ArticleMicrobial genomics2024
Applying rearrangement distances to enable plasmid epidemiology with pling.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
- Genomic global epidemiology and evolution ofMicrobial genomics · 2026Article
- The shared evolutionary capacities of plasmids and extrachromosomal DNA.Nature reviews. Genetics · 2026Review
- pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences.Bioinformatics (Oxford, England) · 2026Article
- Article
- Genome assemblies and annotations are not static and need support for tracking their evolution.Briefings in bioinformatics · 2026Review
- National genomic surveillance reveals global plasmid and chromosomal dissemination routes of blanpj antimicrobials and resistance · 2026Article
- Clinical and genomic determinants associated with emergent ceftazidime-avibactam plus aztreonam non-susceptibility in ceftazidime-avibactam resistantAntimicrobial agents and chemotherapy · 2026Article
- Genomic Epidemiology of Antibiotic-Resistant Bacteria Sampled from Metropolitan Wastewater.Microorganisms · 2026Article
- Decentralized nanopore genomics reveals diverseMicrobial genomics · 2026Article
- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing.Microbial genomics · 2026Article
- Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.Microbial genomics · 2026Article
- A One Health study ofMicrobial genomics · 2026Article
- Coexistence of carbapenemase and hypervirulence-associated genes amongFrontiers in microbiology · 2026Article
- Molecular characterization of mupirocin-resistant MRSA from Germany and South Africa.Frontiers in cellular and infection microbiology · 2026Article
- Genomic phylogeny, taxonomic classification, genetic landscape, and antibiotic resistance of clinicalFrontiers in microbiology · 2026Article
- Genomic characterization ofApplied and environmental microbiology · 2025Article
- Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.Antimicrobial agents and chemotherapy · 2025Review
- Genomic Characterization of NDM-1 ProducerAntibiotics (Basel, Switzerland) · 2025Article
- Article
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7 authors.
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Abstract
Plasmids are a key vector of antibiotic resistance, but the current bioinformatics toolkit is not well suited to tracking them. The rapid structural changes seen in plasmid genomes present considerable challenges to evolutionary and epidemiological analysis. Typical approaches are either low resolution (replicon typing) or use shared k-mer content to define a genetic distance. However, this distance can both overestimate plasmid relatedness by ignoring rearrangements, and underestimate by over-penalizing gene gain/loss. Therefore a model is needed which captures the key components of how plasmid genomes evolve structurally - through gene/block gain or loss, and rearrangement. A secondary requirement is to prevent promiscuous transposable elements (TEs) leading to over-clustering of unrelated plasmids. We choose the 'Double Cut and Join Indel' (DCJ-Indel) model, in which plasmids are studied at a coarse level, as a sequence of signed integers (representing genes or aligned blocks), and the distance between two plasmids is the minimum number of rearrangement events or indels needed to transform one into the other. We show how this gives much more meaningful distances between plasmids. We introduce a software workflow pling (https://github.com/iqbal-lab-org/pling), which uses the DCJ-Indel model, to calculate distances between plasmids and then cluster them. In our approach, we combine containment distances and DCJ-Indel distances to build a TE-aware plasmid network. We demonstrate superior performance and interpretability to other plasmid clustering tools on the 'Russian Doll' dataset and a hospital transmission dataset.
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