Table 1.
Primers used for PCR, size of amplified products, annealing temperatures, origin, and description of target genesa
| Gene | Description of target (DEC pathotype) | Known function (reference) | Primer sequence (5′–3′) | Size of PCR product (bp) | Annealing temp (°C) | Primer source or reference |
|---|---|---|---|---|---|---|
| aida-I | Adhesin involved in diffuse adherence (DAEC) | Adherence and biofilm formation (25) | GTTCTCTCTGATGGTTATGCAACATTGACCATACCGCCG | 342 | 60 | This study (GenBank accession no. GU810159.1) |
| cah | Calcium-binding antigen 43 homologue (EHEC) | Biofilm formation and autoaggregation (26) | CGTATCGCTGTGCCCGATAACCCGTATACGAGTTGTCAGAATCA | 707 | 58 | 27 |
| eatA | ETEC autotransporter A (ETEC) | Serine protease (28) | CAGGAGTGGGAACATTAAGTCACGTACGCCTTTGATTTCAGGAT | 743 | 60 | 27 |
| ehaA | EHEC autotransporter A (EHEC) | Biofilm formation (11) | CACAGATGACAGAAGGGACGTTTACCCCACTCGTCAG | 326 | 59 | This study (GenBank accession no. AE005174.2) |
| ehaB | EHEC autotransporter B (EHEC) | Biofilm formation (11) | CAG GGTTATGAGTGGGAAGCCACTTGCTGCCGTTGTT | 423 | 59 | This study (GenBank accession no. AE005174.2) |
| ehaC | EHEC autotransporter C (EHEC) | Unknown (11) | TAATGACGGCAAAGGTGGTCATTCATCAGGGAGTTGCT | 599 | 59 | This study (GenBank accession no. AE005174.2) |
| ehaD | EHEC autotransporter D (EHEC) | Biofilm formation (11) | GGCAGTTGACACGATTATTACTGTCGCTTTGCCATTATC | 821 | 59 | This study (GenBank accession no. AE005174.2) |
| ehaJ | EHEC autotransporter J (EHEC/EPEC) | Biofilm formation (9) | ACGGGCTGCTGAGTATTTTGTAGTTTGCCACATCACCG | 455 | 60 | This study (GenBank accession no. NC_011601.1) |
| epeA | EHEC plasmid-encoded autotransporter (EHEC) | Protease and mucinolytic activity (29) | GGGAGAGTTCAGGCATTTACAGCGTTACCTTACTTGAG | 783 | 57 | This study (GenBank accession no. AY258503.2) |
| espC | E. coli secreted protein C (EPEC) | Enterotoxic activity and cleavage of spectrin, pepsin, and factor V (30) | TAGTGCAGTGCAGAAAGCAGTTAGTTTTCCTGTTGCTGTATGCC | 301 | 55 | 27 |
| espI | E. coli secreted protease (EHEC) | Degradation of plasma proteins (19) | ATGGACAGAGTGGAGACAGGCCACCTTTATTCTCACCA | 560 | 52 | 19 |
| espP | Extracellular serine protease (EHEC) | Cleavage of spectrin, pepsin, and factor V (31) | GTCCATGCAGGGACATGCCATCACATCAGCACCGTTCTCTAT | 547 | 55 | 27 |
| pet | Plasmid-encoded toxin (EAEC) | Enterotoxic and cytopathic toxin effects and cleavage of spectrin (32) | GGCACAGAATAAAGGGGTGTTTCCTCTTGTTTCCACGACATAC | 302 | 58 | 27 |
| pic | Protein involved in colonization (EAEC) | Mucinase activity and cleavage of factor V (33) | GGGTATTGTCCGTTCCGATACAACGATACCGTCTCCCG | 1,176 | 60 | 33 |
| sab | STEC autotransporter (EHEC) | Biofilm formation (34) | GGTGGATACAGCAGGTAATGTATCTCACCACCTGCTATCG | 163 | 59 | 34 |
| sat | Secreted autotransporter toxin (DAEC) | Cytopathic toxin effects and cleavage of spectrin and factor V (35) | TCAGAAGCTCAGCGAATCATTGCCATTATCACCAGTAAAACGCACC | 930 | 59 | 17 |
| tibA | Tib A (ETEC) | Biofilm formation, adherence, and autoaggregation (36) | ATGGTTGGCAGTGACGGTAGGTTGTTGACGGACGGAAA | 480 | 58 | This study (GenBank accession no. FN649414.1) |
a
EPEC, enteropathogenic E. coli; ETEC, enterotoxigenic E. coli; STEC, Shiga toxin-producing E. coli; EHEC, enterohemorrhagic E. coli; EAEC, enteroaggregative E. coli; DAEC, diffusely adherent E. coli. Positive controls: cah, ehaABCD, and espP, EHEC EDL933 (26); eatA and tibA, ETEC H10407 (28); pet and pic, EAEC 042 (32); ehaJ and espC, EPEC E2348/69 (30); epeA and sab, EHEC EH41 (29); aida-I, DAEC 2787 (25); sat, DAEC FBC114 (37); espI, STEC O113:H21 (38).