# ResFinder phenotype results.
# Sample: BC10.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	No resistance	0	
tobramycin	aminoglycoside	No resistance	0	
streptomycin	aminoglycoside	No resistance	0	
amikacin	aminoglycoside	No resistance	0	
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaZ (blaZ_GQ900471)
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	Resistant	3	blaZ (blaZ_GQ900471)
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	No resistance	0	
meropenem	beta-lactam	No resistance	0	
piperacillin	beta-lactam	Resistant	3	blaZ (blaZ_GQ900471)
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	Resistant	3	blaZ (blaZ_GQ900471)
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	No resistance	0	
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC11.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(6')-Ib (aac(6')-Ib_M21682)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib (aac(6')-Ib_M21682)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ampicillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cefepime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ceftazidime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
piperacillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
unknown beta-lactam	beta-lactam	Resistant	1	blaTEM-234 (blaTEM-234_MH243353), blaTEM-219 (blaTEM-219_KM114268), blaTEM-217 (blaTEM-217_HG934763), blaTEM-198 (blaTEM-198_AB700703), blaTEM-104 (blaTEM-104_AF516719)
aztreonam	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC12.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_X90856), rmtB (rmtB_AB103506)
tobramycin	aminoglycoside	Resistant	2	rmtB (rmtB_AB103506)
streptomycin	aminoglycoside	Resistant	1	aadA10 (aadA10_AM087405), ant(6)-Ia (ant(6)-Ia_AF330699)
amikacin	aminoglycoside	Resistant	2	rmtB (rmtB_AB103506), aph(3')-III (aph(3')-III_M26832)
isepamicin	aminoglycoside	Resistant	2	rmtB (rmtB_AB103506), aph(3')-III (aph(3')-III_M26832)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_X90856), rmtB (rmtB_AB103506), aph(3')-III (aph(3')-III_M26832)
neomycin	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_X90856), aph(3')-III (aph(3')-III_M26832)
lividomycin	aminoglycoside	Resistant	2	aph(3')-III (aph(3')-III_M26832)
paromomycin	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_X90856), aph(3')-III (aph(3')-III_M26832)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_X90856), aph(3')-III (aph(3')-III_M26832)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_X90856)
butirosin	aminoglycoside	Resistant	2	aph(3')-III (aph(3')-III_M26832)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	Resistant	2	rmtB (rmtB_AB103506)
arbekacin	aminoglycoside	Resistant	2	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	1	aadA10 (aadA10_AM087405)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	qnrVC1 (qnrVC1_EU436855), crpP (crpP_HM560971)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaPAO (blaPAO_AY083592), blaOXA-395 (blaOXA-395_AY306133), mecA (mecA_BX571856), blaZ (blaZ_NC_013944), blaZ (blaZ_NZ_CUGR01000082), blaZ (blaZ_NZ_JVBT01000063), blaZ (blaZ_JBTH01000015), blaZ (blaZ_AJ400722), blaNDM-1 (blaNDM-1_FN396876)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
ampicillin	beta-lactam	Resistant	3	blaPAO (blaPAO_AY083592), blaOXA-395 (blaOXA-395_AY306133), mecA (mecA_BX571856), blaZ (blaZ_NC_013944), blaZ (blaZ_NZ_CUGR01000082), blaZ (blaZ_NZ_JVBT01000063), blaZ (blaZ_JBTH01000015), blaZ (blaZ_AJ400722), blaNDM-1 (blaNDM-1_FN396876)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
cefepime	beta-lactam	Resistant	3	blaPAO (blaPAO_AY083592), mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
cefixime	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
cefoxitin	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
ceftazidime	beta-lactam	Resistant	3	blaPAO (blaPAO_AY083592), mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
ertapenem	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
imipenem	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
meropenem	beta-lactam	Resistant	3	blaOXA-395 (blaOXA-395_AY306133), mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
piperacillin	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaZ (blaZ_NC_013944), blaZ (blaZ_NZ_CUGR01000082), blaZ (blaZ_NZ_JVBT01000063), blaZ (blaZ_JBTH01000015), blaZ (blaZ_AJ400722), blaNDM-1 (blaNDM-1_FN396876)
piperacillin+tazobactam	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaNDM-1 (blaNDM-1_FN396876)
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	Resistant	1	blaZ (blaZ_NC_013944), blaZ (blaZ_NZ_CUGR01000082), blaZ (blaZ_NZ_JVBT01000063), blaZ (blaZ_JBTH01000015), blaZ (blaZ_AJ400722)
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	Resistant	2	fosA (fosA_ACWU01000146)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(A) (msr(A)_X52085), mph(C) (mph(C)_AF167161)
azithromycin	macrolide	Resistant	2	msr(A) (msr(A)_X52085)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(C) (mph(C)_AF167161)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	msr(A) (msr(A)_X52085), mph(C) (mph(C)_AF167161)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140), tet(K) (tet(K)_U38656)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140), tet(K) (tet(K)_U38656)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	2	msr(A) (msr(A)_X52085)
pristinamycin ia	streptogramin b	Resistant	2	msr(A) (msr(A)_X52085)
virginiamycin s	streptogramin b	Resistant	2	msr(A) (msr(A)_X52085)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	catB7 (catB7_AF036933)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	Resistant	1	fusB (fusB_AY373761)
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC13.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	1	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876), blaTEM-1D (blaTEM-1D_AF188200)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ampicillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876), blaTEM-1D (blaTEM-1D_AF188200)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefepime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefixime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefoxitin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ceftazidime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ertapenem	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
imipenem	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876), blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876), blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876), blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
unknown beta-lactam	beta-lactam	Resistant	3	blaADC-25 (blaADC-25_EF016355), blaOXA-66 (blaOXA-66_AY750909)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC14.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	2	aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550), aadA1 (aadA1_JQ414041)
amikacin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
neomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
