Table 2. Presence/absence of important virulence factor genes found in HL1 in comparison to USA300 and USA400.

Annotation	Gene number	HL1	USA 400	USA300
Immunoglobulin G binding protein A precursor	SAKer_00085	+	+	+
Lipase (EC 3.1.1.3)	SAKer_00314	+	+	+
Exotoxin	SAKer_00368	+	+	+
Exotoxin	SAKer_00404	+	+	+
Exotoxin	SAKer_00405	+	+	+
Exotoxin	SAKer_00406	+	+	+
Exotoxin	SAKer_00408	+	+	+
Exotoxin	SAKer_00409	+	+	+
Exotoxin	SAKer_00410	+	+	+
Exotoxin	SAKer_00411	+	+	+
Exotoxin	SAKer_00412	+	+	+
Exotoxin	SAKer_00413	+	+	+
Exotoxin	SAKer_00417	+	+	+
Phenol-soluble modulin α4	SAKer_05000	+	+	+
Phenol-soluble modulin α3	SAKer_05001	+	+	+
Phenol-soluble modulin α2	SAKer_05002	+	+	+
Phenol-soluble modulin α1	SAKer_05003	+	+	+
Staphylococcal accessory regulator SarA	SAKer_00611	+	+	+
Lipase (EC 3.1.1.3)	SAKer_00649	+	+	+
Staphylococcal accessory regulator homolog (SarX)	SAKer_00663	+	+	+
Sensory transduction protein kinase SaeS (EC 2.7.13.3)	SAKer_00702	+	+	+
Two-component response regulator SaeR	SAKer_00703	+	+	+
Staphylocoagulase precursor	SAKer_00791	×1	×	+
Thermonuclease (EC 3.1.31.1)	SAKer_00795	+	+	+
Staphostatin B	SAKer_00967	+	+	+
Staphopain (EC 3.4.22.48)	SAKer_00968	+	+	+
Glutamyl endopeptidase precursor (EC 3.4.21.19)	SAKer_00969	+	+	+
Heme uptake protein IsdB	SAKer_01050	+	+	+
Heme uptake heme-iron binding protein IsdA	SAKer_01051	+	+	+
Heme uptake cell surface protein IsdC	SAKer_01052	+	+	+
Heme uptake ABC transporter, membrane component IsdD	SAKer_01053	+	+	+
Heme uptake ABC transporter, heme-binding protein IsdE	SAKer_01054	+	+	+
Heme uptake ABC transporter, permease protein IsdF	SAKer_01055	+	+	+
Sortase B family protein	SAKer_01056	+	+	+
Formyl peptide receptor family 1 inhibitory protein Flipr	SAKer_01077	+	+	+
Alpha-hemolysin	SAKer_01084	+	+	+
Exotoxin	SAKer_01087	+	+	+
Exotoxin	SAKer_01088	+	+	+
Exotoxin	SAKer_01089	+	+	+
Phenol-soluble modulin β1	SAKer_01099	+	+	+
Phenol-soluble modulin β2	SAKer_01100	+	+	+
Peptide deformylase (EC 3.5.1.88)	SAKer_01142	+	+	+
Thermonuclease (EC 3.1.31.1)	SAKer_01259	+	+	+
Lysyltransferase (EC 2.3.2.3) MprF	SAKer_01297	+	+	+
Two-component sensor kinase ArlS (EC 2.7.13.3)	SAKer_01351	+	+	+
Two-component response regulator ArlR	SAKer_01352	+	+	+
Superoxide dismutase (EC 1.15.1.1)	SAKer_01500	+	+	+
Enterotoxin	SAKer_01549	+	+	+
Enterotoxin	SAKer_01550	+	+	+
Heme uptake receptor for hemoglobin-haptoglobin complexes IsdH	SAKer_01672	+	+	+
Staphylococcal accessory regulator homolog (Rot)	SAKer_01705	+	+	+
Serine protease (EC 3.4.21. -) SplD	SAKer_01758	+	+	+
Serine protease (EC 3.4.21. -) SplC	SAKer_01759	+	+	+
Serine protease (EC 3.4.21. -) SplB	SAKer_01760	+	+	+
Serine protease (EC 3.4.21. -) SplA	SAKer_01761	+	+	+
