Table 4  Antimicrobial resistance gene on plasmids predicted by ResFinder and PlasmidFinder after de novo assembly of clinical E. coli strains with ONT reads using Flye, Canu, Wtdbg2, and NECAT assemblers with and without read correcting with Medaka, NextPolish, and Racon. F = Flye, C = Canu, W = Wtdbg2, NE = NECAT, M = Medaka, NP = NextPolish, R = Racon

Barcode 01

IncI1

blaCMY-7

Ampicillin, Amoxicillin/clavulanic acid, Cefoxitin, ceftriaxone

F + M, F + R, C + M, C + NP, C + R, W + M, W + NP, W + R

IncQ1

aph(6)-Id

Kanamycin

All

blaTEM-34

Ampicillin, Amoxicillin/clavulanic acid

All except F + NP

dfrA14

Trimethoprim

All except F + NP

mph(A)

Erythromycin, azithromycin

All except F + NP

strA

Streptomycin

All

sul2

Sulfisoxazole

All

Barcode 03

IncB/O/K/Z

aadA5

Streptomycin

All except NE + NP

aph(6)-Id

Kanamycin

All

blacTX-M-15

Ampicillin, ceftriaxone

All

dfrA17

Trimethoprim

All

mph(A)

Erythromycin, azithromycin

All

qnrS1

Ciprofloxacin I/R

All

strA

Streptomycin

All

sul1

Sulfisoxazole

All

sul2

Sulfisoxazole

All except W + M, W + NP, W + R

tet(A)

Tetracycline

All

Barcode 08

IncFII

blaTEM-S7

Ampicillin

C + M, C + NP

mph(A)

Erythromycin, azithromycin

C + M, C + NP, C + R

blaTEM-79

Ampicillin

C + R

Barcode 09

InCQ1

aph(3'')-Ib

Streptomycin

All

aph(6)-Id

Kanamycin

All

blaTEM-1B

Ampicillin

All except F + M, F + NP, F + R

dfrA7

Trimethoprim

All except F + M, F + NP, F + R

sul1

Sulfisoxazole

All except F + M, F + NP, F + R

sul2

Sulfisoxazole

All except W + NP

tet(A)

Tetracycline

NE + M, NE + NP, NE + R