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. 2018 Feb;138(2):336–343. doi: 10.1016/j.jid.2017.09.023

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© 2017 The Authors

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

PMC Copyright notice

Evidence of selection and genetic adaptation within the host. (a) Evidence of plasmid dynamics and an evolutionary bottleneck. ML core SNPs tree illustrating genetic relationship of colonies from two spatially distinct positions in a single eczema site. Branch label marked with an arrow indicates point in phylogeny where a plasmid (backbone similar to SAP0194) carrying multiple metal resistance genes was gained in the S. aureus population. Tree rooted using MRSA252 reference. Branch labels: E1/3, lateral border; E2/4, medial border of single eczema site. SNP bar is indicated for scale (not applicable to root branches with strikethrough). (b) Convergent evolution of agrA mutants. ML core SNPs tree of colonies from five body sites. Branch labels marked with arrows indicate the point in phylogeny where homoplastic mutations in agrA are predicted to have occurred. Tree rooted using MSSA476 reference. EASI, Eczema Area Severity Index; ML, maximum likelihood; SNP, single-nucleotide polymorphism; ST, sequence type.