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Zheng L, Shen J, Chen R, Hu Y, Zhao W, Leung ELH, Dai L. Genome engineering of the human gut microbiome. J Genet Genomics 2024; 51:479-491. [PMID: 38218395 DOI: 10.1016/j.jgg.2024.01.002] [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: 10/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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Affiliation(s)
- Linggang Zheng
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruiyue Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucan Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Science, University of Macau, Macau 999078, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Foo GW, Leichthammer CD, Saita IM, Lukas ND, Batko IZ, Heinrichs DE, Edgell DR. Intein-based thermoregulated meganucleases for containment of genetic material. Nucleic Acids Res 2024; 52:2066-2077. [PMID: 38180814 PMCID: PMC10899782 DOI: 10.1093/nar/gkad1247] [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: 08/23/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
Limiting the spread of synthetic genetic information outside of the intended use is essential for applications where biocontainment is critical. In particular, biocontainment of engineered probiotics and plasmids that are excreted from the mammalian gastrointestinal tract is needed to prevent escape and acquisition of genetic material that could confer a selective advantage to microbial communities. Here, we built a simple and lightweight biocontainment system that post-translationally activates a site-specific DNA endonuclease to degrade DNA at 18°C and not at higher temperatures. We constructed an orthogonal set of temperature-sensitive meganucleases (TSMs) by inserting the yeast VMA1 L212P temperature-sensitive intein into the coding regions of LAGLIDADG homing endonucleases. We showed that the TSMs eliminated plasmids carrying the cognate TSM target site from laboratory strains of Escherichia coli at the permissive 18°C but not at higher restrictive temperatures. Plasmid elimination is dependent on both TSM endonuclease activity and intein splicing. TSMs eliminated plasmids from E. coli Nissle 1917 after passage through the mouse gut when fecal resuspensions were incubated at 18°C but not at 37°C. Collectively, our data demonstrates the potential of thermoregulated meganucleases as a means of restricting engineered plasmids and probiotics to the mammalian gut.
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Affiliation(s)
- Gary W Foo
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | | | - Ibrahim M Saita
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - Nicholas D Lukas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - Izabela Z Batko
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - David E Heinrichs
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
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3
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Ma W, Cui X, Dong X, Li X, Liu K, Wang Y, Shi X, Chen L, Hao M. Characterization of nontyphoidal Salmonella strains from a tertiary hospital in China: serotype diversity, multidrug resistance, and genetic insights. Front Cell Infect Microbiol 2024; 13:1327092. [PMID: 38264733 PMCID: PMC10803454 DOI: 10.3389/fcimb.2023.1327092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Objective Nontyphoidal Salmonella is a significant public health concern due to its ability to cause foodborne illnesses worldwide. This study aims to characterize the nontyphoidal Salmonella strains isolated from patients in China. Methods A total of 19 nontyphoidal Salmonella strains were characterized through serovar identification, antimicrobial susceptibility testing (AST), biofilm formation assessment. Genetic relatedness was determined using pulsed-field gel electrophoresis (PFGE). WGS was employed to decipher the resistance mechanism and to contextualize the S. serovar Mbandaka strains among previously sequenced isolates in China. The biofilm associated mrkA gene was examined by PCR. Results The predominant serovar identified was S. Enteritidis, followed by S. Mbandaka, S. Thompson, S. Livingston, S. Alachua, and S. Infantis. PFGE analysis indicated a notable genetic similarity among the S. Mbandaka isolates. Phylogenetic analysis suggested that these strains were likely derived from a single source that had persisted in China for over five years. One multidrug resistance (MDR) S. Enteritidis isolate carried a highly transferable IncB/O/K/Z plasmid with bla CTX-M-15. One S. Thompson strain, harboring the mrkABCDF operon in an IncX1 plasmid, isolated from cutaneous lesions, demonstrated robust biofilm formation. However, no mrkABCDF loci were detected in other strains. Conclusion Our study emphasizes the importance of persisted surveillance and prompt response to Salmonella infections to protect public health. The dissemination of bla CTX-M-15-harboring IncB/O/K/Z plasmid and the spread of virulent mrkABCDF operon among Salmonella in China and other global regions warrant close monitoring.
