# 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	
