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Table 1 Detection of plasmids in two avian-associated E. coli isolates using commercial plasmid extraction kits

From: Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing

  

E. coli isolate 4957-3S1

E. coli isolate 4957-C3

Plasmid Extraction Kita

Sequencing Kitb

AB241c

AB690

AA175

AC044

AB690

AB241

AA176

AA378

AB526

AE638

AG799

A

Ligation

+

+

-

-

+

-

-

-

-

-

-

A

Rapid

+

+

-

-

+

+

-

-

-

-

-

B

Ligation

+

+

-

-

+

+

-

-

-

-

-

B

Rapid

+

+

-

-

+

-

-

-

-

-

-

C

Ligation

+

+

-

-

+

-

-

-

-

-

-

C

Rapid

+

+

-

-

+

-

-

-

-

-

-

D

Ligation

+

-

-

-

+

-

-

-

-

+

-

D

Rapid

+

-

-

-

+

-

-

-

-

-

-

E

Ligation

-

-

-

-

+

-

-

-

-

-

-

E

Rapid

+

-

-

-

+

-

-

-

-

-

-

F

Ligation

-

-

-

-

-

-

-

-

-

-

+

F

Rapid

+

-

-

-

+

-

-

-

-

-

-

Combinationsd

            

A/B

Ligation

+

+

-

-

+

-

-

-

-

-

-

A/B

Rapid

+

+

-

-

+

+

-

-

-

-

-

A/C

Ligation

+

-

-

-

+

-

-

-

-

-

-

A/C

Rapid

+

+

-

-

+

-

-

-

-

-

-

A/D

Ligation

+

+

-

-

+

-

-

-

-

-

-

A/D

Rapid

+

-

-

-

+

-

-

-

-

-

-

A/E

Ligation

+

+

-

-

+

-

-

-

-

-

-

A/E

Rapid

+

-

+

-

+

+

-

-

-

-

-

A/F

Ligation

+

-

-

-

+

-

-

-

-

-

-

A/F

Rapid

+

+

-

-

+

+

-

-

-

-

-

B/C

Ligation

+

+

-

-

+

-

-

-

-

-

-

B/C

Rapid

+

+

-

-

+

-

-

-

-

-

-

B/D

Ligation

+

+

-

-

+

-

-

-

-

-

-

B/D

Rapid

+

-

-

-

+

-

-

-

-

-

-

B/E

Ligation

+

+

-

-

+

-

-

-

-

-

-

B/E

Rapid

+

-

-

-

+

-

-

-

-

-

-

B/F

Ligation

-

-

-

-

+

-

-

+

-

-

-

B/F

Rapid

+

+

-

-

+

-

-

-

-

-

-

C/D

Ligation

-

+

-

-

+

-

-

-

-

-

-

C/D

Rapid

+

-

-

-

+

-

-

-

-

-

-

C/E

Ligation

+

-

-

-

+

-

-

-

-

-

-

C/E

Rapid

+

-

-

-

+

-

-

-

-

-

-

C/F

Ligation

+

-

-

+

+

-

-

-

-

+

-

C/F

Rapid

+

-

-

-

+

-

-

-

-

-

-

D/E

Ligation

+

+

-

-

+

-

+

-

-

+

-

D/E

Rapid

+

-

-

-

+

-

-

-

-

-

-

D/F

Ligation

-

-

-

-

-

-

-

-

-

-

-

D/F

Rapid

+

-

-

-

-

-

-

-

+

-

-

E/F

Ligation

+

-

-

-

-

-

+

+

-

-

-

E/F

Rapid

+

-

-

-

+

-

-

-

-

-

-

  1. aPlasmid-containing samples were prepared from the two E. coli isolates using commercial plasmid extraction kits: A – GenElute plasmid miniprep kit (#PLN70; Millipore Sigma); B – NucleoSpin plasmid mini kit (#740588.50; Machery-Nagel); C – Presto mini plasmid kit (#PD100; Geneaid); D – Monarch plasmid miniprep kit (#T1010S; New England Biolabs); E – Plasmid midi kit (#12,143; Qiagen); and F – GeneJET plasmid miniprep kit (#K0502; ThermoFisher)
  2. bSequencing libraries from each plasmid sample were generated using the Nanopore Ligation or Rapid kits with sequencing performed on the Nanopore MinION Mk1C.
  3. cPlasmid clusters were detected by MOB-suite software (v3.1.0) in each finished DNA assembly from each E. coli isolate. The metadata corresponding to each ID listed is in Table S2
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BMC Genomics

ISSN: 1471-2164

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