Table 4.
Antimicrobial resistance phenotype and resistance determinants predicted with various assembly and sequencing techniques in five E. coli isolates.
| 17-AB00050 | ||||
| Class of In Silico Type Phenotype | Subclass of In Silico Type Phenotype | Determined Resistance Gene(s) | Determined Phenotype | Class/Subclass of Determined Phenotype |
| Quinolone | Quinolone | qnrS1 | Ciprofloxacin | Fluoroquinolone |
| β-Lactam | Penicillin, Cephalosporin | blaEC-8, blaSHV-12 | Ampicillin | β-Lactam |
| Cefepime | Cephalosporin | |||
| Cefotaxime | Cephalosporin | |||
| Aminoglycoside | Gentamicin | aac(3)-VIa | Gentamicin | Aminoglycoside |
| Sulfonamide | Sulfonamid | sul1 | Sulphamethoxazole | Sulfonamide |
| Aminoglycoside | Streptomycin | aadA1 | Not within the test panel | Not within the test panel |
| 17-AB00090 | ||||
| Class of In Silico Type Phenotype | Subclass of In Silico Type Phenotype | Determined Resistance Gene(s) | Determined Phenotype | Class/Subclass of Determined Phenotype |
| β-Lactam | Penicillin | blaTEM-1, blaTEM-1*1, blaTEM-135*2 | Ampicillin | β-Lactam |
| β-Lactam | Penicillin, Cephalosporine | bla EC-18 | ||
| Quinolone | Quinolone | qnrS1 | Ciprofloxacin | Fluoroquinolone |
| Nalidixic acid | Quinolone | |||
| Tetracycline | Tetracycline | tet(A) | Tetracycline | Tetracycline |
| 17-AB00432 | ||||
| Class of In Silico Type Phenotype | Subclass of In Silico Type Phenotype | Determined Resistance Gene(s) | Determined Phenotype | Class/Subclass of Determined Phenotype |
| β-Lactam | Penicillin | bla TEM-1 | Ampicillin | β-Lactam |
| β-Lactam | Penicillin, Cephalosporin | blaCTX-M-15, blaEC | Cefepime | Cephalosporin |
| Cefotaxime | Cephalosporin | |||
| Ceftazidime | Cephalosporin | |||
| Aminoglycoside | Kanamycin | aph(3′)-Ia | Not within the test panel | Not within the test panel |
| Quinolone | Quinolone | qnrS1 | Ciprofloxacin | Fluoroquinolone |
| Nalidixic acid | Quinolone | |||
| Aminoglycoside | Streptomycin |
aph(3″)-Ib, aph(3″)-Ib* |
Not within the test panel | Not within the test panel |
| aph(3′)-Ia, | ||||
|
aph(6)-Id, aph(6)-Id* |
||||
| Sulfonamide | Sulfonamide | sul2, sul2* | Sulphamethoxazole | Sulfonamide |
| Tetracycline | Tetracycline | tet(A), tet(A)*3, tet(B) | Tetracycline | Tetracycline |
| 17-AB00587 | ||||
| Class of In Silico Type Phenotype | Subclass of In Silico Type Phenotype | Determined Resistance Gene | Determined Phenotype | Class/Subclass of Determined Phenotype |
| β-Lactam | Cephalosporin | blaCTX-M-1, blaEC-15 | Cefepime | Cephalosporin |
| Cefotaxime | Cephalosporin | |||
| Ceftazidime | Cephalosporin | |||
| Lincosamide | Lincosamide | lnu(F) | Not within the test panel | Not within the test panel |
| Macrolide | Macrolide | mph(A) | ||
| Quinolone | Fluoroquinolone | qnrS1 | Ciprofloxacin | Fluoroquinolone |
| Aminoglycoside | Streptomycin | aadA2 | Not within the test panel | Not within the test panel |
| 17-AB00639 | ||||
| Class of In Silico Type Phenotype | Subclass of In Silico Type Phenotype | Determined Resistance Gene(s) | Determined Phenotype | Class/Subclass of Determined Phenotype |
| β-Lactam | Penicillin | bla TEM-1 | Ampicillin | β-Lactam |
| β-Lactam | Penicillin, Cephalosporin*3 | blaCTX-M-1*4, blaEC, | Cefepime | Cephalosporin |
| blaTEM-1*4, blaTEM-1 | Cefotaxime | Cephalosporine | ||
| Ceftazidime | Cephalosporine | |||
| Aminoglycoside | Gentamicin | aac(3)-Iva | Gentamicin | Aminoglycoside |
| Aminoglycoside | Hygromicin | aph(4)-Ia | Not within the test panel | Not within the test panel |
| Macrolide | Macrolide | mph(A) | ||
| Quinolone | Fluoroquinolone | qnrS1 | Ciprofloxacin | Fluoroquinolon |
| Aminoglycoside | Streptomycin |
aph(3″)-Ib, aph(3″)-Ib*4, |
Not within the test panel | Not within the test panel |
| aph(6)-Id* 5 | ||||
| Sulfonamide | Sulfonamide | sul2 | Sulphamethoxazole | Sulfonamide |
| Diaminopyrimidine | Trimethoprim | dfrA5 | Trimethoprim | Diaminopyrimidine |
*1: duplication detected in all long-read and hybrid assemblies but not in NextSeq assemblies. *2: gene only determined with data Flye-ONT assemblies. *3: duplication detected in all long-read and hybrid assemblies but not in short-read-only assemblies. *4: detected in all long-read and hybrid assemblies but not in NextSeq assemblies. *5: not detected in short-read-only assemblies and Flye-ONT sequences.