Going through phages: A Computational approach to Revealing the role of prophage in Staphylococcus aureus

Abstract Prophages have important roles in virulence, antibiotic resistance and genome evolution in Staphylococcus aureus . Rapid growth in the number of sequenced S. aureus genomes allows for an investigation of prophage sequences in S. aureus at an unprecedented scale. We developed a computational pipeline to detect and analyze prophage sequences in nearly 10,011 S. aureus genomes, discovering thousands of putative prophage sequences with genes encoding virulence factors and antibiotic resistance. Importance Bacteriophages (phages) play key roles in bacterial evolution, governing abundance, adaptation and diversity of bacterial communities. Temperate phage can facilitate bacterial adaptation via transduction of novel genes. This study takes advantage of the unprecedented quantity of genomic sequencing in public repositories to analyze viral genes in 10,000 Staphylococcus aureus genomes. We found 196,727 prophage sequences, with an estimated total of 129,935 genes. We determined the function of these genes, identifying a large quantity of novel genes that benefit the host such as beta-lactamase, enterotoxins and cytotoxins. These results will inform studies of bacterial evolution and adaptation, by identifying the mechanism of horizontal transfer of genes that confer adaptive traits to bacteria, especially in the context of antibiotic resistance.