombinant proteins. No further positive effects were observed when the mutations were combined. Conclusions Our findings confirm that our strain engineering approach involving translational regulation of endogenous proteins, in addition to plasmid-based methods, can be used to manipulate the cellular levels of periplasmic folding assistants and proteases to improve the yields of translocated recombinant proteins. The positive effects of SppA overexpression should be further investigated in E. coli.
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Affiliation(s)
- Agnieszka Gawin
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway
| | - Sine Alise Hartvigsen Hansen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway
| | - Jostein Malmo
- Vectron Biosolutions AS, Abels gt 5, N-7030, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491, Trondheim, Norway.
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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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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: 21] [Impact Index Per Article: 5.3] [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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Volke DC, Friis L, Wirth NT, Turlin J, Nikel PI. Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida. Metab Eng Commun 2020; 10:e00126. [PMID: 32215253 PMCID: PMC7090339 DOI: 10.1016/j.mec.2020.e00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/23/2020] [Accepted: 02/29/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding β-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering. Plasmid-curing is the most time-consuming step in genome engineering approaches. We have developed a system for easy target- and self-curing of plasmid DNA. Synthetic control of replication and highly-specific in vivo DNA digestion were used. Plasmid curing with this system displays an efficiency >90% in a 24-h cultivation. Quick genome engineering facilitated genome reduction of P. putida.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Laura Friis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Justine Turlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion. Commun Biol 2020; 3:98. [PMID: 32139868 PMCID: PMC7058019 DOI: 10.1038/s42003-020-0824-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/12/2020] [Indexed: 12/18/2022] Open
Abstract
Ferulic acid is a ubiquitous phenolic compound in lignocellulose, which is recognized for its role in the microbial carbon catabolism and industrial value. However, its recalcitrance and toxicity poses a challenge for ferulic acid-to-bioproducts bioconversion. Here, we develop a genome editing strategy for Pseudomonas putida KT2440 using an integrated CRISPR/Cas9n-λ-Red system with pyrF as a selection marker, which maintains cell viability and genetic stability, increases mutation efficiency, and simplifies genetic manipulation. Via this method, four functional modules, comprised of nine genes involved in ferulic acid catabolism and polyhydroxyalkanoate biosynthesis, were integrated into the genome, generating the KTc9n20 strain. After metabolic engineering and optimization of C/N ratio, polyhydroxyalkanoate production was increased to ~270 mg/L, coupled with ~20 mM ferulic acid consumption. This study not only establishes a simple and efficient genome editing strategy, but also offers an encouraging example of how to apply this method to improve microbial aromatic compound bioconversion. Yueyue Zhou et al. develop a genetic engineering method that increases the production of polyhydroxyalkanoate from ferulic acid, which is toxic at high concentrations. This study provides insight into the bioconversion of the aromatic compound in Pseudomonas.
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Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR. PLoS One 2020; 15:e0225202. [PMID: 31940351 PMCID: PMC6961859 DOI: 10.1371/journal.pone.0225202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022] Open
Abstract
Plasmids are potent vehicles for spread of antibiotic resistance genes in bacterial populations and often persist in the absence of selection due to efficient maintenance mechanisms. We previously constructed non-conjugative high copy number plasmid vectors that efficiently displace stable plasmids from enteric bacteria in a laboratory context by blocking their replication and neutralising their addiction systems. Here we assess a low copy number broad-host-range self-transmissible IncP-1 plasmid as a vector for such curing cassettes to displace IncF and IncK plasmids. The wild type plasmid carrying the curing cassette displaces target plasmids poorly but derivatives with deletions near the IncP-1 replication origin that elevate copy number about two-fold are efficient. Verification of this in mini IncP-1 plasmids showed that elevated copy number was not sufficient and that the parB gene, korB, that is central to its partitioning and gene control system, also needs to be included. The resulting vector can displace target plasmids from a laboratory population without selection and demonstrated activity in a mouse model although spread is less efficient and requires additional selection pressure.
