Skip to main content

Table 2 Comparison of antibiotic resistance phenotype and clinically relevant resistance genes in cases of bacterial pneumonia. The antibiotic resistance phenotype was detected by clinical culture and clinically relevant resistance genes were detected by Nanopore. Genes conferring resistance phenotype are highlighted in bold

From: Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study

Case

Pathogen by culture & Nanopore

Resistance phenotype by culture

Clinically relevant resistance genes

[N of alignments]

Resistance identified

 Case 1

Stenotrophomonas maltophilia

R: ticarcillin/clavulanic acid

R: ceftazidime

blaTEM-4 [4]

blaTEM-112 [1]

blaTEM-157 [1]

blaACT-5 [1]

I: levofloxacin

oqxB [1]

Tetracycline not tested

tetC [6]

 Case 2

Staphylococcus aureus

R: methicillin

mecA [4]

R: erythromycin, clindamycin

ermA [10]

erm (33) [1]

 

tet38 [11]

ant(4′)-lb [9]

tetC [3]

blaTEM-4 [1]

 Case 3

Staphylococcus aureus

I: tetracycline

tetK [1]

tet38 [1]

tetQ [1]

 Case 4

Escherichia coli

R: tetracycline

tetX [1]

R: Trimethoprim-sulfamethoxazole

R: ciprofloxacin, levofloxacin

sul1 [363]

dfrA [127]

 

acrF [315]a

parE [304]a

mfd [277]a

 

mphA [215]

aadA5 [196]

vgaC [110]

blaACT-5 [7]

blaACT-14 [3]

mefA [1]

mel [1]

No resistance identified

 Case 5

Staphylococcus aureus

S: all tested agents

none

 Case 6

Staphylococcus aureus

S: all tested agents

tet38 [2]

blaTEM4 [2]

 Case 7

Pseudomonas aeruginosa

S: all tested agents

none

Resistance not tested

 Case 8

Streptococcus agalactiae

Not tested

tetM [60]

isaC [55]

sul1 [2]

tetQ [2]

mphA [1]

aadA5 [1]

  1. Abbreviations: R Resistant, I Intermediate, S Susceptible
  2. a Genes conferring antibiotic resistance phenotype but not classified as clinical relevant genes by EPI2ME antimicrobial resistance gene analyses [ARMA workflow]
  3. Tested agents for case 5: Ampicillin/Sulbactum, Oxacillin, Imipenem, Gentamicin, Erthromycin, Tetracycline, Vancomycin, Clindamycin, Linezolid, Rifampin, Trimethoprim-sulfamethoxazole, Synercid
  4. Tested agents for case 6: Ampicillin/Sulbactum, Oxacillin, Imipenem, Gentamicin, Erthromycin, Tetracycline
  5. Tested agents for case 7: Piperacillin/Tazobactum, Ticarcillin/Clavulanic acid, Cefepime, Ceftazidime, Imipenem, Meropenem, Aztreonam, Gentamicin, Tobramycin, Amikacin, Ciprofloxacin, Levofloxacin