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<p>Virulent phages, characterized by an obligatory lytic cycle resulting in the death of their bacterial hosts, are assumed to lack the ability to persist within bacterial colonies. Consequently, when bacterial isolates are sequenced, the resulting assemblies are not expected to contain virulent phage genomes. Here we test this assumption at scale by analysing over 267,000 publicly available <i>Escherichia</i> assemblies. Surprisingly, we identified 373 virulent phage genomes within these assemblies. Such viral genomes are associated with specific phage taxa and especially with very large (jumbo) phages such as the phage nucleus-forming family <i>Chimalliviridae</i>. Multiple lines of evidence from culture experiments and bioinformatic analyses suggest that these virulent phage genomes arise from persistent infections without substantial host mortality. We also identified 285 related phage genomes in bacterial taxa beyond <i>Escherichia</i>, highlighting the frequency of as-yet-uncharacterized persistent phages. Our findings challenge the traditional virulent–temperate dichotomy and point to the prevalence of non-canonical phage lifestyles.</p>

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Persistent virulent phages exist across bacterial isolates

  • 期刊论文

  • 发表日期：

    2025年12月29日

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  • Peter Erdmann Dougherty,
  • Charles Bernard,
  • Alexander Byth Carstens,
  • Emmanuel Bumunang,
  • Milan Gerovac,
  • Mathias Müsken,
  • Kim Stanford,
  • Tim A. McAllister,
  • Eduardo P. C. Rocha,
  • Lars Hestbjerg Hansen

摘要

Virulent phages, characterized by an obligatory lytic cycle resulting in the death of their bacterial hosts, are assumed to lack the ability to persist within bacterial colonies. Consequently, when bacterial isolates are sequenced, the resulting assemblies are not expected to contain virulent phage genomes. Here we test this assumption at scale by analysing over 267,000 publicly available Escherichia assemblies. Surprisingly, we identified 373 virulent phage genomes within these assemblies. Such viral genomes are associated with specific phage taxa and especially with very large (jumbo) phages such as the phage nucleus-forming family Chimalliviridae. Multiple lines of evidence from culture experiments and bioinformatic analyses suggest that these virulent phage genomes arise from persistent infections without substantial host mortality. We also identified 285 related phage genomes in bacterial taxa beyond Escherichia, highlighting the frequency of as-yet-uncharacterized persistent phages. Our findings challenge the traditional virulent–temperate dichotomy and point to the prevalence of non-canonical phage lifestyles.