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Trosvik P, Noordzij HT, de Muinck EJ. Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life. Sci Rep 2024; 14:18701. [PMID: 39134593 PMCID: PMC11319485 DOI: 10.1038/s41598-024-69275-w] [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: 04/24/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.
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Affiliation(s)
- Pål Trosvik
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Hanna Theodora Noordzij
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Eric Jacques de Muinck
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Pharmacy, University of Oslo, Oslo, Norway
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2
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Zhou H, Lu Z, Liu X, Bie X, Cui X, Wang Z, Sun X, Yang J. Characterization and transmission of plasmid-mediated multidrug resistance in foodborne Vibrio parahaemolyticus. Front Microbiol 2024; 15:1437660. [PMID: 39144225 PMCID: PMC11322368 DOI: 10.3389/fmicb.2024.1437660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/19/2024] [Indexed: 08/16/2024] Open
Abstract
Objectives The purpose of this study was to determine the structural features and transferability of the multidrug-resistance (MDR) plasmid, and resistance phenotypes for the tested antimicrobials in foodborne Vibrio parahaemolyticus. Methods Plasmids were isolated from a V. parahaemolyticus strain of seafood origin, then sequenced using the Illumina NovaSeq 6000 and PacBio Sequel II sequencing platforms to obtain the complete genome data. Characterization of the MDR plasmid pVP52-1, including determination of antimicrobial resistance genes (ARGs), plasmid incompatibility groups, and transferability, was carried out. Results V. parahaemolyticus strain NJIFDCVp52 contained two circular chromosomes and two circular plasmids (pVP52-1 and pVP52-2). Plasmid typing indicated that pVP52-1 belonged to the incompatibility group IncA/C2 and the sequence type pST3. pVP52-1 carried 12 different ARGs, an IS110-composite transposon consisting of aac(6')-Ib-cr, qnrVC1, aac(6')-Ib, dfrA14, and the IS26-mphA-IS6100 unit flanked by inverted sequences of IS5075 and IS4321. pVP52-2 carried no ARGs. A plasmid elimination assay showed that only pVP52-1 and its ARGs were lost, the loss of resistance to several antimicrobials, causing a change from the ampicillin-ampicillin/sulbactam-cefazolin-cefoxitin-ceftazidime-cefotaxime-imipenem-trimethoprim/sulfamethoxazole resistance pattern to the ampicillin resistance pattern. In accordance, a conjugation transfer assay showed that only pVP52-1 and its ARGs were horizontally transferred, leading to increased antimicrobial resistance in Escherichia coli strain EC600, causing a change from the ampicillin-nalidixic acid resistance pattern to the ampicillin-ampicillin/sulbactam-cefazolin-cefoxitin-ceftazidime-cefotaxime-imipenem-nalidixic acid-chloramphenicol-tetracycline-trimethoprim/sulfamethoxazole-azithromycin resistance pattern. Further transferability experiments revealed that pVP52-1 could be transferred to other enterobacterial strains of E. coli and Salmonella. Discussion This study emphasizes the urgent need for continued surveillance of resistance plasmids and changes in antimicrobial resistance profiles among the V. parahaemolyticus population.
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Affiliation(s)
- Haibo Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinmei Liu
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinping Cui
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zuwei Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaojie Sun
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Jun Yang
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
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3
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Jung JM, Rahman A, Schiffer AM, Weisberg AJ. Beav: a bacterial genome and mobile element annotation pipeline. mSphere 2024:e0020924. [PMID: 39037262 DOI: 10.1128/msphere.00209-24] [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: 03/12/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024] Open
Abstract
Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional Agrobacterium-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at https://github.com/weisberglab/beav. IMPORTANCE Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.
