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Table 1 Primers used for detection of E. coli molecular markers

From: Diarrhea-associated biofilm formed by enteroaggregative Escherichia coli and aggregative Citrobacter freundii: a consortium mediated by putative F pili

Gene

Locus description

Primer sequence (5'-3')

Amplicon length (bp)

Annealing temperature (°C)

Reference

Enteroaggregative E. coli markers

aat

AA probe (CVD432)

CTGGCGAAAGACTGTATCAT

630

55-60

[9]

  

CCATGTATAGAAATCCGCTGTT

   

aggR

Transcriptional activator

CTAATTGTACAATCGATGTA

324

50

This study

  

CTGAAGTAATTCTTGAAT

   

aggA

Aggregative fimbria I (AAF I)

GCTAACGCTGCGTTAGAAAGACC

421

55-60

[9]

  

GGAGTATCATTCTATATTCGCC

   

aafA

AAF/II

GACAACCGCAACGCTGCGCTG

233

50

[9]

  

GATAGCCGGTGTAATTGAGCC

   

agg3A

AAF/III

GTATCATTGCGAGTCTGGTATTCAG

462

60

[5]

  

GGGCTGTTATAGAGTAACTTCCAG

   

pilS

Type IV pilus

ATGAGCGTCATAACCTGTTC

532

58

[14]

  

CTGTTGGTTTCCAGTTTGAT

   

pic

Mucinase

TTCAGCGGAAAGACGAA

500

55-60

[9]

  

TCTGCGCATTCATACCA

   

pet

Plasmid-encoded toxin

CCGCAAATGGAGCTGCAAC

1,133

55-60

[9]

  

CGAGTTTTCCGCCGTTTTC

   

astA

EAEC heat-stable toxin

CCATCAACACAGTATATCCGA

111

55-60

[9]

  

GGTCGCGAGTGACGGCTTTGT

   

Enteropathogenic E. coli markers

EAF probe

EPEC adhesion factor

CAGGGTAAAAGAAAGATGATAA

396

52

[9]

  

TATGGGGACCATGTATTATCA

   

eae

Intimin (adhesin)

CCCGAATTCGGCACAAGCATAAGC

877

52

[9]

  

CCCGGATCCGTCTCGCCAGTATTCG

   

escC

Locus of enterocyte effacement (LEE) 2

GTCAGCGACAGATATAACATAC

450

54

[44]

  

AACGCATTCACCCTAATC

   

escV

LEE 3

CTAACTTCTTTCCCCACAATC

760

54

[44]

  

TATCCCCAACAGGCAAAC

   

Enterohaemorrhagic E.coli markers

stx

Shiga toxin I and II

TTTACGATAGACTTCTCGAC

227

48

[45]

  

CACATATAAATTATTTCGCTC

   

hlyA

hemolysin

GGTGCAGCAGAAAAAGTTGTAG

1,551

57

[46]

  

TCTCGCCTGATAGTGTTTGGTA

   

Enterotoxigenic E. coli markers

cfaA-B

Colonization factor antigen 1

CTATTGGTGCAATGGCTCTGACC

352

55-60

[47]

  

GCAGCAGCTTCAAATTCTTTGGC

   

cs3

Colonization factor CS3

CCACTCTAACCAAAGAACTGGC

250

60

This study

  

GGTGGTGGCAAAGCTAGCAGAG

   

ltA

Heat-labile enterotoxin

GGCGACAGATTATACCGTGC

696

50

This study

  

CCGAATTCTGTTATATATGTC

   

estA

Heat-stable enterotoxin

CAGGATGCTAAACCAGTAGAGT

174

60

This study

  

TCCCTTTATATTATTAATAGCACCC

   

Uropathogenic E. coli markers

papC

P pili usher

GACGGCTGTACTGCAGGGTGTGGCG

328

60

[48]

  

ATATCCTTTCTGCAGGGATGCAATA

   

sfaD-E

S fimbria

CTCCGGAGAACTGGGTGCATCTTAC

407

60

[48]

  

CGGAGGAGTAATTACAAACCTGGCA