ruleID	organism	gene	nodeID	refseq accession	GenBank accession	HMM accession	ARO accession	mutation	variation type	context	drug	drug class	phenotype	clinical category	breakpoint	breakpoint standard	PMID	evidence code	evidence grade	evidence limitations	rule curation note	Reviewed by
STA0001	s__Staphylococcus aureus	unknown	-	-	-	-	-	-		core	ceftazidime	-	wildtype	R	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01)"	6413485				"Wildtype resistance, but no mechanism described. Most likely is due to the wildtype sequence of PBP3 (primary target of ceftazidime), for which ceftazidime has low affinity."	"NC, SLB"
STA0002	s__Staphylococcus aureus	tet(38)	tet(38)	-	-	NF012176.0	ARO:3000565	-	Gene presence detected	core	tetracycline	-	wildtype	S	MIC <=1 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	29216347	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0003	s__Staphylococcus aureus	mepA	mepA	-	-	NF000131.1	ARO:3000026	-	Gene presence detected	core	tigecycline	-	wildtype	S	MIC <=0.5 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01)"	37432114	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0004	s__Staphylococcus aureus	norA	-	-	BAA14147.1	-	ARO:3004667	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	8517696	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0006	s__Staphylococcus aureus	norA	-	-	BAA14147.1	-	ARO:3004667	-	Gene presence detected	core	norfloxacin	-	wildtype		MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); ECOFF (2025-4-17); CLSI M100Ed35E"	8517696	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0007	s__Staphylococcus aureus	norB	-	-	CCQ22388.1	-	ARO:3000421	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	18723624	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0009	s__Staphylococcus aureus	norB	-	-	CCQ22388.1	-	ARO:3000421	-	Gene presence detected	core	norfloxacin	-	wildtype	S	MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01) + ECOFF (2025-4-17); CLSI M100Ed35E"	18723624	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0010	s__Staphylococcus aureus	norB	-	-	CCQ22388.1	-	ARO:3000421	-	Gene presence detected	core	moxifloxacin	-	wildtype	S	MIC <=0.25 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	18723624	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0011	s__Staphylococcus aureus	norB	-	-	CCQ22388.1	-	ARO:3000421	-	Gene presence detected	core	sparfloxacin	-	wildtype	S	MIC <=0.5 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); CLSI M100Ed35E"	18723624	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0012	s__Staphylococcus aureus	norB	-	-	CCQ22388.1	-	ARO:3000421	-	Gene presence detected	core	tetracycline	-	wildtype	S	MIC <=1 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01) + ECOFF (2025-4-17); CLSI M100Ed35E"	18723624	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0013	s__Staphylococcus aureus	norC	-	-	AGP27106.1	-	ARO:3007010	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	16495280	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0015	s__Staphylococcus aureus	norC	-	-	AGP27106.1	-	ARO:3007010	-	Gene presence detected	core	moxifloxacin	-	wildtype	S	MIC <=0.25 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	16495280	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0016	s__Staphylococcus aureus	mdeA	-	-	WP_002289367.1	-	ARO:3007011	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	14982783	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0018	s__Staphylococcus aureus	mdeA	-	-	WP_002289367.1	-	ARO:3007011	-	Gene presence detected	core	norfloxacin	-	wildtype		MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); ECOFF (2025-4-17); CLSI M100Ed35E"	14982783	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0019	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	"12730173, 21867918"	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0020	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	norfloxacin	-	wildtype		MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); ECOFF (2025-4-17); CLSI M100Ed35E"	"12730173, 21867918"	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0022	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	tetracycline	-	wildtype	S	MIC <=1 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	15774883	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0023	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	-	peptide antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023)
EUCAST v14.0 (2024-01-01)"	15774883	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	NC
STA0024	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	daptomycin	-	wildtype	S	MIC <=1 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	15774883	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0025	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	-	cephalosporin	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	"17277059, 15774883"	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species. The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0026	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	cefoxitin	-	wildtype	S	MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	15774883	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0027	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	-	penicillin beta-lactam	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023)
EUCAST v14.0 (2024-01-01)"	"17277059, 15774883"	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species. The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	NC
STA0028	s__Staphylococcus aureus	mgrA (norR)	-	-	BAB41874.1	-	ARO:3000815	-	Gene presence detected	core	benzylpenicillin	-	wildtype	S	MIC <=0.125 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	15774883	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0029	s__Staphylococcus aureus	sdrM	-	-	BAB43261.1	-	ARO:3007013	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	16508166	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0030	s__Staphylococcus aureus	sdrM	-	-	BAB43261.1	-	ARO:3007013	-	Gene presence detected	core	norfloxacin	-	wildtype		MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); ECOFF (2025-4-17); CLSI M100Ed35E"	16508166	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.	"NC, SLB"
STA0031	s__Staphylococcus aureus	mepR	-	-	BAB56495.1	-	ARO:3000746	-	Gene presence detected	core	tigecycline	-	wildtype	S	MIC <=0.5 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	"15855507, 16569840"	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0032	s__Staphylococcus aureus	mepR	-	-	BAB56495.1	-	ARO:3000746	-	Gene presence detected	core	tetracycline	-	wildtype	S	MIC <=1 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	"15855507, 16569840"	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0033	s__Staphylococcus aureus	arlR	-	-	ATC67679.1	-	ARO:3000838	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	10633099	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species. The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0034	s__Staphylococcus aureus	arlR	-	-	ATC67679.1	-	ARO:3000838	-	Gene presence detected	core	norfloxacin	-	wildtype		MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); ECOFF (2025-4-17); CLSI M100Ed35E"	10633099	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0036	s__Staphylococcus aureus	kdpD	-	-	CYF42523.1	-	ARO:3004047	-	Gene presence detected	core	-	aminoglycoside antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	23555240	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0037	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	-	macrolide antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	20855745	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0038	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	erythromycin	-	wildtype	S	MIC <=1 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01)"	20855745	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0039	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	-	aminoglycoside antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	20855745	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0040	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	kanamycin A	-	wildtype		MIC <=8 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); ECOFF (2025-4-17)"	20855745	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	"NC, SLB"
STA0041	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	-	oxazolidinone antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	20855745	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0042	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	linezolid	-	wildtype	S	MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01)"	20855745	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	NC
STA0043	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	-	diaminopyrimidine antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	20855745	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0044	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	trimethoprim	-	wildtype	S	MIC <=4 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01)"	20855745	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	NC
STA0045	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	-	phenicol antibiotic	wildtype	S	not applicable	"Expected resistant phenotypes v1.2 (13 January, 2023); EUCAST v15.0 (2025-01-01); CLSI M100Ed35E"	20855745	ECO:0001103 natural variation mutant evidence	strong		"Wildtype core gene encoding an efflux pump. This efflux pump is not associated with clinical resistance in this species unless efflux activity is upregulated.The rule is being defined for the whole class on the basis of specific evidence for a subset of drugs, not all drugs have direct evidence but as they are not expected resistances the rule is assumed to apply class-wide."	"NC, SLB"
STA0046	s__Staphylococcus aureus	lmrS	-	-	AAW38464.1	-	ARO:3004572	-	Gene presence detected	core	chloramphenicol	-	wildtype		MIC <=16 mg/L	"Expected resistant phenotypes v1.2 (13 January, 2023); ECOFF (2025-4-17)"	20855745	ECO:0001103 natural variation mutant evidence	strong		Wildtype core gene encoding an efflux pump regulator. This regulator is not associated with clinical resistance in this species.	NC