Figure 4

Phylogenetic relationship among selected E. faecalis strains based on whole genome alignments. The alignment was calculated with Mugsy (http://mugsy.sourceforge.net/ [last access 16.07.2014] [57]) and only aligned regions present in all analyzed strains were extracted. These regions were concatenated and positions with gaps removed. The resulting core alignment was used to infer a Maximum Likelihood tree with RAxML. The GTRGAMMA model for nucleotide substitution and rate heterogeneity was utilized, bootstrap support values of 1000 replicates are shown at the nodes. Names of the ST40 isolates and their origin are indicated at the end of the branches. The highly related ST40 isolates were further zoomed in exemplified by the dotted line and the different scale bar. Metadata are given as follows: Strain no., year of isolation, origin, country: AC, animal colonizer; AI, animal infection; HC, human colonizer; HI, human infection; CU, Cuba; D, Germany; DK, Denmark; ES, Spain; IS, Island; PL, Poland; USA.