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PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level

G Royer1,2,3, J W Decousser1,3, C Branger1

  • 12​Université Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.

Microbial Genomics
|September 29, 2018
PubMed

Insights

PlaScope accurately identifies plasmid DNA in bacterial genomes, outperforming existing tools. This advancement aids in tracking antibiotic resistance and virulence genes, crucial for understanding bacterial pathogenicity and outbreaks.

Area of Science:

  • Bacteriology
  • Genomics
  • Bioinformatics

Background:

  • Plasmids carry critical antibiotic resistance and virulence genes in medically important bacteria like Enterobacteriaceae.
  • Plasmid-borne genes significantly impact bacterial pathogenicity and facilitate the spread of traits like antimicrobial resistance.
  • Existing tools for plasmidome analysis from whole-genome sequences often lack combined high sensitivity and specificity.

Purpose of the Study:

  • To develop and evaluate PlaScope, a novel targeted approach for accurate plasmid sequence recovery from bacterial genome assemblies.
  • To assess PlaScope's performance against existing plasmid identification tools, PlasFlow and cBar.
  • To demonstrate PlaScope's utility in identifying clinically relevant genetic elements, including antibiotic resistance and virulence genes.

Main Methods:

  • PlaScope utilizes Centrifuge, a metagenomic classifier, with a custom database of curated chromosomal and plasmid sequences.
  • The tool classifies assembled contigs based on their predicted genomic location (plasmid vs. chromosome).
  • Performance was evaluated on a dataset of 70 Escherichia coli genomes and a clinical collection of Klebsiella pneumoniae strains.

Main Results:

  • PlaScope achieved superior performance metrics: 0.87 recall, 0.99 specificity, 0.96 precision, and 0.98 accuracy on E. coli.
  • The tool successfully identified chromosomal integrations of extended-spectrum beta-lactamase genes in a clinical E. coli dataset.
  • PlaScope accurately assigned locations for the majority of resistance genes in Klebsiella pneumoniae strains.

Conclusions:

  • PlaScope offers a highly sensitive and specific method for plasmid prediction in bacterial genome assemblies.
  • This tool enhances the ability to study the 'plasmidome' and track the dissemination of resistance and virulence factors.
  • The targeted approach is adaptable for other well-characterized bacterial species, advancing genomic epidemiology.
Keywords:
Escherichia coliantimicrobial resistancebioinformatic methodplasmid detection

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