2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2026
Abstrakt

Karina Ilchenko, Remy A. Bonnin, Eduardo P. C. Rocha, Eugen Pfeifer. Efficient detection and typing of phage-plasmids. mBio, :e0300025. 2026.

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Download from publisher: https://doi.org/10.1128/mbio.03000-25 PubMed

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Abstract:

Phage-plasmids (P-Ps) are temperate phages that replicate as plasmids during 
lysogeny. Despite their high diversity, they carry genes similar to phages and 
plasmids. This leads to gene exchanges and to the formation of hybrid or 
defective elements, which limits accurate detection of P-Ps. To address this 
challenge, we developed tyPPing, an easy-to-use method that efficiently detects 
and types P-Ps with high accuracy. It searches for distinct frequencies and sets 
of conserved proteins to separate P-Ps from plasmids and phages. tyPPing's 
strength comes from both its precise predictions and its ability to 
systematically type P-Ps, including the assignment of confidence levels. We 
tested tyPPing on several databases and a collection of incomplete (draft) 
genomes. While predictions rely on the quality of assemblies, we detected 
high-quality P-Ps and experimentally proved them to be functional. Compared to 
other classification methods, tyPPing is designed to detect distinct P-P types 
and surpasses other tools in terms of sensitivity and scalability. P-Ps are 
highly diverse, making the systematic identification of new types a difficult 
task. By combining tyPPing with other tools, however, we show a valuable 
foundation for addressing this challenge. How to use tyPPing and other approaches 
is documented in our GitHub repository: github.com/EpfeiferNutri/Phage-plasmids/. 
IMPORTANCE: 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.