Efficient detection and typing of phage-plasmids

Mobile genetic elements, such as phages and plasmids, are diverse and drive bacterial evolution through horizontal gene transfer. Phage-plasmids, of which many carry antibiotic resistance genes or virulence factors, are both phages and plasmids and have life cycles of temperate phages and plasmids. This makes accurate classification difficult as current computational tools typically classify them as one or the other. We addressed this problem by developing tyPPing, a new and highly precise method, to systematically identify, separate, and catalog phage-plasmids. We demonstrated that tyPPing is highly accurate and broadly compatible. It provides a reliable foundation for all future studies involving phages and plasmids, ranging from agriculture environments to pathogenic strains of clinical settings.

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Publication Details

Journal
mBio
Published
2026-02-09
DOI
https://doi.org/10.1128/mbio.03000-25
Primary Topic
Bacteriophages and microbial interactions
Type
article
Field-Weighted Citation Impact
0.00

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article

Efficient detection and typing of phage-plasmids

Rémy A. Bonnin, Eugen Pfeifer, Karina Ilchenko, Eduardo P C Rocha
mBio
Bacteriophages and microbial interactions
article

Efficient detection and typing of phage-plasmids

Rémy A. Bonnin, Eugen Pfeifer, Karina Ilchenko, Eduardo P C Rocha
article en

Abstract

Mobile genetic elements, such as phages and plasmids, are diverse and drive bacterial evolution through horizontal gene transfer. Phage-plasmids, of which many carry antibiotic resistance genes or virulence factors, are both phages and plasmids and have life cycles of temperate phages and plasmids. This makes accurate classification difficult as current computational tools typically classify them as one or the other. We addressed this problem by developing tyPPing, a new and highly precise method, to systematically identify, separate, and catalog phage-plasmids. We demonstrated that tyPPing is highly accurate and broadly compatible. It provides a reliable foundation for all future studies involving phages and plasmids, ranging from agriculture environments to pathogenic strains of clinical settings.

mBioVol. 17(3)
Centre National de la Recherche Scientifique (FR), Inserm (FR), Institut Pasteur (FR), Université Paris Cité (FR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Microbiologie de l’alimentation au service de la santé (FR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Assistance Publique – Hôpitaux de Paris (FR), Evolutionary Genomics (United States) (US), CEA Paris-Saclay (FR), Infectious Disease Models and Innovative Therapies (FR), CNR de la Résistance aux Antibiotiques (FR), Bicêtre Hospital (FR)
Infrastructures en Biologie Santé et Agronomie, Agence Nationale de la Recherche, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
Zero hunger
Openalex Percentile: Top 67%
Bacteriophages and microbial interactions
DOIOpen Access PDFOpenAlex
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