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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: 43] [Impact Index Per Article: 8.6] [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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Zainuddin HS, Bai Y, Mansell TJ. CRISPR-based curing and analysis of metabolic burden of cryptic plasmids in Escherichia coli Nissle 1917. Eng Life Sci 2019; 19:478-485. [PMID: 32625025 DOI: 10.1002/elsc.201900003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/28/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
E. coli Nissle 1917 (EcN) has long been used as an over-the-counter probiotic and has shown potential to be used as a live biotherapeutic. It contains two stably replicating cryptic plasmids, pMUT1, and pMUT2, the function of which is unclear but the presence of which may increase the metabolic burden on the cell, particularly in the context of added recombinant plasmids. In this work, we present a clustered regularly interspaced short palindromic repeats-Cas9-based method of curing cryptic plasmids, producing strains cured of one or both plasmids. We then assayed heterologous protein production from three different recombinant plasmids in wild-type and cured EcN derivatives and found that production of reporter proteins was not significantly different across strains. In addition, we replaced pMUT2 with an engineered version containing an inserted antibiotic resistance reporter gene and demonstrated that the engineered plasmid was stable over 90 generations without selection. These findings have broad implications for the curing of cryptic plasmids and for stable heterologous expression of proteins in this host. Specifically, curing of cryptic plasmids may not be necessary for optimal heterologous expression in this host.
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Affiliation(s)
- Halimatun S Zainuddin
- Department of Chemical and Biological Engineering Iowa State University Sweeney Hall Ames IA USA
| | - Yanfen Bai
- Department of Chemical and Biological Engineering Iowa State University Sweeney Hall Ames IA USA
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering Iowa State University Sweeney Hall Ames IA USA
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45
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Lim H, Choi SK. Programmed gRNA Removal System for CRISPR-Cas9-Mediated Multi-Round Genome Editing in Bacillus subtilis. Front Microbiol 2019; 10:1140. [PMID: 31164882 PMCID: PMC6536666 DOI: 10.3389/fmicb.2019.01140] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/06/2019] [Indexed: 01/25/2023] Open
Abstract
CRISPR/Cas9 has become a simple and powerful genome editing tool for many organisms. However, multi-round genome editing should replace single-guide RNA (sgRNA) every round, which is laborious and time-consuming. Here, we have developed a multi-round genome editing system in which genome editing and the programmed removal of the sgRNA have sequentially occurred in a growth-dependent manner in Bacillus subtilis. The system contains two plasmids, one containing a cas9 gene and the other containing two sgRNAs and a donor DNA for homology directed repair (HDR). The two sgRNAs are chromosome-targeting (sgRNAct) and self-targeting (sgRNAst) under the control of a constitutive promoter and sporulation-specific promoter, respectively. In the growth phase, the sgRNAct is transcribed and complexed with the Cas9 to edit the chromosomal target, while the sgRNAst is transcribed in the sporulation phase and complexed with the Cas9 to attack its own plasmid. Therefore, the system automatically makes the cell ready for next-round genome editing during cultivation. The system was approved through the sequential deletion of eight extracellular protease genes in the B. subtilis, suggesting that it can be used for versatile applications in multi-round genome editing.
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Affiliation(s)
- Hayeon Lim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, South Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, South Korea
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Uribe RV, van der Helm E, Misiakou MA, Lee SW, Kol S, Sommer MOA. Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla. Cell Host Microbe 2019; 25:233-241.e5. [PMID: 30737174 DOI: 10.1016/j.chom.2019.01.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/24/2018] [Accepted: 01/02/2019] [Indexed: 01/07/2023]
Abstract
CRISPR-Cas systems in bacteria and archaea provide immunity against bacteriophages and plasmids. To overcome CRISPR immunity, phages have acquired anti-CRISPR genes that reduce CRISPR-Cas activity. Using a synthetic genetic circuit, we developed a high-throughput approach to discover anti-CRISPR genes from metagenomic libraries based on their functional activity rather than sequence homology or genetic context. We identified 11 DNA fragments from soil, animal, and human metagenomes that circumvent Streptococcus pyogenes Cas9 activity in our selection strain. Further in vivo and in vitro characterization of a subset of these hits validated the activity of four anti-CRISPRs. Notably, homologs of some of these anti-CRISPRs were detected in seven different phyla, namely Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, and Balneolaeota, and have high sequence identity suggesting recent horizontal gene transfer. Thus, anti-CRISPRs against type II-A CRISPR-Cas systems are widely distributed across bacterial phyla, suggesting a more complex ecological role than previously appreciated.
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Affiliation(s)
- Ruben V Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Eric van der Helm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Maria-Anna Misiakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Sang-Woo Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark.
