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 |