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
EFM0004	s__Enterococcus_B faecium	aac(6')-I	aac(6')_Entco	WP_008265821.1	-	-	ARO:3002556	-	Gene presence detected	core	amikacin	-	wildtype	R	not applicable	not applicable	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	moderate	lacks evidence of the degree to which MIC is affected	"21159796: Large decrease in the MICs of aminoglycosides that are substrates for AAC(6’)-Ii [ > 2-fold reduction in kanamycin, tobramycin and netilmicin MICs] was observed for the _aac(6_)-Ii strain (BM4681). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT855 (pBADΩaac(6_)-Ii )] conferred on E. coli > 4-fold increase in MIC to kanamycin, tobramycin, amikacin, and netilmicin, while gentamicin only changed 1-fold (Table 1). 8239603: Cloning of the plasmid pAT432 (containg gene aac(6')-Ii) into E. coli BM694 strain conferred resistance to amikacin, kanamycin, 2'-N-ethyl-netilmicin, netilmicin, sisomicin, and tobramycin and susceptible to gentamicin and 6'-N-ethyl-netilmicin."
EFM0005	s__Enterococcus_B faecium	aac(6')-I	aac(6')_Entco	WP_008265821.1	-	-	ARO:3002556	-	Gene presence detected	core	gentamicin	-	wildtype	S	MIC <=32 mg/L	ECOFF	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	strong		"21159796: Large decrease in the MICs of aminoglycosides that are substrates for AAC(6’)-Ii [ > 2-fold reduction in kanamycin, tobramycin and netilmicin MICs] was observed for the _aac(6_)-Ii strain (BM4681). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT855 (pBADΩaac(6_)-Ii )] conferred on E. coli > 4-fold increase in MIC to kanamycin, tobramycin, amikacin, and netilmicin, while gentamicin only changed 1-fold (Table 1). 8239603: Cloning of the plasmid pAT432 (containg gene aac(6')-Ii) into E. coli BM694 strain conferred resistance to amikacin, kanamycin, 2'-N-ethyl-netilmicin, netilmicin, sisomicin, and tobramycin and susceptible to gentamicin and 6'-N-ethyl-netilmicin."
EFM0001	s__Enterococcus_B faecium	aac(6')-I	aac(6')_Entco	WP_008265821.1	-	-	ARO:3002556	-	Gene presence detected	core	kanamycin A	-	wildtype	R	not applicable	not applicable	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	strong		"21159796: Large decrease in the MICs of aminoglycosides that are substrates for AAC(6’)-Ii [ > 2-fold reduction in kanamycin, tobramycin and netilmicin MICs] was observed for the _aac(6_)-Ii strain (BM4681). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT855 (pBADΩaac(6_)-Ii )] conferred on E. coli > 4-fold increase in MIC to kanamycin, tobramycin, amikacin, and netilmicin, while gentamicin only changed 1-fold (Table 1). 8239603: Cloning of the plasmid pAT432 (containg gene aac(6')-Ii) into E. coli BM694 strain conferred resistance to amikacin, kanamycin, 2'-N-ethyl-netilmicin, netilmicin, sisomicin, and tobramycin and susceptible to gentamicin and 6'-N-ethyl-netilmicin."
EFM0003	s__Enterococcus_B faecium	aac(6')-I	aac(6')_Entco	WP_008265821.1	-	-	ARO:3002556	-	Gene presence detected	core	netilmicin	-	wildtype	R	not applicable	not applicable	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	strong		"21159796: The drop in amikacin MIC in knockout strain is moderate, not as pronounced as that for other aminoglycosides. Large decrease in the MICs of aminoglycosides that are substrates for AAC(6’)-Ii [ > 2-fold reduction in kanamycin, tobramycin and netilmicin MICs] was observed for the _aac(6_)-Ii strain (BM4681). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT855 (pBADΩaac(6_)-Ii )] conferred on E. coli > 4-fold increase in MIC to kanamycin, tobramycin, amikacin, and netilmicin, while gentamicin only changed 1-fold (Table 1). 8239603: Cloning of the plasmid pAT432 (containg gene aac(6')-Ii) into E. coli BM694 strain conferred resistance to amikacin, kanamycin, 2'-N-ethyl-netilmicin, netilmicin, sisomicin, and tobramycin and susceptible to gentamicin and 6'-N-ethyl-netilmicin."