Leukocidin F subunit (LukD)	SAKer_01767	+	+	+
Leukocidin S subunit (LukE)	SAKer_01768	+	+	+
Enterotoxin	SAKer_01776	+	+	-
Enterotoxin	SAKer_01777	+	+	+
Enterotoxin	SAKer_01778	+	+	-
Enterotoxin	SAKer_01779	+	+	+
Enterotoxin	SAKer_01780	+	+	+
Enterotoxin	SAKer_01781	+	+	+
Staphopain (EC 3.4.22.48)	SAKer_01871	+	+	+
Phenol-soluble modulin export ABC transporter permease PmtD	SAKer_01904	+	+	+
Phenol-soluble modulin export ABC transporter ATP-binding protein PmtC	SAKer_01905	+	+	+
Phenol-soluble modulin export ABC transporter permease PmtB	SAKer_01906	+	+	+
Phenol-soluble modulin export ABC transporter ATP-binding protein PmtA	SAKer_01907	+	+	+
Phospholipase C (beta-hemolysin) (EC 3.1.4.3), truncated	SAKer_01914	×	×	×
Staphylococcal complement inhibitor SCIN	SAKer_01918	×	+	+
Chemotaxis-inhibiting protein	SAKer_01920	+	-	+
Staphylokinase precursor	SAKer_01923	+	+	+
Leukocidin F subunit	SAKer_01986	+	+	+
Leukocidin S subunit	SAKer_01987	+	+	+
Delta-hemolysin	SAKer_01999	+	+	+
Accessory gene regulator protein B AgrB	SAKer_02000	+	+	+
Autoinducing peptide precursor AgrD	SAKer_02001	+	+	+
Sensory transduction histidine kinase AgrC (EC 2.7.3. -)	SAKer_02002	+	+	+
Accessory gene regulator protein A AgrA	SAKer_02003	+	+	+
RNA polymerase sigma-B factor	SAKer_02029	+	+	+
Staphylococcal accessory regulator homolog (SarV)	SAKer_02230	+	+	+
Staphylococcal accessory regulator homolog (SarR)	SAKer_02260	+	+	+
Staphylococcal accessory regulator homolog (SarY)	SAKer_02262	+	+	+
Esterase (EC 3.1.1. -)	SAKer_02324	+	+	+
Gamma-hemolysin subunit A	SAKer_02399	+	+	+
Gamma-hemolysin subunit C	SAKer_02401	+	+	+
Gamma-hemolysin subunit B	SAKer_02402	+	+	+
Staphylococcal accessory regulator homolog (SarT/SarH3)	SAKer_02485	+	+	+
Staphylococcal accessory regulator homolog (SarU/SarH2)	SAKer_02486	+	+	+
Sortase A	SAKer_02517	+	+	+
Esterase (EC 3.1.1. -)	SAKer_02525	+	+	+
Staphyloxanthin biosynthesis protein CrtN (dehydrosqualene dehydrogenase)	SAKer_02552	+	+	+
Staphyloxanthin biosynthesis protein CrtM (dehydrosqualene synthase)	SAKer_02554	+	+	+
Staphyloxanthin biosynthesis protein CrtQ	SAKer_02555	+	+	+
Staphyloxanthin biosynthesis protein CrtP	SAKer_02556	+	+	+
Staphyloxanthin biosynthesis protein CrtO	SAKer_02557	+	+	+
Esterase/Lipase (EC 3.1. -. -)	SAKer_02575	+	+	+
Zinc metalloproteinase aureolysin (EC 3.4.24.29)	SAKer_02638	+	+	+
N-acetylglucosaminyltransferase (EC 2.4.1. -) IcaA	SAKer_02668	+	+	+
N-acetylglucosaminyltransferase, accessory part IcaD	SAKer_02669	+	+	+
Polysaccharide intercellular adhesin deacetylase IcaB	SAKer_02670	+	+	+
Putative polysaccharide intercellular adhesin exporter IcaC	SAKer_02671	+	+	+
Lipase (EC 3.1.1.3)	SAKer_02673	+	+	+

¹truncated.