Table 2.
Non-synonymous SNPs and InDels found in the group I clinical ST378 S. epidermidis isolates
| ID # | Gene name/function | Amino acid change | Isolates | Phylogenetic cluster |
|---|---|---|---|---|
| 1 | GraR, two-component response regulator | Gly59Arg | 1A, 1B, 1C, 1D, 1E, 1F, 16J, 16N | Group I |
| 2 | Sodium/di- and tricarboxylate cotransporter | Ser161stop | 1A, 1B, 1C, 1D, 1E, 1F, 16J, 16N | Group I |
| 3 | Cold-shock protein CspA | Gly57fs | 1A, 1B, 1C, 1D, 1E, 1F, 16J, 16N | Group I |
| 4 | RodA, rod shape-determining protein/FtsW, cell division protein | Gly161Val | 1A, 1B, 1C, 1D, 1E, 1F, 16J, 16N | Group I |
| 5 | PbuG, hypoxanthine/guanine permease | Ser27Leu | 1A, 1B, 1C, 1D, 1E, 1F, 16J, 16N | Group I |
| 6 | RpoB, DNA-directed RNA polymerase beta subunit | Arg917Leu | 1A, 1B, 1C, 1D, 1E, 1F, 16N | |
| 7 | Sle1, autolysin, N-acetylmuramoyl-L-alanine amidase | Val67Ala | 1A | |
| 8 | NrdI, ribonucleotide reduction protein | Arg14stop | 1A | |
| 9 | SecDF, protein translocase subunit | Ser621Asn | 1A | |
| 10 | Bicyclomycin-resistance protein TcaB/major myo-inositol transporter IolT | Pro64Ala | 1A | |
| 11 | ClpC, ATP-dependent Clp protease ATP-binding subunit | Arg12_Gln18del | 1B, 1E, 16N | Blue star |
| 12 | NrdI, ribonucleotide reduction protein | Glu112fs | 1B, 1E, 16N | Blue star |
| 13 | Isocitrate dehydrogenase | Val356Leu | 1B, 1E, 16N | Blue star |
| 14 | SufB, Fe-S cluster assembly protein | Ala129Gly | 1E | |
| 15 | peptidase, U32 family large subunit [C1] | Glu90Gln | 1E | |
| 17 | PrmA, ribosomal protein L11 methyltransferase | Asp107Gly | 1B, 16N | Blue square |
| 18 | Sialic acid utilization regulator, RpiR family/MurR/RpiR family transcriptional regulator | Val84Ile | 1B, 16N | Blue square |
| 19 | Two-component sensor kinase WalK | Met428Thr | 1B, 16N | Blue square |
| 20 | SarA, Staphylococcal accessory regulator A | Ala70Thr | 16N | |
| 21 | 3’-to-5’ oligoribonuclease A | Pro46fs | 16N | |
| 22 | acetate kinase | Thr239Ala | 16N | |
| 23 | Mqo, malate:quinone oxidoreductase | Ser431_Pro432_ Gly433_Ala434del | 16N | |
| 24 | Salicylate hydroxylase | Ala290Gly | 1C, 1D, 1F | Blue circle |
| 25 | Manganese ABC transporter, inner membrane permease protein SitD | Tyr243fs | 1C | |
| 26 | NrdI, ribonucleotide reduction protein | Gln54stop | 1C | |
| 27 | YrrC, RecD-like DNA helicase, deoxyribonuclease | Ile122Thr | 1C | |
| 28 | RpoC, DNA-directed RNA polymerase beta’ subunit | Gly433Val | 1D, 1F | Blue triangle |
| 29 | RibU, riboflavin transporter | Met1Val | 1D, 1F | Blue triangle |
| 30 | Iron-sulfur cluster assembly scaffold protein NifU | Lys134Glu | 1D | |
| 31 | PurR, pur operon repressor | Phe33Ser | 1F | |
| 32 | SrrB, respiratory response protein | Ile13Ser | 1F | |
| 33 | RpoB, DNA-directed RNA polymerase beta subunit | Gln137Pro | 16J | |
| 34 | Predicted RNA-binding protein, associated with RNAse of E/G family | Val15fs | 16J | |
| 35 | general stress protein 13 (contains ribosomal protein S1 (RPS1) domain) | Thr31fs | 16J | |
| 36 | Mqo, malate:quinone oxidoreductase | Arg375Trp | 16J | |
| 37 | PutP, proline/sodium symporter | Leu353stop | 1A, 1B, 1C, 1D, 1E, 1F, 16J, 16N, 14G, 16L,16O |
Non-synonymous mutations characteristic of all isolates, subclusters or single isolates from the group I phylogenetic cluster (labeled in blue 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)