#Gene_accession	TypeGene	Mutation ID	Codon_pos	Ref_nuc	Ref_codon	Res_codon	Class	Phenotype	PMID	Mechanism of resistance	Notes	Required mutation	% abundance mutation required
penA_1_AB727726.1	AA	ALA-501	501	GCG	A	V,T,P		Cephalosporins	24982323,24982323,27432602
penA_1_AB727726.1	AA	GLY-542	542	GGC	G	S		Cephalosporins	20511367		Only statistically associated with enhanced resistance
penA_1_AB727726.1	AA	PRO-551	551	CCG	P	S,L		Cephalosporins	20511367,20511367		Only statistically associated with enhanced resistance
penA_1_AB727726.1	AA	ALA-311	311	GCA	A	V		Cephalosporins	24982323		Mutation indicates mosaic penA gene
penA_1_AB727726.1	AA	ILE-312	312	ATC	I	M		Cephalosporins	24982323		Mutation indicates mosaic penA gene
penA_1_AB727726.1	AA	VAL-316	316	GTG	V	T		Cephalosporins	24982323		Mutation indicates mosaic penA gene
penA_1_AB727726.1	AA	THR-483	483	ACC	T	S		Cephalosporins	24982323		Mutation indicates mosaic penA gene
penA_1_AB727726.1	AA	ASN-512	512	AAC	N	Y		Cephalosporins	24982323		Mutation indicates mosaic penA gene
penA_1_AB727726.1	AA	GLY-545	545	GGC	G	S		Cephalosporins	24982323		Mutation indicates mosaic penA gene
penA_1_AB727726.1	AA	GLY-546	546	GGC	G	S		Cephalosporins	24982323		Mutation indicates mosaic penA gene
mtrR-promoter-size-66bp_1_CP012026.1	AA	GLY-45	45	GGC	G	D	Beta-lactam, Macrolide, Tetracycline	Penicillin,Tetracycline,Cephalosporins,Macrolide	7773394
pilQ_1_AP023073.1	AA	GLU-666	666	GAA	E	K	Beta-lactam, Macrolide, Quinolone	Penicillin,Tetracycline,Ciprofloxacin	24982323		Only effective in the presents of the mtrR and penB (porB mutation) resistance determinants
rpsJ_1_AE004969.1	AA	VAL-57	57	GTG	V	M,L,Q	Tetracycline	Tetracycline	16189114,16189114,16189114
rpsE_1_AP023075.1	AA	LYS-28	28	AAA	K	E	Aminoglycoside	Spectinomycin	23183436		Mutation seen together with V27 deletion
rpsE_1_AP023075.1	AA	THR-24	24	ACC	T	P	Aminoglycoside	Spectinomycin	23183436		Low-level resistance
gyrA_1_CP034026.1	AA	SER-91	91	TCC	S	F	Quinolone	Fluoroquinolone	12529019		Mutation often seen together with D95N/G mutation (PMID: 23347339)
gyrA_1_CP034026.1	AA	ASP-95	95	GAC	D	N,G	Quinolone	Fluoroquinolone	12529019,12529019		Mutation often seen together with S91F mutation (PMID: 23347339)
parC_1_AE004969.1	AA	GLU-91	91	GAG	E	G,Q,K	Quinolone	Fluoroquinolone	24982323,24982323,24982323	High-level resistance when additional to gyrA S91P and gyrA D95N/G	gyrA_1_CP034026.1_D95N.G,gyrA_1_CP034026.1_S91P
parC_1_AE004969.1	AA	SER-88	88	TCC	S	P	Quinolone	Fluoroquinolone	24982323		High-level resistance when additional to gyrA S91P and gyrA D95N/G	gyrA_1_CP034026.1_D95N.G,gyrA_1_CP034026.1_S91P
porB_1_AE004969.1	AA	GLY-120	120	GGC	G	D	Beta-lactam, Tetracycline	Penicillin, Tetracycline,Cephalosporins	12183233		Solo mutation gives partial resistance	porB_1_AE004969.1_A121D
porB_1_AE004969.1	AA	ALA-121	121	GCC	A	D	Beta-lactam, Tetracycline	Penicillin, Tetracycline,Cephalosporins	12183233		Solo muttaion gives partial resistance	porB_1_AE004969.1_G120D