lividomycin	aminoglycoside	Resistant	2	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA1 (aadA1_JQ414041)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaADC-25 (blaADC-25_EF016355), blaOXA-98 (blaOXA-98_EU255288), blaOXA-66 (blaOXA-66_AY750909), blaOXA-72 (blaOXA-72_AY739646)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	catB8 (catB8_AF227506)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC15.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(3)-I (aac(3)-I_AJ877225)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_CP000971), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA1 (aadA1_JX185132), aadA1 (aadA1_JQ480156), aadA1 (aadA1_JQ414041)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	Resistant	2	aac(3)-I (aac(3)-I_AJ877225)
fortimicin	aminoglycoside	Resistant	2	aac(3)-I (aac(3)-I_AJ877225)
spectinomycin	aminocyclitol	Resistant	1	aadA1 (aadA1_JX185132), aadA1 (aadA1_JQ480156), aadA1 (aadA1_JQ414041)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaOXA-69 (blaOXA-69_AY859527), blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ampicillin	beta-lactam	Resistant	3	blaOXA-69 (blaOXA-69_AY859527), blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cefepime	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ceftazidime	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964), blaKPC-2 (blaKPC-2_AY034847)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964), blaKPC-2 (blaKPC-2_AY034847)
piperacillin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
unknown beta-lactam	beta-lactam	Resistant	1	blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	1	blaCTX-M-27 (blaCTX-M-27_AY156923), blaCTX-M-174 (blaCTX-M-174_KT997886), blaCTX-M-98 (blaCTX-M-98_HM755448)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_AJ746361), sul1 (sul1_AY963803), sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	1	tet(A) (tet(A)_AF534183)
doxycycline	tetracycline	Resistant	1	tet(A) (tet(A)_AF534183)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC16.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555), aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-15 (blaCTX-M-15_AY044436), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-15 (blaCTX-M-15_AY044436), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
cefepime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-15 (blaCTX-M-15_AY044436), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
cefixime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-15 (blaCTX-M-15_AY044436), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-15 (blaCTX-M-15_AY044436), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
piperacillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-15 (blaCTX-M-15_AY044436), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125)
aztreonam	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-15 (blaCTX-M-15_AY044436), blaKPC-3 (blaKPC-3_HM769262)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-15 (blaCTX-M-15_AY044436), blaKPC-3 (blaKPC-3_HM769262)
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaCTX-M-15 (blaCTX-M-15_AY044436)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708), dfrA14 (dfrA14_KF921535)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	catB3 (catB3_AJ009818), catB3 (catB3_U13880), OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC17.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	aac(3)-IId (aac(3)-IId_EU022314), rmtB (rmtB_AB103506), ant(2'')-Ia (ant(2'')-Ia_X04555), aac(3)-IIa (aac(3)-IIa_CP023555)
tobramycin	aminoglycoside	Resistant	3	aac(3)-IId (aac(3)-IId_EU022314), rmtB (rmtB_AB103506), ant(2'')-Ia (ant(2'')-Ia_X04555), aac(3)-IIa (aac(3)-IIa_CP023555), aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967), aadA1 (aadA1_JQ414041)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	aac(3)-IId (aac(3)-IId_EU022314), rmtB (rmtB_AB103506)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967), aadA1 (aadA1_JQ414041)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	2	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	2	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-14 (blaCTX-M-14_AF252622), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-14 (blaCTX-M-14_AF252622), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-1 (blaOXA-1_HQ170510)
cefepime	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-14 (blaCTX-M-14_AF252622), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
cefixime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-14 (blaCTX-M-14_AF252622), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaCTX-M-15 (blaCTX-M-15_AY044436)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569)
ceftazidime	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-14 (blaCTX-M-14_AF252622), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaCTX-M-15 (blaCTX-M-15_AY044436)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
piperacillin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-14 (blaCTX-M-14_AF252622), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaOXA-1 (blaOXA-1_HQ170510)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125)
aztreonam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaCTX-M-15 (blaCTX-M-15_AY044436)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569), blaCTX-M-15 (blaCTX-M-15_AY044436)
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaCTX-M-15 (blaCTX-M-15_AY044436)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaVEB-1 (blaVEB-1_DQ393569)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708), dfrA14 (dfrA14_KF921535)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140), tet(A) (tet(A)_AF534183)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140), tet(A) (tet(A)_AF534183)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	cmlA1 (cmlA1_M64556), catB3 (catB3_AJ009818), catB3 (catB3_U13880), OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	Resistant	3	ARR-2 (ARR-2_HQ141279)
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC18.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	No resistance	0	
tobramycin	aminoglycoside	Resistant	2	aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	No resistance	0	
amikacin	aminoglycoside	Resistant	2	aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_CP006832)
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	2	crpP (crpP_HM560971)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666065), blaOXA-50 (blaOXA-50_AY306130), blaCARB-2 (blaCARB-2_M69058), blaVIM-4 (blaVIM-4_EU581706)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
ampicillin	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666065), blaOXA-50 (blaOXA-50_AY306130), blaCARB-2 (blaCARB-2_M69058), blaVIM-4 (blaVIM-4_EU581706)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
cefepime	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666065), blaVIM-4 (blaVIM-4_EU581706)
cefixime	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
cefotaxime	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
cefoxitin	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
ceftazidime	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666065), blaVIM-4 (blaVIM-4_EU581706)
ertapenem	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
imipenem	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
