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. 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. 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. 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.

中文翻译：

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临床非结核分枝杆菌不同物种内整合前噬菌体的表征。

非结核分枝杆菌 (NTM) 感染的患病率正在增加，目前估计美国每年有超过 100,000 人受到影响。目前尚不清楚某些分枝杆菌物种如何从环境细菌转变为临床病原体，也不清楚哪些遗传因素影响同一物种菌株之间毒力的差异。分枝杆菌内遗传进化和多样性的一个潜在机制是宿主基因组中存在称为原噬菌体的整合病毒。原噬菌体可以作为细菌基因的载体，具有通过水平基因转移改变细菌适应性的潜力。在这项研究中，我们量化了从临床样本中分离出的分枝杆菌中原噬菌体的频率和组成，并将其与环境分枝杆菌噬菌体数据库 PhagesDB 的组成进行比较。通过 VirSorter 和 Phaster 两种发现工具之间的协议来预测原噬菌体，并通过生长速率比较整合的原噬菌体的频率。原噬菌体被分配到 PhagesDB 字母簇。使用基因注释软件 Prokka 中的毒力因子数据库 (VFDB) 和病理系统资源集成中心毒力数据库 (Patric-VF) 的组合来计算细菌毒力基因频率。CRISPR 元件是使用 CRT 发现的。ARAGORN 用于量化 tRNA。快速生长的分枝杆菌 (RGM) 比缓慢生长的分枝杆菌 (SGM) 更可能含有原噬菌体。CRISPR 元件与分枝杆菌中的原噬菌体丰度无关。与 RGM 相比，SGM 中 tRNA 的丰度更高。我们将临床分离株的原噬菌体基因组中细菌毒力基因的丰度与 PhagesDB 的分枝杆菌噬菌体进行了比较。我们的数据表明，相对于 PhagesDB 的环境分枝杆菌噬菌体，来自临床分枝杆菌的原噬菌体富含细菌毒力基因。原噬菌体存在于临床 NTM 分离株中。与 SGM 基因组相比，原噬菌体更有可能存在于 RGM 中。这种通过增长率富集的机制和选择性优势仍不清楚。此外，临床 NTM 的原噬菌体中细菌毒力基因的频率相对于 PhagesDB 环境代理有所丰富。这表明原噬菌体可能充当遗传元件的储存库，细菌可以利用这些遗传元件在临床环境中茁壮成长。