# 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	