meropenem	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
piperacillin	beta-lactam	Resistant	3	blaCARB-2 (blaCARB-2_M69058), blaVIM-4 (blaVIM-4_EU581706)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaVIM-4 (blaVIM-4_EU581706)
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	Resistant	2	fosA (fosA_ACWU01000146)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	catB7 (catB7_AF036933)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	Resistant	3	ARR-7 (ARR-7_FN397623)
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC19.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaOXA-66 (blaOXA-66_AY750909), blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	catA1 (catA1_V00622)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC1.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	No resistance	0	
tobramycin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
streptomycin	aminoglycoside	Resistant	3	aadA5 (aadA5_AF137361)
amikacin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA5 (aadA5_AF137361)
fluoroquinolone	quinolone	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
ciprofloxacin	quinolone	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaOXA-1 (blaOXA-1_HQ170510)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaOXA-1 (blaOXA-1_HQ170510)
cefepime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	No resistance	0	
meropenem	beta-lactam	No resistance	0	
piperacillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaOXA-1 (blaOXA-1_HQ170510)
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	Resistant	3	dfrA17 (dfrA17_FJ460238)
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	1	catB3 (catB3_AJ009818), catB3 (catB3_U13880)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC21.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	2	aac(6')-Ii (aac(6')-Ii_L12710), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
tobramycin	aminoglycoside	Resistant	2	aac(6')-Ii (aac(6')-Ii_L12710), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
streptomycin	aminoglycoside	Resistant	3	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), ant(6)-Ia (ant(6)-Ia_AF330699)
amikacin	aminoglycoside	Resistant	3	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(3')-III (aph(3')-III_M26832)
isepamicin	aminoglycoside	Resistant	3	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(3')-III (aph(3')-III_M26832)
dibekacin	aminoglycoside	Resistant	2	aac(6')-Ii (aac(6')-Ii_L12710), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
kanamycin	aminoglycoside	Resistant	3	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(3')-III (aph(3')-III_M26832)
neomycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832)
lividomycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832)
paromomycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	2	aac(6')-Ii (aac(6')-Ii_L12710), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	Resistant	2	aac(6')-Ii (aac(6')-Ii_L12710)
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	Resistant	1	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	No resistance	0	
meropenem	beta-lactam	No resistance	0	
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	No resistance	0	
trimethoprim	folate pathway antagonist	Resistant	3	dfrG (dfrG_AB205645)
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	Resistant	2	VanHMX (VanHMX_FJ349556), VanHAX (VanHAX_M97297)
teicoplanin	glycopeptide	Resistant	2	VanHMX (VanHMX_FJ349556), VanHAX (VanHAX_M97297)
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	Resistant	2	erm(B) (erm(B)_X72021), erm(B) (erm(B)_JN899585)
clindamycin	lincosamide	Resistant	2	erm(B) (erm(B)_X72021), erm(B) (erm(B)_JN899585)
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	2	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_X72021), erm(B) (erm(B)_JN899585)
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	2	msr(C) (msr(C)_AY004350)
tetracycline	tetracycline	Resistant	2	tet(M) (tet(M)_EU182585), tet(L) (tet(L)_D00006), tet(L) (tet(L)_M11036), tet(L) (tet(L)_M29725)
doxycycline	tetracycline	Resistant	2	tet(M) (tet(M)_EU182585), tet(L) (tet(L)_D00006), tet(L) (tet(L)_M11036), tet(L) (tet(L)_M29725)
minocycline	tetracycline	Resistant	2	tet(M) (tet(M)_EU182585)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	2	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_X72021), erm(B) (erm(B)_JN899585)
pristinamycin ia	streptogramin b	Resistant	2	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_X72021), erm(B) (erm(B)_JN899585)
virginiamycin s	streptogramin b	Resistant	2	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_X72021), erm(B) (erm(B)_JN899585)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC23.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	aac(3)-Ia (aac(3)-Ia_X15852), armA (armA_AY220558)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	2	aadA1 (aadA1_JX185132), aadA1 (aadA1_JQ414041)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VI (aph(3')-VI_KC170992)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	Resistant	2	aac(3)-Ia (aac(3)-Ia_X15852)
fortimicin	aminoglycoside	Resistant	2	aac(3)-Ia (aac(3)-Ia_X15852)
spectinomycin	aminocyclitol	Resistant	2	aadA1 (aadA1_JX185132), aadA1 (aadA1_JQ414041)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaOXA-69 (blaOXA-69_AY859527), blaNDM-1 (blaNDM-1_FN396876)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ampicillin	beta-lactam	Resistant	3	blaOXA-69 (blaOXA-69_AY859527), blaNDM-1 (blaNDM-1_FN396876)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefepime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefixime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefoxitin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ceftazidime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ertapenem	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
imipenem	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876), blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876), blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
unknown beta-lactam	beta-lactam	Resistant	1	blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC24.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	2	aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aadA6 (aadA6_AF140629)
amikacin	aminoglycoside	Resistant	3	aph(3')-VIa (aph(3')-VIa_X07753), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	3	aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	3	aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	Resistant	3	aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	Resistant	2	aph(3')-IIb (aph(3')-IIb_CP006832)
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	3	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA6 (aadA6_AF140629)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	2	crpP (crpP_HM560971)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666073), blaPAO (blaPAO_FJ666065), blaVIM-2 (blaVIM-2_AF302086), blaOXA-10 (blaOXA-10_J03427)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
ampicillin	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666073), blaPAO (blaPAO_FJ666065), blaVIM-2 (blaVIM-2_AF302086), blaOXA-10 (blaOXA-10_J03427)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
