Genome identity (ANIm) between pairs of SE INPer strains
Pairwise whole genome alignments were done with Mummer within the JSspecies program (Richter et al., 2016). The percent of average nucleotide alignment (ANI) was illustrated by a heat-map constructed with ggPlot2 in R (see methods). ANI > 99% are in red color. S. epidermidis ATCC 12228 was included for comparison. S10 strain had ANI = 97% respect all the other SE strains.
Pangenome model of SE strains
The pangenome model of 29 SE strains was performe with GET_HOMOLOGUES (Contreras-Moreira and Vinuesa, 2013) as described in methods. A. Pangenome size (number of gene family clusters, Y axis) as a function of the number of SE genomes (X axis). B. Core genome according to the Tettelin equations.
Clonal relationships of the STs detected in INPer strains respect to the ST database
Alleles for the seven proteins used in the S. epidermidisMLST scheme (Thomas et al., 2007) were looked at the Staphylococcus epidermidis MLST database ( https://pubmlst.org/sepidermidis/ ; Table 1; see methods) (Feil et al., 2004). The clonal relationships among STs were determined by eBURST( http://eburst.mlst.net ). Six out of 8 ST complexes assigned to the SEINPer strains are denoted by numbers in violet color.