Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages Infecting Staphylococcus aureus

Abstract

The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like Podoviridae, Twort-like or K-like Myoviridae, and a more diverse group of temperate Siphoviridae. Here we present 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 Myoviridae that is largely unrelated to other known S. aureus phages. The average genome size for these phages is ~269 kb with each genome encoding ~263 predicted protein-coding genes. Phage genome organization and content is most similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete viral and non-viral 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 of workThis study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus Myoviridae represent a new class of S. aureus phage that have not been described previously. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, not only are these phages an exciting new type of S. aureus phage, they also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. The data and methods presented in this study could be useful for an audience far beyond those working in S. aureus phage biology. This work is original and has not been submitted for publication in any other journal.