EFM0002	s__Enterococcus_B faecium	aac(6')-I	aac(6')_Entco	WP_008265821.1	-	-	ARO:3002556	-	Gene presence detected	core	tobramycin	-	wildtype	R	not applicable	not applicable	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	strong		"no evidence that aac(6')-Ii affects gentamycin MIC according to 21159796, knock-out strain had same MIC as WT. The recombinant plasmid [pAT855 (pBADΩaac(6_)-Ii )] conferred on E. coli conferred only changed 1-fold change in gentamicin MIC (Table 1)."
EFM0009	s__Enterococcus_B faecium	efmM	-	-	AFC64318.1	-	-	-	Gene presence detected	core	amikacin	-	wildtype	R	not available	ECOFF ID	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	weak	lacks evidence of the degree to which MIC is affected	"no amikacin MIC change in knockout strain compared to WT, no evidence of contribution to intrinsic resistance. 21159796: the drop in kanymycin MIC in knockout strain is moderate, aac(6')-Ii seems to be the main determinant of kanamycin intrinsic resistance. Smaller decreases in kanamycin and tobramycin MIC [only 1-fold reduction] were observed for the _efmM strain (BM4682). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT854 (pBADΩefmM)] conferred on E. coli a 4-fold or greater increase in resistance to kanamycin and tobramycin; the MICs of amikacin, gentamicin, and netilmicin remained unchanged (Table 1)."
EFM0010	s__Enterococcus_B faecium	efmM	-	-	AFC64318.1	-	-	-	Gene presence detected	core	gentamicin	-	wildtype	S	MIC <=32 mg/L	ECOFF	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	strong		"no gentamycin MIC change in knockout strain compared to WT, no evidence of contribution to intrinsic resistance. 21159796: the drop in trobamycin MIC in knockout strain is moderate, aac(6')-Ii seems to be the main determinant of trobamycin intrinsic resistance. Smaller decreases in kanamycin and tobramycin MIC [only 1-fold reduction] were observed for the _efmM strain (BM4682). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT854 (pBADΩefmM)] conferred on E. coli a 4-fold or greater increase in resistance to kanamycin and tobramycin; the MICs of amikacin, gentamicin, and netilmicin remained unchanged (Table 1)."
EFM0006	s__Enterococcus_B faecium	efmM	-	-	AFC64318.1	-	-	-	Gene presence detected	core	kanamycin A	-	wildtype	R	not applicable	not applicable	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	moderate	lacks evidence of the degree to which MIC is affected	"21159796: Smaller decreases in kanamycin and tobramycin MIC [only 1-fold reduction] were observed for the _efmM strain (BM4682). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT854 (pBADΩefmM)] conferred on E. coli a 4-fold or greater increase in resistance to kanamycin and tobramycin; the MICs of amikacin, gentamicin, and netilmicin remained unchanged (Table 1)."
EFM0008	s__Enterococcus_B faecium	efmM	-	-	AFC64318.1	-	-	-	Gene presence detected	core	netilmicin	-	wildtype	R	not available	ECOFF ID	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	weak	lacks evidence of the degree to which MIC is affected	"no netilmicin MIC change in knockout strain compared to WT, no evidence of contribution to intrinsic resistance. 21159796: Smaller decreases in kanamycin and tobramycin MIC [only 1-fold reduction] were observed for the _efmM strain (BM4682). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT854 (pBADΩefmM)] conferred on E. coli a 4-fold or greater increase in resistance to kanamycin and tobramycin; the MICs of amikacin, gentamicin, and netilmicin remained unchanged (Table 1)."
EFM0007	s__Enterococcus_B faecium	efmM	-	-	AFC64318.1	-	-	-	Gene presence detected	core	tobramycin	-	wildtype	R	not applicable	not applicable	"21159796, 8239603"	"ECO:0001091 knockout phenotypic evidence, ECO:0005027 genetic transformation evidence"	moderate	lacks evidence of the degree to which MIC is affected	"21159796: Smaller decreases in kanamycin and tobramycin MIC [only 1-fold reduction] were observed for the _efmM strain (BM4682). The lowest kanamycin and tobramycin MICs were observed for the double mutant E. faecium BM4683 [_aac(6_)-Ii/efmM]. The recombinant plasmid [pAT854 (pBADΩefmM)] conferred on E. coli a 4-fold or greater increase in resistance to kanamycin and tobramycin; the MICs of amikacin, gentamicin, and netilmicin remained unchanged (Table 1)."
