Table 3 Non-synonymous SNPs and InDels found in the group II clinical ST378 S. epidermidis isolates

From: In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance

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)

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Table 3 Non-synonymous SNPs and InDels found in the group II clinical ST378 S. epidermidis isolates

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