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Affiliation(s)
- Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Xiaodi Cui
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Xinpeng Li
- Department of Bacterial Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Ke Liu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Yujiao Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Xiaohong Shi
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, United States
| | - Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
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Allard N, Collette A, Paquette J, Rodrigue S, Côté JP. Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids. Commun Biol 2023; 6:1172. [PMID: 37973843 PMCID: PMC10654706 DOI: 10.1038/s42003-023-05534-2] [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: 03/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Arianne Collette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Josianne Paquette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| | - Jean-Philippe Côté
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
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5
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Mousavinasab F, Karimi R, Taheri S, Ahmadvand F, Sanaaee S, Najafi S, Halvaii MS, Haghgoo A, Zamany M, Majidpoor J, Khosravifar M, Baniasadi M, Talebi M, Movafagh A, Aghaei-Zarch SM, Khorram N, Farnia P, Kalhor K. Microbiome modulation in inflammatory diseases: Progress to microbiome genetic engineering. Cancer Cell Int 2023; 23:271. [PMID: 37951913 PMCID: PMC10640760 DOI: 10.1186/s12935-023-03095-2] [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: 03/13/2023] [Accepted: 10/07/2023] [Indexed: 11/14/2023] Open
Abstract
Recent developments in sequencing technology and analytical approaches have allowed researchers to show that the healthy gut microbiome is very varied and capable of performing a wide range of tasks. The importance of gut microbiota in controlling immunological, neurological, and endocrine function is becoming well-recognized. Thereby, numerous inflammatory diseases, including those that impact the gastrointestinal system, as well as less obvious ones, including Rheumatoid arthritis (RA), cancer, gestational diabetes (GD), type 1 diabetes (T1D), and type 2 diabetes (T2D), have been linked to dysbiotic gut microbiota. Microbiome engineering is a rapidly evolving frontier for solutions to improve human health. Microbiome engineering seeks to improve the function of an ecosystem by manipulating the composition of microbes. Thereby, generating potential therapies against metabolic, inflammatory, and immunological diseases will be possible through microbiome engineering. This essay first provides an overview of the traditional technological instruments that might be used for microbiome engineering, such as Fecal Microbiota Transplantation (FMT), prebiotics, and probiotics. Moreover, we will also discuss experimental genetic methods such as Metagenomic Alteration of Gut microbiome by In situ Conjugation (MAGIC), Bacteriophage, and Conjugative plasmids in manipulating intestinal microbiota.
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Affiliation(s)
| | - Ronika Karimi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sima Taheri
- Department of Microbiology, Shahr Qods Branch, Islamic Azad University, Tehran, Iran
| | | | - Saameh Sanaaee
- Department of New Science, Faculty of Cellular and Molecular biology, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Alireza Haghgoo
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Marzieh Zamany
- Shahid Akbarabadi Clinical Research Development Unit, Iran University of medical Science, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Mina Khosravifar
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mohammad Baniasadi
- Department of Basic Sciences, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Mehrdad Talebi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Abolfazl Movafagh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nastaran Khorram
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran.
| | - Poopak Farnia
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Kambiz Kalhor
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, USA
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6
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [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] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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7
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Li G, Jia L, Wan L, Xia L, Gao A, Yang R, Sun R, Wang M, Du J, Lian X, Zhang R, Fang L, Liao X, Liu Y, Liu B, Sun J. Acquisition of a novel conjugative multidrug-resistant hypervirulent plasmid leads to hypervirulence in clinical carbapenem-resistant Klebsiella pneumoniae strains. MLIFE 2023; 2:317-327. [PMID: 38817808 PMCID: PMC10989919 DOI: 10.1002/mlf2.12086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 06/01/2024]
Abstract
The co-occurrence of plasmid-mediated multidrug resistance and hypervirulence in epidemic carbapenem-resistant Klebsiella pneumoniae has emerged as a global public health issue. In this study, an ST23 carbapenem-resistant hypervirulent K. pneumoniae (CR-HvKP) strain VH1-2 was identified from cucumber in China and harbored a novel hybrid plasmid pVH1-2-VIR. The plasmid pVH1-2-VIR carrying both virulence and multidrug-resistance (MDR) genes was likely generated through the recombination of a virulence plasmid and an IncFIIK conjugative MDR plasmid in clinical ST23 18622 isolated from a sputum sample. The plasmid pVH1-2-VIR exhibited the capacity for transfer to the clinical ST11 carbapenem-resistant K. pneumoniae (CRKP) strain via conjugation assay. Acquisition of pVH1-2-VIR plasmid directly converted a CRKP into CR-HvKP strain characterized by hypermucoviscosity, heightened virulence for Galleria mellonella larvae, and increased colonization ability in the mouse intestine. The emergence of such a hybrid plasmid may expedite the spread of CR-HvKP strains, posing a significant risk to human health.