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Affiliation(s)
- Jewell M Jung
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Arafat Rahman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Andrea M Schiffer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
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4
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Hanke DM, Wang Y, Dagan T. Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility. Nucleic Acids Res 2024; 52:7049-7062. [PMID: 38808675 PMCID: PMC11229322 DOI: 10.1093/nar/gkae430] [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: 11/13/2023] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g. obligatory symbionts). Much less is known about the frequency of pseudogenes in prokaryotic plasmids; those are genetic elements that can transfer between cells and may encode beneficial traits for their host. Non-functionalization of plasmid-encoded genes may alter the plasmid characteristics, e.g. mobility, or their effect on the host. Analyzing 10 832 prokaryotic genomes, we find that plasmid genomes are characterized by threefold-higher pseudogene density compared to chromosomes. The majority of plasmid pseudogenes correspond to deteriorated transposable elements. A detailed analysis of enterobacterial plasmids furthermore reveals frequent gene non-functionalization events associated with the loss of plasmid self-transmissibility. Reconstructing the evolution of closely related plasmids reveals that non-functionalization of the conjugation machinery led to the emergence of non-mobilizable plasmid types. Examples are virulence plasmids in Escherichia and Salmonella. Our study highlights non-functionalization of core plasmid mobility functions as one route for the evolution of domesticated plasmids. Pseudogenes in plasmids supply insights into past transitions in plasmid mobility that are akin to transitions in bacterial lifestyle.
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Affiliation(s)
- Dustin M Hanke
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
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5
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Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R. Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans. Cell Host Microbe 2024; 32:875-886.e9. [PMID: 38754416 DOI: 10.1016/j.chom.2024.04.016] [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: 08/07/2023] [Revised: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.
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Affiliation(s)
- Fabienne Benz
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, Paris 75015, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Sarah Camara-Wilpert
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rimvydė Čepaitė
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Manuel Ares-Arroyo
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | | | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Johannes A Kuehn
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Silvana Gloor
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Mario Rodríguez Mestre
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Mònica Aguilà-Sans
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Lorrie Maccario
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lennart Randau
- Department of Biology, Philipps Universität Marburg, Marburg, Germany; SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany
| | - Patrick Pausch
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany; Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Jonas Stenløkke Madsen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, Paris 75015, France
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Søren Johannes Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
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6
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Beamud B, Benz F, Bikard D. Going viral: The role of mobile genetic elements in bacterial immunity. Cell Host Microbe 2024; 32:804-819. [PMID: 38870898 DOI: 10.1016/j.chom.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Bacteriophages and other mobile genetic elements (MGEs) pose a significant threat to bacteria, subjecting them to constant attacks. In response, bacteria have evolved a sophisticated immune system that employs diverse defensive strategies and mechanisms. Remarkably, a growing body of evidence suggests that most of these defenses are encoded by MGEs themselves. This realization challenges our traditional understanding of bacterial immunity and raises intriguing questions about the evolutionary forces at play. Our review provides a comprehensive overview of the latest findings on the main families of MGEs and the defense systems they encode. We also highlight how a vast diversity of defense systems remains to be discovered and their mechanism of mobility understood. Altogether, the composition and distribution of defense systems in bacterial genomes only makes sense in the light of the ecological and evolutionary interactions of a complex network of MGEs.
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Affiliation(s)
- Beatriz Beamud
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
| | - Fabienne Benz
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
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7
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Wang Y, Dagan T. The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages. Nat Commun 2024; 15:4555. [PMID: 38811529 PMCID: PMC11137137 DOI: 10.1038/s41467-024-48352-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is often facilitated by mobile genetic elements that copy or translocate ARGs between DNA molecules. The agglomeration of mobile elements in plasmids generates resistance islands comprising multiple ARGs. However, whether the emergence of resistance islands is restricted to specific MDR plasmid lineages remains understudied. Here we show that the agglomeration of ARGs in resistance islands is biased towards specific large plasmid lineages. Analyzing 6784 plasmids in 2441 Escherichia, Salmonella, and Klebsiella isolates, we quantify that 84% of the ARGs in MDR plasmids are found in resistance islands. We furthermore observe rapid evolution of ARG combinations in resistance islands. Most regions identified as resistance islands are shared among closely related plasmids but rarely among distantly related plasmids. Our results suggest the presence of barriers for the dissemination of ARGs between plasmid lineages, which are related to plasmid genetic properties, host range and the plasmid evolutionary history. The agglomeration of ARGs in plasmids is attributed to the workings of mobile genetic elements that operate within the framework of existing plasmid lineages.
