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Bacteriophages exert strong evolutionary pressure on their microbial hosts. In their lytic lifecycle, complete bacterial subpopulations are utilized as hosts for bacteriophage replication. However, during their lysogenic lifecycle, bacteriophages can integrate into the host chromosome and alter the host’s genomic make-up, possibly resulting in evolutionary important adjustments. Not surprisingly, bacteria have evolved sophisticated immune systems to protect against phage infection.  Streptococcus pyogenes  isolates are frequently lysogenic and their prophages have been shown to be major contributors to the virulence of this pathogen. Most  S. pyogenes  phage research has focused on genomic prophages in relation to virulence, but little is known about the defensive arsenal of  S. pyogenes  against lytic phage infection. Here, we characterized Phage A1, an  S. pyogenes  bacteriophage, and investigated several mechanisms that  S. pyogenes  utilizes to protect itself against phage predation. We show that Phage A1 belongs to the  Siphoviridae  family and contains a circular double-stranded DNA genome that follows a modular organization described for other streptococcal phages. After infection, the Phage A1 genome can be detected in isolated  S. pyogenes  survivor strains, which enables the survival of the bacterial host and Phage A1 resistance. Furthermore, we demonstrate that the type II-A CRISPR-Cas system of  S. pyogenes  acquires new spacers upon phage infection, which are increasingly detectable in the absence of a capsule. Lastly, we show that  S. pyogenes  produces membrane vesicles that bind to phages, thereby limiting the pool of phages available for infection. Altogether, this work provides novel insight into survival strategies employed by  S. pyogenes  to combat phage predation.

Survival Strategies of Streptococcus pyogenes in Response to Phage Infection