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Efficient detection and typing of phage-plasmids.

Karina Ilchenko1, Remy A Bonnin2,3,4, Eduardo P C Rocha5

  • 1Université Paris-Saclay, INRAE, AgroParisTech, MICALIS, Jouy-en-Josas, France.

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|February 9, 2026
PubMed
Summary

We developed tyPPing, a new method to accurately detect and classify diverse phage-plasmids (P-Ps). This tool enhances our understanding of mobile genetic elements and their role in bacterial evolution.

Keywords:
genomicshidden Markov modelsmobile genetic elementsphage-plasmidsphagesplasmids

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Area of Science:

  • Microbiology and Bioinformatics
  • Genomics and Molecular Biology

Background:

  • Mobile genetic elements, including phages and plasmids, are crucial drivers of bacterial evolution via horizontal gene transfer.
  • Phage-plasmids (P-Ps) possess characteristics of both phages and plasmids, complicating their accurate classification by existing computational tools.
  • The diversity and hybrid nature of P-Ps, some carrying antibiotic resistance or virulence genes, necessitate improved detection methods.

Purpose of the Study:

  • To develop and validate tyPPing, a novel, user-friendly computational method for the accurate detection and systematic typing of phage-plasmids.
  • To differentiate P-Ps from standard phages and plasmids by analyzing conserved protein frequencies and sets.
  • To establish a reliable foundation for future research on P-Ps across various settings, from agriculture to clinical environments.

Main Methods:

  • Development of tyPPing, a computational tool utilizing distinct frequencies and sets of conserved proteins for P-P identification.
  • Testing tyPPing on diverse databases and collections of draft genomes to assess its accuracy and compatibility.
  • Comparative analysis of tyPPing's sensitivity and scalability against existing classification methods.

Main Results:

  • tyPPing demonstrated high accuracy in detecting and typing P-Ps, even in incomplete genome assemblies.
  • The method successfully separated P-Ps from phages and plasmids, assigning confidence levels to its predictions.
  • tyPPing outperformed other tools in sensitivity and scalability for identifying distinct P-P types.

Conclusions:

  • tyPPing provides a precise and scalable solution for the systematic identification and classification of diverse phage-plasmids.
  • The tool is broadly compatible and offers a reliable foundation for future studies on P-Ps.
  • tyPPing facilitates the ongoing challenge of identifying new P-P types, contributing to a better understanding of bacterial genetics and evolution.