TABLE 2.
Alignment of forward primers with the 16S rRNA gene of E. coli, Shigella, and other enteric bacteria
| Source | Region from bp 75–99 of 16S rRNA gene (5′-3′)a | GenBank Accession no. | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ECA75F-ECP79Fb | G | G | A | A | G | A | A | G | C | T | T | G | C | T | T | C | T | T | T | G | C | T | G | A | C | |
| E. coli | ||||||||||||||||||||||||||
| rrnA operon | G | G | A | A | G | A | A | G | C | T | T | G | C | T | T | C | T | T | T | G | C | T | G | A | C | CR01508 |
| rrnB operon | G | G | A | A | G | A | A | G | C | T | T | G | C | T | T | C | T | T | T | G | C | T | G | A | C | CR04840 |
| rrnC operon | G | G | A | A | A | C | A | G | C | T | T | G | C | T | C | T | T | T | C | G | C | T | G | A | C | X80723 |
| rrnD operon | G | G | A | A | A | C | A | G | C | T | T | G | C | T | G | T | T | T | C | G | C | T | G | A | C | CR05849 |
| rrnE operon | G | G | A | A | G | A | A | G | C | T | T | G | C | T | T | C | T | T | T | G | C | T | G | A | C | CR01512 |
| rrnG operon | G | G | A | A | G | C | A | G | C | T | T | G | C | T | C | T | T | C | G | C | T | G | A | C | C | R01932 |
| rrnH operon | G | G | A | A | G | A | A | G | C | T | T | G | C | T | T | C | T | T | T | G | C | T | G | A | C | CR01815 |
| Shigella boydii | G | G | A | A | G | C | A | G | C | T | T | G | C | T | G | T | T | T | C | G | C | T | G | A | C | X96965 |
| Shigella dysenteriae | G | G | A | A | G | C | A | G | C | T | T | G | C | T | G | C | T | T | T | G | C | T | G | A | C | X80680 |
| G | A | A | A | G | C | A | G | C | T | T | G | C | T | G | T | T | T | G | C | T | G | A | C | G | X96966 | |
| G | A | A | A | G | C | A | G | C | T | T | G | C | T | G | C | T | T | T | G | C | T | G | A | C | AF207826 | |
| Shigella flexnerii | G | G | A | A | G | C | A | G | C | T | T | G | C | T | G | T | T | T | C | G | C | T | G | A | C | X80679 |
| Shigella sonnei | G | G | A | A | A | C | A | G | C | T | T | G | C | T | G | T | T | T | C | G | C | T | G | A | C | X80726 |
| Salmonella LT2 | G | G | A | A | G | C | A | G | C | T | T | G | C | T | G | C | T | T | T | G | C | T | G | A | C | Z49264 |
| Citrobacter freundii | C | A | G | A | G | G | A | G | C | T | T | G | C | T | C | C | T | T | G | G | G | T | G | A | C | M59291 |
| Edwardsiella tarda | G | G | A | G | A | A | A | G | C | T | T | G | C | T | T | T | C | T | C | C | G | C | T | G | A | AF053975 |
| Enterobacter aerogenes | A | C | A | G | A | G | A | G | C | T | T | G | C | T | C | T | C | G | G | G | T | G | A | C | G | AJ001237 |
| Enterobacter nimipressuralis | A | C | A | G | A | G | A | G | C | T | T | G | C | T | T | C | T | T | C | A | G | G | G | T | G | Z96077 |
| Klebsiella pneumoniae | A | C | A | G | A | G | A | G | C | T | T | G | C | T | C | T | C | G | G | G | T | G | A | C | G | Y17656 |
| Proteus vulgaris | G | G | A | G | A | A | A | G | C | T | T | G | C | T | T | T | C | T | T | G | C | T | G | A | C | J01874 |
| Pseudomonas aeruginosa | G | A | A | G | G | G | A | G | C | T | T | G | C | T | C | C | T | G | G | A | T | C | A | G | C | AJ249451 |
a
Boldface bases are mismatches.
b
Primers ECA75F and ECP79F cover bases 75 to 99 and 79 to 96, respectively.