The complete genome sequence of nine different strains of Streptococcus pyogenes have now been determined, including serotype M1 and M3 (two strains each), M5, M6, M18, M28, and M49. Seven of these strains are included in the class I type, known to be associated with either acute rheumatic fever or an invasive disease. Class II organisms are known to be associated with acute glomerulonephritis (AGN) and one of the best studied of this class is the M49 strain NZ131, the complete sequence of which has now been determined. The NZ131 (M49) genome contains 1,815,858 bp and is essentially colinear with the M1 genome
it contains no inversions around the origin or terminus. NZ131 contains several large blocks of DNA that appear to be insertions when compared to the class I genomes. These blocks do not appear to be mobile genetic elements, range in size from 3 to 28 kb, and contain a number of genes not found in any of the other sequenced strains. It is noteworthy that this genome contains only two complete bacteriophages-the least number of phages present in any of the previously described genomes. Interestingly, one of these phage genomes is inserted into the same location on the M49 genome as phage 370.2 on the M1 genome. Additionally, this phage contains a single superantigen gene (speH) at the attachment site, but not both speH and speI. A second phage genome contains a streptodornase gene at its attachment site. It is now becoming clear that homologous recombination between various prophages which share homology and residing in the same host can lead to host genome rearrangements and new associations with lysogenic conversion genes in phages. Further analysis of the unique M49 genes should provide important new information regarding virulence genes involved in AGN. © 2006.