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Table 7 Primers used in the study

From: Characterizing the pathotype of neonatal meningitis causing Escherichia coli (NMEC)

Primer Name

Gene/Function

Sequence 5’–3’

Product size

Reference

chuA.1

Phylogrouping

GACGAACCAACGGTCAGGAT

279

[17]

chuA.2

 

TGCCGCCAGTACCAAAGACA

  

yjaA.1

Phylogrouping

TGAAGTGTCAGGAGACGCTG

211

[17]

yjaA.2

 

ATGGAGAATGCGTTCCTCAAC

  

TspE4C2.1

Phylogrouping

GAGTAATGTCGGGGCATTCA

152

[17]

TspE4C2.2

 

CGCGCCAACAAAGTATTACG

  

afaF

Afimbrial adhesin

CAT CAA GCT GTT TGT TCG TCC GCC G

750

[52]

afaR

 

GCT GGG CAG CAA ACT GAT AAC TCT C

  

aslAF

Arylsulfatase

GCG TGA TGT TCA TGT CAA CC

463

[44]

aslAR

 

ATC CGC CAG ATC TAC AAT GC

  

aufAF

Auf fimbriae

TGC ACA TCA GGA AAC CAG ATA C

350

This study

aufR

 

GGC TCA CTG ATA TGG ATG ACA A

  

cnfF

Cytotoxic necrotizing factor1

CAT TCA GAG TCC TGC CCT CAT TAT T

498

[53]

cnfR

 

AAG ATG GAG TTT CCT ATG CAG GAG

  

fimHF

Type I fimbriae

GCA GTC ACC TGC CCT CCG GTA

508

[53]

fimHR

 

TGC AGA ACG GAT AAG CCG TGG

  

hlyAF

Alpha hemolysin

ACC ATA TAA GCG GTC ATT CCC GTC A

1177

[53]

hlyAR

 

AAC AAG GAT AAG CAC TGT TCT GGC T

  

hlyDF

Secretion protein for HlyA

CTC CGG TAC GTG AAA AGG AC

904

[54]

hlyDR

 

GCC CTG ATT ACT GAA GCC TG

  

ibeAF

Invasin of brain endothelium A

CAT TAG CTC TCG GTT CAC GCT

171

[55]

ibeAR

 

TTA CCG CCG TTG ATG TTA TCA

  

ibeBF

Invasin of brain endothelium B

GCA TATTCTGCTGGTTTCTAATGTC

660

This study

ibeBR

 

GTT CTG GAT TTT CTG TTC ATA ATT CA

  

issF

Increased serum survival

CAG CAA CCC GAA CCA CTT GAT G

323

[54]

issR

 

AGC ATT GCC AGA GCG GCA GAA

  

iutAF

Aerobactin synthesis

ATGAGCATATCTCCGGACG

587

[52]

iutAR

 

CAGGTCGAAGAACATCTGG

  

iucCF

Aerobactin synthesis

ACC CGT CTG CAA ATC ATG GAT

269

[55]

iucCR

 

AAA CCT GGC TTA CGC AAC TGT

  

sitAF

Periplasmic iron-binding protein

AGG GGG CAC AAC TGA TTC TCG

608

[56]

sitAR

 

TAC CGG GCC GTT TTC TGT GC

  

kpsMTII F

Capsular type II

GCG CAT TTG CTG ATA CTG TTG

272

[57]

kpsMT IIR

 

CAT CCA GAC GAT AAG CAT GAG CA

  

kpsMT K1

K 1 capsule

TAG CAA ACG TTC TAT TGG TGC

153

[57]

kpsMT IIR

 

CAT CCA GAC GAT AAG CAT GAG CA

 

[57]

neuCF

Capsular N-acetylneuraminic acid synthesis

GGT GGT ACA TTC CGG GAT GTC

676

[52]

neuCR

 

AGG TGA AAA GCC TGG TAG TGT G

  

Nlp I F

New lipoprotein I (adhesin/invasin)

AGT AAT ACT TCC TGG CGT AAA AGT GA

662

This study

Nlp I R

 

AAA TAG AAG TTG GTT TCA CTG AGA TG

  

ompAF

Outer membrane protein A

CACTAAATCCAACGTTTATGGTAAAA

 

This study

ompAR

 

GATACCTTTAACTTCGATCTCTACGC

  

papCF

Outer membrane usher protein of P pili

ATA TCC TTT CTG CAG GGA TGC AAT A

205

[57]

papCR

 

GAC GGC TGT ACT GCA GGG TGT GGC G

  

papG IF

Fimbrial adhesin PapG allele I

CTA CTA TAG TTC ATG CTC AGG TC

474

[54]

papG IR

 

CCT GCA TCC TCC ACC ATT ATC GA

  

papG IIF

Fimbrial adhesin PapG allele II

CCC AGC TTT GTT ATT TTC CTT G

190

[54]

papGIIR

 

TTC TTA CCA TGG CTG TAT GTC G

  

papGIIIF

Fimbrial adhesin PapG allele III

GGC CTG CAA TGG ATT TAC CTG G

258

[54]

papGIIIR

 

CCA CCA AAT GAC CAT GCC AGA C

  

satF

Secreted autotransporter toxin

GCAGCAAATATTGATATATCA

630

[58]

satR

 

GTTGTTGACCTCAGCAAGGAA

  

sfa/focF

S fimbrial adhesin

CGG AGG AGT AAT TAC AAA CCT GGC A

410

[57]

sfa/focR

 

CTC CGG AGA ACT GGG TGC ATC TTA C

  

trajF

Conjugal transfer

CAA TGG GGC TTT TAT TGA ACT C

369

This study

trajR

 

TGA CCA ACA CCC AGC ATA TAA A

  

vat1

Vacuolating cytotoxin

TCC TGG GAC ATA ATG GTC AG

900

This study

vat2

 

GTG TCA GAA CGG AAT TGT

  

adkF

MLST

ATTCTGCTTGGCGCTCCGGG

583

[49]

adkR

 

CCGTCAACTTTCGCGTATTT

  

fumCF

MLST

TCACAGGTCGCCAGCGCTTC

806

[49]

fumR

 

GTACGCAGCGAAAAAGATT

  

gyrBF

MLST

TCGGCGACACGGATGACGGC

911

[49]

gyrBR

 

GTCCATGTAGGCGTTCAGGG

  

icdF

MLST

ATGGAAAGTAAAGTAGTTGTTCCGGCACA

878

[49]

icdR

 

GGACGCAGCAGGATCTGTT

  

mdhF

MLST

ATGAAAGTCGCAGTCCTCGGCGCTGCTGGCGG

932

[49]

mdhR

 

TTAACGAACTCCTGCCCCAGAGCGATATCTTTCTT

  

purAF

MLST

TCGGTAACGGTGTTGTGCTG

816

[49]

purAR

 

CATACGGTAAGCCACGCAGA

  

recAF

MLST

CGCATTCGCTTTACCCTGACC

780

[49]

recAR

 

TCGTCGAAATCTACGGACCGGA

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