Primers used
| Primer sequences | Target sequences | References |
|---|---|---|
| SPATE, serine protease autotransporter. | ||
| Autotransporters | ||
| SPATE1 5′ GAGGTCAACAACCTGAACAAACGTATGGG | The genes encoding SPATE | This study |
| SPATE2 5′ CCGGCACGGGCTGTCACTTTCCAG | ||
| E coli phylogenetic groups | ||
| ChuAf 5′ CGGACGAACCAACGGTCAGGAT | The chuA gene is required for haemtransport in E coli O157:H7 | Modified from Clermont et al15 |
| ChuAr 5′ TGCCGCCAGTACCAAAGACACG | ||
| Yjaf 5′ CGTGAAGTGTCAGGAGACGCTGC | The yjaA gene coding for protein of unknown function | Modified from Clermont et al15 |
| Yjar 5′ TGCGTTCCTCAACCTGTGACAAACC | ||
| Tsp1 5′ GGGAGTAATGTCGGGGCATTCAG Tsp2 5′ CATCGCGCCAACAAAGTATTACGCAG | Tsp encodes for a putative DNA fragment (TSPE4.C2) in E coli | Modified from Clermont et al15 |
| E coli toxins | ||
| Cnff 5′ AGTACTGACACTCACTCAAGCCGC | Cytotoxic necrotising factors (Cnf1 and Cnf2) | This study |
| Cnfr 5′ GCAGAACGACGTTCTTCATAAGTATCACC | ||
| IpgDf 5′ CGACTTCTCTTCTGACGCCGAC IpgDr 5′ CAACATTCCTCCAGCCTAAGCCC | ipgD gene modulates entry of bacteria into epithelial cells | This study |
| Vt1f 5′ CGCATAGTGGAACCTCACTGACGC | Verocytotoxin 1 | This study |
| Vt1r 5′ CATCCCCGTACGACTGATCCC | ||
| Vt2f 5′ CGGAATGCAAATCAGTCGTCACTCAC | Verocytotoxin 2 | This study |
| Vt2r 5′ TCCCCGATACTCCGGAAGCAC | ||
| HlyAf 5′ TGCAGCCTCCAGTGCATCCCTC | The hlyA gene encoding α haemolysin | |
| HlyAr 5′ CTTACCACTCTGACTGCGATCAGC | ||
| STaf 5′ GTGAAACAACATGACGGGAGG | Heat-stable enterotoxin 1 | This study |
| STar 5′ ATAACATCCAGCACAGGCAGG | ||
| STbf 5′ GGGGTTAGAGATGGTACTGCTGGAG | Heat-stable enterotoxin 2 | This study |
| STbr 5′ GACAATGTCCGTCTTGCGTTAGGAC | ||
| LTf 5′ CCGTGCTGACTCTAGACCCCCA | Heat-labile enterotoxin LT | This study |
| LTr 5′ CCTGCTAATCTGTAACCATCCTCTGC | ||
| Eaef 5′ CCAGGCTTCGTCACAGTTGCAGGC Eaer 5′ CGCCAGTATTCGCCACCAATACC | The eae gene coding for intimin present in AEEC strains | This study |
| Enterotoxigenic Bacteroides fragilis (ETBF) | ||
| Bf1F 5′ GTTAGTGCCCAGATGCAGGATGCGG | The genes coding for Bacteroides fragilis enterotoxins (Bft1, Bft2 and Bft3) | This study |
| Bf2F 5′ GAACTCGGTTTATGCAGTTCATGGACTG | ||
| Bf3R 5′ TGGGTTGTAGACATCCCACTGGCTT | ||
| Bf4R 5′ GGATACATCAGCTGGGTTGTAGACATCCC | ||
| E coli adhesins | ||
| PapF 5′ CCGGCGTTCAGGCTGTAGCTG PapR 5′ GCTACAGTGGCAGTATGAGTAATGACCGTTA | The genes coding for pathogenicity islands (PAI I, PAI II)16 and sfp gene cluster | This study |
| PAI1 5′ TAGCTCAGACGCCAGGATTTTCCCTG | ||
| pai2 5′ CCTGGCGCCTGCGGGCTGACTATCAGGG | ||
| BmaEf 5′ CTAACTTGCCATGCTGTGACAGTA | The bmaE gene for M-agglutinin subunit; Afa-8 gene cluster | Martin et al17 |
| BmaEr 5′ TTATCCCCTGCGTAGTTGTGAATC | ||
| Sfaf 5′ CGGAGGAGTAATTACAAACCTGGCA | S-fimbrial adhesins encoded by sfaD to sfaE | Martin et al17 |
| Sfar 5′ CTCCGGAGAACTGGGTGCATCTTAC | ||
| Afaf 5′ TATGGTGAGTTGGCGGGGATGTACAGTTACA | AfaE-3 gene cluster | This study |
| Afar 5′ CCGGGAAAGTTGTCGGATCCAGTGT | ||
| AIDA1 5′ TATGCCACCTGGTATGCCGATGAC AIDA2 5′ ACGCCCACATTCCCCCAGAC | The aidA gene coding E coli AIDA-I adhesin in DAEC strains | This study |
| AggRf 5′ GAGTTAGGTCACTCTAACGCAGAGTTG | The aggR gene for adhesin of aggregative adherence fimbria I | This study |
| AggRr 5′ GACCAATTCGGACAACTGCAAGCATCTAC | ||
| Ag43F 5′TGACACAGGCAATGGACTATGACCG Ag43R 5′GGCATCATCCCGGACCGTGC | The agn43 gene coding for antigen involved in E coli autoaggregation | This study |
| Flagella and type 1 fimbrae typing | ||
| Primer1 5′CAAGTCATTAATAC(A/C)AACAGCC | The fliC genes coding for flagellin proteins | Machado et al18 |
| Primer2 5′GACAT(A/G)TT(A/G)GA(G/A/C)ACTTC(G/C)GT | ||
| FimHf 5′ CTGGTCATTCGCCTGTAAAACCGCCA FimHr 5′ GTCACGCCAATAATCGATTGCACATTCCCT | The fimH gene encoding FimH subunit of type 1 pili | This study |
| Ribosomal DNA-based primers | ||
| ITSF 5′ GTCGTAACAAGGTAGCCGTA | 16S-23S rRNA intergenic transcribed spacers | Cardinale et al13 |
| ITSReub 5′ GCCAAGGCATCCACC | ||
| 27f 5′ AGAGTTTGATCMTGGCTCAG | Conserved 16S rDNA used to amplify ribosomal genes | Lane19 |
| 342r 5′ CTGCTGCSYCCCGTAG | ||