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Volume 5, Issue 6

Going through phages: a computational approach to revealing the role of prophage in Open Access

Abstract

Prophages have important roles in virulence, antibiotic resistance, and genome evolution in . Rapid growth in the number of sequenced genomes allows for an investigation of prophage sequences at an unprecedented scale. We developed a novel computational pipeline for phage discovery and annotation. We combined PhiSpy, a phage discovery tool, with VGAS and PROKKA, genome annotation tools to detect and analyse prophage sequences in nearly 10 011 . genomes, discovering thousands of putative prophage sequences with genes encoding virulence factors and antibiotic resistance. To our knowledge, this is the first large-scale application of PhiSpy on a large-scale set of genomes (10 011 . ). Determining the presence of virulence and resistance encoding genes in prophage has implications for the potential transfer of these genes/functions to other bacteria via transduction and thus can provide insight into the evolution and spread of these genes/functions between bacterial strains. While the phage we have identified may be known, these phages were not necessarily known or characterized in and the clustering and comparison we did for phage based on their gene content is novel. Moreover, the reporting of these genes with the genomes is novel.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacteriophages , computational biology , Staphylococcus aureus , transduction and whole genome sequences
Funding
This study was supported by the:
  • National GEM Consortium
    • Principle Award Recipient: Tyromesteven Sweet Jr.
  • National Science Foundation (Award 1633722)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation (Award ACI-1429783)
    • Principle Award Recipient: NotApplicable
© 2023
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-06-16
2024-04-30
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Going through phages: a computational approach to revealing the role of prophage in Staphylococcus aureus
Access Microbiology 5, 000424 (2023); https://doi.org/10.1099/acmi.0.000424
/content/journal/acmi/10.1099/acmi.0.000424
/content/journal/acmi/10.1099/acmi.0.000424
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