Table 3. Comparison of genomic predictions of antibiotic resistance with susceptibility testing at the ARS reference laboratory.
| Antibiotic class | Antibiotic | Resistant isolates | False positive | False negative | Concordance (%) | Resistance genes/SNPs |
|---|---|---|---|---|---|---|
| Cephalosporin | Cefixime | 0 | 0 | 0 | 100 | - |
| Cephalosporin | Ceftriaxone | 0 | 0 | 0 | 100 | - |
| Penicillin | Penicillin | 18 | 0 | 1 | 95.24 | blaTEM, mtrR_promoter_–57delA, mtrR_A39T, mtrR_disrupted, penA_ins346D, ponA1_L421P, porB1b_A121D, porB1b_G120K |
| Tetracycline | Tetracycline | 14 | 7 | 0 | 66.67 |
tetM, rpsJ-V57M, mtrR_promoter_ –57delA, mtrR_A39T, mtrR_disrupted |
| Fluoroquinolone | Ciprofloxacin | 19 | 0 | 0 | 100 | gyrA_D95G, gyrA_D95A, gyrA_S91F, parC_D86N, parC_S87N, parC_E91K |