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Affiliation(s)
- Gong Li
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Ling Jia
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Lijuan Xia
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Ang Gao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Runshi Yang
- Department of Pathogen Biology and MicrobiologyZhejiang University School of MedicineHangzhouChina
| | - Ruanyang Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Minge Wang
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Juan Du
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Xinlei Lian
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Rongmin Zhang
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Liangxing Fang
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Xiaoping Liao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Yahong Liu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Bao‐Tao Liu
- College of Veterinary MedicineQingdao Agricultural UniversityQingdaoChina
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
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8
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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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9
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Gharesi N, Luneau L, Kalaska JF, Baillet S. Evaluation of abstract rule-based associations in the human premotor cortex during passive observation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543581. [PMID: 37333191 PMCID: PMC10274620 DOI: 10.1101/2023.06.06.543581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Decision-making often manifests in behavior, typically yielding overt motor actions. This complex process requires the registration of sensory information with one's internal representation of the current context, before a categorical judgment of the most appropriate motor behavior can be issued. The construct concept of embodied decision-making encapsulates this sequence of complex processes, whereby behaviorally salient information from the environment is represented in an abstracted space of potential motor actions rather than only in an abstract cognitive "decision" space. Theoretical foundations and some empirical evidence account for support the involvement of premotor cortical circuits in embodied cognitive functions. Animal models show that premotor circuits participate in the registration and evaluation of actions performed by peers in social situations, that is, prior to controlling one's voluntary movements guided by arbitrary stimulus-response rules. However, such evidence from human data is currently limited. Here we used time-resolved magnetoencephalography imaging to characterize activations of the premotor cortex as human participants observed arbitrary, non-biological visual stimuli that either respected or violated a simple stimulus-response association rule. The participants had learned this rule previously, either actively, by performing a motor task (active learning), or passively, by observing a computer perform the same task (passive learning). We discovered that the human premotor cortex is activated during the passive observation of the correct execution of a sequence of events according to a rule learned previously. Premotor activation also differs when the subjects observe incorrect stimulus sequences. These premotor effects are present even when the observed events are of a non-motor, abstract nature, and even when the stimulus-response association rule was learned via passive observations of a computer agent performing the task, without requiring overt motor actions from the human participant. We found evidence of these phenomena by tracking cortical beta-band signaling in temporal alignment with the observation of task events and behavior. We conclude that premotor cortical circuits that are typically engaged during voluntary motor behavior are also involved in the interpretation of events of a non-ecological, unfamiliar nature but related to a learned abstract rule. As such, the present study provides the first evidence of neurophysiological processes of embodied decision-making in human premotor circuits when the observed events do not involve motor actions of a third party.
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Affiliation(s)
- Niloofar Gharesi
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
| | - Lucie Luneau
- Groupe de recherche sur la signalisation neuronale et la circuiterie, Département de Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - John F Kalaska
- Groupe de recherche sur la signalisation neuronale et la circuiterie, Département de Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Sylvain Baillet
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
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10
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Oxendine A, Walsh AA, Young T, Dixon B, Hoke A, Rogers EE, Lee MD, Maurer JJ. Conditions Necessary for the Transfer of Antimicrobial Resistance in Poultry Litter. Antibiotics (Basel) 2023; 12:1006. [PMID: 37370325 DOI: 10.3390/antibiotics12061006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Animal manures contain a large and diverse reservoir of antimicrobial resistance (AMR) genes that could potentially spillover into the general population through transfer of AMR to antibiotic-susceptible pathogens. The ability of poultry litter microbiota to transmit AMR was examined in this study. Abundance of phenotypic AMR was assessed for litter microbiota to the antibiotics: ampicillin (Ap; 25 μg/mL), chloramphenicol (Cm; 25 μg/mL), streptomycin (Sm; 100 μg/mL), and tetracycline (Tc; 25 μg/mL). qPCR was used to estimate gene load of streptomycin-resistance and sulfonamide-resistance genes aadA1 and sul1, respectively, in the poultry litter community. AMR gene load was determined relative to total bacterial abundance using 16S rRNA qPCR. Poultry litter contained 108 CFU/g, with Gram-negative enterics representing a minor population (<104 CFU/g). There was high abundance of resistance to Sm (106 to 107 CFU/g) and Tc (106 to 107 CFU/g) and a sizeable antimicrobial-resistance gene load in regards to gene copies per bacterial genome (aadA1: 0.0001-0.0060 and sul1: 0.0355-0.2455). While plasmid transfer was observed from Escherichia coli R100, as an F-plasmid donor control, to the Salmonella recipient in vitro, no AMR Salmonella were detected in a poultry litter microcosm with the inclusion of E. coli R100. Confirmatory experiments showed that isolated poultry litter bacteria were not interfering with plasmid transfer in filter matings. As no R100 transfer was observed at 25 °C, conjugative plasmid pRSA was chosen for its high plasmid transfer frequency (10-4 to 10-5) at 25 °C. While E. coli strain background influenced the persistence of pRSA in poultry litter, no plasmid transfer to Salmonella was ever observed. Although poultry litter microbiota contains a significant AMR gene load, potential to transmit resistance is low under conditions commonly used to assess plasmid conjugation.
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Affiliation(s)
- Aaron Oxendine
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Allison A Walsh
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Tamesha Young
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Brandan Dixon
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Alexa Hoke
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Eda Erdogan Rogers
- Department of Biomedical Science and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Margie D Lee
- Department of Biomedical Science and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - John J Maurer
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
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11
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Moura de Sousa J, Lourenço M, Gordo I. Horizontal gene transfer among host-associated microbes. Cell Host Microbe 2023; 31:513-527. [PMID: 37054673 DOI: 10.1016/j.chom.2023.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.
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Affiliation(s)
- Jorge Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015 Paris, France
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015 Paris, France
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,6, Oeiras, Portugal.