cefepime	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666073), blaPAO (blaPAO_FJ666065), blaVIM-2 (blaVIM-2_AF302086)
cefixime	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
cefotaxime	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
cefoxitin	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
ceftazidime	beta-lactam	Resistant	3	blaPAO (blaPAO_FJ666073), blaPAO (blaPAO_FJ666065), blaVIM-2 (blaVIM-2_AF302086)
ertapenem	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
imipenem	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
meropenem	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086)
piperacillin	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086), blaOXA-10 (blaOXA-10_J03427)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaVIM-2 (blaVIM-2_AF302086), blaOXA-10 (blaOXA-10_J03427)
unknown beta-lactam	beta-lactam	Resistant	2	blaOXA-488 (blaOXA-488_CP017969)
aztreonam	beta-lactam	Resistant	3	blaOXA-10 (blaOXA-10_J03427)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	Resistant	2	fosA (fosA_ACWU01000146)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	catB7 (catB7_AF036933)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC25.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555), aadD (aadD_M19465), aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aadD (aadD_M19465), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
cefepime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
cefixime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
piperacillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125)
aztreonam	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262)
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708), dfrA14 (dfrA14_KF921535)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	Resistant	3	vga(A)LC (vga(A)LC_DQ823382), erm(C) (erm(C)_M13761)
clindamycin	lincosamide	Resistant	3	vga(A)LC (vga(A)LC_DQ823382), erm(C) (erm(C)_M13761)
dalfopristin	streptogramin a	Resistant	1	vga(A)LC (vga(A)LC_DQ823382)
pristinamycin iia	streptogramin a	Resistant	1	vga(A)LC (vga(A)LC_DQ823382)
virginiamycin m	streptogramin a	Resistant	1	vga(A)LC (vga(A)LC_DQ823382)
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	Resistant	1	vga(A)LC (vga(A)LC_DQ823382)
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251), erm(C) (erm(C)_M13761)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	erm(C) (erm(C)_M13761)
pristinamycin ia	streptogramin b	Resistant	3	erm(C) (erm(C)_M13761)
virginiamycin s	streptogramin b	Resistant	3	erm(C) (erm(C)_M13761)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	catA1 (catA1_V00622), catB3 (catB3_AJ009818), catB3 (catB3_U13880), OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC26.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	No resistance	0	
tobramycin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
streptomycin	aminoglycoside	No resistance	0	
amikacin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
ciprofloxacin	quinolone	Resistant	3	aac(6')-Ib-cr (aac(6')-Ib-cr_DQ303918)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaOXA-1 (blaOXA-1_HQ170510)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaOXA-1 (blaOXA-1_HQ170510)
cefepime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	No resistance	0	
meropenem	beta-lactam	No resistance	0	
piperacillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaOXA-1 (blaOXA-1_HQ170510)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaOXA-1 (blaOXA-1_HQ170510)
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436)
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	No resistance	0	
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	1	catB3 (catB3_AJ009818), catB3 (catB3_U13880)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC27.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(6')-Ib (aac(6')-Ib_M21682)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib (aac(6')-Ib_M21682)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ampicillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cefepime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ceftazidime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
piperacillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
unknown beta-lactam	beta-lactam	Resistant	1	blaTEM-234 (blaTEM-234_MH243353), blaTEM-219 (blaTEM-219_KM114268), blaTEM-217 (blaTEM-217_HG934763), blaTEM-198 (blaTEM-198_AB700703), blaTEM-104 (blaTEM-104_AF516719)
aztreonam	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	2	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC28.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaADC-25 (blaADC-25_EF016355), blaOXA-66 (blaOXA-66_AY750909)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC29.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaOXA-66 (blaOXA-66_AY750909), blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC30.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	2	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cefepime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
piperacillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125)
aztreonam	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC31.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	2	aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550), aadA1 (aadA1_JQ414041)
amikacin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
neomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
lividomycin	aminoglycoside	Resistant	2	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA1 (aadA1_JQ414041)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaADC-25 (blaADC-25_EF016355), blaOXA-98 (blaOXA-98_EU255288), blaOXA-66 (blaOXA-66_AY750909), blaOXA-72 (blaOXA-72_AY739646)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	catB8 (catB8_AF227506)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC32.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(2'')-Ia (aph(2'')-Ia_AP009486), aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(2'')-Ia (aph(2'')-Ia_AP009486)
streptomycin	aminoglycoside	Resistant	3	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), ant(6)-Ia (ant(6)-Ia_AF330699), aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(2'')-Ia (aph(2'')-Ia_AP009486), aph(3')-III (aph(3')-III_M26832), aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(3')-III (aph(3')-III_M26832)
dibekacin	aminoglycoside	Resistant	1	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
kanamycin	aminoglycoside	Resistant	3	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(2'')-Ia (aph(2'')-Ia_AP009486), aph(3')-III (aph(3')-III_M26832), aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832), aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832)
paromomycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832), aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832), aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	3	aph(3')-III (aph(3')-III_M26832), aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	Resistant	1	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaOXA-66 (blaOXA-66_AY750909), blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	Resistant	2	fosB (fosB_X54227)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391), mph(C) (mph(C)_AF167161), msr(A) (msr(A)_AB013298)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), msr(A) (msr(A)_AB013298)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	2	mph(C) (mph(C)_AF167161)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	2	mph(C) (mph(C)_AF167161), msr(A) (msr(A)_AB013298)
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518), msr(A) (msr(A)_AB013298)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518), msr(A) (msr(A)_AB013298)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518), msr(A) (msr(A)_AB013298)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	catA1 (catA1_V00622)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	Resistant	1	fusB (fusB_AY373761)
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC33.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaOXA-66 (blaOXA-66_AY750909), blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC34.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555), aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510), blaCTX-M-15 (blaCTX-M-15_AY044436)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510), blaCTX-M-15 (blaCTX-M-15_AY044436)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
cefepime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510), blaCTX-M-15 (blaCTX-M-15_AY044436)
cefixime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaCTX-M-15 (blaCTX-M-15_AY044436)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaCTX-M-15 (blaCTX-M-15_AY044436)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262)
piperacillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510), blaCTX-M-15 (blaCTX-M-15_AY044436)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-1 (blaNDM-1_FN396876), blaKPC-3 (blaKPC-3_HM769262), blaOXA-1 (blaOXA-1_HQ170510)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125)
aztreonam	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaCTX-M-15 (blaCTX-M-15_AY044436)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262), blaCTX-M-15 (blaCTX-M-15_AY044436)
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaCTX-M-15 (blaCTX-M-15_AY044436)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	catB3 (catB3_AJ009818), catB3 (catB3_U13880), OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC35.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	2	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aac(6')-Ii (aac(6')-Ii_L12710)
tobramycin	aminoglycoside	Resistant	2	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aac(6')-Ii (aac(6')-Ii_L12710)
streptomycin	aminoglycoside	Resistant	3	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), ant(6)-Ia (ant(6)-Ia_AF330699)
amikacin	aminoglycoside	Resistant	2	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(3')-III (aph(3')-III_M26832)
isepamicin	aminoglycoside	Resistant	2	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(3')-III (aph(3')-III_M26832)
dibekacin	aminoglycoside	Resistant	2	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aac(6')-Ii (aac(6')-Ii_L12710)
kanamycin	aminoglycoside	Resistant	2	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aph(3')-III (aph(3')-III_M26832)
neomycin	aminoglycoside	Resistant	2	aph(3')-III (aph(3')-III_M26832)
lividomycin	aminoglycoside	Resistant	2	aph(3')-III (aph(3')-III_M26832)
paromomycin	aminoglycoside	Resistant	2	aph(3')-III (aph(3')-III_M26832)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-III (aph(3')-III_M26832)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-III (aph(3')-III_M26832)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	2	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771), aac(6')-Ii (aac(6')-Ii_L12710)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	Resistant	2	aac(6')-Ii (aac(6')-Ii_L12710)
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	Resistant	1	aac(6')-aph(2'') (aac(6')-aph(2'')_M13771)
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	No resistance	0	
meropenem	beta-lactam	No resistance	0	
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	No resistance	0	
trimethoprim	folate pathway antagonist	Resistant	3	dfrG (dfrG_AB205645)
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	Resistant	2	VanHMX (VanHMX_FJ349556), VanHAX (VanHAX_M97297)
teicoplanin	glycopeptide	Resistant	2	VanHMX (VanHMX_FJ349556), VanHAX (VanHAX_M97297)
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	Resistant	3	erm(B) (erm(B)_AF299292)
clindamycin	lincosamide	Resistant	3	erm(B) (erm(B)_AF299292)
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_AF299292)
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	2	msr(C) (msr(C)_AY004350)
tetracycline	tetracycline	Resistant	2	tet(M) (tet(M)_EU182585), tet(L) (tet(L)_D00006), tet(L) (tet(L)_M11036), tet(L) (tet(L)_M29725)
doxycycline	tetracycline	Resistant	2	tet(M) (tet(M)_EU182585), tet(L) (tet(L)_D00006), tet(L) (tet(L)_M11036), tet(L) (tet(L)_M29725)
minocycline	tetracycline	Resistant	2	tet(M) (tet(M)_EU182585)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_AF299292)
pristinamycin ia	streptogramin b	Resistant	3	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_AF299292)
virginiamycin s	streptogramin b	Resistant	3	msr(C) (msr(C)_AY004350), erm(B) (erm(B)_AF299292)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC36.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaOXA-66 (blaOXA-66_AY750909), blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_U12338)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC37.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(6')-Ib (aac(6')-Ib_M21682)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967), aadA1 (aadA1_JQ480156)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib (aac(6')-Ib_M21682)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967), aadA1 (aadA1_JQ480156)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	2	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	2	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaTEM-1A (blaTEM-1A_HM749966), blaKPC-2 (blaKPC-2_AY034847), blaOXA-232 (blaOXA-232_JX423831), blaNDM-5 (blaNDM-5_JN104597), blaOXA-9 (blaOXA-9_KQ089875)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaOXA-232 (blaOXA-232_JX423831), blaNDM-5 (blaNDM-5_JN104597)
ampicillin	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaTEM-1A (blaTEM-1A_HM749966), blaKPC-2 (blaKPC-2_AY034847), blaOXA-232 (blaOXA-232_JX423831), blaNDM-5 (blaNDM-5_JN104597), blaOXA-9 (blaOXA-9_KQ089875)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaOXA-232 (blaOXA-232_JX423831), blaNDM-5 (blaNDM-5_JN104597)
cefepime	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaNDM-5 (blaNDM-5_JN104597)
cefixime	beta-lactam	Resistant	3	blaNDM-5 (blaNDM-5_JN104597)
cefotaxime	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaNDM-5 (blaNDM-5_JN104597)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-5 (blaNDM-5_JN104597)
ceftazidime	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaNDM-5 (blaNDM-5_JN104597)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-5 (blaNDM-5_JN104597)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-5 (blaNDM-5_JN104597)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaNDM-5 (blaNDM-5_JN104597)
