Fig. 2

Genomic comparison of COL923, USA300-LV and USA300-FPR3757 clones. a Read mapping coverage of sequencing reads of COL923 clone (5sau489 isolate as representative for the most frequent pulsotype, blue circle) and USA300-LV (5sau003, orange circle), compared to the USA300-FPR3757 genome (GenBank number: CP000255.1), the black most inner ring. The outer circle (alternating red-blue) represents the USA300 SmaI fragments (responsible for the PFGE pulsotype). Black and grey fragments represent fragments that change in the COL923 clone, by loss of the SmaI recognition sites. Matches with less than 80% of nucleotide identity or regions without match to the reference genome appear as blank in each ring. The image was prepared using BRIG. b SmaI-restriction PFGE pulsotypes of USA300 and COL923 (5sau489 isolate) clones. Black arrows show the two new fragments in the COL923 clone which were produced for the loss of the SmaI cuts between the fragments 12 and 13, and fragments 15 and 16 (black and grey fragments in figure a). c Maximun likelihood phylogenetic analysis using core genomes from representative isolates belonging to the COL923 clone (clade 2) and USA300-LV (clade 1). The USA300 clone grouped in a different clade more related to the USA300-LV