porB_1_AE004969.1	AA	GLY-120	120	GGC	G	R	Beta-lactam, Tetracycline	Penicillin, Tetracycline,Cephalosporins	12183233			porB_1_AE004969.1_A121H
porB_1_AE004969.1	AA	ALA-121	121	GCC	A	H	Beta-lactam, Tetracycline	Penicillin, Tetracycline,Cephalosporins	12183233			porB_1_AE004969.1_G120R
porB_1_AE004969.1	AA	GLY-120	120	GGC	G	P	Beta-lactam, Tetracycline	Penicillin, Tetracycline,Cephalosporins	12183233			porB_1_AE004969.1_A121P
porB_1_AE004969.1	AA	ALA-121	121	GCC	A	P	Beta-lactam, Tetracycline	Penicillin, Tetracycline,Cephalosporins	12183233			porB_1_AE004969.1_G120P
porB_1_AE004969.1	AA	GLY-120	120	GGC	G	K	Beta-lactam, Tetracycline	Penicillin, Tetracycline,Cephalosporins	12183233
ponA_1_AB727680.1	AA	LEU-421	421	CTG	L	P	Beta-lactam	Penicillin	11850260		Mediates transformation of intermediate-level penicillin-resistant transformants to high-level penicillin resistance
16S-rRNA_1_CP043871.1	NUC	C-1192	1192	C	C	T	Aminoglycoside	Spectinomycin	24982323
23S-rRNA-a1_1_AE004969.1	NUC	C-2604	2604	C	C	T	Macrolide	Macrolide	12183262		C2611T mutation (Escherichia coli numbering)
23S-rRNA-a2_1_AE004969.1	NUC	C-2603	2603	C	C	T	Macrolide	Macrolide	12183262		C2611T mutation (Escherichia coli numbering)
23S-rRNA-a3_1_AE004969.1	NUC	C-2603	2603	C	C	T	Macrolide	Macrolide	12183262		C2611T mutation (Escherichia coli numbering)
23S-rRNA-a4_1_AE004969.1	NUC	C-2610	2610	C	C	T	Macrolide	Macrolide	12183262		C2611T mutation (Escherichia coli numbering)
23S-rRNA-a1_1_AE004969.1	NUC	A-2051	2051	A	A	G	Macrolide	Macrolide	12183262,20585125		A2058G mutation (Escherichia coli numbering)
23S-rRNA-a2_1_AE004969.1	NUC	A-2050	2050	A	A	G	Macrolide	Macrolide	12183262,20585125		A2058G mutation (Escherichia coli numbering)
23S-rRNA-a3_1_AE004969.1	NUC	A-2050	2050	A	A	G	Macrolide	Macrolide	12183262,20585125		A2058G mutation (Escherichia coli numbering)
23S-rRNA-a4_1_AE004969.1	NUC	A-2054	2054	A	A	G	Macrolide	Macrolide	12183262,20585125		A2058G mutation (Escherichia coli numbering)
mtrC-promoter-size-174bp_1_U14993.1	AA	CYS--120	-120	C	C	T	Beta-lactam, Macrolide, Tetracycline, Rifamycin	Penicillin, Tetracycline, Cephalosporins, Macrolide, Rifampicin, Erythromycin	21933917		-10 hexamer (TATAAC->TATAAT) is created as an alternative transcription start point
macAB-promoter-size-225bp_1_AE004969.1	AA	GLY--48	-48	G	G	T	Macrolide	Macrolide	16162665
#Indels
#Gene_accession	TypeGene	Mutation ID	Codon_pos	Ref_nuc	Ref_codon	Res_codon	Class	Phenotype	PMID	Mechanism of resistance	Notes	Required mutation	% abundance mutation required
#penA_1_AB727726.1	AA		346	-	ins	D		Cephalosporins	24982323		Often denoted 'D345a' or 'D345 insertion'
#rpsE_1_AP023075.1	AA	VAL-27	27	GTT	V	del	Aminoglycoside	Spectinomycin	23183436
penA_1_AB727726.1	NUC		1035	-	ins	GAT,GAC		Cephalosporins	24982323,24982323		Often denoted 'D345a' or 'D345 insertion'
mtrR-promoter-size-66bp_1_CP012026.1	NUC		-57	-	del	A	Beta-lactam, Macrolide, Tetracycline	Penicillin, Tetracycline, Cephalosporins, Macrolide	24982323		Deletion in 13bp inverted repeat
rpsE_1_AP023075.1	NUC		78	-	del	GTT	Aminoglycoside	Spectinomycin	23183436