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12
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Patkowski JB, Dahlberg T, Amin H, Gahlot DK, Vijayrajratnam S, Vogel JP, Francis MS, Baker JL, Andersson M, Costa TRD. The F-pilus biomechanical adaptability accelerates conjugative dissemination of antimicrobial resistance and biofilm formation. Nat Commun 2023; 14:1879. [PMID: 37019921 PMCID: PMC10076315 DOI: 10.1038/s41467-023-37600-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Conjugation is used by bacteria to propagate antimicrobial resistance (AMR) in the environment. Central to this process are widespread conjugative F-pili that establish the connection between donor and recipient cells, thereby facilitating the spread of IncF plasmids among enteropathogenic bacteria. Here, we show that the F-pilus is highly flexible but robust at the same time, properties that increase its resistance to thermochemical and mechanical stresses. By a combination of biophysical and molecular dynamics methods, we establish that the presence of phosphatidylglycerol molecules in the F-pilus contributes to the structural stability of the polymer. Moreover, this structural stability is important for successful delivery of DNA during conjugation and facilitates rapid formation of biofilms in harsh environmental conditions. Thus, our work highlights the importance of F-pilus structural adaptations for the efficient spread of AMR genes in a bacterial population and for the formation of biofilms that protect against the action of antibiotics.
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Affiliation(s)
- Jonasz B Patkowski
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Tobias Dahlberg
- Department of Physics, Umeå University, 901 87, Umeå, Sweden
| | - Himani Amin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | | | - Sukhithasri Vijayrajratnam
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joseph P Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Matthew S Francis
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Joseph L Baker
- Department of Chemistry, The College of New Jersey, Ewing, NJ, 08628, USA.
| | | | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK.
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13
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Kirundi J, Moghadamrad S, Urbaniak C. Microbiome-liver crosstalk: A multihit therapeutic target for liver disease. World J Gastroenterol 2023; 29:1651-1668. [PMID: 37077519 PMCID: PMC10107210 DOI: 10.3748/wjg.v29.i11.1651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/05/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023] Open
Abstract
Liver disease has become a leading cause of death, particularly in the West, where it is attributed to more than two million deaths annually. The correlation between gut microbiota and liver disease is still not fully understood. However, it is well known that gut dysbiosis accompanied by a leaky gut causes an increase in lipopolysaccharides in circulation, which in turn evoke massive hepatic inflammation promoting liver cirrhosis. Microbial dysbiosis also leads to poor bile acid metabolism and low short-chain fatty acids, all of which exacerbate the inflammatory response of liver cells. Gut microbial homeostasis is maintained through intricate processes that ensure that commensal microbes adapt to the low oxygen potential of the gut and that they rapidly occupy all the intestinal niches, thus outcompeting any potential pathogens for available nutrients. The crosstalk between the gut microbiota and its metabolites also guarantee an intact gut barrier. These processes that protect against destabilization of gut microbes by potential entry of pathogenic bacteria are collectively called colonization resistance and are equally essential for liver health. In this review, we shall investigate how the mechanisms of colonization resistance influence the liver in health and disease and the microbial-liver crosstalk potential as therapeutic target areas.
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Affiliation(s)
- Jorum Kirundi
- Department of Biomedical Research, University of Bern, Bern 3014, Switzerland
| | - Sheida Moghadamrad
- Department of Gastroenterology/Hepatology, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona and Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano 6900, Switzerland
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14
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Djermoun S, Reuter A, Derollez E, Lesterlin C, Bigot S. Reprogramming targeted-antibacterial-plasmids (TAPs) to achieve broad-host range antibacterial activity. Plasmid 2023; 126:102680. [PMID: 37001687 DOI: 10.1016/j.plasmid.2023.102680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
The emergence and spread of antimicrobial resistance results in antibiotic inefficiency against multidrug resistant bacterial strains. Alternative treatment to antibiotics must be investigated to fight bacterial infections and limit this global public health problem. We recently developed an innovative strategy based on mobilizable Targeted-Antibacterial-Plasmids (TAPs) that deliver CRISPR/Cas systems with strain-specific antibacterial activity, using the F plasmid conjugation machinery for transfer into the targeted strains. These TAPs were shown to specifically kill a variety of Enterobacteriaceae strains, including E. coli K12 and the pathogen strains EPEC, Enterobacter cloacae and Citrobacter rodentium. Here, we extend the host-range of TAPs using the RP4 plasmid conjugation system for their mobilization, thus allowing the targeting of E. coli but also phylogenetically distant species, including Salmonella enterica Thyphimurium, Klebsiella pneumoniae, Vibrio cholerae, and Pseudomonas aeruginosa. This work demonstrates the versatility of the TAP strategy and represents a significant step toward the development of non-antibiotic strain-specific antimicrobial treatments.
