ArticleThe ISME journal2021
Genomic network analysis of environmental and livestock F-type plasmid populations.
Article in The ISME journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Stabilizing features of cefotaximase harbouring plasmids enable persistence in UK livestock.Microbial genomics · 2026Article
- Transfer potential of F-like plasmids inISME communications · 2026Article
- Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.Antimicrobial agents and chemotherapy · 2025Review
- Bacterial warfare is associated with virulence and antimicrobial resistance.Nature communications · 2025Article
- Plasmid genomic epidemiology ofMicrobial genomics · 2025Article
- The dark matter of bacterial genomic surveillance-antimicrobial resistance plasmid transmissions in the hospital setting.Journal of clinical microbiology · 2025Article
- A phylogenetic approach to comparative genomics.Nature reviews. Genetics · 2025Review
- The pet café is a neglected site for transmission of antimicrobial-resistantMicrobial genomics · 2025Article
- Activation, incompatibility, and displacement of FIB replicons in E. coli.Nucleic acids research · 2025Article
- Emergence and polyclonal dissemination of NDM-5/OXA-181 carbapenemase-producing Escherichia coli in the French Indian Ocean territories.Annals of clinical microbiology and antimicrobials · 2025Article
- Molecular epidemiology and genetic dynamics of carbapenem-resistant hypervirulentFrontiers in cellular and infection microbiology · 2025Article
- Limited clonality but widespread plasmid sharing of ESBL-producingCurrent research in microbial sciences · 2025Article
- Towards quantifying plasmid similarity.Microbial genomics · 2024Review
- The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.Nature communications · 2024Article
- Carbapenem-resistant Escherichia coli exhibit diverse spatiotemporal epidemiological characteristics across the globe.Communications biology · 2024Article
- Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles ofAntibiotics (Basel, Switzerland) · 2023Article
- From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production.Microbiology spectrum · 2023Article
- Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission.The ISME journal · 2023Article
- The highly diverse plasmid population found inMicrobial genomics · 2023Article
- Article
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Authors and funding
22 authors.
Funding
Abstract
F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.