Genomes of SEfrom the GenBank used in this work
Prophage sequences and their homologs found in SEINPer genomes
CRISPR-Cas elements present in SE INPer strains
Survey of staphylococci at Instituto Nacional de Perinatología, México City Alone eight years
A. Species classification and proportion. B. Origin of the isolates and proportion. C. Isolation sites proportion.
Frequency cumulation of antibiotic resistant strains in Staphylococcus
A. S. epidermidis. B. S. aureus. The absolute number of antibiotic resistances (x-axis) by the number of strains (y-axis) was counted from 2006 to 2013.
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.
Phylogenetic tree of the SCCmec recombinases
A. ccrA. B. ccrB. C. ccrB