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15
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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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16
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Yu Z, Henderson IR, Guo J. Non-caloric artificial sweeteners modulate conjugative transfer of multi-drug resistance plasmid in the gut microbiota. Gut Microbes 2023; 15:2157698. [PMID: 36524841 PMCID: PMC9762752 DOI: 10.1080/19490976.2022.2157698] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Non-caloric artificial sweeteners have been widely permitted as table sugar substitutes with high intensities of sweetness. They can pass through the intestinal tract without significant metabolization and frequently encounter the gut microbiome, which is composed of diverse bacterial species and is a pool of antibiotic resistance genes (ARGs). However, little is known about whether these sweeteners could accelerate the spread of ARGs in the gut microbiome. Here, we established an in vitro conjugation model by using Escherichia coli that carries chromosome-inserted Tn7 lacIq-pLpp-mCherry and plasmid-encoded gfpmut3b gene as the donor and murine fecal bacteria as the recipient. We found that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) can increase reactive oxygen species (ROS) production and promote plasmid-mediated conjugative transfer to the gut microbiome. Cell sorting and 16S rRNA gene amplicon sequencing analysis of fecal samples reveal that the tested sweeteners can promote the broad-host-range plasmid permissiveness to both Gram-negative and Gram-positive gut bacteria. The increased plasmid permissiveness was also validated with a human pathogen Klebsiella pneumoniae. Collectively, our study demonstrates that non-caloric artificial sweeteners can induce oxidative stress and boost the plasmid-mediated conjugative transfer of ARGs among the gut microbiota and a human pathogen. Considering the soaring consumption of these sweeteners and the abundance of mobile ARGs in the human gut, our results highlight the necessity of performing a thorough risk assessment of antibiotic resistance associated with the usage of artificial sweeteners as food additives.
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Affiliation(s)
- Zhigang Yu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
| | - Ian R Henderson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
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17
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Kessler C, Hou J, Neo O, Buckner MMC. In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome. FEMS Microbiol Rev 2022; 47:6807411. [PMID: 36341518 PMCID: PMC9841969 DOI: 10.1093/femsre/fuac044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.
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Affiliation(s)
- Celia Kessler
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Jingping Hou
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Onalenna Neo
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Michelle M C Buckner
- Corresponding author: Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel: +44 (0)121 415 8758; E-mail:
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18
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Knecht CA, García Allende N, Álvarez VE, Prack McCormick B, Massó MG, Piekar M, Campos J, Fox B, Camicia G, Gambino AS, Leguina ACDV, Donis N, Fernández-Canigia L, Quiroga MP, Centrón D. Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche. Front Cell Infect Microbiol 2022; 12:951049. [DOI: 10.3389/fcimb.2022.951049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
According to the World Health Organization, carbapenem-resistant Enterobacteriaceae (CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria: Klebsiella pneumoniae and Enterobacter cloacae Complex (ECC). This scenario is mirrored in our hospital. It is known that K. pneumoniae and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one Enterobacter hormaechei and one K. pneumoniae) and in vitro competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing K. pneumoniae (KPC-Kp) high-risk clones from our institution. A KPC-producing E. hormaechei and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring blaKPC-2. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of blaKPC-2 within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.
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19
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Cochrane RR, Shrestha A, Severo de Almeida MM, Agyare-Tabbi M, Brumwell SL, Hamadache S, Meaney JS, Nucifora DP, Say HH, Sharma J, Soltysiak MPM, Tong C, Van Belois K, Walker EJL, Lachance MA, Gloor GB, Edgell DR, Shapiro RS, Karas BJ. Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi. BIODESIGN RESEARCH 2022; 2022:9802168. [PMID: 37850145 PMCID: PMC10521675 DOI: 10.34133/2022/9802168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/28/2022] [Indexed: 10/19/2023] Open
Abstract
Fungi are nature's recyclers, allowing for ecological nutrient cycling and, in turn, the continuation of life on Earth. Some fungi inhabit the human microbiome where they can provide health benefits, while others are opportunistic pathogens that can cause disease. Yeasts, members of the fungal kingdom, have been domesticated by humans for the production of beer, bread, and, recently, medicine and chemicals. Still, the great untapped potential exists within the diverse fungal kingdom. However, many yeasts are intractable, preventing their use in biotechnology or in the development of novel treatments for pathogenic fungi. Therefore, as a first step for the domestication of new fungi, an efficient DNA delivery method needs to be developed. Here, we report the creation of superior conjugative plasmids and demonstrate their transfer via conjugation from bacteria to 7 diverse yeast species including the emerging pathogen Candida auris. To create our superior plasmids, derivatives of the 57 kb conjugative plasmid pTA-Mob 2.0 were built using designed gene deletions and insertions, as well as some unintentional mutations. Specifically, a cluster mutation in the promoter of the conjugative gene traJ had the most significant effect on improving conjugation to yeasts. In addition, we created Golden Gate assembly-compatible plasmid derivatives that allow for the generation of custom plasmids to enable the rapid insertion of designer genetic cassettes. Finally, we demonstrated that designer conjugative plasmids harboring engineered restriction endonucleases can be used as a novel antifungal agent, with important applications for the development of next-generation antifungal therapeutics.
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Affiliation(s)
- Ryan R. Cochrane
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Arina Shrestha
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Mariana M. Severo de Almeida
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Michelle Agyare-Tabbi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Stephanie L. Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Samir Hamadache
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Jordyn S. Meaney
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Daniel P. Nucifora
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Henry Heng Say
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | | | - Cheryl Tong
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Katherine Van Belois
- Department of Biology, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Emma J. L. Walker
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Marc-André Lachance
- Department of Biology, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Gregory B. Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - David R. Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Bogumil J. Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
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20
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Ott LC, Mellata M. Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation. Front Microbiol 2022; 13:891548. [PMID: 35847067 PMCID: PMC9280185 DOI: 10.3389/fmicb.2022.891548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.
