Table 4.
Time-line of resistance gene detection from the K. pneumoniae samples
| Time | genes | Class | TP/FP | Sensitivity | Specificity | Data |
|---|---|---|---|---|---|---|
| (mins) | (%) | (%) | (no. of reads) | |||
| K. pneumoniae ATCC BAA-2146 | ||||||
| 30 | 1228 | |||||
| mphA | macrolide | TP | ||||
| blaSHV | beta-lactamase | FP ∗ | ||||
| strA | aminoglycoside | TP | ||||
| blaTEM | beta-lactamase | TP | ||||
| strB | aminoglycoside | TP | ||||
| blaCTX | beta-lactamase | TP | 26.67 | 87.50 | ||
| 60 | 2613 | |||||
| blaLEN | beta-lactamase | TP | ||||
| sul2 | sulphonamide | TP | ||||
| blaOXA | beta-lactamase | TP | ||||
| aac3 | aminoglycoside | TP | ||||
| aac6 | aminoglycoside | TP | ||||
| blaCMY | beta-lactamase | TP | ||||
| blaCFE | beta-lactamase | TP | ||||
| blaLAT | beta-lactamase | TP | ||||
| blaBIL | beta-lactamase | TP | 53.33 | 94.12 | ||
| 90 | 3844 | |||||
| QnrB | quinolone | TP | ||||
| aadA | aminoglycoside | TP | ||||
| oqxA | quinolone | TP | ||||
| tetA | tetracycline | TP | ||||
| oqxB | quinolone | TP | 76.67 | 95.83 | ||
| 120 | 5258 | |||||
| dfrA | trimethoprim | TP | 80.00 | 96.00 | ||
| 240 | 10 788 | |||||
| blaOKP | beta-lactamase | TP | 83.33 | 96.15 | ||
| 270 | 11 931 | |||||
| rmtC | aminoglycoside | TP | 86.67 | 96.43 | ||
| 300 | 13 022 | |||||
| sul1 | sulphonamide | TP | ||||
| sul3 | sulphonamide | TP | 93.33 | 96.55 | ||
| 540 | 20 200 | |||||
| fosA | fosfomycin | TP | 96.67 | 96.67 | ||
| 600 | 21 546 | |||||
| blaNDM | beta-lactamase | TP | 100.00 | 96.77 | ||
| K. quasipneumoniae ATCC 700603 | ||||||
| 30 | 582 | |||||
| oqxA | quinolone | TP | ||||
| blaSHV | beta-lactamase | TP | ||||
| oqxB | quinolone | TP | 27.27 | 100.00 | ||
| 60 | 1090 | |||||
| aadB | aminoglycoside | TP | 36.36 | 100.00 | ||
| 390 | 3704 | |||||
| sul1 | sulphonamide | TP | ||||
| sul3 | sulphonamide | TP | 54.55 | 100.00 | ||
| 420 | 3810 | |||||
| blaOXA | beta-lactamase | TP | 63.64 | 100.00 | ||
| 540 | 4156 | |||||
| blaOKP | beta-lactamase | TP | 72.73 | 100.00 | ||
| K. pneumoniae ATCC 13883 | ||||||
| 30 | 1264 | |||||
| fosA | fosfomycin | TP | 16.67 | 100.00 | ||
| 60 | 2186 | |||||
| blaSHV | beta-lactamase | TP | ||||
| blaOKP | beta-lactamase | TP | 50.00 | 100.00 | ||
| 90 | 2952 | |||||
| blaLEN | beta-lactamase | TP | 66.67 | 100.00 | ||
| 120 | 3584 | |||||
| oqxA | quinolone | TP | 83.33 | 100.00 | ||
| 570 | 8112 | |||||
| oqxB | quinolone | TP | 100.00 | 100.00 | ||
TP/FP: true positives/false positives according to the resistance gene profiles obtained from MiSeq sequencing. ∗Gene blaSHV was detected from MinION sequencing of K. pneumoniae ATCC BAA-2146 but not from MiSeq sequencing due to the inability to resolve a repeat in the gene