Extended Data Fig. 5: Detailed phylogenetic distribution of tarIJLM2-5 among selected S. epidermidis clones and evolutionary relation of tarL from different gene clusters.
a, Maximum-likelihood phylogeny of 33 tarL genes from representative S. epidermidis (Se) and S. aureus (Sa) isolates and other Staphylococcus spp. isolates that carried tarIJL with or without tarM, including S. warneri (Sw), S. hominis (Sh), S. capitis (Sc), and uncharacterised Staphylococcus species (Ssp) (Source Data). The tarL2 gene found in S. epidermidis is more closely related to the two tarL genes in S. aureus than to S. epidermidis tarL1. The S. epidermidis tarL3, tarL4, and tarL5 genes, but not tarL2, were also found in other Staphylococcus species. Phylogenetic reconstruction was carried out using the maximum-likelihood program PhyML with a GTR model of nucleotide substitution, and support for the nodes was assessed using aBayes (see Methods). The tree was midpoint rooted. The scale bar denotes substitutions per variable sites. b, Maximum-likelihood phylogeny of 261 S. epidermidis isolates, comprising 25 tarIJLM-positive S. epidermidis isolates collected in this study, nine tarIJLM-positive S. epidermidis genomes from in the NCBI Reference Sequence Database (accessed July 3 2018), and a global collection of 227 S. epidermidis isolates originating from 96 healthcare institutions across 24 countries3 was inferred from an alignment of 39,298 single-nucleotide polymorphisms (Supplementary Table 2). Four tarIJLM-negative isolates (BPH0677, BPH0704, BPH0737, and SEI) were manually removed from the phylogeny due to their extreme divergence, and clades containing isolates with the same or closely related STs were collapsed to reduce complexity. The tarIJLM2 genes in E73 (Fig. 1b) were used as queries in BLASTN searches. The multilocus sequence types (STs) are indicated. Phylogenetic reconstruction was carried out using the maximum-likelihood program PhyML with a GTR model of nucleotide substitution, and support for the nodes was assessed using aBayes (see Methods). The tree was rooted according to work of Lee et al.3 The scale bar denotes substitutions per variable sites. Expanded subtrees illustrate the phylogenetic relationships of isolates belonging to ST5/ST87, ST10, ST23/single-locus variant (SLV), and ST2/ST188. The presence of tarIJLM2-5 is indicated in colors. A single ST23 isolate, VCU117, carried both, tarIJLM2 and tarIJLM3.