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Affiliation(s)
- Logan C. Ott
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Melha Mellata,
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21
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Chiș AA, Rus LL, Morgovan C, Arseniu AM, Frum A, Vonica-Țincu AL, Gligor FG, Mureșan ML, Dobrea CM. Microbial Resistance to Antibiotics and Effective Antibiotherapy. Biomedicines 2022; 10:biomedicines10051121. [PMID: 35625857 PMCID: PMC9138529 DOI: 10.3390/biomedicines10051121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
Currently, the efficacy of antibiotics is severely affected by the emergence of the antimicrobial resistance phenomenon, leading to increased morbidity and mortality worldwide. Multidrug-resistant pathogens are found not only in hospital settings, but also in the community, and are considered one of the biggest public health concerns. The main mechanisms by which bacteria develop resistance to antibiotics include changes in the drug target, prevention of entering the cell, elimination through efflux pumps or inactivation of drugs. A better understanding and prediction of resistance patterns of a pathogen will lead to a better selection of active antibiotics for the treatment of multidrug-resistant infections.
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22
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Allard N, Neil K, Grenier F, Rodrigue S. The Type IV Pilus of Plasmid TP114 Displays Adhesins Conferring Conjugation Specificity and Is Important for DNA Transfer in the Mouse Gut Microbiota. Microbiol Spectr 2022; 10:e0230321. [PMID: 35293798 PMCID: PMC9045228 DOI: 10.1128/spectrum.02303-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Type IV pili (T4P) are common bacterial surface appendages involved in different biological processes such as adherence, motility, competence, pathogenesis, and conjugation. In this work, we describe the T4P of TP114, an IncI2 enterobacterial conjugative plasmid recently shown to disseminate at high rates in the mouse intestinal tract. This pilus is composed of the major PilS and minor PilV pilins that are both important for conjugation in broth and in the gut microbiota but not on a solid support. The PilV-coding sequence is part of a shufflon and can bear different C-terminal domains. The shufflon is a multiple DNA inversion system containing many DNA cassettes flanked by recombination sites that are recognized by a shufflon-specific tyrosine recombinase (shufflase) promoting the recombination between DNA segments. The different PilV variants act as adhesins that can modify the affinity for different recipient bacteria. Eight PilV variants were identified in TP114, including one that has not been described in other shufflons. All PilV variants allowed conjugative transfer with different recipient Escherichia coli strains. We conclude that the T4P carried by TP114 plays a major role in mating pair stabilization in broth as well as in the gut microbiota and that the shufflon acts as a biological switch modifying the conjugative host range specificity. IMPORTANCE Conjugative plasmids are involved in horizontal gene transfer in the gut microbiota, which constitutes an important antibiotic resistance gene reservoir. However, the molecular mechanisms used by conjugative plasmids to select recipient bacteria and transfer at high rates in the mouse gut microbiota remain poorly characterized. We studied the type IV pilus carried by TP114 and demonstrated that the minor pilin PilV acts as an adhesin that can efficiently select target cells for conjugative transfer. Moreover, the pilV gene can be rapidly modified by a shufflon, hence modulating the nature of the recipient bacteria during conjugation. Our study highlights the role of mating pair stabilization for conjugation in broth as well as in the gut microbiome and explains how the host spectrum of a plasmid can be expanded simply by remodeling the PilV adhesin.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Kevin Neil
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Frédéric Grenier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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23
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Rehabilitation of a misbehaving microbiome: phages for the remodeling of bacterial composition and function. iScience 2022; 25:104146. [PMID: 35402871 PMCID: PMC8991392 DOI: 10.1016/j.isci.2022.104146] [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: 12/02/2022] Open
Abstract
The human gut microbiota is considered an adjunct metabolic organ owing to its health impact. Recent studies have shown correlations between gut phage composition and host health. Whereas phage therapy has popularized virulent phages as antimicrobials, both virulent and temperate phages have a natural ecological relationship with their cognate bacteria. Characterization of this evolutionary coadaptation has led to other emergent therapeutic phage applications that do not necessarily rely on bacterial eradication or target pathogens. Here, we present an overview of the tripartite relationship between phages, bacteria, and the mammalian host, and highlight applications of the wildtype and genetically engineered phage for gut microbiome remodeling. In light of new and varied strategies, we propose to categorize phage applications aiming to modulate bacterial composition or function as “phage rehabilitation.” By delineating phage rehab from phage therapy, we believe it will enable greater nuance and understanding of these new phage-based technologies.
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24
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Heavey MK, Durmusoglu D, Crook N, Anselmo AC. Discovery and delivery strategies for engineered live biotherapeutic products. Trends Biotechnol 2022; 40:354-369. [PMID: 34481657 PMCID: PMC8831446 DOI: 10.1016/j.tibtech.2021.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
Genetically engineered microbes that secrete therapeutics, sense and respond to external environments, and/or target specific sites in the gut fall under an emergent class of therapeutics, called live biotherapeutic products (LBPs). As live organisms that require symbiotic host interactions, LBPs offer unique therapeutic opportunities, but also face distinct challenges in the gut microenvironment. In this review, we describe recent approaches (often demonstrated using traditional probiotic microorganisms) to discover LBP chassis and genetic parts utilizing omics-based methods and highlight LBP delivery strategies, with a focus on addressing physiological challenges that LBPs encounter after oral administration. Finally, we share our perspective on the opportunity to apply an integrated approach, wherein discovery and delivery strategies are utilized synergistically, towards tailoring and optimizing LBP efficacy.
