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Pneumococcal prophages are diverse, but not without structure or history
Angela B Brueggemann1, Caroline L Harrold1, Reza Rezaei Javan1
1Nuffield Department of Medicine, University of Oxford, United Kingdom.
Scientific Reports
|February 21, 2017
Summary
Nearly 500 bacterial genomes revealed that all pneumococcus strains contain prophage DNA. These integrated bacteriophages (phages) show diversity, virulence genes, and influence bacterial evolution.
Area of Science:
- Microbiology
- Genomics
- Virology
Background:
- Bacteriophages (phages) are viruses that infect bacteria, playing a role in bacterial evolution.
- Pneumococcus is a significant bacterial pathogen, but its associated phages remain understudied.
- Prophages, integrated phage DNA, are common in bacterial genomes.
Purpose of the Study:
- To investigate the prevalence, diversity, and molecular epidemiology of prophages in *Streptococcus pneumoniae* (pneumococcus).
- To explore the gene expression of prophages within the pneumococcal genome.
- To understand the role of prophages in pneumococcal biology and evolution.
Main Methods:
- Analysis of nearly 500 pneumococcal genomes.
- RNA sequencing to assess prophage gene expression.
- Bioinformatic identification and clustering of prophages.
Main Results:
- Every pneumococcal genome examined contained prophage DNA.
- 286 full-length or putatively full-length prophages were identified, with 163 being novel.
- Prophages clustered into four main groups, integrated into specific genomic sites, and often carried virulence genes (pblA/pblB).
- Strong associations were observed between specific prophages and pneumococcal genetic lineages, with some prophages persisting for decades.
- RNA sequencing confirmed prophage gene expression.
Conclusions:
- Pneumococcal prophages are ubiquitous, diverse, and genetically structured.
- Prophages contribute virulence factors and are expressed within the host.
- These findings highlight the significant, previously underestimated role of prophages in pneumococcal biology and evolution.
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