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Updated: Nov 15, 2025
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Genomic network analysis of environmental and livestock F-type plasmid populations
William Matlock1, Kevin K Chau2, Manal AbuOun3
1Nuffield Department of Medicine, University of Oxford, Oxford, UK. william.matlock@ndm.ox.ac.uk.
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.
Insights
F-type plasmids in the environment show stable backbones but diverse accessory genes, potentially linked to antimicrobial resistance (AMR) and niche adaptation. This study analyzes plasmid networks from wastewater and livestock settings.
Area of Science:
- Microbiology
- Genomics
- Environmental Science
Background:
- F-type plasmids are clinically significant, often carrying antimicrobial resistance (AMR) genes like extended-spectrum β-lactamases, especially in Enterobacterales.
- Current understanding of F-type plasmid diversity is primarily derived from clinical isolates, limiting insights into their environmental prevalence and evolution.
Purpose of the Study:
- To analyze the diversity and structure of F-type plasmids in environmental and livestock settings using network community analysis.
- To investigate the relationship between plasmid metadata, network communities, and niche partitioning (sampling compartment, host genera).
- To explore the link between core and accessory genes within F-type plasmid communities and their potential role in niche adaptation and AMR.
Main Methods:
- Network community analysis of a large dataset of F-type plasmids from environmental (wastewater treatment works, waterways) and livestock sources.
- Pangenome-style analyses applied to identified plasmid network communities.
- Plasmid phylogeny construction based on core gene alignments to correlate core and accessory gene content.
Main Results:
- Network community analysis revealed distinct F-type plasmid communities shaped by environmental niche and host genera.
- Each community exhibited unique core gene combinations with minimal overlap between communities.
- Plasmid accessory gene content was found to be closely linked to core gene content, suggesting stable backbone structures facilitate accessory gene variation for niche adaptation.
Conclusions:
- Stable F-type plasmid backbone structures can persist in environmental settings, accommodating significant variation in accessory genes.
- This accessory gene variation may be crucial for niche adaptation, potentially explaining the association of F-type plasmids with antimicrobial resistance (AMR).
- Environmental surveillance provides valuable insights into plasmid diversity and evolution beyond clinical settings.
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