A phylogeny was inferred that confirmed the close relationship among all isolates, with TPS3106 more distantly related to the others (Figure  4B). The unmapped reads from each isolate were also subjected to de

novo assembly to identify DNA not present in JKD6159. TPS3104 and TPS3105 contained no new sequences, while TPS3106 contained 34 kb of additional DNA, predominantly spanning the SCCmecV region. Figure 4 Whole genome sequence analysis and comparison of JKD6159 with other ST93 CA-MRSA isolates. (A) Circular diagram CP-690550 molecular weight of the JKD6159, TPS3104, TPS3105 and TPS3106 chromosomes (from inner to outer circles). TPS3104, TPS3105 and TPS3106 contigs were mapped by BLASTN to JKD6159. TPS3104 contained SCCmecIV and ϕSA2 with lukSF-PV; TPS3105 contained SCCmecIV but lacked ϕSA2 and lukSF-PV; TPS3106 contained SCCmecV, and ϕSA2

without lukSF-PV. (B) ST93 S. aureus phylogeny inferred by split decomposition analysis from pairwise comparisons of the 253 learn more variable nucleotide positions identified from the ST93 core chromosome of 2,720,685 bp. Figures indicate the number of nucleotide substitutions per branch. All nodes have 100% bootstrap support. Comparative genomics of ST93 and the importance of agr in the virulence of ST93 CA-MRSA We next explored the contribution of specific mutations to the differential virulence of the ST93 strains. Using our read mapping approach described above, we compared the genome sequences of TPS3104, TPS3105

and TPS3106 with each other and with JKD6159. There were a number of single nucleotide Depsipeptide molecular weight polymorphisms (SNPs) and insertions and deletions (indels) differentiating the strains from JKD6159 (Additional files 8, 9, 10). We searched for mutations in regulatory genes that could potentially explain the different virulence phenotypes of the strains. Notably, both avirulent ST93 strains, TPS3105 and TPS3106 contained mutations within the agr locus. We have since completed whole genome sequencing of TPS3151 and TPS3161 and found they contain predicted amino acid substitutions in AgrC that might disrupt agr function (Stinear et al., submitted). These isolates demonstrated low expression of Hla (Additional file 3). Additionally, TPS3106 also contained a mutation in a gene encoding a previously uncharacterized AraC/XylS family regulatory protein. This was also of particular interest as members of this class have been shown to contribute to the regulation of exotoxin expression [24, 25]. TPS3105 contained a frame-shift mutation within agrA (Sa_JKD6159 nucleotide 2096502) and a further substitution (G to A) within agrA at nucleotide 2096569), while TPS3106 contained an ~356 bp deletion spanning the agr effector molecule, RNAIII (deletion spanning nucleotides 2093372 to 2093728). These mutations suggested these isolates were agr deficient.