EFM0011	s__Enterococcus_B faecium	msr(C)	msr(C)	-	AFC64749.1	-	ARO:3002819	-	Gene presence detected	core	azithromycin	-	wildtype	R	not applicable	not applicable	11120975	ECO:0001091 knockout phenotypic evidence	strong		"11120975: ""Disruption of msrC was associated with a two- to eightfold decrease in MICs of erythromycin azithromycin, tylosin, and quinupristin, suggesting that it may explain in part the apparent greater intrinsic resistance to macrolides of isolates of E. faecium"""
EFM0012	s__Enterococcus_B faecium	msr(C)	msr(C)	-	AFC64749.1	-	ARO:3002819	-	Gene presence detected	core	erythromycin	-	wildtype	R	not applicable	not applicable	11120975	ECO:0001091 knockout phenotypic evidence	strong		"11120975: ""Disruption of msrC was associated with a two- to eightfold decrease in MICs of erythromycin azithromycin, tylosin, and quinupristin, suggesting that it may explain in part the apparent greater intrinsic resistance to macrolides of isolates of E. faecium"""
EFM0014	s__Enterococcus_B faecium	msr(C)	msr(C)	-	AFC64749.1	-	ARO:3002819	-	Gene presence detected	core	quinupristin	-	wildtype	R	not applicable	not applicable	11120975	ECO:0001091 knockout phenotypic evidence	strong		"11120975: ""Disruption of msrC was associated with a two- to eightfold decrease in MICs of erythromycin azithromycin, tylosin, and quinupristin, suggesting that it may explain in part the apparent greater intrinsic resistance to macrolides of isolates of E. faecium"""
EFM0013	s__Enterococcus_B faecium	msr(C)	msr(C)	-	AFC64749.1	-	ARO:3002819	-	Gene presence detected	core	tylosin	-	wildtype	R	not applicable	not applicable	11120975	ECO:0001091 knockout phenotypic evidence	strong		"11120975: ""Disruption of msrC was associated with a two- to eightfold decrease in MICs of erythromycin azithromycin, tylosin, and quinupristin, suggesting that it may explain in part the apparent greater intrinsic resistance to macrolides of isolates of E. faecium"""
EFM0017	s__Enterococcus_B faecium	pbp5	-	-	AZV36500.1	-	-	-	Gene presence detected	core	cefepime	-	wildtype	R	not applicable	not applicable	19304851	ECO:0001091 knockout phenotypic evidence	strong		"the native pbp5 sequence in E. faecium is responsible for intrinsic cephalosporin resistance, mutations in this protein are known to alter beta-lactam resistance profiles, e.g. increase resistance to ampicillin. 19304851: ""Ceftriaxone MIC determinations (Table 2) indicated that Pbp5 was required for resistance to cephalosporins, as previously described (12)."" ""The only other cephalosporin tested that exhibited the heterogeneous resistance phenotype was cefepime, which, like ceftriaxone, has an oxyimino-aminothiazolyl 7-acyl side chain."""
EFM0015	s__Enterococcus_B faecium	pbp5	-	-	AZV36500.1	-	-	-	Gene presence detected	core	ceftobiprole	-	wildtype	S	not available	ECOFF ID	19917749	"ECO:0000024 protein-binding evidence, ECO:0000005 enzymatic activity assay evidence"	strong		"Previous work have showed that most ampicillin-resistant E. faecium clinical isolates were resistant to ceftobiprole, and that amino acid substitutions in PBP5 are necessary for high-level resistance. Therefore it is only the wildtype/unmutated PBP5 protein that is responsible for ceftobiprole susceptibility. 19917749: ""Ceftobiprole binds to unmutated PBP5 in Enterococcus faecium. It demonstrates bactericidal activity against penicillin-resistant strains. Ceftobiprole is effective against overproduced unmutated PBP5"""
EFM0016	s__Enterococcus_B faecium	pbp5	-	-	AZV36500.1	-	-	-	Gene presence detected	core	ceftriaxone	-	wildtype	R	not applicable	not applicable	"3734749, 19304851"	ECO:0001091 knockout phenotypic evidence	strong		"the native pbp5 sequence in E. faecium is responsible for intrinsic cephalosporin resistance, mutations in this protein are known to alter beta-lactam resistance profiles, e.g. increase resistance to ampicillin. 3734749: “cefotaxime showed a very low affinity for PBPs 4, 5 and 6 (which it saturated at a concentration of 2000 _g ml-1) and an affinity for the other PBPs that was close to that of benzylpenicillin.” 19304851: ""Ceftriaxone MIC determinations (Table 2) indicated that Pbp5 was required for resistance to cephalosporins, as previously described (12)."""
