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. 2017 Apr 1;9(4):830–842. doi: 10.1093/gbe/evx037

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© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 2.— — Genetic relatedness of S. aureus isolates from different hosts. (a) Host origin of all S. aureus isolates from chicken (blue), human (red), and other species (yellow). Clonal complex (CC) designations are based on shared MLST housekeeping loci. Chicken isolates were found in five sequence clusters, corresponding to CCs 1, 5, 30, 358, and 398 which are highlighted. The tree was constructed from a core genome alignment (2,789,909 bp) of 1,700 genes using an approximation of the maximum likelihood algorithm. (b) Reconstruction of the clonal frame with putative recombination regions removed of CC5, including 20 chicken (blue) and 26 human (red) isolates (2,302,773 bp alignment in ClonalFrame).