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Affiliation(s)
- Mairead K. Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Aaron C. Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Correspondence: (A.C. Anselmo), (N. Crook)
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25
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Lipke PN, Rauceo JM, Viljoen A. Cell-Cell Mating Interactions: Overview and Potential of Single-Cell Force Spectroscopy. Int J Mol Sci 2022; 23:ijms23031110. [PMID: 35163034 PMCID: PMC8835621 DOI: 10.3390/ijms23031110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
It is an understatement that mating and DNA transfer are key events for living organisms. Among the traits needed to facilitate mating, cell adhesion between gametes is a universal requirement. Thus, there should be specific properties for the adhesion proteins involved in mating. Biochemical and biophysical studies have revealed structural information about mating adhesins, as well as their specificities and affinities, leading to some ideas about these specialized adhesion proteins. Recently, single-cell force spectroscopy (SCFS) has added important findings. In SCFS, mating cells are brought into contact in an atomic force microscope (AFM), and the adhesive forces are monitored through the course of mating. The results have shown some remarkable characteristics of mating adhesins and add knowledge about the design and evolution of mating adhesins.
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Affiliation(s)
- Peter N. Lipke
- Biology Department, Brooklyn College of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Correspondence: (P.N.L.); (A.V.)
| | - Jason M. Rauceo
- Department of Sciences, John Jay College of the City University of New York, New York, NY 10019, USA;
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4–5, bte L7.07.07, 1348 Louvain-la-Neuve, Belgium
- Correspondence: (P.N.L.); (A.V.)
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26
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Liu G, Thomsen LE, Olsen JE. Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review. J Antimicrob Chemother 2021; 77:556-567. [PMID: 34894259 DOI: 10.1093/jac/dkab450] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.
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Affiliation(s)
- Gang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Line Elnif Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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27
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Neil K, Allard N, Roy P, Grenier F, Menendez A, Burrus V, Rodrigue S. High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. Mol Syst Biol 2021; 17:e10335. [PMID: 34665940 PMCID: PMC8527022 DOI: 10.15252/msb.202110335] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
Antibiotic resistance threatens our ability to treat infectious diseases, spurring interest in alternative antimicrobial technologies. The use of bacterial conjugation to deliver CRISPR-cas systems programmed to precisely eliminate antibiotic-resistant bacteria represents a promising approach but requires high in situ DNA transfer rates. We have optimized the transfer efficiency of conjugative plasmid TP114 using accelerated laboratory evolution. We hence generated a potent conjugative delivery vehicle for CRISPR-cas9 that can eliminate > 99.9% of targeted antibiotic-resistant Escherichia coli in the mouse gut microbiota using a single dose. We then applied this system to a Citrobacter rodentium infection model, achieving full clearance within four consecutive days of treatment.
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Affiliation(s)
- Kevin Neil
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Nancy Allard
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Patricia Roy
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Frédéric Grenier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Alfredo Menendez
- Département de Microbiologie et d'InfectiologieUniversité de SherbrookeSherbrookeQCCanada
| | - Vincent Burrus
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
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28
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Neil K, Allard N, Rodrigue S. Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota. Front Microbiol 2021; 12:673260. [PMID: 34149661 PMCID: PMC8213034 DOI: 10.3389/fmicb.2021.673260] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial conjugation is a widespread and particularly efficient strategy to horizontally disseminate genes in microbial populations. With a rich and dense population of microorganisms, the intestinal microbiota is often considered a fertile environment for conjugative transfer and a major reservoir of antibiotic resistance genes. In this mini-review, we summarize recent findings suggesting that few conjugative plasmid families present in Enterobacteriaceae transfer at high rates in the gut microbiota. We discuss the importance of mating pair stabilization as well as additional factors influencing DNA transfer efficiency and conjugative host range in this environment. Finally, we examine the potential repurposing of bacterial conjugation for microbiome editing.
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Affiliation(s)
- Kevin Neil
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nancy Allard
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Sébastien Rodrigue
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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29
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Moralez J, Szenkiel K, Hamilton K, Pruden A, Lopatkin AJ. Quantitative analysis of horizontal gene transfer in complex systems. Curr Opin Microbiol 2021; 62:103-109. [PMID: 34098510 DOI: 10.1016/j.mib.2021.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 11/24/2022]
Abstract
Horizontal gene transfer (HGT) plays a significant role in rapidly propagating diverse traits throughout bacterial populations, thereby accelerating natural evolution and leading to complex community structures. Critical gene transfer rates underlying these occurrences dictate the efficiency and speed of gene spread; these rates are often highly specific to HGT mechanism and environmental context, and have historically been challenging to reliably quantify. In this review, we examine recent works that leverage rigorous quantitative methods to precisely measure these rates in a variety of settings beginning with in vitro studies and advancing to in situ measurements; we emphasize contexts where quantification across multiple scales of complexity has led to fundamental biological insights. Finally, we highlight the applications of these measurements and suggest potential methodological advances to improve our understanding.
