Table 3. Comparison of genomic predictions of antibiotic resistance with laboratory susceptibility testing at the ARSP reference laboratory.

Antibiotic class	Antibiotic	Resistant isolates	False-positive	False-negative	Concordance (%)	Resistance genes/SNPs
Penicillin	Penicillin	116	0	0	100	blaZ, mecA
Penicillin	Oxacillin	116	0	2	98.28	mecA
Folate pathway antagonist	Sulfamethoxazole/ Trimethoprim	9	1	0	99.14	dfrG
Aminoglycoside	Gentamicin	2	0	0	100.00	aacA_aphD
Lincosamide	Clindamycin	2	0	0	100	ermC
Macrolide	Erythromycin	3	0	0	100	ermC, msrA
Tetracycline	Tetracycline	2	0	0	100	tetM, tetK
Fluoroquinolone	Ciprofloxacin	2	0	0	100	GyrA_S84L, GyrA_G106D, GrlA_S80F