Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA.
Computational Modeling and Data Analytics Program, Virginia Tech, Blacksburg, Virginia, USA.
mSphere. 2024 Jun 25;9(6):e0003124. doi: 10.1128/msphere.00031-24. Epub 2024 May 22.
The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion to a new environment, such as a host. While previous studies have focused on identifying and characterizing the genetic diversity of prophages, analyses characterizing the cargo that prophages carry have not been extensively explored. We characterized prophage regions from 303 spp. genomes (representing 254 unique serovars) to assess the distribution of prophages in diverse . On average, prophages accounted for 3.7% (0.1%-8.8%) of the total genomic content of each isolate. Prophage regions annotated as Gifsy 1 and Salmon Fels 1 were the most commonly identified intact prophages, suggesting that they are common throughout the genus. Among 21,687 total coding sequences (CDSs) from intact prophage regions in subsp. genomes, 7.5% (median; range: 1.1%-47.6%) were categorized as having a function not related to prophage integration or phage structure, some of which could potentially provide a functional attribute to the host cell. These predicted functions could be broadly categorized into CDSs involved in: (i) modification of cell surface structures (i.e., glycosyltransferases); (ii) modulation of host responses (e.g., SodC/SodA, SopE, ArtAB, and typhoid toxin); (iii) conferring resistance to heavy metals and antimicrobials; (iv) metabolism of carbohydrates, amino acids, and nucleotides; and (v) DNA replication, repair, and regulation. Overall, our systematic analysis of prophage cargo highlights a broader role for prophage cargo in influencing the metabolic, virulence, and resistance characteristics of .
Lysogenic bacteriophages (phages) can integrate their genome into a bacterial host's genome, potentially introducing genetic elements that can affect the fitness of the host bacterium. The functions of prophage-encoded genes are important to understand as these genes could be mobilized and transferred to a new host. Using a large genomic dataset representing >300 isolates from all known subspecies and species of , our study contributes important new findings on the distribution of prophages and the types of cargo that diverse prophages carry. We identified a number of coding sequences (CDSs) annotated as having cell surface-modifying attributes, suggesting that prophages may have played an important role in shaping 's diverse surface antigen repertoire. Furthermore, our characterization of prophages suggests that they play a broader role in facilitating the acquisition and transfer of CDSs associated with metabolism, DNA replication and repair, virulence factors, and to a lesser extent, antimicrobial resistance.
移动元件（如噬菌体）的获得可以将货物引入受体细菌，从而有助于其在新环境（如宿主）中存活或扩展。尽管先前的研究集中于识别和描述噬菌体的遗传多样性，但对噬菌体携带的货物进行分析的研究尚未广泛开展。我们对 303 株 spp. 基因组（代表 254 个独特血清型）中的噬菌体区域进行了特征描述，以评估噬菌体在不同血清型中的分布。平均而言，噬菌体占每个分离株总基因组含量的 3.7%（0.1%-8.8%）。被注释为 Gifsy 1 和 Salmon Fels 1 的完整噬菌体区域是最常见的完整噬菌体，表明它们在整个 属中普遍存在。在 亚种基因组中完整噬菌体区域的 21687 个总编码序列（CDS）中，7.5%（中位数；范围：1.1%-47.6%）被归类为与噬菌体整合或噬菌体结构无关的功能，其中一些功能可能为宿主细胞提供功能属性。这些预测的功能可以大致分为参与以下方面的 CDS：（i）修饰细胞表面结构（即糖基转移酶）；（ii）调节宿主反应（例如 SodC/SodA、SopE、ArtAB 和伤寒毒素）；（iii）赋予对重金属和抗菌药物的抗性；（iv）碳水化合物、氨基酸和核苷酸的代谢；以及（v）DNA 复制、修复和调控。总体而言，我们对噬菌体货物的系统分析强调了噬菌体货物在影响 代谢、毒力和耐药性特征方面的更广泛作用。
溶源噬菌体（噬菌体）可以将其基因组整合到细菌宿主的基因组中，从而潜在地引入可能影响宿主细菌适应性的遗传元素。了解噬菌体编码基因的功能很重要，因为这些基因可以被转移并转移到新的宿主中。使用一个代表所有已知亚种和种的 >300 个分离株的大型基因组数据集，我们的研究对不同血清型 噬菌体的分布和携带的货物类型提供了重要的新发现。我们确定了一些被注释为具有细胞表面修饰属性的编码序列（CDS），表明噬菌体可能在塑造 's 多样化的表面抗原库方面发挥了重要作用。此外，我们对噬菌体的特征描述表明，它们在促进与代谢、DNA 复制和修复、毒力因子以及在较小程度上与抗菌药物耐药性相关的 CDS 的获取和转移方面发挥了更广泛的作用。
