先前描述的大多数金黄色葡萄球菌噬菌体属于三个主要类别,即,像P68一样的Podophages,Twort样或K样的肌细胞,和更多样化的温带虹吸管群。这里,我们介绍了以下三种新的金黄色葡萄球菌“巨型”噬菌体:MarsHill,Madawaska,还有Machias.这些噬菌体从美国的猪生产环境中分离,并且代表金黄色葡萄球菌肌细胞的新型进化枝。这些噬菌体的平均基因组大小为269kb,每个基因组编码263个预测的蛋白质编码基因。噬菌体基因组的组织和含量与已知的芽孢杆菌属巨型噬菌体相似。,包括AR9和vB_BpuM-BpSp。所有三个噬菌体都具有编码完整病毒体和非病毒体RNA聚合酶的基因,多种归巢核酸内切酶,和一个类似于retron的逆转录酶.与AR9一样,所有这些噬菌体都被认为具有尿嘧啶取代的DNA,这会干扰DNA测序。这些噬菌体还能够转导宿主质粒,这是显著的,因为发现这些噬菌体在猪生产环境中循环,并且还可以感染人金黄色葡萄球菌分离株。重要性本研究描述了以下三种新型金黄色葡萄球菌巨型噬菌体的比较基因组学:MarsHill,Madawaska,还有Machias.这三种金黄色葡萄球菌噬菌体代表了金黄色葡萄球菌噬菌体的新兴类别。这些基因组包含丰富的内含子,显示出与重复获取一致的模式,而不是垂直遗传,表明内含子的获取和丢失是这些噬菌体进化的活跃过程。这些噬菌体可能具有超修饰的DNA,其抑制了几种不同的常见平台的测序。因此,这些噬菌体还代表了由于标准测序技术的局限性而错过的潜在基因组多样性.特别是,由于它们对标准测序技术的抗性,这种超修饰的基因组可能被宏基因组研究遗漏.发现噬菌体MarsHill能够以与其他转导金黄色葡萄球菌噬菌体相当的水平转导宿主DNA,使其成为环境中水平基因转移的潜在载体。
The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups, namely, P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. Here, we present the following three novel S. aureus \"jumbo\" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus myophage. The average genome size for these phages is ∼269 kb with each genome encoding ∼263 predicted protein-coding genes. Phage genome organization and content are similar to those of known jumbo phages of Bacillus sp., including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and nonvirion RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. IMPORTANCE This study describes the comparative genomics of the following three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus myophages represent an emerging class of S. aureus phage. These genomes contain abundant introns which show a pattern consistent with repeated acquisition rather than vertical inheritance, suggesting intron acquisition and loss are active processes in the evolution of these phages. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, these phages also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. In particular, such hypermodified genomes may be missed by metagenomic studies due to their resistance to standard sequencing techniques. Phage MarsHill was found to be able to transduce host DNA at levels comparable to that found for other transducing S. aureus phages, making it a potential vector for horizontal gene transfer in the environment.