Table 5. Comparison of antimicrobial resistance (AMR) genotype and AMR phenotype.
| AMR Genes | Genbank No. | AMR Family | Antibiotics Tested to AMR Phenotype | Gene detected | Resistance dedected | Sensitivity detected | Correlation (%) |
| aac6II | AY123251.1 | Aminoglycoside | Gentamicin, Tobramycin | 1 | 1 | 0 | 100 |
| aadA1 | AB126599.1 | Aminoglycoside | Streptomycin | 14 | 14 | 0 | 100 |
| aadA2 | AB126602.1 | Aminoglycoside | Streptomycin | 5 | 5 | 0 | 100 |
| aphA1 | AB366440.1 | Aminoglycoside | Kanamycin | 5 | 5 | 0 | 100 |
| sph | AB366441.1 | Aminoglycoside | Streptomycin | 1 | 1 | 0 | 100 |
| strA | AB366440.1 | Aminoglycoside | Streptomycin | 10 | 10 | 0 | 100 |
| strB | AB366440.1 | Aminoglycoside | Streptomycin | 14 | 14 | 0 | 100 |
| catA1 | AB366440.1 | Chloramphenicol | Chloramphenicol | 5 | 5 | 0 | 100 |
| cmlA | AJ487033.2 | Chloramphenicol | Chloramphenicol | 4 | 4 | 0 | 100 |
| floR | AF118107.1 | Chloramphenicol | Chloramphenicol | 2 | 2 | 0 | 100 |
| sul1 | AF261825.2 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 8 | 1 | 7 | -a |
| sul2 | AB366440.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 3 | 2 | 1 | -a |
| sul1, sul2 | AF261825.2, AB366440.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 0 | 1 | -a |
| sul1, dfrA1 | AF261825.2, AF203818.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul1, dfrA1, dfrA15 | AF261825.2, AF203818.1, AJ867237.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul1, dfrA12 | AF261825.2, AB366440.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul1, dfrA13 | AF261825.2, AM932669.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul1, dfrV | AF261825.2, DQ133160.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul1, sul2, dfrA1 | AF261825.2, AB366440.1, AF203818.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 2 | 2 | 0 | 100 |
| sul1, sul2, dfrA12 | AF261825.2, AB366440.1, AB366440.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul2, dfrA14 | AB366440.1, DQ388123.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul3, dfrA1 | AY316203.1, AF203818.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 1 | 1 | 0 | 100 |
| sul3, dfrA12 | AY316203.1, AB366440.1 | Sulfonamide/Trimethoprim | Co-trimoxazol (Sulfamethoxazol/Trimethoprim) | 3 | 3 | 0 | 100 |
| ctxM1 | FJ654733.1 | Beta-Lactam | Ampicillin, Piperacillin, Cefuroxime, Cefpodoxime, Ceftazidime | 1 | 1 | 0 | 100 |
| oxa1 | AB218659.1 | Beta-Lactam | Ampicillin, Piperacillin, Cefuroxime | 2 | 2 | 0 | 100 |
| tem1 | AB366440.1 | Beta-Lactam | Ampicillin, Piperacillin | 15 | 15 | 0 | 100 |
| tetA | AB366441.1 | Tetracycline | Tetracycline | 10 | 10 | 0 | 100 |
| tetB | AB366440.1 | Tetracycline | Tetracycline | 13 | 13 | 0 | 100 |
| tetG | AF261825.2 | Tetracycline | Tetracycline | 1 | 1 | 0 | 100 |
| mphA | AY333434.1 | Macrolide | 1 | - | - | -b | |
| no gene detected | Aminoglycoside | Streptomycin | 0 | 2 | 0 | -c | |
| no gene detected | Beta-Lactam | Ampicillin | 0 | 1 | 0 | -c | |
a
only co-trimoxazol was tested, sulfamethoxazol was not available.
b
potential resistance against erythromycin was not tested.
c
AMR phenotype without AMR genotype was detected.
All AMR genes detected in 34 Salmonella strains listed and compared with the AMR phenotype. The phenotype was defined using a VITEK 2 system with an AST-N111 panel and a disk diffusion assay using Oxoid discs with chloramphinicol (30 mg), streptomycin (10 mg) and kanamycin (30 mg).