Phylogenetic diversity of the sequenced S. pyogenes strains: unrooted neighbor-joining tree constructed using concatenated sequences of the seven loci used in MLST for a representative selection of STs from the S. pyogenes MLST database (www.mlst.net). The tree was constructed using ClustalX (23) and Phylip (9) with the Kimura two-parameter method, and the plot was generated using NJplot (17). The positions of all 12 strains for which complete genome sequences are available are shown.

Comparative nucleotide sequence analysis of S. pyogenes prophages: dot matrix showing the relatedness of the nucleotide sequences of prophages generated with DOTTER (21). The prophages used in the comparison (in order) were joined end to end and were obtained from Manfredo (φMan.1, φMan.2, φMan.3, φMan.4, and φMan.5), SSI-1 (SPsP1, SPsP2, SPsP3, SPsP4, and SPsP5) (14), SF370 (370.1, 370.2, 370.3, and 370.4) (10), MGAS315 (φ315.1, φ315.2, φ315.3, φ315.4, φ315.5, and φ315.6) (5), MGAS8232 (φ_speA, φ_speC, φ_speL/M, φ_370.3-like, and φ_sda) (20), MGAS10394 (φ10394.1, φ10394.2, φ10394.3, φ10394.4, φ10394.5, φ10394.6, φ10394.7, and φ10394.8) (3), MGAS6180 (φ6180.1, φ6180.2, φ6180.3, and φ6180.4) (11), MGAS5005 (φ5005.1, φ5005.2, and φ5005.3) (22), MGAS2096 (φ2096.1 and φ2096.2) (4), MGAS9429 (φ9429.1, φ9429.2, and φ9429.3) (4), MGAS10270 (φ10270.1, φ10270.2, φ10270.3, 10270.4, and 10270.5) (4), and MGAS10750 (φ10270.1, φ10270.2, φ10270.3, and φ10270.4) (4). The colored bars indicate the extents of the concatenated prophages for the strains, and the vertical and horizontal lines indicate the extents of the individual prophages. The green arrows indicate prophages referred to in the text.

Comparison of the genome structures of S. pyogenes: pairwise comparisons of the S. pyogenes MGAS315, SSI-1, Manfredo, MGAS10394, and MGAS8232 chromosomes displayed using the Artemis Comparison Tool (ACT) (6). The sequences were aligned using the predicted replication origins (oriC) (left), with the terminus of replication in the center. The colored bars separating the genomes (red and blue) represent matches identified by BLASTN (1). Red lines link matches in the same orientation, and blue lines link matches in the reverse orientation. Regions of the chromosomes containing prophages are indicated by pink boxes.