EFM0022	s__Enterococcus_B faecium	pbpA	-	-	AZV36123.1	-	-	-	Gene presence detected	core	ceftriaxone	-	wildtype	R	not applicable	not applicable	32041714	ECO:0001583 small interfering RNA knockdown evidence	strong		32041714: Antimicrobial susceptibility assays of pbpA knock down E. faecium 1141733 strain revealed that PbpA(2b) also promotes cephalosporin resistance in E. faecium (Table 2).
EFM0019	s__Enterococcus_B faecium	pbpF	-	-	AFC64635.1	-	-	-	Gene presence detected	core	cefepime	-	wildtype	R	not applicable	not applicable	19304851	ECO:0001091 knockout phenotypic evidence	strong		"Pbp5 is the main determinant of cephalosporin resistance in E. faecium but it needs to cooperate with the glycosyltransferase domain of specific class A PBPs (PbpF or PonA) for peptidoglycan polymerization in the presence of cephalosporins (i.e. resistance phenotype). 19304851: The deletion of either pbpF or ponA genes results in susceptibility to extended-spectrum cephalosporins, indicating that these class A PBPs are essential partners for PBP5 in maintaining resistance. The presence of either PbpF or PonA is necessary for the effective polymerization of peptidoglycan, which is vital for cell wall integrity and resistance "
EFM0018	s__Enterococcus_B faecium	pbpF	-	-	AFC64635.1	-	-	-	Gene presence detected	core	ceftriaxone	-	wildtype	R	not applicable	not applicable	19304851	ECO:0001091 knockout phenotypic evidence	strong		"Pbp5 is the main determinant of cephalosporin resistance in E. faecium but it needs to cooperate with the glycosyltransferase domain of specific class A PBPs (PbpF or PonA) for peptidoglycan polymerization in the presence of cephalosporins (i.e. resistance phenotype). 19304851: The deletion of either pbpF or ponA genes results in susceptibility to extended-spectrum cephalosporins, indicating that these class A PBPs are essential partners for PBP5 in maintaining resistance. The presence of either PbpF or PonA is necessary for the effective polymerization of peptidoglycan, which is vital for cell wall integrity and resistance "
EFM0021	s__Enterococcus_B faecium	ponA	-	-	AFC63082.1	-	-	-	Gene presence detected	core	cefepime	-	wildtype	R	not applicable	not applicable	19304851	ECO:0001091 knockout phenotypic evidence	strong		"Pbp5 is the main determinant of cephalosporin resistance in E. faecium but it needs to cooperate with the glycosyltransferase domain of specific class A PBPs (PbpF or PonA) for peptidoglycan polymerization in the presence of cephalosporins (i.e. resistance phenotype). 19304851: The deletion of either pbpF or ponA genes results in susceptibility to extended-spectrum cephalosporins, indicating that these class A PBPs are essential partners for PBP5 in maintaining resistance. The presence of either PbpF or PonA is necessary for the effective polymerization of peptidoglycan, which is vital for cell wall integrity and resistance "
EFM0020	s__Enterococcus_B faecium	ponA	-	-	AFC63082.1	-	-	-	Gene presence detected	core	ceftriaxone	-	wildtype	R	not applicable	not applicable	19304851	ECO:0001091 knockout phenotypic evidence	strong		"Pbp5 is the main determinant of cephalosporin resistance in E. faecium but it needs to cooperate with the glycosyltransferase domain of specific class A PBPs (PbpF or PonA) for peptidoglycan polymerization in the presence of cephalosporins (i.e. resistance phenotype). 19304851: The deletion of either pbpF or ponA genes results in susceptibility to extended-spectrum cephalosporins, indicating that these class A PBPs are essential partners for PBP5 in maintaining resistance. The presence of either PbpF or PonA is necessary for the effective polymerization of peptidoglycan, which is vital for cell wall integrity and resistance "