README.md

Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

The repository storing the data and scripts for the open access publication availible at Virology Journal.

Conclusions

Prophages are present in clinical NTM isolates. Prophages are more likely to be present in RGM compared to SGM genomes. The mechanism and selective advantage of this enrichment by growth rate remain unclear. In addition, the frequency of bacterial virulence genes in prophages from clinical NTM is enriched relative to the PhagesDB environmental proxy. This suggests prophages may act as a reservoir of genetic elements bacteria could use to thrive within a clinical environment.

Prophages in NTM

Bacterial Virulence Gene Enrichment

Location of datasets

Raw Genomes

• The raw clinical isolates are availible from BioProject 319839
• The raw complete genomes are availible from NCBI Assembly and are named in Supplementary File 1
• Prophages from PhagesDB are availible on the PhagesDB webpage and via the API

Predicted Prophages

• The prophages predicted using the pipeline descibed in the paper are availible in the data/fasta folder. They are labeled Combined_Phaster_Overlapped_Integrases.fasta.
• Gene annotations of these predicted prophages is availible under the data/Prophage_Proteins