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Fig. 3 | Genome Biology

Fig. 3

From: Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

Fig. 3

Diversity and distribution of SCCmec type I elements in the archetypal MRSA population. a Parsimonious minimal spanning tree of SCCmec type I elements present in the archetypal MRSA isolates present in the clade credibility tree in b. The tree is built with core SNPs identified in the SCCmec type I elements, and excludes SNP in the pls gene that were predicted to have arisen by recombination. In total, ten genotypes were observed, and the genetic events that distinguish each genotype from the founder genotype are indicated. The tree is centred on the majority genotype inferred as the founder population, and colour-coded according to their genotype. Black asterisks indicate isolates that lack the type I SCCmec element. The sizes of the circles illustrate the relative sizes of the genotype populations. The key below the tree describes the canonical SNPs differentiating SCCmec type I genotypes and the number of variants with that genotype. b Maximum clade credibility tree of the archetypal MRSA clone population based on BEAST analysis. Tips of the tree are constrained by isolation dates; the time scale is shown below the tree. The tree is built with core genome SNPs from a subset of the total collection’s isolates (n = 122), which had precise dates of isolation, and whose origins could be linked back to the original submission documentation. The branches of the tree are coloured according to the genotype of the SCCmec type I element present in that strain (illustrated in a). Internal branches are coloured according to parsimonious reconstruction of the predicted genotype. Where terminal branches are black and highlighted by a black asterisk, this indicates the absence of an SCCmec element, which is predicted to reflect loss of the element. An arrow indicates the point in the phylogenetic reconstruction where an ancestral type I SCCmec element was acquired. The root of the tree corresponds to the basal node of the ST250/ST247 population in Fig. 1 rooted by the RH12000692_7401696 outgroup. From the analysis the estimated mutation rate of population is 1.8 × 10−6 SNPs/site/year. This substitution rate falls within the reported ranges of multiple successful S. aureus lineages [31] and therefore it is unlikely likely that long-term storage of the isolates has created any temporal artefacts

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