TABLE 1.

Known AMR genes identified by the k-mer-based AMR classifiers^a

Antibiotic	Drug class	Known AMR gene(s) to the antibioticb	Known AMR genes associated with other antibioticsb
Ampicillin	Beta-lactam	TEM-1**, CTX-M-15, yicJ*	sul1**, folP**, APH(3′′)-Ib, katE*, yadV*, arnC, fsr, nmpC, pepT, yeeJ, yhdJ
Aztreonam	Beta-lactam	CTX-M-55*	AAC(6′)-Ib-cr, acrD, catIII, nmpC, pitA, yicI, cpdB, yoaE, rapA, dinG, yeeJ, oppA, arnC
Cefepime	Beta-lactam	CTX-M-1**, CTX-M-15, CTX-M-55	dfrA25*, AAC(6′)-Ib10*, AAC(3)-IId, catB3, AAC(6′)-Ib-cr, folA*, yadV*, citF, yeeJ, ftsI
Cefoxitin	Beta-lactam	CMY-2*, ybiW*, betT, chiP, cra, envZ, htrE, lyxK, mdlA, yeeJ, yghA	dfrA25, AAC(3)-IId, catIII, blc, yaiY, folA, putA, lpoA
Ciprofloxacin	Fluoroquinolone	gyrA**	OXA-1*, CTX-M-15*, arnC, nmpC, htrE, cpdB, arcA, flu
Gentamicin	Aminoglycoside	AAC(3)-IId**, AAC(6′)-Ib7**, aadA13*, AAC(3)-IIe*, AAC(6′)-Ib9*, aadA7, ANT(2′′)-Ia	floR, CTX-M-15, dfrA17, mphA, intS*, fliC*, arnC, yicJ
Levofloxacin	Fluoroquinolone	gyrA**	lacI*, yqiK, flu, arcA, fimC, phoE, ybiH, dadA
Tetracycline	Tetracycline	tet(A)**, tet(B)**, mdfA	APH(6)-Id, sul2, yeeJ, folP, csiD
Tobramycin	Aminoglycoside	AAC(3)-IId**, AAC(6′)-Ib-cr**, AAC(3)-IIe, AAC(6′)-Ib7	catB3*, CTX-M-55, dfrA17, OXA-1, fliC*, pinR, ydfU, dnaQ
Trimethoprim	Diaminopyrimidine		ANT(2′′)-Ia**, sul2*, aadA16*, aadA25*, APH(3′′)-Ib*, TEM-1, tet(A), APH(6)-Id, mphA, TEM-150, sul1, folP*, dosP, valS, nmpC, htrE, groL, putP

^aGenes in the top 10% features, ranked according to their maximum feature important assigned by the GBC classifier, are presented.

^bSymbols: **, gene was associated with feature in the top 10% features; *, gene was associated with feature in the top 50% features.