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Table 5 Primers used in the present study

From: Antimicrobial resistance, virulence associated genes and phylogenetic background versus plasmid replicon types: the possible associations in avian pathogenic Escherichia coli (APEC)

Panel

Primer pair

Sequence (5′ to 3′)

Annealing temp (°C)

Product size (bp)

Ref.

Phylogenetic grouping

 Quadruplex

chuA

F: ATGGTACCGGACGAACCAAC

R: TGCCGCCAGTACCAAAGACA

59

288

[23]

yjaA

F: CAAACGTGAAGTGTCAGGAG

R: AATGCGTTCCTCAACCTGTG

211

TspE4.C2

F: CACTATTCGTAAGGTCATCC

R: AGTTTATCGCTGCGGGTCGC

152

arpA

F: AACGCTATTCGCCAGCTTGC

R: TCTCCCCATACCGTACGCTA

400

 Group E

arpA

F: GATTCCATCTTGTCAAAATATGCC

R: GAAAAGAAAAAGAATTCCCAAGAG

57

219

 Group C

trpA

F: AGTTTTATGCCCAGTGCGAG

R: TCTGCGCCGGTCACGCCC

59

489

β- Lactamase/ESBL genes

 Triplex

BlaTEM

F: CATTTCCGTGTCGCCCTTATTC

R: CGTTCATCCATAGTTGCCTGAC

57

800

[50]

BlaSHV

F: AGCCGCTTGAGCAAATTAAAC

R: ATCCCGCAGATAAATCACCAC

713

BlaOXA

F: GGCACCAGATTCAACTTTCAAG

R: GACCCCAAGTTTCCTGTAAGTG

564

 Uniplex

BlaCTX-M

F: ATGTGCAGYACCAGTAARGTKATGGC

R: TGGGTRAARTARGTSACCAGAAYCAGCGG

61

593

[51]

APEC virulence genotyping

 iroN

F: AATCCGGCAAAGAGACGAACCGCCT

R: GTTCGGGCAACCCCTGCTTTGACTTT

60

553

[5]

 ompT

F: TCATCCCGGAAGCCTCCCTCACTACTAT

R: TAGCGTTTGCTGCACTGGCTTCTGATAC

496

 hlyF

F: GGCCACAGTCGTTTAGGGTGCTTACC

R: GGCGGTTTAGGCATTCCGATACTCAG

450

 iss

F: CAGCAACCCGAACCACTTGATG

R: AGCATTGCCAGAGCGGCAGAA

323

 iutA

F: GGCTGGACATCATGGGAACTGG

R: CGTCGGGAACGGGTAGAATCG

302

Plasmid replicon typing

 1

B/O

F: GCGGTCCGGAAAGCCAGAAAAC

R: TCTGCGTTCCGCCAAGTTCGA

60

159

[35]

FIC

F: GTGAACTGGCAGATGAGGAAGG

R: TTCTCCTCGTCGCCAAACTAGAT

262

A/C

F: GAGAACCAAAGACAAAGACCTGGA

R: ACGACAAACCTGAATTGCCTCCTT

465

P

F: CTATGGCCCTGCAAACGCGCCAGAAA

R: TCACGCGCCAGGGCGCAGCC

534

T

F: TTGGCCTGTTTGTGCCTAAACCAT

R: CGTTGATTACACTTAGCTTTGGAC

750

 2

K/B

F: GCGGTCCGGAAAGCCAGAAAAC

R: TCTTTCACGAGCCCGCCAAA

60

160

W

F: CCTAAGAACAACAAAGCCCCCG

R: GGTGCGCGGCATAGAACCGT

242

FIIA

F: CTGTCGTAAGCTGATGGC

R: CTCTGCCACAAACTTCAGC

270

FIA

F: CCATGCTGGTTCTAGAGAAGGTG

R: GTATATCCTTACTGGCTTCCGCAG

462

FIB

F: GGAGTTCTGACACACGATTTTCTG

R: CTCCCGTCGCTTCAGGGCATT

702

Y

F: AATTCAAACAACACTGTGCAGCCTG

R: GCGAGAATGGACGATTACAAAACTTT

765

 3

I1

F: CGAAAGCCGGACGGCAGAA

R: TCGTCGTTCCGCCAAGTTCGT

60

139

Frep

F: TGATCGTTTAAGGAATTTTG

R: GAAGATCAGTCACACCATCC

270

X

F: AACCTTAGAGGCTATTTAAGTTGCTGAT

R: TGAGAGTCAATTTTTATCTCATGTTTTAGC

376

HI1

F: GGAGCGATGGATTACTTCAGTAC

R: TGCCGTTTCACCTCGTGAGTA

471

N

F: GTCTAACGAGCTTACCGAAG

R: GTTTCAACTCTGCCAAGTTC

559

HI2

F: TTTCTCCTGAGTCACCTGTTAACAC

R: GGCTCACTACCGTTGTCATCCT

644

L/M

F: GGATGAAAACTATCAGCATCTGAAG

R: CTGCAGGGGCGATTCTTTAGG

785