# 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	
