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 | Â | TGCCGCCAGTACCAAAGACA | Â | Â |
yjaA.1 | Phylogrouping | TGAAGTGTCAGGAGACGCTG | 211 | [17] |
yjaA.2 | Â | ATGGAGAATGCGTTCCTCAAC | Â | Â |
TspE4C2.1 | Phylogrouping | GAGTAATGTCGGGGCATTCA | 152 | [17] |
TspE4C2.2 | Â | CGCGCCAACAAAGTATTACG | Â | Â |
afaF | Afimbrial adhesin | CAT CAA GCT GTT TGT TCG TCC GCC G | 750 | [52] |
afaR | Â | GCT GGG CAG CAA ACT GAT AAC TCT C | Â | Â |
aslAF | Arylsulfatase | GCG TGA TGT TCA TGT CAA CC | 463 | [44] |
aslAR | Â | ATC CGC CAG ATC TAC AAT GC | Â | Â |
aufAF | Auf fimbriae | TGC ACA TCA GGA AAC CAG ATA C | 350 | This study |
aufR | Â | GGC TCA CTG ATA TGG ATG ACA A | Â | Â |
cnfF | Cytotoxic necrotizing factor1 | CAT TCA GAG TCC TGC CCT CAT TAT T | 498 | [53] |
cnfR | Â | AAG ATG GAG TTT CCT ATG CAG GAG | Â | Â |
fimHF | Type I fimbriae | GCA GTC ACC TGC CCT CCG GTA | 508 | [53] |
fimHR | Â | TGC AGA ACG GAT AAG CCG TGG | Â | Â |
hlyAF | Alpha hemolysin | ACC ATA TAA GCG GTC ATT CCC GTC A | 1177 | [53] |
hlyAR | Â | AAC AAG GAT AAG CAC TGT TCT GGC T | Â | Â |
hlyDF | Secretion protein for HlyA | CTC CGG TAC GTG AAA AGG AC | 904 | [54] |
hlyDR | Â | GCC CTG ATT ACT GAA GCC TG | Â | Â |
ibeAF | Invasin of brain endothelium A | CAT TAG CTC TCG GTT CAC GCT | 171 | [55] |
ibeAR | Â | TTA CCG CCG TTG ATG TTA TCA | Â | Â |
ibeBF | Invasin of brain endothelium B | GCA TATTCTGCTGGTTTCTAATGTC | 660 | This study |
ibeBR | Â | GTT CTG GAT TTT CTG TTC ATA ATT CA | Â | Â |
issF | Increased serum survival | CAG CAA CCC GAA CCA CTT GAT G | 323 | [54] |
issR | Â | AGC ATT GCC AGA GCG GCA GAA | Â | Â |
iutAF | Aerobactin synthesis | ATGAGCATATCTCCGGACG | 587 | [52] |
iutAR | Â | CAGGTCGAAGAACATCTGG | Â | Â |
iucCF | Aerobactin synthesis | ACC CGT CTG CAA ATC ATG GAT | 269 | [55] |
iucCR | Â | AAA CCT GGC TTA CGC AAC TGT | Â | Â |
sitAF | Periplasmic iron-binding protein | AGG GGG CAC AAC TGA TTC TCG | 608 | [56] |
sitAR | Â | TAC CGG GCC GTT TTC TGT GC | Â | Â |
kpsMTII F | Capsular type II | GCG CAT TTG CTG ATA CTG TTG | 272 | [57] |
kpsMT IIR | Â | CAT CCA GAC GAT AAG CAT GAG CA | Â | Â |
kpsMT K1 | K 1 capsule | TAG CAA ACG TTC TAT TGG TGC | 153 | [57] |
kpsMT IIR | Â | CAT CCA GAC GAT AAG CAT GAG CA | Â | [57] |
neuCF | Capsular N-acetylneuraminic acid synthesis | GGT GGT ACA TTC CGG GAT GTC | 676 | [52] |
neuCR | Â | AGG TGA AAA GCC TGG TAG TGT G | Â | Â |
Nlp I F | New lipoprotein I (adhesin/invasin) | AGT AAT ACT TCC TGG CGT AAA AGT GA | 662 | This study |
Nlp I R | Â | AAA TAG AAG TTG GTT TCA CTG AGA TG | Â | Â |
ompAF | Outer membrane protein A | CACTAAATCCAACGTTTATGGTAAAA | Â | This study |
ompAR | Â | GATACCTTTAACTTCGATCTCTACGC | Â | Â |
papCF | Outer membrane usher protein of P pili | ATA TCC TTT CTG CAG GGA TGC AAT A | 205 | [57] |
papCR | Â | GAC GGC TGT ACT GCA GGG TGT GGC G | Â | Â |
papG IF | Fimbrial adhesin PapG allele I | CTA CTA TAG TTC ATG CTC AGG TC | 474 | [54] |
papG IR | Â | CCT GCA TCC TCC ACC ATT ATC GA | Â | Â |
papG IIF | Fimbrial adhesin PapG allele II | CCC AGC TTT GTT ATT TTC CTT G | 190 | [54] |
papGIIR | Â | TTC TTA CCA TGG CTG TAT GTC G | Â | Â |
papGIIIF | Fimbrial adhesin PapG allele III | GGC CTG CAA TGG ATT TAC CTG G | 258 | [54] |
papGIIIR | Â | CCA CCA AAT GAC CAT GCC AGA C | Â | Â |
satF | Secreted autotransporter toxin | GCAGCAAATATTGATATATCA | 630 | [58] |
satR | Â | GTTGTTGACCTCAGCAAGGAA | Â | Â |
sfa/focF | S fimbrial adhesin | CGG AGG AGT AAT TAC AAA CCT GGC A | 410 | [57] |
sfa/focR | Â | CTC CGG AGA ACT GGG TGC ATC TTA C | Â | Â |
trajF | Conjugal transfer | CAA TGG GGC TTT TAT TGA ACT C | 369 | This study |
trajR | Â | TGA CCA ACA CCC AGC ATA TAA A | Â | Â |
vat1 | Vacuolating cytotoxin | TCC TGG GAC ATA ATG GTC AG | 900 | This study |
vat2 | Â | GTG TCA GAA CGG AAT TGT | Â | Â |
adkF | MLST | ATTCTGCTTGGCGCTCCGGG | 583 | [49] |
adkR | Â | CCGTCAACTTTCGCGTATTT | Â | Â |
fumCF | MLST | TCACAGGTCGCCAGCGCTTC | 806 | [49] |
fumR | Â | GTACGCAGCGAAAAAGATT | Â | Â |
gyrBF | MLST | TCGGCGACACGGATGACGGC | 911 | [49] |
gyrBR | Â | GTCCATGTAGGCGTTCAGGG | Â | Â |
icdF | MLST | ATGGAAAGTAAAGTAGTTGTTCCGGCACA | 878 | [49] |
icdR | Â | GGACGCAGCAGGATCTGTT | Â | Â |
mdhF | MLST | ATGAAAGTCGCAGTCCTCGGCGCTGCTGGCGG | 932 | [49] |
mdhR | Â | TTAACGAACTCCTGCCCCAGAGCGATATCTTTCTT | Â | Â |
purAF | MLST | TCGGTAACGGTGTTGTGCTG | 816 | [49] |
purAR | Â | CATACGGTAAGCCACGCAGA | Â | Â |
recAF | MLST | CGCATTCGCTTTACCCTGACC | 780 | [49] |
recAR | Â | TCGTCGAAATCTACGGACCGGA | Â | Â |