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Affiliation(s)
- Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany.
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8
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Pfeifer E, Rocha EPC. Phage-plasmids promote recombination and emergence of phages and plasmids. Nat Commun 2024; 15:1545. [PMID: 38378896 PMCID: PMC10879196 DOI: 10.1038/s41467-024-45757-3] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
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Affiliation(s)
- Eugen Pfeifer
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
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9
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Camargo AP, Call L, Roux S, Nayfach S, Huntemann M, Palaniappan K, Ratner A, Chu K, Mukherjeep S, Reddy TBK, Chen IM, Ivanova N, Eloe-Fadrosh E, Woyke T, Baltrus D, Castañeda-Barba S, de la Cruz F, Funnell BE, Hall JJ, Mukhopadhyay A, Rocha EC, Stalder T, Top E, Kyrpides N. IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. Nucleic Acids Res 2024; 52:D164-D173. [PMID: 37930866 PMCID: PMC10767988 DOI: 10.1093/nar/gkad964] [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: 08/29/2023] [Revised: 10/09/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023] Open
Abstract
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.
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Affiliation(s)
- Antonio Pedro Camargo
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lee Call
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen Nayfach
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Anna Ratner
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ken Chu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Supratim Mukherjeep
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - I-Min A Chen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalia N Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson AZ, USA
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA
| | | | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas – Universidad de Cantabria), Cantabria, Spain
| | - Barbara E Funnell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Eva Top
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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10
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Hamilton T, Joris BR, Shrestha A, Browne TS, Rodrigue S, Karas BJ, Gloor GB, Edgell DR. De Novo Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials. ACS Synth Biol 2023; 12:3578-3590. [PMID: 38049144 PMCID: PMC10729033 DOI: 10.1021/acssynbio.3c00319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 12/06/2023]
Abstract
Metagenomic sequences represent an untapped source of genetic novelty, particularly for conjugative systems that could be used for plasmid-based delivery of Cas9-derived antimicrobial agents. However, unlocking the functional potential of conjugative systems purely from metagenomic sequences requires the identification of suitable candidate systems as starting scaffolds for de novo DNA synthesis. Here, we developed a bioinformatics approach that searches through the metagenomic "trash bin" for genes associated with conjugative systems present on contigs that are typically excluded from common metagenomic analysis pipelines. Using a human metagenomic gut data set representing 2805 taxonomically distinct units, we identified 1598 contigs containing conjugation genes with a differential distribution in human cohorts. We synthesized de novo an entire Citrobacter spp. conjugative system of 54 kb containing at least 47 genes and assembled it into a plasmid, pCitro. We found that pCitro conjugates from Escherichia coli to Citrobacter rodentium with a 30-fold higher frequency than to E. coli, and is compatible with Citrobacter resident plasmids. Mutations in the traV and traY conjugation components of pCitro inhibited conjugation. We showed that pCitro can be repurposed as an antimicrobial delivery agent by programming it with the TevCas9 nuclease and Citrobacter-specific sgRNAs to kill C. rodentium. Our study reveals a trove of uncharacterized conjugative systems in metagenomic data and describes an experimental framework to animate these large genetic systems as novel target-adapted delivery vectors for Cas9-based editing of bacterial genomes.