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47
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CRISPR-Cas9 and CRISPR-Assisted Cytidine Deaminase Enable Precise and Efficient Genome Editing in Klebsiella pneumoniae. Appl Environ Microbiol 2018; 84:AEM.01834-18. [PMID: 30217854 DOI: 10.1128/aem.01834-18] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/10/2018] [Indexed: 12/21/2022] Open
Abstract
Klebsiella pneumoniae is a promising industrial microorganism as well as a major human pathogen. The recent emergence of carbapenem-resistant K. pneumoniae has posed a serious threat to public health worldwide, emphasizing a dire need for novel therapeutic means against drug-resistant K. pneumoniae Despite the critical importance of genetics in bioengineering, physiology studies, and therapeutic-means development, genome editing, in particular, the highly desirable scarless genetic manipulation in K. pneumoniae, is often time-consuming and laborious. Here, we report a two-plasmid system, pCasKP-pSGKP, used for precise and iterative genome editing in K. pneumoniae By harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome cleavage system and the lambda Red recombination system, pCasKP-pSGKP enabled highly efficient genome editing in K. pneumoniae using a short repair template. Moreover, we developed a cytidine base-editing system, pBECKP, for precise C→T conversion in both the chromosomal and plasmid-borne genes by engineering the fusion of the cytidine deaminase APOBEC1 and a Cas9 nickase. By using both the pCasKP-pSGKP and the pBECKP tools, the bla KPC-2 gene was confirmed to be the major factor that contributed to the carbapenem resistance of a hypermucoviscous carbapenem-resistant K. pneumoniae strain. The development of the two editing tools will significantly facilitate the genetic engineering of K. pneumoniae IMPORTANCE Genetics is a key means to study bacterial physiology. However, the highly desirable scarless genetic manipulation is often time-consuming and laborious for the major human pathogen K. pneumoniae We developed a CRISPR-Cas9-mediated genome-editing method and a cytidine base-editing system, enabling rapid, highly efficient, and iterative genome editing in both industrial and clinically isolated K. pneumoniae strains. We applied both tools in dissecting the drug resistance mechanism of a hypermucoviscous carbapenem-resistant K. pneumoniae strain, elucidating that the bla KPC-2 gene was the major factor that contributed to the carbapenem resistance of the hypermucoviscous carbapenem-resistant K. pneumoniae strain. Utilization of the two tools will dramatically accelerate a wide variety of investigations in diverse K. pneumoniae strains and relevant Enterobacteriaceae species, such as gene characterization, drug discovery, and metabolic engineering.
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Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142-155. [DOI: 10.1016/j.ymben.2018.05.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
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Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context. Trends Microbiol 2018; 26:978-985. [PMID: 30049587 DOI: 10.1016/j.tim.2018.06.007] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/11/2018] [Accepted: 06/27/2018] [Indexed: 12/29/2022]
Abstract
Antibiotic-resistant infections are an urgent problem in clinical settings because they sharply increase mortality risk in critically ill patients. The horizontal spread of antibiotic resistance genes among bacteria is driven by bacterial plasmids, promoting the evolution of resistance. Crucially, particular associations exist between resistance plasmids and bacterial clones that become especially successful in clinical settings. However, the factors underlying the success of these associations remain unknown. Recent in vitro evidence reveals (i) that plasmids produce fitness costs in bacteria, and (ii) that these costs are alleviated over time through compensatory mutations. I argue that plasmid-imposed costs and subsequent compensatory adaptation may determine the success of associations between plasmids and bacteria in clinical settings, shaping the in vivo evolution of antibiotic resistance.
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50
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Górski A, Międzybrodzki R, Łobocka M, Głowacka-Rutkowska A, Bednarek A, Borysowski J, Jończyk-Matysiak E, Łusiak-Szelachowska M, Weber-Dąbrowska B, Bagińska N, Letkiewicz S, Dąbrowska K, Scheres J. Phage Therapy: What Have We Learned? Viruses 2018; 10:E288. [PMID: 29843391 PMCID: PMC6024844 DOI: 10.3390/v10060288] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/11/2018] [Accepted: 05/22/2018] [Indexed: 02/07/2023] Open
Abstract
In this article we explain how current events in the field of phage therapy may positively influence its future development. We discuss the shift in position of the authorities, academia, media, non-governmental organizations, regulatory agencies, patients, and doctors which could enable further advances in the research and application of the therapy. In addition, we discuss methods to obtain optimal phage preparations and suggest the potential of novel applications of phage therapy extending beyond its anti-bacterial action.
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Affiliation(s)
- Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warsaw, Poland.
| | - Aleksandra Głowacka-Rutkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
| | - Agnieszka Bednarek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Natalia Bagińska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Sławomir Letkiewicz
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Medical Sciences Institute, Katowice School of Economics, Harcerzy Września Street 3, 40-659 Katowice, Poland.
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Research and Development Center, Regional Specialized Hospital, Kamieńskiego 73a, 51-124 Wrocław, Poland.
| | - Jacques Scheres
- National Institute of Public Health NIZP, Chocimska Street 24, 00-971 Warsaw, Poland.
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