# 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	