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Affiliation(s)
- Thomas
A. Hamilton
- Department
of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London N6A 5C1, ON, Canada
| | - Benjamin R. Joris
- Department
of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London N6A 5C1, ON, Canada
| | - Arina Shrestha
- Department
of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London N6A 5C1, ON, Canada
| | - Tyler S. Browne
- Department
of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London N6A 5C1, ON, Canada
| | - Sébastien Rodrigue
- Départment
de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada
| | - Bogumil J. Karas
- Department
of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London N6A 5C1, ON, Canada
| | - Gregory B. Gloor
- Department
of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London N6A 5C1, ON, Canada
| | - David R. Edgell
- Department
of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London N6A 5C1, ON, Canada
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11
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Zhang J, Xu Y, Wang M, Li X, Liu Z, Kuang D, Deng Z, Ou HY, Qu J. Mobilizable plasmids drive the spread of antimicrobial resistance genes and virulence genes in Klebsiella pneumoniae. Genome Med 2023; 15:106. [PMID: 38041146 PMCID: PMC10691111 DOI: 10.1186/s13073-023-01260-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a notorious clinical pathogen and frequently carries various plasmids, which are the main carriers of antimicrobial resistance and virulence genes. In comparison to self-transmissible conjugative plasmids, mobilizable plasmids have received much less attention due to their defects in conjugative elements. However, the contribution of mobilizable plasmids to the horizontal transfer of antimicrobial resistance genes and virulence genes of K. pneumoniae remains unclear. In this study, the transfer, stability, and cargo genes of the mobilizable plasmids of K. pneumoniae were examined via genetic experiments and genomic analysis. METHODS Carbapenem-resistant (CR) plasmid pHSKP2 and multidrug-resistant (MDR) plasmid pHSKP3 of K. pneumoniae HS11286, virulence plasmid pRJF293 of K. pneumoniae RJF293 were employed in conjugation assays to assess the transfer ability of mobilizable plasmids. Mimic mobilizable plasmids and genetically modified plasmids were constructed to confirm the cotransfer models. The plasmid morphology was evaluated through XbaI and S1 nuclease pulsed-field gel electrophoresis and/or complete genome sequencing. Mobilizable plasmid stability in transconjugants was analyzed via serial passage culture. In addition, in silico genome analysis of 3923 plasmids of 1194 completely sequenced K. pneumoniae was performed to investigate the distribution of the conjugative elements, the cargo genes, and the targets of the CRISPR-Cas system. The mobilizable MDR plasmid and virulence plasmid of K. pneumoniae were investigated, which carry oriT but lack other conjugative elements. RESULTS Our results showed that mobilizable MDR and virulence plasmids carrying oriT but lacking the relaxase gene were able to cotransfer with a helper conjugative CR plasmid across various Klebsiella and Escherichia coli strains. The transfer and stability of mobilizable plasmids rather than conjugative plasmids were not interfered with by the CRISPR-Cas system of recipient strains. According to the in silico analysis, the mobilizable plasmids carry about twenty percent of acquired antimicrobial resistance genes and more than seventy-five percent of virulence genes in K. pneumoniae. CONCLUSIONS Our work observed that a mobilizable MDR or virulence plasmid that carries oriT but lacks the relaxase genes transferred with the helper CR conjugative plasmid and mobilizable plasmids escaped from CRISPR-Cas defence and remained stable in recipients. These results highlight the threats of mobilizable plasmids as vital vehicles in the dissemination of antibiotic resistance and virulence genes in K. pneumoniae.
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Affiliation(s)
- Jianfeng Zhang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yanping Xu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Meng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, 519000, China
| | - Zhiyuan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Dai Kuang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- National Health Commission (NHC) Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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12
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Dorado-Morales P, Lambérioux M, Mazel D. Unlocking the potential of microbiome editing: A review of conjugation-based delivery. Mol Microbiol 2023. [PMID: 37658686 DOI: 10.1111/mmi.15147] [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: 04/07/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023]
Abstract
In recent decades, there has been a rapid increase in the prevalence of multidrug-resistant pathogens, posing a challenge to modern antibiotic-based medicine. This has highlighted the need for novel treatments that can specifically affect the target microorganism without disturbing other co-inhabiting species, thus preventing the development of dysbiosis in treated patients. Moreover, there is a pressing demand for tools to effectively manipulate complex microbial populations. One of the approaches suggested to address both issues was to use conjugation as a tool to modify the microbiome by either editing the genome of specific bacterial species and/or the removal of certain taxonomic groups. Conjugation involves the transfer of DNA from one bacterium to another, which opens up the possibility of introducing, modifying or deleting specific genes in the recipient. In response to this proposal, there has been a significant increase in the number of studies using this method for gene delivery in bacterial populations. This MicroReview aims to provide a detailed overview on the use of conjugation for microbiome engineering, and at the same time, to initiate a discussion on the potential, limitations and possible future directions of this approach.
