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Table 1 Primers used for PCR analysis of known virulence genes of extra-intestinal pathogenic E. coli

From: Adherent-invasive Escherichia coli (AIEC) in pediatric Crohn’s disease patients: phenotypic and genetic pathogenic features

Virulence traits

Genes

Primer sequence (5′à 3′)

Expected amplicon size (bp)

References

P fimbriae

papA

ATGGCAGTGGTGTCTTTTGGTG

720

[33]

CGTCCCACCATACGTGCTCTTC

papEF

GCAACAGCAACGCTGGTTGCATCAT

336

[33]

AGAGAGAGCCACTCTTATACGGACA

P pili-associated G-adhesins

papC

GACGGCTGTACTGCAGGGTGTGGCG

328

[33]

ATATCCTTTCTGCAGGGATGCAATA

Pyelonephritis-associated pili

papG allele II e III

CTGTAATTACGGAAGTGATTTCTG

1070

[33]

ACTATCCGGCTCCGGATAAACCAT

papG allele II

GGGATGAGCGGGCCTTTGAT

190

[33]

CGGGCCCCCAAGTAACTCG

papG allele III

GGCCTGCAATGGATTTACCTGG

258

[33]

CCACCAAATGACCATGCCAGAC

S and F1C fimbriae

sfa//focDE

CTCCGGAGAACTGGGTGCATCTTAC

410

[33]

CGGAGGAGTAATTACAAACCTGGCA

F1C fimbriae

focG

CAGCACAGGCAGTGGATACGA

360

[33]

GAATGTCGCCTGCCCATTGCT

Dr-binding adhesin

afa/draBC

GGCAGAGGGCCGGCAACAGGC

559

[33]

CCCGTAACGCGCCAGCATCTC

G fimbriae

gafD

TGTTGGACCGTCTCAGGGCTC

952

[33]

CTCCCGGAACTCGCTGTTACT

Nonfimbrial adhesin type 1

nfaE

GCTTACTGATTCTGGGATGGA

559

[33]

CGGTGGCCGAGTCATATGCCA

Mannose-specific adhesion gene. Type1 fimbriae.

fimH

TGCAGAACGGATAAGCCGTGG

508

[33]

GCAGTCACCTGCCCTCCGGTA

Haemolysin A

hlyA

AACAAGGATAAGCACTGTTCTGGCT

1177

[33]

ACCATATAAGCGGTCATTCCCGTCA

Cytotoxic necrotizing factor 1

cnf1

GTGATAATATATCACATTATTC

498

[33]

GAATTCGTCTCGTTGAGCTTCACTG

Yersiniabactin siderophore receptor

fyuA

TGATTAACCCCGCGACGGGAA

880

[33]

CGCAGTAGGCACGATGTTGTA

Aerobactin siderophore receptor

iutA

GGCTGGACATCATGGGAACTGG

300

[33]

CGTCGGGAACGGGTAGAATCG

Capsule synthesis primers

kpsMT II

GCGCATTTGCTGATACTGTTG

272

[33]

CATCCAGACGATAAGCATGAGCA

kpsMT III

TCCTCTTGCTACTATTCCCCCT

392

[33]

AGGCGTATCCATCCCTCCTAAC

kpsMT1 (K1)

TAGCAAACGTTCTATTGGTGC

153

[33]

CATCCAGACGATAAGCATGAGCA

kpsMT 5 (K5)

CAGTATCAGCAATCGTTCTGTA

159

[33]

CATCCAGACGATAAGCATGAGCA

Invasion of brain endothelium gene (associate with neonatal meningitis)

IbeA

AGGCAGGTGTGCGCCGCGTAC

170

[33]

TGGTGCTCCGGCAAACCATGC

Encodes colicin V

cvaC

CACACACAAACGGGAGCTGTT

680

[33]

CTTCCCGCAGCATAGTTCCAT

Serum resistance gene

traT

GGTGTGGTGCGATGAGCACAG

290

[33]

CACGGTTCAGCCATCCCTGAG

Pathogenicity islands described in a virulent uropathogen.

PAI

GGACATCCTGTTACAGCGCGCA

930

[33]

TCGCCACCAATCACAGCCGAAC

Transcriptional Activator gene of aggregative adhesion fimbriae

aggR

GTATACACAAAAGAAGGAAGC

254

[34]

ACAGAATCGTCAGCATCAGC

CVD432 gene probe sequence of the plasmid of aggregative adhesion

pAA (CVD432)

CTGGCCAAAGACTGTATCAT

630

[34]

CAATGTATAGAAATCCGCTGTT