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Affiliation(s)
- Jenifer Moralez
- Department of Biology, Barnard College, New York, NY 10027, USA
| | | | - Kerry Hamilton
- School of Sustainable Engineering and the Built Environment, 660 S College Ave, Tempe AZ 85281, USA; The Biodesign Center for Environmental Health Engineering, 1001 S McAllister Ave, Tempe AZ 85287, USA
| | - Amy Pruden
- Virginia Tech, Department of Civil & Environmental Engineering, Blacksburg, VA 24060, USA
| | - Allison J Lopatkin
- Department of Biology, Barnard College, New York, NY 10027, USA; Department Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; Data Science Institute, Columbia University, New York, NY 10027, USA.
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30
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Reuter A, Hilpert C, Dedieu-Berne A, Lematre S, Gueguen E, Launay G, Bigot S, Lesterlin C. Targeted-antibacterial-plasmids (TAPs) combining conjugation and CRISPR/Cas systems achieve strain-specific antibacterial activity. Nucleic Acids Res 2021; 49:3584-3598. [PMID: 33660775 PMCID: PMC8034655 DOI: 10.1093/nar/gkab126] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 12/25/2022] Open
Abstract
The global emergence of drug-resistant bacteria leads to the loss of efficacy of our antibiotics arsenal and severely limits the success of currently available treatments. Here, we developed an innovative strategy based on targeted-antibacterial-plasmids (TAPs) that use bacterial conjugation to deliver CRISPR/Cas systems exerting a strain-specific antibacterial activity. TAPs are highly versatile as they can be directed against any specific genomic or plasmid DNA using the custom algorithm (CSTB) that identifies appropriate targeting spacer sequences. We demonstrate the ability of TAPs to induce strain-selective killing by introducing lethal double strand breaks (DSBs) into the targeted genomes. TAPs directed against a plasmid-born carbapenem resistance gene efficiently resensitise the strain to the drug. This work represents an essential step toward the development of an alternative to antibiotic treatments, which could be used for in situ microbiota modification to eradicate targeted resistant and/or pathogenic bacteria without affecting other non-targeted bacterial species.
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Affiliation(s)
- Audrey Reuter
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Cécile Hilpert
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Annick Dedieu-Berne
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Sophie Lematre
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Erwan Gueguen
- University of Lyon, Université Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathogénie, 69622 Villeurbanne, France
| | - Guillaume Launay
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Sarah Bigot
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France
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31
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Al-Mir H, Osman M, Drapeau A, Hamze M, Madec JY, Haenni M. WGS Analysis of Clonal and Plasmidic Epidemiology of Colistin-Resistance Mediated by mcr Genes in the Poultry Sector in Lebanon. Front Microbiol 2021; 12:624194. [PMID: 33763043 PMCID: PMC7982416 DOI: 10.3389/fmicb.2021.624194] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/11/2021] [Indexed: 12/19/2022] Open
Abstract
Poultry and poultry meat are important contributors to the global antimicrobial burden. Unregulated and illegal use of extended-spectrum cephalosporins (ESC) in this sector has long been identified as a major cause of massive spread of ESC-resistant Escherichia coli, and colistin usage is considered a main driver of plasmid-mediated mcr genes dissemination. In Lebanon, the first mcr-1-positive E. coli found in poultry dates back to 2015, followed by a few reports of mcr-1-positive E. coli in poultry, swine, humans, and the environment. On the contrary, a comprehensive picture of the population structure of mcr-1-positive E. coli and mcr-1-bearing plasmids carrying the mcr-1 gene using whole-genome analysis is largely lacking. This study reports the prevalence of mcr-1-positive E. coli in poultry originating from 32 farms across three Lebanese governorates and slaughtered in the same place. We report 27/32 (84.4%) mcr-1 positive farms, leading to a total of 84 non-duplicate E. coli collected, of which 62 presented the mcr-1 gene. Numerous associated resistances were identified, including to ESC through the presence of bla CTX-M or bla CMY genes. The mcr-1 gene was mostly carried by IncX4 (n = 36) and IncI2 (n = 24) plasmids, which are both known for their efficient transfer capacities. A high genetic diversity was detected, arguing for the lack of contamination during the slaughter process. ST744 and ST1011 were the most widely identified clones, which have been both regularly associated to mcr-1-carrying E. coli and to the poultry sector. The wide dissemination of colistin-resistance, coupled to resistances to ESC and numerous other molecules, should urge authorities to implement efficient guidelines for the use of antibiotics in the poultry sector in Lebanon.
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Affiliation(s)
- Hiba Al-Mir
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
- Université de Lyon – ANSES Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Antoine Drapeau
- Université de Lyon – ANSES Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Yves Madec
- Université de Lyon – ANSES Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- Université de Lyon – ANSES Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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