TABLE 5.
Possible ways to name organisms to capture all the information available by 16S rRNA gene sequence analysisa
| Specimen name | Nomenclature or possible nomenclature | Reason for example |
|---|---|---|
| 6703 | Streptococcus anginosus | Present system |
| 6703 | Streptococcus anginosus (0%) | Designates that there are no sequence differences between the specimen sequence and type strain |
| 6703 | Streptococcus anginosus (0%) (blood, pharynx) | As above, with clinical source of other genetically identical strains |
| VAMC5210 | Streptococcus anginosus | Present system |
| VAMC5210 | Streptococcus anginosus (0.37%) | Designates the percent difference between the specimen sequence and type strain |
| VAMC5210 | Streptococcus anginosus sequevar (274A, 288A) | Designates the position and base change of the two differences between the specimen sequence and type strain |
| S7745 | Streptococcus anginosus | Present system |
| S7745 | Streptococcus anginosus (0.55%) | Designates the percent difference between the specimen sequence and type strain |
| S7745 | Streptococcus anginosus (0.55%) sequevar (137A, 288A, 487G) | As above and designates the position and substitution of the three differences between the specimen sequence and type strain |
| S7745 | Streptococcus anginosus (0.55%) sequevar (137A, 288A, 487G) (urogenital) | All known information is included, including the most common site of isolation |
| VAMC5366 | Streptococcus anginosus | Present system |
| VAMC5366 | Streptococcus anginosus (1.10%) | Designates the percent difference between the specimen sequence and type strain; since there is more than 1% difference, consider naming as a new species |
| VAMC5366 | Streptococcus anginosus sequevar: differs from type strain at positions 71, 97, 186, 274, 288, and 463 | Designates the position of the six differences between the specimen sequence and type strain |
| VAMC5366 | Streptococcus anginosus (1.10%) (pharynx) | Designates the percent difference between the specimen sequence and type strain and the most common site of isolation |
a
The genotypic information makes naming organisms more complex but at times may have clinical importance. All examples are of S. anginosus subspecies or sequevars shown in Fig. 4.