The majority of previously described
Staphylococcus aureus
bacteriophages belong to three major groups: P68-like podophages, Twort-like or K-like myophages, and a more diverse group of temperate siphophages. 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
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 is similar to known jumbo phages of
Bacillus
, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete virion and non-virion 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 work:
This study describes the comparative genomics of 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 is an active process 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 them a potential vector for horizontal gene transfer in the environment.