piperacillin	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaTEM-1A (blaTEM-1A_HM749966), blaKPC-2 (blaKPC-2_AY034847), blaOXA-232 (blaOXA-232_JX423831), blaNDM-5 (blaNDM-5_JN104597)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaOXA-232 (blaOXA-232_JX423831), blaNDM-5 (blaNDM-5_JN104597)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125), blaSHV-28 (blaSHV-28_AF299299)
aztreonam	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-5 (blaNDM-5_JN104597)
ticarcillin	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622), blaTEM-1A (blaTEM-1A_HM749966), blaKPC-2 (blaKPC-2_AY034847)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaSHV-106 (blaSHV-106_AM922307), blaCTX-M-14 (blaCTX-M-14_AF252622)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cephalothin	beta-lactam	Resistant	2	blaTEM-1A (blaTEM-1A_HM749966)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708)
fosfomycin	fosfomycin	Resistant	2	fosA (fosA_ACZD01000244)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	Resistant	2	erm(B) (erm(B)_JN899585)
clindamycin	lincosamide	Resistant	2	erm(B) (erm(B)_JN899585)
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	2	mph(A) (mph(A)_D16251), erm(B) (erm(B)_JN899585)
azithromycin	macrolide	Resistant	1	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	1	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	1	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	2	erm(B) (erm(B)_JN899585)
pristinamycin ia	streptogramin b	Resistant	2	erm(B) (erm(B)_JN899585)
virginiamycin s	streptogramin b	Resistant	2	erm(B) (erm(B)_JN899585)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC38.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(6')-Ib (aac(6')-Ib_M21682)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib (aac(6')-Ib_M21682)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ampicillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cefepime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
ceftazidime	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
piperacillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
unknown beta-lactam	beta-lactam	Resistant	1	blaTEM-234 (blaTEM-234_MH243353), blaTEM-219 (blaTEM-219_KM114268), blaTEM-217 (blaTEM-217_HG934763), blaTEM-198 (blaTEM-198_AB700703), blaTEM-104 (blaTEM-104_AF516719)
aztreonam	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaSHV-12 (blaSHV-12_KF976405), blaCTX-M-14 (blaCTX-M-14_AF252622)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC39.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	2	aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550), aadA1 (aadA1_JQ414041)
amikacin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
neomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
lividomycin	aminoglycoside	Resistant	2	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753), aph(3')-Ia (aph(3')-Ia_X62115)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA1 (aadA1_JQ414041)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaADC-25 (blaADC-25_EF016355), blaOXA-98 (blaOXA-98_EU255288), blaOXA-66 (blaOXA-66_AY750909), blaOXA-72 (blaOXA-72_AY739646)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	catB8 (catB8_AF227506)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC3.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaOXA-66 (blaOXA-66_AY750909), blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC4.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	No resistance	0	
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_X62115), aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaADC-25 (blaADC-25_EF016355), blaOXA-66 (blaOXA-66_AY750909)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC5.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), aac(3)-IIa (aac(3)-IIa_CP023555), aac(6')-Ib3 (aac(6')-Ib3_X60321)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Ib3 (aac(6')-Ib3_X60321)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
cefepime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
cefixime	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876)
piperacillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262), blaNDM-1 (blaNDM-1_FN396876), blaOXA-1 (blaOXA-1_HQ170510)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125)
aztreonam	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaKPC-3 (blaKPC-3_HM769262)
ceftazidime+avibactam	beta-lactam	Resistant	3	blaNDM-1 (blaNDM-1_FN396876)
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-15 (blaCTX-M-15_AY044436), blaCTX-M-14 (blaCTX-M-14_AF252622)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaKPC-3 (blaKPC-3_HM769262)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708), dfrA14 (dfrA14_KF921535)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	Resistant	1	erm(B) (erm(B)_U35228), erm(B) (erm(B)_X66468), erm(B) (erm(B)_U86375), erm(B) (erm(B)_JN899585)
clindamycin	lincosamide	Resistant	1	erm(B) (erm(B)_U35228), erm(B) (erm(B)_X66468), erm(B) (erm(B)_U86375), erm(B) (erm(B)_JN899585)
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251), erm(B) (erm(B)_U35228), erm(B) (erm(B)_X66468), erm(B) (erm(B)_U86375), erm(B) (erm(B)_JN899585)
azithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(A) (mph(A)_D16251)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	1	erm(B) (erm(B)_U35228), erm(B) (erm(B)_X66468), erm(B) (erm(B)_U86375), erm(B) (erm(B)_JN899585)
pristinamycin ia	streptogramin b	Resistant	1	erm(B) (erm(B)_U35228), erm(B) (erm(B)_X66468), erm(B) (erm(B)_U86375), erm(B) (erm(B)_JN899585)
virginiamycin s	streptogramin b	Resistant	1	erm(B) (erm(B)_U35228), erm(B) (erm(B)_X66468), erm(B) (erm(B)_U86375), erm(B) (erm(B)_JN899585)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	3	catA1 (catA1_V00622), catB3 (catB3_AJ009818), catB3 (catB3_U13880), OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC6.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
tobramycin	aminoglycoside	Resistant	3	armA (armA_AY220558)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF024602), aph(3'')-Ib (aph(3'')-Ib_AF321551), aph(3'')-Ib (aph(3'')-Ib_AF313472), aph(3'')-Ib (aph(3'')-Ib_AF321550)
amikacin	aminoglycoside	Resistant	3	armA (armA_AY220558), aph(3')-VIa (aph(3')-VIa_X07753)
isepamicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
neomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
ribostamycin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	Resistant	2	aph(3')-VIa (aph(3')-VIa_X07753)
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	3	armA (armA_AY220558)
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	No resistance	0	
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
meropenem	beta-lactam	Resistant	3	blaOXA-23 (blaOXA-23_AY795964)
piperacillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	Resistant	3	blaOXA-66 (blaOXA-66_AY750909), blaADC-25 (blaADC-25_EF016355)
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	Resistant	3	blaTEM-1D (blaTEM-1D_AF188200)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518), mph(E) (mph(E)_DQ839391)
