Table 3.
Non-synonymous SNPs and InDels found in the group II clinical ST378 S. epidermidis isolates
| ID # | Gene name/function | Amino acid change | Isolates | Phylogenetic cluster |
|---|---|---|---|---|
| 38 | Pta, phosphate acetyltransferase | Asp245Tyr | 14G, 16H,16I, 16K, 16L, 16M,16O | Group II |
| 39 | Penicillin-binding protein 1/Cell division protein FtsI | Val605Leu | 14G, 16H,16I, 16K, 16L, 16M,16O | Group II |
| 40 | RsbU, sigma factor B regulator | Thr325Asn | 14G, 16H,16I, 16K, 16L, 16M,16O | Group II |
| 41 | RNA-binding protein, conserved protein domain family EVE RNA binding | Trp17Cys | 14G, 16H,16I, 16K, 16L, 16M,16O | Group II |
| 42 | ArlR, two-component response regulator | Leu51fs | 14G, 16H,16I, 16K, 16L, 16M,16O | Group II |
| 43 | Mqo, malate:quinone oxidoreductase | Arg132stop | 14G, 16H,16I, 16K, 16L, 16M,16O | Group II |
| 44 | RpoB, DNA-directed RNA polymerase beta subunit | Gly491_Gly492 insProGly | 14G, 16L,16O | Red star |
| 45 | MsrC, free methionine-(R)-sulfoxide reductase | Gly64Asp | 14G, 16L,16O | Red star |
| 46 | Sat, sulfate adenylyltransferase | Pro348Gln | 14G, 16L,16O | Red star |
| 47 | pyruvate dehydrogenase subunit beta/branched-chain alpha-keto acid dehydrogenase E1 | Glu201Lys | 14G, 16L,16O | Red star |
| 48 | MprF virulence factor, phosphatidylglycerol lysyltransferase | Glu791_His792 insLeuGlu | 16L | |
| 49 | GTP-sensing transcriptional pleiotropic repressor CodY | Glu254fs | 16H, 16I, 16K, 16M | Red square |
| 50 | glycerol-3-phosphate responsive antiterminator | Gly129Ala | 16H, 16I, 16K, 16M | Red square |
| 51 | PrmA, ribosomal protein L11 methyltransferase | Glu238Ala | 16H, 16I, 16K, 16M | Red square |
| 52 | RpoB, DNA-directed RNA polymerase beta subunit | Gly492Val | 16I | |
| 53 | RelQ, (p)ppGpp synthetase | Phe40fs | 16I | |
| 54 | RSH, (p)ppGpp synthase/hydrolase | Leu533Phe | 16H, 16K, 16M | Red circle |
| 55 | RpoB, DNA-directed RNA polymerase beta subunit | Ala473_Asn474 insAla | 16H, 16K, 16M | Red circle |
| 56 | HssR, heme response regulator | Thr95Ala | 16H, 16K, 16M | Red circle |
| 57 | AgrA, accessory gene regulator protein A | Glu42fs | 16H | |
| 58 | Hypothetical serine protease | Arg78Ile | 16H | |
| 59 | AgrA, accessory gene regulator protein A | Arg218Pro | 16M | |
| 60 | L-Cystine ABC transporter, periplasmic cystine-binding protein TcyA | Thr45_Tyr46del | 16M |
Non-synonymous mutations characteristic of all isolates, subclusters or single isolates from the group II phylogenetic cluster (labeled in red in Fig. 2). The numbering in the first column is an identification number for each of the mutations reported (starting from 1 in Table 2, going up to 60 in Table 3). The isolates in which the mutations were found are given in the column “Isolates” and the symbols denotations in the “Phylogenetic cluster” column refer to the colored symbols shown on the phylogenetic tree branches to characterize subclusters (Fig. 2b). An extended version of this table, allowing a color-guided visualization and showing the mutations' localization in the S. epidermidis RP62A reference genome, can be found in the Supplementary Information (Supplementary Table 3)