# ResFinder phenotype results for salmonella.
# Sample: gdS337.fa
# 
# 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
trimethoprim	folate pathway antagonist	No resistance	0	
azithromycin	macrolide	No resistance	0	
ciprofloxacin	quinolone	Resistant	3	qnrS1 (qnrS1_AB187515)
ertapenem	beta-lactam	No resistance	0	
cefotaxime	beta-lactam	No resistance	0	
imipenem	beta-lactam	No resistance	0	
cefoxitin	beta-lactam	No resistance	0	
nalidixic acid	quinolone	No resistance	0	
tobramycin	aminoglycoside	Resistant	2	aac(6')-Iaa (aac(6')-Iaa_NC_003197)
tigecycline	tetracycline	No resistance	0	
sulfamethoxazole	folate pathway antagonist	Resistant	3	sul2 (sul2_AY034138)
tetracycline	tetracycline	Resistant	2	tet(A) (tet(A)_AJ517790)
chloramphenicol	amphenicol	Resistant	1	floR (floR_AF118107)
amikacin	aminoglycoside	Resistant	2	aac(6')-Iaa (aac(6')-Iaa_NC_003197)
gentamicin	aminoglycoside	No resistance	0	
pipercallin+tazobactam	NA	NA	NA	Not in database
ceftazidime	beta-lactam	No resistance	0	
colistin	polymyxin	No resistance	0	
meropenem	beta-lactam	No resistance	0	
temocillin	beta-lactam	No resistance	0	
ampicillin+clavulanic acid	beta-lactam	No resistance	0	
cefepime	beta-lactam	No resistance	0	
ampicillin	beta-lactam	No resistance	0	

# WARNING: Missing features from phenotype database:
# Feature_ID	Region	Database	Hit
acrB_28_l	acrB		
acrB_40_p	acrB		
parC_255_s	parC		
parC_395_s	parC		
parC_469_a	parC		
parE_135_r	parE		
16S_rrsD_92_b	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_249_k	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_471_r	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1005_s	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1006_w	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1007_w	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1020_y	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1022_k	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1133_r	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1135_y	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1136_m	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		
16S_rrsD_1139_y	16S_rrsD;;16S_rrsD;;shgx;;16S_rrsD;;vmai		