azithromycin	macrolide	Resistant	3	msr(E) (msr(E)_FR751518)
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
doxycycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
minocycline	tetracycline	Resistant	1	tet(B) (tet(B)_AP000342)
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
pristinamycin ia	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
virginiamycin s	streptogramin b	Resistant	3	msr(E) (msr(E)_FR751518)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC7.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	No resistance	0	
tobramycin	aminoglycoside	Resistant	2	aadD (aadD_AF181950)
streptomycin	aminoglycoside	No resistance	0	
amikacin	aminoglycoside	Resistant	2	aadD (aadD_AF181950)
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	ant(9)-Ia (ant(9)-Ia_X02588)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaZ (blaZ_JDXN01000019)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	mecA (mecA_BX571856)
ampicillin	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaZ (blaZ_JDXN01000019)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	mecA (mecA_BX571856)
cefepime	beta-lactam	Resistant	3	mecA (mecA_BX571856)
cefixime	beta-lactam	Resistant	3	mecA (mecA_BX571856)
cefotaxime	beta-lactam	Resistant	3	mecA (mecA_BX571856)
cefoxitin	beta-lactam	Resistant	3	mecA (mecA_BX571856)
ceftazidime	beta-lactam	Resistant	3	mecA (mecA_BX571856)
ertapenem	beta-lactam	Resistant	3	mecA (mecA_BX571856)
imipenem	beta-lactam	Resistant	3	mecA (mecA_BX571856)
meropenem	beta-lactam	Resistant	3	mecA (mecA_BX571856)
piperacillin	beta-lactam	Resistant	3	mecA (mecA_BX571856), blaZ (blaZ_JDXN01000019)
piperacillin+tazobactam	beta-lactam	Resistant	3	mecA (mecA_BX571856)
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	Resistant	3	blaZ (blaZ_JDXN01000019)
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	No resistance	0	
trimethoprim	folate pathway antagonist	No resistance	0	
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	Resistant	3	bleO (bleO_AF051917)
lincomycin	lincosamide	Resistant	3	erm(A) (erm(A)_X03216)
clindamycin	lincosamide	Resistant	3	erm(A) (erm(A)_X03216)
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	erm(A) (erm(A)_X03216)
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	Resistant	3	erm(A) (erm(A)_X03216)
pristinamycin ia	streptogramin b	Resistant	3	erm(A) (erm(A)_X03216)
virginiamycin s	streptogramin b	Resistant	3	erm(A) (erm(A)_X03216)
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC8.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), ant(2'')-Ia (ant(2'')-Ia_X04555)
tobramycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314), ant(2'')-Ia (ant(2'')-Ia_X04555), aac(6')-Il (aac(6')-Il_U13880)
streptomycin	aminoglycoside	Resistant	3	aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551), aadA2 (aadA2_JQ364967), aadA1 (aadA1_JX185132), aadA1 (aadA1_JQ414041)
amikacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(6')-Il (aac(6')-Il_U13880)
isepamicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
dibekacin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
kanamycin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aph(3')-Ia (aph(3')-Ia_V00359)
neomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
lividomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
paromomycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
ribostamycin	aminoglycoside	Resistant	3	aph(3')-Ia (aph(3')-Ia_V00359)
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
apramycin	aminoglycoside	Resistant	1	aac(3)-IId (aac(3)-IId_EU022314)
sisomicin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506), aac(3)-IId (aac(3)-IId_EU022314)
arbekacin	aminoglycoside	Resistant	3	rmtB (rmtB_AB103506)
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA2 (aadA2_JQ364967), aadA1 (aadA1_JX185132), aadA1 (aadA1_JQ414041)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), qnrS1 (qnrS1_AB187515)
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	Resistant	2	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
amoxicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaVIM-1 (blaVIM-1_Y18050)
amoxicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVEB-1 (blaVEB-1_DQ393569), blaVIM-1 (blaVIM-1_Y18050)
ampicillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaVIM-1 (blaVIM-1_Y18050)
ampicillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVEB-1 (blaVEB-1_DQ393569), blaVIM-1 (blaVIM-1_Y18050)
cefepime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569), blaVIM-1 (blaVIM-1_Y18050)
cefixime	beta-lactam	Resistant	3	blaVIM-1 (blaVIM-1_Y18050)
cefotaxime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569), blaVIM-1 (blaVIM-1_Y18050)
cefoxitin	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVEB-1 (blaVEB-1_DQ393569), blaVIM-1 (blaVIM-1_Y18050)
ceftazidime	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569), blaVIM-1 (blaVIM-1_Y18050)
ertapenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVIM-1 (blaVIM-1_Y18050)
imipenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVIM-1 (blaVIM-1_Y18050)
meropenem	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVIM-1 (blaVIM-1_Y18050)
piperacillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaVIM-1 (blaVIM-1_Y18050)
piperacillin+tazobactam	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427), blaVIM-1 (blaVIM-1_Y18050)
unknown beta-lactam	beta-lactam	Resistant	2	blaSHV-182 (blaSHV-182_KP050489), blaSHV-159 (blaSHV-159_JX121126), blaSHV-158 (blaSHV-158_JX121125)
aztreonam	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569), blaOXA-10 (blaOXA-10_J03427)
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaKPC-2 (blaKPC-2_AY034847), blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016), blaSHV-99 (blaSHV-99_AM941845), blaVEB-1 (blaVEB-1_DQ393569)
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	Resistant	3	blaCTX-M-14 (blaCTX-M-14_AF252622), blaSHV-99 (blaSHV-99_AM941845)
ticarcillin+clavulanic acid	beta-lactam	Resistant	3	blaKPC-2 (blaKPC-2_AY034847), blaVEB-1 (blaVEB-1_DQ393569)
cephalothin	beta-lactam	Resistant	2	blaTEM-1C (blaTEM-1C_FJ560503), blaTEM-1B (blaTEM-1B_AY458016)
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138), sul1 (sul1_EU780013)
trimethoprim	folate pathway antagonist	Resistant	3	OqxB (OqxB_EU370913), OqxA (OqxA_EU370913), dfrA12 (dfrA12_AM040708), dfrA23 (dfrA23_AJ746361), dfrA1 (dfrA1_AF203818), dfrA1 (dfrA1_AJ238350), dfrA1 (dfrA1_X00926)
fosfomycin	fosfomycin	Resistant	2	fosA6 (fosA6_KU254579), fosA7 (fosA7_LAPJ01000014)
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	Resistant	3	mph(B) (mph(B)_D85892)
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	Resistant	3	mph(B) (mph(B)_D85892)
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	Resistant	3	mph(B) (mph(B)_D85892)
tetracycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140), tet(A) (tet(A)_AF534183)
doxycycline	tetracycline	Resistant	3	tet(G) (tet(G)_AF133140), tet(A) (tet(A)_AF534183)
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	Resistant	2	cmlA1 (cmlA1_M64556), OqxB (OqxB_EU370913), OqxA (OqxA_EU370913)
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	Resistant	3	ARR-2 (ARR-2_HQ141279)
