Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

Abstract

Background: Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic evolution and diversity within mycobacteria is the presence of integrated viruses called prophages in the host genome. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhagesDB, an environmental mycobacteriophage database. Methods: Prophages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhagesDB lettered clusters. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs. Results: Rapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM. We compared the abundance of bacterial virulence genes within prophage genomes from clinical isolates to mycobacteriophages from PhagesDB. Our data suggests that prophages from clinical mycobacteria are enriched for bacterial virulence genes relative to environmental mycobacteriophage from PhagesDB.

Mycobacterium abscessus Strain Morphotype Determines Phage Susceptibility, the Repertoire of Therapeutically Useful Phages, and Phage Resistance

“…Bioinformatic analyses shows that prophages are abundant in the GD strains, as has been reported for other M. abscessus strains ( 38 ). These prophages, along with plasmids from these strains, are described in detail elsewhere ( 36 ) (Tables S5 and S6) ( https://phagesdb.org/documents/categories/15/ ), and their inclusion in each strain is indicated in Fig.…”

The Prophage and Plasmid Mobilome as a Likely Driver of Mycobacterium abscessus Diversity

“…Clinical isolates of M. abscessus differ greatly in their phage infection profiles, presenting challenges in broadening phage therapeutic applications ( 17 ). However, the phage infection profiles do not correlate with whole-genome phylogenies, and mobile elements, including prophages and plasmids, are likely major contributors ( 18 , 19 ). To understand the potential roles of the mycobacterial mobilome in these properties, we have characterized the prophages and plasmids of a recently genomically defined set of 82 recent M. abscessus clinical isolates with well-defined phage infection profiles ( 17 ).…”

Considerations for Phage Therapy Against Mycobacterium abscessus

“…Prophages are abundant in bacterial genomes including mycobacteria. A recent study of prophages within clinical NTM concluded that it was more likely to find prophages in rapidly compared to slowly growing bacteria and also suggested that prophages from clinical mycobacteria may contain more virulence genes than environmental mycobacteria ( Glickman et al, 2020 ). Importantly, a genome analysis of 48 M. abscessus strains concluded that at least 17 mycobacteriophages have infected M. abscessus during its evolution and the authors located one to eight prophage regions in 47 out of the 48 genomes, from intact prophages to small prophage-like elements ( Sassi et al, 2014 ).…”