genome into a second set of non-overlapping 11-mers, offset by four base pairs from the initial indexing, and into a third set of non-overlapping 9-mers. By performing three independent alignments using the staggered genomic indices and then superimposing the resulting alignments to show all aligning sequences, the enhanced-BLAT (eBLAT) detects as much as 75% more conserved sequences when evolutionary distant sequences are aligned [22]. NCBI BLAST database searches Database homology BLAST searches against 988 microbial genomes were performed using the standard tBLASTn, BLASTn and BLASTp options at the National Center for Biotechnology Information web site (http://www.ncbi.nlm.nih.gov). Supporting Information Table S1 MRSA252-RF122 uniquely shared chromosomal DNA sequence blocks. Found at: doi:10.1371/journal.pone.0003074.s001 (0.06 MB DOC) Figure S1 An EvoUnique profile identifies a putative nitric oxide reductase gene in the human S. aureus MRSA252 genome that is not present in the genomes of 16 other Staphylococci. EvoUnique analysis of the human S. aureus MRSA252 genomic DNA (bases 303,347 to 306,097) with 16 other Staphylococcus genomes (S. aureus COL; S. aureus MSSA476, S. aureus Mu50; S. aureus MW2; S. aureus N315; S. aureus NCTC 8325; S. aureus RF122; S. aureus USA300; S. aureus JH1; S. aureus JH9; S. aureus Mu3; S. aureus Newman; S. epidermidis ATCC 12228; S. epidermidis RP62; S. haemolyticus JCSC1435; and S. saprophy- ticus) reveals a unique 2,750 bp region that contains a 763 amino acid protein encoding ORF identified as encoding a nitric oxide reductase (SAR0261). Upper case, red-colored letters represent sequences that are unique to S. aureus MRSA252 and were not found in the other 16 Staphylococci genomes analyzed; green bases are shared with one other isolate and lowercase gray-colored References 1. Klevens RM, Edwards JR, Tenover FC, McDonald LC, Horan T, et al. (2006) Changes in the epidemiology of methicillin-resistant Staphylococcus aureus in intensive care units in US hospitals, 1992–2003. Clin Infect Dis 42: 389–91. 2. Jarvis WR, Schlosser J, Chinn RY, Tweeten S, Jackson M (2006) National prevalence of methicillin-resistant Staphylococcus aureus in inpatients at US health care facilities, 2006. Am J Infection Control 35: 631–637. 3. Barkema HW, Schukken YH, Zadoks RN (2006) Invited Review: The role of cow, pathogen, and treatment regimen in the therapeutic success of bovine Staphylococcus aureus mastitis. J Dairy Sci 89: 1877–95. 4. 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Found at: doi:10.1371/journal.pone.0003074.s002 (4.89 MB TIF) Figure S2 Identification of HGT exchanges between plasmid and bacterial genomes. EvoPrinter comparative analysis of the Staphylococcus pTZ2162 plasmid with the S. aureus COL; S. aureus MRSA252; S. aureus MSSA476, S. aureus Mu50; S. aureus MW2; S. aureus N315; S. aureus NCTC 8325; S. aureus RF122; S. aureus USA300; S. aureus JH1; S. aureus JH9; S. aureus Mu3 and S. aureus Newman genomes identifies HGT sequences that are uniquely shared with different bacterial genomes. Shown is a pTZ2162 plasmid DNA EvoDifferences profile (25,815 to 30,799 bp) that highlights two different putative HGT events. Highlighted with green-colored letters, pTZ2162 uniquely shares a 766 bp sequence with the human MRSA252 genome that includes a partial match to the blaZ gene (ORF boxed). 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(2004) Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci USA 101: 9786–91. PLoS ONE | www.plosone.org 7 August 2008 | Volume 3 | Issue 8 | e3074