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
# ResFinder phenotype results.
# Sample: BC9.fasta
# 
# The phenotype 'No resistance' should be interpreted with
# caution, as it only means that nothing in the used
# database indicate resistance, but resistance could exist
# from 'unknown' or not yet implemented sources.
# 
# The 'Match' column stores one of the integers 0, 1, 2, 3.
#      0: No match found
#      1: Match < 100% ID AND match length < ref length
#      2: Match = 100% ID AND match length < ref length
#      3: Match = 100% ID AND match length = ref length
# If several hits causing the same resistance are found,
# the highest number will be stored in the 'Match' column.

# Antimicrobial	Class	WGS-predicted phenotype	Match	Genetic background
gentamicin	aminoglycoside	No resistance	0	
tobramycin	aminoglycoside	No resistance	0	
streptomycin	aminoglycoside	Resistant	3	aadA5 (aadA5_AF137361), aph(6)-Id (aph(6)-Id_M28829), aph(3'')-Ib (aph(3'')-Ib_AF321551)
amikacin	aminoglycoside	No resistance	0	
isepamicin	aminoglycoside	No resistance	0	
dibekacin	aminoglycoside	No resistance	0	
kanamycin	aminoglycoside	No resistance	0	
neomycin	aminoglycoside	No resistance	0	
lividomycin	aminoglycoside	No resistance	0	
paromomycin	aminoglycoside	No resistance	0	
ribostamycin	aminoglycoside	No resistance	0	
unknown aminoglycoside	aminoglycoside	No resistance	0	
butiromycin	aminoglycoside	No resistance	0	
butirosin	aminoglycoside	No resistance	0	
hygromycin	aminoglycoside	No resistance	0	
netilmicin	aminoglycoside	No resistance	0	
apramycin	aminoglycoside	No resistance	0	
sisomicin	aminoglycoside	No resistance	0	
arbekacin	aminoglycoside	No resistance	0	
kasugamycin	aminoglycoside	No resistance	0	
astromicin	aminoglycoside	No resistance	0	
fortimicin	aminoglycoside	No resistance	0	
spectinomycin	aminocyclitol	Resistant	3	aadA5 (aadA5_AF137361)
fluoroquinolone	quinolone	No resistance	0	
ciprofloxacin	quinolone	No resistance	0	
unknown quinolone	quinolone	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
amoxicillin	beta-lactam	No resistance	0	
amoxicillin+clavulanic acid	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
cefixime	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
ceftazidime	beta-lactam	No resistance	0	
ertapenem	beta-lactam	No resistance	0	
imipenem	beta-lactam	No resistance	0	
meropenem	beta-lactam	No resistance	0	
piperacillin	beta-lactam	No resistance	0	
piperacillin+tazobactam	beta-lactam	No resistance	0	
unknown beta-lactam	beta-lactam	No resistance	0	
aztreonam	beta-lactam	No resistance	0	
cefotaxime+clavulanic acid	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ticarcillin	beta-lactam	No resistance	0	
ceftazidime+avibactam	beta-lactam	No resistance	0	
penicillin	beta-lactam	No resistance	0	
ceftriaxone	beta-lactam	No resistance	0	
ticarcillin+clavulanic acid	beta-lactam	No resistance	0	
cephalothin	beta-lactam	No resistance	0	
piperacillin+clavulanic acid	beta-lactam	No resistance	0	
ceftiofur	under_development	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul1 (sul1_U12338), sul2 (sul2_HQ840942)
trimethoprim	folate pathway antagonist	Resistant	3	dfrA17 (dfrA17_FJ460238)
fosfomycin	fosfomycin	No resistance	0	
vancomycin	glycopeptide	No resistance	0	
teicoplanin	glycopeptide	No resistance	0	
bleomycin	glycopeptide	No resistance	0	
lincomycin	lincosamide	No resistance	0	
clindamycin	lincosamide	No resistance	0	
dalfopristin	streptogramin a	No resistance	0	
pristinamycin iia	streptogramin a	No resistance	0	
virginiamycin m	streptogramin a	No resistance	0	
quinupristin+dalfopristin	streptogramin a	No resistance	0	
tiamulin	pleuromutilin	No resistance	0	
carbomycin	macrolide	No resistance	0	
erythromycin	macrolide	No resistance	0	
azithromycin	macrolide	No resistance	0	
oleandomycin	macrolide	No resistance	0	
spiramycin	macrolide	No resistance	0	
tylosin	macrolide	No resistance	0	
telithromycin	macrolide	No resistance	0	
tetracycline	tetracycline	No resistance	0	
doxycycline	tetracycline	No resistance	0	
minocycline	tetracycline	No resistance	0	
tigecycline	tetracycline	No resistance	0	
quinupristin	streptogramin b	No resistance	0	
pristinamycin ia	streptogramin b	No resistance	0	
virginiamycin s	streptogramin b	No resistance	0	
linezolid	oxazolidinone	No resistance	0	
chloramphenicol	amphenicol	No resistance	0	
florfenicol	amphenicol	No resistance	0	
colistin	polymyxin	No resistance	0	
fusidic acid	steroid antibacterial	No resistance	0	
mupirocin	pseudomonic acid	No resistance	0	
rifampicin	rifamycin	No resistance	0	
metronidazole	nitroimidazole	No resistance	0	
narasin	ionophores	No resistance	0	
salinomycin	ionophores	No resistance	0	
maduramicin	ionophores	No resistance	0	