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Affiliation(s)
- Pedro Dorado-Morales
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, et CNRS, UMR3525, Paris, France
| | - Morgan Lambérioux
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, et CNRS, UMR3525, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, et CNRS, UMR3525, Paris, France
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13
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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14
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Rodrigues C, Lanza VF, Peixe L, Coque TM, Novais Â. Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0339522. [PMID: 37098951 PMCID: PMC10269502 DOI: 10.1128/spectrum.03395-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/26/2023] [Indexed: 04/27/2023] Open
Abstract
Klebsiella pneumoniae sequence type 14 (ST14) and ST15 caused outbreaks of CTX-M-15 and/or carbapenemase producers worldwide, but their phylogeny and global dynamics remain unclear. We clarified the evolution of K. pneumoniae clonal group 14 (CG14) and CG15 by analyzing the capsular locus (KL), resistome, virulome, and plasmidome of public genomes (n = 481) and de novo sequences (n = 9) representing main sublineages circulating in Portugal. CG14 and CG15 evolved independently within 6 main subclades defined according to the KL and the accessory genome. The CG14 (n = 65) clade was structured in two large monophyletic subclades, CG14-I (KL2, 86%) and CG14-II (KL16, 14%), whose emergences were dated to 1932 and 1911, respectively. Genes encoding extended-spectrum β-lactamase (ESBL), AmpC, and/or carbapenemases were mostly observed in CG14-I (71% versus 22%). CG15 clade (n = 170) was segregated into subclades CG15-IA (KL19/KL106, 9%), CG15-IB (variable KL types, 6%), CG15-IIA (KL24, 43%) and CG15-IIB (KL112, 37%). Most CG15 genomes carried specific GyrA and ParC mutations and emerged from a common ancestor in 1989. CTX-M-15 was especially prevalent in CG15 (68% CG15 versus 38% CG14) and in CG15-IIB (92%). Plasmidome analysis revealed 27 predominant plasmid groups (PG), including particularly pervasive and recombinant F-type (n = 10), Col (n = 10), and new plasmid types. While blaCTX-M-15 was acquired multiple times by a high diversity of F-type mosaic plasmids, other antibiotic resistance genes (ARGs) were dispersed by IncL (blaOXA-48) or IncC (blaCMY/TEM-24) plasmids. We first demonstrate an independent evolutionary trajectory for CG15 and CG14 and how the acquisition of specific KL, quinolone-resistance determining region (QRDR) mutations (CG15), and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-I and CG15-IIA/IIB). IMPORTANCE Klebsiella pneumoniae represents a major threat in the burden of antibiotic resistance (ABR). Available studies to explain the origin, the diversity, and the evolution of certain ABR K. pneumoniae populations have mainly been focused on a few clonal groups (CGs) using phylogenetic analysis of the core genome, the accessory genome being overlooked. Here, we provide unique insights into the phylogenetic evolution of CG14 and CG15, two poorly characterized CGs which have contributed to the global dissemination of genes responsible for resistance to first-line antibiotics such as β-lactams. Our results point out an independent evolution of these two CGs and highlight the existence of different subclades structured by the capsular type and the accessory genome. Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome reflect the exposure and adaptation of K. pneumoniae under different selective pressures.
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Affiliation(s)
- Carla Rodrigues
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Val F. Lanza
- Unidad de Genómica Traslacional Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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15
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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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16
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Horne T, Orr VT, Hall JP. How do interactions between mobile genetic elements affect horizontal gene transfer? Curr Opin Microbiol 2023; 73:102282. [PMID: 36863168 DOI: 10.1016/j.mib.2023.102282] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 03/03/2023]
Abstract
Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.
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Affiliation(s)
- Tanya Horne
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Victoria T Orr
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - James Pj Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
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