Integrating proteomics, genomics, and bioinformatics tools to define unique features of the clonal M1T1 strain of Streptococcus pyogenes

In this study, we compare the globally disseminated and more virulent group A streptococcal (GAS) M1T1 clone to the fully sequenced M1 SF370 strain. Using proteomics, DNA microarrays, and bioinformatics tools, we identified 3 mosaic prophages in the M1T1 genome that carry 3 toxin genes, speA2, mf4, and the novel streptodornase, sda1. These prophages closely resemble phages of an M3 strain associated with severe diseases. By examining a set of highly conserved prophage sequences flanking the toxin genes, we suggest a recombination-based model for toxin exchange between GAS prophages, which, together with the phage mosaicism, is likely to have contributed to the emergence and diversification of the M1T1 clone.