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Table 4 Time-line of resistance gene detection from the K. pneumoniae samples

From: Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing

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  
  1. 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